@article {1212, title = {Bangladesh{\textquoteright}s digital health journey: reflections on a decade of quiet revolution.}, journal = {WHO South East Asia J Public Health}, volume = {8}, year = {2019}, month = {2019 09}, pages = {71-76}, abstract = {

Bangladesh has made remarkable progress in digital health in recent years. Through one of the world{\textquoteright}s largest deployments to date of the open-source District Health Information Software 2 (DHIS2), the country now has a national public sector health data warehouse. Information from previously fragmented data systems is now unified in a common data repository, enabling data exchange for health information systems and decision-making. Work is ongoing to create lifetime electronic health records for all citizens that can be transferred between health facilities. Extensive customization of open-source software has laid the foundations for a national digital networking system. Initiatives have focused on producing digital solutions to aid priorities such as strengthening the health system as a whole as well as supporting specific technical interventions, for example improving the civil registration and vital statistics system. Digital solutions have also supported the Bangladesh health workforce strategy through a set of registries that electronically captures and maintains human resource information for the entire public health sector, including monitoring staff attendance through the use of low-cost biometric fingerprint time-attendance machines. Citizens are encouraged to engage in shaping health services via a web-based complaints and suggestions system, and a new system to raise health awareness via public digital displays has started in Dhaka. Strong support at the highest political level has been critical to the success of efforts to introduce these innovations. The endeavour has also generated a cadre of enthusiastic eHealth proponents, who are focused on further strengthening and expanding the existing systems and on harnessing the vast amount of information amassed at the central data repository through big data analysis, artificial intelligence and machine learning.

}, issn = {2304-5272}, doi = {10.4103/2224-3151.264849}, author = {Khan, Muhammad Abdul Hannan and Cruz, Valeria de Oliveira and Azad, Abul Kalam} } @article {1220, title = {CODE STROKE ALERT-Concept and Development of a Novel Open-Source Platform to Streamline Acute Stroke Management.}, journal = {Front Neurol}, volume = {10}, year = {2019}, month = {2019}, pages = {725}, abstract = {

Effective, time-critical intervention in acute stroke is crucial to mitigate mortality rate and morbidity, but delivery of reperfusion treatments is often hampered by pre-, in-, or inter-hospital system level delays. Disjointed, repetitive, and inefficient communication is a consistent contributor to avoidable treatment delay. In the era of rapid reperfusion therapy for ischemic stroke, there is a need for a communication system to synchronize the flow of clinical information across the entire stroke journey. A multi-disciplinary development team designed an electronic communications platform, integrated between web browsers and a mobile application, to link all relevant members of the stroke treatment pathway. The platform uses tiered notifications, geotagging, incorporates multiple clinical score calculators, and is compliant with security regulations. The system safely saves relevant information for audit and research. Code Stroke Alert is a platform that can be accessed by emergency medical services (EMS) and hospital staff, coordinating the flow of information during acute stroke care, reducing duplication, and error in clinical information handover. Electronic data logs provide an auditable trail of relevant quality improvement metrics, facilitating quality improvement, and research. Code Stroke Alert will be freely available to health networks globally. The open-source nature of the software offers valuable potential for future development of plug-ins and add-ons, based on individual institutional needs. Prospective, multi-site implementation, and measurement of clinical impact are underway.

}, issn = {1664-2295}, doi = {10.3389/fneur.2019.00725}, author = {Seah, Huey Ming and Burney, Moe and Phan, Michael and Shell, Daniel and Wu, Jamin and Zhou, Kevin and Brooks, Owen and Coulton, Bronwyn and Maingard, Julian and Tang, Jennifer and Yazdabadi, Gohar and Tahayori, Bahman and Barras, Christen and Kok, Hong Kuan and Chandra, Ronil and Thijs, Vincent and Brooks, Duncan Mark and Asadi, Hamed} } @article {1223, title = {Health4Afrika - Implementing HL7 FHIR Based Interoperability.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {20-24}, abstract = {

Supported by the European Commission under Horizon 2020, mHealth4Afrika is co-designing and validating a modular, multilingual, state-of-the-art health information system addressing primary healthcare requirements in resource constrained environments. mHealth4Afrika has co-designed a comprehensive range of functionality and medical programs in partnership with Ministries of Health, district health officers, clinic managers and primary healthcare workers from urban, rural and deep rural health facilities in Ethiopia, Kenya, Malawi and South Africa. This paper provides insights into how mHealth4Afrika is leveraging HL7 FHIR to support standards-based data exchange and interoperability between Electronic Medical Records and DHIS2. This work is currently being validated in the field.

}, issn = {1879-8365}, doi = {10.3233/SHTI190175}, author = {Baskaya, Mert and Yuksel, Mustafa and Erturkmen, Gokce Banu Laleci and Cunningham, Miriam and Cunningham, Paul} } @article {1271, title = {The impact of PEPFAR transition on HIV service delivery at health facilities in Uganda.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0223426}, abstract = {

BACKGROUND: Since 2004, the President{\textquoteright}s Emergency Plan for AIDS Relief (PEPFAR) has played a large role in Uganda{\textquoteright}s HIV/AIDS response. To better target resources to high burden regions and facilities, PEPFAR planned to withdraw from 29\% of previously-supported health facilities in Uganda between 2015 and 2017.

METHODS: We conducted a cross-sectional survey of 226 PEPFAR-supported health facilities in Uganda in mid-2017. The survey gathered information on availability, perceived quality, and access to HIV services before and after transition. We compare responses for facilities transitioned to those maintained on PEPFAR, accounting for survey design. We also extracted data from DHIS2 for the period October 2013-December 2017 on the number of HIV tests and counseling (HTC), number of patients on antiretroviral therapy (Current on ART), and retention on first-line ART (Retention) at 12 months. Using mixed effect models, we compare trends in service volume around the transition period.

RESULTS: There were 206 facilities that reported transition and 20 that reported maintenance on PEPFAR. Some facilities reporting transition may have been in a gap between implementing partners. The median transition date was September 2016, nine months prior to the survey. Transition facilities were more likely to discontinue HIV outreach following transition (51.6\% vs. 1.4\%, p<0.001) and to report declines in HIV care access (43.5\% vs. 3.1\%, p<0.001) and quality (35.6\% vs. 0\%, p<0.001). However, transition facilities did not differ in their trends in HIV service volume relative to maintenance facilities.

CONCLUSIONS: Transition from PEPFAR resulted in facilities reporting worsening patient access and service quality for HIV care, but there is insufficient evidence to suggest negative impacts on volume of HIV services. Facility respondents{\textquoteright} perceptions about access and quality may be overly pessimistic, or they may signal forthcoming impacts. Unrelated to transition, declining retention on ART in Uganda is a cause for concern.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0223426}, author = {Wilhelm, Jess Alan and Qiu, Mary and Paina, Ligia and Colantuoni, Elizabeth and Mukuru, Moses and Ssengooba, Freddie and Bennett, Sara} } @article {1278, title = {Large care gaps in primary care management of asthma: a longitudinal practice audit.}, journal = {BMJ Open}, volume = {9}, year = {2019}, month = {2019 01 29}, pages = {e022506}, abstract = {

OBJECTIVES: Care gaps in asthma may be highly prevalent but are poorly characterised. We sought to prospectively measure adherence to key evidence-based adult asthma practices in primary care, and predictors of these behaviours.

DESIGN: One-year prospective cohort study employing an electronic chart audit.

SETTING: Three family health teams (two academic, one community-based) in Ontario, Canada.

PARTICIPANTS: 884 patients (72.1\% female; 46.0{\textpm}17.5 years old) (4199 total visits; 4.8{\textpm}4.8 visits/patient) assigned to 23 physicians (65\% female; practising for 10.0{\textpm}8.6 years).

MAIN OUTCOME MEASURES: The primary outcome was the proportion of visits during which practitioners assessed asthma control according to symptom-based criteria. Secondary outcomes included the proportion of: patients who had asthma control assessed at least once; visits during which a controller medication was initiated or escalated; and patients who received a written asthma action plan. Behavioural predictors were established a priori and tested in a multivariable model.

RESULTS: Primary outcome: Providers assessed asthma control in 4.9\% of visits and 15.4\% of patients. Factors influencing assessment included clinic site (p=0.019) and presenting symptom, with providers assessing control more often during visits for asthma symptoms (35.0\%) or any respiratory symptoms (18.8\%) relative to other visits (1.6\%) (p<0.01).

SECONDARY OUTCOMES: Providers escalated controller therapy in 3.3\% of visits and 15.4\% of patients. Factors influencing escalation included clinic site, presenting symptom and prior objective asthma diagnosis. Escalation occurred more frequently during visits for asthma symptoms (21.0\%) or any respiratory symptoms (11.9\%) relative to other visits (1.5\%) (p<0.01) and in patients without a prior objective asthma diagnosis (3.5\%) relative to those with (1.3\%) (p=0.025). No asthma action plans were delivered.

CONCLUSIONS: Major gaps in evidence-based asthma practice exist in primary care. Targeted knowledge translation interventions are required to address these gaps, and can be tailored by leveraging the identified behavioural predictors.

TRIAL REGISTRATION NUMBER: NCT01070095; Pre-results.

}, issn = {2044-6055}, doi = {10.1136/bmjopen-2018-022506}, author = {Price, Courtney and Agarwal, Gina and Chan, David and Goel, Sanjeev and Kaplan, Alan G and Boulet, Louis-Philippe and Mamdani, Muhammad M and Straus, Sharon E and Lebovic, Gerald and Gupta, Samir} } @article {1210, title = {Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses.}, journal = {JCO Clin Cancer Inform}, volume = {3}, year = {2019}, month = {2019 Aug}, pages = {1-16}, abstract = {

PURPOSE: We have created a cloud-based machine learning system (CLOBNET) that is an open-source, lean infrastructure for electronic health record (EHR) data integration and is capable of extract, transform, and load (ETL) processing. CLOBNET enables comprehensive analysis and visualization of structured EHR data. We demonstrate the utility of CLOBNET by predicting primary therapy outcomes of patients with high-grade serous ovarian cancer (HGSOC) on the basis of EHR data.

MATERIALS AND METHODS: CLOBNET is built using open-source software to make data preprocessing, analysis, and model training user friendly. The source code of CLOBNET is available in GitHub. The HGSOC data set was based on a prospective cohort of 208 patients with HGSOC who were treated at Turku University Hospital, Finland, from 2009 to 2019 for whom comprehensive clinical and EHR data were available.

RESULTS: We trained machine learning (ML) models using clinical data, including a herein developed dissemination score that quantifies the disease burden at the time of diagnosis, to identify patients with progressive disease (PD) or a complete response (CR) on the basis of RECIST (version 1.1). The best performance was achieved with a logistic regression model, which resulted in an area under receiver operating characteristic curve (AUROC) of 0.86, with a specificity of 73\% and a sensitivity of 89\%, when it classified between patients who experienced PD and CR.

CONCLUSION: We have developed an open-source computational infrastructure, CLOBNET, that enables effective and rapid analysis of EHR and other clinical data. Our results demonstrate that CLOBNET allows predictions to be made on the basis of EHR data to address clinically relevant questions.

}, issn = {2473-4276}, doi = {10.1200/CCI.18.00132}, author = {Isoviita, Veli-Matti and Salminen, Liina and Azar, Jimmy and Lehtonen, Rainer and Roering, Pia and Carp{\'e}n, Olli and Hietanen, Sakari and Gr{\'e}nman, Seija and Hynninen, Johanna and F{\"a}rkkil{\"a}, Anniina and Hautaniemi, Sampsa} } @article {1221, title = {RADAR-Base: Open Source Mobile Health Platform for Collecting, Monitoring, and Analyzing Data Using Sensors, Wearables, and Mobile Devices.}, journal = {JMIR Mhealth Uhealth}, volume = {7}, year = {2019}, month = {2019 08 01}, pages = {e11734}, abstract = {

BACKGROUND: With a wide range of use cases in both research and clinical domains, collecting continuous mobile health (mHealth) streaming data from multiple sources in a secure, highly scalable, and extensible platform is of high interest to the open source mHealth community. The European Union Innovative Medicines Initiative Remote Assessment of Disease and Relapse-Central Nervous System (RADAR-CNS) program is an exemplary project with the requirements to support the collection of high-resolution data at scale; as such, the Remote Assessment of Disease and Relapse (RADAR)-base platform is designed to meet these needs and additionally facilitate a new generation of mHealth projects in this nascent field.

OBJECTIVE: Wide-bandwidth networks, smartphone penetrance, and wearable sensors offer new possibilities for collecting near-real-time high-resolution datasets from large numbers of participants. The aim of this study was to build a platform that would cater for large-scale data collection for remote monitoring initiatives. Key criteria are around scalability, extensibility, security, and privacy.

METHODS: RADAR-base is developed as a modular application; the backend is built on a backbone of the highly successful Confluent/Apache Kafka framework for streaming data. To facilitate scaling and ease of deployment, we use Docker containers to package the components of the platform. RADAR-base provides 2 main mobile apps for data collection, a Passive App and an Active App. Other third-Party Apps and sensors are easily integrated into the platform. Management user interfaces to support data collection and enrolment are also provided.

RESULTS: General principles of the platform components and design of RADAR-base are presented here, with examples of the types of data currently being collected from devices used in RADAR-CNS projects: Multiple Sclerosis, Epilepsy, and Depression cohorts.

CONCLUSIONS: RADAR-base is a fully functional, remote data collection platform built around Confluent/Apache Kafka and provides off-the-shelf components for projects interested in collecting mHealth datasets at scale.

}, issn = {2291-5222}, doi = {10.2196/11734}, author = {Ranjan, Yatharth and Rashid, Zulqarnain and Stewart, Callum and Conde, Pauline and Begale, Mark and Verbeeck, Denny and Boettcher, Sebastian and Dobson, Richard and Folarin, Amos} } @article {1214, title = {Towards an Open-Source Oncology Electronic Medical Records System for Low-Resource Settings: Development of Chemotherapy Management in OpenMRS.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {634-638}, abstract = {

Cancer is a major public health challenge in low and middle income countries (LMICs). In this paper, we describe work in progress to develop functionality within an open-source electronic medical records system to support safe and standardized cancer care in low-resource settings. We engaged cancer care providers from LMICs to elicit and prioritize requirement, and following a rapid application development approach we developed chemotherapy prescription and documentation functionality within OpenMRS.

}, issn = {1879-8365}, doi = {10.3233/SHTI190300}, author = {Kabukye, Johnblack K and Casaceli, Alexis M and Ball, Ellen and De Armas, Mario and Cornet, Ronald} } @article {1238, title = {Design and implementation of an affordable, public sector electronic medical record in rural Nepal.}, journal = {J Innov Health Inform}, volume = {24}, year = {2017}, month = {2017 Jun 23}, pages = {862}, abstract = {

INTRODUCTION: Globally, electronic medical records are central to the infrastructure of modern healthcare systems. Yet the vast majority of electronic medical records have been designed for resource-rich environments and are not feasible in settings of poverty. Here we describe the design and implementation of an electronic medical record at a public sector district hospital in rural Nepal, and its subsequent expansion to an additional public sector facility.DevelopmentThe electronic medical record was designed to solve for the following elements of public sector healthcare delivery: 1) integration of the systems across inpatient, surgical, outpatient, emergency, laboratory, radiology, and pharmacy sites of care; 2) effective data extraction for impact evaluation and government regulation; 3) optimization for longitudinal care provision and patient tracking; and 4) effectiveness for quality improvement initiatives.

APPLICATION: For these purposes, we adapted Bahmni, a product built with open-source components for patient tracking, clinical protocols, pharmacy, laboratory, imaging, financial management, and supply logistics. In close partnership with government officials, we deployed the system in February of 2015, added on additional functionality, and iteratively improved the system over the following year. This experience enabled us then to deploy the system at an additional district-level hospital in a different part of the country in under four weeks. We discuss the implementation challenges and the strategies we pursued to build an electronic medical record for the public sector in rural Nepal.DiscussionOver the course of 18 months, we were able to develop, deploy and iterate upon the electronic medical record, and then deploy the refined product at an additional facility within only four weeks. Our experience suggests the feasibility of an integrated electronic medical record for public sector care delivery even in settings of rural poverty.

}, keywords = {Delivery of Health Care, Integrated, electronic health records, Global Health, Health Plan Implementation, Hospitals, Public, Humans, Nepal, Public Sector, Rural Population}, issn = {2058-4563}, doi = {10.14236/jhi.v24i2.862}, author = {Raut, Anant and Yarbrough, Chase and Singh, Vivek and Gauchan, Bikash and Citrin, David and Verma, Varun and Hawley, Jessica and Schwarz, Dan and Harsha Bangura, Alex and Shrestha, Biplav and Schwarz, Ryan and Adhikari, Mukesh and Maru, Duncan} } @article {1236, title = {Development and Deployment of the OpenMRS-Ebola Electronic Health Record System for an Ebola Treatment Center in Sierra Leone.}, journal = {J Med Internet Res}, volume = {19}, year = {2017}, month = {2017 08 21}, pages = {e294}, abstract = {

BACKGROUND: Stringent infection control requirements at Ebola treatment centers (ETCs), which are specialized facilities for isolating and treating Ebola patients, create substantial challenges for recording and reviewing patient information. During the 2014-2016 West African Ebola epidemic, paper-based data collection systems at ETCs compromised the quality, quantity, and confidentiality of patient data. Electronic health record (EHR) systems have the potential to address such problems, with benefits for patient care, surveillance, and research. However, no suitable software was available for deployment when large-scale ETCs opened as the epidemic escalated in 2014.

OBJECTIVE: We present our work on rapidly developing and deploying OpenMRS-Ebola, an EHR system for the Kerry Town ETC in Sierra Leone. We describe our experience, lessons learned, and recommendations for future health emergencies.

METHODS: We used the OpenMRS platform and Agile software development approaches to build OpenMRS-Ebola. Key features of our work included daily communications between the development team and ground-based operations team, iterative processes, and phased development and implementation. We made design decisions based on the restrictions of the ETC environment and regular user feedback. To evaluate the system, we conducted predeployment user questionnaires and compared the EHR records with duplicate paper records.

RESULTS: We successfully built OpenMRS-Ebola, a modular stand-alone EHR system with a tablet-based application for infectious patient wards and a desktop-based application for noninfectious areas. OpenMRS-Ebola supports patient tracking (registration, bed allocation, and discharge); recording of vital signs and symptoms; medication and intravenous fluid ordering and monitoring; laboratory results; clinician notes; and data export. It displays relevant patient information to clinicians in infectious and noninfectious zones. We implemented phase 1 (patient tracking; drug ordering and monitoring) after 2.5 months of full-time development. OpenMRS-Ebola was used for 112 patient registrations, 569 prescription orders, and 971 medication administration recordings. We were unable to fully implement phases 2 and 3 as the ETC closed because of a decrease in new Ebola cases. The phase 1 evaluation suggested that OpenMRS-Ebola worked well in the context of the rollout, and the user feedback was positive.

CONCLUSIONS: To our knowledge, OpenMRS-Ebola is the most comprehensive adaptable clinical EHR built for a low-resource setting health emergency. It is designed to address the main challenges of data collection in highly infectious environments that require robust infection prevention and control measures and it is interoperable with other electronic health systems. Although we built and deployed OpenMRS-Ebola more rapidly than typical software, our work highlights the challenges of having to develop an appropriate system during an emergency rather than being able to rapidly adapt an existing one. Lessons learned from this and previous emergencies should be used to ensure that a set of well-designed, easy-to-use, pretested health software is ready for quick deployment in future.

}, keywords = {electronic health records, Epidemics, Hemorrhagic Fever, Ebola, Humans, Infection Control, Sierra Leone, Telemedicine}, issn = {1438-8871}, doi = {10.2196/jmir.7881}, author = {Oza, Shefali and Jazayeri, Darius and Teich, Jonathan M and Ball, Ellen and Nankubuge, Patricia Alexandra and Rwebembera, Job and Wing, Kevin and Sesay, Alieu Amara and Kanter, Andrew S and Ramos, Glauber D and Walton, David and Cummings, Rachael and Checchi, Francesco and Fraser, Hamish S} } @article {1175, title = {Easy {Handling} of {Sensors} and {Actuators} over {TCP}/{IP} {Networks} by {Open} {Source} {Hardware}/{Software}}, journal = {Sensors (Basel, Switzerland)}, volume = {17}, year = {2017}, abstract = {There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)-this one designed using the intuitive graphical system of EJS-located on the user{\textquoteright}s computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented.}, keywords = {Arduino, collaborative access, data acquisition, EJS, HMI, Internet-of-Things, Modbus, open source hardware/software, remote access}, issn = {1424-8220}, doi = {10.3390/s17010094}, author = {Mej{\'\i}as, Andr{\'e}s and Herrera, Reyes S. and M{\'a}rquez, Marco A. and Calder{\'o}n, Antonio Jos{\'e} and Gonz{\'a}lez, Isa{\'\i}as and And{\'u}jar, Jos{\'e} Manuel} } @article {1231, title = {Home Behavior Monitoring Module in OpenEMR: Use of home sensors as Patient-Generated Data (PGD) for elderly care.}, journal = {AMIA Annu Symp Proc}, volume = {2017}, year = {2017}, month = {2017}, pages = {2279-2283}, issn = {1942-597X}, author = {Casanova-Perez, Regina A and Padilla-Huamantinco, Pierre G and De Freitas-Vidal, Catharine I and Choi, Yong K} } @article {1273, title = {Leveraging the Value of Human Relationships to Improve Health Outcomes. Lessons learned from the OpenMRS Electronic Health Record System.}, journal = {Appl Clin Inform}, volume = {8}, year = {2017}, month = {2017 Feb 01}, pages = {108-121}, abstract = {

OBJECTIVES: Despite significant awareness on the value of leveraging patient relationships across the healthcare continuum, there is no research on the potential of using Electronic Health Record (EHR) systems to store structured patient relationship data, or its impact on enabling better healthcare. We sought to identify which EHR systems supported effective patient relationship data collection, and for systems that do, what types of relationship data is collected, how this data is used, and the perceived value of doing so.

MATERIALS AND METHODS: We performed a literature search to identify EHR systems that supported patient relationship data collection. Based on our results, we defined attributes of an effective patient relationship model. The Open Medical Record System (OpenMRS), an open source medical record platform for underserved settings met our eligibility criteria for effective patient relationship collection. We performed a survey to understand how the OpenMRS patient relationship model was used, and how it brought value to implementers.

RESULTS: The OpenMRS patient relationship model has won widespread adoption across many implementations and is perceived to be valuable in enabling better health care delivery. Patient relationship information is widely used for community health programs and enabling chronic care. Additionally, many OpenMRS implementers were using this feature to collect custom relationship types for implementation specific needs.

CONCLUSIONS: We believe that flexible patient relationship data collection is critical for better healthcare, and can inform community care and chronic care initiatives across the world. Additionally, patient relationship data could also be leveraged for many other initiatives such as patient centric care and in the field of precision medicine.

}, keywords = {Data Collection, Delivery of Health Care, electronic health records, Humans, Interpersonal Relations}, issn = {1869-0327}, doi = {10.4338/ACI-2016-08-RA-0139}, author = {Kasthurirathne, Suranga N and Mamlin, Burke W and Cullen, Theresa} } @article {1285, title = {Long-Term Outcomes of Aflibercept Treatment for Neovascular Age-Related Macular Degeneration in a Clinical Setting.}, journal = {Am J Ophthalmol}, volume = {174}, year = {2017}, month = {2017 Feb}, pages = {160-168}, abstract = {

PURPOSE: To report 2-year treatment outcomes with intravitreal aflibercept for neovascular age-related macular degeneration (nAMD) in routine clinical practice.

DESIGN: Retrospective, nonrandomized, interventional case series.

METHODS: Retrospective analysis of electronic medical record (EMR) notes (OpenEyes) and paper case notes and review of spectral-domain optical coherence tomography (SDOCT) imaging of patients with consecutively treated eyes with previously untreated nAMD. Patients were commenced on aflibercept injections in 1 or both eyes from October 1, 2013 to December 31, 2013. Data including age, sex, visual acuity (VA) measured on Early Treatment Diabetic Retinopathy Study charts, injection episodes, and complications were recorded. Additionally, SDOCT data, including presence or absence of macular fluid and automated central subfield macular thickness (CSMT) at year 1 and 2, were recorded.

RESULTS: Of the 109 eyes of 102 patients treated, data from 94 eyes of 88 patients were available at 2-year follow-up (86\% of patients). In the analysis of 2-year outcomes, there were 58 women (65.9\%); the mean ({\textpm} standard deviation) age was 77.5 {\textpm} 8 years. Over the 2 years, these eyes received a median of 12 (mean, 11.4 {\textpm} 4) injections at a median of 100 (mean, 99.3 {\textpm} 5.3) weeks of follow-up. The mean VA changed from 55.9 {\textpm} 15 letters at baseline to 61.3 {\textpm} 16.9 letters (VA gain 5.4 letters) at 1 year and to 61 {\textpm} 17.1 letters (VA gain 5.1 {\textpm} 14.9 letters) at 2 years. The reduction in CSMT was 79~μm with absence of macular fluid in 72.7\% of the 88 eyes with SDOCT data available at 2-year follow-up.

CONCLUSIONS: The VA and SDOCT results compare favorably with outcomes seen in randomized controlled trials. The results suggest that good long-term outcomes can be achieved using aflibercept for nAMD in clinical settings.

}, keywords = {Aged, Dose-Response Relationship, Drug, Female, Fluorescein Angiography, Follow-Up Studies, Fundus Oculi, Humans, Intravitreal Injections, Macula Lutea, Macular Degeneration, Male, Receptors, Vascular Endothelial Growth Factor, Recombinant Fusion Proteins, Retinal Neovascularization, Retrospective Studies, Time Factors, Tomography, Optical Coherence, Treatment Outcome, Visual Acuity}, issn = {1879-1891}, doi = {10.1016/j.ajo.2016.09.038}, author = {Eleftheriadou, Maria and Vazquez-Alfageme, Clara and Citu, Cristina Maria and Crosby-Nwaobi, Roxanne and Sivaprasad, Sobha and Hykin, Philip and Hamilton, Robin D and Patel, Praveen J} } @article {1276, title = {A Mobile-Based Community Health Management Information System for Community Health Workers and Their Supervisors in 2 Districts of Zambia.}, journal = {Glob Health Sci Pract}, volume = {5}, year = {2017}, month = {2017 09 27}, pages = {486-494}, abstract = {

INTRODUCTION: Effective community health management information systems (C-HMIS) are important in low-resource countries that rely heavily on community-based health care providers. Zambia currently lacks a functioning C-HMIS to provide real-time, community-based health information from community health workers (CHWs) to health center staff and higher levels of the health system.

PROGRAM DESCRIPTION: We developed a C-HMIS mobile platform for use by CHWs providing integrated community case management (iCCM) services and their supervisors to address challenges of frequent stock-outs and inadequate supportive supervision of iCCM-trained CHWs. The platform used simple feature mobile phones on which were loaded the District Health Information System version 2 (DHIS2) software and Java 2 platform micro edition (J2ME) aggregation and tracker applications. This project was implemented in Chipata and Chadiza districts, which supported previous mHealth programs and had cellular coverage from all 3 major network carriers in Zambia. A total of 40 CHWs and 20 CHW supervisors received mobile phones with data bundles and training in the mobile application, after which they implemented the program over a period of 5.5 months, from February to mid-July 2016. CHWs used the mobile phones to submit data on iCCM cases seen, managed, and referred, as well as iCCM medical and diagnostic supplies received and dispensed. Using their mobile phones, the supervisors tracked CHWs{\textquoteright} reported cases with medicine consumption, sent CHWs feedback on their referrals, and received SMS reminders to set up mentorship sessions.

OBSERVATIONS: CHWs were able to use the mobile application to send weekly reports to health center supervisors on disease caseloads and medical commodities consumed, to make drug and supply requisitions, and to send pre-referral notices to health centers. Health center staff used the mobile system to provide feedback to CHWs on the case outcomes of referred patients and to receive automated monthly SMS reminders to invite CHWs to the facility for mentorship. District- and central-level staff were able to access community-level health data in real time using passwords.

LESSONS LEARNED: C-HMIS, using simple feature phones, was feasible and viable for the provision of real-time community-based health information to all levels of the health care system in Zambia, but smartphones, laptops, or desktop computers are needed to perform data analysis and visualization. Ongoing technical support is needed to address the hardware and software challenges CHWs face in their day-to-day interaction with the application on their mobile phones.

}, keywords = {Community Health Services, Community Health Workers, Delivery of Health Care, Health information systems, Humans, Mobile Applications, Referral and Consultation, Zambia}, issn = {2169-575X}, doi = {10.9745/GHSP-D-16-00275}, author = {Biemba, Godfrey and Chiluba, Boniface and Yeboah-Antwi, Kojo and Silavwe, Vichaels and Lunze, Karsten and Mwale, Rodgers K and Russpatrick, Scott and Hamer, Davidson H} } @article {1300, title = {QuPath: Open source software for digital pathology image analysis.}, journal = {Sci Rep}, volume = {7}, year = {2017}, month = {2017 12 04}, pages = {16878}, abstract = {

QuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath{\textquoteright}s flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research.

}, keywords = {Algorithms, Biomarkers, Tumor, Colonic Neoplasms, Humans, Image Interpretation, Computer-Assisted, Kaplan-Meier Estimate, Programmed Cell Death 1 Ligand 2 Protein, User-Computer Interface}, issn = {2045-2322}, doi = {10.1038/s41598-017-17204-5}, author = {Bankhead, Peter and Loughrey, Maurice B and Fern{\'a}ndez, Jos{\'e} A and Dombrowski, Yvonne and McArt, Darragh G and Dunne, Philip D and McQuaid, Stephen and Gray, Ronan T and Murray, Liam J and Coleman, Helen G and James, Jacqueline A and Salto-Tellez, Manuel and Hamilton, Peter W} } @article {1176, title = {Three-dimensional image reconstruction with free open-source {OsiriX} software in video-assisted thoracoscopic lobectomy and segmentectomy}, journal = {International Journal of Surgery (London, England)}, year = {2017}, abstract = {OBJECTIVE: The aim of this retrospective study was to evaluate the practice and the feasibility of Osirix, a free and open-source medical imaging software, in performing accurate video-assisted thoracoscopic lobectomy and segmentectomy. METHODS: From July 2014 to April 2016, 63 patients received anatomical video-assisted thoracoscopic surgery (VATS), either lobectomy or segmentectomy, in our department. Three-dimensional (3D) reconstruction images of 61 (96.8\%) patients were preoperatively obtained with contrast-enhanced computed tomography (CT). Preoperative resection simulations were accomplished with patient-individual reconstructed 3D images. For lobectomy, pulmonary lobar veins, arteries and bronchi were identified meticulously by carefully reviewing the 3D images on the display. For segmentectomy, the intrasegmental veins in the affected segment for division and the intersegmental veins to be preserved were identified on the 3D images. Patient preoperative characteristics, surgical outcomes and postoperative data were reviewed from a prospective database. RESULTS: The study cohort of 63 patients included 33 (52.4\%) men and 30 (47.6\%) women, of whom 46 (73.0\%) underwent VATS lobectomy and 17 (37.0\%) underwent VATS segmentectomy. There was 1 conversion from VATS lobectomy to open thoracotomy because of fibrocalcified lymph nodes. A VATS lobectomy was performed in 1 case after completing the segmentectomy because invasive adenocarcinoma was detected by intraoperative frozen-section analysis. There were no 30-day or 90-day operative mortalities CONCLUSIONS: The free, simple, and user-friendly software program Osirix can provide a 3D anatomic structure of pulmonary vessels and a clear vision into the space between the lesion and adjacent tissues, which allows surgeons to make preoperative simulations and improve the accuracy and safety of actual surgery.}, keywords = {Lobectomy, Segmentectomy, Three-dimensional reconstruction technique, Video-assisted thoracoscopic surgery}, issn = {1743-9159}, doi = {10.1016/j.ijsu.2017.01.079}, author = {Yao, Fei and Wang, Jian and Yao, Ju and Hang, Fangrong and Lei, Xu and Cao, Yongke} } @inbook {1119, title = {BiobankCloud: A Platform for the Secure Storage, Sharing, and Processing of Large Biomedical Data Sets}, booktitle = {Biomedical Data Management and Graph Online Querying: VLDB 2015 Workshops, Big-O(Q) and DMAH, Waikoloa, HI, USA, August 31 {\textendash} September 4, 2015, Revised Selected Papers}, year = {2016}, pages = {89{\textendash}105}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {Biobanks store and catalog human biological material that is increasingly being digitized using next-generation sequencing (NGS). There is, however, a computational bottleneck, as existing software systems are not scalable and secure enough to store and process the incoming wave of genomic data from NGS machines. In the BiobankCloud project, we are building a Hadoop-based platform for the secure storage, sharing, and parallel processing of genomic data. We extended Hadoop to include support for multi-tenant studies, reduced storage requirements with erasure coding, and added support for extensible and consistent metadata. On top of Hadoop, we built a scalable scientific workflow engine featuring a proper workflow definition language focusing on simple integration and chaining of existing tools, adaptive scheduling on Apache Yarn, and support for iterative dataflows. Our platform also supports the secure sharing of data across different, distributed Hadoop clusters. The software is easily installed and comes with a user-friendly web interface for running, managing, and accessing data sets behind a secure 2-factor authentication. Initial tests have shown that the engine scales well to dozens of nodes. The entire system is open-source and includes pre-defined workflows for popular tasks in biomedical data analysis, such as variant identification, differential transcriptome analysis using RNA-Seq, and analysis of miRNA-Seq and ChIP-Seq data.}, isbn = {978-3-319-41576-5}, doi = {10.1007/978-3-319-41576-5_7}, url = {http://dx.doi.org/10.1007/978-3-319-41576-5_7}, author = {Bessani, Alysson and Brandt, J{\"o}rgen and Bux, Marc and Cogo, Vinicius and Dimitrova, Lora and Dowling, Jim and Gholami, Ali and Hakimzadeh, Kamal and Hummel, Micheal and Ismail, Mahmoud and Laure, Erwin and Leser, Ulf and Litton, Jan-Eric and Martinez, Roxanna and Niazi, Salman and Reichel, Jane and Zimmermann, Karin}, editor = {Wang, Fusheng and Luo, Gang and Weng, Chunhua and Khan, Arijit and Mitra, Prasenjit and Yu, Cong} } @article {1146, title = {A HTML5 open source tool to conduct studies based on Libet{\textquoteright}s clock paradigm.}, journal = {Sci Rep}, volume = {6}, year = {2016}, month = {2016}, pages = {32689}, abstract = {

Libet{\textquoteright}s clock is a well-known procedure in experiments in psychology and neuroscience. Examples of its use include experiments exploring the subjective sense of agency, action-effect binding, and subjective timing of conscious decisions and perceptions. However, the technical details of the apparatus used to conduct these types of experiments are complex, and are rarely explained in sufficient detail as to guarantee an exact replication of the procedure. With this in mind, we developed Labclock Web, a web tool designed to conduct online and offline experiments using Libet{\textquoteright}s clock. After describing its technical features, we explain how to configure specific experiments using this tool. Its degree of accuracy and precision in the presentation of stimuli has been technically validated, including the use of two cognitive experiments conducted with voluntary participants who performed the experiment both in our laboratory and via the Internet. Labclock Web is distributed without charge under a free software license (GPLv3) since one of our main objectives is to facilitate the replication of experiments and hence the advancement of knowledge in this area.

}, issn = {2045-2322}, doi = {10.1038/srep32689}, author = {Garaizar, Pablo and Cubillas, Carmelo P and Matute, Helena} } @article {1133, title = {Integrating Heterogeneous Biomedical Data for Cancer Research: the CARPEM infrastructure.}, journal = {Appl Clin Inform}, volume = {7}, year = {2016}, month = {2016}, pages = {260-74}, abstract = {

Cancer research involves numerous disciplines. The multiplicity of data sources and their heterogeneous nature render the integration and the exploration of the data more and more complex. Translational research platforms are a promising way to assist scientists in these tasks. In this article, we identify a set of scientific and technical principles needed to build a translational research platform compatible with ethical requirements, data protection and data-integration problems. We describe the solution adopted by the CARPEM cancer research program to design and deploy a platform able to integrate retrospective, prospective, and day-to-day care data. We designed a three-layer architecture composed of a data collection layer, a data integration layer and a data access layer. We leverage a set of open-source resources including i2b2 and tranSMART.

}, issn = {1869-0327}, doi = {10.4338/ACI-2015-09-RA-0125}, author = {Rance, Bastien and Canuel, Vincent and Countouris, Hector and Laurent-Puig, Pierre and Burgun, Anita} } @article {1168, title = {Methods for {Specifying} {Scientific} {Data} {Standards} and {Modeling} {Relationships} with {Applications} to {Neuroscience}}, journal = {Frontiers in Neuroinformatics}, volume = {10}, year = {2016}, pages = {48}, abstract = {Neuroscience continues to experience a tremendous growth in data; in terms of the volume and variety of data, the velocity at which data is acquired, and in turn the veracity of data. These challenges are a serious impediment to sharing of data, analyses, and tools within and across labs. Here, we introduce BRAINformat, a novel data standardization framework for the design and management of scientific data formats. The BRAINformat library defines application-independent design concepts and modules that together create a general framework for standardization of scientific data. We describe the formal specification of scientific data standards, which facilitates sharing and verification of data and formats. We introduce the concept of Managed Objects, enabling semantic components of data formats to be specified as self-contained units, supporting modular and reusable design of data format components and file storage. We also introduce the novel concept of Relationship Attributes for modeling and use of semantic relationships between data objects. Based on these concepts we demonstrate the application of our framework to design and implement a standard format for electrophysiology data and show how data standardization and relationship-modeling facilitate data analysis and sharing. The format uses HDF5, enabling portable, scalable, and self-describing data storage and integration with modern high-performance computing for data-driven discovery. The BRAINformat library is open source, easy-to-use, and provides detailed user and developer documentation and is freely available at: https://bitbucket.org/oruebel/brainformat.}, keywords = {data format specification, electrophysiology, neuroscience, relationship modeling}, doi = {10.3389/fninf.2016.00048}, author = {R{\"u}bel, Oliver and Dougherty, Max and Prabhat, null and Denes, Peter and Conant, David and Chang, Edward F. and Bouchard, Kristofer} } @article {1170, title = {Open {Source} {Drug} {Discovery}: {Highly} {Potent} {Antimalarial} {Compounds} {Derived} from the {Tres} {Cantos} {Arylpyrroles}}, journal = {ACS central science}, volume = {2}, year = {2016}, pages = {687{\textendash}701}, abstract = {The development of new antimalarial compounds remains a pivotal part of the strategy for malaria elimination. Recent large-scale phenotypic screens have provided a wealth of potential starting points for hit-to-lead campaigns. One such public set is explored, employing an open source research mechanism in which all data and ideas were shared in real time, anyone was able to participate, and patents were not sought. One chemical subseries was found to exhibit oral activity but contained a labile ester that could not be replaced without loss of activity, and the original hit exhibited remarkable sensitivity to minor structural change. A second subseries displayed high potency, including activity within gametocyte and liver stage assays, but at the cost of low solubility. As an open source research project, unexplored avenues are clearly identified and may be explored further by the community; new findings may be cumulatively added to the present work.}, issn = {2374-7943}, doi = {10.1021/acscentsci.6b00086}, author = {Williamson, Alice E. and Ylioja, Paul M. and Robertson, Murray N. and Antonova-Koch, Yevgeniya and Avery, Vicky and Baell, Jonathan B. and Batchu, Harikrishna and Batra, Sanjay and Burrows, Jeremy N. and Bhattacharyya, Soumya and Calderon, Felix and Charman, Susan A. and Clark, Julie and Crespo, Benigno and Dean, Matin and Debbert, Stefan L. and Delves, Michael and Dennis, Adelaide S. M. and Deroose, Frederik and Duffy, Sandra and Fletcher, Sabine and Giaever, Guri and Hallyburton, Irene and Gamo, Francisco-Javier and Gebbia, Marinella and Guy, R. Kiplin and Hungerford, Zoe and Kirk, Kiaran and Lafuente-Monasterio, Maria J. and Lee, Anna and Meister, Stephan and Nislow, Corey and Overington, John P. and Papadatos, George and Patiny, Luc and Pham, James and Ralph, Stuart A. and Ruecker, Andrea and Ryan, Eileen and Southan, Christopher and Srivastava, Kumkum and Swain, Chris and Tarnowski, Matthew J. and Thomson, Patrick and Turner, Peter and Wallace, Iain M. and Wells, Timothy N. C. and White, Karen and White, Laura and Willis, Paul and Winzeler, Elizabeth A. and Wittlin, Sergio and Todd, Matthew H.} } @article {1121, title = {Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond.}, journal = {PLoS Pathog}, volume = {12}, year = {2016}, month = {2016 Jul}, pages = {e1005763}, abstract = {

A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34\%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal chemistry programs. The data for all of these assays are presented and analyzed to show how outstanding leads for many indications can be selected. These results reveal the immense potential for translating the dispersed expertise in biological assays involving human pathogens into drug discovery starting points, by providing open access to new families of molecules, and emphasize how a small additional investment made to help acquire and distribute compounds, and sharing the data, can catalyze drug discovery for dozens of different indications. Another lesson is that when multiple screens from different groups are run on the same library, results can be integrated quickly to select the most valuable starting points for subsequent medicinal chemistry efforts.

}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1005763}, author = {Van Voorhis, Wesley C and Adams, John H and Adelfio, Roberto and Ahyong, Vida and Akabas, Myles H and Alano, Pietro and Alday, Aintzane and Alem{\'a}n Resto, Yesmalie and Alsibaee, Aishah and Alzualde, Ainhoa and Andrews, Katherine T and Avery, Simon V and Avery, Vicky M and Ayong, Lawrence and Baker, Mark and Baker, Stephen and Ben Mamoun, Choukri and Bhatia, Sangeeta and Bickle, Quentin and Bounaadja, Lotfi and Bowling, Tana and Bosch, J{\"u}rgen and Boucher, Lauren E and Boyom, Fabrice F and Brea, Jose and Brennan, Marian and Burton, Audrey and Caffrey, Conor R and Camarda, Grazia and Carrasquilla, Manuela and Carter, Dee and Belen Cassera, Maria and Chih-Chien Cheng, Ken and Chindaudomsate, Worathad and Chubb, Anthony and Colon, Beatrice L and Col{\'o}n-L{\'o}pez, Daisy D and Corbett, Yolanda and Crowther, Gregory J and Cowan, Noemi and D{\textquoteright}Alessandro, Sarah and Le Dang, Na and Delves, Michael and DeRisi, Joseph L and Du, Alan Y and Duffy, Sandra and Abd El-Salam El-Sayed, Shimaa and Ferdig, Michael T and Fern{\'a}ndez Robledo, Jos{\'e} A and Fidock, David A and Florent, Isabelle and Fokou, Patrick V T and Galstian, Ani and Gamo, Francisco Javier and Gokool, Suzanne and Gold, Ben and Golub, Todd and Goldgof, Gregory M and Guha, Rajarshi and Guiguemde, W Armand and Gural, Nil and Guy, R Kiplin and Hansen, Michael A E and Hanson, Kirsten K and Hemphill, Andrew and Hooft van Huijsduijnen, Rob and Horii, Takaaki and Horrocks, Paul and Hughes, Tyler B and Huston, Christopher and Igarashi, Ikuo and Ingram-Sieber, Katrin and Itoe, Maurice A and Jadhav, Ajit and Naranuntarat Jensen, Amornrat and Jensen, Laran T and Jiang, Rays H Y and Kaiser, Annette and Keiser, Jennifer and Ketas, Thomas and Kicka, Sebastien and Kim, Sunyoung and Kirk, Kiaran and Kumar, Vidya P and Kyle, Dennis E and Lafuente, Maria Jose and Landfear, Scott and Lee, Nathan and Lee, Sukjun and Lehane, Adele M and Li, Fengwu and Little, David and Liu, Liqiong and Llin{\'a}s, Manuel and Loza, Maria I and Lubar, Aristea and Lucantoni, Leonardo and Lucet, Isabelle and Maes, Louis and Mancama, Dalu and Mansour, Nuha R and March, Sandra and McGowan, Sheena and Medina Vera, Iset and Meister, Stephan and Mercer, Luke and Mestres, Jordi and Mfopa, Alvine N and Misra, Raj N and Moon, Seunghyun and Moore, John P and Morais Rodrigues da Costa, Francielly and M{\"u}ller, Joachim and Muriana, Arantza and Nakazawa Hewitt, Stephen and Nare, Bakela and Nathan, Carl and Narraidoo, Nathalie and Nawaratna, Sujeevi and Ojo, Kayode K and Ortiz, Diana and Panic, Gordana and Papadatos, George and Parapini, Silvia and Patra, Kailash and Pham, Ngoc and Prats, Sarah and Plouffe, David M and Poulsen, Sally-Ann and Pradhan, Anupam and Quevedo, Celia and Quinn, Ronald J and Rice, Christopher A and Abdo Rizk, Mohamed and Ruecker, Andrea and St Onge, Robert and Salgado Ferreira, Rafaela and Samra, Jasmeet and Robinett, Natalie G and Schlecht, Ulrich and Schmitt, Marjorie and Silva Villela, Filipe and Silvestrini, Francesco and Sinden, Robert and Smith, Dennis A and Soldati, Thierry and Spitzm{\"u}ller, Andreas and Stamm, Serge Maximilian and Sullivan, David J and Sullivan, William and Suresh, Sundari and Suzuki, Brian M and Suzuki, Yo and Swamidass, S Joshua and Taramelli, Donatella and Tchokouaha, Lauve R Y and Theron, Anjo and Thomas, David and Tonissen, Kathryn F and Townson, Simon and Tripathi, Abhai K and Trofimov, Valentin and Udenze, Kenneth O and Ullah, Imran and Vallieres, Cindy and Vigil, Edgar and Vinetz, Joseph M and Voong Vinh, Phat and Vu, Hoan and Watanabe, Nao-Aki and Weatherby, Kate and White, Pamela M and Wilks, Andrew F and Winzeler, Elizabeth A and Wojcik, Edward and Wree, Melanie and Wu, Wesley and Yokoyama, Naoaki and Zollo, Paul H A and Abla, Nada and Blasco, Benjamin and Burrows, Jeremy and Laleu, Beno{\^\i}t and Leroy, Didier and Spangenberg, Thomas and Wells, Timothy and Willis, Paul A} } @article {1148, title = {Open-source, small-animal magnetic resonance-guided focused ultrasound system.}, journal = {J Ther Ultrasound}, volume = {4}, year = {2016}, month = {2016}, pages = {22}, abstract = {

BACKGROUND: MR-guided focused ultrasound or high-intensity focused ultrasound (MRgFUS/MRgHIFU) is a non-invasive therapeutic modality with many potential applications in areas such as cancer therapy, drug delivery, and blood-brain barrier opening. However, the large financial costs involved in developing preclinical MRgFUS systems represent a barrier to research groups interested in developing new techniques and applications. We aim to mitigate these challenges by detailing a validated, open-source preclinical MRgFUS system capable of delivering thermal and mechanical FUS in a quantifiable and repeatable manner under real-time MRI guidance.

METHODS: A hardware and software package was developed that includes closed-loop feedback controlled thermometry code and CAD drawings for a therapy table designed for a preclinical MRI scanner. For thermal treatments, the modular software uses a proportional integral derivative controller to maintain a precise focal temperature rise in the target given input from MR phase images obtained concurrently. The software computes the required voltage output and transmits it to a FUS transducer that is embedded in the delivery table within the magnet bore. The delivery table holds the FUS transducer, a small animal and its monitoring equipment, and a transmit/receive RF coil. The transducer is coupled to the animal via a water bath and is translatable in two dimensions from outside the magnet. The transducer is driven by a waveform generator and amplifier controlled by real-time software in Matlab. MR acoustic radiation force imaging is also implemented to confirm the position of the focus for mechanical and thermal treatments.

RESULTS: The system was validated in tissue-mimicking phantoms and in vivo during murine tumor hyperthermia treatments. Sonications were successfully controlled over a range of temperatures and thermal doses for up to 20 min with minimal temperature overshoot. MR thermometry was validated with an optical temperature probe, and focus visualization was achieved with acoustic radiation force imaging.

CONCLUSIONS: We developed an MRgFUS platform for small-animal treatments that robustly delivers accurate, precise, and controllable sonications over extended time periods. This system is an open source and could increase the availability of low-cost small-animal systems to interdisciplinary researchers seeking to develop new MRgFUS applications and technology.

}, issn = {2050-5736}, doi = {10.1186/s40349-016-0066-7}, author = {Poorman, Megan E and Chaplin, Vandiver L and Wilkens, Ken and Dockery, Mary D and Giorgio, Todd D and Grissom, William A and Caskey, Charles F} } @article {1164, title = {Process control charts in infection prevention: {Make} it simple to make it happen}, journal = {American Journal of Infection Control}, year = {2016}, abstract = {BACKGROUND: Quality improvement is central to Infection Prevention and Control (IPC) programs. Challenges may occur when applying quality improvement methodologies like process control charts, often due to the limited exposure of typical IPs. Because of this, our team created an open-source database with a process control chart generator for IPC programs. The objectives of this report are to outline the development of the application and demonstrate application using simulated data. METHODS: We used Research Electronic Data Capture (REDCap Consortium, Vanderbilt University, Nashville, TN), R (R Foundation for Statistical Computing, Vienna, Austria), and R Studio Shiny (R Foundation for Statistical Computing) to create an open source data collection system with automated process control chart generation. We used simulated data to test and visualize both in-control and out-of-control processes for commonly used metrics in IPC programs. RESULTS: The R code for implementing the control charts and Shiny application can be found on our Web site (https://github.com/ul-research-support/spcapp). Screen captures of the workflow and simulated data indicating both common cause and special cause variation are provided. CONCLUSIONS: Process control charts can be easily developed based on individual facility needs using freely available software. Through providing our work free to all interested parties, we hope that others will be able to harness the power and ease of use of the application for improving the quality of care and patient safety in their facilities.}, keywords = {Health care-associated infection, Quality Improvement, Surveillance}, issn = {1527-3296}, doi = {10.1016/j.ajic.2016.09.021}, author = {Wiemken, Timothy L. and Furmanek, Stephen P. and Carrico, Ruth M. and Mattingly, William A. and Persaud, Annuradha K. and Guinn, Brian E. and Kelley, Robert R. and Ramirez, Julio A.} } @article {1161, title = {Reliability of infarct volumetry: {Its} relevance and the improvement by a software-assisted approach}, journal = {Journal of Cerebral Blood Flow and Metabolism: Official Journal of the International Society of Cerebral Blood Flow and Metabolism}, year = {2016}, abstract = {Despite the efficacy of neuroprotective approaches in animal models of stroke, their translation has so far failed from bench to bedside. One reason is presumed to be a low quality of preclinical study design, leading to bias and a low a priori power. In this study, we propose that the key read-out of experimental stroke studies, the volume of the ischemic damage as commonly measured by free-handed planimetry of TTC-stained brain sections, is subject to an unrecognized low inter-rater and test-retest reliability with strong implications for statistical power and bias. As an alternative approach, we suggest a simple, open-source, software-assisted method, taking advantage of automatic-thresholding techniques. The validity and the improvement of reliability by an automated method to tMCAO infarct volumetry are demonstrated. In addition, we show the probable consequences of increased reliability for precision, p-values, effect inflation, and power calculation, exemplified by a systematic analysis of experimental stroke studies published in the year 2015. Our study reveals an underappreciated quality problem in translational stroke research and suggests that software-assisted infarct volumetry might help to improve reproducibility and therefore the robustness of bench to bedside translation.}, keywords = {experimental stroke, Image analysis, middle cerebral artery occlusion, Neuroprotection, power}, issn = {1559-7016}, doi = {10.1177/0271678X16681311}, author = {Friedl{\"a}nder, Felix and Bohmann, Ferdinand and Brunkhorst, Max and Chae, Ju-Hee and Devraj, Kavi and K{\"o}hler, Yvette and Kraft, Peter and Kuhn, Hannah and Lucaciu, Alexandra and Luger, Sebastian and Pfeilschifter, Waltraud and Sadler, Rebecca and Liesz, Arthur and Scholtyschik, Karolina and Stolz, Leonie and Vutukuri, Rajkumar and Brunkhorst, Robert} } @article {1159, title = {{SIproc}: an open-source biomedical data processing platform for large hyperspectral images}, journal = {The Analyst}, year = {2016}, abstract = {There has recently been significant interest within the vibrational spectroscopy community to apply quantitative spectroscopic imaging techniques to histology and clinical diagnosis. However, many of the proposed methods require collecting spectroscopic images that have a similar region size and resolution to the corresponding histological images. Since spectroscopic images contain significantly more spectral samples than traditional histology, the resulting data sets can approach hundreds of gigabytes to terabytes in size. This makes them difficult to store and process, and the tools available to researchers for handling large spectroscopic data sets are limited. Fundamental mathematical tools, such as MATLAB, Octave, and SciPy, are extremely powerful but require that the data be stored in fast memory. This memory limitation becomes impractical for even modestly sized histological images, which can be hundreds of gigabytes in size. In this paper, we propose an open-source toolkit designed to perform out-of-core processing of hyperspectral images. By taking advantage of graphical processing unit (GPU) computing combined with adaptive data streaming, our software alleviates common workstation memory limitations while achieving better performance than existing applications.}, issn = {1364-5528}, doi = {10.1039/c6an02082h}, author = {Berisha, Sebastian and Chang, Shengyuan and Saki, Sam and Daeinejad, Davar and He, Ziqi and Mankar, Rupali and Mayerich, David} } @article {1165, title = {A systematic literature review of open source software quality assessment models}, journal = {SpringerPlus}, volume = {5}, year = {2016}, pages = {1936}, abstract = {BACKGROUND: Many open source software (OSS) quality assessment models are proposed and available in the literature. However, there is little or no adoption of these models in practice. In order to guide the formulation of newer models so they can be acceptable by practitioners, there is need for clear discrimination of the existing models based on their specific properties. Based on this, the aim of this study is to perform a systematic literature review to investigate the properties of the existing OSS quality assessment models by classifying them with respect to their quality characteristics, the methodology they use for assessment, and their domain of application so as to guide the formulation and development of newer models. Searches in IEEE Xplore, ACM, Science Direct, Springer and Google Search is performed so as to retrieve all relevant primary studies in this regard. Journal and conference papers between the year 2003 and 2015 were considered since the first known OSS quality model emerged in 2003. RESULTS: A total of 19 OSS quality assessment model papers were selected. To select these models we have developed assessment criteria to evaluate the quality of the existing studies. Quality assessment models are classified into five categories based on the quality characteristics they possess namely: single-attribute, rounded category, community-only attribute, non-community attribute as well as the non-quality in use models. Our study reflects that software selection based on hierarchical structures is found to be the most popular selection method in the existing OSS quality assessment models. Furthermore, we found that majority (47\%) of the existing models do not specify any domain of application. CONCLUSIONS: In conclusion, our study will be a valuable contribution to the community and helps the quality assessment model developers in formulating newer models and also to the practitioners (software evaluators) in selecting suitable OSS in the midst of alternatives.}, keywords = {Analysis, Community, ISO 25010, open source software, Quality assessment models}, doi = {10.1186/s40064-016-3612-4}, author = {Adewumi, Adewole and Misra, Sanjay and Omoregbe, Nicholas and Crawford, Broderick and Soto, Ricardo} } @article {1032, title = {Anterior loop of the inferior alveolar nerve: Averages and prevalence based on CT scans.}, journal = {J Prosthet Dent}, year = {2015}, month = {2015 Oct 9}, abstract = {

STATEMENT OF PROBLEM: The treatment of edentulous patients by using a complete implant-supported fixed prosthetic with distal extension has been widely studied; success is mainly dependent upon the placement of the distal implants. The location of the inferior alveolar nerve determines implant placement, but the length, prevalence, and symmetry between the left and right side of the anterior loop of the alveolar nerve are unknown.

PURPOSE: The purpose of this clinical study was to measure the anterior loop of the inferior alveolar nerve, which determines the placement of distal implants, in a group of 55 Mexican participants. The study expected to ascertain the average length, prevalence, and symmetry between left and right side and any sex differences. To differentiate the inferior alveolar nerve path, a new technique was applied using Hounsfield unit (HU) thresholds. The null hypothesis was that no significant differences would be found between the left and right sides or between men and women for the anterior loop of the inferior alveolar nerve.

MATERIAL AND METHODS: Fifty-five computed tomography (CT) scans were made (Somatom Sensation 16; Siemens Healthcare) and were visualized with InVesalius software. Anterior loop measurements were made on 3-dimensional surfaces. To determine statistical differences between the left and right side and between the sexes, the t test was used. The interclass correlation coefficient test was also applied to verify the reliability of the measurements.

RESULTS: Ninety percent of participants showed the anterior loop of the inferior alveolar nerve. The length of the anterior loop ranged between 0 and 6.68 mm, with a mean of 2.19 mm. No significant differences were found between the left and right sides or between men and women.

CONCLUSIONS: The mean length for the anterior loop in the sample was 2.19 mm. As the anterior loop length shows a high degree of variability, these findings suggest that a CT scan for each patient is recommended in order to visualize a safety zone before placing implants close to the mental foramen.

}, issn = {1097-6841}, doi = {10.1016/j.prosdent.2015.06.025}, author = {Juan, Del Valle Lovato and Grageda, Edgar and Crespo, Salvador G{\'o}mez} } @article {981, title = {Going open source: some lessons learned from the development of OpenRecLink.}, journal = {Cad Saude Publica}, volume = {31}, year = {2015}, month = {2015 Feb}, pages = {257-63}, abstract = {

Record linkage is the process of identifying and merging records across different databases belonging to the same entity. The health sector is one of the pioneering areas of record linkage techniques applications. In 1998 we began the development of a software package, called RecLink that implemented probabilistic record linkage techniques. In this article we report the development of a new, open-source version of that program, now named OpenRecLink. The aim of this article is to present the main characteristics of the new version and some of the lessons learned during its development. The new version is a total rewrite of the program, based on three goals: (1) to migrate to a free and open source software (FOSS) platform; (2) to implement a multiplatform version; (3) to implement the support for internationalization. We describe the tools that we adopted, the process of development and some of the problems encountered.

}, keywords = {Databases, Factual, Medical Record Linkage, Software, Software Design}, issn = {1678-4464}, author = {Camargo Jr, Kenneth Rochel de and Coeli, Claudia Medina} } @article {1279, title = {Identifying patients with asthma in primary care electronic medical record systems Chart analysis-based electronic algorithm validation study.}, journal = {Can Fam Physician}, volume = {61}, year = {2015}, month = {2015 Oct}, pages = {e474-83}, abstract = {

OBJECTIVE: To develop and test a variety of electronic medical record (EMR) search algorithms to allow clinicians to accurately identify their patients with asthma in order to enable improved care.

DESIGN: A retrospective chart analysis identified 5 relevant unique EMR information fields (electronic disease registry, cumulative patient profile, billing diagnostic code, medications, and chart notes); asthma-related search terms were designated for each field. The accuracy of each term was tested for its ability to identify the asthma patients among all patients whose charts were reviewed. Increasingly sophisticated search algorithms were then designed and evaluated by serially combining individual searches with Boolean operators.

SETTING: Two large academic primary care clinics in Hamilton, Ont.

PARTICIPANTS: Charts for 600 randomly selected patients aged 16 years and older identified in an initial EMR search as likely having asthma (n = 150), chronic obstructive pulmonary disease (n = 150), other respiratory conditions (n = 150), or nonrespiratory conditions (n = 150) were reviewed until 100 patients per category were identified (or until all available names were exhausted). A total of 398 charts were reviewed in full and included.

MAIN OUTCOME MEASURES: Sensitivity and specificity of each search for asthma diagnosis (against the reference standard of a physician chart review-based diagnosis).

RESULTS: Two physicians reviewed the charts identified in the initial EMR search using a standardized data collection form and ascribed the following diagnoses in 398 patients: 112 (28.1\%) had asthma, 81 (20.4\%) had chronic obstructive pulmonary disease, 104 (26.1\%) had other respiratory conditions, and 101 (25.4\%) had nonrespiratory conditions. Concordance between reviewers in chart abstraction diagnosis was high (κ = 0.89, 95\% CI 0.80 to 0.97). Overall, the algorithm searching for patients who had asthma in their cumulative patient profiles or for whom an asthma billing code had been used was the most accurate (sensitivity of 90.2\%, 95\% CI 87.3\% to 93.1\%; specificity of 83.9\%, 95\% CI 80.3\% to 87.5\%).

CONCLUSION: Usable, practical search algorithms that accurately identify patients with asthma in existing EMRs are presented. Clinicians can apply 1 of these algorithms to generate asthma registries for targeted quality improvement initiatives and outcome measurements. This methodology can be emulated for other diseases.

}, keywords = {Adult, Aged, Algorithms, Asthma, Data Accuracy, electronic health records, Female, Humans, Male, Middle Aged, Ontario, Primary Health Care, Pulmonary Disease, Chronic Obstructive, Registries, Retrospective Studies, Sensitivity and Specificity}, issn = {1715-5258}, author = {Xi, Nancy and Wallace, Rebecca and Agarwal, Gina and Chan, David and Gershon, Andrea and Gupta, Samir} } @article {977, title = {Implementation, reliability, and feasibility test of an Open-Source PACS.}, journal = {Radiol Med}, year = {2015}, month = {2015 Jun 19}, abstract = {

PURPOSE: To implement a hardware and software system able to perform the major functions of an Open-Source PACS, and to analyze it in a simulated real-world environment.

MATERIALS AND METHODS: A small home network was implemented, and the Open-Source operating system Ubuntu 11.10 was installed in a laptop containing the Dcm4chee suite with the software devices needed.

RESULTS: The Open-Source PACS implemented is compatible with Linux OS, Microsoft OS, and Mac OS X; furthermore, it was used with operating systems that guarantee the operation in portable devices (smartphone, tablet) Android and iOS.

CONCLUSIONS: An OSS PACS is useful for making tutorials and workshops on post-processing techniques for educational and training purposes.

}, issn = {1826-6983}, doi = {10.1007/s11547-015-0560-y}, author = {Valeri, Gianluca and Zuccaccia, Matteo and Badaloni, Andrea and Ciriaci, Damiano and La Riccia, Luigi and Mazzoni, Giovanni and Maggi, Stefania and Giovagnoni, Andrea} } @article {993, title = {Open Source Software For Patient Data Management In Critical Care.}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {920}, abstract = {

We have previously developed a Patient Data Management System for Intensive Care based on Open Source Software. The aim of this work was to adapt this software to use in Emergency Departments in low resource environments. The new software includes facilities for utilization of the South African Triage Scale and prediction of mortality based on independent predictive factors derived from data from the Tabarre Emergency Trauma Center in Port au Prince, Haiti.

}, issn = {0926-9630}, author = {Massaut, Jacques and Charretk, Nicolas and Gayraud, Olivia and Van Den Bergh, Rafael and Charles, Adelin and Edema, Nathalie} } @article {1058, title = {OpenNCP: a novel framework to foster cross-border e-Health services.}, journal = {Stud Health Technol Inform}, volume = {210}, year = {2015}, month = {2015}, pages = {617-21}, abstract = {

The continuity of cross-border health care in the European Union depends on the ability to set up shared practices with respect to patient data exchange across Member States. This flow of data must comply with demanding security, legal and interoperability requirements, as defined by the epSOS project specifications. In this paper, we describe the OpenNCP framework that offers a comprehensive set of interoperability services to enable national and regional e-Health platforms to set up cross-border health information networks compliant with epSOS, with minimal adaptation of the existing infrastructure. The OpenNCP, available as open source software, has been adopted in 10 Member States, allowing them to securely interconnect their eHealth infrastructures.

}, issn = {0926-9630}, author = {Fonseca, Marcelo and Karkaletsis, Kostas and Cruz, Isabel A and Berler, Alexander and Oliveira, Il{\'\i}dio C} } @article {1098, title = {Open-source health information technology: A case study of electronic medical records}, journal = {Health Policy and Technology}, volume = {4}, year = {2015}, pages = {14{\textendash}28}, author = {Safadi, Hani and Chan, David and Dawes, Martin and Roper, Mark and Faraj, Samer} } @article {982, title = {Patient Access to Their Health Record Using Open Source EHR.}, journal = {Stud Health Technol Inform}, volume = {208}, year = {2015}, month = {2015}, pages = {104-8}, abstract = {

In both Europe and North America, patients are beginning to gain access to their health records in electronic form. Using the open source cityEHR as an example, we have focussed on the needs of clinical users to gather requirements for patient access and have implemented these requirements in a new application called cityEHR-PA. The development of a separate application for patient access was necessary to address requirements for security and ease of use. The use of open standards throughout the design of the EHR allows the possibility of third parties to develop applications for patient access, consuming the individual patient record extracted from the full EHR.

}, issn = {0926-9630}, author = {Chelsom, John and Dogar, Naveed} } @article {1052, title = {Translational research platforms integrating clinical and omics data: a review of publicly available solutions.}, journal = {Brief Bioinform}, volume = {16}, year = {2015}, month = {2015 Mar}, pages = {280-90}, abstract = {

The rise of personalized medicine and the availability of high-throughput molecular analyses in the context of clinical care have increased the need for adequate tools for translational researchers to manage and explore these data. We reviewed the biomedical literature for translational platforms allowing the management and exploration of clinical and omics data, and identified seven platforms: BRISK, caTRIP, cBio Cancer Portal, G-DOC, iCOD, iDASH and tranSMART. We analyzed these platforms along seven major axes. (1) The community axis regrouped information regarding initiators and funders of the project, as well as availability status and references. (2) We regrouped under the information content axis the nature of the clinical and omics data handled by each system. (3) The privacy management environment axis encompassed functionalities allowing control over data privacy. (4) In the analysis support axis, we detailed the analytical and statistical tools provided by the platforms. We also explored (5) interoperability support and (6) system requirements. The final axis (7) platform support listed the availability of documentation and installation procedures. A large heterogeneity was observed in regard to the capability to manage phenotype information in addition to omics data, their security and interoperability features. The analytical and visualization features strongly depend on the considered platform. Similarly, the availability of the systems is variable. This review aims at providing the reader with the background to choose the platform best suited to their needs. To conclude, we discuss the desiderata for optimal translational research platforms, in terms of privacy, interoperability and technical features.

}, issn = {1477-4054}, doi = {10.1093/bib/bbu006}, author = {Canuel, Vincent and Rance, Bastien and Avillach, Paul and Degoulet, Patrice and Burgun, Anita} } @article {980, title = {Virtualization of Open-Source Secure Web Services to Support Data Exchange in a Pediatric Critical Care Research Network.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Mar 21}, abstract = {

OBJECTIVES: To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality.

MATERIAL AND METHODS: Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers.

RESULTS: Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56\% to 1\% and demonstrated that 99\% of the data consistently transferred using the data dictionary and 1\% needed human curation.

CONCLUSIONS: Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv009}, author = {Frey, Lewis J and Sward, Katherine A and Newth, Christopher Jl and Khemani, Robinder G and Cryer, Martin E and Thelen, Julie L and Enriquez, Rene and Shaoyu, Su and Pollack, Murray M and Harrison, Rick E and Meert, Kathleen L and Berg, Robert A and Wessel, David L and Shanley, Thomas P and Dalton, Heidi and Carcillo, Joseph and Jenkins, Tammara L and Dean, J Michael} } @article {1000, title = {Why open source?}, journal = {Cad Saude Publica}, volume = {31}, year = {2015}, month = {2015 Feb}, pages = {221-2}, keywords = {Access to Information, Periodicals as Topic, Reproducibility of Results, Software, Software Design}, issn = {1678-4464}, author = {Carvalho, Marilia S{\'a}} } @article {1025, title = {Experience of using an open source clinical trials data management software system in Kenya.}, journal = {BMC Res Notes}, volume = {7}, year = {2014}, month = {2014}, pages = {845}, abstract = {

BACKGROUND: Clinical trials data management (CTDM) remains one of the many challenges in running state of the art trials in resource-poor settings since most trials do not allocate, or have available, sufficient resources for CTDM and because of poor internet connectivity. Open-source software like OpenClinica could be a solution in such scenarios.

FINDINGS: In 2007, the KEMRI-Wellcome Trust Research Programme (KWTRP) adopted OpenClinica (OC) community edition, an open-source software system and we share our experience and lessons learnt since its adoption. We have used OC in three different modes; direct remote data entry from sites through Global System for Mobile Communications (GSM) modems, a centralized data centre approach where all data from paper records were entered at a central location and an off-line approach where data entry was done from a copy of database hosted on a field-site server laptop, then data uploaded to a centralized server later. We have used OC in eleven trials/studies with a cumulative number of participants in excess of 6000. These include large and complex trials, with multiple sites recruiting in different regions of East Africa. In the process, we have developed substantial local capacity through hands-on training and mentorship, which we have now begun to share with other institutions in the region.

CONCLUSIONS: Our experience demonstrates that an open source data management system to manage trials{\textquoteright} data can be utilized to international industry standards in resource-poor countries.

}, issn = {1756-0500}, doi = {10.1186/1756-0500-7-845}, author = {Ngari, Moses M and Waithira, Naomi and Chilengi, Roma and Njuguna, Patricia and Lang, Trudie and Fegan, Greg} } @article {1023, title = {A framework for integration of heterogeneous medical imaging networks.}, journal = {Open Med Inform J}, volume = {8}, year = {2014}, month = {2014}, pages = {20-32}, abstract = {

Medical imaging is increasing its importance in matters of medical diagnosis and in treatment support. Much is due to computers that have revolutionized medical imaging not only in acquisition process but also in the way it is visualized, stored, exchanged and managed. Picture Archiving and Communication Systems (PACS) is an example of how medical imaging takes advantage of computers. To solve problems of interoperability of PACS and medical imaging equipment, the Digital Imaging and Communications in Medicine (DICOM) standard was defined and widely implemented in current solutions. More recently, the need to exchange medical data between distinct institutions resulted in Integrating the Healthcare Enterprise (IHE) initiative that contains a content profile especially conceived for medical imaging exchange: Cross Enterprise Document Sharing for imaging (XDS-i). Moreover, due to application requirements, many solutions developed private networks to support their services. For instance, some applications support enhanced query and retrieve over DICOM objects metadata. This paper proposes anintegration framework to medical imaging networks that provides protocols interoperability and data federation services. It is an extensible plugin system that supports standard approaches (DICOM and XDS-I), but is also capable of supporting private protocols. The framework is being used in the Dicoogle Open Source PACS.

}, issn = {1874-4311}, doi = {10.2174/1874431101408010020}, author = {Viana-Ferreira, Carlos and Ribeiro, Lu{\'\i}s S and Costa, Carlos} } @article {931, title = {Managing multicentre clinical trials with open source.}, journal = {Inform Health Soc Care}, volume = {39}, year = {2014}, month = {2014 Mar}, pages = {67-80}, abstract = {

Background: Multicentre clinical trials are challenged by high administrative burden, data management pitfalls and costs. This leads to a reduced enthusiasm and commitment of the physicians involved and thus to a reluctance in conducting multicentre clinical trials. Objective: The purpose of this study was to develop a web-based open source platform to support a multi-centre clinical trial. Methods: We developed on Drupal, an open source software distributed under the terms of the General Public License, a web-based, multi-centre clinical trial management system with the design science research approach. Results: This system was evaluated by user-testing and well supported several completed and on-going clinical trials and is available for free download. Conclusion: Open source clinical trial management systems are capable in supporting multi-centre clinical trials by enhancing efficiency, quality of data management and collaboration.

}, issn = {1753-8165}, doi = {10.3109/17538157.2013.812647}, author = {Raptis, Dimitri Aristotle and Mettler, Tobias and Fischer, Michael Alexander and Patak, Michael and Lesurtel, Mickael and Eshmuminov, Dilmurodjon and de Rougemont, Olivier and Graf, Rolf and Clavien, Pierre-Alain and Breitenstein, Stefan} } @article {1001, title = {tranSMART: An Open Source Knowledge Management and High Content Data Analytics Platform.}, journal = {AMIA Jt Summits Transl Sci Proc}, volume = {2014}, year = {2014}, month = {2014}, pages = {96-101}, abstract = {

The tranSMART knowledge management and high-content analysis platform is a flexible software framework featuring novel research capabilities. It enables analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research. tranSMART bridges the prolific world of basic science and clinical practice data at the point of care by merging multiple types of data from disparate sources into a common environment. The application supports data harmonization and integration with analytical pipelines. The application code was released into the open source community in January 2012, with 32 instances in operation. tranSMART{\textquoteright}s extensible data model and corresponding data integration processes, rapid data analysis features, and open source nature make it an indispensable tool in translational or clinical research.

}, issn = {2153-4063}, author = {Scheufele, Elisabeth and Aronzon, Dina and Coopersmith, Robert and McDuffie, Michael T and Kapoor, Manish and Uhrich, Christopher A and Avitabile, Jean E and Liu, Jinlei and Housman, Dan and Palchuk, Matvey B} } @article {1009, title = {AccessMRS: integrating OpenMRS with smart forms on Android.}, journal = {Stud Health Technol Inform}, volume = {192}, year = {2013}, month = {2013}, pages = {866-70}, abstract = {

We present a new open-source Android application, AccessMRS, for interfacing with an electronic medical record system (OpenMRS) and loading {\textquoteright}Smart Forms{\textquoteright} on a mobile device. AccessMRS functions as a patient-centered interface for viewing OpenMRS data; managing patient information in reminders, task lists, and previous encounters; and launching patient-specific {\textquoteright}Smart Forms{\textquoteright} for electronic data collection and dissemination of health information. We present AccessMRS in the context of related software applications we developed to serve Community Health Workers, including AccessInfo, AccessAdmin, AccessMaps, and AccessForms. The specific features and design of AccessMRS are detailed in relationship to the requirements that drove development: the workflows of the Kenyan Ministry of Health Community Health Volunteers (CHVs) supported by the AMPATH Primary Health Care Program. Specifically, AccessMRS was designed to improve the quality of community-based Maternal and Child Health services delivered by CHVs in Kosirai Division. AccessMRS is currently in use by more than 80 CHVs in Kenya and undergoing formal assessment of acceptability, effectiveness, and cost.

}, keywords = {electronic health records, Forms and Records Control, Information Storage and Retrieval, Medical Record Linkage, Mobile Applications, Programming Languages, Software Design, Systems Integration, User-Computer Interface}, issn = {0926-9630}, author = {Fazen, Louis E and Chemwolo, Benjamin T and Songok, Julia J and Ruhl, Laura J and Kipkoech, Carolyne and Green, James M and Ikemeri, Justus E and Christoffersen-Deb, Astrid} } @article {860, title = {A case study of private{\textendash}public collaboration for humanitarian free and open source disaster management software deployment}, journal = {Decision Support Systems}, volume = {55}, year = {2013}, pages = {1 - 11}, abstract = {Abstract Free and open source software (FOSS) has been increasingly adopted for humanitarian purpose worldwide, yet the factors for successful deployment of humanitarian \{FOSS\} in a disaster situation remain largely unexplored. Drawing upon the Technology{\textendash}Organization{\textendash}Environment (TOE) framework, this study identifies the key issues in collaborative deployment of \{FOSS\} for humanitarian relief operations. The research further elaborates the key research issues by adopting a case study approach in which qualitative data were gathered from key informants from both private and public sectors. The results suggest that task{\textendash}technology fit, expertise management, and inter-organizational relationship management play critical roles in humanitarian \{FOSS\} deployment.}, keywords = {Private{\textendash}public partnership}, issn = {0167-9236}, doi = {http://dx.doi.org/10.1016/j.dss.2012.10.030}, url = {http://www.sciencedirect.com/science/article/pii/S0167923612002850}, author = {Jessica P. Li and Rui Chen and JinKyu Lee and H. Raghav Rao} } @article {856, title = {Clinician-led development of electronic health records systems.}, journal = {Stud Health Technol Inform}, volume = {183}, year = {2013}, month = {2013}, pages = {3-8}, abstract = {

The open source cityEHR system was evaluated as a toolkit for clinician-led development of an Electronic Health Record for management of patients in the Ponseti clinic of a major London hospital. As a toolkit, it was found that the ontology-driven approach of cityEHR was too complex for clinicians to use. The toolkit was refined to use more familiar spreadsheet s to represent the ontology and was then used successfully to create an effective clinical system, generated automatically from the information model.

}, issn = {0926-9630}, author = {Chelsom, John and Ahluwalia, Raju and Dogar, Naveed} } @article {848, title = {A common type system for clinical natural language processing.}, journal = {J Biomed Semantics}, volume = {4}, year = {2013}, month = {2013}, pages = {1}, abstract = {

UNLABELLED:

BACKGROUND: 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.

RESULTS: 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.

CONCLUSIONS: 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.

}, issn = {2041-1480}, doi = {10.1186/2041-1480-4-1}, author = {Wu, Stephen T and Kaggal, Vinod C and Dligach, Dmitriy and Masanz, James J and Chen, Pei and Becker, Lee and Chapman, Wendy W and Savova, Guergana K and Liu, Hongfang and Chute, Christopher G} } @article {890, title = {Comparison of femoral tunnel widening between outside-in and trans-tibial double-bundle ACL reconstruction.}, journal = {Knee Surg Sports Traumatol Arthrosc}, year = {2013}, month = {2013 Jul 13}, abstract = {

PURPOSE: The objectives of this study were to compare (1) the degree of widening by comparing the diameter at the most widened area and the site of widening by measuring the distance from the tunnel entrance to the most widened area in two femoral tunnels (anteromedial and posterolateral), and (2) the morphologic change at the tunnel entrance between outside-in and trans-tibial double-bundle anterior cruciate ligament (ACL) reconstruction.

METHODS: A retrospective study that included 17 trans-tibial and 19 outside-in double-bundle ACL reconstructed patients was conducted for evaluation of serial computed tomography (CT) scan (immediate post-operation and post-operative 1~year). Digital image communication in medicine (DICOM) data was extracted from the PiViewSTAR and imported into OsiriX({\textregistered}), which was installed on a Macbook Pro laptop computer. Diameter of the most widened area and distance from the entrance to this point were measured from each of two perpendicular (sagittal and coronal) planes that were accurately realigned parallel to the tunnel direction. Change in the morphology of the tunnel entrance between immediate post-operation and 1-year post-operation was evaluated.

RESULTS: Widening was observed in both planes of both tunnels in the two techniques. However, no statistical significances in the diameter of most widened area and distance from the tunnel entrance to the most widened point were observed between the both techniques (n.s.). Distances from the centre point to each four sections showed an increase in all four sections of all both tunnels in both techniques. However, no statistical significance was observed between the two techniques (n.s.).

CONCLUSION: Widening was observed in all tunnels using both techniques and degrees, and sites of the widening did not differ between groups. Morphologic change at the tunnel entrance was not limited to the specific direction and occurred in all directions without significant difference between groups.

LEVEL OF EVIDENCE: Retrospective comparative study, Level III.

}, issn = {1433-7347}, doi = {10.1007/s00167-013-2597-6}, author = {Lee, Yong Seuk and Lee, Beom Koo and Oh, Won Seok and Cho, Yong Kyun} } @article {1010, title = {E-health systems for management of MDR-TB in resource-poor environments: a decade of experience and recommendations for future work.}, journal = {Stud Health Technol Inform}, volume = {192}, year = {2013}, month = {2013}, pages = {627-31}, abstract = {

INTRODUCTION: Multi-drug resistant TB (MDR-TB) is a complex infectious disease that is a growing threat to global health. It requires lengthy treatment with multiple drugs and specialized laboratory testing. To effectively scale up treatment to thousands of patients requires good information systems to support clinical care, reporting, drug forecasting, supply chain management and monitoring.

METHODS: Over the last decade we have developed the PIH-EMR electronic medical record system, and subsequently OpenMRS-TB, to support the treatment of MDR-TB in Peru, Haiti, Pakistan, and other resource-poor environments.

RESULTS: We describe here the experience with implementing these systems and evaluating many aspects of their performance, and review other systems for MDR-TB management.

CONCLUSIONS: We recommend a new approach to information systems to address the barriers to scale up MDR-TB treatment, particularly access to the appropriate drugs and lab data. We propose moving away from fragmented, vertical systems to focus on common platforms, addressing all stages of TB care, support for open data standards and interoperability, care for a wide range of diseases including HIV, integration with mHealth applications, and ability to function in resource-poor environments.

}, keywords = {Developing Countries, electronic health records, Electronic Prescribing, Extensively Drug-Resistant Tuberculosis, Haiti, Health Information Management, Humans, Medication Systems, Hospital, Pakistan, Remote Consultation}, issn = {0926-9630}, author = {Fraser, Hamish S F and Habib, Ali and Goodrich, Mark and Thomas, David and Blaya, Joaquin A and Fils-Aime, Joseph Reginald and Jazayeri, Darius and Seaton, Michael and Khan, Aamir J and Choi, Sharon S and Kerrison, Foster and Falzon, Dennis and Becerra, Mercedes C} } @article {1035, title = {A hybrid approach to telepathology in Cambodia.}, journal = {J Telemed Telecare}, volume = {19}, year = {2013}, month = {2013 Dec}, pages = {475-8}, abstract = {

We established a hybrid telepathology network at the Children{\textquoteright}s Surgical Centre (CSC) in Cambodia, based on store-and-forward communication using iPATH and videoconferencing using Skype. We retrospectively analysed all data from the CSC stored on the iPATH server and reviewed the patient notes over an 8-month period. Of 115 patients for histopathology diagnosis during the study period, 38 cases were uploaded onto iPATH for further telemedicine discussion. The median number of days it took a specialist, other than the local one, to comment on the case on iPATH was 5 days (range 0-15). In three cases (8\%) there was no reply from a specialist on iPATH. During the study period, seven clinical conferences were held, with an average of 6 cases (range 4-7) discussed at each conference. All 38 cases discussed had a final agreed diagnosis and firm management plans were made. Of the 24 cases where proactive management was advised, 17 patients followed through with the recommendations. Although the combination of video consultations and store-and-forward communication has not been used much before in the developing world, it has benefited patient care and outcomes at the CSC.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Cambodia, Child, Child, Preschool, Female, Humans, Internet, Male, Middle Aged, Remote Consultation, Retrospective Studies, Surgical Procedures, Operative, telepathology, Videoconferencing, Young Adult}, issn = {1758-1109}, doi = {10.1177/1357633X13512071}, author = {Kadaba, Varsha and Ly, Tho and Noor, Saqib and Chhut, Serey V and Hinsch, Nora and Stauch, Gerhard and Gollogly, James} } @article {892, title = {Integration of advanced 3D SPECT modeling into the open-source STIR framework}, journal = {Medical Physics}, volume = {40}, year = {2013}, pages = {092502}, keywords = {C++ language, image reconstruction, medical image processing, object-oriented programming, public domain software, single photon emission computed tomography, software libraries, software packages}, doi = {10.1118/1.4816676}, url = {http://link.aip.org/link/?MPH/40/092502/1}, author = {Berta Marti Fuster and Carles Falcon and Charalampos Tsoumpas and Lefteris Livieratos and Pablo Aguiar and Albert Cot and Domenec Ros and Kris Thielemans} } @article {858, title = {Open source electronic health records and chronic disease management.}, journal = {J Am Med Inform Assoc}, year = {2013}, month = {2013 Jun 29}, abstract = {

OBJECTIVE: To study and report on the use of open source electronic health records (EHR) to assist with chronic care management within safety net medical settings, such as community health centers (CHC).

METHODS AND MATERIALS: The study was conducted by NORC at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to CHC that currently use an open source EHR.

RESULTS: Two of the sites chosen by NORC were actively using an open source EHR to assist in the redesign of their care delivery system to support more effective chronic disease management. This included incorporating the chronic care model into an CHC and using the EHR to help facilitate its elements, such as care teams for patients, in addition to maintaining health records on indigent populations, such as tuberculosis status on homeless patients.

DISCUSSION: The ability to modify the open-source EHR to adapt to the CHC environment and leverage the ecosystem of providers and users to assist in this process provided significant advantages in chronic care management. Improvements in diabetes management, controlled hypertension and increases in tuberculosis vaccinations were assisted through the use of these open source systems.

CONCLUSIONS: The flexibility and adaptability of open source EHR demonstrated its utility and viability in the provision of necessary and needed chronic disease care among populations served by CHC.

}, issn = {1527-974X}, doi = {10.1136/amiajnl-2013-001672}, author = {Goldwater, Jason C and Kwon, Nancy J and Nathanson, Ashley and Muckle, Alison E and Brown, Alexa and Cornejo, Kerri} } @article {895, title = {Revolutionizing patient control of health information.}, journal = {Can Fam Physician}, volume = {59}, year = {2013}, month = {2013 Aug}, pages = {823-4}, issn = {1715-5258}, author = {Chan, David and Howard, Michelle and Dolovich, Lisa and Bartlett, Gillian and Price, David} } @article {899, title = {SIVIC: Open-source, standards-based software for DICOM MR spectroscopy workflows}, journal = {International Journal of Biomedical Imaging}, volume = {2013}, year = {2013}, abstract = {Quantitative analysis of magnetic resonance spectroscopic imaging (MRSI) data provides maps of metabolic parameters that show promise for improving medical diagnosis and therapeutic monitoring. While anatomical images are routinely reconstructed on the scanner, formatted using the DICOM standard, and interpreted using PACS workstations, this is not the case for MRSI data. The evaluation of MRSI data is made more complex because files are typically encoded with vendor-specific file formats and there is a lack of standardized tools for reconstruction, processing, and visualization. SIVIC is a flexible open-source software framework and application suite that enables a complete scanner-to-PACS workflow for evaluation and interpretation of MRSI data. It supports conversion of vendor-specific formats into the DICOM MR spectroscopy (MRS) standard, provides modular and extensible reconstruction and analysis pipelines, and provides tools to support the unique visualization requirements associated with such data. Workflows are presented which demonstrate the routine use of SIVIC to support the acquisition, analysis, and delivery to PACS of clinical 1H MRSI datasets at UCSF. {\textcopyright} 2013 Jason C. Crane et al.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84881398824\&partnerID=40\&md5=dbbc0d09b4153fd2609d0bb01b37bb30}, author = {Crane, J C and Olson, M P and Nelson, S J} } @article {859, title = {The use of open source electronic health records within the federal safety net.}, journal = {J Am Med Inform Assoc}, year = {2013}, month = {2013 Jun 6}, abstract = {

OBJECTIVE: To conduct a federally funded study that examines the acquisition, implementation and operation of open source electronic health records (EHR) within safety net medical settings, such as federally qualified health centers (FQHC). METHODS AND MATERIALS: The study was conducted by the National Opinion Research Center (NORC) at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to West Virginia, California and Arizona FQHC that were currently using an open source EHR. RESULTS: Five of the six sites that were chosen as part of the study found a number of advantages in the use of their open source EHR system, such as utilizing a large community of users and developers to modify their EHR to fit the needs of their provider and patient communities, and lower acquisition and implementation costs as compared to a commercial system. DISCUSSION: Despite these advantages, many of the informants and site visit participants felt that widespread dissemination and use of open source was restrained due to a negative connotation regarding this type of software. In addition, a number of participants stated that there is a necessary level of technical acumen needed within the FQHC to make an open source EHR effective. CONCLUSIONS: An open source EHR provides advantages for FQHC that have limited resources to acquire and implement an EHR, but additional study is needed to evaluate its overall effectiveness.

}, issn = {1527-974X}, doi = {10.1136/amiajnl-2013-001671}, author = {Goldwater, Jason C and Kwon, Nancy J and Nathanson, Ashley and Muckle, Alison E and Brown, Alexa and Cornejo, Kerri} } @article {896, title = {Utility of an open-source DICOM viewer software (OsiriX) to assess pulmonary fibrosis in systemic sclerosis: preliminary results.}, journal = {Rheumatol Int}, year = {2013}, month = {2013 Aug 15}, abstract = {

To investigate the utility of an open-source Digital Imaging and Communication in Medicine viewer software-OsiriX-to assess pulmonary fibrosis (PF) in patients with systemic sclerosis (SSc). Chest high-resolution computed tomography (HRCT) examinations obtained from 10 patients with diagnosis of SSc were analysed by two radiologists adopting a standard semiquantitative scoring for PF. Pulmonary involvement was evaluated in three sections (superior, middle and inferior). For the assessment of the extension of PF, the adopted semiquantitative HRCT score ranged from 0 to 3 (0~=~absence of PF; 1~=~1-20~\% of lung section involvement; 2~=~21-40~\% of lung section involvement; 3~=~41-100~\% of lung section involvement). Further, a quantitative assessment (i.e. parameters of distribution of lung attenuation such as kurtosis and mean lung attenuation) of PF was independently performed on the same sections by a rheumatologist, independently and blinded to radiologists{\textquoteright} scoring, using OsiriX. The results obtained were compared with those of HRCT semiquantitative analysis. Intra-reader reliability of HRCT findings and feasibility of OsiriX quantitative segmentation was recorded. A significant association between the median values of kurtosis by both the quantitative OsiriX assessment and the HRCT semiquantitative analysis was found (p~<~0.0001). Moreover, kurtosis correlated significantly with the mean lung attenuation (Spearman{\textquoteright}s rho~=~0.885; p~=~0.0001). An excellent intra-reader reliability of HRCT findings among both readers was obtained. A significant difference between the mean time spent on the OsiriX quantitative analysis (mean 1.85~{\textpm}~SD 1.3~min) and the mean time spent by the radiologist for the HRCT semiquantitative assessment (mean 8.5~{\textpm}~SD 4.5~min, p~<~0.00001) was noted. The study provides the new working hypothesis that OsiriX may be a useful and feasible tool to achieve a quantitative evaluation of PF in SSc patients.

}, issn = {1437-160X}, doi = {10.1007/s00296-013-2845-6}, author = {Ariani, Alarico and Carotti, Marina and Gutierrez, Marwin and Bichisecchi, Elisabetta and Grassi, Walter and Giuseppetti, Gian Marco and Salaffi, Fausto} } @article {721, title = {Accuracy and Reliability of Length Measurements on Three-Dimensional Computed Tomography Using Open-Source OsiriX Software.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, year = {2012}, month = {2012 Jan 20}, abstract = {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.}, issn = {1618-727X}, doi = {10.1007/s10278-012-9458-6}, author = {Kim, Gihyeon and Jung, Ho-Joong and Lee, Han-Jun and Lee, Jae-Sung and Koo, Seungbum and Chang, Seung-Hwan} } @article {776, title = {Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: The SHARPn project.}, journal = {J Biomed Inform}, year = {2012}, month = {2012 Feb 4}, abstract = {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{\textquoteright}s health. One of the primary informatics problem areas in this endeavor is the standardization of disparate health data from the nation{\textquoteright}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 {\textquoteright}liquidity{\textquoteright} 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.}, issn = {1532-0480}, doi = {10.1016/j.jbi.2012.01.009}, author = {Rea, Susan and Pathak, Jyotishman and Savova, Guergana and Oniki, Thomas A and Westberg, Les and Beebe, Calvin E and Tao, Cui and Parker, Craig G and Haug, Peter J and Huff, Stanley M and Chute, Christopher G} } @article {816, title = {Developing open source, self-contained disease surveillance software applications for use in resource-limited settings.}, journal = {BMC Med Inform Decis Mak}, volume = {12}, year = {2012}, month = {2012}, pages = {99}, abstract = {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.}, issn = {1472-6947}, doi = {10.1186/1472-6947-12-99}, author = {Campbell, Timothy C and Hodanics, Charles J and Babin, Steven M and Poku, Adjoa M and Wojcik, Richard A and Skora, Joseph F and Coberly, Jacqueline S and Mistry, Zarna S and Lewis, Sheri H} } @inbook {1080, title = {Development of an mHealth Open Source Platform for Diabetic Foot Ulcers Tele-consultations}, booktitle = {Wireless Mobile Communication and Healthcare}, series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering}, volume = {83}, year = {2012}, pages = {158-164}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, keywords = {diabetic foot ulcers, m-health, Telemedicine}, isbn = {978-3-642-29733-5}, doi = {10.1007/978-3-642-29734-2_22}, url = {http://dx.doi.org/10.1007/978-3-642-29734-2_22}, author = {Dafoulas, GeorgeE. and Koutsias, Stylianos and Behar, Joachim and Osorio, Juan and Malley, Brian and Gruentzig, Alexander and Celi, LeoAnthony and Angelidis, Pantelis and Theodorou, Kyriaki and Giannoukas, Athanasios}, editor = {Nikita, KonstantinaS. and Lin, JamesC. and Fotiadis, DimitriosI. and Arredondo Waldmeyer, Maria-Teresa} } @inbook {851, title = {Development of an mHealth Open Source Platform for Diabetic Foot Ulcers Tele-consultations}, booktitle = {Wireless Mobile Communication and Healthcare}, series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering}, volume = {83}, year = {2012}, pages = {158-164}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Diabetes is one of the foremost causes of death in many countries and a leading cause of blindness, renal failure, and non-traumatic amputation. Therefore, diabetic foot ulceration and amputation cause extensive burden on individuals and health care systems in developed and developing countries. Due to the multi-disciplinary requirements for the treatment of diabetic foot ulceration, telemedicine has been introduced to facilitate the access of the patients to specialized health professionals. In this paper the development of an open source mobile health platform is presented, able to support diagnostic algorithms, with the use of a smartphone.}, keywords = {diabetic foot ulcers, m-health, Telemedicine}, isbn = {978-3-642-29733-5}, doi = {10.1007/978-3-642-29734-2_22}, url = {http://dx.doi.org/10.1007/978-3-642-29734-2_22}, author = {Dafoulas, GeorgeE. and Koutsias, Stylianos and Behar, Joachim and Osorio, Juan and Malley, Brian and Gruentzig, Alexander and Celi, LeoAnthony and Angelidis, Pantelis and Theodorou, Kyriaki and Giannoukas, Athanasios}, editor = {Nikita, KonstantinaS. and Lin, JamesC. and Fotiadis, DimitriosI. and Arredondo Waldmeyer, Maria-Teresa} } @article {799, title = {A framework for mapping, visualisation and automatic model creation of signal-transduction networks.}, journal = {Mol Syst Biol}, volume = {8}, year = {2012}, month = {2012}, pages = {578}, abstract = {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.}, issn = {1744-4292}, doi = {10.1038/msb.2012.12}, author = {Tiger, Carl-Fredrik and Krause, Falko and Cedersund, Gunnar and Palm{\'e}r, Robert and Klipp, Edda and Hohmann, Stefan and Kitano, Hiroaki and Krantz, Marcus} } @article {905, title = {Informatics in radiology: An open-source and open-access cancer Biomedical Informatics Grid Annotation and Image Markup Template Builder}, journal = {Radiographics}, volume = {32}, year = {2012}, pages = {1223{\textendash}1232}, abstract = {In a routine clinical environment or clinical trial, a case report form or structured reporting template can be used to quickly generate uniform and consistent reports. Annotation and Image Markup (AIM), a project supported by the National Cancer Institute{\textquoteright}s cancer Biomedical Informatics Grid, can be used to collect information for a case report form or structured reporting template. AIM is designed to store, in a single information source, (a) the description of pixel data with use of markups or graphical drawings placed on the image, (b) calculation results (which may or may not be directly related to the markups), and (c) supplemental information. To facilitate the creation of AIM annotations with data entry templates, an AIM template schema and an open-source template creation application were developed to assist clinicians, image researchers, and designers of clinical trials to quickly create a set of data collection items, thereby ultimately making image information more readily accessible. {\textcopyright} RSNA, 2012.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84863860787\&partnerID=40\&md5=154429b57f255f957ea8a13055866456}, author = {Mongkolwat, P.a and Channin, D.S.b and Kleper, V.a and Rubin, D.L.c} } @conference {838, title = {Interactive Electromechanical Model of the Heart for Patient-Specific Therapy Planning and Training using SOFA}, booktitle = {VPH 2012}, year = {2012}, address = {Londres, United Kingdom}, abstract = {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.}, url = {http://hal.inria.fr/hal-00751537}, author = {Talbot, Hugo and Marchesseau, St{\'e}phanie and Duriez, Christian and Courtecuisse, Hadrien and Relan, Jatin and Sermesant, Maxime and Cotin, St{\'e}phane and Delingette, Herv{\'e}} } @conference {819, title = {Net4Care: Towards a Mission-Critical Software Ecosystem}, booktitle = {Software Architecture (WICSA) and European Conference on Software Architecture (ECSA), 2012 Joint Working IEEE/IFIP Conference on}, year = {2012}, month = {aug.}, abstract = {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.}, doi = {10.1109/WICSA-ECSA.212.34}, author = {Christensen, Henrik Baerbak and Hansen, Klaus Marius} } @article {1055, title = {The NIH National Center for Integrative Biomedical Informatics (NCIBI).}, journal = {J Am Med Inform Assoc}, volume = {19}, year = {2012}, month = {2012 Mar-Apr}, pages = {166-70}, abstract = {

The National Center for Integrative and Biomedical Informatics (NCIBI) is one of the eight NCBCs. NCIBI supports information access and data analysis for biomedical researchers, enabling them to build computational and knowledge models of biological systems to address the Driving Biological Problems (DBPs). The NCIBI DBPs have included prostate cancer progression, organ-specific complications of type 1 and 2 diabetes, bipolar disorder, and metabolic analysis of obesity syndrome. Collaborating with these and other partners, NCIBI has developed a series of software tools for exploratory analysis, concept visualization, and literature searches, as well as core database and web services resources. Many of our training and outreach initiatives have been in collaboration with the Research Centers at Minority Institutions (RCMI), integrating NCIBI and RCMI faculty and students, culminating each year in an annual workshop. Our future directions include focusing on the TranSMART data sharing and analysis initiative.

}, keywords = {Biomedical Research, Databases as Topic, Forecasting, Goals, Information Dissemination, Integrative Medicine, Medical Informatics, National Institutes of Health (U.S.), United States}, issn = {1527-974X}, doi = {10.1136/amiajnl-2011-000552}, author = {Athey, Brian D and Cavalcoli, James D and Jagadish, H V and Omenn, Gilbert S and Mirel, Barbara and Kretzler, Matthias and Burant, Charles and Isokpehi, Raphael D and DeLisi, Charles} } @article {1050, title = {S2DIA: a diagnostic system for Diabetes mellitus using SANA platform.}, journal = {Conf Proc IEEE Eng Med Biol Soc}, volume = {2012}, year = {2012}, month = {2012}, pages = {6078-81}, abstract = {

Currently, Diabetes is a very common disease around the world, and with an increase in sedentary lifestyles, obesity and an aging population the number of people with Diabetes worldwide will increase by more than 50\%. In this context, the MIT (Massachusetts Institute of Technology) developed the SANA platform, which brings the benefits of information technology to the field of healthcare. It offers healthcare delivery in remote areas, improves patient access to medical specialists for faster, higher quality, and more cost effective diagnosis and intervention. For these reasons, we developed a system for diagnosis of Diabetes using the SANA platform, called S2DIA. It is the first step towards knowing the risks for type 2 Diabetes, and it will be evaluated, especially, in remote/poor areas of Brazil.

}, keywords = {Diabetes Mellitus, Type 2, Diagnosis, Computer-Assisted, Humans, Risk Factors}, issn = {1557-170X}, doi = {10.1109/EMBC.2012.6347380}, author = {Costa, Clayton M and Gondim, Dikson D and Gondim, Dibson D and Soares, Heliana B and Ribeiro, Anna G C D and Silva, Ikaro and Winkler, Erick and Celi, Leo and Guerreiro, Ana M G and Leite, Cic{\'\i}lia R M} } @inbook {789, title = {SOFA: A Multi-Model Framework for Interactive Physical Simulation}, booktitle = {Soft Tissue Biomechanical Modeling for Computer Assisted Surgery}, series = {Studies in Mechanobiology, Tissue Engineering and Biomaterials}, volume = {11}, year = {2012}, pages = {283-321}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {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.}, isbn = {978-3-642-29013-8}, doi = {10.1007/8415_2012_125}, url = {http://dx.doi.org/10.1007/8415_2012_125}, author = {Faure, Fran{\c c}ois and Duriez, Christian and Delingette, Herv{\'e} and Allard, J{\'e}r{\'e}mie and Gilles, Benjamin and Marchesseau, St{\'e}phanie and Talbot, Hugo and Courtecuisse, Hadrien and Bousquet, Guillaume and Peterlik, Igor and Cotin, St{\'e}phane}, editor = {Payan, Yohan} } @inbook {786, title = {VURTIGO: Visualization Platform for Real-Time, MRI-Guided Cardiac Electroanatomic Mapping}, booktitle = {Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges}, series = {Lecture Notes in Computer Science}, volume = {7085}, year = {2012}, pages = {244-253}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {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.}, isbn = {978-3-642-28325-3}, url = {http://dx.doi.org/10.1007/978-3-642-28326-0_25}, author = {Radau, Perry and Pintilie, Stefan and Flor, Roey and Biswas, Labonny and Oduneye, Samuel and Ramanan, Venkat and Anderson, Kevan and Wright, Graham}, editor = {Camara, Oscar and Konukoglu, Ender and Pop, Mihaela and Rhode, Kawal and Sermesant, Maxime and Young, Alistair} } @article {868, title = {The caBIG{\textregistered} Life Science Business Architecture Model.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 May 15}, pages = {1429-35}, abstract = {

MOTIVATION: Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG{\textregistered}) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research.

RESULTS: LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model{\textquoteright}s current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases. Availability and Implementation: The LS BAM is freely available as UML, PDF and HTML (https://wiki.nci.nih.gov/x/OFNyAQ).

}, keywords = {Biomedical Research, Computational Biology, Computer Systems, National Cancer Institute (U.S.), Neoplasms, Software, United States, Vocabulary, Controlled}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btr141}, author = {Boyd, Lauren Becnel and Hunicke-Smith, Scott P and Stafford, Grace A and Freund, Elaine T and Ehlman, Michele and Chandran, Uma and Dennis, Robert and Fernandez, Anna T and Goldstein, Stephen and Steffen, David and Tycko, Benjamin and Klemm, Juli D} } @article {1047, title = {[Central online quality assurance in radiology: an IT solution exemplified by the German Breast Cancer Screening Program].}, journal = {Rofo}, volume = {183}, year = {2011}, month = {2011 Sep}, pages = {849-54}, abstract = {

PURPOSE: Physical-technical quality assurance is one of the essential tasks of the National Reference Centers in the German Breast Cancer Screening Program. For this purpose the mammography units are required to transfer the measured values of the constancy tests on a daily basis and all phantom images created for this purpose on a weekly basis to the reference centers. This is a serious logistical challenge. To meet these requirements, we developed an innovative software tool.

MATERIALS AND METHODS: By the end of 2005, we had already developed web-based software (MammoControl) allowing the transmission of constancy test results via entry forms. For automatic analysis and transmission of the phantom images, we then introduced an extension (MammoControl DIANA). This was based on Java, Java Web Start, the NetBeans Rich Client Platform, the Pixelmed Java DICOM Toolkit and the ImageJ library.

RESULTS: MammoControl DIANA was designed to run locally in the mammography units. This allows automated on-site image analysis. Both results and compressed images can then be transmitted to the reference center. We developed analysis modules for the daily and monthly consistency tests and additionally for a homogeneity test.

CONCLUSION: The software we developed facilitates the immediate availability of measurement results, phantom images, and DICOM header data in all reference centers. This allows both targeted guidance and short response time in the case of errors. We achieved a consistent IT-based evaluation with standardized tools for the entire screening program in Germany.

}, keywords = {Data Compression, Female, Germany, Guideline Adherence, Humans, Image Processing, Computer-Assisted, Mammography, Mass Screening, Online Systems, Phantoms, Imaging, Quality Assurance, Health Care, Radiology Information Systems, Reference Standards, Software}, issn = {1438-9010}, doi = {10.1055/s-0031-1281599}, author = {Czwoydzinski, J and Girnus, R and Sommer, A and Heindel, W and Lenzen, H} } @article {869, title = {DDN: a caBIG{\textregistered} analytical tool for differential network analysis.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 Apr 1}, pages = {1036-8}, abstract = {

UNLABELLED: Differential dependency network (DDN) is a caBIG{\textregistered} (cancer Biomedical Informatics Grid) analytical tool for detecting and visualizing statistically significant topological changes in transcriptional networks representing two biological conditions. Developed under caBIG{\textregistered}{\textquoteright}s In Silico Research Centers of Excellence (ISRCE) Program, DDN enables differential network analysis and provides an alternative way for defining network biomarkers predictive of phenotypes. DDN also serves as a useful systems biology tool for users across biomedical research communities to infer how genetic, epigenetic or environment variables may affect biological networks and clinical phenotypes. Besides the standalone Java application, we have also developed a Cytoscape plug-in, CytoDDN, to integrate network analysis and visualization seamlessly.

AVAILABILITY: The Java and MATLAB source code can be downloaded at the authors{\textquoteright} web site http://www.cbil.ece.vt.edu/software.htm.

}, keywords = {Animals, Computational Biology, Epigenesis, Genetic, Female, Gene Regulatory Networks, Mammary Glands, Animal, Rats, Software, Systems Biology}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btr052}, author = {Zhang, Bai and Tian, Ye and Jin, Lu and Li, Huai and Shih, Ie-Ming and Madhavan, Subha and Clarke, Robert and Hoffman, Eric P and Xuan, Jianhua and Hilakivi-Clarke, Leena and Wang, Yue} } @article {660, title = {Dicoogle - an Open Source Peer-to-Peer PACS.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {24}, year = {2011}, month = {2011 Oct}, pages = {848-56}, abstract = {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.}, issn = {1618-727X}, doi = {10.1007/s10278-010-9347-9}, author = {Costa, Carlos and Ferreira, Carlos and Basti{\~a}o, Lu{\'\i}s and Ribeiro, Lu{\'\i}s and Silva, Augusto and Oliveira, Jos{\'e} Lu{\'\i}s} } @article {597, title = {Forward field computation with OpenMEEG.}, journal = {Computational intelligence and neuroscience}, volume = {2011}, year = {2011}, month = {2011}, pages = {923703}, abstract = {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.}, issn = {1687-5273}, author = {Gramfort, Alexandre and Papadopoulo, Th{\'e}odore and Olivi, Emmanuel and Clerc, Maureen} } @inbook {springerlink:10.1007/978-3-642-24418-6_29, title = {Health Informatics: The Relevance of Open Source and Multilevel Modeling}, booktitle = {Open Source Systems: Grounding Research}, series = {IFIP Advances in Information and Communication Technology}, volume = {365}, year = {2011}, note = {10.1007/978-3-642-24418-6_29}, pages = {338-347}, publisher = {Springer Boston}, organization = {Springer Boston}, abstract = {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.}, isbn = {978-3-642-24417-9}, url = {http://dx.doi.org/10.1007/978-3-642-24418-6_29}, author = {Cavalini, Luciana and Cook, Timothy}, editor = {Hissam, Scott and Russo, Barbara and de Mendon{\c c}a Neto, Manoel and Kon, Fabio} } @article {594, title = {Implementation of the Zambia electronic perinatal record system for comprehensive prenatal and delivery care.}, journal = {International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics}, volume = {113}, year = {2011}, month = {2011 May}, pages = {131-6}, abstract = {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.}, issn = {1879-3479}, author = {Chi, Benjamin H and Vwalika, Bellington and Killam, William P and Wamalume, Chibesa and Giganti, Mark J and Mbewe, Reuben and Stringer, Elizabeth M and Chintu, Namwinga T and Putta, Nande B and Liu, Katherine C and Chibwesha, Carla J and Rouse, Dwight J and Stringer, Jeffrey S A} } @article {538, title = {Integration of 3D anatomical data obtained by CT imaging and 3D optical scanning for Computer Aided Implant Surgery.}, journal = {BMC medical imaging}, volume = {11}, year = {2011}, month = {2011 Feb 21}, pages = {5}, abstract = {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.}, issn = {1471-2342}, author = {Frisardi, Gianni and Chessa, Giacomo and Barone, Sandro and Paoli, Alessandro and Razionale, Armando and Frisardi, Flavio} } @article {10.1371/journal.pone.0027372, title = {An Open Environment CT-US Fusion for Tissue Segmentation during Interventional Guidance}, journal = {PLoS ONE}, volume = {6}, number = {11}, year = {2011}, month = {11}, pages = {e27372}, publisher = {Public Library of Science}, abstract = {

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\>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 mm2 ROI resulted in mean HU of 68{\textpm}44 within the tumor and -97{\textpm}52 within the fat pad adjacent to the tumor (p\<0.005). The tumor area measured by CT and histology was correlated (r2 = 0.92), while the area designated as fat decreased with increasing tumor size (r2 = 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 \<75 mm3, 75{\textendash}150 mm3 and \>150 mm3, 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.

}, doi = {10.1371/journal.pone.0027372}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0027372}, author = {Caskey, , Charles F. and Hlawitschka, , Mario and Qin, , Shengping and Mahakian, , Lisa M. and Cardiff, , Robert D. and Boone, , John M. and Ferrara, , Katherine W.} } @article {1048, title = {PopHealth primer. ONC funds open-source software to streamline clinical quality measures reporting for meaningful use program.}, journal = {J AHIMA}, volume = {82}, year = {2011}, month = {2011 Sep}, pages = {48-50}, keywords = {Benchmarking, Financing, Government, Government Agencies, Mandatory Reporting, Organizational Case Studies, Quality Assurance, Health Care, Reimbursement, Incentive, Software, United States, User-Computer Interface}, issn = {1060-5487}, author = {Cottington, Sarah} } @article {1155, title = {The {SHARPn} project on secondary use of {Electronic} {Medical} {Record} data: progress, plans, and possibilities}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2011}, year = {2011}, pages = {248{\textendash}256}, abstract = {SHARPn is a collaboration among 16 academic and industry partners committed to the production and distribution of high-quality software artifacts that support the secondary use of EMR data. Areas of emphasis are data normalization, natural language processing, high-throughput phenotyping, and data quality metrics. Our work avails the industrial scalability afforded by the Unstructured Information Management Architecture (UIMA) from IBM Watson Research labs, the same framework which underpins the Watson Jeopardy demonstration. This descriptive paper outlines our present work and achievements, and presages our trajectory for the remainder of the funding period. The project is one of the four Strategic Health IT Advanced Research Projects (SHARP) projects funded by the Office of the National Coordinator in 2010.}, keywords = {Algorithms, Biomedical Research, Cooperative Behavior, Data Mining, electronic health records, Natural Language Processing, Software}, issn = {1942-597X}, author = {Chute, Christopher G. and Pathak, Jyotishman and Savova, Guergana K. and Bailey, Kent R. and Schor, Marshall I. and Hart, Lacey A. and Beebe, Calvin E. and Huff, Stanley M.} } @article {910, title = {Staying open. Open-source health IT gets boost from foundation.}, journal = {Modern healthcare}, volume = {41}, year = {2011}, pages = {10{\textendash}11}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79958716512\&partnerID=40\&md5=034fdbb492b4a355ae02dfa560abe1cd}, author = {Conn, J} } @article {599, title = {Wikipedia: a key tool for global public health promotion.}, journal = {Journal of medical Internet research}, volume = {13}, year = {2011}, month = {2011}, pages = {e14}, abstract = {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{\textquoteright}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{\textquoteright}s health-related entries. Several examples of partnerships already show that there is enthusiasm to strengthen Wikipedia{\textquoteright}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.}, keywords = {Consumer Health Information, Encyclopedias as Topic, Health Promotion, Humans, Information Dissemination, Information Services, Internet, Patient Education as Topic, Public Health, World Health}, issn = {1438-8871}, author = {Heilman, James M and Kemmann, Eckhard and Bonert, Michael and Chatterjee, Anwesh and Ragar, Brent and Beards, Graham M and Iberri, David J and Harvey, Matthew and Thomas, Brendan and Stomp, Wouter and Martone, Michael F and Lodge, Daniel J and Vondracek, Andrea and de Wolff, Jacob F and Liber, Casimir and Grover, Samir C and Vickers, Tim J and Mesk{\'o}, Bertalan and Laurent, Micha{\"e}l R} } @article {529, title = {AngioLab: Integrated technology for patient-specific management of intracranial aneurysms.}, journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference}, volume = {1}, year = {2010}, month = {2010}, pages = {6801-4}, abstract = {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.}, issn = {1557-170X}, author = {Villa-Uriol, M C and Larrabide, I and Geers, A J and Pozo, J and Bogunovic, H and Mazzeo, M and Omedas, P and Barbarito, V and Carotenuto, L and Riccobene, C and Planes, X and Martelli, Y and Frangi, A F} } @article {871, title = {The caBIG annotation and image Markup project.}, journal = {J Digit Imaging}, volume = {23}, year = {2010}, month = {2010 Apr}, pages = {217-25}, abstract = {

Image annotation and markup are at the core of medical interpretation in both the clinical and the research setting. Digital medical images are managed with the DICOM standard format. While DICOM contains a large amount of meta-data about whom, where, and how the image was acquired, DICOM says little about the content or meaning of the pixel data. An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human or machine observer. An image markup is the graphical symbols placed over the image to depict an annotation. While DICOM is the standard for medical image acquisition, manipulation, transmission, storage, and display, there are no standards for image annotation and markup. Many systems expect annotation to be reported verbally, while markups are stored in graphical overlays or proprietary formats. This makes it difficult to extract and compute with both of them. The goal of the Annotation and Image Markup (AIM) project is to develop a mechanism, for modeling, capturing, and serializing image annotation and markup data that can be adopted as a standard by the medical imaging community. The AIM project produces both human- and machine-readable artifacts. This paper describes the AIM information model, schemas, software libraries, and tools so as to prepare researchers and developers for their use of AIM.

}, keywords = {Computational Biology, Computer Communication Networks, Databases, Factual, Diagnostic Imaging, Humans, Interdisciplinary Communication, Medical Records Systems, Computerized, National Cancer Institute (U.S.), National Institutes of Health (U.S.), Neoplasms, Program Evaluation, Quality of Health Care, Radiographic Image Enhancement, Radiology Information Systems, Software, Systems Integration, United States, User-Computer Interface}, issn = {1618-727X}, doi = {10.1007/s10278-009-9193-9}, author = {Channin, David S and Mongkolwat, Pattanasak and Kleper, Vladimir and Sepukar, Kastubh and Rubin, Daniel L} } @article {20226035, title = {CASE: a framework for computer supported outbreak detection.}, journal = {BMC medical informatics and decision making}, volume = {10}, year = {2010}, month = {2010}, pages = {14}, abstract = {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.}, author = {Cakici, Baki and Hebing, Kenneth and Gr{\"u}newald, Maria and Saretok, Paul and Hulth, Anette} } @proceedings {513, title = {Comprehensive Yet Scalable Health Information Systems for Low Resource Settings: A Collaborative Effort in Sierra Leone}, year = {2010}, month = {11/2010}, abstract = {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.}, url = {http://proceedings.amia.org/127frh}, author = {Braaa, J{\o}rn and Kanterb, Andrew S. and Leshc, Neal and Crichtond, Ryan and Jolliffea, Bob and S{\ae}b{\o}e, Johan and Kossia, Edem and Seebregts, Christopher J} } @article {1015, title = {Experience implementing OpenMRS to support maternal and reproductive health in Northern Nigeria.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {332-6}, abstract = {

In Northern Nigeria a deteriorating health system has resulted in one of the World{\textquoteright}s highest rates of maternal and infant deaths. The dire situation in Northern Nigeria is only amplified by the lack of an effective health information system, leaving hospitals and clinics to make decisions about patient care with only uninformed guesses about medical history and access to unreliable and unintelligible patient registers and summary reports. In 2009 we implemented an electronic medical records system using OpenMRS for the Family Health Unit of the Shehu Idris College. The three-month process resulted in electronic forms for all clinical areas, greatly reduced data duplication and a monthly reporting process that takes minutes instead of days. This system provides not only access to the first patient-based health indicators in Nigeria (as opposed to previously error-prone aggregate data) but is also an example of the potential to overcome the harsh computing environment in Nigeria to implement eHealth systems that will improve the quality of patient care.

}, keywords = {Delivery of Health Care, electronic health records, Maternal Health Services, Maternal Welfare, Models, Organizational, Needs Assessment, Nigeria, Reproductive Medicine, Utilization Review}, issn = {0926-9630}, author = {Thompson, Adam and Castle, Evelyn and Lubeck, Paul and Makarfi, Provost Shehu} } @article {20663165, title = {Heterogeneity prevails: the state of clinical trial data management in Europe - results of a survey of ECRIN centres.}, journal = {Trials}, volume = {11}, year = {2010}, month = {2010 Jul 21}, pages = {79}, abstract = {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 "electronic Case Report Forms". 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{\textquoteright}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.}, url = {http://www.trialsjournal.com/content/11/1/79}, author = {Kuchinke, Wolfgang and Ohmann, Christian and Yang, Qin and Salas, Nader and Lauritsen, Jens and Gueyffier, Francois and Leizorovicz, Alan and Schade-Brittinger, Carmen and Wittenberg, Michael and Voko, Zoltan and Gaynor, Siobhan and Cooney, Margaret and Doran, Peter and Maggioni, Aldo and Lorimer, Andrea and Torres, Ferran and McPherson, Gladys and Charvill, Jim and Hellstrom, Mats and Lejeune, Stephane} } @article {10.1371/journal.pone.0014094, title = {JULIDE: A Software Tool for 3D Reconstruction and Statistical Analysis of Autoradiographic Mouse Brain Sections}, journal = {PLoS ONE}, volume = {5}, number = {11}, year = {2010}, month = {11}, pages = {e14094}, publisher = {Public Library of Science}, abstract = {

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.

}, doi = {10.1371/journal.pone.0014094}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0014094}, author = {Ribes, Delphine and Parafita, Julia and Charrier, R{\'e}mi and Magara, Fulvio and Magistretti, Pierre J. and Thiran, Jean-Philippe} } @article {1042, title = {JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.}, journal = {PLoS One}, volume = {5}, year = {2010}, month = {2010}, pages = {e14094}, abstract = {

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.

}, keywords = {Animals, Autoradiography, Brain, Carbon Radioisotopes, Deoxyglucose, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Male, Maze Learning, Mice, Mice, Inbred C57BL, Reproducibility of Results, Software}, issn = {1932-6203}, doi = {10.1371/journal.pone.0014094}, author = {Ribes, Delphine and Parafita, Julia and Charrier, R{\'e}mi and Magara, Fulvio and Magistretti, Pierre J and Thiran, Jean-Philippe} } @article {20646816, title = {Mandibular reconstruction with fibula free flap. Experience of virtual reconstruction using Osirix((R)), a free and open source software for medical imagery.}, journal = {Annales de chirurgie plastique et esthetique}, year = {2010}, month = {2010 Jun 18}, abstract = {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.}, author = {Albert, S and Cristofari, J-P and Cox, A and Bensimon, J-L and Guedon, C and Barry, B} } @article {847, title = {Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications.}, journal = {J Am Med Inform Assoc}, volume = {17}, year = {2010}, month = {2010 Sep-Oct}, pages = {507-13}, abstract = {

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.

}, keywords = {Biomedical Research, electronic health records, Information Storage and Retrieval, Natural Language Processing}, issn = {1527-974X}, doi = {10.1136/jamia.2009.001560}, author = {Savova, Guergana K and Masanz, James J and Ogren, Philip V and Zheng, Jiaping and Sohn, Sunghwan and Kipper-Schuler, Karin C and Chute, Christopher G} } @article {20398366, title = {Open source challenges for hospital information system (HIS) in developing countries: a pilot project in Mali.}, journal = {BMC medical informatics and decision making}, volume = {10}, year = {2010}, month = {2010}, pages = {22}, abstract = {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 "La Timone" 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{\textquoteright} 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.}, doi = {10.1186/1472-6947-10-22}, url = {http://www.biomedcentral.com/1472-6947/10/22}, author = {Bagayoko, Cheick-Oumar and Dufour, Jean-Charles and Chaacho, Saad and Bouhaddou, Omar and Fieschi, Marius} } @article {596, title = {OpenMEEG: opensource software for quasistatic bioelectromagnetics.}, journal = {Biomedical engineering online}, volume = {9}, year = {2010}, month = {2010}, pages = {45}, abstract = {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.}, keywords = {Benchmarking, Computers, Electric Impedance, Electricity, Electroencephalography, Electromagnetic Phenomena, Licensure, Magnetics, Magnetoencephalography, Models, Theoretical, Quality Control, Software, Time Factors, Tomography}, issn = {1475-925X}, author = {Gramfort, Alexandre and Papadopoulo, Th{\'e}odore and Olivi, Emmanuel and Clerc, Maureen} } @inbook {springerlink:10.1007/978-3-642-12197-5_85, title = {rtMEG: A Real-Time Software Toolbox for Brain-Machine Interfaces Using Magnetoencephelography}, booktitle = {17th International Conference on Biomagnetism Advances in Biomagnetism {\textendash} Biomag2010}, series = {IFMBE Proceedings}, volume = {28}, year = {2010}, note = {10.1007/978-3-642-12197-5_85}, pages = {362-365}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, isbn = {978-3-642-12197-5}, url = {http://dx.doi.org/10.1007/978-3-642-12197-5_85}, author = {Sudre, Gustavo and Wang, Wei and Song, Tao and Kajola, Matti and Vinjamuri, Ramana and Collinger, Jennifer and Degenhart, Alan and Bagic, Anto and Weber, Doug J.}, editor = {Magjarevic, R. and Nagel, J. H. and Supek, Selma and Su{\v s}ac, Ana} } @article {20482787, title = {Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities.}, journal = {BMC bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {260}, abstract = {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.}, author = {Tolopko, Andrew N and Sullivan, John P and Erickson, Sean D and Wrobel, David and Chiang, Su L and Rudnicki, Katrina and Rudnicki, Stewart and Nale, Jennifer and Selfors, Laura M and Greenhouse, Dara and Muhlich, Jeremy L and Shamu, Caroline E} } @article {499, title = {Bayesian analysis of neuroimaging data in FSL.}, journal = {NeuroImage}, volume = {45}, year = {2009}, month = {2009 Mar}, pages = {S173-86}, abstract = {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.}, keywords = {Bayes Theorem, Brain, Diffusion Magnetic Resonance Imaging, Humans, Image Interpretation, Computer-Assisted, Software}, issn = {1095-9572}, author = {Woolrich, Mark W and Jbabdi, Saad and Patenaude, Brian and Chappell, Michael and Makni, Salima and Behrens, Timothy and Beckmann, Christian and Jenkinson, Mark and Smith, Stephen M} } @article {873, title = {The caBIG terminology review process.}, journal = {J Biomed Inform}, volume = {42}, year = {2009}, month = {2009 Jun}, pages = {571-80}, abstract = {

The National Cancer Institute (NCI) is developing an integrated biomedical informatics infrastructure, the cancer Biomedical Informatics Grid (caBIG), to support collaboration within the cancer research community. A key part of the caBIG architecture is the establishment of terminology standards for representing data. In order to evaluate the suitability of existing controlled terminologies, the caBIG Vocabulary and Data Elements Workspace (VCDE WS) working group has developed a set of criteria that serve to assess a terminology{\textquoteright}s structure, content, documentation, and editorial process. This paper describes the evolution of these criteria and the results of their use in evaluating four standard terminologies: the Gene Ontology (GO), the NCI Thesaurus (NCIt), the Common Terminology for Adverse Events (known as CTCAE), and the laboratory portion of the Logical Objects, Identifiers, Names and Codes (LOINC). The resulting caBIG criteria are presented as a matrix that may be applicable to any terminology standardization effort.

}, keywords = {Medical Informatics, National Institutes of Health (U.S.), Terminology as Topic, United States}, issn = {1532-0480}, doi = {10.1016/j.jbi.2008.12.003}, author = {Cimino, James J and Hayamizu, Terry F and Bodenreider, Olivier and Davis, Brian and Stafford, Grace A and Ringwald, Martin} } @conference {1086, title = {Commercial Open Source RIS/PACS: The ClearCanvas Experience}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001827400220027}, author = {Norman Young and Clinton Chau and John Adziovsky} } @conference {1088, title = {Concept Matching between OpenEHR and SONHO}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001828400450053}, author = {Ricardo Cruz-Correia and Carla {\'A}vila and Rong Chen} } @article {19230726, title = {Demonstration of the Adamkiewicz artery by multidetector computed tomography angiography analysed with the open-source software OsiriX.}, journal = {European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery}, volume = {37}, year = {2009}, month = {2009 Apr}, pages = {395-400}, abstract = {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.}, author = {Melissano, G and Bertoglio, L and Civelli, V and Amato, A C Moraes and Coppi, G and Civilini, E and Calori, G and De Cobelli, F and Del Maschio, A and Chiesa, R} } @article {18952940, title = {Electronic Support for Public Health: validated case finding and reporting for notifiable diseases using electronic medical data.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {16}, year = {2009}, month = {2009 Jan-Feb}, pages = {18-24}, abstract = {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.}, author = {Lazarus, Ross and Klompas, Michael and Campion, Francis X and McNabb, Scott J N and Hou, Xuanlin and Daniel, James and Haney, Gillian and DeMaria, Alfred and Lenert, Leslie and Platt, Richard} } @inbook {springerlink:10.1007/978-3-642-01932-6_45, title = {GIMIAS: An Open Source Framework for Efficient Development of Research Tools and Clinical Prototypes}, booktitle = {Functional Imaging and Modeling of the Heart}, series = {Lecture Notes in Computer Science}, volume = {5528}, year = {2009}, note = {10.1007/978-3-642-01932-6_45}, pages = {417-426}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {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.}, url = {http://dx.doi.org/10.1007/978-3-642-01932-6_45}, author = {Larrabide, Ignacio and Omedas, Pedro and Martelli, Yves and Planes, Xavier and Nieber, Maarten and Moya, Juan and Butakoff, Constantine and Sebasti{\'a}n, Rafael and Camara, Oscar and De Craene, Mathieu and Bijnens, Bart and Frangi, Alejandro}, editor = {Ayache, Nicholas and Delingette, Herv{\'e} and Sermesant, Maxime} } @article {20044607, title = {Image analysis of breast cancer immunohistochemistry-stained sections using ImageJ: an RGB-based model.}, journal = {Anticancer research}, volume = {29}, year = {2009}, month = {2009 Dec}, pages = {4995-8}, abstract = {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.}, author = {Vrekoussis, T and Chaniotis, V and Navrozoglou, I and Dousias, V and Pavlakis, K and Stathopoulos, E N and Zoras, O} } @article {1018, title = {Mobile Care (Moca) for Remote Diagnosis and Screening.}, journal = {J Health Inform Dev Ctries}, volume = {3}, year = {2009}, month = {2009 Jan 1}, pages = {17-21}, abstract = {

Moca is a cell phone-facilitated clinical information system to improve diagnostic, screening and therapeutic capabilities in remote resource-poor settings. The software allows transmission of any medical file, whether a photo, x-ray, audio or video file, through a cell phone to (1) a central server for archiving and incorporation into an electronic medical record (to facilitate longitudinal care, quality control, and data mining), and (2) a remote specialist for real-time decision support (to leverage expertise). The open source software is designed as an end-to-end clinical information system that seamlessly connects health care workers to medical professionals. It is integrated with OpenMRS, an existing open source medical records system commonly used in developing countries.

}, issn = {1178-4407}, author = {Celi, Leo Anthony and Sarmenta, Luis and Rotberg, Jhonathan and Marcelo, Alvin and Clifford, Gari} } @article {19534858, title = {OsiriX, a useful tool for processing tomographic images in patients with facial fracture}, journal = {Cirugia y cirujanos}, volume = {77}, year = {2009}, month = {2009 Mar-Apr}, pages = {95-9}, abstract = {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 Traumatolog{\'\i}a y Ortopedia "Lomas Verdes" 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.}, author = {Sierra-Mart{\'\i}nez, Eduardo and Cienfuegos-Monroy, Ricardo and Fern{\'a}ndez-Sobrino, Gerardo} } @article {18612462, title = {Automated identification of acute hepatitis B using electronic medical record data to facilitate public health surveillance.}, journal = {PloS one}, volume = {3}, year = {2008}, month = {2008}, pages = {e2626}, abstract = {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.}, author = {Klompas, Michael and Haney, Gillian and Church, Daniel and Lazarus, Ross and Hou, Xuanlin and Platt, Richard} } @article {18999296, title = {caBIG compatibility review system: software to support the evaluation of applications using defined interoperability criteria.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2008}, month = {2008}, pages = {197-201}, abstract = {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.}, author = {Freimuth, Robert R and Schauer, Michael W and Lodha, Preeti and Govindrao, Poornima and Nagarajan, Rakesh and Chute, Christopher G} } @article {18096909, title = {caGrid 1.0: an enterprise Grid infrastructure for biomedical research.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {15}, year = {2008}, month = {2008 Mar-Apr}, pages = {138-49}, abstract = {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.}, author = {Oster, Scott and Langella, Stephen and Hastings, Shannon and Ervin, David and Madduri, Ravi and Phillips, Joshua and Kurc, Tahsin and Siebenlist, Frank and Covitz, Peter and Shanbhag, Krishnakant and Foster, Ian and Saltz, Joel} } @article {803, title = {Designing Tracking Software for Image-Guided Surgery Applications: IGSTK Experience.}, journal = {Int J Comput Assist Radiol Surg}, volume = {3}, year = {2008}, month = {2008 Nov 1}, pages = {395-403}, abstract = {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.}, issn = {1861-6429}, doi = {10.1007/s11548-008-0243-4}, author = {Enquobahrie, Andinet and Gobbi, David and Turek, Matt and Cheng, Patrick and Yaniv, Ziv and Lindseth, Frank and Cleary, Kevin} } @article {18302744, title = {Epigrass: a tool to study disease spread in complex networks.}, journal = {Source code for biology and medicine}, volume = {3}, year = {2008}, month = {2008}, pages = {3}, abstract = {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.}, author = {Coelho, Fl{\'a}vio C and Cruz, Oswaldo G and Code{\c c}o, Cl{\'a}udia T} } @article {802, title = {The image-guided surgery toolkit IGSTK: an open source C++ software toolkit.}, journal = {J Digit Imaging}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {21-33}, abstract = {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{\textquoteright} mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences.}, keywords = {Computer Systems, Data Display, Database Management Systems, Humans, Information Dissemination, Information Storage and Retrieval, Safety, Software, Software Design, Software Validation, Surgery, Computer-Assisted, Systems Integration, User-Computer Interface}, issn = {0897-1889}, doi = {10.1007/s10278-007-9054-3}, author = {Enquobahrie, Andinet and Cheng, Patrick and Gary, Kevin and Ibanez, Luis and Gobbi, David and Lindseth, Frank and Yaniv, Ziv and Aylward, Stephen and Jomier, Julien and Cleary, Kevin} } @article {17850667, title = {Indivo: a personally controlled health record for health information exchange and communication.}, journal = {BMC medical informatics and decision making}, volume = {7}, year = {2007}, month = {2007}, pages = {25}, abstract = {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{\textquoteright}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.}, url = {http://www.biomedcentral.com/1472-6947/7/25/}, author = {Mandl, Kenneth D and Simons, William W and Crawford, William C R and Abbett, Jonathan M} } @article {17700904, title = {Reflections on the role of open source in health information system interoperability.}, journal = {Yearbook of medical informatics}, year = {2007}, month = {2007}, pages = {50-60}, abstract = {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.}, author = {Sfakianakis, S and Chronaki, C E and Chiarugi, F and Conforti, F and Katehakis, D G} } @conference {SOFA07, title = {SOFA - an Open Source Framework for Medical Simulation}, booktitle = {Medicine Meets Virtual Reality (MMVR{\textquoteright}15)}, year = {2007}, month = {February}, address = {Long Beach, USA}, url = {http://www.sofa-framework.org/docs/SOFA_MMVR07.pdf}, author = {Allard, J{\'e}r{\'e}mie and Cotin, St{\'e}phane and Faure, Fran{\c c}ois and Bensoussan, Pierre-Jean and Poyer, Fran{\c c}ois and Duriez, Christian and Delingette, Herv{\'e} and Grisoni, Laurent} } @article {566, title = {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.}, journal = {Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society}, volume = {30}, year = {2006}, month = {2006 Sep-Oct}, pages = {391-406}, abstract = {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).}, keywords = {Data Display, Database Management Systems, Diagnostic Imaging, Equipment Design, Equipment Failure Analysis, Guidelines as Topic, Information Storage and Retrieval, Internationality, Medical Records Systems, Computerized, Programming Languages, Radiology Information Systems, Systems Integration, User-Computer Interface}, issn = {0895-6111}, author = {Inchingolo, Paolo and Beltrame, Marco and Bosazzi, Pierpaolo and Cicuta, Davide and Faustini, Giorgio and Mininel, Stefano and Poli, Andrea and Vatta, Federica} } @conference {782, title = {Remote Large Data Visualization in the ParaView Framework.}, booktitle = {EGPGV}, year = {2006}, publisher = {Eurographics Association}, organization = {Eurographics Association}, keywords = {dblp}, isbn = {3-905673-40-1}, url = {http://dblp.uni-trier.de/db/conf/egpgv/egpgv2006.html$\#$CedilnikGMAF06}, author = {Cedilnik, Andy and Geveci, Berk and Moreland, Kenneth and Ahrens, James P. and Favre, Jean M.}, editor = {Heirich, Alan and Raffin, Bruno and dos Santos, Lu{\'\i}s Paulo Peixoto} } @article {15924271, title = {Establishing a Web-based DICOM teaching file authoring tool using open-source public software.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {18}, year = {2005}, month = {2005 Sep}, pages = {169-75}, abstract = {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.}, author = {Lee, Wen-Jeng and Yang, Chung-Yi and Liu, Kao-Lang and Liu, Hon-Man and Ching, Yu-Tai and Chen, Shyh-Jye} } @article {16257947, title = {Information technology as a tool to improve the quality of American Indian health care.}, journal = {American journal of public health}, volume = {95}, year = {2005}, month = {2005 Dec}, pages = {2173-9}, abstract = {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.}, author = {Sequist, Thomas D and Cullen, Theresa and Ayanian, John Z} } @article {15361001, title = {The RODS Open Source Project: removing a barrier to syndromic surveillance.}, journal = {Studies in health technology and informatics}, volume = {107}, year = {2004}, month = {2004}, pages = {1192-6}, abstract = {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.}, author = {Espino, Jeremy U and Wagner, Michael M and Tsui, Fu-Chang and Su, Hoah-Der and Olszewski, Robert T and Lie, Zhen and Chapman, Wendy and Zeng, Xiaoming and Ma, Lili and Lu, Zhong Wei and Dara, Jagan} } @article {11679206, title = {LIPSIA - a new software system for the evaluation of functional magnetic resonance images of the human brain.}, journal = {Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society}, volume = {25}, year = {2001}, month = {2001 Nov-Dec}, pages = {449-57}, abstract = {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.}, author = {Lohmann, G and M{\"u}ller, K and Bosch, V and Mentzel, H and Hessler, S and Chen, L and Zysset, S and von Cramon, D Y} }