<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wu, Stephen T</style></author><author><style face="normal" font="default" size="100%">Kaggal, Vinod C</style></author><author><style face="normal" font="default" size="100%">Dligach, Dmitriy</style></author><author><style face="normal" font="default" size="100%">Masanz, James J</style></author><author><style face="normal" font="default" size="100%">Chen, Pei</style></author><author><style face="normal" font="default" size="100%">Becker, Lee</style></author><author><style face="normal" font="default" size="100%">Chapman, Wendy W</style></author><author><style face="normal" font="default" size="100%">Savova, Guergana K</style></author><author><style face="normal" font="default" size="100%">Liu, Hongfang</style></author><author><style face="normal" font="default" size="100%">Chute, Christopher G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A common type system for clinical natural language processing.</style></title><secondary-title><style face="normal" font="default" size="100%">J Biomed Semantics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Biomed Semantics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">1</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;UNLABELLED: &lt;/b&gt;&lt;/p&gt;&lt;p&gt;&lt;b&gt;BACKGROUND: &lt;/b&gt;One challenge in reusing clinical data stored in electronic medical records is that these data are heterogenous. Clinical Natural Language Processing (NLP) plays an important role in transforming information in clinical text to a standard representation that is comparable and interoperable. Information may be processed and shared when a type system specifies the allowable data structures. Therefore, we aim to define a common type system for clinical NLP that enables interoperability between structured and unstructured data generated in different clinical settings.&lt;/p&gt;&lt;p&gt;&lt;b&gt;RESULTS: &lt;/b&gt;We describe a common type system for clinical NLP that has an end target of deep semantics based on Clinical Element Models (CEMs), thus interoperating with structured data and accommodating diverse NLP approaches. The type system has been implemented in UIMA (Unstructured Information Management Architecture) and is fully functional in a popular open-source clinical NLP system, cTAKES (clinical Text Analysis and Knowledge Extraction System) versions 2.0 and later.&lt;/p&gt;&lt;p&gt;&lt;b&gt;CONCLUSIONS: &lt;/b&gt;We have created a type system that targets deep semantics, thereby allowing for NLP systems to encapsulate knowledge from text and share it alongside heterogenous clinical data sources. Rather than surface semantics that are typically the end product of NLP algorithms, CEM-based semantics explicitly build in deep clinical semantics as the point of interoperability with more structured data types.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">David Ingram</style></author><author><style face="normal" font="default" size="100%">Sevket Seref Arikan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Evolving Role of Open Source Software in Medicine and Health Services</style></title><secondary-title><style face="normal" font="default" size="100%">Technology Innovation Management Review</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">electronic health care record</style></keyword><keyword><style  face="normal" font="default" size="100%">information retrieval</style></keyword><keyword><style  face="normal" font="default" size="100%">open source framework</style></keyword><keyword><style  face="normal" font="default" size="100%">openEHR Foundation</style></keyword><keyword><style  face="normal" font="default" size="100%">persistence</style></keyword><keyword><style  face="normal" font="default" size="100%">standards based</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">01/2013</style></date></pub-dates></dates><pages><style face="normal" font="default" size="100%">32-39</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The past five decades have witnessed immense coevolution of methods and tools of information technology, and their practical and experimental application within the medical and healthcare domain. Healthcare itself continues to evolve in response to change in healthcare needs, progress in the scientific foundations of treatments, and in professional and managerial organization of affordable and effective services, in which patients and their families and carers increasingly participate. Taken together, these trends impose highly complex underlying challenges for the design, development, and sustainability of the quality of supporting information services and software infrastructure that are needed. The challenges are multidisciplinary and multiprofessional in scope, and they require deeper study and learning to inform policy and promote public awareness of the problems health services have faced in this area for many years. The repeating pattern of failure to live up to expectations of policy-driven national health IT initiatives has proved very costly and remains frustrating and unproductive for all involved. In this article, we highlight the barriers to progress and discuss the dangers of pursuing a standardization framework devoid of empirical testing and iterative development. We give the example of the openEHR Foundation, which was established at University College London (UCL) in London, England, with members in 80 countries. The Foundation is a not-for-profit company providing open specifications and working for generic standards for electronic records, informed directly by a wide range of implementation experience. We also introduce the Opereffa open source framework, which was developed at UCL based on these specifications and which has been downloaded in some 70 countries. We argue that such an approach is now essential to support good discipline, innovation, and governance at the heart of medicine and health services, in line with the new mandate for health commissioning in the United Kingdom’s National Health Service (NHS), which emphasizes patient participation, innovation, transparency, and accountability.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kim, Gihyeon</style></author><author><style face="normal" font="default" size="100%">Jung, Ho-Joong</style></author><author><style face="normal" font="default" size="100%">Lee, Han-Jun</style></author><author><style face="normal" font="default" size="100%">Lee, Jae-Sung</style></author><author><style face="normal" font="default" size="100%">Koo, Seungbum</style></author><author><style face="normal" font="default" size="100%">Chang, Seung-Hwan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Accuracy and Reliability of Length Measurements on Three-Dimensional Computed Tomography Using Open-Source OsiriX Software.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Jan 20</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">ENG</style></language><abstract><style face="normal" font="default" size="100%">There is a growing interest in three-dimensional computed tomography (3D-CT) as a research tool for the study of bone, joint anatomy, and kinematics. However, when CT data are processed and handled manually using image processing programs to yield 3D image and coordinate value, systematic and random errors should be validated. We evaluated the accuracy and reliability of length measurement on CT with OsiriX software. 3D-CT scans were made of 14 frozen pig knees with five transosseous holes in the metaphyseal portion of femur. The lengths between tunnel orifices were measured using Mitutoyo Digimatic digital calipers to establish the gold standard, and with the OsiriX program in 3D multi-planar reformatting mode for comparison. All measurements were recorded by a principal (replicate 1, trial 1) and a secondary observer (replicate 2, trial 1) and were repeated once by each observer (trial 2). The mean differences between OsiriX and real measurements were less than 0.1 mm in both replicates, and maximum differences were less than 0.3 mm. There were no significant differences between the replicates and real measurements (p = 0.544 and 0.622 for replicates 1 and 2, respectively). The intraclass correlation coefficients (ICC) were very high between trials and between replicates (ICC = 0.998 and 0.999, respectively). For kinematic analysis of the knees, length measurements on 3D-CT using OsiriX program can be used as alternatives to real measurements with less than 0.3-mm accuracy and very high reliability.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22270788?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fraser, Hamish S F</style></author><author><style face="normal" font="default" size="100%">Thomas, David</style></author><author><style face="normal" font="default" size="100%">Tomaylla, Juan</style></author><author><style face="normal" font="default" size="100%">Garcia, Nadia</style></author><author><style face="normal" font="default" size="100%">Lecca, Leonid</style></author><author><style face="normal" font="default" size="100%">Murray, Megan</style></author><author><style face="normal" font="default" size="100%">Becerra, Mercedes C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Adaptation of a web-based, open source electronic medical record system platform to support a large study of tuberculosis epidemiology.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Med Inform Decis Mak</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Med Inform Decis Mak</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">125</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">UNLABELLED: ABSTRACT:

BACKGROUND: In 2006, we were funded by the US National Institutes of Health to implement a study of tuberculosis epidemiology in Peru. The study required a secure information system to manage data from a target goal of 16,000 subjects who needed to be followed for at least one year. With previous experience in the development and deployment of web-based medical record systems for TB treatment in Peru, we chose to use the OpenMRS open source electronic medical record system platform to develop the study information system. Supported by a core technical and management team and a large and growing worldwide community, OpenMRS is now being used in more than 40 developing countries. We adapted the OpenMRS platform to better support foreign languages. We added a new module to support double data entry, linkage to an existing laboratory information system, automatic upload of GPS data from handheld devices, and better security and auditing of data changes. We added new reports for study managers, and developed data extraction tools for research staff and statisticians. Further adaptation to handle direct entry of laboratory data occurred after the study was launched.

RESULTS: Data collection in the OpenMRS system began in September 2009. By August 2011 a total of 9,256 participants had been enrolled, 102,274 forms and 13,829 laboratory results had been entered, and there were 208 users. The system is now entirely supported by the Peruvian study staff and programmers.

CONCLUSIONS: The information system served the study objectives well despite requiring some significant adaptations mid-stream. OpenMRS has more tools and capabilities than it did in 2008, and requires less adaptations for future projects. OpenMRS can be an effective research data system in resource poor environments, especially for organizations using or considering it for clinical care as well as research.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">van Valkenhoef, G.</style></author><author><style face="normal" font="default" size="100%">Tervonen, T.</style></author><author><style face="normal" font="default" size="100%">Zwinkels, T.</style></author><author><style face="normal" font="default" size="100%">de Brock, B.</style></author><author><style face="normal" font="default" size="100%">Hillege, H.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">ADDIS: a decision support system for evidence-based medicine</style></title><secondary-title><style face="normal" font="default" size="100%">Decision Support Systems</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">clinicaltrial</style></keyword><keyword><style  face="normal" font="default" size="100%">datamodel</style></keyword><keyword><style  face="normal" font="default" size="100%">decisionanalysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Evidence-basedmedicine</style></keyword><keyword><style  face="normal" font="default" size="100%">evidencesynthesis</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><volume><style face="normal" font="default" size="100%">in press</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Clinical trials are the main source of information for the efficacy and safety evaluation of medical treatments. Al- though they are of pivotal importance in evidence-based medicine, there is a lack of usable information systems providing data-analysis and decision support capabilities for aggregate clinical trial results. This is partly caused by unavailability (i) of trial data in a structured format suitable for re-analysis, and (ii) of a complete data model for ag- gregate level results. In this paper, we develop a unifying data model that enables the development of evidence-based decision support in the absence of a complete data model. We describe the supported decision processes and show how these are implemented in the open source ADDIS software. ADDIS enables semi-automated construction of meta-analyses, network meta-analyses and benefit-risk decision models, and provides visualization of all results.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>13</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhao, J.</style></author><author><style face="normal" font="default" size="100%">van Valkenhoef, G.</style></author><author><style face="normal" font="default" size="100%">de Brock, B.</style></author><author><style face="normal" font="default" size="100%">Hillege, H.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">ADDIS: an automated way to do network meta-analysis</style></title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kankaanpää, Pasi</style></author><author><style face="normal" font="default" size="100%">Paavolainen, Lassi</style></author><author><style face="normal" font="default" size="100%">Tiitta, Silja</style></author><author><style face="normal" font="default" size="100%">Karjalainen, Mikko</style></author><author><style face="normal" font="default" size="100%">Päivärinne, Joacim</style></author><author><style face="normal" font="default" size="100%">Nieminen, Jonna</style></author><author><style face="normal" font="default" size="100%">Marjomäki, Varpu</style></author><author><style face="normal" font="default" size="100%">Heino, Jyrki</style></author><author><style face="normal" font="default" size="100%">White, Daniel J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">BioImageXD: an open, general-purpose and high-throughput image-processing platform.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Methods</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat. Methods</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">683-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rea, Susan</style></author><author><style face="normal" font="default" size="100%">Pathak, Jyotishman</style></author><author><style face="normal" font="default" size="100%">Savova, Guergana</style></author><author><style face="normal" font="default" size="100%">Oniki, Thomas A</style></author><author><style face="normal" font="default" size="100%">Westberg, Les</style></author><author><style face="normal" font="default" size="100%">Beebe, Calvin E</style></author><author><style face="normal" font="default" size="100%">Tao, Cui</style></author><author><style face="normal" font="default" size="100%">Parker, Craig G</style></author><author><style face="normal" font="default" size="100%">Haug, Peter J</style></author><author><style face="normal" font="default" size="100%">Huff, Stanley M</style></author><author><style face="normal" font="default" size="100%">Chute, Christopher G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: The SHARPn project.</style></title><secondary-title><style face="normal" font="default" size="100%">J Biomed Inform</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Feb 4</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Strategic Health IT Advanced Research Projects (SHARP) Program, established by the Office of the National Coordinator for Health Information Technology in 2010 supports research findings that remove barriers for increased adoption of health IT. The improvements envisioned by the SHARP Area 4 Consortium (SHARPn) will enable the use of the electronic health record (EHR) for secondary purposes, such as care process and outcomes improvement, biomedical research and epidemiologic monitoring of the nation's health. One of the primary informatics problem areas in this endeavor is the standardization of disparate health data from the nation's many health care organizations and providers. The SHARPn team is developing open source services and components to support the ubiquitous exchange, sharing and reuse or 'liquidity' of operational clinical data stored in electronic health records. One year into the design and development of the SHARPn framework, we demonstrated end to end data flow and a prototype SHARPn platform, using thousands of patient electronic records sourced from two large healthcare organizations: Mayo Clinic and Intermountain Healthcare. The platform was deployed to (1) receive source EHR data in several formats, (2) generate structured data from EHR narrative text, and (3) normalize the EHR data using common detailed clinical models and Consolidated Health Informatics standard terminologies, which were (4) accessed by a phenotyping service using normalized data specifications. The architecture of this prototype SHARPn platform is presented. The EHR data throughput demonstration showed success in normalizing native EHR data, both structured and narrative, from two independent organizations and EHR systems. Based on the demonstration, observed challenges for standardization of EHR data for interoperable secondary use are discussed.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Patrick Vandewalle</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Code Sharing is Associated with Research Impact in Image Processing</style></title><secondary-title><style face="normal" font="default" size="100%">IEEE Computing in Science and Engineering</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">April</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://rr.epfl.ch/37/</style></url></web-urls></urls><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In computational sciences such as image processing, the publication itself is often not enough to allow other researchers to verify the results by repeating the described experiments. In many cases, supplementary material such as source code and measurement data are required, or can at least be very helpful. Still, only approximately 10% of recently published papers in image processing have code available online. One of the arguments for not making code available is the extra time required to prepare the material. In this paper, we claim that this additional time may be well spent, as the availability of code for a publication is associated with an increase in the expected number of citations. We show this with exploratory analyses of the relationship between code availability and the number of citations for image processing papers.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Vemuri, Anant S</style></author><author><style face="normal" font="default" size="100%">Wu, Jungle Chi-Hsiang</style></author><author><style face="normal" font="default" size="100%">Liu, Kai-Che</style></author><author><style face="normal" font="default" size="100%">Wu, Hurng-Sheng</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Deformable three-dimensional model architecture for interactive augmented reality in minimally invasive surgery.</style></title><secondary-title><style face="normal" font="default" size="100%">Surg Endosc</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Jun 27</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Surgical procedures have undergone considerable advancement during the last few decades. More recently, the availability of some imaging methods intraoperatively has added a new dimension to minimally invasive techniques. Augmented reality in surgery has been a topic of intense interest and research. METHODS: Augmented reality involves usage of computer vision algorithms on video from endoscopic cameras or cameras mounted in the operating room to provide the surgeon additional information that he or she otherwise would have to recognize intuitively. One of the techniques combines a virtual preoperative model of the patient with the endoscope camera using natural or artificial landmarks to provide an augmented reality view in the operating room. The authors' approach is to provide this with the least number of changes to the operating room. Software architecture is presented to provide interactive adjustment in the registration of a three-dimensional (3D) model and endoscope video. RESULTS: Augmented reality including adrenalectomy, ureteropelvic junction obstruction, and retrocaval ureter and pancreas was used to perform 12 surgeries. The general feedback from the surgeons has been very positive not only in terms of deciding the positions for inserting points but also in knowing the least change in anatomy. CONCLUSIONS: The approach involves providing a deformable 3D model architecture and its application to the operating room. A 3D model with a deformable structure is needed to show the shape change of soft tissue during the surgery. The software architecture to provide interactive adjustment in registration of the 3D model and endoscope video with adjustability of every 3D model is presented.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Campbell, Timothy C</style></author><author><style face="normal" font="default" size="100%">Hodanics, Charles J</style></author><author><style face="normal" font="default" size="100%">Babin, Steven M</style></author><author><style face="normal" font="default" size="100%">Poku, Adjoa M</style></author><author><style face="normal" font="default" size="100%">Wojcik, Richard A</style></author><author><style face="normal" font="default" size="100%">Skora, Joseph F</style></author><author><style face="normal" font="default" size="100%">Coberly, Jacqueline S</style></author><author><style face="normal" font="default" size="100%">Mistry, Zarna S</style></author><author><style face="normal" font="default" size="100%">Lewis, Sheri H</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Developing open source, self-contained disease surveillance software applications for use in resource-limited settings.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Med Inform Decis Mak</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Med Inform Decis Mak</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">99</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">UNLABELLED: ABSTRACT:

BACKGROUND: Emerging public health threats often originate in resource-limited countries. In recognition of this fact, the World Health Organization issued revised International Health Regulations in 2005, which call for significantly increased reporting and response capabilities for all signatory nations. Electronic biosurveillance systems can improve the timeliness of public health data collection, aid in the early detection of and response to disease outbreaks, and enhance situational awareness.

METHODS: As components of its Suite for Automated Global bioSurveillance (SAGES) program, The Johns Hopkins University Applied Physics Laboratory developed two open-source, electronic biosurveillance systems for use in resource-limited settings. OpenESSENCE provides web-based data entry, analysis, and reporting. ESSENCE Desktop Edition provides similar capabilities for settings without internet access. Both systems may be configured to collect data using locally available cell phone technologies.

RESULTS: ESSENCE Desktop Edition has been deployed for two years in the Republic of the Philippines. Local health clinics have rapidly adopted the new technology to provide daily reporting, thus eliminating the two-to-three week data lag of the previous paper-based system.

CONCLUSIONS: OpenESSENCE and ESSENCE Desktop Edition are two open-source software products with the capability of significantly improving disease surveillance in a wide range of resource-limited settings. These products, and other emerging surveillance technologies, can assist resource-limited countries compliance with the revised International Health Regulations.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kim, Youngjun</style></author><author><style face="normal" font="default" size="100%">Kim, Kyunghwan</style></author><author><style face="normal" font="default" size="100%">Roy, Frédérick</style></author><author><style face="normal" font="default" size="100%">Park, Sehyung</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Dohi, Takeyoshi</style></author><author><style face="normal" font="default" size="100%">Liao, Hongen</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Development of a Laparoscopic Surgical Training System with Simulation Open Framework Architecture (SOFA)</style></title><secondary-title><style face="normal" font="default" size="100%">Computer Aided Surgery</style></secondary-title><tertiary-title><style face="normal" font="default" size="100%">Proceedings in Information and Communications Technology</style></tertiary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/978-4-431-54094-6_10</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer Japan</style></publisher><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">83-91</style></pages><isbn><style face="normal" font="default" size="100%">978-4-431-54094-6</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">With a number of advantages over traditional laparotomy, laparoscopic surgery is a successful minimally invasive surgical procedure. However, laparoscopy demands high surgical skill. For efficient and safe training, virtual surgery simulation systems have been developed recently. In this paper, we describe the development of a laparoscopic surgery training system using Simulation Open Framework Architecture (SOFA). The simulation software was integrated with a two-hand haptic device specially developed for laparoscopic surgical training. As an example, we focused on the simulation of gallbladder removal surgery using laparoscopic instruments. Gallbladder removal was successfully simulated by the proposed methods. We expect this training system to be similarly successful in simulating a number of other surgical procedures.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ziegler, Scott E</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Development of a Next-Generation Automated DICOM Processing System in a PACS-Less Research Environment.</style></title><secondary-title><style face="normal" font="default" size="100%">J Digit Imaging</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 May 1</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The use of clinical imaging modalities within the pharmaceutical research space provides value and challenges. Typical clinical settings will utilize a Picture Archive and Communication System (PACS) to transmit and manage Digital Imaging and Communications in Medicine (DICOM) images generated by clinical imaging systems. However, a PACS is complex and provides many features that are not required within a research setting, making it difficult to generate a business case and determine the return on investment. We have developed a next-generation DICOM processing system using open-source software, commodity server hardware such as Apple Xserve®, high-performance network-attached storage (NAS), and in-house-developed preprocessing programs. DICOM-transmitted files are arranged in a flat file folder hierarchy easily accessible via our downstream analysis tools and a standard file browser. This next-generation system had a minimal construction cost due to the reuse of all the components from our first-generation system with the addition of a second server for a few thousand dollars. Performance metrics were gathered and the system was found to be highly scalable, performed significantly better than the first-generation system, is modular, has satisfactory image integrity, and is easier to maintain than the first-generation system. The resulting system is also portable across platforms and utilizes minimal hardware resources, allowing for easier upgrades and migration to smaller form factors at the hardware end-of-life. This system has been in production successfully for 8 months and services five clinical instruments and three pre-clinical instruments. This system has provided us with the necessary DICOM C-Store functionality, eliminating the need for a clinical PACS for day-to-day image processing.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Archie, Kevin A</style></author><author><style face="normal" font="default" size="100%">Marcus, Daniel S</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">DicomBrowser: Software for Viewing and Modifying DICOM Metadata.</style></title><secondary-title><style face="normal" font="default" size="100%">J Digit Imaging</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Feb 15</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Digital Imaging and Communications in Medicine (DICOM) is the dominant standard for medical imaging data. DICOM-compliant devices and the data they produce are generally designed for clinical use and often do not match the needs of users in research or clinical trial settings. DicomBrowser is software designed to ease the transition between clinically oriented DICOM tools and the specialized workflows of research imaging. It supports interactive loading and viewing of DICOM images and metadata across multiple studies and provides a rich and flexible system for modifying DICOM metadata. Users can make ad hoc changes in a graphical user interface, write metadata modification scripts for batch operations, use partly automated methods that guide users to modify specific attributes, or combine any of these approaches. DicomBrowser can save modified objects as local files or send them to a DICOM storage service using the C-STORE network protocol. DicomBrowser is open-source software, available for download at http://nrg.wustl.edu/software/dicom-browser .</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tiger, Carl-Fredrik</style></author><author><style face="normal" font="default" size="100%">Krause, Falko</style></author><author><style face="normal" font="default" size="100%">Cedersund, Gunnar</style></author><author><style face="normal" font="default" size="100%">Palmér, Robert</style></author><author><style face="normal" font="default" size="100%">Klipp, Edda</style></author><author><style face="normal" font="default" size="100%">Hohmann, Stefan</style></author><author><style face="normal" font="default" size="100%">Kitano, Hiroaki</style></author><author><style face="normal" font="default" size="100%">Krantz, Marcus</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A framework for mapping, visualisation and automatic model creation of signal-transduction networks.</style></title><secondary-title><style face="normal" font="default" size="100%">Mol Syst Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Mol. Syst. Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">578</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal-transduction networks that avoids the combinatorial explosion by breaking down the network in reaction and contingency information. It provides two new visualisation methods and automatic export to mathematical models. We use this framework to compile the presently most comprehensive map of the yeast MAP kinase network. Our method improves previous strategies by combining (I) more concise mapping adapted to empirical data, (II) individual referencing for each piece of information, (III) visualisation without simplifications or added uncertainty, (IV) automatic visualisation in multiple formats, (V) automatic export to mathematical models and (VI) compatibility with established formats. The framework is supported by an open source software tool that facilitates integration of the three levels of network analysis: definition, visualisation and mathematical modelling. The framework is species independent and we expect that it will have wider impact in signalling research on any system.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hadlich, Marcelo Souza</style></author><author><style face="normal" font="default" size="100%">Oliveira, Gláucia Maria Moraes</style></author><author><style face="normal" font="default" size="100%">Feijóo, Raúl A</style></author><author><style face="normal" font="default" size="100%">Azevedo, Clerio F</style></author><author><style face="normal" font="default" size="100%">Tura, Bernardo Rangel</style></author><author><style face="normal" font="default" size="100%">Ziemer, Paulo Gustavo Portela</style></author><author><style face="normal" font="default" size="100%">Blanco, Pablo Javier</style></author><author><style face="normal" font="default" size="100%">Pina, Gustavo</style></author><author><style face="normal" font="default" size="100%">Meira, Márcio</style></author><author><style face="normal" font="default" size="100%">Souza E Silva, Nelson Albuquerque de</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Free and open-source software application for the evaluation of coronary computed tomography angiography images.</style></title><secondary-title><style face="normal" font="default" size="100%">Arq Bras Cardiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Arq. Bras. Cardiol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Oct 2</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: The standardization of images used in Medicine in 1993 was performed using the DICOM (Digital Imaging and Communications in Medicine) standard. Several tests use this standard and it is increasingly necessary to design software applications capable of handling this type of image; however, these software applications are not usually free and open-source, and this fact hinders their adjustment to most diverse interests. OBJECTIVE: To develop and validate a free and open-source software application capable of handling DICOM coronary computed tomography angiography images. METHODS: We developed and tested the ImageLab software in the evaluation of 100 tests randomly selected from a database. We carried out 600 tests divided between two observers using ImageLab and another software sold with Philips Brilliance computed tomography appliances in the evaluation of coronary lesions and plaques around the left main coronary artery (LMCA) and the anterior descending artery (ADA). To evaluate intraobserver, interobserver and intersoftware agreements, we used simple and kappa statistics agreements. RESULTS: The agreements observed between software applications were generally classified as substantial or almost perfect in most comparisons. CONCLUSION: The ImageLab software agreed with the Philips software in the evaluation of coronary computed tomography angiography tests, especially in patients without lesions, with lesions &lt; 50% in the LMCA and &lt; 70% in the ADA. The agreement for lesions &gt; 70% in the ADA was lower, but this is also observed when the anatomical reference standard is used.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wang, Changji</style></author><author><style face="normal" font="default" size="100%">Liu, Xuan</style></author><author><style face="normal" font="default" size="100%">Li, Wentao</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Implementing a Personal Health Record Cloud Platform Using Ciphertext-Policy Attribute-Based Encryption</style></title><secondary-title><style face="normal" font="default" size="100%">Intelligent Networking and Collaborative Systems (INCoS), 2012 4th International Conference on</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">sept.</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Work on designing and implementing a patient-centric, personal health record cloud platform based on open-source Indivo X system. We adopt cipher text-policy attribute-based encryption to provide privacy protection and fine-grained access control.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Andrew S. Kanter, Rob Borland, Mourice Barasa, Casey Iiams-Hauser, Olivia Velez, Nadi Nina Kaonga, Matt Berg</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Importance of Using Open Source Technologies and Common Standards for Interoperability within eHealth: Perspectives from the Millennium Villages Project</style></title><secondary-title><style face="normal" font="default" size="100%">Advances in Health Care Management</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><volume><style face="normal" font="default" size="100%">Advances in Health Care Management</style></volume><pages><style face="normal" font="default" size="100%">189–204</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Purpose – The purpose of this chapter is to illustrate the importance of using open source technologies and common standards for interoperability when implementing eHealth systems, and to illustrate this through case studies, where possible.
Design/methodology/approach – The sources used to inform this chapter draw from the implementation and evaluation of the eHealth Program in the context of the Millennium Villages Project (MVP).
Findings – As the eHealth Team was tasked to deploy an eHealth architecture, the Millennium Villages Global-Network (MVG-Net), across all 14 of the MVP sites in sub-Saharan Africa, the team not only recognized the need for standards and uniformity but also realized that context would be an important factor. Therefore, the team decided to utilize open source solutions.
Practical implications – The MVP implementation of MVG-Net provides a model for those looking to implement informatics solutions across disciplines and countries. Furthermore, there are valuable lessons learned that the eHealth community can benefit from.
Originality/value – By sharing lessons learned and developing an accessible, open source eHealth platform, we believe that we can more efficiently and rapidly achieve the health-related and collaborative Millennium Development Goals.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Braa, Jørn</style></author><author><style face="normal" font="default" size="100%">Heywood, Arthur</style></author><author><style face="normal" font="default" size="100%">Sahay, Sundeep</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Improving quality and use of data through data-use workshops: Zanzibar, United Republic of Tanzania.</style></title><secondary-title><style face="normal" font="default" size="100%">Bull World Health Organ</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bull. World Health Organ.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 May 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">90</style></volume><pages><style face="normal" font="default" size="100%">379-84</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">PROBLEM: In Zanzibar, United Republic of Tanzania, as in many developing countries, health managers lack faith in the national Health Management Information System (HMIS). The establishment of parallel data collection systems generates a vicious cycle: national health data are used little because they are of poor quality, and their relative lack of use, in turn, makes their quality remain poor.

APPROACH: An action research approach was applied to strengthen the use of information and improve data quality in Zanzibar. The underlying premise was that encouraging use in small incremental steps could help to break the vicious cycle and improve the HMIS.

LOCAL SETTING: To test the hypothesis at the national and district levels a project to strengthen the HMIS was established in Zanzibar. The project included quarterly data-use workshops during which district staff assessed their own routine data and critiqued their colleagues' data.

RELEVANT CHANGES: The data-use workshops generated inputs that were used by District Health Information Software developers to improve the tool. The HMIS, which initially covered only primary care outpatients and antenatal care, eventually grew to encompass all major health programmes and district and referral hospitals. The workshops directly contributed to improvements in data coverage, data set quality and rationalization, and local use of target indicators.

LESSONS LEARNT: Data-use workshops with active engagement of data users themselves can improve health information systems overall and enhance staff capacity for information use, presentation and analysis for decision-making.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Klompas, Michael</style></author><author><style face="normal" font="default" size="100%">McVetta, Jason</style></author><author><style face="normal" font="default" size="100%">Lazarus, Ross</style></author><author><style face="normal" font="default" size="100%">Eggleston, Emma</style></author><author><style face="normal" font="default" size="100%">Haney, Gillian</style></author><author><style face="normal" font="default" size="100%">Kruskal, Benjamin A</style></author><author><style face="normal" font="default" size="100%">Yih, W Katherine</style></author><author><style face="normal" font="default" size="100%">Daly, Patricia</style></author><author><style face="normal" font="default" size="100%">Oppedisano, Paul</style></author><author><style face="normal" font="default" size="100%">Beagan, Brianne</style></author><author><style face="normal" font="default" size="100%">Lee, Michael</style></author><author><style face="normal" font="default" size="100%">Kirby, Chaim</style></author><author><style face="normal" font="default" size="100%">Heisey-Grove, Dawn</style></author><author><style face="normal" font="default" size="100%">DeMaria, Alfred</style></author><author><style face="normal" font="default" size="100%">Platt, Richard</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Integrating clinical practice and public health surveillance using electronic medical record systems.</style></title><secondary-title><style face="normal" font="default" size="100%">Am J Prev Med</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Am J Prev Med</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">42</style></volume><pages><style face="normal" font="default" size="100%">S154-62</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Electronic medical record (EMR) systems have rich potential to improve integration between primary care and the public health system at the point of care. EMRs make it possible for clinicians to contribute timely, clinically detailed surveillance data to public health practitioners without changing their existing workflows or incurring extra work. New surveillance systems can extract raw data from providers' EMRs, analyze them for conditions of public health interest, and automatically communicate results to health departments. The current paper describes a model EMR-based public health surveillance platform called Electronic Medical Record Support for Public Health (ESP). The ESP platform provides live, automated surveillance for notifiable diseases, influenza-like illness, and diabetes prevalence, care, and complications. Results are automatically transmitted to state health departments.</style></abstract><issue><style face="normal" font="default" size="100%">6 Suppl 2</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lu, Tong</style></author><author><style face="normal" font="default" size="100%">Liang, Ping</style></author><author><style face="normal" font="default" size="100%">Wu, Wen-Bo</style></author><author><style face="normal" font="default" size="100%">Xue, Jin</style></author><author><style face="normal" font="default" size="100%">Lei, Cheng-Long</style></author><author><style face="normal" font="default" size="100%">Li, Yin-Yan</style></author><author><style face="normal" font="default" size="100%">Sun, Yun-Na</style></author><author><style face="normal" font="default" size="100%">Liu, Fang-Yi</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Integration of the Image-Guided Surgery Toolkit (IGSTK) into the Medical Imaging Interaction Toolkit (MITK).</style></title><secondary-title><style face="normal" font="default" size="100%">J Digit Imaging</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Apr 26</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The development cycle of an image-guided surgery navigation system is too long to meet current clinical needs. This paper presents an integrated system developed by the integration of two open-source software (IGSTK and MITK) to shorten the development cycle of the image-guided surgery navigation system and save human resources simultaneously. An image-guided surgery navigation system was established by connecting the two aforementioned open-source software libraries. It used the Medical Imaging Interaction Toolkit (MITK) as a framework providing image processing tools for the image-guided surgery navigation system of medical imaging software with a high degree of interaction and used the Image-Guided Surgery Toolkit (IGSTK) as a library that provided the basic components of the system for location, tracking, and registration. The electromagnetic tracking device was used to measure the real-time position of surgical tools and fiducials attached to the patient's anatomy. IGSTK was integrated into MITK; at the same time, the compatibility and the stability of this system were emphasized. Experiments showed that an integrated system of the image-guided surgery navigation system could be developed in 2 months. The integration of IGSTK into MITK is feasible. Several techniques for 3D reconstruction, geometric analysis, mesh generation, and surface data analysis for medical image analysis of MITK can connect with the techniques for location, tracking, and registration of IGSTK. This integration of advanced modalities can decrease software development time and emphasize the precision, safety, and robustness of the image-guided surgery navigation system.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Talbot, Hugo</style></author><author><style face="normal" font="default" size="100%">Marchesseau, Stéphanie</style></author><author><style face="normal" font="default" size="100%">Duriez, Christian</style></author><author><style face="normal" font="default" size="100%">Courtecuisse, Hadrien</style></author><author><style face="normal" font="default" size="100%">Relan, Jatin</style></author><author><style face="normal" font="default" size="100%">Sermesant, Maxime</style></author><author><style face="normal" font="default" size="100%">Cotin, Stéphane</style></author><author><style face="normal" font="default" size="100%">Delingette, Hervé</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Interactive Electromechanical Model of the Heart for Patient-Specific Therapy Planning and Training using SOFA</style></title><secondary-title><style face="normal" font="default" size="100%">VPH 2012</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://hal.inria.fr/hal-00751537</style></url></web-urls></urls><pub-location><style face="normal" font="default" size="100%">Londres, United Kingdom</style></pub-location><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The contributions of this work are twofold. First, we developed an electrophysiological training simulator in SOFA which tackles the interactive issue in the context of cardiac arrhythmias. Coupled with this electrophysiology, we developed a mechanical model of the heart that can be personalized from MRI datasets. Our simulations are based on the SOFA platform. SOFA is an open-source framework targeted at real-time simulation with an emphasis on medical simulation, mainly developed at Inria. A large choice of efficient solvers, hyperelastic or viscous material laws are already implemented in SOFA. Moreover, it enables interactivity during the simulation (pacing, surgery planning, ...) and gives a good trade-off between accuracy and computational efficiency.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fritzsche, K H</style></author><author><style face="normal" font="default" size="100%">Neher, P F</style></author><author><style face="normal" font="default" size="100%">Reicht, I</style></author><author><style face="normal" font="default" size="100%">van Bruggen, T</style></author><author><style face="normal" font="default" size="100%">Goch, C</style></author><author><style face="normal" font="default" size="100%">Reisert, M</style></author><author><style face="normal" font="default" size="100%">Nolden, M</style></author><author><style face="normal" font="default" size="100%">Zelzer, S</style></author><author><style face="normal" font="default" size="100%">Meinzer, H-P</style></author><author><style face="normal" font="default" size="100%">Stieltjes, B</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">MITK Diffusion Imaging.</style></title><secondary-title><style face="normal" font="default" size="100%">Methods Inf Med</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Methods Inf Med</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Oct 11</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">51</style></volume><pages><style face="normal" font="default" size="100%">441-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Background: Diffusion-MRI provides a unique window on brain anatomy and insights into aspects of tissue structure in living humans that could not be studied previously. There is a major effort in this rapidly evolving field of research to develop the algorithmic tools necessary to cope with the complexity of the datasets. Objectives: This work illustrates our strategy that encompasses the development of a modularized and open software tool for data processing, visualization and interactive exploration in diffusion imaging research and aims at reinforcing sustainable evaluation and progress in the field. Methods: In this paper, the usability and capabilities of a new application and toolkit component of the Medical Imaging and Interaction Toolkit (MITK, www.mitk.org), MITK-DI, are demonstrated using in-vivo datasets. Results: MITK-DI provides a comprehensive software framework for high-performance data processing, analysis and interactive data exploration, which is designed in a modular, extensible fashion (using CTK) and in adherence to widely accepted coding standards (e.g. ITK, VTK). MITK-DI is available both as an open source software development toolkit and as a ready-to-use installable application. Conclusions: The open source release of the modular MITK-DI tools will increase verifiability and comparability within the research community and will also be an important step towards bringing many of the current techniques towards clinical application.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Peter F. Neher</style></author><author><style face="normal" font="default" size="100%">Bram Stieltjes</style></author><author><style face="normal" font="default" size="100%">Marco Reisert</style></author><author><style face="normal" font="default" size="100%">Ignaz Reicht</style></author><author><style face="normal" font="default" size="100%">Meinzer, Hans-Peter</style></author><author><style face="normal" font="default" size="100%">Klaus H. Fritzsche</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">David R. Haynor</style></author><author><style face="normal" font="default" size="100%">Sebastien Ourselin</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">MITK global tractography</style></title><secondary-title><style face="normal" font="default" size="100%">Medical Imaging 2012: Image Processing</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://link.aip.org/link/?PSI/8314/83144D/1</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">SPIE</style></publisher><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Fiber tracking algorithms yield valuable information for neurosurgery as well as automated diagnostic approaches. However, they have not yet arrived in the daily clinical practice. In this paper we present an open source integration of the global tractography algorithm proposed by Reisert et.al.1 into the open source Medical Imaging Interaction Toolkit (MITK) developed and maintained by the Division of Medical and Biological Informatics at the German Cancer Research Center (DKFZ). The integration of this algorithm into a standardized and open development environment like MITK enriches accessibility of tractography algorithms for the science community and is an important step towards bringing neuronal tractography closer to a clinical application. The MITK diffusion imaging application, downloadable from www.mitk.org, combines all the steps necessary for a successful tractography: preprocessing, reconstruction of the images, the actual tracking, live monitoring of intermediate results, postprocessing and visualization of the final tracking results. This paper presents typical tracking results and demonstrates the steps for pre- and post-processing of the images.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zijlmans, Mariken</style></author><author><style face="normal" font="default" size="100%">Langø, Thomas</style></author><author><style face="normal" font="default" size="100%">Hofstad, Erlend Fagertun</style></author><author><style face="normal" font="default" size="100%">Van Swol, Christiaan F P</style></author><author><style face="normal" font="default" size="100%">Rethy, Anna</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Navigated laparoscopy - liver shift and deformation due to pneumoperitoneum in an animal model.</style></title><secondary-title><style face="normal" font="default" size="100%">Minim Invasive Ther Allied Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Minim Invasive Ther Allied Technol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">21</style></volume><pages><style face="normal" font="default" size="100%">241-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Abstract Background: Precise laparoscopic liver resection requires accurate planning and visualization of important anatomy such as vessels and tumors. Combining laparoscopic ultrasound with navigation technology could provide this. Preoperative images are valuable for planning and overview of the procedure, while intraoperative images provide an updated view of the surgical field. Purpose: To validate the accuracy of navigation technology based on preoperative images, we need to understand how much the liver shifts and deforms due to heartbeat, breathing, surgical manipulation and pneumoperitoneum. In this study, we evaluated liver tumor shift and deformation due to pneumoperitoneum in an animal model. Methods: Tumor models were injected into the liver of the animal, and 3D CT images were acquired before and after insufflation. Tumor shifts and deformation were determined. Results: The results showed significant tumor position shift due to pneumoperitoneum, with a maximum of 28 mm in cranio-caudal direction. No significant tumor deformation was detected. Small standard deviations suggest rigid body transformation of the liver as a whole, but this needs further investigation. Conclusion: The findings indicate a need for anatomic shift correction of preoperative images before they are used in combination with LUS guidance during a laparoscopic liver resection procedure.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Christensen, Henrik Baerbak</style></author><author><style face="normal" font="default" size="100%">Hansen, Klaus Marius</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Net4Care: Towards a Mission-Critical Software Ecosystem</style></title><secondary-title><style face="normal" font="default" size="100%">Software Architecture (WICSA) and European Conference on Software Architecture (ECSA), 2012 Joint Working IEEE/IFIP Conference on</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">aug.</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The demographics of the western world is changing: people are getting older and as a partial consequence get an increasing number of chronic diseases such as diabetes, chronic obstructive pulmonary disease (COPD), and coronary disease. At the same time, healthcare systems are stressed for resources, health centers are getting larger and more distributed, and the number of healthcare professionals does not follow the trend in chronic diseases. All of this leads to a need for telemedical and mobile health applications. In a Danish context, these applications are often developed through local (innovative) initiatives with little regards for national and global (standardization) initiatives. A reason for this discrepancy is that the software architecture for national (and global) systems and standards are hard to understand, hard to develop systems based on, and hard to deploy. To counter this, we propose a software ecosystem approach for telemedicine applications, providing a framework, Net4Care, encapsulating national/global design decisions with respect to standardization while allowing for local innovation. This paper presents an analysis of existing systems, of requirements for a software ecosystem for telemedicine, and a summary of initial design decisions for the Net4Care framework.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>12</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shinji Kobayashi</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open Sourse Software Development on Medical Domain</style></title><secondary-title><style face="normal" font="default" size="100%">Modern Information Systems</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.intechopen.com/books/modern-information-systems/open-source-software-in-medicine</style></url></web-urls></urls><edition><style face="normal" font="default" size="100%">Christos Kalloniatis</style></edition><publisher><style face="normal" font="default" size="100%">InTech</style></publisher><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Millard, Peter S</style></author><author><style face="normal" font="default" size="100%">Bru, Juan</style></author><author><style face="normal" font="default" size="100%">Berger, Christopher A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open-source point-of-care electronic medical records for use in resource-limited settings: systematic review and questionnaire surveys.</style></title><secondary-title><style face="normal" font="default" size="100%">BMJ Open</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMJ Open</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Point-of-care electronic medical records (EMRs) are a key tool to manage chronic illness. Several EMRs have been developed for use in treating HIV and tuberculosis, but their applicability to primary care, technical requirements and clinical functionalities are largely unknown.

OBJECTIVES: This study aimed to address the needs of clinicians from resource-limited settings without reliable internet access who are considering adopting an open-source EMR.

STUDY ELIGIBILITY CRITERIA: Open-source point-of-care EMRs suitable for use in areas without reliable internet access.

STUDY APPRAISAL AND SYNTHESIS METHODS: The authors conducted a comprehensive search of all open-source EMRs suitable for sites without reliable internet access. The authors surveyed clinician users and technical implementers from a single site and technical developers of each software product. The authors evaluated availability, cost and technical requirements.

RESULTS: The hardware and software for all six systems is easily available, but they vary considerably in proprietary components, installation requirements and customisability.

LIMITATIONS: This study relied solely on self-report from informants who developed and who actively use the included products. CONCLUSIONS AND IMPLICATIONS OF KEY FINDINGS: Clinical functionalities vary greatly among the systems, and none of the systems yet meet minimum requirements for effective implementation in a primary care resource-limited setting. The safe prescribing of medications is a particular concern with current tools. The dearth of fully functional EMR systems indicates a need for a greater emphasis by global funding agencies to move beyond disease-specific EMR systems and develop a universal open-source health informatics platform.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sainz de Abajo, Beatriz</style></author><author><style face="normal" font="default" size="100%">Agustín Llamas Ballestero</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Overview of the Most Important Open Source Software: Analysis of the Benefits of OpenMRS, OpenEMR, and VistA</style></title><secondary-title><style face="normal" font="default" size="100%">Telemedicine and E-Health Services, Policies, and Applications: Advancements and Developments</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/978-1-4666-0888-7.ch012</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">IGI Global</style></publisher><pub-location><style face="normal" font="default" size="100%">Hershey, PA, USA</style></pub-location><pages><style face="normal" font="default" size="100%">315–346</style></pages><isbn><style face="normal" font="default" size="100%">9781466608887</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In this chapter, the authors review software that enables the proper management of EHR. The different types of software share the feature of being open source and offer the best opportunity in health care to developing countries—an overall integrated approach. The authors analyze the main free software programs (technical features, programming languages, places for introduction, etc.). Then they focus on the description and the comparison of the three most important open source software programs EHR (OpenMRS, OpenVistA, and OpenEMR) that are installed on two operating systems (Linux Ubuntu and Windows). Finally, the authors show the results of the various parameters measured in these systems after using different Web browsers. The results show us how the three main EHR applications work depending on which operating system is installed and which web browser is used.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Morin, Andrew</style></author><author><style face="normal" font="default" size="100%">Urban, Jennifer</style></author><author><style face="normal" font="default" size="100%">Sliz, Piotr</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A quick guide to software licensing for the scientist-programmer.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS Comput Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS Comput. Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">e1002598</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">7</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lu Xiaoqi</style></author><author><style face="normal" font="default" size="100%">Yu Ning</style></author><author><style face="normal" font="default" size="100%">Gu Yu</style></author><author><style face="normal" font="default" size="100%">Jia Weitao</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Research and implementation of Electronic Medical Records Editing System based on CDA</style></title><secondary-title><style face="normal" font="default" size="100%">Consumer Electronics, Communications and Networks (CECNet), 2012 2nd International Conference on</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">CDA document structure</style></keyword><keyword><style  face="normal" font="default" size="100%">CDA standards</style></keyword><keyword><style  face="normal" font="default" size="100%">clinical document architecture</style></keyword><keyword><style  face="normal" font="default" size="100%">document handling</style></keyword><keyword><style  face="normal" font="default" size="100%">electronic medical records editing system</style></keyword><keyword><style  face="normal" font="default" size="100%">EMR</style></keyword><keyword><style  face="normal" font="default" size="100%">health level 7</style></keyword><keyword><style  face="normal" font="default" size="100%">HIS</style></keyword><keyword><style  face="normal" font="default" size="100%">HL7</style></keyword><keyword><style  face="normal" font="default" size="100%">hospital information systems</style></keyword><keyword><style  face="normal" font="default" size="100%">information exchange</style></keyword><keyword><style  face="normal" font="default" size="100%">medical information systems</style></keyword><keyword><style  face="normal" font="default" size="100%">regional medical system establishment</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">april</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&amp;arnumber=6201451&amp;contentType=Conference+Publications&amp;queryText%3DResearch+and+implementation+of+Electronic+Medical+Records+Editing+System+based+on+CDA</style></url></web-urls></urls><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">It is difficult to exchange information between heterogeneous Hospital Information Systems (HIS). It becomes the obstacle of regional medical system establishment. The coming forth of HL7 (Health Level 7) CDA (Clinical Document Architecture) standard provides the technical basic conditions. This paper describes CDA standards and CDA document structure. Through a complete analysis of Electronic Medical Record (EMR), the model of Electronic Medical Records Editing Subsystem is given. Based on this model, functional modules of Electronic Medical Records Editing Subsystem are designed and implemented. Through Electronic Medical Records Editing Subsystem, clinical documents can effectively produce, parse, validate and view. It provides a technical support for exchanges of medical and health information.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mandl, Kenneth D</style></author><author><style face="normal" font="default" size="100%">Mandel, Joshua C</style></author><author><style face="normal" font="default" size="100%">Murphy, Shawn N</style></author><author><style face="normal" font="default" size="100%">Bernstam, Elmer Victor</style></author><author><style face="normal" font="default" size="100%">Ramoni, Rachel L</style></author><author><style face="normal" font="default" size="100%">Kreda, David A</style></author><author><style face="normal" font="default" size="100%">McCoy, J Michael</style></author><author><style face="normal" font="default" size="100%">Adida, Ben</style></author><author><style face="normal" font="default" size="100%">Kohane, Isaac S.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The SMART Platform: early experience enabling substitutable applications for electronic health records.</style></title><secondary-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Mar 17</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">ObjectiveThe Substitutable Medical Applications, Reusable Technologies (SMART) Platforms project seeks to develop a health information technology platform with substitutable applications (apps) constructed around core services. The authors believe this is a promising approach to driving down healthcare costs, supporting standards evolution, accommodating differences in care workflow, fostering competition in the market, and accelerating innovation.Materials and methodsThe Office of the National Coordinator for Health Information Technology, through the Strategic Health IT Advanced Research Projects (SHARP) Program, funds the project. The SMART team has focused on enabling the property of substitutability through an app programming interface leveraging web standards, presenting predictable data payloads, and abstracting away many details of enterprise health information technology systems. Containers-health information technology systems, such as electronic health records (EHR), personally controlled health records, and health information exchanges that use the SMART app programming interface or a portion of it-marshal data sources and present data simply, reliably, and consistently to apps.ResultsThe SMART team has completed the first phase of the project (a) defining an app programming interface, (b) developing containers, and (c) producing a set of charter apps that showcase the system capabilities. A focal point of this phase was the SMART Apps Challenge, publicized by the White House, using http://www.challenge.gov website, and generating 15 app submissions with diverse functionality.ConclusionKey strategic decisions must be made about the most effective market for further disseminating SMART: existing market-leading EHR vendors, new entrants into the EHR market, or other stakeholders such as health information exchanges.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Faure, François</style></author><author><style face="normal" font="default" size="100%">Duriez, Christian</style></author><author><style face="normal" font="default" size="100%">Delingette, Hervé</style></author><author><style face="normal" font="default" size="100%">Allard, Jérémie</style></author><author><style face="normal" font="default" size="100%">Gilles, Benjamin</style></author><author><style face="normal" font="default" size="100%">Marchesseau, Stéphanie</style></author><author><style face="normal" font="default" size="100%">Talbot, Hugo</style></author><author><style face="normal" font="default" size="100%">Courtecuisse, Hadrien</style></author><author><style face="normal" font="default" size="100%">Bousquet, Guillaume</style></author><author><style face="normal" font="default" size="100%">Peterlik, Igor</style></author><author><style face="normal" font="default" size="100%">Cotin, Stéphane</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Payan, Yohan</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">SOFA: A Multi-Model Framework for Interactive Physical Simulation</style></title><secondary-title><style face="normal" font="default" size="100%">Soft Tissue Biomechanical Modeling for Computer Assisted Surgery</style></secondary-title><tertiary-title><style face="normal" font="default" size="100%">Studies in Mechanobiology, Tissue Engineering and Biomaterials</style></tertiary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/8415_2012_125</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer Berlin Heidelberg</style></publisher><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">283-321</style></pages><isbn><style face="normal" font="default" size="100%">978-3-642-29013-8</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Simulation Open Framework Architecture (SOFA) is an open-source C++ library primarily targeted at interactive computational medical simulation. SOFA facilitates collaborations between specialists from various domains, by decomposing complex simulators into components designed independently and organized in a scenegraph data structure. Each component encapsulates one of the aspects of a simulation, such as the degrees of freedom, the forces and constraints, the differential equations, the main loop algorithms, the linear solvers, the collision detection algorithms or the interaction devices. The simulated objects can be represented using several models, each of them optimized for a different task such as the computation of internal forces, collision detection, haptics or visual display. These models are synchronized during the simulation using a mapping mechanism. CPU and GPU implementations can be transparently combined to exploit the computational power of modern hardware architectures. Thanks to this flexible yet efficient architecture, SOFA can be used as a test-bed to compare models and algorithms, or as a basis for the development of complex, high-performance simulators.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hirschmann, Michael T</style></author><author><style face="normal" font="default" size="100%">Wagner, Christopher R</style></author><author><style face="normal" font="default" size="100%">Rasch, Helmut</style></author><author><style face="normal" font="default" size="100%">Henckel, Johann</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Standardized volumetric 3D-analysis of SPECT/CT imaging in orthopaedics: overcoming the limitations of qualitative 2D analysis.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Med Imaging</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Med Imaging</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">UNLABELLED: ABSTRACT:

BACKGROUND: SPECT/CT combines high resolution anatomical 3D computerized tomography (CT) and single photon emission computerized tomography (SPECT) as functional imaging, which provides 3D information about biological processes into a single imaging modality. The clinical utility of SPECT/CT imaging has been recognized in a variety of medical fields and most recently in orthopaedics; however, clinical adoption has been limited due to shortcomings of analytical tools available. Specifically, SPECT analyses are mainly qualitative due to variation in overall metabolic uptake among patients. Furthermore, most analyses are done in 2D, although rich 3D data are available. Consequently, it is difficult to quantitatively compare the position, size, and intensity of SPECT uptake regions among patients, and therefore difficult to draw meaningful clinical conclusions.

METHODS: We propose a method for normalizing orthopaedic SPECT/CT data that enables standardised 3D volumetric quantitative measurements and comparison among patients. Our method is based on 3D localisation using clinically relevant anatomical landmarks and frames of reference, along with intensity value normalisation using clinically relevant reference regions. Using the normalised data, we describe a thresholding technique to distinguish clinically relevant hot spots from background activity.

RESULTS: Using an exemplar comparison of two patients, we demonstrate how the normalised, 3D-rendered data can provide a richer source of clinical information and allow quantitative comparison of SPECT/CT measurements across patients. Specifically, we demonstrate how non-normalized SPECT/CT analysis can lead to different clinical conclusions than the normalized SPECT/CT analysis, and that normalized quantitative analysis can be a more accurate indicator of pathology.

CONCLUSIONS: Conventional orthopaedic frames of reference, 3D volumetric data analysis and thresholding are used to distinguish clinically relevant hot spots from background activity. Our goal is to facilitate a standardised approach to quantitative data collection and comparison of clinical studies using SPECT/CT, enabling more widespread clinical use of this powerful imaging tool.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gainer, Alex</style></author><author><style face="normal" font="default" size="100%">Roth, Mary</style></author><author><style face="normal" font="default" size="100%">Strong, Phil</style></author><author><style face="normal" font="default" size="100%">Davis, James</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A Standards-Based Open Source Application to Gather Health Assessment Data in Developing Countries</style></title><secondary-title><style face="normal" font="default" size="100%">Global Humanitarian Technology Conference (GHTC), 2012 IEEE</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">and Telemedicine</style></keyword><keyword><style  face="normal" font="default" size="100%">Ash</style></keyword><keyword><style  face="normal" font="default" size="100%">Communities</style></keyword><keyword><style  face="normal" font="default" size="100%">Computers</style></keyword><keyword><style  face="normal" font="default" size="100%">Health</style></keyword><keyword><style  face="normal" font="default" size="100%">Medical services</style></keyword><keyword><style  face="normal" font="default" size="100%">Medical Technology</style></keyword><keyword><style  face="normal" font="default" size="100%">Mobile communication</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Standards</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">oct.</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Many organizations are working in developing coun- tries to support local health care organizations and infrastructure to provide sustainable, community-based health care. This requires not only the influx of medical staff and supplies, but also requires maintaining individual health care records and enabling the ability to collect, analyze and aggregate data in the field to customize care to the local needs of the community, and to provide continuity of care to its citizens. The recent rise of adoption of standards for electronic health records(EHR) provides an alternative to using paper forms in mobile health clinics that often serve these countries. In this paper, we describe an open-source, standards-based health assessment software application developed by the non-profit organization Health Records For Everyone (HR4E) and field tested in a mobile health clinic in rural Ethiopia in the fall of 2011. The application allows mobile health clinic staff to quickly deploy medical clinics and collect patient data electronically in the face of various environmental challenges. In addition to producing electronic patient records which are validated in-field using HL7's Clinical Document Architecture standard, the application allows medical practitioners to view and summarize patient data for in-field analysis.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Thielemans, Kris</style></author><author><style face="normal" font="default" size="100%">Tsoumpas, Charalampos</style></author><author><style face="normal" font="default" size="100%">Mustafovic, Sanida</style></author><author><style face="normal" font="default" size="100%">Beisel, Tobias</style></author><author><style face="normal" font="default" size="100%">Aguiar, Pablo</style></author><author><style face="normal" font="default" size="100%">Dikaios, Nikolaos</style></author><author><style face="normal" font="default" size="100%">Jacobson, Matthew W</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">STIR: software for tomographic image reconstruction release 2.</style></title><secondary-title><style face="normal" font="default" size="100%">Phys Med Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Phys Med Biol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Algorithms</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Computers</style></keyword><keyword><style  face="normal" font="default" size="100%">Image Processing, Computer-Assisted</style></keyword><keyword><style  face="normal" font="default" size="100%">Mice</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Tomography</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Feb 21</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">57</style></volume><pages><style face="normal" font="default" size="100%">867-83</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We present a new version of STIR (Software for Tomographic Image Reconstruction), an open source object-oriented library implemented in C++ for 3D positron emission tomography reconstruction. This library has been designed such that it can be used for many algorithms and scanner geometries, while being portable to various computing platforms. This second release enhances its flexibility and modular design and includes additional features such as Compton scatter simulation, an additional iterative reconstruction algorithm and parametric image reconstruction (both indirect and direct). We discuss the new features in this release and present example results. STIR can be downloaded from http://stir.sourceforge.net.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Prlić, Andreas</style></author><author><style face="normal" font="default" size="100%">Procter, James B</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Ten simple rules for the open development of scientific software.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS Comput Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS Comput. Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">e1002802</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">12</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Suominen, Hanna</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Towards an international electronic repository and virtual laboratory of open data and open-source software for telehealth research: comparison of international, Australian and finnish privacy policies.</style></title><secondary-title><style face="normal" font="default" size="100%">Stud Health Technol Inform</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Stud Health Technol Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">182</style></volume><pages><style face="normal" font="default" size="100%">153-60</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Health data includes all content related to health in all data formats, document types, information systems, publication media and languages from all specialties, organisations, regions, states and countries. Capabilities to share, integrate and compare these data contents, clinical trial results and other evaluation outcomes together with telehealth applications for data processing are critical to accelerate discovery and its diffusion to clinical practice. However, the same ethical and legal frameworks that protect privacy hinder this open data and open-source code approach and the issues accumulate if moving data across national, regional or organisational borders. This can be seen as one of the reasons why many telehealth applications and health-research findings tend to be limited to very narrow domains and global results are lacking. The aim of this paper is to take steps towards establishing an international electronic repository and virtual laboratory of open data and open-source code for research purposes by comparing international, Australian and Finnish frameworks. The frameworks seem to be fundamentally similar; they apply the principles of accountability and adequacy to using and disclosing personal data. Their requirements to inform data subjects about the purposes of data collection and use before the dataset is collected, assure that individuals are no longer identifiable and to destruct data when the research activities are finished make sharing data and even secondary data difficult. Using the Internet or cloud services for sharing without proper approvals by ethics committees is technically not allowed if the data are stored in another country. The research community needs to overcome these barriers and develop a virtual laboratory, which operates on distributed data repositories. This empowers the community by enabling systematic evaluations of new technologies and research hypotheses on a rich variety of data and against existing applications, and subsequent tracking of quality improvements in time.&lt;/p&gt;</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Maglogiannis, Ilias</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Towards the Adoption of Open Source and Open Access Electronic Health Record Systems</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Healthcare Engineering</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">03</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1260/2040-2295.3.1.141</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">141–162</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">As the Electronic Health Record (EHR) systems constantly expand to support more clinical activities and their implementations in healthcare organizations become more widespread, several communities have been working intensively for several years to develop open access and open source EHR software, aiming at reducing the costs of EHR deployment and maintenance. In this paper, we describe and evaluate the most popular open source electronic medical records such as openEMR, openMRS and patientOS, providing their technical features and potentials. These systems are considered quite important due to their prevalence. The article presents the key features of each system and outlines the advantages and problems of Open Source Software (OSS) Systems through a review of the literature, in order to demonstrate the possibility of their adoption in modern electronic healthcare systems. Also discussed are the future trends of OS EHRs in the context of the Personal Health Records and mobile computing paradigm.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Radau, Perry</style></author><author><style face="normal" font="default" size="100%">Pintilie, Stefan</style></author><author><style face="normal" font="default" size="100%">Flor, Roey</style></author><author><style face="normal" font="default" size="100%">Biswas, Labonny</style></author><author><style face="normal" font="default" size="100%">Oduneye, Samuel</style></author><author><style face="normal" font="default" size="100%">Ramanan, Venkat</style></author><author><style face="normal" font="default" size="100%">Anderson, Kevan</style></author><author><style face="normal" font="default" size="100%">Wright, Graham</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Camara, Oscar</style></author><author><style face="normal" font="default" size="100%">Konukoglu, Ender</style></author><author><style face="normal" font="default" size="100%">Pop, Mihaela</style></author><author><style face="normal" font="default" size="100%">Rhode, Kawal</style></author><author><style face="normal" font="default" size="100%">Sermesant, Maxime</style></author><author><style face="normal" font="default" size="100%">Young, Alistair</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">VURTIGO: Visualization Platform for Real-Time, MRI-Guided Cardiac Electroanatomic Mapping</style></title><secondary-title><style face="normal" font="default" size="100%">Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges</style></secondary-title><tertiary-title><style face="normal" font="default" size="100%">Lecture Notes in Computer Science</style></tertiary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/978-3-642-28326-0_25</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer Berlin / Heidelberg</style></publisher><volume><style face="normal" font="default" size="100%">7085</style></volume><pages><style face="normal" font="default" size="100%">244-253</style></pages><isbn><style face="normal" font="default" size="100%">978-3-642-28325-3</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Guidance of electrophysiological (EP) procedures by magnetic resonance imaging (MRI) has significant advantages over x-ray fluoroscopy. Display of electroanatomic mapping (EAM) during an intervention fused with a prior MR volume and DE-MRI derived tissue classification should improve the accuracy of cardiac resynchronization therapy (CRT) for ventricular arrhythmias. Improved accuracy in the spatial localization of recorded EP points will produce an EAM to constrain and customize patient-specific cardiac electroanatomic models being developed for understanding the patterns of arrhythmogenic slow conduction zones causing reentry circuits and treatment planning. The Vurtigo software presented here is a four dimensional (3D+time) real-time visualization application for guiding interventions capable of displaying prior volumes, real-time MRI scan planes, EAM (voltage or activation times), segmented models, and tracked catheters. This paper will describe the architecture and features of Vurtigo followed by the application example of guiding percutaneous cardiac electroanatomic mapping in porcine models.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gietzelt, Matthias</style></author><author><style face="normal" font="default" size="100%">Goltz, Ursula</style></author><author><style face="normal" font="default" size="100%">Grunwald, Daniel</style></author><author><style face="normal" font="default" size="100%">Lochau, Malte</style></author><author><style face="normal" font="default" size="100%">Marschollek, Michael</style></author><author><style face="normal" font="default" size="100%">Song, Bianying</style></author><author><style face="normal" font="default" size="100%">Wolf, Klaus-Hendrik</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Arden2ByteCode: A one-pass Arden Syntax compiler for service-oriented decision support systems based on the OSGi platform.</style></title><secondary-title><style face="normal" font="default" size="100%">Comput Methods Programs Biomed</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1016/j.cmpb.2011.11.003} note = {Epub ahead of print</style></url></web-urls></urls><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Müller, Oliver</style></author><author><style face="normal" font="default" size="100%">Lipp, Peter</style></author><author><style face="normal" font="default" size="100%">Kaestner, Lars</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">ATOM - an OMERO add-on for automated import of image data.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC research notes</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Res Notes</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">382</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">UNLABELLED: ABSTRACT:

BACKGROUND: Modern microscope platforms are able to generate multiple gigabytes of image data in a single experimental session. In a routine research laboratory workflow, these data are initially stored on the local acquisition computer from which files need to be transferred to the experimenter's (remote) image repository (e.g., DVDs, portable hard discs or server-based storage) because of limited local data storage. Although manual solutions for this migration, such as OMERO - a client-server software for visualising and managing large amounts of image data - exist, this import process may be a time-consuming and tedious task.

FINDINGS: We have developed ATOM, a Java-based and thus platform-independent add-on for OMERO enabling automated transfer of image data from a wide variety of acquisition software packages into OMERO. ATOM provides a graphical user interface and allows pre-organisation of experimental data for the transfer.

CONCLUSIONS: ATOM is a convenient extension of the OMERO software system. An automated interface to OMERO will be a useful tool for scientists working with file formats supported by the Bio-Formats file format library, a platform-independent library for reading the most common file formats of microscope images.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21978452?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">François Tadel</style></author><author><style face="normal" font="default" size="100%">Sylvain Baillet</style></author><author><style face="normal" font="default" size="100%">John C. Mosher</style></author><author><style face="normal" font="default" size="100%">Dimitrios Pantazis</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Brainstorm: A User-Friendly Application for MEG/EEG Analysis</style></title><secondary-title><style face="normal" font="default" size="100%">Computational Intelligence and Neuroscience</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">01/2011</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.hindawi.com/journals/cin/2011/879716/</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">2011</style></volume><abstract><style face="normal" font="default" size="100%">Brainstorm is a collaborative open-source application dedicated to magnetoencephalography (MEG) and electroencephalography (EEG) data visualization and processing, with an emphasis on cortical source estimation techniques and their integration with anatomical magnetic resonance imaging (MRI) data. The primary objective of the software is to connect MEG/EEG neuroscience investigators with both the best-established and cutting-edge methods through a simple and intuitive graphical user interface (GUI).</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ferranti, Jeffrey M</style></author><author><style face="normal" font="default" size="100%">Gilbert, William</style></author><author><style face="normal" font="default" size="100%">McCall, Jonathan</style></author><author><style face="normal" font="default" size="100%">Shang, Howard</style></author><author><style face="normal" font="default" size="100%">Barros, Tanya</style></author><author><style face="normal" font="default" size="100%">Horvath, Monica M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The design and implementation of an open-source, data-driven cohort recruitment system: the Duke Integrated Subject Cohort and Enrollment Research Network (DISCERN)</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of the American Medical Informatics Association</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://jamia.bmj.com/content/early/2011/09/23/amiajnl-2011-000115.abstract</style></url></web-urls></urls><abstract><style face="normal" font="default" size="100%">Objective Failure to reach research subject recruitment goals is a significant impediment to the success of many clinical trials. Implementation of health-information technology has allowed retrospective analysis of data for cohort identification and recruitment, but few institutions have also leveraged real-time streams to support such activities.Design Duke Medicine has deployed a hybrid solution, The Duke Integrated Subject Cohort and Enrollment Research Network (DISCERN), that combines both retrospective warehouse data and clinical events contained in prospective Health Level 7 (HL7) messages to immediately alert study personnel of potential recruits as they become eligible.Results DISCERN analyzes more than 500‚Äà000 messages daily in service of 12 projects. Users may receive results via email, text pages, or on-demand reports. Preliminary results suggest DISCERN's unique ability to reason over both retrospective and real-time data increases study enrollment rates while reducing the time required to complete recruitment-related tasks. The authors have introduced a preconfigured DISCERN function as a self-service feature for users.Limitations The DISCERN framework is adoptable primarily by organizations using both HL7 message streams and a data warehouse. More efficient recruitment may exacerbate competition for research subjects, and investigators uncomfortable with new technology may find themselves at a competitive disadvantage in recruitment.Conclusion DISCERN's hybrid framework for identifying real-time clinical events housed in HL7 messages complements the traditional approach of using retrospective warehoused data. DISCERN is helpful in instances when the required clinical data may not be loaded into the warehouse and thus must be captured contemporaneously during patient care. Use of an open-source tool supports generalizability to other institutions at minimal cost.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Costa, Carlos</style></author><author><style face="normal" font="default" size="100%">Ferreira, Carlos</style></author><author><style face="normal" font="default" size="100%">Bastião, Luís</style></author><author><style face="normal" font="default" size="100%">Ribeiro, Luís</style></author><author><style face="normal" font="default" size="100%">Silva, Augusto</style></author><author><style face="normal" font="default" size="100%">Oliveira, José Luís</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Dicoogle - an Open Source Peer-to-Peer PACS.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Digit Imaging</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">24</style></volume><pages><style face="normal" font="default" size="100%">848-56</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Picture Archiving and Communication Systems (PACS) have been widely deployed in healthcare institutions, and they now constitute a normal commodity for practitioners. However, its installation, maintenance, and utilization are still a burden due to their heavy structures, typically supported by centralized computational solutions. In this paper, we present Dicoogle, a PACS archive supported by a document-based indexing system and by peer-to-peer (P2P) protocols. Replacing the traditional database storage (RDBMS) by a documental organization permits gathering and indexing data from file-based repositories, which allows searching the archive through free text queries. As a direct result of this strategy, more information can be extracted from medical imaging repositories, which clearly increases flexibility when compared with current query and retrieval DICOM services. The inclusion of P2P features allows PACS internetworking without the need for a central management framework. Moreover, Dicoogle is easy to install, manage, and use, and it maintains full interoperability with standard DICOM services.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20981467?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zerbe, Norman</style></author><author><style face="normal" font="default" size="100%">Hufnagl, Peter</style></author><author><style face="normal" font="default" size="100%">Schluns, Karsten</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Distributed computing in image analysis using open source frameworks and application to image sharpness assessment of histological whole slide images</style></title><secondary-title><style face="normal" font="default" size="100%">Diagnostic Pathology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.diagnosticpathology.org/content/6/S1/S16</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">Suppl 1</style></number><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">S16</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND:Automated image analysis on virtual slides is evolving rapidly and will play an important role in the future of digital pathology. Due to the image size, the computational cost of processing whole slide images (WSIs) in full resolution is immense. Moreover, image analysis requires well focused images in high magnification.METHODS:We present a system that merges virtual microscopy techniques, open source image analysis software, and distributed parallel processing. We have integrated the parallel processing framework JPPF, so batch processing can be performed distributed and in parallel. All resulting meta data and image data are collected and merged. As an example the system is applied to the specific task of image sharpness assessment. ImageJ is an open source image editing and processing framework developed at the NIH having a large user community that contributes image processing algorithms wrapped as plug-ins in a wide field of life science applications. We developed an ImageJ plug-in that supports both basic interactive virtual microscope and batch processing functionality. For the application of sharpness inspection we employ an approach with non-overlapping tiles. Compute nodes retrieve image tiles of moderate size from the streaming server and compute the focus measure. Each tile is divided into small sub images to calculate an edge based sharpness criterion which is used for classification. The results are aggregated in a sharpness map.RESULTS:Based on the system we calculate a sharpness measure and classify virtual slides into one of the following categories - excellent, okay, review and defective. Generating a scaled sharpness map enables the user to evaluate sharpness of WSIs and shows overall quality at a glance thus reducing tedious assessment work.CONCLUSIONS:Using sharpness assessment as an example, the introduced system can be used to process, analyze and parallelize analysis of whole slide images based on open source software.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Helms, Eric</style></author><author><style face="normal" font="default" size="100%">Williams, Laurie</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evaluating access control of open source electronic health record systems</style></title><secondary-title><style face="normal" font="default" size="100%">Proceeding of the 3rd workshop on Software engineering in health care</style></secondary-title><tertiary-title><style face="normal" font="default" size="100%">SEHC '11</style></tertiary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">access control</style></keyword><keyword><style  face="normal" font="default" size="100%">electronic health records</style></keyword><keyword><style  face="normal" font="default" size="100%">health it</style></keyword><keyword><style  face="normal" font="default" size="100%">healthcare</style></keyword><keyword><style  face="normal" font="default" size="100%">privacy</style></keyword><keyword><style  face="normal" font="default" size="100%">role-based access control</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><publisher><style face="normal" font="default" size="100%">ACM</style></publisher><pub-location><style face="normal" font="default" size="100%">New York, NY, USA</style></pub-location><pages><style face="normal" font="default" size="100%">63–70</style></pages><isbn><style face="normal" font="default" size="100%">978-1-4503-0585-3</style></isbn><abstract><style face="normal" font="default" size="100%">Incentives and penalties for healthcare providers as laid out in the American Recovery and Reinvestment Act of 2009 have caused tremendous growth in the development and installation of electronic health record (EHR) systems in the US. For the benefit of protecting patient privacy, regulations and certification criteria related to EHR systems stipulate the use of access control of protected health information. The goal of this research is to guide development teams, regulators, and certification bodies by assessing the state of the practice in EHR access control. In this paper, we present a compilation of 25 criteria relative to access control in EHR systems found in the Health Insurance Portability and Accountability Act (HIPAA) regulation, meaningful use certification criteria, best practices embodied in the National Institute for Standards and Technology (NIST) role-based access control standard, and other best practices found in the literature. We then examine the state of the practice in access control by evaluating four open source EHR systems using these 25 evaluation criteria. Our research indicates that the NIST Meaningful Use criteria provide HIPAA compliance, but none of the regulatory and certification criteria address the implementation standards, and best practices related to access control. Additionally, our results indicate that open source EHR system designers are not implementing robust access control mechanisms for the adequate protection of patient data.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Oostenveld, Robert</style></author><author><style face="normal" font="default" size="100%">Fries, Pascal</style></author><author><style face="normal" font="default" size="100%">Maris, Eric</style></author><author><style face="normal" font="default" size="100%">Schoffelen, Jan-Mathijs</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data.</style></title><secondary-title><style face="normal" font="default" size="100%">Computational intelligence and neuroscience</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Comput Intell Neurosci</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electroencephalography</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrophysiological Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Magnetoencephalography</style></keyword><keyword><style  face="normal" font="default" size="100%">Numerical Analysis, Computer-Assisted</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2011</style></volume><pages><style face="normal" font="default" size="100%">156869</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21253357?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gramfort, Alexandre</style></author><author><style face="normal" font="default" size="100%">Papadopoulo, Théodore</style></author><author><style face="normal" font="default" size="100%">Olivi, Emmanuel</style></author><author><style face="normal" font="default" size="100%">Clerc, Maureen</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Forward field computation with OpenMEEG.</style></title><secondary-title><style face="normal" font="default" size="100%">Computational intelligence and neuroscience</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Comput Intell Neurosci</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2011</style></volume><pages><style face="normal" font="default" size="100%">923703</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">To recover the sources giving rise to electro- and magnetoencephalography in individual measurements, realistic physiological modeling is required, and accurate numerical solutions must be computed. We present OpenMEEG, which solves the electromagnetic forward problem in the quasistatic regime, for head models with piecewise constant conductivity. The core of OpenMEEG consists of the symmetric Boundary Element Method, which is based on an extended Green Representation theorem. OpenMEEG is able to provide lead fields for four different electromagnetic forward problems: Electroencephalography (EEG), Magnetoencephalography (MEG), Electrical Impedance Tomography (EIT), and intracranial electric potentials (IPs). OpenMEEG is open source and multiplatform. It can be used from Python and Matlab in conjunction with toolboxes that solve the inverse problem; its integration within FieldTrip is operational since release 2.0.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21437231?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Cavalini, Luciana</style></author><author><style face="normal" font="default" size="100%">Cook, Timothy</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Hissam, Scott</style></author><author><style face="normal" font="default" size="100%">Russo, Barbara</style></author><author><style face="normal" font="default" size="100%">de Mendonça Neto, Manoel</style></author><author><style face="normal" font="default" size="100%">Kon, Fabio</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Health Informatics: The Relevance of Open Source and Multilevel Modeling</style></title><secondary-title><style face="normal" font="default" size="100%">Open Source Systems: Grounding Research</style></secondary-title><tertiary-title><style face="normal" font="default" size="100%">IFIP Advances in Information and Communication Technology</style></tertiary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/978-3-642-24418-6_29</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer Boston</style></publisher><volume><style face="normal" font="default" size="100%">365</style></volume><pages><style face="normal" font="default" size="100%">338-347</style></pages><isbn><style face="normal" font="default" size="100%">978-3-642-24417-9</style></isbn><abstract><style face="normal" font="default" size="100%">Health information features significant spatial-temporal and domain complexities, which brings challenges to the implementation of patient-centered, interoperable and semantically coherent healthcare information systems. This position paper supports the idea that the multilevel modeling approach is essential to ensure interoperability at the semantic level, but true interoperability is only achieved by the adoption of open standards, and open source implementations are needed for promote competition based on software quality. The Multilevel Healthcare Information Modelling (MLHIM) specifications are presented as the fully open source multilevel modeling reference implementation, and best practices for the development of multilevel-based open source healthcare applications are suggested.</style></abstract><notes><style face="normal" font="default" size="100%">10.1007/978-3-642-24418-6_29</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Birkle, Markus</style></author><author><style face="normal" font="default" size="100%">Schneider, Benjamin</style></author><author><style face="normal" font="default" size="100%">Beck, Tobias</style></author><author><style face="normal" font="default" size="100%">Deuster, Thomas</style></author><author><style face="normal" font="default" size="100%">Fischer, Markus</style></author><author><style face="normal" font="default" size="100%">Flatow, Florian</style></author><author><style face="normal" font="default" size="100%">Heinrich, Robert</style></author><author><style face="normal" font="default" size="100%">Kapp, Christian</style></author><author><style face="normal" font="default" size="100%">Riemer, Jasmin</style></author><author><style face="normal" font="default" size="100%">Simon, Michael</style></author><author><style face="normal" font="default" size="100%">Bergh, Björn</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Implementation of an open source provider organization registry service.</style></title><secondary-title><style face="normal" font="default" size="100%">Studies in health technology and informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Stud Health Technol Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">169</style></volume><pages><style face="normal" font="default" size="100%">265-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Healthcare Information Exchange Networks (HIEN) enables the exchange of medical information between different institutions. One of the biggest problems running a HIEN is the unique identification of the care providers. The provider and organisation registry service (PORS) has to provide a unique identifier for care providers. The concept and the implementation of PORS will be described in this article. Finally the PORS implementation will be compared with the Integrating the Healthcare Enterprise (IHE) profile for a Healthcare Provider Directory (HPD).</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21893754?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chi, Benjamin H</style></author><author><style face="normal" font="default" size="100%">Vwalika, Bellington</style></author><author><style face="normal" font="default" size="100%">Killam, William P</style></author><author><style face="normal" font="default" size="100%">Wamalume, Chibesa</style></author><author><style face="normal" font="default" size="100%">Giganti, Mark J</style></author><author><style face="normal" font="default" size="100%">Mbewe, Reuben</style></author><author><style face="normal" font="default" size="100%">Stringer, Elizabeth M</style></author><author><style face="normal" font="default" size="100%">Chintu, Namwinga T</style></author><author><style face="normal" font="default" size="100%">Putta, Nande B</style></author><author><style face="normal" font="default" size="100%">Liu, Katherine C</style></author><author><style face="normal" font="default" size="100%">Chibwesha, Carla J</style></author><author><style face="normal" font="default" size="100%">Rouse, Dwight J</style></author><author><style face="normal" font="default" size="100%">Stringer, Jeffrey S A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Implementation of the Zambia electronic perinatal record system for comprehensive prenatal and delivery care.</style></title><secondary-title><style face="normal" font="default" size="100%">International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int J Gynaecol Obstet</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">113</style></volume><pages><style face="normal" font="default" size="100%">131-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">OBJECTIVE:
To characterize prenatal and delivery care in an urban African setting.

METHODS:
The Zambia Electronic Perinatal Record System (ZEPRS) was implemented to record demographic characteristics, past medical and obstetric history, prenatal care, and delivery and newborn care for pregnant women across 25 facilities in the Lusaka public health sector.

RESULTS:
From June 1, 2007, to January 31, 2010, 115552 pregnant women had prenatal and delivery information recorded in ZEPRS. Median gestation age at first prenatal visit was 23weeks (interquartile range [IQR] 19-26). Syphilis screening was documented in 95663 (83%) pregnancies: 2449 (2.6%) women tested positive, of whom 1589 (64.9%) were treated appropriately. 111108 (96%) women agreed to HIV testing, of whom 22% were diagnosed with HIV. Overall, 112813 (98%) of recorded pregnancies resulted in a live birth, and 2739 (2%) in a stillbirth. The median gestational age was 38weeks (IQR 35-40) at delivery; the median birth weight of newborns was 3000g (IQR 2700-3300g).

CONCLUSION:
The results demonstrate the feasibility of using a comprehensive electronic medical record in an urban African setting, and highlight its important role in ongoing efforts to improve clinical care.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21315347?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Frisardi, Gianni</style></author><author><style face="normal" font="default" size="100%">Chessa, Giacomo</style></author><author><style face="normal" font="default" size="100%">Barone, Sandro</style></author><author><style face="normal" font="default" size="100%">Paoli, Alessandro</style></author><author><style face="normal" font="default" size="100%">Razionale, Armando</style></author><author><style face="normal" font="default" size="100%">Frisardi, Flavio</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Integration of 3D anatomical data obtained by CT imaging and 3D optical scanning for Computer Aided Implant Surgery.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC medical imaging</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Feb 21</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">5</style></pages><language><style face="normal" font="default" size="100%">ENG</style></language><abstract><style face="normal" font="default" size="100%">ABSTRACT: BACKGROUND: A precise placement of dental implants is a crucial step to optimize both prosthetic aspects and functional constraints. In this context, the use of virtual guiding systems has been recognized as a fundamental tool to control the ideal implant position. In particular, complex periodontal surgeries can be performed using preoperative planning based on CT data. The critical point of the procedure relies on the lack of accuracy in transferring CT planning information to surgical field through custom-made stereo-lithographic surgical guides. METHODS: In this work, a novel methodology is proposed for monitoring loss of accuracy in transferring CT dental information into periodontal surgical field. The methodology is based on integrating 3D data of anatomical (impression and cast) and preoperative (radiographic template) models, obtained by both CT and optical scanning processes. RESULTS: A clinical case, relative to a fully edentulous jaw patient, has been used as test case to assess the accuracy of the various steps concurring in manufacturing surgical guides. In particular, a surgical guide has been designed to place implants in the bone structure of the patient. The analysis of the results has allowed the clinician to monitor all the errors, which have been occurring step by step manufacturing the physical templates. CONCLUSIONS: The use of an optical scanner, which has a higher resolution and accuracy than CT scanning, has demonstrated to be a valid support to control the precision of the various physical models adopted and to point out possible error sources. A case study regarding a fully edentulous patient has confirmed the feasibility of the proposed methodology.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21338504?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mejia, Ismael</style></author><author><style face="normal" font="default" size="100%">Südholt, Mario</style></author><author><style face="normal" font="default" size="100%">Benavides Navarro, Luis Daniel</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Invasive composition for the evolution of a health information system</style></title><secondary-title><style face="normal" font="default" size="100%">Variability &amp; Composition (VariComp)</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Aspect-oriented programming</style></keyword><keyword><style  face="normal" font="default" size="100%">Distributed systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Health information systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Invasive software composition</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">03</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://hal.inria.fr/inria-00567598/PDF/mejia-sudholt-benavides_varicomp-AOSD2011.pdf</style></url></web-urls></urls><pub-location><style face="normal" font="default" size="100%">Pernambuco Brazil</style></pub-location><abstract><style face="normal" font="default" size="100%">{I}n this paper we show that some of the evolution tasks in {O}pen{MRS}, a health information system, may require the invasive modification of interfaces and implementations in order to offer an appropriate modularization. {W}e introduce a new composition framework in {J}ava that supports the definition of expressive pattern-based invasive compositions. {F}ur thermore, we show that the composition framework allows us to concisely define an evolution scenario of {O}pen{MRS} that supports the consolidation of patient data from differ- ent remote instances.</style></abstract><notes><style face="normal" font="default" size="100%">{ACM} 978-1-4503-0646-1/11/03 {D}.: {S}oftware/{D}.3: {PROGRAMMING} {LANGUAGES}/{D}.3.3: {L}anguage {C}onstructs and {F}eatures</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Henttonen, Katja</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Hissam, Scott</style></author><author><style face="normal" font="default" size="100%">Russo, Barbara</style></author><author><style face="normal" font="default" size="100%">de Mendonça Neto, Manoel</style></author><author><style face="normal" font="default" size="100%">Kon, Fabio</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Libre Software as an Innovation Enabler in India Experiences of a Bangalorian Software SME</style></title><secondary-title><style face="normal" font="default" size="100%">Open Source Systems: Grounding Research</style></secondary-title><tertiary-title><style face="normal" font="default" size="100%">IFIP Advances in Information and Communication Technology</style></tertiary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/978-3-642-24418-6_15</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer Boston</style></publisher><volume><style face="normal" font="default" size="100%">365</style></volume><pages><style face="normal" font="default" size="100%">220-232</style></pages><isbn><style face="normal" font="default" size="100%">978-3-642-24417-9</style></isbn><abstract><style face="normal" font="default" size="100%">Free/Libre and open source software (FLOSS) has been advocated for its presumed capacity to support native software industries in developing countries. It is said to create new spaces for exploration and to lower entry barriers to mature software markets, for example. However, little empirical research has been conducted concerning FLOSS business in a developing country setting and, thus, there is not much evidence to support or refute these claims. This paper presents a business case study conducted in India, a country branded as a ’software powerhouse’ of the developing world. The findings show how FLOSS has opened up significant opportunities for the case company, especially in terms of improving its innovative capability and upgrading in the software value chain. On the other hand, they also highlight some challenges to FLOSS involvement that rise specifically from the Indian context.</style></abstract><notes><style face="normal" font="default" size="100%">10.1007/978-3-642-24418-6_15</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Garcia Ruiz, Manuel</style></author><author><style face="normal" font="default" size="100%">Garcia Chaves, Alvin</style></author><author><style face="normal" font="default" size="100%">Ruiz Ibañez, Carlos</style></author><author><style face="normal" font="default" size="100%">Gutierrez Mazo, Jorge Mario</style></author><author><style face="normal" font="default" size="100%">Ramirez Giraldo, Juan Carlos</style></author><author><style face="normal" font="default" size="100%">Pelaez Echavarria, Alejandro</style></author><author><style face="normal" font="default" size="100%">Valencia Diaz, Edison</style></author><author><style face="normal" font="default" size="100%">Pelaez Restrepo, Gustavo</style></author><author><style face="normal" font="default" size="100%">Montoya Munera, Edwin Nelson</style></author><author><style face="normal" font="default" size="100%">Garcia Loaiza, Bernardo</style></author><author><style face="normal" font="default" size="100%">Gomez Gonzalez, Sebastian</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">mantisGRID: A Grid Platform for DICOM Medical Images Management in Colombia and Latin America.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Digit Imaging</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">24</style></volume><pages><style face="normal" font="default" size="100%">271-83</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">This paper presents the mantisGRID project, an interinstitutional initiative from Colombian medical and academic centers aiming to provide medical grid services for Colombia and Latin America. The mantisGRID is a GRID platform, based on open source grid infrastructure that provides the necessary services to access and exchange medical images and associated information following digital imaging and communications in medicine (DICOM) and health level 7 standards. The paper focuses first on the data abstraction architecture, which is achieved via Open Grid Services Architecture Data Access and Integration (OGSA-DAI) services and supported by the Globus Toolkit. The grid currently uses a 30-Mb bandwidth of the Colombian High Technology Academic Network, RENATA, connected to Internet 2. It also includes a discussion on the relational database created to handle the DICOM objects that were represented using Extensible Markup Language Schema documents, as well as other features implemented such as data security, user authentication, and patient confidentiality. Grid performance was tested using the three current operative nodes and the results demonstrated comparable query times between the mantisGRID (OGSA-DAI) and Distributed mySQL databases, especially for a large number of records.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20127269?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Aladl, Usaf E.</style></author><author><style face="normal" font="default" size="100%">Peters, Terry</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">El-Baz, Ayman S.</style></author><author><style face="normal" font="default" size="100%">Acharya U, Rajendra</style></author><author><style face="normal" font="default" size="100%">Laine, Andrew F.</style></author><author><style face="normal" font="default" size="100%">Suri, Jasjit S.</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Medical Image Registration</style></title><secondary-title><style face="normal" font="default" size="100%">Multi Modality State-of-the-Art Medical Image Segmentation and Registration Methodologies</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/978-1-4419-8204-9_9</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer New York</style></publisher><pages><style face="normal" font="default" size="100%">227-245</style></pages><isbn><style face="normal" font="default" size="100%">978-1-4419-8204-9</style></isbn><abstract><style face="normal" font="default" size="100%">In this chapter, we cover the necessary background information required to understand medical image registration, the basic tools required to implement registration algorithms, and demonstrate a complete application for various types of registration between different modalities using freely available and maintained software.</style></abstract><notes><style face="normal" font="default" size="100%">10.1007/978-1-4419-8204-9_9</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Seitel, Alexander</style></author><author><style face="normal" font="default" size="100%">Yung, Kwong</style></author><author><style face="normal" font="default" size="100%">Mersmann, Sven</style></author><author><style face="normal" font="default" size="100%">Kilgus, Thomas</style></author><author><style face="normal" font="default" size="100%">Groch, Anja</style></author><author><style face="normal" font="default" size="100%">Dos Santos, Thiago R</style></author><author><style face="normal" font="default" size="100%">Franz, Alfred M</style></author><author><style face="normal" font="default" size="100%">Nolden, Marco</style></author><author><style face="normal" font="default" size="100%">Meinzer, Hans-Peter</style></author><author><style face="normal" font="default" size="100%">Maier-Hein, Lena</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">MITK-ToF-Range data within MITK.</style></title><secondary-title><style face="normal" font="default" size="100%">International journal of computer assisted radiology and surgery</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 May 31</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">ENG</style></language><abstract><style face="normal" font="default" size="100%">PURPOSE: The time-of-flight (ToF) technique is an emerging technique for rapidly acquiring distance information and is becoming increasingly popular for intra-operative surface acquisition. Using the ToF technique as an intra-operative imaging modality requires seamless integration into the clinical workflow. We thus aim to integrate ToF support in an existing framework for medical image processing. METHODS: MITK-ToF was implemented as an extension of the open-source C++ Medical Imaging Interaction Toolkit (MITK) and provides the basic functionality needed for rapid prototyping and development of image-guided therapy (IGT) applications that utilize range data for intra-operative surface acquisition. This framework was designed with a module-based architecture separating the hardware-dependent image acquisition task from the processing of the range data. RESULTS: The first version of MITK-ToF has been released as an open-source toolkit and supports several ToF cameras and basic processing algorithms. The toolkit, a sample application, and a tutorial are available from http://mitk.org . CONCLUSIONS: With the increased popularity of time-of-flight cameras for intra-operative surface acquisition, integration of range data supports into medical image processing toolkits such as MITK is a necessary step. Handling acquisition of range data from different cameras and processing of the data requires the establishment and use of software design principles that emphasize flexibility, extendibility, robustness, performance, and portability. The open-source toolkit MITK-ToF satisfies these requirements for the image-guided therapy community and was already used in several research projects.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21626396?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Raptis, Dimitri A.</style></author><author><style face="normal" font="default" size="100%">Mettler, Tobias</style></author><author><style face="normal" font="default" size="100%">Tzanas, Kostas</style></author><author><style face="normal" font="default" size="100%">Graf, Rolf</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A novel open-source web-based platform promoting collaboration of healthcare professionals and biostatisticians: A design science approach</style></title><secondary-title><style face="normal" font="default" size="100%">Informatics for Health and Social Care</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">clinician</style></keyword><keyword><style  face="normal" font="default" size="100%">collaboration</style></keyword><keyword><style  face="normal" font="default" size="100%">design science research</style></keyword><keyword><style  face="normal" font="default" size="100%">open source</style></keyword><keyword><style  face="normal" font="default" size="100%">quality of research</style></keyword><keyword><style  face="normal" font="default" size="100%">relationship</style></keyword><keyword><style  face="normal" font="default" size="100%">statisticians</style></keyword><keyword><style  face="normal" font="default" size="100%">user-centred</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://informahealthcare.com/doi/abs/10.3109/17538157.2011.590257</style></url></web-urls></urls><pages><style face="normal" font="default" size="100%">1-15</style></pages><abstract><style face="normal" font="default" size="100%">Collaboration among clinicians and statisticians is relatively poor, with many cases leading to poor quality research, reflected by low level of evidence studies published in the literature, thus affecting the overall quality of healthcare. We have developed a novel open-source web-based platform aiming in reinforcing the clinician–statistician relationship, using an iterative design research process by involving all end-users. Evaluation of this platform by healthcare professionals and biostatisticians was highly positive, as we first identified the pitfalls of their relationship and overcame them through the use of this platform. We are hoping that this will strengthen the clinician–statistician relationship in the short term and ultimately improve the quality of research and hence the quality of healthcare in the long term.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Caskey, , Charles F.</style></author><author><style face="normal" font="default" size="100%">Hlawitschka, , Mario</style></author><author><style face="normal" font="default" size="100%">Qin, , Shengping</style></author><author><style face="normal" font="default" size="100%">Mahakian, , Lisa M.</style></author><author><style face="normal" font="default" size="100%">Cardiff, , Robert D.</style></author><author><style face="normal" font="default" size="100%">Boone, , John M.</style></author><author><style face="normal" font="default" size="100%">Ferrara, , Katherine W.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">An Open Environment CT-US Fusion for Tissue Segmentation during Interventional Guidance</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS ONE</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">11</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1371%2Fjournal.pone.0027372</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">11</style></number><publisher><style face="normal" font="default" size="100%">Public Library of Science</style></publisher><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">e27372</style></pages><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Therapeutic ultrasound (US) can be noninvasively focused to activate drugs, ablate tumors and deliver drugs beyond the blood brain barrier. However, well-controlled guidance of US therapy requires fusion with a navigational modality, such as magnetic resonance imaging (MRI) or X-ray computed tomography (CT). Here, we developed and validated tissue characterization using a fusion between US and CT. The performance of the CT/US fusion was quantified by the calibration error, target registration error and fiducial registration error. Met-1 tumors in the fat pads of 12 female FVB mice provided a model of developing breast cancer with which to evaluate CT-based tissue segmentation. Hounsfield units (HU) within the tumor and surrounding fat pad were quantified, validated with histology and segmented for parametric analysis (fat: −300 to 0 HU, protein-rich: 1 to 300 HU, and bone: HU&amp;gt;300). Our open source CT/US fusion system differentiated soft tissue, bone and fat with a spatial accuracy of ∼1 mm. Region of interest (ROI) analysis of the tumor and surrounding fat pad using a 1 mm&lt;sup&gt;2&lt;/sup&gt; ROI resulted in mean HU of 68±44 within the tumor and −97±52 within the fat pad adjacent to the tumor (p&amp;lt;0.005). The tumor area measured by CT and histology was correlated (r&lt;sup&gt;2&lt;/sup&gt; = 0.92), while the area designated as fat decreased with increasing tumor size (r&lt;sup&gt;2&lt;/sup&gt; = 0.51). Analysis of CT and histology images of the tumor and surrounding fat pad revealed an average percentage of fat of 65.3% vs. 75.2%, 36.5% vs. 48.4%, and 31.6% vs. 38.5% for tumors &amp;lt;75 mm&lt;sup&gt;3&lt;/sup&gt;, 75–150 mm&lt;sup&gt;3&lt;/sup&gt; and &amp;gt;150 mm&lt;sup&gt;3&lt;/sup&gt;, respectively. Further, CT mapped bone-soft tissue interfaces near the acoustic beam during real-time imaging. Combined CT/US is a feasible method for guiding interventions by tracking the acoustic focus within a pre-acquired CT image volume and characterizing tissues proximal to and surrounding the acoustic focus.&lt;/p&gt;</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Locatelli, Paolo</style></author><author><style face="normal" font="default" size="100%">Baj, Emanuele</style></author><author><style face="normal" font="default" size="100%">Restifo, Nicola</style></author><author><style face="normal" font="default" size="100%">Origgi, Gianni</style></author><author><style face="normal" font="default" size="100%">Bragagia, Silvia</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Arabnia, Hamid R. R.</style></author><author><style face="normal" font="default" size="100%">Tran, Quoc-Nam</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Open Source Clinical Portals: A Model for Healthcare Information Systems to Support Care Processes and Feed Clinical Research</style></title><secondary-title><style face="normal" font="default" size="100%">Software Tools and Algorithms for Biological Systems</style></secondary-title><tertiary-title><style face="normal" font="default" size="100%">Advances in Experimental Medicine and Biology</style></tertiary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/978-1-4419-7046-6_68</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer New York</style></publisher><volume><style face="normal" font="default" size="100%">696</style></volume><pages><style face="normal" font="default" size="100%">667-677</style></pages><isbn><style face="normal" font="default" size="100%">978-1-4419-7046-6</style></isbn><abstract><style face="normal" font="default" size="100%">Open source is a still unexploited chance for healthcare organizations and technology providers to answer to a growing demand for innovation and to join economical benefits with a new way of managing hospital information systems. This chapter will present the case of the web enterprise clinical portal developed in Italy by Niguarda Hospital in Milan with the support of Fondazione Politecnico di Milano, to enable a paperless environment for clinical and administrative activities in the ward. This represents also one rare case of open source technology and reuse in the healthcare sector, as the system’s porting is now taking place at Besta Neurological Institute in Milan. This institute is customizing the portal to feed researchers with structured clinical data collected in its portal’s patient records, so that they can be analyzed, e.g., through business intelligence tools. Both organizational and clinical advantages are investigated, from process monitoring, to semantic data structuring, to recognition of common patterns in care processes.</style></abstract><notes><style face="normal" font="default" size="100%">10.1007/978-1-4419-7046-6_68</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Reynolds, J. Carl</style></author><author><style face="normal" font="default" size="100%">Wyatt, C. Jeremy</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open Source, Open Standards, and Health Care Information Systems</style></title><secondary-title><style face="normal" font="default" size="100%">J Med Internet Res</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Health Care Information Systems</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">Feb</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.jmir.org/2011/1/e24/</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">1</style></number><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">e24</style></pages></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chung-Yueh Lien</style></author><author><style face="normal" font="default" size="100%">Onken, Michael</style></author><author><style face="normal" font="default" size="100%">Marco Eichelberg</style></author><author><style face="normal" font="default" size="100%">Tsair Kao</style></author><author><style face="normal" font="default" size="100%">Andreas Hein</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">William W. Boonn</style></author><author><style face="normal" font="default" size="100%">Brent J. Liu</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Open source tools for standardized privacy protection of medical images</style></title><secondary-title><style face="normal" font="default" size="100%">Medical Imaging 2011: Advanced PACS-based Imaging Informatics and Therapeutic Applications</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://link.aip.org/link/?PSI/7967/79670M/1</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">1</style></number><publisher><style face="normal" font="default" size="100%">SPIE</style></publisher><volume><style face="normal" font="default" size="100%">7967</style></volume><pages><style face="normal" font="default" size="100%">79670M</style></pages><abstract><style face="normal" font="default" size="100%">In addition to the primary care context, medical images are often useful for research projects and community healthcare networks, so-called &quot;secondary use&quot;. Patient privacy becomes an issue in such scenarios since the disclosure of personal health information (PHI) has to be prevented in a sharing environment. In general, most PHIs should be completely removed from the images according to the respective privacy regulations, but some basic and alleviated data is usually required for accurate image interpretation. Our objective is to utilize and enhance these specifications in order to provide reliable software implementations for de- and re-identification of medical images suitable for online and offline delivery. DICOM (Digital Imaging and Communications in Medicine) images are de-identified by replacing PHI-specific information with values still being reasonable for imaging diagnosis and patient indexing. In this paper, this approach is evaluated based on a prototype implementation built on top of the open source framework DCMTK (DICOM Toolkit) utilizing standardized de- and re-identification mechanisms. A set of tools has been developed for DICOM de-identification that meets privacy requirements of an offline and online sharing environment and fully relies on standard-based methods.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mohammed-Rajput, Nareesa A</style></author><author><style face="normal" font="default" size="100%">Smith, Dawn C</style></author><author><style face="normal" font="default" size="100%">Mamlin, Burke</style></author><author><style face="normal" font="default" size="100%">Biondich, Paul</style></author><author><style face="normal" font="default" size="100%">Doebbeling, Brad N</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">for the Open MRS Collaborative Investigators</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">OpenMRS, A Global Medical Records System Collaborative: Factors Influencing Successful Implementation.</style></title><secondary-title><style face="normal" font="default" size="100%">AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2011</style></volume><pages><style face="normal" font="default" size="100%">960-968</style></pages><language><style face="normal" font="default" size="100%">ENG</style></language><abstract><style face="normal" font="default" size="100%">OpenMRS is an open-source, robust electronic health record (EHR) platform that is supported by a large global network and used in over forty countries. We explored what factors lead to successful implementation of OpenMRS in resource constrained settings. Data sources included in-person and telephone key informant interviews, focus groups and responses to an electronic survey from 10 sites in 7 countries. Qualitative data was coded through independent coding, discussion and consensus. The most common perceived benefits of implementation were for providing clinical care, reporting to funders, managing operations and research. Successful implementation factors include securing adequate infrastructure, and sociotechnical system factors, particularly adequate staffing, computers, and ability to use software. Strategic and tactical planning were successful strategies, including understanding and addressing the infrastructure and human costs involved, training or hiring personnel technically capable of modifying the software and integrating it into the daily work flow to meet clinicians' needs.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22195155?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">John Noll</style></author><author><style face="normal" font="default" size="100%">Sarah Beecham</style></author><author><style face="normal" font="default" size="100%">Dominik Seichter</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A Qualitative Study of Open Source Software Development: The Open EMR Project</style></title><secondary-title><style face="normal" font="default" size="100%">Empirical Software Engineering and Measurement, International Symposium on</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><publisher><style face="normal" font="default" size="100%">IEEE Computer Society</style></publisher><pub-location><style face="normal" font="default" size="100%">Los Alamitos, CA, USA</style></pub-location><pages><style face="normal" font="default" size="100%">30-39</style></pages><isbn><style face="normal" font="default" size="100%">978-0-7695-4604-9</style></isbn><abstract><style face="normal" font="default" size="100%">Open Source software is competing successfully in many areas. The commercial sector is recognizing the benefits offered by Open Source development methods that lead to high quality software. Can these benefits be realized in specialized domains where expertise is rare? This study examined discussion forums of an Open Source project in a particular specialized application domain -- electronic medical records -- to see how development roles are carried out, and by whom. We found through a qualitative analysis that the core developers in this system include doctors and clinicians who also use the product. We also found that the size of the community associated with the project is an order of magnitude smaller than predicted, yet still maintains a high degree of responsiveness to issues raised by users. The implication is that a few experts and a small core of dedicated programmers can achieve success using an Open Source approach in a specialized domain.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>13</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">D Mason</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">SU-E-T-33: Pydicom: An Open Source DICOM Library</style></title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/doi/10.1118/1.3611983</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">6</style></number><publisher><style face="normal" font="default" size="100%">AAPM</style></publisher><volume><style face="normal" font="default" size="100%">38</style></volume><pages><style face="normal" font="default" size="100%">3493-3493</style></pages></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Karopka, T</style></author><author><style face="normal" font="default" size="100%">Schmuhl, H</style></author><author><style face="normal" font="default" size="100%">Marcelo, A</style></author><author><style face="normal" font="default" size="100%">Molin, J Dal</style></author><author><style face="normal" font="default" size="100%">Wright, G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Towards Open Collaborative Health Informatics - The Role of Free/Libre Open Source Principles. Contribution of the IMIA Open Source Health Informatics Working Group.</style></title><secondary-title><style face="normal" font="default" size="100%">Yearbook of medical informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Yearb Med Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">63-72</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">OBJECTIVES: : To analyze the contribution of Free/Libre Open Source Software in health care (FLOSS-HC) and to give perspectives for future developments.

METHODS: The paper summarizes FLOSS-related trends in health care as anticipated by members of the IMIA Open Source Working Group. Data were obtained through literature review and personal experience and observations of the authors in the last two decades. A status quo is given by a frequency analysis of the database of Medfloss.org, one of the world's largest platforms dedicated to FLOSS-HC. The authors discuss current problems in the field of health care and finally give a prospective roadmap, a projection of the potential influences of FLOSS in health care.

RESULTS: FLOSS-HC already exists for more than 2 decades. Several projects have shown that FLOSS may produce highly competitive alternatives to proprietary solutions that are at least equivalent in usability and have a better total cost of ownership ratio. The Medfloss.org database currently lists 221 projects of diverse application types.

CONCLUSIONS: FLOSS principles hold a great potential for addressing several of the most critical problems in health care IT. The authors argue that an ecosystem perspective is relevant and that FLOSS principles are best suited to create health IT systems that are able to evolve over time as medical knowledge, technologies, insights, workflows etc. continuously change. All these factors that inherently influence the development of health IT systems are changing at an ever growing pace. Traditional models of software engineering are not able to follow these changes and provide up-to-date systems for an acceptable cost/value ratio. To allow FLOSS to positively influence Health IT in the future a &quot;FLOSS-friendly&quot; environment has to be provided. Policy makers should resolve uncertainties in the legal framework that disfavor FLOSS. Certification procedures should be specified in a way that they do not raise additional barriers for FLOSS.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21938327?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Spero, Julie C</style></author><author><style face="normal" font="default" size="100%">McQuide, Pamela A</style></author><author><style face="normal" font="default" size="100%">Matte, Rita</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Tracking and monitoring the health workforce: a new human resources information system (HRIS) in Uganda.</style></title><secondary-title><style face="normal" font="default" size="100%">Human resources for health</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Feb 17</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">6</style></pages><language><style face="normal" font="default" size="100%">ENG</style></language><abstract><style face="normal" font="default" size="100%">ABSTRACT: BACKGROUND: Health workforce planning is important in ensuring that the recruitment, training and deployment of health workers are conducted in the most efficient way possible. However, in many developing countries, human resources for health data are limited, inconsistent, out-dated, or unavailable. Consequently, policy-makers are unable to use reliable data to make informed decisions about the health workforce. Computerized human resources information systems (HRIS) enable countries to collect, maintain, and analyze health workforce data. METHODS: The purpose of this article is twofold. First, we describe Uganda's transition from a paper filing system to an electronic HRIS capable of providing information about country-specific health workforce questions. We examine the ongoing five-step HRIS strengthening process used to implement an HRIS that tracks health worker data at the Uganda Nurses and Midwives Council (UNMC). Secondly, we describe how HRIS data can be used to address workforce planning questions via an initial analysis of the UNMC training, licensure and registration records from 1970 through May 2009. RESULTS: The data indicate that, for the 25 482 nurses and midwives who entered training before 2006, 72% graduated, 66% obtained a council registration, and 28% obtained a license to practice. Of the 17 405 nurses and midwives who obtained a council registration as of May 2009, 96% are of Ugandan nationality and just 3% received their training outside of the country. Thirteen per cent obtained a registration for more than one type of training. Most (34%) trainings with a council registration are for the enrolled nurse training, followed by enrolled midwife (25%), registered (more advanced) nurse (21%), registered midwife (11%), and more specialized trainings (9%). CONCLUSION: The UNMC database is valuable in monitoring and reviewing information about nurses and midwives. However, information obtained from this system is also important in improving strategic planning for the greater health care system in Uganda. We hope that the use of a real-world example of HRIS strengthening provides guidance for the implementation of similar projects in other countries or contexts.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21329516?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Asiimwe, Caroline</style></author><author><style face="normal" font="default" size="100%">Gelvin, David</style></author><author><style face="normal" font="default" size="100%">Lee, Evan</style></author><author><style face="normal" font="default" size="100%">Ben Amor, Yanis</style></author><author><style face="normal" font="default" size="100%">Quinto, Ebony</style></author><author><style face="normal" font="default" size="100%">Katureebe, Charles</style></author><author><style face="normal" font="default" size="100%">Sundaram, Lakshmi</style></author><author><style face="normal" font="default" size="100%">Bell, David</style></author><author><style face="normal" font="default" size="100%">Berg, Matt</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Use of an innovative, affordable, and open-source short message service-based tool to monitor malaria in remote areas of Uganda.</style></title><secondary-title><style face="normal" font="default" size="100%">The American journal of tropical medicine and hygiene</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Am. J. Trop. Med. Hyg.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">85</style></volume><pages><style face="normal" font="default" size="100%">26-33</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Abstract. Quality health management requires timely and accurate data, and paper-based reporting does not fill this role adequately. The introduction of malaria rapid diagnostic tests and the availability of wireless communications present an opportunity to open direct data transmission and feedback between peripheral health workers and central managers. In November 2009, the Uganda Ministry of Health deployed a short message service-based reporting system in two districts. At a set-up cost of $100/health facility, local technician support of $ 400 per month, and a cost of $0.53/week/clinic, the SMS reporting system was started at more than 140 clinics. Positivity rates for rapid diagnostic tests and artemisinin combination therapy stock outs were 48% and 54% in Kabale and 71% and 54% in Gulu, among other reports, at more than 85% health facilities reporting weekly and without monetary incentives or additional supervision. The SMS-based reporting systems have potential to improve timeliness in reporting of specific, time-sensitive metrics at modest cost, while by-passing current bottlenecks in the flow of data. With the development of specific capacity to manage stock data at district level, the availability of timely data offers potential to address commodity distribution problems and reduce stock-outs.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21734120?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Heilman, James M</style></author><author><style face="normal" font="default" size="100%">Kemmann, Eckhard</style></author><author><style face="normal" font="default" size="100%">Bonert, Michael</style></author><author><style face="normal" font="default" size="100%">Chatterjee, Anwesh</style></author><author><style face="normal" font="default" size="100%">Ragar, Brent</style></author><author><style face="normal" font="default" size="100%">Beards, Graham M</style></author><author><style face="normal" font="default" size="100%">Iberri, David J</style></author><author><style face="normal" font="default" size="100%">Harvey, Matthew</style></author><author><style face="normal" font="default" size="100%">Thomas, Brendan</style></author><author><style face="normal" font="default" size="100%">Stomp, Wouter</style></author><author><style face="normal" font="default" size="100%">Martone, Michael F</style></author><author><style face="normal" font="default" size="100%">Lodge, Daniel J</style></author><author><style face="normal" font="default" size="100%">Vondracek, Andrea</style></author><author><style face="normal" font="default" size="100%">de Wolff, Jacob F</style></author><author><style face="normal" font="default" size="100%">Liber, Casimir</style></author><author><style face="normal" font="default" size="100%">Grover, Samir C</style></author><author><style face="normal" font="default" size="100%">Vickers, Tim J</style></author><author><style face="normal" font="default" size="100%">Meskó, Bertalan</style></author><author><style face="normal" font="default" size="100%">Laurent, Michaël R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Wikipedia: a key tool for global public health promotion.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of medical Internet research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Med. Internet Res.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Consumer Health Information</style></keyword><keyword><style  face="normal" font="default" size="100%">Encyclopedias as Topic</style></keyword><keyword><style  face="normal" font="default" size="100%">Health Promotion</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Information Dissemination</style></keyword><keyword><style  face="normal" font="default" size="100%">Information Services</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Patient Education as Topic</style></keyword><keyword><style  face="normal" font="default" size="100%">Public Health</style></keyword><keyword><style  face="normal" font="default" size="100%">World Health</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">e14</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Internet has become an important health information resource for patients and the general public. Wikipedia, a collaboratively written Web-based encyclopedia, has become the dominant online reference work. It is usually among the top results of search engine queries, including when medical information is sought. Since April 2004, editors have formed a group called WikiProject Medicine to coordinate and discuss the English-language Wikipedia's medical content. This paper, written by members of the WikiProject Medicine, discusses the intricacies, strengths, and weaknesses of Wikipedia as a source of health information and compares it with other medical wikis. Medical professionals, their societies, patient groups, and institutions can help improve Wikipedia's health-related entries. Several examples of partnerships already show that there is enthusiasm to strengthen Wikipedia's biomedical content. Given its unique global reach, we believe its possibilities for use as a tool for worldwide health promotion are underestimated. We invite the medical community to join in editing Wikipedia, with the goal of providing people with free access to reliable, understandable, and up-to-date health information.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21282098?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Trevena, Lyndal</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">WikiProject Medicine.</style></title><secondary-title><style face="normal" font="default" size="100%">BMJ (Clinical research ed.)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMJ</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">342</style></volume><pages><style face="normal" font="default" size="100%">d3387</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21653617?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Masoom Alam</style></author><author><style face="normal" font="default" size="100%">Xinwen Zhang</style></author><author><style face="normal" font="default" size="100%">Kamran H Khan</style></author><author><style face="normal" font="default" size="100%">Gohar Ali</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">xDAuth: A Scalable and Lightweight Framework for Cross Domain Access Control and Delegation</style></title><secondary-title><style face="normal" font="default" size="100%">SACMAT’11</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://profsandhu.com/zhang/pub/sacmat11-xdauth.pdf</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">ACM</style></publisher><pub-location><style face="normal" font="default" size="100%">Innsbruck, Austria</style></pub-location><abstract><style face="normal" font="default" size="100%">Cross domain resource sharing and collaborations have be-
come pervasive in today's service oriented organizations.
Existing approaches for the realization of cross domain ac-
cess control are either focused on the model level only with-
out concrete implementation mechanisms, or not general
enough to provide a 
exible framework for enterprise web
applications. In this paper, we present xDAuth, a frame-
work for the realization of cross domain access control and
delegation with RESTful web service architecture. While
focusing on real issues under the context of cross domain
access scenarios such as no predened trust relationship be-
tween a service provider domain and service requestor do-
main, xDAuth leverages existing web technologies to real-
ize desired security requirements while supporting 
exible
and scalable security policies and privacy protection with
low performance overhead. We have implemented xDAuth
in a medical module in OpenERP, an open source ERP sys-
tem. Our evaluation demonstrates that xDAuth is a feasible
framework towards general cross domain access control for
service oriented architectures.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Garla, Vijay</style></author><author><style face="normal" font="default" size="100%">Lo Re, Vincent</style></author><author><style face="normal" font="default" size="100%">Dorey-Stein, Zachariah</style></author><author><style face="normal" font="default" size="100%">Kidwai, Farah</style></author><author><style face="normal" font="default" size="100%">Scotch, Matthew</style></author><author><style face="normal" font="default" size="100%">Womack, Julie</style></author><author><style face="normal" font="default" size="100%">Justice, Amy</style></author><author><style face="normal" font="default" size="100%">Brandt, Cynthia</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Yale cTAKES extensions for document classification: architecture and application.</style></title><secondary-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Connecticut</style></keyword><keyword><style  face="normal" font="default" size="100%">Data Mining</style></keyword><keyword><style  face="normal" font="default" size="100%">Decision Support Systems, Clinical</style></keyword><keyword><style  face="normal" font="default" size="100%">electronic health records</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Liver Failure</style></keyword><keyword><style  face="normal" font="default" size="100%">Natural Language Processing</style></keyword><keyword><style  face="normal" font="default" size="100%">Pattern Recognition, Automated</style></keyword><keyword><style  face="normal" font="default" size="100%">Radiology Information Systems</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Sep-Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">18</style></volume><pages><style face="normal" font="default" size="100%">614-20</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;BACKGROUND: &lt;/b&gt;Open-source clinical natural-language-processing (NLP) systems have lowered the barrier to the development of effective clinical document classification systems. Clinical natural-language-processing systems annotate the syntax and semantics of clinical text; however, feature extraction and representation for document classification pose technical challenges.&lt;/p&gt;&lt;p&gt;&lt;b&gt;METHODS: &lt;/b&gt;The authors developed extensions to the clinical Text Analysis and Knowledge Extraction System (cTAKES) that simplify feature extraction, experimentation with various feature representations, and the development of both rule and machine-learning based document classifiers. The authors describe and evaluate their system, the Yale cTAKES Extensions (YTEX), on the classification of radiology reports that contain findings suggestive of hepatic decompensation.&lt;/p&gt;&lt;p&gt;&lt;b&gt;RESULTS AND DISCUSSION: &lt;/b&gt;The F(1)-Score of the system for the retrieval of abdominal radiology reports was 96%, and was 79%, 91%, and 95% for the presence of liver masses, ascites, and varices, respectively. The authors released YTEX as open source, available at http://code.google.com/p/ytex.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Søvik, Aste</style></author><author><style face="normal" font="default" size="100%">Rødal, Jan</style></author><author><style face="normal" font="default" size="100%">Skogmo, Hege K</style></author><author><style face="normal" font="default" size="100%">Lervåg, Christoffer</style></author><author><style face="normal" font="default" size="100%">Eilertsen, Karsten</style></author><author><style face="normal" font="default" size="100%">Malinen, Eirik</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Adaptive radiotherapy based on contrast enhanced cone beam CT imaging.</style></title><secondary-title><style face="normal" font="default" size="100%">Acta oncologica (Stockholm, Sweden)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Acta Oncol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Carcinoma</style></keyword><keyword><style  face="normal" font="default" size="100%">Cone-Beam Computed Tomography</style></keyword><keyword><style  face="normal" font="default" size="100%">Contrast Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Dog Diseases</style></keyword><keyword><style  face="normal" font="default" size="100%">Dogs</style></keyword><keyword><style  face="normal" font="default" size="100%">Female</style></keyword><keyword><style  face="normal" font="default" size="100%">Maxillary Neoplasms</style></keyword><keyword><style  face="normal" font="default" size="100%">Patient Positioning</style></keyword><keyword><style  face="normal" font="default" size="100%">Radiographic Image Enhancement</style></keyword><keyword><style  face="normal" font="default" size="100%">Radiotherapy Planning, Computer-Assisted</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">49</style></volume><pages><style face="normal" font="default" size="100%">972-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Cone beam CT (CBCT) imaging has become an integral part of radiation therapy, with images typically used for offline or online patient setup corrections based on bony anatomy co-registration. Ideally, the co-registration should be based on tumor localization. However, soft tissue contrast in CBCT images may be limited. In the present work, contrast enhanced CBCT (CECBCT) images were used for tumor visualization and treatment adaptation. Material and methods. A spontaneous canine maxillary tumor was subjected to repeated cone beam CT imaging during fractionated radiotherapy (10 fractions in total). At five of the treatment fractions, CECBCT images, employing an iodinated contrast agent, were acquired, as well as pre-contrast CBCT images. The tumor was clearly visible in post-contrast minus pre-contrast subtraction images, and these contrast images were used to delineate gross tumor volumes. IMRT dose plans were subsequently generated. Four different strategies were explored: 1) fully adapted planning based on each CECBCT image series, 2) planning based on images acquired at the first treatment fraction and patient repositioning following bony anatomy co-registration, 3) as for 2), but with patient repositioning based on co-registering contrast images, and 4) a strategy with no patient repositioning or treatment adaptation. The equivalent uniform dose (EUD) and tumor control probability (TCP) calculations to estimate treatment outcome for each strategy. Results. Similar translation vectors were found when bony anatomy and contrast enhancement co-registration were compared. Strategy 1 gave EUDs closest to the prescription dose and the highest TCP. Strategies 2 and 3 gave EUDs and TCPs close to that of strategy 1, with strategy 3 being slightly better than strategy 2. Even greater benefits from strategies 1 and 3 are expected with increasing tumor movement or deformation during treatment. The non-adaptive strategy 4 was clearly inferior to all three adaptive strategies. Conclusion. CECBCT may prove useful for adaptive radiotherapy.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20831484?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Villa-Uriol, M C</style></author><author><style face="normal" font="default" size="100%">Larrabide, I</style></author><author><style face="normal" font="default" size="100%">Geers, A J</style></author><author><style face="normal" font="default" size="100%">Pozo, J</style></author><author><style face="normal" font="default" size="100%">Bogunovic, H</style></author><author><style face="normal" font="default" size="100%">Mazzeo, M</style></author><author><style face="normal" font="default" size="100%">Omedas, P</style></author><author><style face="normal" font="default" size="100%">Barbarito, V</style></author><author><style face="normal" font="default" size="100%">Carotenuto, L</style></author><author><style face="normal" font="default" size="100%">Riccobene, C</style></author><author><style face="normal" font="default" size="100%">Planes, X</style></author><author><style face="normal" font="default" size="100%">Martelli, Y</style></author><author><style face="normal" font="default" size="100%">Frangi, A F</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">AngioLab: Integrated technology for patient-specific management of intracranial aneurysms.</style></title><secondary-title><style face="normal" font="default" size="100%">Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Conf Proc IEEE Eng Med Biol Soc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">1</style></volume><pages><style face="normal" font="default" size="100%">6801-4</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">AngioLab is a software tool developed within the GIMIAS framework and is part of a more ambitious pipeline for the integrated management of cerebral aneurysms. AngioLab currently includes three plug-ins: angio segmentation, angio morphology and stenting, as well as supports advanced rendering techniques for the visualization of virtual angiographies. In December 2009, 23 clinicians completed an evaluation questionnaire about AngioLab. This activity was part of a teaching course held during the 2(nd) European Society for Minimally Invasive Neurovascular Treatment (ESMINT) Teaching Course held at the Universitat Pompeu Fabra, Barcelona, Spain. The Automated Morphological Analysis (angio morphology plug-in) and the Endovascular Treatment Planning (stenting plug-in) were evaluated. In general, the results provided by these tools were considered as relevant and as an emerging need in their clinical field.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21095844?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">de Oliveira, Ana Cláudia Melo Tiessi Gomes</style></author><author><style face="normal" font="default" size="100%">Nunes, Fátima de Lourdes dos Santos</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Building a open source framework for virtual medical training.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Digit Imaging</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">23</style></volume><pages><style face="normal" font="default" size="100%">706-20</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">This paper presents a framework to build medical training applications by using virtual reality and a tool that helps the class instantiation of this framework. The main purpose is to make easier the building of virtual reality applications in the medical training area, considering systems to simulate biopsy exams and make available deformation, collision detection, and stereoscopy functionalities. The instantiation of the classes allows quick implementation of the tools for such a purpose, thus reducing errors and offering low cost due to the use of open source tools. Using the instantiation tool, the process of building applications is fast and easy. Therefore, computer programmers can obtain an initial application and adapt it to their needs. This tool allows the user to include, delete, and edit parameters in the functionalities chosen as well as storing these parameters for future use. In order to verify the efficiency of the framework, some case studies are presented.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19789924?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Cakici, Baki</style></author><author><style face="normal" font="default" size="100%">Hebing, Kenneth</style></author><author><style face="normal" font="default" size="100%">Grünewald, Maria</style></author><author><style face="normal" font="default" size="100%">Saretok, Paul</style></author><author><style face="normal" font="default" size="100%">Hulth, Anette</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">CASE: a framework for computer supported outbreak detection.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC medical informatics and decision making</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Med Inform Decis Mak</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">14</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: In computer supported outbreak detection, a statistical method is applied to a collection of cases to detect any excess cases for a particular disease. Whether a detected aberration is a true outbreak is decided by a human expert. We present a technical framework designed and implemented at the Swedish Institute for Infectious Disease Control for computer supported outbreak detection, where a database of case reports for a large number of infectious diseases can be processed using one or more statistical methods selected by the user. RESULTS: Based on case information, such as diagnosis and date, different statistical algorithms for detecting outbreaks can be applied, both on the disease level and the subtype level. The parameter settings for the algorithms can be configured independently for different diagnoses using the provided graphical interface. Input generators and output parsers are also provided for all supported algorithms. If an outbreak signal is detected, an email notification is sent to the persons listed as receivers for that particular disease. CONCLUSIONS: The framework is available as open source software, licensed under GNU General Public License Version 3. By making the code open source, we wish to encourage others to contribute to the future development of computer supported outbreak detection systems, and in particular to the development of the CASE framework.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20226035?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Braaa, Jørn</style></author><author><style face="normal" font="default" size="100%">Kanterb, Andrew S.</style></author><author><style face="normal" font="default" size="100%">Leshc, Neal</style></author><author><style face="normal" font="default" size="100%">Crichtond, Ryan</style></author><author><style face="normal" font="default" size="100%">Jolliffea, Bob</style></author><author><style face="normal" font="default" size="100%">Sæbøe, Johan</style></author><author><style face="normal" font="default" size="100%">Kossia, Edem</style></author><author><style face="normal" font="default" size="100%">Seebregts, Christopher J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comprehensive Yet Scalable Health Information Systems for Low Resource Settings: A Collaborative Effort in Sierra Leone</style></title><secondary-title><style face="normal" font="default" size="100%">AMIA 2010 Symposium</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">11/2010</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://proceedings.amia.org/127frh</style></url></web-urls></urls><abstract><style face="normal" font="default" size="100%">We address the problem of how to integrate health informa- tion systems in low-income African countries in which techni- cal infrastructure and human resources vary wildly within countries. We describe a set of tools to meet the needs of dif- ferent service areas including managing aggregate indicators, patient level record systems, and mobile tools for community outreach. We present the case of Sierra Leone and use this case to motivate and illustrate an architecture that allows us to provide services at each level of the health system (na- tional, regional, facility and community) and provide different configurations of the tools as appropriate for the individual area. Finally, we present a, collaborative implementation of this approach in Sierra Leone.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Scolozzi, Paolo</style></author><author><style face="normal" font="default" size="100%">Momjian, Armen</style></author><author><style face="normal" font="default" size="100%">Heuberger, Joris</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Computer-aided volumetric comparison of reconstructed orbits for blow-out fractures with nonpreformed versus 3-dimensionally preformed titanium mesh plates: a preliminary study.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of computer assisted tomography</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Comput Assist Tomogr</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">34</style></volume><pages><style face="normal" font="default" size="100%">98-104</style></pages><abstract><style face="normal" font="default" size="100%">OBJECTIVES: To compare and evaluate, using computer-aided volumetric measurements, the accuracy and reliability of nonpreformed mesh plates (NPMPs) versus 3-dimensionally preformed titanium mesh plates (PMPs) in posttraumatic orbital volume restoration. PATIENTS AND METHODS: Facial coronal computed tomographic scan slices from 20 patients (10 in the NPMP and 10 in the PMP group) were used to measure bony orbital volume using OsiriX Medical Image software (version 3.3.2, www.osirix-viewer.com). The procedure was performed on both orbits; thereafter, the volume of the contralateral health orbit was used as a control for comparison in the 2 groups of patients. The difference in orbital volume between the 2 groups and between the reconstructed versus uninjured side in both groups have been statistically correlated. RESULTS: The mean orbital volume between the reconstructed (19.215 mL in NPMP and 21.791 mL in PMP) and the contralateral uninjured side (18.955 mL in NPMP and 21.710 mL in PMP) was not statistically significant (P &gt; 0.05). The mean orbital volumes of the reconstructed orbits were 19.215 mL in the NPMP and 21.791 mL in the PMP group, with no statistically significant difference (P &gt; 0.05). The volume data of the reconstructed orbit fitted that of the contralateral uninjured orbit with an accuracy of a maximum of 1.85 mL in the NPMP group and 2.5 mL in the PMP group. CONCLUSIONS: The current study demonstrated that there were no significant differences in the orbital volume restoration using either technique. In fact, both techniques allow for close reproduction of natural orbital volume and shape, and its use in posttraumatic orbital wall reconstruction was successful.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20118730?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Syed-Mohamad, Sharifa Mastura</style></author><author><style face="normal" font="default" size="100%">Ali, Siti Hawa</style></author><author><style face="normal" font="default" size="100%">Mat-Husin, Mohd Nazri</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The development and design of an electronic patient record using open source web-based technology.</style></title><secondary-title><style face="normal" font="default" size="100%">The HIM journal</style></secondary-title><alt-title><style face="normal" font="default" size="100%">HIM J</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">39</style></volume><pages><style face="normal" font="default" size="100%">30-5</style></pages><abstract><style face="normal" font="default" size="100%">This paper describes the method used to develop the One Stop Crisis Centre (OSCC) Portal, an open source web-based electronic patient record system (EPR) for the One Stop Crisis Center, Hospital Universiti Sains Malaysia (HUSM) in Kelantan, Malaysia. Features and functionalities of the system are presented to demonstrate the workflow. Use of the OSCC Portal improved data integration and data communication and contributed to improvements in care management. With implementation of the OSCC portal, improved coordination between disciplines and standardisation of data in HUSM were noticed. It is expected that this will in turn result in improved data confidentiality and data integrity. The collected data will also be useful for quality assessment and research. Other low-resource centers with limited computer hardware and access to open-source software could benefit from this endeavour.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20335647?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Dinevski, Dejan</style></author><author><style face="normal" font="default" size="100%">Poli, Andrea</style></author><author><style face="normal" font="default" size="100%">Krajnc, Ivan</style></author><author><style face="normal" font="default" size="100%">Sustersic, Olga</style></author><author><style face="normal" font="default" size="100%">Arh, Tanja</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">E-health integration and interoperability based on open-source information technology.</style></title><secondary-title><style face="normal" font="default" size="100%">Wiener klinische Wochenschrift</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Wien. Klin. Wochenschr.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">122 Suppl 2</style></volume><pages><style face="normal" font="default" size="100%">3-10</style></pages><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20517664?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wright, Pauliina</style></author><author><style face="normal" font="default" size="100%">Muren, Ludvig P</style></author><author><style face="normal" font="default" size="100%">Høyer, Morten</style></author><author><style face="normal" font="default" size="100%">Malinen, Eirik</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evaluation of adaptive radiotherapy of bladder cancer by image-based tumour control probability modelling.</style></title><secondary-title><style face="normal" font="default" size="100%">Acta oncologica (Stockholm, Sweden)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Acta Oncol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Carcinoma</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Simulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Image Processing, Computer-Assisted</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Statistical</style></keyword><keyword><style  face="normal" font="default" size="100%">Probability</style></keyword><keyword><style  face="normal" font="default" size="100%">Radiotherapy Dosage</style></keyword><keyword><style  face="normal" font="default" size="100%">Radiotherapy Planning, Computer-Assisted</style></keyword><keyword><style  face="normal" font="default" size="100%">Radiotherapy, Conformal</style></keyword><keyword><style  face="normal" font="default" size="100%">Tumor Burden</style></keyword><keyword><style  face="normal" font="default" size="100%">Urinary Bladder</style></keyword><keyword><style  face="normal" font="default" size="100%">Urinary Bladder Neoplasms</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">49</style></volume><pages><style face="normal" font="default" size="100%">1045-51</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Clinical implementation of adaptive radiotherapy strategies could benefit from extended tools for plan evaluation and selection. For this purpose we investigated the feasibility of image-based tumour control probability (TCP) modelling using the bladder as example of a tumour site with potential benefit from adaptive strategies.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20831494?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Stein, D</style></author><author><style face="normal" font="default" size="100%">Fritzsche, K H</style></author><author><style face="normal" font="default" size="100%">Nolden, M</style></author><author><style face="normal" font="default" size="100%">Meinzer, H P</style></author><author><style face="normal" font="default" size="100%">Wolf, I</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The extensible open-source rigid and affine image registration module of the Medical Imaging Interaction Toolkit (MITK).</style></title><secondary-title><style face="normal" font="default" size="100%">Computer methods and programs in biomedicine</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Comput Methods Programs Biomed</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computers</style></keyword><keyword><style  face="normal" font="default" size="100%">Diagnostic Imaging</style></keyword><keyword><style  face="normal" font="default" size="100%">Image Enhancement</style></keyword><keyword><style  face="normal" font="default" size="100%">Image Interpretation, Computer-Assisted</style></keyword><keyword><style  face="normal" font="default" size="100%">Pattern Recognition, Automated</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">100</style></volume><pages><style face="normal" font="default" size="100%">79-86</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Although non-rigid registration methods are available or under development for many specific problems in medicine, rigid and affine registration is an important task that is often performed for pre-aligning images before using non-rigid registration. In this paper, we present a free and open-source application for rigid and affine image registration, which is designed both for developers and for end-users. The application is based on the Medical Imaging Interaction Toolkit (MITK) and allows for inter-modality and intra-modality rigid 2D-2D and 3D-3D registration of medical images such as CT, MRI, or ultrasound. The framework as well as the application can be easily extended by adding new transforms, metrics and optimizers. Thus, developers of new algorithms are enabled to test and use their algorithms more quickly, spending less work on user interfaces. Additionally, the framework provides the possibility to use image masks to restrict the evaluation of metric values by the optimizer on certain areas of the images.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20409608?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Stein, D</style></author><author><style face="normal" font="default" size="100%">Fritzsche, K H</style></author><author><style face="normal" font="default" size="100%">Nolden, M</style></author><author><style face="normal" font="default" size="100%">Meinzer, H P</style></author><author><style face="normal" font="default" size="100%">Wolf, I</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The extensible open-source rigid and affine image registration module of the Medical Imaging Interaction Toolkit (MITK).</style></title><secondary-title><style face="normal" font="default" size="100%">Computer methods and programs in biomedicine</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr 19</style></date></pub-dates></dates><abstract><style face="normal" font="default" size="100%">Although non-rigid registration methods are available or under development for many specific problems in medicine, rigid and affine registration is an important task that is often performed for pre-aligning images before using non-rigid registration. In this paper, we present a free and open-source application for rigid and affine image registration, which is designed both for developers and for end-users. The application is based on the Medical Imaging Interaction Toolkit (MITK) and allows for inter-modality and intra-modality rigid 2D-2D and 3D-3D registration of medical images such as CT, MRI, or ultrasound. The framework as well as the application can be easily extended by adding new transforms, metrics and optimizers. Thus, developers of new algorithms are enabled to test and use their algorithms more quickly, spending less work on user interfaces. Additionally, the framework provides the possibility to use image masks to restrict the evaluation of metric values by the optimizer on certain areas of the images.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20409608?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Flores Zuniga, Alejandro Enrique</style></author><author><style face="normal" font="default" size="100%">Win, Khin Than</style></author><author><style face="normal" font="default" size="100%">Susilo, Willy</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Functionalities of free and open electronic health record systems.</style></title><secondary-title><style face="normal" font="default" size="100%">International journal of technology assessment in health care</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int J Technol Assess Health Care</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">26</style></volume><pages><style face="normal" font="default" size="100%">382-9</style></pages><abstract><style face="normal" font="default" size="100%">Objectives: The aim of this study was to examine open-source electronic health record (EHR) software to determine their level of functionalities according to the International Organization for Standardization (ISO) standards.Methods: ISO standards were used as a guideline to determine and describe the reference architecture and functionalities of a standard electronic health record system as well the environmental context for which the software has been built. Twelve open-source EHR systems were selected and evaluated according to two-dimensional criteria based on ISO/TS 18308:2004 functional requirements and ISO/TR 20514:2005 context of the EHR system.Results: Open EHR software programs mostly fulfill structural, procedural, evolutional, and medicolegal requirements at the minimal and full functionality levels. Communication, privacy, and security requirements are accomplished in less than 23 percent of the cases, mainly at minimal functional level. Ethical, cultural, and consumer requirements still need to be fulfilled by free and open-source EHR applications.Conclusions: Most analyzed systems had several functional limitations. Nevertheless, especially for clinicians and decision makers in developing countries, open-source EHR systems are an option. The limited functionalities are likely to become requirements for further releases of open-source EHR systems.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20974022?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kuchinke, Wolfgang</style></author><author><style face="normal" font="default" size="100%">Ohmann, Christian</style></author><author><style face="normal" font="default" size="100%">Yang, Qin</style></author><author><style face="normal" font="default" size="100%">Salas, Nader</style></author><author><style face="normal" font="default" size="100%">Lauritsen, Jens</style></author><author><style face="normal" font="default" size="100%">Gueyffier, Francois</style></author><author><style face="normal" font="default" size="100%">Leizorovicz, Alan</style></author><author><style face="normal" font="default" size="100%">Schade-Brittinger, Carmen</style></author><author><style face="normal" font="default" size="100%">Wittenberg, Michael</style></author><author><style face="normal" font="default" size="100%">Voko, Zoltan</style></author><author><style face="normal" font="default" size="100%">Gaynor, Siobhan</style></author><author><style face="normal" font="default" size="100%">Cooney, Margaret</style></author><author><style face="normal" font="default" size="100%">Doran, Peter</style></author><author><style face="normal" font="default" size="100%">Maggioni, Aldo</style></author><author><style face="normal" font="default" size="100%">Lorimer, Andrea</style></author><author><style face="normal" font="default" size="100%">Torres, Ferran</style></author><author><style face="normal" font="default" size="100%">McPherson, Gladys</style></author><author><style face="normal" font="default" size="100%">Charvill, Jim</style></author><author><style face="normal" font="default" size="100%">Hellstrom, Mats</style></author><author><style face="normal" font="default" size="100%">Lejeune, Stephane</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Heterogeneity prevails: the state of clinical trial data management in Europe - results of a survey of ECRIN centres.</style></title><secondary-title><style face="normal" font="default" size="100%">Trials</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Jul 21</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.trialsjournal.com/content/11/1/79</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">79</style></pages><abstract><style face="normal" font="default" size="100%">ABSTRACT: BACKGROUND: The use of Clinical Data Management Systems (CDMS) has become essential in clinical trials to handle the increasing amount of data that must be collected and analyzed. With a CDMS trial data are captured at investigator sites with &quot;electronic Case Report Forms&quot;. Although more and more of these electronic data management systems are used in academic research centres an overview of CDMS products and of available data management and quality management resources for academic clinical trials in Europe is missing. METHODS: The ECRIN (European Clinical Research Infrastructure Network) data management working group conducted a two-part standardized survey on data management, software tools, and quality management for clinical trials. The questionnaires were answered by nearly 80 centres / units (with an overall response rate of 47% and 43%) from 12 European countries and EORTC. RESULTS: Our survey shows that about 90% of centres have a CDMS in routine use. Of these CDMS nearly 50% are commercial systems; Open Source solutions don't play a major role. In general, solutions used for clinical data management are very heterogeneous: 20 different commercial CDMS products (7 Open Source solutions) in addition to 17/18 proprietary systems are in use. The most widely employed CDMS products are MACRO TM and Capture System TM, followed by solutions that are used in at least 3 centres: eResearch Network TM, CleanWeb TM, GCP Base TM and SAS TM. Although quality management systems for data management are in place in most centres / units, there exist some deficits in the area of system validation. CONCLUSIONS: Because the considerable heterogeneity of data management software solutions may be a hindrance to cooperation based on trial data exchange, standards like CDISC (Clinical Data Interchange Standard Consortium) should be implemented more widely. In a heterogeneous environment the use of data standards can simplify data exchange, increase the quality of data and prepare centres for new developments (e.g. the use of EHR for clinical research). Because data management and the use of electronic data capture systems in clinical trials are characterized by the impact of regulations and guidelines, ethical concerns are discussed. In this context quality management becomes an important part of compliant data management. To address these issues ECRIN will establish certified data centres to support electronic data management and associated compliance needs of clinical trial centres in Europe.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20663165?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tuominen, Vilppu J</style></author><author><style face="normal" font="default" size="100%">Ruotoistenmaki, Sanna</style></author><author><style face="normal" font="default" size="100%">Viitanen, Arttu</style></author><author><style face="normal" font="default" size="100%">Jumppanen, Mervi</style></author><author><style face="normal" font="default" size="100%">Isola, Jorma</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67.</style></title><secondary-title><style face="normal" font="default" size="100%">Breast cancer research : BCR</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Jul 27</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">R56</style></pages><abstract><style face="normal" font="default" size="100%">ABSTRACT: INTRODUCTION: Accurate assessment of estrogen receptor (ER), progesterone receptor (PR), and Ki-67 is essential in the histopathologic diagnostics of breast cancer. Commercially available image analysis systems are usually bundled with dedicated analysis hardware and, to our knowledge, no easily installable, free software for immunostained slide scoring has been described. In this study, we describe a free, Internet-based web application for quantitative image analysis of ER, PR, and Ki-67 immunohistochemistry in breast cancer tissue sections. METHODS: The application, named ImmunoRatio, calculates the percentage of positively stained nuclear area (labeling index) by using a color deconvolution algorithm for separating the staining components (diaminobenzidine and hematoxylin) and adaptive thresholding for nuclear area segmentation. ImmunoRatio was calibrated using cell counts defined visually as the gold standard (training set, n=50). Validation was done using a separate set of 50 ER, PR, and Ki-67 stained slides (test set, n=50). In addition, Ki-67 labeling indexes determined by ImmunoRatio were studied for their prognostic value in a retrospective cohort of 123 breast cancer patients. RESULTS: The labeling indexes by calibrated ImmunoRatio analyses correlated well with those defined visually in the test set (correlation coefficient r=0.98). Using the median Ki-67 labeling index (20%) as a cutoff, a hazard ratio of 2.2 was obtained in the survival analysis (n=123, P=0.01). ImmunoRatio was shown to adapt to various staining protocols, microscope setups, digital camera models, and image acquisition settings. The application can be used directly with web browsers running on modern operating systems (e.g., Microsoft Windows, Linux distributions, and Mac OS). No software downloads or installations are required. ImmunoRatio is open source software, and the web application is publicly accessible on our website. CONCLUSIONS: We anticipate that free web applications, such as ImmunoRatio, will make the quantitative image analysis of ER, PR, and Ki-67 easy and straightforward in the diagnostic assessment of breast cancer specimens.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20663194?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fraser, Hamish S F</style></author><author><style face="normal" font="default" size="100%">Blaya, Joaquin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Implementing medical information systems in developing countries, what works and what doesn't.</style></title><secondary-title><style face="normal" font="default" size="100%">AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium</style></secondary-title><alt-title><style face="normal" font="default" size="100%">AMIA Annu Symp Proc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2010</style></volume><pages><style face="normal" font="default" size="100%">232-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Global Health Informatics is an emerging field, as demonstrated by several substantial and widely used electronic medical record (EMR) systems along with the emergence of mobile based or&quot;mhealth&quot; systems. We describe here many of the practical lessons we have learned from implementing systems in a wide range of challenging environments over the last decade. Some requirements, like data backups, skilled staff and local leadership are universally important. Others, such as limited power, poor network access and distributed populations, require different designs and strategies in resource poor environments.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21346975?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Adida, Ben</style></author><author><style face="normal" font="default" size="100%">Sanyal, Arjun</style></author><author><style face="normal" font="default" size="100%">Zabak, Steve</style></author><author><style face="normal" font="default" size="100%">Kohane, Isaac S.</style></author><author><style face="normal" font="default" size="100%">Mandl, Kenneth D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Indivo X: Developing a Fully Substitutable Personally Controlled Health Record Platform</style></title><secondary-title><style face="normal" font="default" size="100%">AMIA 2010 Symposium</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">11/2010</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://proceedings.amia.org/127eoo</style></url></web-urls></urls><abstract><style face="normal" font="default" size="100%">To support a rich ecosystem of third-party applications around a personally controlled health record (PCHR), we have redesigned Indivo, the original PCHR, as a web- based platform with feature-level substitutability. Core to this new release is the Indivo X Application Program- ming Interface (API), the contract between the PCHR platform and the end-user apps. Using rapid iterative de- velopment to build a minimal feature set from real-world requirements, the resulting Indivo X API, now in public stable beta, is enabling developers, including third-party contributors, to quickly create and integrate novel fea- tures into patients’ online records, ultimately building a fully customizable experience for diverse patient needs.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ribes, Delphine</style></author><author><style face="normal" font="default" size="100%">Parafita, Julia</style></author><author><style face="normal" font="default" size="100%">Charrier, Rémi</style></author><author><style face="normal" font="default" size="100%">Magara, Fulvio</style></author><author><style face="normal" font="default" size="100%">Magistretti, Pierre J.</style></author><author><style face="normal" font="default" size="100%">Thiran, Jean-Philippe</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">JULIDE: A Software Tool for 3D Reconstruction and Statistical Analysis of Autoradiographic Mouse Brain Sections</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS ONE</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">11</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1371%2Fjournal.pone.0014094</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">11</style></number><publisher><style face="normal" font="default" size="100%">Public Library of Science</style></publisher><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">e14094</style></pages><abstract><style face="normal" font="default" size="100%">&lt;p&gt;In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.&lt;/p&gt;</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Albert, S</style></author><author><style face="normal" font="default" size="100%">Cristofari, J-P</style></author><author><style face="normal" font="default" size="100%">Cox, A</style></author><author><style face="normal" font="default" size="100%">Bensimon, J-L</style></author><author><style face="normal" font="default" size="100%">Guedon, C</style></author><author><style face="normal" font="default" size="100%">Barry, B</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Mandibular reconstruction with fibula free flap. Experience of virtual reconstruction using Osirix((R)), a free and open source software for medical imagery.</style></title><secondary-title><style face="normal" font="default" size="100%">Annales de chirurgie plastique et esthetique</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Jun 18</style></date></pub-dates></dates><abstract><style face="normal" font="default" size="100%">The techniques of free tissue transfers are mainly used for mandibular reconstruction by specialized surgical teams. This type of reconstruction is mostly realized in matters of head and neck cancers affecting mandibular bone and requiring a wide surgical resection and interruption of the mandible. To decrease the duration of the operation, surgical procedure involves generally two teams, one devoted to cancer resection and the other one to raise the fibular flap and making the reconstruction. For a better preparation of this surgical procedure, we propose here the use of a medical imaging software enabling mandibular reconstructions in three dimensions using the CT-scan done during the initial disease-staging checkup. The software used is Osirix((R)), developed since 2004 by a team of radiologists from Geneva and UCLA, working on Apple((R)) computers and downloadable free of charge in its basic version. We report here our experience of this software in 17 patients, with a preoperative modelling in three dimensions of the mandible, of the segment of mandible to be removed. It also forecasts the numbers of fragments of fibula needed and the location of osteotomies.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20646816?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Savova, Guergana K</style></author><author><style face="normal" font="default" size="100%">Masanz, James J</style></author><author><style face="normal" font="default" size="100%">Ogren, Philip V</style></author><author><style face="normal" font="default" size="100%">Zheng, Jiaping</style></author><author><style face="normal" font="default" size="100%">Sohn, Sunghwan</style></author><author><style face="normal" font="default" size="100%">Kipper-Schuler, Karin C</style></author><author><style face="normal" font="default" size="100%">Chute, Christopher G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications.</style></title><secondary-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biomedical Research</style></keyword><keyword><style  face="normal" font="default" size="100%">electronic health records</style></keyword><keyword><style  face="normal" font="default" size="100%">Information Storage and Retrieval</style></keyword><keyword><style  face="normal" font="default" size="100%">Natural Language Processing</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Sep-Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">507-13</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;We aim to build and evaluate an open-source natural language processing system for information extraction from electronic medical record clinical free-text. We describe and evaluate our system, the clinical Text Analysis and Knowledge Extraction System (cTAKES), released open-source at http://www.ohnlp.org. The cTAKES builds on existing open-source technologies-the Unstructured Information Management Architecture framework and OpenNLP natural language processing toolkit. Its components, specifically trained for the clinical domain, create rich linguistic and semantic annotations. Performance of individual components: sentence boundary detector accuracy=0.949; tokenizer accuracy=0.949; part-of-speech tagger accuracy=0.936; shallow parser F-score=0.924; named entity recognizer and system-level evaluation F-score=0.715 for exact and 0.824 for overlapping spans, and accuracy for concept mapping, negation, and status attributes for exact and overlapping spans of 0.957, 0.943, 0.859, and 0.580, 0.939, and 0.839, respectively. Overall performance is discussed against five applications. The cTAKES annotations are the foundation for methods and modules for higher-level semantic processing of clinical free-text.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mühler, Konrad</style></author><author><style face="normal" font="default" size="100%">Tietjen, Christian</style></author><author><style face="normal" font="default" size="100%">Ritter, Felix</style></author><author><style face="normal" font="default" size="100%">Preim, Bernhard</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The medical exploration toolkit: an efficient support for visual computing in surgical planning and training.</style></title><secondary-title><style face="normal" font="default" size="100%">IEEE transactions on visualization and computer graphics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">IEEE Trans Vis Comput Graph</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Jan-Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">16</style></volume><pages><style face="normal" font="default" size="100%">133-46</style></pages><abstract><style face="normal" font="default" size="100%">Application development is often guided by the usage of software libraries and toolkits. For medical applications, the toolkits currently available focus on image analysis and volume rendering. Advance interactive visualizations and user interface issues are not adequately supported. Hence, we present a toolkit for application development in the field of medical intervention planning, training, and presentation--the MEDICALEXPLORATIONTOOLKIT (METK). The METK is based on the rapid prototyping platform MeVisLab and offers a large variety of facilities for an easy and efficient application development process. We present dedicated techniques for advanced medical visualizations, exploration, standardized documentation, adn interface widgets for common tasks. These include, e.g., advanced animation facilities, viewpoint selection, several illustrative rendering techniques, and new techniques for object selection in 3D surface models. No extended programming skills are needed for application building, since a graphical programming approach can be used. the toolkit is freely available and well documented to facilitate the use and extension of the toolkit.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19910667?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wilder, Bruce</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Need for open-source electronic health records.</style></title><secondary-title><style face="normal" font="default" size="100%">Health affairs (Project Hope)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Health Aff (Millwood)</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">29</style></volume><pages><style face="normal" font="default" size="100%">332-4; author reply 332</style></pages><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20348080?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bagayoko, Cheick-Oumar</style></author><author><style face="normal" font="default" size="100%">Dufour, Jean-Charles</style></author><author><style face="normal" font="default" size="100%">Chaacho, Saad</style></author><author><style face="normal" font="default" size="100%">Bouhaddou, Omar</style></author><author><style face="normal" font="default" size="100%">Fieschi, Marius</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open source challenges for hospital information system (HIS) in developing countries: a pilot project in Mali.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC medical informatics and decision making</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Med Inform Decis Mak</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.biomedcentral.com/1472-6947/10/22</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">22</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: We are currently witnessing a significant increase in use of Open Source tools in the field of health. Our study aims to research the potential of these software packages for developing countries. Our experiment was conducted at the Centre Hospitalier Mere Enfant in Mali. METHODS: After reviewing several Open Source tools in the field of hospital information systems, Mediboard software was chosen for our study. To ensure the completeness of Mediboard in relation to the functionality required for a hospital information system, its features were compared to those of a well-defined comprehensive record management tool set up at the University Hospital &quot;La Timone&quot; of Marseilles in France. It was then installed on two Linux servers: a first server for testing and validation of different modules, and a second one for the deployed full implementation. After several months of use, we have evaluated the usability aspects of the system including feedback from end-users through a questionnaire. RESULTS: Initial results showed the potential of Open Source in the field of health IT for developing countries like Mali.Five main modules have been fully implemented: patient administrative and medical records management of hospital activities, tracking of practitioners' activities, infrastructure management and the billing system. This last component of the system has been fully developed by the local Mali team.The evaluation showed that the system is broadly accepted by all the users who participated in the study. 77% of the participants found the system useful; 85% found it easy; 100% of them believe the system increases the reliability of data. The same proportion encourages the continuation of the experiment and its expansion throughout the hospital. CONCLUSIONS: In light of the results, we can conclude that the objective of our study was reached. However, it is important to take into account the recommendations and the challenges discussed here to avoid several potential pitfalls specific to the context of Africa.Our future work will target the full integration of the billing module in Mediboard and an expanded implementation throughout the hospital.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20398366?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Isken, Mark W</style></author><author><style face="normal" font="default" size="100%">Ward, Timothy J</style></author><author><style face="normal" font="default" size="100%">Littig, Steven J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">An open source software project for obstetrical procedure scheduling and occupancy analysis.</style></title><secondary-title><style face="normal" font="default" size="100%">Health care management science</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Oct 27</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">ENG</style></language><abstract><style face="normal" font="default" size="100%">Increases in the rate of births via cesarean section and induced labor have led to challenging scheduling and capacity planning problems for hospital inpatient obstetrical units. We present occupancy and patient scheduling models to help address these challenges. These patient flow models can be used to explore the relationship between procedure scheduling practices and the resulting occupancy on inpatient obstetrical units such as labor and delivery and postpartum. The models capture numerous important characteristics of inpatient obstetrical patient flow such as time of day and day of week dependent arrivals and length of stay, multiple patient types and clinical interventions, and multiple patient care units with inter-unit patient transfers. We have used these models in several projects at different hospitals involving design of procedure scheduling templates and analysis of inpatient obstetrical capacity. In the development of these models, we made heavy use of open source software tools and have released the entire project as a free and open source model and software toolkit.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20978855?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gramfort, Alexandre</style></author><author><style face="normal" font="default" size="100%">Papadopoulo, Théodore</style></author><author><style face="normal" font="default" size="100%">Olivi, Emmanuel</style></author><author><style face="normal" font="default" size="100%">Clerc, Maureen</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">OpenMEEG: opensource software for quasistatic bioelectromagnetics.</style></title><secondary-title><style face="normal" font="default" size="100%">Biomedical engineering online</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biomed Eng Online</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Benchmarking</style></keyword><keyword><style  face="normal" font="default" size="100%">Computers</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Impedance</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electroencephalography</style></keyword><keyword><style  face="normal" font="default" size="100%">Electromagnetic Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Licensure</style></keyword><keyword><style  face="normal" font="default" size="100%">Magnetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Magnetoencephalography</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Theoretical</style></keyword><keyword><style  face="normal" font="default" size="100%">Quality Control</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Time Factors</style></keyword><keyword><style  face="normal" font="default" size="100%">Tomography</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">45</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Interpreting and controlling bioelectromagnetic phenomena require realistic physiological models and accurate numerical solvers. A semi-realistic model often used in practise is the piecewise constant conductivity model, for which only the interfaces have to be meshed. This simplified model makes it possible to use Boundary Element Methods. Unfortunately, most Boundary Element solutions are confronted with accuracy issues when the conductivity ratio between neighboring tissues is high, as for instance the scalp/skull conductivity ratio in electro-encephalography. To overcome this difficulty, we proposed a new method called the symmetric BEM, which is implemented in the OpenMEEG software. The aim of this paper is to present OpenMEEG, both from the theoretical and the practical point of view, and to compare its performances with other competing software packages.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20819204?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Reinert, Knut</style></author><author><style face="normal" font="default" size="100%">Kohlbacher, Oliver</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">OpenMS and TOPP: open source software for LC-MS data analysis.</style></title><secondary-title><style face="normal" font="default" size="100%">Methods in molecular biology (Clifton, N.J.)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Methods Mol. Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">604</style></volume><pages><style face="normal" font="default" size="100%">201-11</style></pages><abstract><style face="normal" font="default" size="100%">The automatic analysis of mass spectrometry data is becoming more and more important since increasingly larger datasets are readily available that cannot be evaluated manually. This has triggered the development of several open-source software libraries for the automatic analysis of such data. Among those is OpenMS together with TOPP (The OpenMS Proteomics Pipeline). OpenMS is a C++ library for rapid prototyping of complex algorithms for the analysis of mass spectrometry data. Based on the OpenMS library, TOPP provides a collection of tools for the most important tasks in proteomics analysis. The tight coupling of OpenMS and TOPP makes it easy to extend TOPP by adding new tools to the OpenMS library. We describe the overall concepts behind the software and illustrate its use with several examples.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20013373?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Messroghli, Daniel</style></author><author><style face="normal" font="default" size="100%">Rudolph, Andre</style></author><author><style face="normal" font="default" size="100%">Abdel-Aty, Hassan</style></author><author><style face="normal" font="default" size="100%">Wassmuth, Ralf</style></author><author><style face="normal" font="default" size="100%">Kuhne, Titus</style></author><author><style face="normal" font="default" size="100%">Dietz, Rainer</style></author><author><style face="normal" font="default" size="100%">Schulz-Menger, Jeanette</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Medical Imaging</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.biomedcentral.com/1471-2342/10/16</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">1</style></number><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">16</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND:In magnetic resonance (MR) imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization.  RESULTS:After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/ TOMROP T1; modified Look-Locker inversion recovery (MOLLI) T1; single-echo T2/ T2*; and multi-echo T2/ T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data. CONCLUSIONS:MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet. </style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>13</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Morrison, Cecily</style></author><author><style face="normal" font="default" size="100%">Iosif, Adona</style></author><author><style face="normal" font="default" size="100%">Danka, Miklos</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Report on existing open-source electronic medical records</style></title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.cl.cam.ac.uk/techreports/UCAM-CL-TR-768.pdf</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">UCAM-CL-TR-768</style></number><publisher><style face="normal" font="default" size="100%">University of Cambridge, Computer Laboratory</style></publisher><abstract><style face="normal" font="default" size="100%">In this report we provide an overview of existing open-source electronic medical records and assess them against the criteria established by the EViDence group.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Safadi, Hani</style></author><author><style face="normal" font="default" size="100%">Faraj, Samer</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Role of Workarounds during an Open Source Electronic Medical Record System Implementation</style></title><secondary-title><style face="normal" font="default" size="100%">ICIS 2010 Proceedings</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://aisel.aisnet.org/icis2010_submissions/47</style></url></web-urls></urls><abstract><style face="normal" font="default" size="100%">A significant degree of customization of medical information technology is required to effectively integrate the promise of IT with the diversity and complexity of medical work. In the absence of such customizations, dissatisfaction and resistance toward the system arise. Indeed, the complexity of the medical work and the inability of software to tailor to the diverse medical practices may explain the limited diffusion of health information systems especially in North America. We study the role of workarounds during an open-source Electronic Medical Record System (EMR) implementation at a medium-size urgent care clinic in a major Canadian city. We found that the technology appropriation process involved the evolving of number of non-trivial workarounds in order to match the EMR to medical work. The emergence of workarounds is conceptualized as a knowledge creation and integration process. This perspective allows us to look at the antecedents and the change dynamics of workarounds in the clinic. Furthermore diverging from the negative view toward workarounds, we discuss the importance of incorporating workarounds during and following system development. The workaround perspective shed the light on how users’ behavior can be channeled into a constructive development effort. This paper contributes by examining the workaround of medical practitioners using an open-source electronic medical record system as well as offering a knowledge perspective for the study of EMR appropriation.</style></abstract><issue><style face="normal" font="default" size="100%">Paper 47</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sudre, Gustavo</style></author><author><style face="normal" font="default" size="100%">Wang, Wei</style></author><author><style face="normal" font="default" size="100%">Song, Tao</style></author><author><style face="normal" font="default" size="100%">Kajola, Matti</style></author><author><style face="normal" font="default" size="100%">Vinjamuri, Ramana</style></author><author><style face="normal" font="default" size="100%">Collinger, Jennifer</style></author><author><style face="normal" font="default" size="100%">Degenhart, Alan</style></author><author><style face="normal" font="default" size="100%">Bagic, Anto</style></author><author><style face="normal" font="default" size="100%">Weber, Doug J.</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Magjarevic, R.</style></author><author><style face="normal" font="default" size="100%">Nagel, J. H.</style></author><author><style face="normal" font="default" size="100%">Supek, Selma</style></author><author><style face="normal" font="default" size="100%">Sušac, Ana</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">rtMEG: A Real-Time Software Toolbox for Brain-Machine Interfaces Using Magnetoencephelography</style></title><secondary-title><style face="normal" font="default" size="100%">17th International Conference on Biomagnetism Advances in Biomagnetism – Biomag2010</style></secondary-title><tertiary-title><style face="normal" font="default" size="100%">IFMBE Proceedings</style></tertiary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/978-3-642-12197-5_85</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer Berlin Heidelberg</style></publisher><volume><style face="normal" font="default" size="100%">28</style></volume><pages><style face="normal" font="default" size="100%">362-365</style></pages><isbn><style face="normal" font="default" size="100%">978-3-642-12197-5</style></isbn><notes><style face="normal" font="default" size="100%">10.1007/978-3-642-12197-5_85</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tolopko, Andrew N</style></author><author><style face="normal" font="default" size="100%">Sullivan, John P</style></author><author><style face="normal" font="default" size="100%">Erickson, Sean D</style></author><author><style face="normal" font="default" size="100%">Wrobel, David</style></author><author><style face="normal" font="default" size="100%">Chiang, Su L</style></author><author><style face="normal" font="default" size="100%">Rudnicki, Katrina</style></author><author><style face="normal" font="default" size="100%">Rudnicki, Stewart</style></author><author><style face="normal" font="default" size="100%">Nale, Jennifer</style></author><author><style face="normal" font="default" size="100%">Selfors, Laura M</style></author><author><style face="normal" font="default" size="100%">Greenhouse, Dara</style></author><author><style face="normal" font="default" size="100%">Muhlich, Jeremy L</style></author><author><style face="normal" font="default" size="100%">Shamu, Caroline E</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC bioinformatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Bioinformatics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">260</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. RESULTS: We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. CONCLUSIONS: The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20482787?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">A Panchal</style></author><author><style face="normal" font="default" size="100%">R Keyes</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">SU-GG-T-260: Dicompyler: An Open Source Radiation Therapy Research Platform with a Plugin Architecture</style></title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://link.aip.org/link/?MPH/37/3245/2</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">6</style></number><publisher><style face="normal" font="default" size="100%">AAPM</style></publisher><volume><style face="normal" font="default" size="100%">37</style></volume><pages><style face="normal" font="default" size="100%">3245-3245</style></pages></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kalpathy-Cramer, Jayashree</style></author><author><style face="normal" font="default" size="100%">Fuller, Clifton David</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Target Contour Testing/Instructional Computer Software (TaCTICS): A Novel Training and Evaluation Platform for Radiotherapy Target Delineation.</style></title><secondary-title><style face="normal" font="default" size="100%">AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium</style></secondary-title><alt-title><style face="normal" font="default" size="100%">AMIA Annu Symp Proc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2010</style></volume><pages><style face="normal" font="default" size="100%">361-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Target volume delineation is a critical step in the creation of treatment plans in radiation therapy. However, intra-observer and inter-observer variability in target volume definitions can introduce substantial differences in resulting doses between treatments plans from different users and institutions Consequently, there is a need for tools that allow quantitative metrics to be collected and reported regarding inter-and intra-user performance in target volume delineation. We describe TaCTICS, a web-based educational training software application targeted towards residents and non-expert users. TaCTICS allows users to delineate target structures in DICOM-RT compatible formats using their preferred treatment planning system. After uploading the resulting structure file, users are provided a scoring of their structures based on comparison to reference sets derived from expert users using a variety of metrics for volume overlap and surface distances.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21347001?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Meyer dos Santos, Sascha</style></author><author><style face="normal" font="default" size="100%">Klinkhardt, Ute</style></author><author><style face="normal" font="default" size="100%">Schneppenheim, Reinhard</style></author><author><style face="normal" font="default" size="100%">Harder, Sebastian</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Using ImageJ for the quantitative analysis of flow-based adhesion assays in real-time under physiologic flow conditions.</style></title><secondary-title><style face="normal" font="default" size="100%">Platelets</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Platelets</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">21</style></volume><pages><style face="normal" font="default" size="100%">60-6</style></pages><abstract><style face="normal" font="default" size="100%">This article intends to close the gap between the abundance of regular articles focusing on adhesive mechanisms of cells in a flow field and purely technical reports confined to the description of newly developed algorithms, not yet ready to be used by users without programming skills. A simple and robust method is presented for analysing raw videomicroscopic data of flow-based adhesion assays using the freely available public domain software ImageJ. We describe in detail the image processing routines used to rapidly and reliably evaluate the number of adherent and translocating platelets in videomicroscopic recordings. The depicted procedures were exemplified by analysing platelet interaction with immobilized von Willebrand factor and fibrinogen in flowing blood under physiological wall shear rates. Neutralizing GPIbalpha function reduced shear-dependent platelet translocation on von Willebrand factor and abolished firm platelet adhesion. Abciximab, Tirofiban and Eptifibatide completely inhibited GPIIb/IIIa-dependent stable platelet deposition on fibrinogen. The presented method to analyse videomicroscopic recordings from flow-based adhesion assays offers the advantage of providing a simple and reliable way to quantify flow-based adhesion assays, which is completely based on ImageJ and can easily be applied to study adhesion mechanisms of cells in non-fluorescent modes without the need to deviate from the presented protocol.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20001786?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Weitzman, Elissa R</style></author><author><style face="normal" font="default" size="100%">Kaci, Liljana</style></author><author><style face="normal" font="default" size="100%">Mandl, Kenneth D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Acceptability of a personally controlled health record in a community-based setting: implications for policy and design.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of medical Internet research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Med. Internet Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">e14</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: Consumer-centered health information systems that address problems related to fragmented health records and disengaged and disempowered patients are needed, as are information systems that support public health monitoring and research. Personally controlled health records (PCHRs) represent one response to these needs. PCHRs are a special class of personal health records (PHRs) distinguished by the extent to which users control record access and contents. Recently launched PCHR platforms include Google Health, Microsoft's HealthVault, and the Dossia platform, based on Indivo. OBJECTIVE: To understand the acceptability, early impacts, policy, and design requirements of PCHRs in a community-based setting. METHODS: Observational and narrative data relating to acceptability, adoption, and use of a personally controlled health record were collected and analyzed within a formative evaluation of a PCHR demonstration. Subjects were affiliates of a managed care organization run by an urban university in the northeastern United States. Data were collected using focus groups, semi-structured individual interviews, and content review of email communications. Subjects included: n = 20 administrators, clinicians, and institutional stakeholders who participated in pre-deployment group or individual interviews; n = 52 community members who participated in usability testing and/or pre-deployment piloting; and n = 250 subjects who participated in the full demonstration of which n = 81 initiated email communications to troubleshoot problems or provide feedback. All data were formatted as narrative text and coded thematically by two independent analysts using a shared rubric of a priori defined major codes. Sub-themes were identified by analysts using an iterative inductive process. Themes were reviewed within and across research activities (ie, focus group, usability testing, email content review) and triangulated to identify patterns. RESULTS: Low levels of familiarity with PCHRs were found as were high expectations for capabilities of nascent systems. Perceived value for PCHRs was highest around abilities to co-locate, view, update, and share health information with providers. Expectations were lowest for opportunities to participate in research. Early adopters perceived that PCHR benefits outweighed perceived risks, including those related to inadvertent or intentional information disclosure. Barriers and facilitators at institutional, interpersonal, and individual levels were identified. Endorsement of a dynamic platform model PCHR was evidenced by preferences for embedded searching, linking, and messaging capabilities in PCHRs; by high expectations for within-system tailored communications; and by expectation of linkages between self-report and clinical data. CONCLUSIONS: Low levels of awareness/preparedness and high expectations for PCHRs exist as a potentially problematic pairing. Educational and technical assistance for lay users and providers are critical to meet challenges related to: access to PCHRs, especially among older cohorts; workflow demands and resistance to change among providers; inadequate health and technology literacy; clarification of boundaries and responsibility for ensuring accuracy and integrity of health information across distributed data systems; and understanding confidentiality and privacy risks. Continued demonstration and evaluation of PCHRs is essential to advancing their use.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19403467?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Paré, Guy</style></author><author><style face="normal" font="default" size="100%">Wybo, Michael D</style></author><author><style face="normal" font="default" size="100%">Delannoy, Charles</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Barriers to open source software adoption in Quebec's health care organizations.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of medical systems</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Med Syst</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Attitude of Health Personnel</style></keyword><keyword><style  face="normal" font="default" size="100%">Delivery of Health Care</style></keyword><keyword><style  face="normal" font="default" size="100%">Health Facility Administrators</style></keyword><keyword><style  face="normal" font="default" size="100%">Health Policy</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Medical Informatics</style></keyword><keyword><style  face="normal" font="default" size="100%">Organizational Innovation</style></keyword><keyword><style  face="normal" font="default" size="100%">Quebec</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Systems Integration</style></keyword><keyword><style  face="normal" font="default" size="100%">Technology Transfer</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">33</style></volume><pages><style face="normal" font="default" size="100%">1-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We conducted in-depth interviews with 15 CIOs to identify the principal impediments to adoption of open source software in the Quebec health sector. We found that key factors for not adopting an open source solution were closely linked to the orientations of ministry level policy makers and a seeming lack of information on the part of operational level IT managers concerning commercially oriented open source providers. We use the case of recent changes in the structure of Quebec's health care organizations and a change in the commercial policies of a key vendor to illustrate our conclusions regarding barriers to adoption of open source products.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19238891?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Woolrich, Mark W</style></author><author><style face="normal" font="default" size="100%">Jbabdi, Saad</style></author><author><style face="normal" font="default" size="100%">Patenaude, Brian</style></author><author><style face="normal" font="default" size="100%">Chappell, Michael</style></author><author><style face="normal" font="default" size="100%">Makni, Salima</style></author><author><style face="normal" font="default" size="100%">Behrens, Timothy</style></author><author><style face="normal" font="default" size="100%">Beckmann, Christian</style></author><author><style face="normal" font="default" size="100%">Jenkinson, Mark</style></author><author><style face="normal" font="default" size="100%">Smith, Stephen M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Bayesian analysis of neuroimaging data in FSL.</style></title><secondary-title><style face="normal" font="default" size="100%">NeuroImage</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Neuroimage</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bayes Theorem</style></keyword><keyword><style  face="normal" font="default" size="100%">Brain</style></keyword><keyword><style  face="normal" font="default" size="100%">Diffusion Magnetic Resonance Imaging</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Image Interpretation, Computer-Assisted</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">45</style></volume><pages><style face="normal" font="default" size="100%">S173-86</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Typically in neuroimaging we are looking to extract some pertinent information from imperfect, noisy images of the brain. This might be the inference of percent changes in blood flow in perfusion FMRI data, segmentation of subcortical structures from structural MRI, or inference of the probability of an anatomical connection between an area of cortex and a subthalamic nucleus using diffusion MRI. In this article we will describe how Bayesian techniques have made a significant impact in tackling problems such as these, particularly in regards to the analysis tools in the FMRIB Software Library (FSL). We shall see how Bayes provides a framework within which we can attempt to infer on models of neuroimaging data, while allowing us to incorporate our prior belief about the brain and the neuroimaging equipment in the form of biophysically informed or regularising priors. It allows us to extract probabilistic information from the data, and to probabilistically combine information from multiple modalities. Bayes can also be used to not only compare and select between models of different complexity, but also to infer on data using committees of models. Finally, we mention some analysis scenarios where Bayesian methods are impractical, and briefly discuss some practical approaches that we have taken in these cases.</style></abstract><issue><style face="normal" font="default" size="100%">1 Suppl</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19059349?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gouws, André</style></author><author><style face="normal" font="default" size="100%">Woods, Will</style></author><author><style face="normal" font="default" size="100%">Millman, Rebecca</style></author><author><style face="normal" font="default" size="100%">Morland, Antony</style></author><author><style face="normal" font="default" size="100%">Green, Gary</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool.</style></title><secondary-title><style face="normal" font="default" size="100%">Frontiers in neuroinformatics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">9</style></pages><abstract><style face="normal" font="default" size="100%">Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK's low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user's operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19352444?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Melissano, G</style></author><author><style face="normal" font="default" size="100%">Bertoglio, L</style></author><author><style face="normal" font="default" size="100%">Civelli, V</style></author><author><style face="normal" font="default" size="100%">Amato, A C Moraes</style></author><author><style face="normal" font="default" size="100%">Coppi, G</style></author><author><style face="normal" font="default" size="100%">Civilini, E</style></author><author><style face="normal" font="default" size="100%">Calori, G</style></author><author><style face="normal" font="default" size="100%">De Cobelli, F</style></author><author><style face="normal" font="default" size="100%">Del Maschio, A</style></author><author><style face="normal" font="default" size="100%">Chiesa, R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Demonstration of the Adamkiewicz artery by multidetector computed tomography angiography analysed with the open-source software OsiriX.</style></title><secondary-title><style face="normal" font="default" size="100%">European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Eur J Vasc Endovasc Surg</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">37</style></volume><pages><style face="normal" font="default" size="100%">395-400</style></pages><abstract><style face="normal" font="default" size="100%">OBJECTIVE: To evaluate the feasibility of the Adamkiewicz artery (AKA) detection by multidetector computed tomography (CT) data analysis without the need of a dedicated workstation, using low-cost hardware and the freeware OsiriX. METHODS: CT scans of 67 patients undergoing a thoracic or thoraco-abdominal aortic procedure between April 2006 and August 2008 were evaluated with respect to detection rate and AKA level and side using the OsiriX software version 3.2 on Mac OS X computer and compared to results obtained by standard workstation analysis, in a fully blinded analysis. The results were also compared with data compiled from a review of the English-language literature on this topic. RESULTS: (1) AKA identification showed a substantial agreement of 85.07% between the methods (k=0.636). (2) The comparison of AKA level showed a substantial agreement (weighted k=0.661), with consensus in 70.14%. (3) From the literature review, we found that recognition of the AKA was achieved in 466 of 555 cases (83.96%). (4) In 384 (83.3%) cases the AKA originated from a left intercostal artery. (5) The proposed method and literature-compiled data showed a similar AKA level distribution. CONCLUSIONS: Noninvasive AKA location with open-source software and low-cost hardware is feasible. The OsiriX software allows to effectively navigate through CT data not only to study the aorta, but also to detect the AKA, as in the case of the standard method and the literature data. Its availability and ease of use may contribute to make identification of the AKA part of the routine evaluation of CT scans in patients with aortic disease, even where dedicated workstations are not available, with potential benefits for planning therapeutic procedures.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19230726?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ibrahim, Danilo</style></author><author><style face="normal" font="default" size="100%">Broilo, Tiago Leonardo</style></author><author><style face="normal" font="default" size="100%">Heitz, Claiton</style></author><author><style face="normal" font="default" size="100%">Gerhardt de Oliveira, Marília</style></author><author><style face="normal" font="default" size="100%">de Oliveira, Helena Willhelm</style></author><author><style face="normal" font="default" size="100%">Nobre, Stella Maris Wanderlei</style></author><author><style face="normal" font="default" size="100%">Dos Santos Filho, José Henrique Gomes</style></author><author><style face="normal" font="default" size="100%">Silva, Daniela Nascimento</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Dimensional error of selective laser sintering, three-dimensional printing and PolyJet models in the reproduction of mandibular anatomy.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Craniomaxillofac Surg</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">37</style></volume><pages><style face="normal" font="default" size="100%">167-73</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: Selective laser sintering (SLS), three-dimensional printing (3DP) and PolyJet are rapid prototyping (RP) techniques to fabricate prototypes from virtual biomedical images. To be used in maxillofacial surgery, these models must accurately reproduce the craniofacial skeleton. PURPOSE: To analyze the capacity of SLS, 3DP and PolyJet models to reproduce mandibular anatomy and their dimensional error. MATERIAL: Dry mandible, helical CT images, SLS, 3DP and PolyJet prototypes, and digital electronic caliper. METHODS: Helical CT images were acquired from a dry mandible (criterion standard) and manipulated with the InVesalius software. Prototypes were produced using SLS, 3DP and PolyJet techniques. Thirteen linear measurements of each prototype were made and compared with the dry mandible measurements. RESULTS: The results showed a dimensional error of 1.79%, 3.14% and 2.14% for SLS, 3DP and PolyJet models, respectively. The models satisfactorily reproduced anatomic details and the SLS and PolyJet prototypes showed greater dimensional precision and reproduced mandibular anatomy more accurately than the 3DP model. CONCLUSIONS: The SLS prototype had a greater dimensional accuracy than the PolyJet and 3DP models. The PolyJet technique reproduced anatomic details of the mandible more accurately.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19056288?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lazarus, Ross</style></author><author><style face="normal" font="default" size="100%">Klompas, Michael</style></author><author><style face="normal" font="default" size="100%">Campion, Francis X</style></author><author><style face="normal" font="default" size="100%">McNabb, Scott J N</style></author><author><style face="normal" font="default" size="100%">Hou, Xuanlin</style></author><author><style face="normal" font="default" size="100%">Daniel, James</style></author><author><style face="normal" font="default" size="100%">Haney, Gillian</style></author><author><style face="normal" font="default" size="100%">DeMaria, Alfred</style></author><author><style face="normal" font="default" size="100%">Lenert, Leslie</style></author><author><style face="normal" font="default" size="100%">Platt, Richard</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electronic Support for Public Health: validated case finding and reporting for notifiable diseases using electronic medical data.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of the American Medical Informatics Association : JAMIA</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Jan-Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">16</style></volume><pages><style face="normal" font="default" size="100%">18-24</style></pages><abstract><style face="normal" font="default" size="100%">Health care providers are legally obliged to report cases of specified diseases to public health authorities, but existing manual, provider-initiated reporting systems generally result in incomplete, error-prone, and tardy information flow. Automated laboratory-based reports are more likely accurate and timely, but lack clinical information and treatment details. Here, we describe the Electronic Support for Public Health (ESP) application, a robust, automated, secure, portable public health detection and messaging system for cases of notifiable diseases. The ESP application applies disease specific logic to any complete source of electronic medical data in a fully automated process, and supports an optional case management workflow system for case notification control. All relevant clinical, laboratory and demographic details are securely transferred to the local health authority as an HL7 message. The ESP application has operated continuously in production mode since January 2007, applying rigorously validated case identification logic to ambulatory EMR data from more than 600,000 patients. Source code for this highly interoperable application is freely available under an approved open-source license at http://esphealth.org.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18952940?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Heinze, Oliver</style></author><author><style face="normal" font="default" size="100%">Brandner, Antje</style></author><author><style face="normal" font="default" size="100%">Bergh, Björn</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Establishing a personal electronic health record in the Rhine-Neckar region.</style></title><secondary-title><style face="normal" font="default" size="100%">Studies in health technology and informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Stud Health Technol Inform</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Germany</style></keyword><keyword><style  face="normal" font="default" size="100%">Medical Records Systems, Computerized</style></keyword><keyword><style  face="normal" font="default" size="100%">Organizational Case Studies</style></keyword><keyword><style  face="normal" font="default" size="100%">Program Development</style></keyword><keyword><style  face="normal" font="default" size="100%">Regional Health Planning</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">150</style></volume><pages><style face="normal" font="default" size="100%">119</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We present an approach to establish a personal and electronic health record (PEHR) system in our region, and describe the underlying vision, the technical aspects, the current status as well as the gained experiences. Applied are international standards (HL7, DICOM) and technologies existing today. Obstacles to overcome during the implementation have been the management of access rights, data privacy as well as the integration of the primary systems.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19745279?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Solomon, Robert W</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Free and open source software for the manipulation of digital images.</style></title><secondary-title><style face="normal" font="default" size="100%">AJR. American journal of roentgenology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">AJR Am J Roentgenol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">192</style></volume><pages><style face="normal" font="default" size="100%">W330-4</style></pages><abstract><style face="normal" font="default" size="100%">OBJECTIVE: Free and open source software is a type of software that is nearly as powerful as commercial software but is freely downloadable. This software can do almost everything that the expensive programs can. GIMP (gnu image manipulation program) is the free program that is comparable to Photoshop, and versions are available for Windows, Macintosh, and Linux platforms. This article briefly describes how GIMP can be installed and used to manipulate radiology images. CONCLUSION: It is no longer necessary to budget large amounts of money for high-quality software to achieve the goals of image processing and document creation because free and open source software is available for the user to download at will.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19457798?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yamamoto, Shuji</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Fundamental of medical image processing with personal computer system--Image processing of computed tomography with imageJ</style></title><secondary-title><style face="normal" font="default" size="100%">Nippon Hoshasen Gijutsu Gakkai zasshi</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nippon Hoshasen Gijutsu Gakkai Zasshi</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Dec 20</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">65</style></volume><pages><style face="normal" font="default" size="100%">1680-2</style></pages><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20124747?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Larrabide, Ignacio</style></author><author><style face="normal" font="default" size="100%">Omedas, Pedro</style></author><author><style face="normal" font="default" size="100%">Martelli, Yves</style></author><author><style face="normal" font="default" size="100%">Planes, Xavier</style></author><author><style face="normal" font="default" size="100%">Nieber, Maarten</style></author><author><style face="normal" font="default" size="100%">Moya, Juan</style></author><author><style face="normal" font="default" size="100%">Butakoff, Constantine</style></author><author><style face="normal" font="default" size="100%">Sebastián, Rafael</style></author><author><style face="normal" font="default" size="100%">Camara, Oscar</style></author><author><style face="normal" font="default" size="100%">De Craene, Mathieu</style></author><author><style face="normal" font="default" size="100%">Bijnens, Bart</style></author><author><style face="normal" font="default" size="100%">Frangi, Alejandro</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Ayache, Nicholas</style></author><author><style face="normal" font="default" size="100%">Delingette, Hervé</style></author><author><style face="normal" font="default" size="100%">Sermesant, Maxime</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">GIMIAS: An Open Source Framework for Efficient Development of Research Tools and Clinical Prototypes</style></title><secondary-title><style face="normal" font="default" size="100%">Functional Imaging and Modeling of the Heart</style></secondary-title><tertiary-title><style face="normal" font="default" size="100%">Lecture Notes in Computer Science</style></tertiary-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/978-3-642-01932-6_45</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer Berlin / Heidelberg</style></publisher><volume><style face="normal" font="default" size="100%">5528</style></volume><pages><style face="normal" font="default" size="100%">417-426</style></pages><abstract><style face="normal" font="default" size="100%">GIMIAS is a workflow-oriented environment for addressing advanced biomedical image computing and build personalized computational models, which is extensible through the development of application-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Virtual Physiological Human community while allowing business-friendly technology transfer and commercial product development. This framework has been fully developed in ANSI-C++ on top of well known open source libraries like VTK, ITK and wxWidgets among others. Based on GIMIAS, in this paper is presented a workflow for medical image analysis and simulation of the heart.</style></abstract><notes><style face="normal" font="default" size="100%">10.1007/978-3-642-01932-6_45</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Vrekoussis, T</style></author><author><style face="normal" font="default" size="100%">Chaniotis, V</style></author><author><style face="normal" font="default" size="100%">Navrozoglou, I</style></author><author><style face="normal" font="default" size="100%">Dousias, V</style></author><author><style face="normal" font="default" size="100%">Pavlakis, K</style></author><author><style face="normal" font="default" size="100%">Stathopoulos, E N</style></author><author><style face="normal" font="default" size="100%">Zoras, O</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Image analysis of breast cancer immunohistochemistry-stained sections using ImageJ: an RGB-based model.</style></title><secondary-title><style face="normal" font="default" size="100%">Anticancer research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Anticancer Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">29</style></volume><pages><style face="normal" font="default" size="100%">4995-8</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: Image analysis of tissue sections using RGB image profiling is a modern accepted technique. MATERIALS AND METHODS: A new method of RGB analysis, using the freeware ImageJ, is presented which can be applied to sections with either nuclear or cytoplasmic staining. The step-by-step process is presented and the method is tested using breast cancer specimens immunostained for CK-19 and estrogen receptors. RESULTS: This image analysis easily discriminates CK-19 and estrogen receptor positivity in prepared breast cancer specimens. The method is easy to perform, without the need for previous image transformations. CONCLUSION: Compared to previous methods, this method proved more accurate in estimating the actual colours that an observer recognizes as positive after immunostaining. Further studies are needed to evaluate whether this method is efficient enough to be applied in clinical practice.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20044607?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Maleike, D</style></author><author><style face="normal" font="default" size="100%">Nolden, M</style></author><author><style face="normal" font="default" size="100%">Meinzer, H-P</style></author><author><style face="normal" font="default" size="100%">Wolf, I</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Interactive segmentation framework of the Medical Imaging Interaction Toolkit.</style></title><secondary-title><style face="normal" font="default" size="100%">Computer methods and programs in biomedicine</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Comput Methods Programs Biomed</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">96</style></volume><pages><style face="normal" font="default" size="100%">72-83</style></pages><abstract><style face="normal" font="default" size="100%">Interactive methods are indispensable for real world applications of segmentation in medicine, at least to allow for convenient and fast verification and correction of automated techniques. Besides traditional interactive tasks such as adding or removing parts of a segmentation, adjustment of contours or the placement of seed points, the relatively recent Graph Cut and Random Walker segmentation methods demonstrate an interest in advanced interactive strategies for segmentation. Though the value of toolkits and extensible applications is generally accepted for the development of new segmentation algorithms, the topic of interactive segmentation applications is rarely addressed by current toolkits and applications. In this paper, we present the extension of the Medical Imaging Interaction Toolkit (MITK) with a framework for the development of interactive applications for image segmentation. The framework provides a clear structure for the development of new applications and offers a plugin mechanism to easily extend existing applications with additional segmentation tools. In addition, the framework supports shape-based interpolation and multi-level undo/redo of modifications to binary images. To demonstrate the value of the framework, we also present a free, open-source application named InteractiveSegmentation for manual segmentation of medical images (including 3D+t), which is built based on the extended MITK framework. The application includes several features to effectively support manual segmentation, which are not found in comparable freely available applications. InteractiveSegmentation is fully developed and successfully and regularly used in several projects. Using the plugin mechanism, the application enables developers of new algorithms to begin algorithmic work more quickly.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19439392?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bourgeois, Fabienne C</style></author><author><style face="normal" font="default" size="100%">Mandl, Kenneth D</style></author><author><style face="normal" font="default" size="100%">Shaw, Danny</style></author><author><style face="normal" font="default" size="100%">Flemming, Daisy</style></author><author><style face="normal" font="default" size="100%">Nigrin, Daniel J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Mychildren's: integration of a personally controlled health record with a tethered patient portal for a pediatric and adolescent population.</style></title><secondary-title><style face="normal" font="default" size="100%">AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium</style></secondary-title><alt-title><style face="normal" font="default" size="100%">AMIA Annu Symp Proc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2009</style></volume><pages><style face="normal" font="default" size="100%">65-9</style></pages><abstract><style face="normal" font="default" size="100%">Personally controlled health records (PCHRs) and patient portals are increasingly being offered by healthcare institutions, employers, insurance companies and commercial entities to allow patients access to their health information. Both applications offer unique services to provide patients with tools to manage their health. While PCHRs allow users ubiquitous, portable, patient controlled access to their health information, traditional patient portals provide provider-tethered applications allowing patients access, but not control of, certain healthcare information, as well as communication and administrative functions, such as secure messaging, appointment management and prescription refill requests, facilitating care at a specific healthcare facility.We describe our approach for the design, content creation, policy development, and implementation of MyChildren's, a unique web-based application leveraging the advantages of both a provider-tethered patient portal and a PCHR to allow patients and their guardians access to the functionality and convenience of a traditional patient portal, as well as the portability and flexibility of a PCHR.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20351824?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Murray, Peter J</style></author><author><style face="normal" font="default" size="100%">Wright, Graham</style></author><author><style face="normal" font="default" size="100%">Karopka, Thomas</style></author><author><style face="normal" font="default" size="100%">Betts, Helen</style></author><author><style face="normal" font="default" size="100%">Orel, Andrej</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open source and healthcare in Europe - time to put leading edge ideas into practice.</style></title><secondary-title><style face="normal" font="default" size="100%">Studies in health technology and informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Stud Health Technol Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">150</style></volume><pages><style face="normal" font="default" size="100%">963-7</style></pages><abstract><style face="normal" font="default" size="100%">Free/Libre and Open Source Software (FLOSS) is a process of software development, a method of licensing and a philosophy. Although FLOSS plays a significant role in several market areas, the impact in the health care arena is still limited. FLOSS is promoted as one of the most effective means for overcoming fragmentation in the health care sector and providing a basis for more efficient, timely and cost effective health care provision. The 2008 European Federation for Medical Informatics (EFMI) Special Topic Conference (STC) explored a range of current and future issues related to FLOSS in healthcare (FLOSS-HC). In particular, there was a focus on health records, ubiquitous computing, knowledge sharing, and current and future applications. Discussions resulted in a list of main barriers and challenges for use of FLOSS-HC. Based on the outputs of this event, the 2004 Open Steps events and subsequent workshops at OSEHC2009 and Med-e-Tel 2009, a four-step strategy has been proposed for FLOSS-HC: 1) a FLOSS-HC inventory; 2) a FLOSS-HC collaboration platform, use case database and knowledge base; 3) a worldwide FLOSS-HC network; and 4) FLOSS-HC dissemination activities. The workshop will further refine this strategy and elaborate avenues for FLOSS-HC from scientific, business and end-user perspectives. To gain acceptance by different stakeholders in the health care industry, different activities have to be conducted in collaboration. The workshop will focus on the scientific challenges in developing methodologies and criteria to support FLOSS-HC in becoming a viable alternative to commercial and proprietary software development and deployment.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19745456?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Seebregts, Christopher J</style></author><author><style face="normal" font="default" size="100%">Mamlin, Burke W</style></author><author><style face="normal" font="default" size="100%">Biondich, Paul G</style></author><author><style face="normal" font="default" size="100%">Fraser, Hamish S F</style></author><author><style face="normal" font="default" size="100%">Wolfe, Benjamin A</style></author><author><style face="normal" font="default" size="100%">Jazayeri, Darius</style></author><author><style face="normal" font="default" size="100%">Allen, Christian</style></author><author><style face="normal" font="default" size="100%">Miranda, Justin</style></author><author><style face="normal" font="default" size="100%">Baker, Elaine</style></author><author><style face="normal" font="default" size="100%">Musinguzi, Nicholas</style></author><author><style face="normal" font="default" size="100%">Kayiwa, Daniel</style></author><author><style face="normal" font="default" size="100%">Fourie, Carl</style></author><author><style face="normal" font="default" size="100%">Lesh, Neal</style></author><author><style face="normal" font="default" size="100%">Kanter, Andrew</style></author><author><style face="normal" font="default" size="100%">Yiannoutsos, Constantin T</style></author><author><style face="normal" font="default" size="100%">Bailey, Christopher</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">OpenMRS Implementers Network</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">The OpenMRS Implementers Network.</style></title><secondary-title><style face="normal" font="default" size="100%">International journal of medical informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int J Med Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Nov</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.healthware.org/openmrs/openmrs.pdf</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">78</style></volume><pages><style face="normal" font="default" size="100%">711-20</style></pages><abstract><style face="normal" font="default" size="100%">OBJECTIVE: OpenMRS (www.openmrs.org) is a configurable open source electronic medical record application developed and maintained by a large network of open source developers coordinated by the Regenstrief Institute and Partners in Health and mainly used for HIV patient and treatment information management in Africa. Our objective is to develop an open Implementers Network for OpenMRS to provide regional support for the growing number of OpenMRS implementations in Africa and to include African developers and implementers in the future growth of OpenMRS. METHODS: We have developed the OpenMRS Implementers Network using a dedicated Wiki site and e-mail server. We have also organized annual meetings in South Africa and regional training courses at African locations where OpenMRS is being implemented. An OpenMRS Internship program has been initiated and we have started collaborating with similar networks and projects working in Africa. To evaluate its potential, OpenMRS was implemented initially at one site in South Africa by a single implementer using a downloadable OpenMRS application and only the OpenMRS Implementers Network for support. RESULTS: The OpenMRS Implementers Network Wiki and list server have grown into effective means of providing implementation support and forums for exchange of implementation experiences. The annual OpenMRS Implementers meeting has been held in South Africa for the past three years and is attracting successively larger numbers of participants with almost 200 implementers and developers attending the 2008 meeting in Durban, South Africa. Six African developers are presently registered on the first intake of the OpenMRS Internship program. Successful collaborations have been started with several African developer groups and projects initiated to develop interoperability between OpenMRS and various applications. The South African OpenMRS Implementer group successfully configured, installed and maintained an integrated HIV/TB OpenMRS application without significant programming support. Since then, this model has been replicated in several other African sites. The OpenMRS Implementers Network has contributed substantially to the growth and sustainability of OpenMRS in Africa and has become a useful way of including Africans in the development and implementation of OpenMRS in developing countries. The Network provides valuable support and enables a basic OpenMRS application to be implemented in the absence of onsite programmers.</style></abstract><issue><style face="normal" font="default" size="100%">11</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19157968?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sierra-Martínez, Eduardo</style></author><author><style face="normal" font="default" size="100%">Cienfuegos-Monroy, Ricardo</style></author><author><style face="normal" font="default" size="100%">Fernández-Sobrino, Gerardo</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">OsiriX, a useful tool for processing tomographic images in patients with facial fracture</style></title><secondary-title><style face="normal" font="default" size="100%">Cirugia y cirujanos</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Cir Cir</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Mar-Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">77</style></volume><pages><style face="normal" font="default" size="100%">95-9</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: OsiriX, a Mac OS X-based open source program, is presented as a useful tool to process tomographic images for diagnosis and preoperative planning in patients with facial fractures. METHODS: CT scans were performed on 124 patients with facial fractures treated at the Department of Maxillofacial and Reconstructive Surgery of the Hospital de Traumatología y Ortopedia &quot;Lomas Verdes&quot; in Mexico City. Information obtained was recorded in DICOM format in CDs and processed in a Macintosh laptop with OsiriX software, doing multiplanar and 3D reconstructions. Surgical findings were compared to the images obtained by the software. RESULTS: Of the surgical findings, 96.5% matched with the OsiriX images. Only 3.5% of the OsiriX images were not consistent because of distortion or artifacts in the CT due to firearm projectiles and Erich arch bars near the involved area. CONCLUSIONS: Based on the results obtained, the authors consider that the OsiriX software is a useful tool for diagnosis and preoperative planning in patients with facial fractures. Furthermore, it prevents the loss of information due to the process of image selection by the radiology staff.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19534858?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hanke, Michael</style></author><author><style face="normal" font="default" size="100%">Halchenko, Yaroslav O</style></author><author><style face="normal" font="default" size="100%">Sederberg, Per B</style></author><author><style face="normal" font="default" size="100%">Hanson, Stephen José</style></author><author><style face="normal" font="default" size="100%">Haxby, James V</style></author><author><style face="normal" font="default" size="100%">Pollmann, Stefan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">PyMVPA: A python toolbox for multivariate pattern analysis of fMRI data.</style></title><secondary-title><style face="normal" font="default" size="100%">Neuroinformatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Neuroinformatics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Spring</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">37-53</style></pages><abstract><style face="normal" font="default" size="100%">Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19184561?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hanke, Michael</style></author><author><style face="normal" font="default" size="100%">Halchenko, Yaroslav O</style></author><author><style face="normal" font="default" size="100%">Sederberg, Per B</style></author><author><style face="normal" font="default" size="100%">Olivetti, Emanuele</style></author><author><style face="normal" font="default" size="100%">Fründ, Ingo</style></author><author><style face="normal" font="default" size="100%">Rieger, Jochem W</style></author><author><style face="normal" font="default" size="100%">Herrmann, Christoph S</style></author><author><style face="normal" font="default" size="100%">Haxby, James V</style></author><author><style face="normal" font="default" size="100%">Hanson, Stephen José</style></author><author><style face="normal" font="default" size="100%">Pollmann, Stefan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">PyMVPA: A Unifying Approach to the Analysis of Neuroscientific Data.</style></title><secondary-title><style face="normal" font="default" size="100%">Frontiers in neuroinformatics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">3</style></pages><abstract><style face="normal" font="default" size="100%">The Python programming language is steadily increasing in popularity as the language of choice for scientific computing. The ability of this scripting environment to access a huge code base in various languages, combined with its syntactical simplicity, make it the ideal tool for implementing and sharing ideas among scientists from numerous fields and with heterogeneous methodological backgrounds. The recent rise of reciprocal interest between the machine learning (ML) and neuroscience communities is an example of the desire for an inter-disciplinary transfer of computational methods that can benefit from a Python-based framework. For many years, a large fraction of both research communities have addressed, almost independently, very high-dimensional problems with almost completely non-overlapping methods. However, a number of recently published studies that applied ML methods to neuroscience research questions attracted a lot of attention from researchers from both fields, as well as the general public, and showed that this approach can provide novel and fruitful insights into the functioning of the brain. In this article we show how PyMVPA, a specialized Python framework for machine learning based data analysis, can help to facilitate this inter-disciplinary technology transfer by providing a single interface to a wide array of machine learning libraries and neural data-processing methods. We demonstrate the general applicability and power of PyMVPA via analyses of a number of neural data modalities, including fMRI, EEG, MEG, and extracellular recordings.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19212459?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sugimoto, Maki</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Recent advances in visualization, imaging, and navigation in hepatobiliary and pancreatic sciences.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of hepato-biliary-pancreatic surgery</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Oct 6</style></date></pub-dates></dates><abstract><style face="normal" font="default" size="100%">BACKGROUND/PURPOSE: Recent introduction of multi-detector CT (MDCT) and high-speed magnetic resonance (MR) imaging have dramatically advanced visualization and imaging technology in diagnostic and therapeutic strategy in hepatobiliary pancreatic disease. However, image diagnostics have progressed with a background of the essence of anatomy, pathology, and physiology. It is important to object the reflection of the patient's condition and pathology of each disease and remove pattern recognition in what they were depicted as an image. Visualization plays another important role in various medical diagnostics. Trends in scientific visualization will depend on advancements in molecular technology and computer hardware as well as trends in engineering disciplines. METHODS: In this special issue, the recent advances in visualization and imaging in the field of hepatobiliary and pancreatic sciences are featured including application of advanced visualization techniques, data management, data compression, feature extraction. RESULTS: We discuss the potential benefits of new technologies and procedures in hepatobiliary and pancreatic areas, that are circulating tumor cells, MR imaging for hepatocellular carcinoma, indocyanine green using fluorescence under infrared light observation, carbon dioxide enhanced MDCT virtual cholangiopancreatography, endoscopic ultrasonography-guided biliary drainage, natural orifice translumenal endoscopic surgery, MR-laparoscopy, and image overlay navigation surgery by OsiriX. CONCLUSION: Some of the recent trends are discussed in terms of visualization and imaging in hapatobiliary and pancreatic sciences. The goal in using visualization is to assist existing scientific procedures by providing new insight through visual representation.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19806300?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Onken, Michael</style></author><author><style face="normal" font="default" size="100%">Riesmeier, Jörg</style></author><author><style face="normal" font="default" size="100%">Engel, Marcel</style></author><author><style face="normal" font="default" size="100%">Yabanci, Adem</style></author><author><style face="normal" font="default" size="100%">Zabel, Bernhard</style></author><author><style face="normal" font="default" size="100%">Després, Stefan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Reversible anonymization of DICOM images using automatically generated policies.</style></title><secondary-title><style face="normal" font="default" size="100%">Studies in health technology and informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Stud Health Technol Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">150</style></volume><pages><style face="normal" font="default" size="100%">861-5</style></pages><abstract><style face="normal" font="default" size="100%">Many real-world applications in the area of medical imaging like case study databases require separation of identifying (IDATA) and non-identifying (MDATA) data, specifically those offering Internet-based data access. These kinds of projects also must provide a role-based access system, controlling, how patient data must be organized and how it can be accessed. On DICOM image level, different image types support different kind of information, intermixing IDATA and MDATA in a single object. To separate them, it is possible to reversibly anonymize DICOM objects by substituting IDATA by a unique anonymous token. In case that later an authenticated user needs full access to an image, this token can be used for re-linking formerly separated IDATA and MDATA, thus resulting in a dynamically generated, exact copy of the original image. The approach described in this paper is based on the automatic generation of anonymization policies from the DICOM standard text, providing specific support for all kinds of DICOM images. The policies are executed by a newly developed framework based on the DICOM toolkit DCMTK and offer a reliable approach to reversible anonymization. The implementation is evaluated in a German BMBF-supported expert network in the area of skeletal dysplasias, SKELNET, but may generally be applicable to related projects, enormously improving quality and integrity of diagnostics in a field focused on images. It performs effectively and efficiently on real-world test images from the project and other kind of DICOM images.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19745435?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Janamanchi, Balaji</style></author><author><style face="normal" font="default" size="100%">Katsamakas, Evangelos</style></author><author><style face="normal" font="default" size="100%">Raghupathi, Wullianallur</style></author><author><style face="normal" font="default" size="100%">Gao, Wei</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The state and profile of open source software projects in health and medical informatics.</style></title><secondary-title><style face="normal" font="default" size="100%">International journal of medical informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int J Med Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">78</style></volume><pages><style face="normal" font="default" size="100%">457-72</style></pages><abstract><style face="normal" font="default" size="100%">PURPOSE: Little has been published about the application profiles and development patterns of open source software (OSS) in health and medical informatics. This study explores these issues with an analysis of health and medical informatics related OSS projects on SourceForge, a large repository of open source projects. METHODOLOGY: A search was conducted on the SourceForge website during the period from May 1 to 15, 2007, to identify health and medical informatics OSS projects. This search resulted in a sample of 174 projects. A Java-based parser was written to extract data for several of the key variables of each project. Several visually descriptive statistics were generated to analyze the profiles of the OSS projects. RESULTS: Many of the projects have sponsors, implying a growing interest in OSS among organizations. Sponsorship, we discovered, has a significant impact on project success metrics. Nearly two-thirds of the projects have a restrictive license type. Restrictive licensing may indicate tighter control over the development process. Our sample includes a wide range of projects that are at various stages of development (status). Projects targeted towards the advanced end user are primarily focused on bio-informatics, data formats, database and medical science applications. CONCLUSION: We conclude that there exists an active and thriving OSS development community that is focusing on health and medical informatics. A wide range of OSS applications are in development, from bio-informatics to hospital information systems. A profile of OSS in health and medical informatics emerges that is distinct and unique to the health care field. Future research can focus on OSS acceptance and diffusion and impact on cost, efficiency and quality of health care.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19321384?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sturm, Marc</style></author><author><style face="normal" font="default" size="100%">Kohlbacher, Oliver</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">TOPPView: an open-source viewer for mass spectrometry data.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of proteome research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Proteome Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">3760-3</style></pages><abstract><style face="normal" font="default" size="100%">Visualization of complex mass spectrometric data sets is becoming increasingly important in proteomics and metabolomics. We present TOPPView, an integrated data visualization and analysis tool for mass spectrometric data sets. TOPPView allows the visualization and comparison of individual mass spectra, two-dimensional LC-MS data sets and their accompanying metadata. By supporting standardized XML-based data exchange formats, data import is possible from any type of mass spectrometer. The integrated analysis tools of the OpenMS Proteomics Pipeline (TOPP) allow efficient data analysis from within TOPPView through a convenient graphical user interface. TOPPView runs on all major operating systems and is available free of charge under an open-source license at http://www.openms.de.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19425593?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Pintilie, Stefan</style></author><author><style face="normal" font="default" size="100%">Biswas, Labonny</style></author><author><style face="normal" font="default" size="100%">Anderson, Kevan</style></author><author><style face="normal" font="default" size="100%">Dick, Sandy</style></author><author><style face="normal" font="default" size="100%">Wright, Graham</style></author><author><style face="normal" font="default" size="100%">Radau, Perry</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Visualization Software for Real-time, Image-guided Therapeutics in Cardiovascular Interventions</style></title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computer Science/Medical Imaging</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://hal.archives-ouvertes.fr/inria-00417831/en/</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">CCSd/HAL : e-articles server (based on gBUS) [http://hal.ccsd.cnrs.fr/oai/oai.php] (France)</style></publisher><abstract><style face="normal" font="default" size="100%">This paper introduces RtViewer, a four-dimensional (3D + time) real-time visualization software for guiding cardiovascular interventions that is open source and freely available. RtViewer was designed to be part of a pipeline that can connect it to a magnetic resonance imaging (MRI) scanner, actively tracked catheters, and navigational devices. The architecture and features of RtViewer will be described with examples of guiding percutaneous cardiovascular interventions. The paper concludes with a brief description of the work in progress on the next generation of this platform, named Vurtigo.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Klompas, Michael</style></author><author><style face="normal" font="default" size="100%">Haney, Gillian</style></author><author><style face="normal" font="default" size="100%">Church, Daniel</style></author><author><style face="normal" font="default" size="100%">Lazarus, Ross</style></author><author><style face="normal" font="default" size="100%">Hou, Xuanlin</style></author><author><style face="normal" font="default" size="100%">Platt, Richard</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Automated identification of acute hepatitis B using electronic medical record data to facilitate public health surveillance.</style></title><secondary-title><style face="normal" font="default" size="100%">PloS one</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS ONE</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">e2626</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: Automatic identification of notifiable diseases from electronic medical records can potentially improve the timeliness and completeness of public health surveillance. We describe the development and implementation of an algorithm for prospective surveillance of patients with acute hepatitis B using electronic medical record data. METHODS: Initial algorithms were created by adapting Centers for Disease Control and Prevention diagnostic criteria for acute hepatitis B into electronic terms. The algorithms were tested by applying them to ambulatory electronic medical record data spanning 1990 to May 2006. A physician reviewer classified each case identified as acute or chronic infection. Additional criteria were added to algorithms in serial fashion to improve accuracy. The best algorithm was validated by applying it to prospective electronic medical record data from June 2006 through April 2008. Completeness of case capture was assessed by comparison with state health department records. FINDINGS: A final algorithm including a positive hepatitis B specific test, elevated transaminases and bilirubin, absence of prior positive hepatitis B tests, and absence of an ICD9 code for chronic hepatitis B identified 112/113 patients with acute hepatitis B (sensitivity 97.4%, 95% confidence interval 94-100%; specificity 93.8%, 95% confidence interval 87-100%). Application of this algorithm to prospective electronic medical record data identified 8 cases without false positives. These included 4 patients that had not been reported to the health department. There were no known cases of acute hepatitis B missed by the algorithm. CONCLUSIONS: An algorithm using codified electronic medical record data can reliably detect acute hepatitis B. The completeness of public health surveillance may be improved by automatically identifying notifiable diseases from electronic medical record data.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18612462?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Freimuth, Robert R</style></author><author><style face="normal" font="default" size="100%">Schauer, Michael W</style></author><author><style face="normal" font="default" size="100%">Lodha, Preeti</style></author><author><style face="normal" font="default" size="100%">Govindrao, Poornima</style></author><author><style face="normal" font="default" size="100%">Nagarajan, Rakesh</style></author><author><style face="normal" font="default" size="100%">Chute, Christopher G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">caBIG compatibility review system: software to support the evaluation of applications using defined interoperability criteria.</style></title><secondary-title><style face="normal" font="default" size="100%">AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><pages><style face="normal" font="default" size="100%">197-201</style></pages><abstract><style face="normal" font="default" size="100%">The caBIG Compatibility Review System (CRS) is a web-based application to support compatibility reviews, which certify that software applications that pass the review meet a specific set of criteria that allow them to interoperate. The CRS contains workflows that support both semantic and syntactic reviews, which are performed by the caBIG Vocabularies and Common Data Elements (VCDE) and Architecture workspaces, respectively. The CRS increases the efficiency of compatibility reviews by reducing administrative overhead and it improves uniformity by ensuring that each review is conducted according to a standard process. The CRS provides metrics that allow the review team to evaluate the level of data element reuse in an application, a first step towards quantifying the extent of harmonization between applications. Finally, functionality is being added that will provide automated validation of checklist criteria, which will further simplify the review process.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18999296?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Oster, Scott</style></author><author><style face="normal" font="default" size="100%">Langella, Stephen</style></author><author><style face="normal" font="default" size="100%">Hastings, Shannon</style></author><author><style face="normal" font="default" size="100%">Ervin, David</style></author><author><style face="normal" font="default" size="100%">Madduri, Ravi</style></author><author><style face="normal" font="default" size="100%">Phillips, Joshua</style></author><author><style face="normal" font="default" size="100%">Kurc, Tahsin</style></author><author><style face="normal" font="default" size="100%">Siebenlist, Frank</style></author><author><style face="normal" font="default" size="100%">Covitz, Peter</style></author><author><style face="normal" font="default" size="100%">Shanbhag, Krishnakant</style></author><author><style face="normal" font="default" size="100%">Foster, Ian</style></author><author><style face="normal" font="default" size="100%">Saltz, Joel</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">caGrid 1.0: an enterprise Grid infrastructure for biomedical research.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of the American Medical Informatics Association : JAMIA</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Mar-Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">15</style></volume><pages><style face="normal" font="default" size="100%">138-49</style></pages><abstract><style face="normal" font="default" size="100%">OBJECTIVE: To develop software infrastructure that will provide support for discovery, characterization, integrated access, and management of diverse and disparate collections of information sources, analysis methods, and applications in biomedical research. DESIGN: An enterprise Grid software infrastructure, called caGrid version 1.0 (caGrid 1.0), has been developed as the core Grid architecture of the NCI-sponsored cancer Biomedical Informatics Grid (caBIG) program. It is designed to support a wide range of use cases in basic, translational, and clinical research, including 1) discovery, 2) integrated and large-scale data analysis, and 3) coordinated study. MEASUREMENTS: The caGrid is built as a Grid software infrastructure and leverages Grid computing technologies and the Web Services Resource Framework standards. It provides a set of core services, toolkits for the development and deployment of new community provided services, and application programming interfaces for building client applications. RESULTS: The caGrid 1.0 was released to the caBIG community in December 2006. It is built on open source components and caGrid source code is publicly and freely available under a liberal open source license. The core software, associated tools, and documentation can be downloaded from the following URL: https://cabig.nci.nih.gov/workspaces/Architecture/caGrid. CONCLUSIONS: While caGrid 1.0 is designed to address use cases in cancer research, the requirements associated with discovery, analysis and integration of large scale data, and coordinated studies are common in other biomedical fields. In this respect, caGrid 1.0 is the realization of a framework that can benefit the entire biomedical community.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18096909?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fegan, Greg W</style></author><author><style face="normal" font="default" size="100%">Lang, Trudie A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Could an open-source clinical trial data-management system be what we have all been looking for?</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS medicine</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS Med.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Mar 4</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0050006</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">e6</style></pages><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18318594?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Enquobahrie, Andinet</style></author><author><style face="normal" font="default" size="100%">Gobbi, David</style></author><author><style face="normal" font="default" size="100%">Turek, Matt</style></author><author><style face="normal" font="default" size="100%">Cheng, Patrick</style></author><author><style face="normal" font="default" size="100%">Yaniv, Ziv</style></author><author><style face="normal" font="default" size="100%">Lindseth, Frank</style></author><author><style face="normal" font="default" size="100%">Cleary, Kevin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Designing Tracking Software for Image-Guided Surgery Applications: IGSTK Experience.</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Comput Assist Radiol Surg</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int J Comput Assist Radiol Surg</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Nov 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">395-403</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">OBJECTIVE: Many image-guided surgery applications require tracking devices as part of their core functionality. The Image-Guided Surgery Toolkit (IGSTK) was designed and developed to interface tracking devices with software applications incorporating medical images. METHODS: IGSTK was designed as an open source C++ library that provides the basic components needed for fast prototyping and development of image-guided surgery applications. This library follows a component-based architecture with several components designed for specific sets of image-guided surgery functions. At the core of the toolkit is the tracker component that handles communication between a control computer and navigation device to gather pose measurements of surgical instruments present in the surgical scene. The representations of the tracked instruments are superimposed on anatomical images to provide visual feedback to the clinician during surgical procedures. RESULTS: The initial version of the IGSTK toolkit has been released in the public domain and several trackers are supported. The toolkit and related information are available at www.igstk.org. CONCLUSION: With the increased popularity of minimally invasive procedures in health care, several tracking devices have been developed for medical applications. Designing and implementing high-quality and safe software to handle these different types of trackers in a common framework is a challenging task. It requires establishing key software design principles that emphasize abstraction, extensibility, reusability, fault-tolerance, and portability. IGSTK is an open source library that satisfies these needs for the image-guided surgery community.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Halamka, John D</style></author><author><style face="normal" font="default" size="100%">Mandl, Kenneth D</style></author><author><style face="normal" font="default" size="100%">Tang, Paul C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Early experiences with personal health records.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of the American Medical Informatics Association : JAMIA</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Jan-Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">15</style></volume><pages><style face="normal" font="default" size="100%">1-7</style></pages><abstract><style face="normal" font="default" size="100%">Over the past year, several payers, employers, and commercial vendors have announced personal health record projects. Few of these are widely deployed and few are fully integrated into ambulatory or hospital-based electronic record systems. The earliest adopters of personal health records have many lessons learned that can inform these new initiatives. We present three case studies--MyChart at Palo Alto Medical Foundation, PatientSite at Beth Israel Deaconess Medical Center, and Indivo at Children's Hospital Boston. We describe our implementation challenges from 1999 to 2007 and postulate the evolving challenges we will face over the next five years.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17947615?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Coelho, Flávio C</style></author><author><style face="normal" font="default" size="100%">Cruz, Oswaldo G</style></author><author><style face="normal" font="default" size="100%">Codeço, Cláudia T</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Epigrass: a tool to study disease spread in complex networks.</style></title><secondary-title><style face="normal" font="default" size="100%">Source code for biology and medicine</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">3</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: The construction of complex spatial simulation models such as those used in network epidemiology, is a daunting task due to the large amount of data involved in their parameterization. Such data, which frequently resides on large geo-referenced databases, has to be processed and assigned to the various components of the model. All this just to construct the model, then it still has to be simulated and analyzed under different epidemiological scenarios. This workflow can only be achieved efficiently by computational tools that can automate most, if not all, these time-consuming tasks. In this paper, we present a simulation software, Epigrass, aimed to help designing and simulating network-epidemic models with any kind of node behavior. RESULTS: A Network epidemiological model representing the spread of a directly transmitted disease through a bus-transportation network connecting mid-size cities in Brazil. Results show that the topological context of the starting point of the epidemic is of great importance from both control and preventive perspectives. CONCLUSION: Epigrass is shown to facilitate greatly the construction, simulation and analysis of complex network models. The output of model results in standard GIS file formats facilitate the post-processing and analysis of results by means of sophisticated GIS software.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18302744?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>12</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ignacio Valdes</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Free and Open Source Software in Healthcare 1.0</style></title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electronic Health Record</style></keyword><keyword><style  face="normal" font="default" size="100%">Electronic Medical Record</style></keyword><keyword><style  face="normal" font="default" size="100%">Free and Open Source</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">https://www.amia.org/files/Final-OS-WG%20White%20Paper_11_19_08_0.pdf</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">American Medical Informatics Association Open Source Working Group</style></publisher><abstract><style face="normal" font="default" size="100%">The possible benefits of widespread adoption of Electronic Health Record/Electronic Medical Record (EHR/EMR) technologies are widely documented, yet progress is slow and few propose a viable mechanism to achieve shared goals. Multiple problems of cost, interoperability, vendor lock-in, standardization and longevity have been identified and have persisted. Even “successes” have problems. While multiple initiatives and much money is spent on finding answers, Free/Open Source Software (FOSS) licensing holds promise for solving these problems or at least making them more tractable. Multiple deployments, novel applications, and multiple companies offering support appear to be occurring. Interoperability and connectivity may be an area of particular proliferation. By vendor and site self-report there are a substantial number of patient records, 3,959,065 in 898 non-Federal government sites and 24,442,000 patient records in 1607 Federal government sites that use FOSS or public domain software EHR/EMR’s. To date, 232 Open Source titled works on various aspects are listed in PubMed. Local and national education is needed to ensure that equal attention be given to FOSS licensed EHR/EMR software.</style></abstract><work-type><style face="normal" font="default" size="100%">White Paper</style></work-type></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Peirce, Jonathan W</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Generating Stimuli for Neuroscience Using PsychoPy.</style></title><secondary-title><style face="normal" font="default" size="100%">Frontiers in neuroinformatics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2</style></volume><pages><style face="normal" font="default" size="100%">10</style></pages><abstract><style face="normal" font="default" size="100%">PsychoPy is a software library written in Python, using OpenGL to generate very precise visual stimuli on standard personal computers. It is designed to allow the construction of as wide a variety of neuroscience experiments as possible, with the least effort. By writing scripts in standard Python syntax users can generate an enormous variety of visual and auditory stimuli and can interact with a wide range of external hardware (enabling its use in fMRI, EEG, MEG etc.). The structure of scripts is simple and intuitive. As a result, new experiments can be written very quickly, and trying to understand a previously written script is easy, even with minimal code comments. PsychoPy can also generate movies and image sequences to be used in demos or simulated neuroscience experiments. This paper describes the range of tools and stimuli that it provides and the environment in which experiments are conducted.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19198666?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Protti, Denis</style></author><author><style face="normal" font="default" size="100%">Groen, Peter</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Implementation of the Veterans Health Administration VistA clinical information system around the world.</style></title><secondary-title><style face="normal" font="default" size="100%">Healthcare quarterly (Toronto, Ont.)</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">83-9</style></pages><abstract><style face="normal" font="default" size="100%">The success story of the Veterans Health Administration (VHA) within the US Department of Veterans Affairs has been well documented and is generally well known. What is generally not known is that the VHA's clinical information system, known as VistA, and the computerized patient record system clinical user interface front end have been successfully transported and implemented to a number of non-VHA healthcare organizations across the United States. Moreover, VistA software modules have been installed, or are being considered for installation, in healthcare institutions around the world in countries such as Mexico, Finland, Jordan, Germany, Nigeria, Egypt, Malaysia, India, Brazil, Pakistan and Samoa.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19068935?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Letunic, Ivica</style></author><author><style face="normal" font="default" size="100%">Yamada, Takuji</style></author><author><style face="normal" font="default" size="100%">Kanehisa, Minoru</style></author><author><style face="normal" font="default" size="100%">Bork, Peer</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">iPath: interactive exploration of biochemical pathways and networks.</style></title><secondary-title><style face="normal" font="default" size="100%">Trends in biochemical sciences</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Trends Biochem. Sci.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">33</style></volume><pages><style face="normal" font="default" size="100%">101-3</style></pages><abstract><style face="normal" font="default" size="100%">iPath is an open-access online tool (http://pathways.embl.de) for visualizing and analyzing metabolic pathways. An interactive viewer provides straightforward navigation through various pathways and enables easy access to the underlying chemicals and enzymes. Customized pathway maps can be generated and annotated using various external data. For example, by merging human genome data with two important gut commensals, iPath can pinpoint the complementarity of the host-symbiont metabolic capacities.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18276143?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Jens H. Weber-Jahnke</style></author><author><style face="normal" font="default" size="100%">Glen McCallum</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A Light-Weight Component for Adding Decision Support to Electronic Medical Records</style></title><secondary-title><style face="normal" font="default" size="100%">Hawaii International Conference on System Sciences</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><publisher><style face="normal" font="default" size="100%">IEEE Computer Society</style></publisher><pub-location><style face="normal" font="default" size="100%">Los Alamitos, CA, USA</style></pub-location><pages><style face="normal" font="default" size="100%">251</style></pages></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Jens H. Jahnke-Weber</style></author><author><style face="normal" font="default" size="100%">Morgan Price</style></author><author><style face="normal" font="default" size="100%">Glen McCallum</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Making available Clinical Decision Support in Service-Oriented Architectures</style></title><secondary-title><style face="normal" font="default" size="100%">Journal on Information Technology in Healthcare</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.88.5385&amp;rep=rep1&amp;type=pdf</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">54</style></pages><abstract><style face="normal" font="default" size="100%">Computer-based clinical decision support (CDS) has great potential for cost savings and for increasing patient safety and quality of care. The cost of owning and particularly maintaining CDS systems is significant. Therefore, it makes good economic sense to share a CDS service installation among a larger set of client systems. The emerging paradigm of serviceoriented architectures (SOAs) embraces the idea of sharing and interaction between loosely coupled, co-operative services. Canada has based its planned architecture for realizing the electronic medical record (EMR) on the SOA paradigm. While CDS components are currently not in the set of services to be constructed for Canada’s health information infrastructure, they seems to be growing interest in adding them in the future, after the more essential services have been implemented. In this paper, we discuss the status of clinical decision support systems today and some challenges of making them available in SOA-based infrastructures. We report on design choices and solutions we have selected during the construction of the EGADSS (Electronic Guideline and Decision Support System) component. Our design decisions are based on domainspecific challenges such as knowledge, data and workflow interoperability as well as on technical considerations about construction high quality services for SOA-based infrastructures. EGADSS has been released under open-source license and is freely available.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><section><style face="normal" font="default" size="100%">42</style></section></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Massaut, Jacques</style></author><author><style face="normal" font="default" size="100%">Reper, Pascal</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open source electronic health record and patient data management system for intensive care.</style></title><secondary-title><style face="normal" font="default" size="100%">Studies in health technology and informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Stud Health Technol Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">141</style></volume><pages><style face="normal" font="default" size="100%">139-45</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND AND OBJECTIVES: In Intensive Care Units, the amount of data to be processed for patients care, the turn over of the patients, the necessity for reliability and for review processes indicate the use of Patient Data Management Systems (PDMS) and electronic health records (EHR). To respond to the needs of an Intensive Care Unit and not to be locked with proprietary software, we developed a PDMS and EHR based on open source software and components. METHODS: The software was designed as a client-server architecture running on the Linux operating system and powered by the PostgreSQL data base system. The client software was developed in C using GTK interface library. The application offers to the users the following functions: medical notes captures, observations and treatments, nursing charts with administration of medications, scoring systems for classification, and possibilities to encode medical activities for billing processes. RESULTS: Since his deployment in February 2004, the PDMS was used to care more than three thousands patients with the expected software reliability and facilitated data management and review processes. Communications with other medical software were not developed from the start, and are realized by the use of the Mirth HL7 communication engine. Further upgrade of the system will include multi-platform support, use of typed language with static analysis, and configurable interface. CONCLUSION: The developed system based on open source software components was able to respond to the medical needs of the local ICU environment. The use of OSS for development allowed us to customize the software to the preexisting organization and contributed to the acceptability of the whole system.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18953134?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sturm, Marc</style></author><author><style face="normal" font="default" size="100%">Bertsch, Andreas</style></author><author><style face="normal" font="default" size="100%">Gröpl, Clemens</style></author><author><style face="normal" font="default" size="100%">Hildebrandt, Andreas</style></author><author><style face="normal" font="default" size="100%">Hussong, Rene</style></author><author><style face="normal" font="default" size="100%">Lange, Eva</style></author><author><style face="normal" font="default" size="100%">Pfeifer, Nico</style></author><author><style face="normal" font="default" size="100%">Schulz-Trieglaff, Ole</style></author><author><style face="normal" font="default" size="100%">Zerck, Alexandra</style></author><author><style face="normal" font="default" size="100%">Reinert, Knut</style></author><author><style face="normal" font="default" size="100%">Kohlbacher, Oliver</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">OpenMS - an open-source software framework for mass spectrometry.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC bioinformatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Bioinformatics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.biomedcentral.com/1471-2105/9/163</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">163</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever increasing amounts of data. Consequently, analysis of the data is currently often the bottleneck for experimental studies. Although software tools for many data analysis tasks are available today, they are often hard to combine with each other or not flexible enough to allow for rapid prototyping of a new analysis workflow. RESULTS: We present OpenMS, a software framework for rapid application development in mass spectrometry. OpenMS has been designed to be portable, easy-to-use and robust while offering a rich functionality ranging from basic data structures to sophisticated algorithms for data analysis. This has already been demonstrated in several studies. CONCLUSION: OpenMS is available under the Lesser GNU Public License (LGPL) from the project website at http://www.openms.de.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18366760?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Stott, Will</style></author><author><style face="normal" font="default" size="100%">Ryan, Andy</style></author><author><style face="normal" font="default" size="100%">Jacobs, Ian J</style></author><author><style face="normal" font="default" size="100%">Menon, Usha</style></author><author><style face="normal" font="default" size="100%">Bessant, Conrad</style></author><author><style face="normal" font="default" size="100%">Jones, Christopher</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">OSPACS: Ultrasound image management system.</style></title><secondary-title><style face="normal" font="default" size="100%">Source code for biology and medicine</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442597/</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">11</style></pages><abstract><style face="normal" font="default" size="100%">ABSTRACT: BACKGROUND: Ultrasound scanning uses the medical imaging format, DICOM, for electronically storing the images and data associated with a particular scan. Large health care facilities typically use a picture archiving and communication system (PACS) for storing and retrieving such images. However, these systems are usually not suitable for managing large collections of anonymized ultrasound images gathered during a clinical screening trial. RESULTS: We have developed a system enabling the accurate archiving and management of ultrasound images gathered during a clinical screening trial. It is based upon a Windows application utilizing an open-source DICOM image viewer and a relational database. The system automates the bulk import of DICOM files from removable media by cross-validating the patient information against an external database, anonymizing the data as well as the image, and then storing the contents of the file as a field in a database record. These image records may then be retrieved from the database and presented in a tree-view control so that the user can select particular images for display in a DICOM viewer or export them to external media. CONCLUSION: This system provides error-free automation of ultrasound image archiving and management, suitable for use in a clinical trial. An open-source project has been established to promote continued development of the system.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18570637?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yellowlees, Peter M</style></author><author><style face="normal" font="default" size="100%">Marks, Shayna L</style></author><author><style face="normal" font="default" size="100%">Hogarth, Michael</style></author><author><style face="normal" font="default" size="100%">Turner, Stuart</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Standards-based, open-source electronic health record systems: a desirable future for the U.S. health industry.</style></title><secondary-title><style face="normal" font="default" size="100%">Telemedicine journal and e-health : the official journal of the American Telemedicine Association</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Telemed J E Health</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">14</style></volume><pages><style face="normal" font="default" size="100%">284-8</style></pages><abstract><style face="normal" font="default" size="100%">Many healthcare systems are moving toward a fully electronic health record (EHR) in order to better manage patient care. Unfortunately, in the United States, many current EHR systems leave much to be desired. Among well-documented criticisms are that they tend to be inflexible, proprietary, nonintuitive, expensive, difficult to maintain and rarely interoperable across health systems. From the clinician's perspective, these flaws sometimes make having an EHR system seem no better than retaining a paper-based system. Open-source software, a great success in other information-intensive industries, is one possible solution to these problems, and may help integrate a functional EHR system into, and across, more health systems and clinics because of the greater potential for local customization. We believe that the advantages of an open-source EHR system outweigh the costs of a more traditional, proprietary EHR system, and recommend that more work be done to advance an interoperable open-source EHR system in the United States. Open-source EHR systems have the potential to improve healthcare in the United States as they have done in many other areas around the world.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18570554?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bourgeois, Fabienne C</style></author><author><style face="normal" font="default" size="100%">Taylor, Patrick L</style></author><author><style face="normal" font="default" size="100%">Emans, S Jean</style></author><author><style face="normal" font="default" size="100%">Nigrin, Daniel J</style></author><author><style face="normal" font="default" size="100%">Mandl, Kenneth D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Whose personal control? Creating private, personally controlled health records for pediatric and adolescent patients.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of the American Medical Informatics Association : JAMIA</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Nov-Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">15</style></volume><pages><style face="normal" font="default" size="100%">737-43</style></pages><abstract><style face="normal" font="default" size="100%">Personally controlled health records (PCHRs) enable patients to store, manage, and share their own health data, and promise unprecedented consumer access to medical information. To deploy a PCHR in the pediatric population requires crafting of access and security policies, tailored to a record that is not only under patient control, but one that may also be accessed by parents, guardians, and third-party entities. Such hybrid control of health information requires careful consideration of both the PCHR vendor's access policies, as well as institutional policies regulating data feeds to the PCHR, to ensure that the privacy and confidentiality of each user is preserved. Such policies must ensure compliance with legal mandates to prevent unintended disclosures and must preserve the complex interactions of the patient-provider relationship. Informed by our own operational involvement in the implementation of the Indivo PCHR, we provide a framework for understanding and addressing the challenges posed by child, adolescent, and family access to PCHRs.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18755989?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Warnock, Max J</style></author><author><style face="normal" font="default" size="100%">Toland, Christopher</style></author><author><style face="normal" font="default" size="100%">Evans, Damien</style></author><author><style face="normal" font="default" size="100%">Wallace, Bill</style></author><author><style face="normal" font="default" size="100%">Nagy, Paul</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Benefits of using the DCM4CHE DICOM archive.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Digit Imaging</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Nov</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2039778</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">20 Suppl 1</style></volume><pages><style face="normal" font="default" size="100%">125-9</style></pages><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17917780?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bitter, Ingmar</style></author><author><style face="normal" font="default" size="100%">Van Uitert, Robert</style></author><author><style face="normal" font="default" size="100%">Wolf, Ivo</style></author><author><style face="normal" font="default" size="100%">Ibáñez, Luis</style></author><author><style face="normal" font="default" size="100%">Kuhnigk, Jan-Martin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comparison of four freely available frameworks for image processing and visualization that use ITK.</style></title><secondary-title><style face="normal" font="default" size="100%">IEEE transactions on visualization and computer graphics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">IEEE Trans Vis Comput Graph</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 May-Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">483-93</style></pages><abstract><style face="normal" font="default" size="100%">Most image processing and visualization applications allow users to configure computation parameters and manipulate the resulting visualizations. SCIRun, VolView, MeVisLab, and the Medical Interaction Toolkit (MITK) are four image processing and visualization frameworks that were built for these purposes. All frameworks are freely available and all allow the use of the ITK C++ library. In this paper, the benefits and limitations of each visualization framework are presented to aid both application developers and users in the decision of which framework may be best to use for their application. The analysis is based on more than 50 evaluation criteria, functionalities, and example applications. We report implementation times for various steps in the creation of a reference application in each of the compared frameworks. The data-flow programming frameworks, SCIRun and MeVisLab, were determined to be best for developing application prototypes, while VolView was advantageous for nonautomatic end-user applications based on existing ITK functionalities, and MITK was preferable for automated end-user applications that might include new ITK classes specifically designed for the application.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17356215?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Leong, T Y</style></author><author><style face="normal" font="default" size="100%">Kaiser, K</style></author><author><style face="normal" font="default" size="100%">Miksch, S</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Free and open source enabling technologies for patient-centric, guideline-based clinical decision support: a survey.</style></title><secondary-title><style face="normal" font="default" size="100%">Yearbook of medical informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Yearb Med Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007</style></date></pub-dates></dates><pages><style face="normal" font="default" size="100%">74-86</style></pages><abstract><style face="normal" font="default" size="100%">OBJECTIVES: Guideline-based clinical decision support is an emerging paradigm to help reduce error, lower cost, and improve quality in evidence-based medicine. The free and open source (FOS) approach is a promising alternative for delivering cost-effective information technology (IT) solutions in health care. In this paper, we survey the current FOS enabling technologies for patient-centric, guideline-based care, and discuss the current trends and future directions of their role in clinical decision support. METHODS: We searched PubMed, major biomedical informatics websites, and the web in general for papers and links related to FOS health care IT systems. We also relied on our background and knowledge for specific subtopics. We focused on the functionalities of guideline modeling tools, and briefly examined the supporting technologies for terminology, data exchange and electronic health record (EHR) standards. RESULTS: To effectively support patient-centric, guideline-based care, the computerized guidelines and protocols need to be integrated with existing clinical information systems or EHRs. Technologies that enable such integration should be accessible, interoperable, and scalable. A plethora of FOS tools and techniques for supporting different knowledge management and quality assurance tasks involved are available. Many challenges, however, remain in their implementation. CONCLUSIONS: There are active and growing trends of deploying FOS enabling technologies for integrating clinical guidelines, protocols, and pathways into the main care processes. The continuing development and maturation of such technologies are likely to make increasingly significant contributions to patient-centric, guideline-based clinical decision support.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17700908?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Enquobahrie, Andinet</style></author><author><style face="normal" font="default" size="100%">Cheng, Patrick</style></author><author><style face="normal" font="default" size="100%">Gary, Kevin</style></author><author><style face="normal" font="default" size="100%">Ibanez, Luis</style></author><author><style face="normal" font="default" size="100%">Gobbi, David</style></author><author><style face="normal" font="default" size="100%">Lindseth, Frank</style></author><author><style face="normal" font="default" size="100%">Yaniv, Ziv</style></author><author><style face="normal" font="default" size="100%">Aylward, Stephen</style></author><author><style face="normal" font="default" size="100%">Jomier, Julien</style></author><author><style face="normal" font="default" size="100%">Cleary, Kevin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The image-guided surgery toolkit IGSTK: an open source C++ software toolkit.</style></title><secondary-title><style face="normal" font="default" size="100%">J Digit Imaging</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Digit Imaging</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computer Systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Data Display</style></keyword><keyword><style  face="normal" font="default" size="100%">Database Management Systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Information Dissemination</style></keyword><keyword><style  face="normal" font="default" size="100%">Information Storage and Retrieval</style></keyword><keyword><style  face="normal" font="default" size="100%">Safety</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Software Design</style></keyword><keyword><style  face="normal" font="default" size="100%">Software Validation</style></keyword><keyword><style  face="normal" font="default" size="100%">Surgery, Computer-Assisted</style></keyword><keyword><style  face="normal" font="default" size="100%">Systems Integration</style></keyword><keyword><style  face="normal" font="default" size="100%">User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">20 Suppl 1</style></volume><pages><style face="normal" font="default" size="100%">21-33</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers' mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mandl, Kenneth D</style></author><author><style face="normal" font="default" size="100%">Simons, William W</style></author><author><style face="normal" font="default" size="100%">Crawford, William C R</style></author><author><style face="normal" font="default" size="100%">Abbett, Jonathan M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Indivo: a personally controlled health record for health information exchange and communication.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC medical informatics and decision making</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Med Inform Decis Mak</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.biomedcentral.com/1472-6947/7/25/</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">25</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: Personally controlled health records (PCHRs), a subset of personal health records (PHRs), enable a patient to assemble, maintain and manage a secure copy of his or her medical data. Indivo (formerly PING) is an open source, open standards PCHR with an open application programming interface (API). RESULTS: We describe how the PCHR platform can provide standard building blocks for networked PHR applications. Indivo allows the ready integration of diverse sources of medical data under a patient's control through the use of standards-based communication protocols and APIs for connecting PCHRs to existing and future health information systems. CONCLUSION: The strict and transparent personal control model is designed to encourage widespread participation by patients, healthcare providers and institutions, thus creating the ecosystem for development of innovative, consumer-focused healthcare applications.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17850667?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Potter, Glenn</style></author><author><style face="normal" font="default" size="100%">Busbridge, Rick</style></author><author><style face="normal" font="default" size="100%">Toland, Michael</style></author><author><style face="normal" font="default" size="100%">Nagy, Paul</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Mastering DICOM with DVTk.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Digit Imaging</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Nov</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.springerlink.com/content/r17t75244k2376n0/</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">20 Suppl 1</style></volume><pages><style face="normal" font="default" size="100%">47-62</style></pages><abstract><style face="normal" font="default" size="100%">The Digital Imaging and Communications in Medicine (DICOM) Validation Toolkit (DVTk) is an open-source framework with potential value for anyone working with the DICOM standard. DICOM's flexibility requires hands-on experience in understanding ways in which the standard's interpretation may vary among vendors. DVTk was developed as a clinical engineering tool to aid and accelerate DICOM integration at clinical sites. DVTk is used to provide an independent measurement of the accuracy of a product's DICOM interface, according to both the DICOM standard and the product's conformance statement. DVTk has stand-alone tools and a framework with which developers can create new tools. We provide an overview of the architecture of the toolkit, sample scenarios of its utility, and evidence of its relative ease of use. Our goal is to encourage involvement in this open-source project and attract developers to build off and further enrich this platform for DICOM integration testing.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17680308?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Faustini, Giorgio</style></author><author><style face="normal" font="default" size="100%">Inchingolo, P.</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Magjarevic, Ratko</style></author><author><style face="normal" font="default" size="100%">Jarm, Tomaz</style></author><author><style face="normal" font="default" size="100%">Kramar, Peter</style></author><author><style face="normal" font="default" size="100%">Zupanic, Anze</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">O3-RWS: a Java-based, IHE-compliant open-source radiology workstation</style></title><secondary-title><style face="normal" font="default" size="100%">11th Mediterranean Conference on Medical and Biomedical Engineering and Computing 2007</style></secondary-title><tertiary-title><style face="normal" font="default" size="100%">IFMBE Proceedings</style></tertiary-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/978-3-540-73044-6_189</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer Berlin Heidelberg</style></publisher><volume><style face="normal" font="default" size="100%">16</style></volume><pages><style face="normal" font="default" size="100%">727-731</style></pages><isbn><style face="normal" font="default" size="100%">978-3-540-73044-6</style></isbn><abstract><style face="normal" font="default" size="100%">Within the Open Three Consortium (O3) an open source radiological reporting workstation, called O3- RWS, has been studied, developed and experimented in the routine of European and US hospitals. The O3 Consortium is an international open-source project constituted in 2005 by Higher Education in Clinical Engineering (HECE) of the University of Trieste; it deals with the multi-centric integration of hospitals, RHIOs and citizen (care at home and on the move, and ambient assisted living). O3-RWS has been studied and developed with the goal to give a solution for the needs of the physician, who wants to have an easy-to-use, light and complete solution for the radiology reporting and report creation. O3-RWS, a very versatile platform-independent radiology workstation, providing user authentication and being easy to use also for private users, is able to retrieve, visualize and manage medical images; in an universal version, it is going to be able to deal with vital signs like ECG, hemodynamical and pneumological data.</style></abstract><notes><style face="normal" font="default" size="100%">10.1007/978-3-540-73044-6_189</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nagy, Paul</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open source in imaging informatics.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Digit Imaging</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Nov</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.springerlink.com/content/ux777t47g638k402/</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">20 Suppl 1</style></volume><pages><style face="normal" font="default" size="100%">1-10</style></pages><abstract><style face="normal" font="default" size="100%">The open source community within radiology is a vibrant collection of developers and users working on scores of collaborative projects with the goal of promoting the use of information technology within radiology for education, clinical, and research purposes. This community, which includes many commercial partners, has a rich history in supporting the success of the digital imaging and communication in medicine (DICOM) standard and today is pioneering interoperability limits by embracing the Integrating the Healthcare Enterprise. This article describes only a small portion of the more successful open source applications and is written to help end users see these projects as practical aids for the imaging informaticist and picture archiving and communication system (PACS) administrator.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17674101?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Prior, Fred W</style></author><author><style face="normal" font="default" size="100%">Erickson, Bradley J</style></author><author><style face="normal" font="default" size="100%">Tarbox, Lawrence</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open source software projects of the caBIG In Vivo Imaging Workspace Software special interest group.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Digit Imaging</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">20 Suppl 1</style></volume><pages><style face="normal" font="default" size="100%">94-100</style></pages><abstract><style face="normal" font="default" size="100%">The Cancer Bioinformatics Grid (caBIG) program was created by the National Cancer Institute to facilitate sharing of IT infrastructure, data, and applications among the National Cancer Institute-sponsored cancer research centers. The program was launched in February 2004 and now links more than 50 cancer centers. In April 2005, the In Vivo Imaging Workspace was added to promote the use of imaging in cancer clinical trials. At the inaugural meeting, four special interest groups (SIGs) were established. The Software SIG was charged with identifying projects that focus on open-source software for image visualization and analysis. To date, two projects have been defined by the Software SIG. The eXtensible Imaging Platform project has produced a rapid application development environment that researchers may use to create targeted workflows customized for specific research projects. The Algorithm Validation Tools project will provide a set of tools and data structures that will be used to capture measurement information and associated needed to allow a gold standard to be defined for the given database against which change analysis algorithms can be tested. Through these and future efforts, the caBIG In Vivo Imaging Workspace Software SIG endeavors to advance imaging informatics and provide new open-source software tools to advance cancer research.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17846835?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gatta, R</style></author><author><style face="normal" font="default" size="100%">Abeni, F</style></author><author><style face="normal" font="default" size="100%">Buglione, M</style></author><author><style face="normal" font="default" size="100%">Peveri, A</style></author><author><style face="normal" font="default" size="100%">Barbera, F</style></author><author><style face="normal" font="default" size="100%">Tonoli, S</style></author><author><style face="normal" font="default" size="100%">Fratta, P</style></author><author><style face="normal" font="default" size="100%">Magrini, S M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open-source, low-cost, high-reliability solutions for digital imaging systems: example of a &quot;dicom router&quot;.</style></title><secondary-title><style face="normal" font="default" size="100%">La Radiologia medica</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Radiol Med</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">112</style></volume><pages><style face="normal" font="default" size="100%">1252-9</style></pages><abstract><style face="normal" font="default" size="100%">PURPOSE: The purpose of this article is to illustrate a case where acquisition of digital imaging know-how by a modern radiotherapy division has helped to solve a technical problem while allowing substantial savings through the use of free and open-source resources. The problem was related to the necessity to route, with complex policies, the images produced by different digital imaging and communications in medicine (DICOM) sources within the department or in other divisions and/or hospitals. MATERIALS AND METHODS: The problem was solved by using completely free, well-tested and stable technologies (PHP, Apache, MySQL, DCMTK OFFIS, Red Hat Linux 9A and Linux Fedora Core 4) and low-cost hardware to contain costs. In the development, we also considered integration of the routed images with the existing electronic clinical records. RESULTS: The system developed, called the dicom router, implemented two kinds of routing: manual and automatic, both oriented to link the images acquired with the existing electronic clinical records. System stability was enhanced in a second phase by using a low-cost hardware redundancy solution. The system has now been operating for 1 year and has proved the value of the technologies used. CONCLUSIONS: The need to operate with more than one provider creates a series of integration issues, so that it becomes economically appealing to acquire internally the knowledge needed to interact more precisely with providers of big information technology (IT) solutions. This need is well catered for by open-source technologies, which are well documented and available to everyone. By using them, in-house IT technicians are able to implement valuable technical solutions for small-to medium-sized informatization problems, which would otherwise remain unsolved except with great economic efforts.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18074196?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bui, Alex A T</style></author><author><style face="normal" font="default" size="100%">Morioka, Craig</style></author><author><style face="normal" font="default" size="100%">Dionisio, John David N</style></author><author><style face="normal" font="default" size="100%">Johnson, David B</style></author><author><style face="normal" font="default" size="100%">Sinha, Usha</style></author><author><style face="normal" font="default" size="100%">Ardekani, Siamak</style></author><author><style face="normal" font="default" size="100%">Taira, Ricky K</style></author><author><style face="normal" font="default" size="100%">Aberle, Denise R</style></author><author><style face="normal" font="default" size="100%">El-Saden, Suzie</style></author><author><style face="normal" font="default" size="100%">Kangarloo, Hooshang</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">OpenSourcePACS: an extensible infrastructure for medical image management.</style></title><secondary-title><style face="normal" font="default" size="100%">IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society</style></secondary-title><alt-title><style face="normal" font="default" size="100%">IEEE Trans Inf Technol Biomed</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Jan</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://escholarship.org/uc/item/186368fv</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">94-109</style></pages><abstract><style face="normal" font="default" size="100%">The development of comprehensive picture archive and communication systems (PACS) has mainly been limited to proprietary developments by vendors, though a number of freely available software projects have addressed specific image management tasks. The openSourcePACS project aims to provide an open source, common foundation upon which not only can a basic PACS be readily implemented, but to also support the evolution of new PACS functionality through the development of novel imaging applications and services. openSourcePACS consists of four main software modules: 1) image order entry, which enables the ordering and tracking of structured image requisitions; 2) an agent-based image server framework that coordinates distributed image services including routing, image processing, and querying beyond the present digital image and communications in medicine (DICOM) capabilities; 3) an image viewer, supporting standard display and image manipulation tools, DICOM presentation states, and structured reporting; and 4) reporting and result dissemination, supplying web-based widgets for creating integrated reports. All components are implemented using Java to encourage cross-platform deployment. To demonstrate the usage of openSourcePACS, a preliminary application supporting primary care/specialist communication was developed and is described herein. Ultimately, the goal of openSourcePACS is to promote the wide-scale development and usage of PACS and imaging applications within academic and research communities.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17249408?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Peirce, Jonathan W</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">PsychoPy--Psychophysics software in Python.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of neuroscience methods</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Neurosci. Methods</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 May 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">162</style></volume><pages><style face="normal" font="default" size="100%">8-13</style></pages><abstract><style face="normal" font="default" size="100%">The vast majority of studies into visual processing are conducted using computer display technology. The current paper describes a new free suite of software tools designed to make this task easier, using the latest advances in hardware and software. PsychoPy is a platform-independent experimental control system written in the Python interpreted language using entirely free libraries. PsychoPy scripts are designed to be extremely easy to read and write, while retaining complete power for the user to customize the stimuli and environment. Tools are provided within the package to allow everything from stimulus presentation and response collection (from a wide range of devices) to simple data analysis such as psychometric function fitting. Most importantly, PsychoPy is highly extensible and the whole system can evolve via user contributions. If a user wants to add support for a particular stimulus, analysis or hardware device they can look at the code for existing examples, modify them and submit the modifications back into the package so that the whole community benefits.</style></abstract><issue><style face="normal" font="default" size="100%">1-2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17254636?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Geller, Aaron S</style></author><author><style face="normal" font="default" size="100%">Schlefer, Ian K</style></author><author><style face="normal" font="default" size="100%">Sederberg, Per B</style></author><author><style face="normal" font="default" size="100%">Jacobs, Joshua</style></author><author><style face="normal" font="default" size="100%">Kahana, Michael J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">PyEPL: a cross-platform experiment-programming library.</style></title><secondary-title><style face="normal" font="default" size="100%">Behavior research methods</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">39</style></volume><pages><style face="normal" font="default" size="100%">950-8</style></pages><abstract><style face="normal" font="default" size="100%">PyEPL (the Python Experiment-Programming Library) is a Python library which allows cross-platform and object-oriented coding of behavioral experiments. It provides functions for displaying text and images onscreen, as well as playing and recording sound, and is capable of rendering 3-D virtual environments forspatial-navigation tasks. It is currently tested for Mac OS X and Linux. It interfaces with Activewire USB cards (on Mac OS X) and the parallel port (on Linux) for synchronization of experimental events with physiological recordings. In this article, we first present two sample programs which illustrate core PyEPL features. The examples demonstrate visual stimulus presentation, keyboard input, and simulation and exploration of a simple 3-D environment. We then describe the components and strategies used in implementing PyEPL.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18183912?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sfakianakis, S</style></author><author><style face="normal" font="default" size="100%">Chronaki, C E</style></author><author><style face="normal" font="default" size="100%">Chiarugi, F</style></author><author><style face="normal" font="default" size="100%">Conforti, F</style></author><author><style face="normal" font="default" size="100%">Katehakis, D G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Reflections on the role of open source in health information system interoperability.</style></title><secondary-title><style face="normal" font="default" size="100%">Yearbook of medical informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Yearb Med Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007</style></date></pub-dates></dates><pages><style face="normal" font="default" size="100%">50-60</style></pages><abstract><style face="normal" font="default" size="100%">OBJECTIVES: This paper reflects on the role of open source in health information system interoperability. Open source is a driving force in computer science research and the development of information systems. It facilitates the sharing of information and ideas, enables evolutionary development and open collaborative testing of code, and broadens the adoption of interoperability standards. In health care, information systems have been developed largely ad hoc following proprietary specifications and customized design. However, the wide deployment of integrated services such as Electronic Health Records (EHRs) over regional health information networks (RHINs) relies on interoperability of the underlying information systems and medical devices. METHODS: This reflection is built on the experiences of the PICNIC project that developed shared software infrastructure components in open source for RHINs and the OpenECG network that offers open source components to lower the implementation cost of interoperability standards such as SCP-ECG, in electrocardiography. RESULTS: Open source components implementing standards and a community providing feedback from real-world use are key enablers of health care information system interoperability. CONCLUSIONS: Investing in open source is investing in interoperability and a vital aspect of a long term strategy towards comprehensive health services and clinical research.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17700904?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Graves, Edward E</style></author><author><style face="normal" font="default" size="100%">Quon, Andrew</style></author><author><style face="normal" font="default" size="100%">Loo, Billy W</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">RT_Image: an open-source tool for investigating PET in radiation oncology.</style></title><secondary-title><style face="normal" font="default" size="100%">Technology in cancer research &amp; treatment</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Technol. Cancer Res. Treat.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">111-21</style></pages><abstract><style face="normal" font="default" size="100%">Positron emission tomography (PET) has emerged as a valuable imaging modality for the diagnosis and staging of cancer. However, despite evidence that PET may be useful for defining target volumes for radiation therapy, no standardized methodology for accomplishing this task exists. To facilitate the investigation of the utility of PET imaging in radiotherapy treatment planning and accelerate its integration into clinical radiation oncology, we have developed software for exploratory analysis and segmentation of functional imaging datasets. The application, RT_Image, allows display of multiple imaging datasets and associated three-dimensional regions-of-interest (ROIs) at arbitrary view angles and fields of view. It also includes semi-automated image segmentation tools for defining metabolically active tumor volumes that may aid creation of target volumes for treatment planning. RT_Image is DICOM compliant, permitting the transfer of imaging data and DICOM-RT structure sets between the application and treatment planning software. RT_Image has been used by radiation oncologists, nuclear medicine physicians, and radiation physicists to analyze over 200 PET datasets. Novel segmentation techniques have been implemented within this programming framework for therapy planning and for evaluation of molecular imaging-derived parameters as prognostic indicators. RT_Image represents a freely-available software base on which further investigations of the utlity of PET and molecular imaging in radiation oncology may be built. The development of tools such as this is critical in order to realize the potential of molecular imaging-guided radiation therapy.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17375973?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Allard, Jérémie</style></author><author><style face="normal" font="default" size="100%">Cotin, Stéphane</style></author><author><style face="normal" font="default" size="100%">Faure, François</style></author><author><style face="normal" font="default" size="100%">Bensoussan, Pierre-Jean</style></author><author><style face="normal" font="default" size="100%">Poyer, François</style></author><author><style face="normal" font="default" size="100%">Duriez, Christian</style></author><author><style face="normal" font="default" size="100%">Delingette, Hervé</style></author><author><style face="normal" font="default" size="100%">Grisoni, Laurent</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">SOFA - an Open Source Framework for Medical Simulation</style></title><secondary-title><style face="normal" font="default" size="100%">Medicine Meets Virtual Reality (MMVR'15)</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">February</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.sofa-framework.org/docs/SOFA_MMVR07.pdf</style></url></web-urls></urls><pub-location><style face="normal" font="default" size="100%">Long Beach, USA</style></pub-location></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mamlin, Burke W</style></author><author><style face="normal" font="default" size="100%">Biondich, Paul G</style></author><author><style face="normal" font="default" size="100%">Wolfe, Ben A</style></author><author><style face="normal" font="default" size="100%">Fraser, Hamish</style></author><author><style face="normal" font="default" size="100%">Jazayeri, Darius</style></author><author><style face="normal" font="default" size="100%">Allen, Christian</style></author><author><style face="normal" font="default" size="100%">Miranda, Justin</style></author><author><style face="normal" font="default" size="100%">Tierney, William M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Cooking up an open source EMR for developing countries: OpenMRS - a recipe for successful collaboration.</style></title><secondary-title><style face="normal" font="default" size="100%">AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1839638</style></url></web-urls></urls><pages><style face="normal" font="default" size="100%">529-33</style></pages><abstract><style face="normal" font="default" size="100%">Millions of people are continue to die each year from HIV/AIDS. The majority of infected persons (&gt;95%) live in the developing world. A worthy response to this pandemic will require coordinated, scalable, and flexible information systems. We describe the OpenMRS system, an open source, collaborative effort that can serve as a foundation for EMR development in developing countries. We report our progress to date, lessons learned, and future directions.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17238397?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Morisawa, Hiraku</style></author><author><style face="normal" font="default" size="100%">Hirota, Mikako</style></author><author><style face="normal" font="default" size="100%">Toda, Tosifusa</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC bioinformatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Bioinformatics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">430</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies. RESULTS: We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. CONCLUSION: Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17018156?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Inchingolo, Paolo</style></author><author><style face="normal" font="default" size="100%">Beltrame, Marco</style></author><author><style face="normal" font="default" size="100%">Bosazzi, Pierpaolo</style></author><author><style face="normal" font="default" size="100%">Cicuta, Davide</style></author><author><style face="normal" font="default" size="100%">Faustini, Giorgio</style></author><author><style face="normal" font="default" size="100%">Mininel, Stefano</style></author><author><style face="normal" font="default" size="100%">Poli, Andrea</style></author><author><style face="normal" font="default" size="100%">Vatta, Federica</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">O3-DPACS Open-Source Image-Data Manager/Archiver and HDW2 Image-Data Display: an IHE-compliant project pushing the e-health integration in the world.</style></title><secondary-title><style face="normal" font="default" size="100%">Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Comput Med Imaging Graph</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Data Display</style></keyword><keyword><style  face="normal" font="default" size="100%">Database Management Systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Diagnostic Imaging</style></keyword><keyword><style  face="normal" font="default" size="100%">Equipment Design</style></keyword><keyword><style  face="normal" font="default" size="100%">Equipment Failure Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Guidelines as Topic</style></keyword><keyword><style  face="normal" font="default" size="100%">Information Storage and Retrieval</style></keyword><keyword><style  face="normal" font="default" size="100%">Internationality</style></keyword><keyword><style  face="normal" font="default" size="100%">Medical Records Systems, Computerized</style></keyword><keyword><style  face="normal" font="default" size="100%">Programming Languages</style></keyword><keyword><style  face="normal" font="default" size="100%">Radiology Information Systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Systems Integration</style></keyword><keyword><style  face="normal" font="default" size="100%">User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Sep-Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">30</style></volume><pages><style face="normal" font="default" size="100%">391-406</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">After many years of study, development and experimentation of open PACS and Image workstation solutions including management of medical data and signals (DPACS project), the research and development at the University of Trieste have recently been directed towards Java-based, IHE compliant and multi-purpose servers and clients. In this paper an original Image-Data Manager/Archiver (O3-DPACS) and a universal Image-Data Display (HDW2) are described. O3-DPACS is also part of a new project called Open Three (O3) Consortium, promoting Open Source adoption in e-health at European and world-wide levels. This project aims to give a contribution to the development of e-health through the study of Healthcare Information Systems and the contemporary proposal of new concepts, designs and solutions for the management of health data in an integrated environment: hospitals, Regional Health Information Organizations and citizens (home-care, mobile-care and ambient assisted living).</style></abstract><issue><style face="normal" font="default" size="100%">6-7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17055700?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wolfe, Benjamin A</style></author><author><style face="normal" font="default" size="100%">Mamlin, Burke W</style></author><author><style face="normal" font="default" size="100%">Biondich, Paul G</style></author><author><style face="normal" font="default" size="100%">Fraser, Hamish S F</style></author><author><style face="normal" font="default" size="100%">Jazayeri, Darius</style></author><author><style face="normal" font="default" size="100%">Allen, Christian</style></author><author><style face="normal" font="default" size="100%">Miranda, Justin</style></author><author><style face="normal" font="default" size="100%">Tierney, William M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The OpenMRS system: collaborating toward an open source EMR for developing countries.</style></title><secondary-title><style face="normal" font="default" size="100%">AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006</style></date></pub-dates></dates><pages><style face="normal" font="default" size="100%">1146</style></pages><abstract><style face="normal" font="default" size="100%">OpenMRS is an open source infrastructure for the creation of medical record systems in developing countries. Produced and maintained collaboratively across multiple institutions, this framework consists of an open source data model, a set of core application functions, and a default implementation. The goal of this implementation is to provide the beginnings of an EMR that is suitable for all groups involved with healthcare in developing countries.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17238765?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Cedilnik, Andy</style></author><author><style face="normal" font="default" size="100%">Geveci, Berk</style></author><author><style face="normal" font="default" size="100%">Moreland, Kenneth</style></author><author><style face="normal" font="default" size="100%">Ahrens, James P.</style></author><author><style face="normal" font="default" size="100%">Favre, Jean M.</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Heirich, Alan</style></author><author><style face="normal" font="default" size="100%">Raffin, Bruno</style></author><author><style face="normal" font="default" size="100%">dos Santos, Luís Paulo Peixoto</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Remote Large Data Visualization in the ParaView Framework.</style></title><secondary-title><style face="normal" font="default" size="100%">EGPGV</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">dblp</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dblp.uni-trier.de/db/conf/egpgv/egpgv2006.html#CedilnikGMAF06</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Eurographics Association</style></publisher><isbn><style face="normal" font="default" size="100%">3-905673-40-1</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yushkevich, Paul A</style></author><author><style face="normal" font="default" size="100%">Piven, Joseph</style></author><author><style face="normal" font="default" size="100%">Hazlett, Heather Cody</style></author><author><style face="normal" font="default" size="100%">Smith, Rachel Gimpel</style></author><author><style face="normal" font="default" size="100%">Ho, Sean</style></author><author><style face="normal" font="default" size="100%">Gee, James C</style></author><author><style face="normal" font="default" size="100%">Gerig, Guido</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability.</style></title><secondary-title><style face="normal" font="default" size="100%">NeuroImage</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Neuroimage</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Jul 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">31</style></volume><pages><style face="normal" font="default" size="100%">1116-28</style></pages><abstract><style face="normal" font="default" size="100%">Active contour segmentation and its robust implementation using level set methods are well-established theoretical approaches that have been studied thoroughly in the image analysis literature. Despite the existence of these powerful segmentation methods, the needs of clinical research continue to be fulfilled, to a large extent, using slice-by-slice manual tracing. To bridge the gap between methodological advances and clinical routine, we developed an open source application called ITK-SNAP, which is intended to make level set segmentation easily accessible to a wide range of users, including those with little or no mathematical expertise. This paper describes the methods and software engineering philosophy behind this new tool and provides the results of validation experiments performed in the context of an ongoing child autism neuroimaging study. The validation establishes SNAP intrarater and interrater reliability and overlap error statistics for the caudate nucleus and finds that SNAP is a highly reliable and efficient alternative to manual tracing. Analogous results for lateral ventricle segmentation are provided.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16545965?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Joel West</style></author><author><style face="normal" font="default" size="100%">Siobhán O'Mahony</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Contrasting Community Building in Sponsored and Community Founded Open Source Projects</style></title><secondary-title><style face="normal" font="default" size="100%">Hawaii International Conference on System Sciences</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year></dates><publisher><style face="normal" font="default" size="100%">IEEE Computer Society</style></publisher><pub-location><style face="normal" font="default" size="100%">Los Alamitos, CA, USA</style></pub-location><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">196c</style></pages></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lee, Wen-Jeng</style></author><author><style face="normal" font="default" size="100%">Yang, Chung-Yi</style></author><author><style face="normal" font="default" size="100%">Liu, Kao-Lang</style></author><author><style face="normal" font="default" size="100%">Liu, Hon-Man</style></author><author><style face="normal" font="default" size="100%">Ching, Yu-Tai</style></author><author><style face="normal" font="default" size="100%">Chen, Shyh-Jye</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Establishing a Web-based DICOM teaching file authoring tool using open-source public software.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Digit Imaging</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">18</style></volume><pages><style face="normal" font="default" size="100%">169-75</style></pages><abstract><style face="normal" font="default" size="100%">Online teaching files are an important source of educational and referential materials in the radiology community. The commonly used Digital Imaging and Communications in Medicine (DICOM) file format of the radiology community is not natively supported by common Web browsers. The ability of the Web server to convert and parse DICOM is important when the DICOM-converting tools are not available. In this paper, we describe our approach to develop a Web-based teaching file authoring tool. Our server is built using Apache Web server running on FreeBSD operating system. The dynamic page content is produced by Hypertext Preprocessor (PHP). Digital Imaging and Communications in Medicine images are converted by ImageMagick into Joint Photographic Experts Group (JPEG) format. Digital Imaging and Communications in Medicine attributes are parsed by dicom3tools and stored in PostgreSQL database. Using free software available from the Internet, we build a Web service that allows radiologists to create their own online teaching file cases with a common Web browser.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15924271?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hackländer, Thomas</style></author><author><style face="normal" font="default" size="100%">Martin, Jens</style></author><author><style face="normal" font="default" size="100%">Kleber, Klaus</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Informatics in radiology (infoRAD): an open source framework for modification and communication of DICOM objects.</style></title><secondary-title><style face="normal" font="default" size="100%">Radiographics : a review publication of the Radiological Society of North America, Inc</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Radiographics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Nov-Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">25</style></volume><pages><style face="normal" font="default" size="100%">1709-21</style></pages><abstract><style face="normal" font="default" size="100%">A configurable framework has been developed that can receive, modify, and export images in different picture archiving and communication system scenarios. The framework has three main components: a receiver for Digital Imaging and Communications in Medicine (DICOM) objects, a processing pipeline to apply one or more modifications to these objects, and one or more senders to send the processed objects to predefined addresses. The toolbox programming was implemented as an open source project in Java. The processing pipeline uses the concept of configurable plug-ins. One plug-in is user programmable by means of extensible stylesheet language files and allows conversion of DICOM objects to extensible markup language documents or other file types. Input and output channels are the DICOM Storage service, DICOM compact disks-read-only memory (CD-ROMs), and the local file system. The toolbox has been successfully applied to different clinical scenarios, including the correction of DICOM objects from non-Integrating the Healthcare Enterprise (IHE) conform modalities, pseudonaming of DICOM images, and use of the IHE Portable Data for Imaging profile with import and export of CD-ROMs. The toolbox has proved reliability in the clinical routine. Because of the open programming interfaces, the functionality can easily be adapted to future applications.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16284146?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sequist, Thomas D</style></author><author><style face="normal" font="default" size="100%">Cullen, Theresa</style></author><author><style face="normal" font="default" size="100%">Ayanian, John Z</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Information technology as a tool to improve the quality of American Indian health care.</style></title><secondary-title><style face="normal" font="default" size="100%">American journal of public health</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Am J Public Health</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">95</style></volume><pages><style face="normal" font="default" size="100%">2173-9</style></pages><abstract><style face="normal" font="default" size="100%">The American Indian/Alaska Native population experiences a disproportionate burden of disease across a spectrum of conditions. While the recent National Healthcare Disparities Report highlighted differences in quality of care among racial and ethnic groups, there was only very limited information available for American Indians. The Indian Health Service (IHS) is currently enhancing its information systems to improve the measurement of health care quality as well as to support quality improvement initiatives. We summarize current knowledge regarding health care quality for American Indians, highlighting the variation in reported measures in the existing literature. We then discuss how the IHS is using information systems to produce standardized performance measures and present future directions for improving American Indian health care quality.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16257947?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Brauchli, K</style></author><author><style face="normal" font="default" size="100%">O'mahony, D</style></author><author><style face="normal" font="default" size="100%">Banach, L</style></author><author><style face="normal" font="default" size="100%">Oberholzer, M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">iPath - a Telemedicine Platform to Support Health Providers in Low Resource Settings.</style></title><secondary-title><style face="normal" font="default" size="100%">Studies in health technology and informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Stud Health Technol Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">114</style></volume><pages><style face="normal" font="default" size="100%">11-7</style></pages><abstract><style face="normal" font="default" size="100%">In many developing countries there is an acute shortage of medical specialists. The specialists and services that are available are usually concentrated in cities and health workers in rural health care, who serve most of the population, are isolated from specialist support [1]. Besides, the few remaining specialist are often isolated from colleagues. With the recent development in information and communication technologies, new option for telemedicine and generally for sharing knowledge at a distance are becoming increasingly accessible to health workers also in developing countries. Since 2001 the Department of Pathology in Basel, Switzerland is operating an Internet based telemedicine platform to assist health workers in developing countries. Over 1800 consultation have been performed since. This paper will give an introduction to iPath - the telemedicine platform developed for this project - and analyse two case studies: a teledermatology project from South Africa and a telepathology project from Solomon Islands.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15923755?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Brauchli, Kurt</style></author><author><style face="normal" font="default" size="100%">Oberholzer, Martin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The iPath telemedicine platform.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of telemedicine and telecare</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Telemed Telecare</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11 Suppl 2</style></volume><pages><style face="normal" font="default" size="100%">S3-7</style></pages><abstract><style face="normal" font="default" size="100%">An early, point-to-point telepathology system at the University of Basel developed into an open-source, Internet-based platform for telemedicine in 2001. The Internet Pathology Suite (iPath) is a Web-based telepathology platform that permits the online presentation and discussion of cases within user groups. It also allows realtime telemicroscopy across firewalls. After four years, the telepathology network has over 700 active users. More than 6,300 cases with a total of about 39,000 images have been diagnosed. The diagnostic workload of all these cases is not exclusively handled by the Department of Pathology in Basel, but by a growing number of independent groups who also use the server simply as a case repository. What started as a small project for hospitals in Switzerland has become a global network.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16375782?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tolentino, Herman</style></author><author><style face="normal" font="default" size="100%">Marcelo, Alvin</style></author><author><style face="normal" font="default" size="100%">Marcelo, Portia</style></author><author><style face="normal" font="default" size="100%">Maramba, Inocencio</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Linking primary care information systems and public health information networks: lessons from the Philippines.</style></title><secondary-title><style face="normal" font="default" size="100%">Studies in health technology and informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Stud Health Technol Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">116</style></volume><pages><style face="normal" font="default" size="100%">955-60</style></pages><abstract><style face="normal" font="default" size="100%">Community-based primary care information systems are one of the building blocks for national health information systems. In the Philippines, after the devolution of health care to local governments, we observed &quot;health information system islands&quot; connected to national vertical programs being implemented in devolved health units. These structures lead to a huge amount of &quot;information work&quot; in the transformation of health information at the community level. This paper describes work done to develop and implement the open-source Community Based Health Information Tracking System (CHITS) Project, which was implemented to address this information management problem and its outcomes. Several lessons learned from the field as well as software development strategies are highlighted in building community level information systems that link to national level health information systems.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16160381?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Herman, Tolentino</style></author><author><style face="normal" font="default" size="100%">Marcelo, Alvin</style></author><author><style face="normal" font="default" size="100%">Marcelo, Portia</style></author><author><style face="normal" font="default" size="100%">Maramba, Inocencio</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Linking primary care information systems and public health vertical programs in the Philippines: an open-source experience.</style></title><secondary-title><style face="normal" font="default" size="100%">AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005</style></date></pub-dates></dates><pages><style face="normal" font="default" size="100%">311-5</style></pages><abstract><style face="normal" font="default" size="100%">Community-based primary care information systems are one of the building blocks for national health information systems. In the Philippines, after the devolution of health care to local governments, we observed &quot;health information system islands&quot; connected to national vertical programs being implemented in devolved health units. These structures lead to a huge amount of &quot;information work&quot; in the transformation of health information at the community level. This paper describes work done to develop and implement the open-source Community Based Health Information Tracking System (CHITS) Project, which was implemented to address this information management problem and its outcomes. Several lessons learned from the field as well as software development strategies are highlighted in building community level information systems that link to national level health information systems.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16779052?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wolf, Ivo</style></author><author><style face="normal" font="default" size="100%">Vetter, Marcus</style></author><author><style face="normal" font="default" size="100%">Wegner, Ingmar</style></author><author><style face="normal" font="default" size="100%">Böttger, Thomas</style></author><author><style face="normal" font="default" size="100%">Nolden, Marco</style></author><author><style face="normal" font="default" size="100%">Schöbinger, Max</style></author><author><style face="normal" font="default" size="100%">Hastenteufel, Mark</style></author><author><style face="normal" font="default" size="100%">Kunert, Tobias</style></author><author><style face="normal" font="default" size="100%">Meinzer, Hans-Peter</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The medical imaging interaction toolkit.</style></title><secondary-title><style face="normal" font="default" size="100%">Medical image analysis</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Med Image Anal</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Algorithms</style></keyword><keyword><style  face="normal" font="default" size="100%">Artificial Intelligence</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Graphics</style></keyword><keyword><style  face="normal" font="default" size="100%">Diagnostic Imaging</style></keyword><keyword><style  face="normal" font="default" size="100%">Image Enhancement</style></keyword><keyword><style  face="normal" font="default" size="100%">Image Interpretation, Computer-Assisted</style></keyword><keyword><style  face="normal" font="default" size="100%">Imaging, Three-Dimensional</style></keyword><keyword><style  face="normal" font="default" size="100%">Pattern Recognition, Automated</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">594-604</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Thoroughly designed, open-source toolkits emerge to boost progress in medical imaging. The Insight Toolkit (ITK) provides this for the algorithmic scope of medical imaging, especially for segmentation and registration. But medical imaging algorithms have to be clinically applied to be useful, which additionally requires visualization and interaction. The Visualization Toolkit (VTK) has powerful visualization capabilities, but only low-level support for interaction. In this paper, we present the Medical Imaging Interaction Toolkit (MITK). The goal of MITK is to significantly reduce the effort required to construct specifically tailored, interactive applications for medical image analysis. MITK allows an easy combination of algorithms developed by ITK with visualizations created by VTK and extends these two toolkits with those features, which are outside the scope of both. MITK adds support for complex interactions with multiple states as well as undo-capabilities, a very important prerequisite for convenient user interfaces. Furthermore, MITK facilitates the realization of multiple, different views of the same data (as a multiplanar reconstruction and a 3D rendering) and supports the visualization of 3D+t data, whereas VTK is only designed to create one kind of view of 2D or 3D data. MITK reuses virtually everything from ITK and VTK. Thus, it is not at all a competitor to ITK or VTK, but an extension, which eases the combination of both and adds the features required for interactive, convenient to use medical imaging software. MITK is an open-source project (www.mitk.org).</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15896995?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Drury, Peter</style></author><author><style face="normal" font="default" size="100%">Dahlman, Bruce</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open source approaches to health information systems in Kenya.</style></title><secondary-title><style face="normal" font="default" size="100%">World hospitals and health services : the official journal of the International Hospital Federation</style></secondary-title><alt-title><style face="normal" font="default" size="100%">World Hosp Health Serv</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">41</style></volume><pages><style face="normal" font="default" size="100%">36-9</style></pages><abstract><style face="normal" font="default" size="100%">This paper focuses on the experience to date of an installation of a Free Open Source Software (FOSS) product, Care2X, at a church hospital in Kenya. The FOSS movement has been maturing rapidly. In developed countries, its benefits relative to proprietary software have been extensively discussed and ways of quantifying the total costs of the development have been developed. Nevertheless, empirical data on the impact of FOSS, particularly in the developing world, concerning its use and development is still quite limited, although the possibilities of FOSS are becoming increasingly attractive.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16300164?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ahrens, James</style></author><author><style face="normal" font="default" size="100%">Geveci, Berk</style></author><author><style face="normal" font="default" size="100%">Law, Charles</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Hansen, C R</style></author><author><style face="normal" font="default" size="100%">Johnson, C DEditors</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">ParaView : An End-User Tool for Large Data Visualization</style></title><secondary-title><style face="normal" font="default" size="100%">Energy</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://scholar.google.com/scholar?hl=en&amp;btnG=Search&amp;q=intitle:ParaView:+An+end-user+tool+for+large+data+visualization#0</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">836</style></volume><pages><style face="normal" font="default" size="100%">717–732</style></pages><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Good, Thomas</style></author><author><style face="normal" font="default" size="100%">DiTommaso, Marianne</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">SQL Clinic: the open-source alternative for electronic medical records.</style></title><secondary-title><style face="normal" font="default" size="100%">Psychiatr Serv</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Psychiatr Serv</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Medical Records Systems, Computerized</style></keyword><keyword><style  face="normal" font="default" size="100%">Psychiatry</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">56</style></volume><pages><style face="normal" font="default" size="100%">269-71</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">3</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Smith, Stephen M</style></author><author><style face="normal" font="default" size="100%">Jenkinson, Mark</style></author><author><style face="normal" font="default" size="100%">Woolrich, Mark W</style></author><author><style face="normal" font="default" size="100%">Beckmann, Christian F</style></author><author><style face="normal" font="default" size="100%">Behrens, Timothy E J</style></author><author><style face="normal" font="default" size="100%">Johansen-Berg, Heidi</style></author><author><style face="normal" font="default" size="100%">Bannister, Peter R</style></author><author><style face="normal" font="default" size="100%">De Luca, Marilena</style></author><author><style face="normal" font="default" size="100%">Drobnjak, Ivana</style></author><author><style face="normal" font="default" size="100%">Flitney, David E</style></author><author><style face="normal" font="default" size="100%">Niazy, Rami K</style></author><author><style face="normal" font="default" size="100%">Saunders, James</style></author><author><style face="normal" font="default" size="100%">Vickers, John</style></author><author><style face="normal" font="default" size="100%">Zhang, Yongyue</style></author><author><style face="normal" font="default" size="100%">De Stefano, Nicola</style></author><author><style face="normal" font="default" size="100%">Brady, J Michael</style></author><author><style face="normal" font="default" size="100%">Matthews, Paul M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Advances in functional and structural MR image analysis and implementation as FSL.</style></title><secondary-title><style face="normal" font="default" size="100%">NeuroImage</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Neuroimage</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bayes Theorem</style></keyword><keyword><style  face="normal" font="default" size="100%">Brain</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Factual</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Image Processing, Computer-Assisted</style></keyword><keyword><style  face="normal" font="default" size="100%">Magnetic Resonance Imaging</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Neurological</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Statistical</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">23 Suppl 1</style></volume><pages><style face="normal" font="default" size="100%">S208-19</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The techniques available for the interrogation and analysis of neuroimaging data have a large influence in determining the flexibility, sensitivity, and scope of neuroimaging experiments. The development of such methodologies has allowed investigators to address scientific questions that could not previously be answered and, as such, has become an important research area in its own right. In this paper, we present a review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB). This research has focussed on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data. The majority of the research laid out in this paper has been implemented as freely available software tools within FMRIB's Software Library (FSL).</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15501092?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Dickhaus, H</style></author><author><style face="normal" font="default" size="100%">Floca, R</style></author><author><style face="normal" font="default" size="100%">Eisenmann, U</style></author><author><style face="normal" font="default" size="100%">Metzner, R</style></author><author><style face="normal" font="default" size="100%">Wirtz, C R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A flexible registration framework for multimodal image data.</style></title><secondary-title><style face="normal" font="default" size="100%">Conf Proc IEEE Eng Med Biol Soc</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Conf Proc IEEE Eng Med Biol Soc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">1755-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">This paper describes a registration framework based on the insight segmentation and registration toolkit (ITK) which can be used for matching multimodal image data. Different target groups with individual needs and precognition are addressed. The framework offers tools for supporting different matching tasks in a clinical environment. A setup editor defines specific rigid or non rigid matching approaches and the appropriate parameters. Different metrics including a correlation metric, a difference metric and mutual information based metrics are available. Furthermore, a test series editor can be used to evaluate the selected setup. The evaluation results, which are expressed in statistical figures, trends and performance measures, can be visualized and used for an optimal adapted setup configuration. Tests for matching precision, quality and parameter adjustments are offered. For export and import of image data, the most frequently used file formats of clinical environments like DICOM and ANALYZE are supported. We demonstrate some registration examples which frequently occur in the neurosurgical routine of a University Hospital.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Espino, Jeremy U</style></author><author><style face="normal" font="default" size="100%">Wagner, Michael M</style></author><author><style face="normal" font="default" size="100%">Tsui, Fu-Chang</style></author><author><style face="normal" font="default" size="100%">Su, Hoah-Der</style></author><author><style face="normal" font="default" size="100%">Olszewski, Robert T</style></author><author><style face="normal" font="default" size="100%">Lie, Zhen</style></author><author><style face="normal" font="default" size="100%">Chapman, Wendy</style></author><author><style face="normal" font="default" size="100%">Zeng, Xiaoming</style></author><author><style face="normal" font="default" size="100%">Ma, Lili</style></author><author><style face="normal" font="default" size="100%">Lu, Zhong Wei</style></author><author><style face="normal" font="default" size="100%">Dara, Jagan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The RODS Open Source Project: removing a barrier to syndromic surveillance.</style></title><secondary-title><style face="normal" font="default" size="100%">Studies in health technology and informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Stud Health Technol Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">107</style></volume><pages><style face="normal" font="default" size="100%">1192-6</style></pages><abstract><style face="normal" font="default" size="100%">The goal of the Real-time Outbreak and Disease Surveillance (RODS) Open Source Project is to accelerate deployment of computer-based syndromic surveillance. To this end, the project has released the RODS software under the GNU General Public License and created an organizational structure to catalyze its development. This paper describes the design of the software, requested extensions, and the structure of the development effort.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15361001?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Parvin, B</style></author><author><style face="normal" font="default" size="100%">Yang, Qing</style></author><author><style face="normal" font="default" size="100%">Fontenay, G</style></author><author><style face="normal" font="default" size="100%">Barcellos-Hoff, M H</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">BioSig: an imaging bioinformatics system for phenotypic analysis.</style></title><secondary-title><style face="normal" font="default" size="100%">IEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society</style></secondary-title><alt-title><style face="normal" font="default" size="100%">IEEE Trans Syst Man Cybern B Cybern</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">33</style></volume><pages><style face="normal" font="default" size="100%">814-24</style></pages><abstract><style face="normal" font="default" size="100%">Organisms express their genomes in a cell-specific manner, resulting in a variety of cellular phenotypes or phenomes. Mapping cell phenomes under a variety of experimental conditions is necessary in order to understand the responses of organisms to stimuli. Representing such data requires an integrated view of experimental and informatic protocols. The proposed system, named BioSig, provides the foundation for cataloging cellular responses as a function of specific conditioning, treatment, staining, etc., for either fixed tissue or living cell studies. A data model has been developed to capture experimental variables and map them to image collections and their computed representation. This representation is hierarchical and spans across sample tissues, cells, and organelles, which are imaged with light microscopy. At each layer, content is represented with an attributed graph, which contains information about cellular morphology, protein localization, and cellular organization in tissue or cell culture. The Web-based multilayer informatics architecture uses the data model to provide guided workflow access for content exploration.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18238234?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">McDonald, Clement J</style></author><author><style face="normal" font="default" size="100%">Schadow, Gunther</style></author><author><style face="normal" font="default" size="100%">Barnes, Michael</style></author><author><style face="normal" font="default" size="100%">Dexter, Paul</style></author><author><style face="normal" font="default" size="100%">Overhage, J Marc</style></author><author><style face="normal" font="default" size="100%">Mamlin, Burke</style></author><author><style face="normal" font="default" size="100%">McCoy, J Michael</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open Source software in medical informatics--why, how and what.</style></title><secondary-title><style face="normal" font="default" size="100%">International journal of medical informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int J Med Inform</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">69</style></volume><pages><style face="normal" font="default" size="100%">175-84</style></pages><abstract><style face="normal" font="default" size="100%">'Open Source' is a 20-40 year old approach to licensing and distributing software that has recently burst into public view. Against conventional wisdom this approach has been wildly successful in the general software market--probably because the openness lets programmers the world over obtain, critique, use, and build upon the source code without licensing fees. Linux, a UNIX-like operating system, is the best known success. But computer scientists at the University of California, Berkeley began the tradition of software sharing in the mid 1970s with BSD UNIX and distributed the major internet network protocols as source code without a fee. Medical informatics has its own history of Open Source distribution: Massachusetts General's COSTAR and the Veterans Administration's VISTA software have been distributed as source code at no cost for decades. Bioinformatics, our sister field, has embraced the Open Source movement and developed rich libraries of open-source software. Open Source has now gained a tiny foothold in health care (OSCAR GEHR, OpenEMed). Medical informatics researchers and funding agencies should support and nurture this movement. In a world where open-source modules were integrated into operational health care systems, informatics researchers would have real world niches into which they could engraft and test their software inventions. This could produce a burst of innovation that would help solve the many problems of the health care system. We at the Regenstrief Institute are doing our part by moving all of our development to the open-source model.</style></abstract><issue><style face="normal" font="default" size="100%">2-3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12810121?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kantor, Gareth S</style></author><author><style face="normal" font="default" size="100%">Wilson, Wayne D</style></author><author><style face="normal" font="default" size="100%">Midgley, Adrian</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Open-source software and the primary care EMR.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of the American Medical Informatics Association : JAMIA</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Nov-Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">616; author reply 617</style></pages><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12925540?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">van der Linden, Helma</style></author><author><style face="normal" font="default" size="100%">Boers, Gerrit</style></author><author><style face="normal" font="default" size="100%">Tange, Huibert</style></author><author><style face="normal" font="default" size="100%">Talmon, Jan</style></author><author><style face="normal" font="default" size="100%">Hasman, Arie</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">PropeR: a multi disciplinary EPR system.</style></title><secondary-title><style face="normal" font="default" size="100%">International journal of medical informatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int J Med Inform</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computer Systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Delivery of Health Care, Integrated</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Interprofessional Relations</style></keyword><keyword><style  face="normal" font="default" size="100%">Medical Records Systems, Computerized</style></keyword><keyword><style  face="normal" font="default" size="100%">Stroke</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">70</style></volume><pages><style face="normal" font="default" size="100%">149-60</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">This article describes the architecture of an EPR system developed for the PropeR project. This EPR system not only aims at supporting home care of stroke patients, but is also designed in such a way that it can be ported to other medical services without much effort. We will briefly describe the Stroke Service and the related PropeR project. Starting from a list of requirements to construct a generic EPR system we will outline the architecture and describe the standards and methods used. Subsequently we describe the implementation and the problems encountered. In the discussion, we will go into the advantages and disadvantages of the tools and techniques we have used.</style></abstract><issue><style face="normal" font="default" size="100%">2-3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12909166?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tsui, Fu-Chiang</style></author><author><style face="normal" font="default" size="100%">Espino, Jeremy U</style></author><author><style face="normal" font="default" size="100%">Dato, Virginia M</style></author><author><style face="normal" font="default" size="100%">Gesteland, Per H</style></author><author><style face="normal" font="default" size="100%">Hutman, Judith</style></author><author><style face="normal" font="default" size="100%">Wagner, Michael M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Technical description of RODS: a real-time public health surveillance system.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of the American Medical Informatics Association : JAMIA</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Sep-Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">399-408</style></pages><abstract><style face="normal" font="default" size="100%">This report describes the design and implementation of the Real-time Outbreak and Disease Surveillance (RODS) system, a computer-based public health surveillance system for early detection of disease outbreaks. Hospitals send RODS data from clinical encounters over virtual private networks and leased lines using the Health Level 7 (HL7) message protocol. The data are sent in real time. RODS automatically classifies the registration chief complaint from the visit into one of seven syndrome categories using Bayesian classifiers. It stores the data in a relational database, aggregates the data for analysis using data warehousing techniques, applies univariate and multivariate statistical detection algorithms to the data, and alerts users of when the algorithms identify anomalous patterns in the syndrome counts. RODS also has a Web-based user interface that supports temporal and spatial analyses. RODS processes sales of over-the-counter health care products in a similar manner but receives such data in batch mode on a daily basis. RODS was used during the 2002 Winter Olympics and currently operates in two states-Pennsylvania and Utah. It has been and continues to be a resource for implementing, evaluating, and applying new methods of public health surveillance.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12807803?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Van Essen, D C</style></author><author><style face="normal" font="default" size="100%">Drury, H A</style></author><author><style face="normal" font="default" size="100%">Dickson, J</style></author><author><style face="normal" font="default" size="100%">Harwell, J</style></author><author><style face="normal" font="default" size="100%">Hanlon, D</style></author><author><style face="normal" font="default" size="100%">Anderson, C H</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">An integrated software suite for surface-based analyses of cerebral cortex.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of the American Medical Informatics Association : JAMIA</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Am Med Inform Assoc</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2001</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2001 Sep-Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">443-59</style></pages><abstract><style face="normal" font="default" size="100%">The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11522765?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lohmann, G</style></author><author><style face="normal" font="default" size="100%">Müller, K</style></author><author><style face="normal" font="default" size="100%">Bosch, V</style></author><author><style face="normal" font="default" size="100%">Mentzel, H</style></author><author><style face="normal" font="default" size="100%">Hessler, S</style></author><author><style face="normal" font="default" size="100%">Chen, L</style></author><author><style face="normal" font="default" size="100%">Zysset, S</style></author><author><style face="normal" font="default" size="100%">von Cramon, D Y</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">LIPSIA - a new software system for the evaluation of functional magnetic resonance images of the human brain.</style></title><secondary-title><style face="normal" font="default" size="100%">Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Comput Med Imaging Graph</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2001</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2001 Nov-Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">25</style></volume><pages><style face="normal" font="default" size="100%">449-57</style></pages><abstract><style face="normal" font="default" size="100%">This paper describes the non-commercial software system LIPSIA that was developed for the processing of functional magnetic resonance images (fMRI) of the human brain. The analysis of fMRI data comprises various aspects including filtering, spatial transformation, statistical evaluation as well as segmentation and visualization. In LIPSIA, particular emphasis was placed on the development of new visualization and segmentation techniques that support visualizations of individual brain anatomy so that experts can assess the exact location of activation patterns in individual brains. As the amount of data that must be handled is enormous, another important aspect in the development LIPSIA was the efficiency of the software implementation. Well established statistical techniques were used whenever possible.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11679206?dopt=Abstract</style></custom1></record></records></xml>