@article {1301, title = {Use of cost-effective technologies for a routine clinical pathology laboratory}, journal = {Lab on a Chip}, year = {2021}, month = {2021}, pages = { - }, abstract = {Classically, the need for highly sophisticated instruments with important economic costs has been a major limiting factor for clinical pathology laboratories, especially in developing countries. With the aim of making clinical pathology more accessible, a wide variety of free or economical technologies have been developed worldwide in the last years. 3D printing and Arduino approaches can provide up to 94\% economical savings in hardware and instrumentation in comparison to commercial alternatives. The vast selection of Point-of-Care-Tests (POCT) currently available also limits the need for specific instruments or personnel, as they can be used almost anywhere and by anyone. Lastly, there are dozens of free and libre digital tools available in health informatics. This review provides an overview of the state-of-the-art on cost-effective alternatives with applications in routine clinical pathology laboratories. In this context, a variety of technologies including 3D printing and Arduino, lateral flow assays, plasmonic biosensors, and microfluidics, as well as laboratory information systems, are discussed. This review aims to serve as an introduction to different technologies that can make clinical pathology more accessible and, therefore, contribute to achieve universal health coverage.}, isbn = {1473-0197}, url = {http://dx.doi.org/10.1039/D1LC00658D}, author = {Vazquez, Mercedes and Anfossi, L. and Ben-Yoav, Hader and Di{\'e}guez, Lorena and Karopka, Thomas and Della Ventura, Bartolomeo and Abalde-Cela, Sara and Minopoli, Antonio and Di Nardo, Fabio and Kumar Shukla, Vikas and Teixeira, Alexandra and Tvarijonaviciute, Asta and Franco, Lorena} } @article {1299, title = {Using Open Source, Open Data, and Civic Technology to Address the COVID-19 Pandemic and Infodemic.}, journal = {Yearb Med Inform}, year = {2021}, month = {2021 Apr 21}, abstract = {

OBJECTIVES: The emerging COVID-19 pandemic has caused one of the world{\textquoteright}s worst health disasters compounded by social confusion with misinformation, the so-called "Infodemic". In this paper, we discuss how open technology approaches - including data sharing, visualization, and tooling - can address the COVID-19 pandemic and infodemic.

METHODS: In response to the call for participation in the 2020 International Medical Informatics Association (IMIA) Yearbook theme issue on Medical Informatics and the Pandemic, the IMIA Open Source Working Group surveyed recent works related to the use of Free/Libre/Open Source Software (FLOSS) for this pandemic.

RESULTS: FLOSS health care projects including GNU Health, OpenMRS, DHIS2, and others, have responded from the early phase of this pandemic. Data related to COVID-19 have been published from health organizations all over the world. Civic Technology, and the collaborative work of FLOSS and open data groups were considered to support collective intelligence on approaches to managing the pandemic.

CONCLUSION: FLOSS and open data have been effectively used to contribute to managing the COVID-19 pandemic, and open approaches to collaboration can improve trust in data.

}, issn = {2364-0502}, doi = {10.1055/s-0041-1726488}, author = {Kobayashi, Shinji and Falc{\'o}n, Luis and Fraser, Hamish and Braa, J{\o}rn and Amarakoon, Pamod and Marcelo, Alvin and Paton, Chris} } @article {1303, title = {Machado: Open source genomics data integration framework.}, journal = {Gigascience}, volume = {9}, year = {2020}, month = {2020 09 14}, abstract = {

BACKGROUND: Genome projects and multiomics experiments generate huge volumes of data that must be stored, mined, and transformed into useful knowledge. All this information is supposed to be accessible and, if possible, browsable afterwards. Computational biologists have been dealing with this scenario for more than a decade and have been implementing software and databases to meet this challenge. The GMOD{\textquoteright}s (Generic Model Organism Database) biological relational database schema, known as Chado, is one of the few successful open source initiatives; it is widely adopted and many software packages are able to connect to it.

FINDINGS: We have been developing an open source software package named Machado, a genomics data integration framework implemented in Python, to enable research groups to both store and visualize genomics data. The framework relies on the Chado database schema and, therefore, should be very intuitive for current developers to adopt it or have it running on top of already existing databases. It has several data-loading tools for genomics and transcriptomics data and also for annotation results from tools such as BLAST, InterproScan, OrthoMCL, and LSTrAP. There is an API to connect to JBrowse, and a web visualization tool is implemented using Django Views and Templates. The Haystack library integrated with the ElasticSearch engine was used to implement a Google-like search, i.e., single auto-complete search box that provides fast results and filters.

CONCLUSION: Machado aims to be a modern object-relational framework that uses the latest Python libraries to produce an effective open source resource for genomics research.

}, issn = {2047-217X}, doi = {10.1093/gigascience/giaa097}, author = {Mudadu, Mauricio de Alvarenga and Zerlotini, Adhemar} } @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 {1289, title = {Community-led data collection using Open Data Kit for surveillance of animal African trypanosomiasis in Shimba hills, Kenya.}, journal = {BMC Res Notes}, volume = {12}, year = {2019}, month = {2019 Mar 18}, pages = {151}, abstract = {

OBJECTIVE: In Sub-Saharan Africa, there is an increase in trypanosome non-susceptibility to multiple trypanocides, but limited information on judicious trypanocide use is accessible to smallholder farmers and agricultural stakeholders in disease endemic regions, resulting in widespread multi-drug resistance. Huge economic expenses and the laborious nature of extensive field studies have hindered collection of the requisite large-scale prospective datasets required to inform disease management. We examined the efficacy of community-led data collection strategies using smartphones by smallholder farmers to acquire robust datasets from the trypanosomiasis endemic Shimba hills region in Kenya. We used Open Data Kit, an open-source smartphone application development software, to create a data collection App.

RESULTS: Our study provides proof of concept for the viability of using smartphone Apps to remotely collect reliable large-scale information from smallholder farmers and veterinary health care givers in resource poor settings. We show that these datasets can be reliably collated remotely, analysed, and the findings can inform policies that improve farming practices and economic wellbeing while restricting widespread multi-drug resistance. Moreover, this strategy can be used to monitor and manage other infectious diseases in other rural, resource poor settings.

}, keywords = {Adult, Animals, Cattle, Cattle Diseases, Community-Based Participatory Research, Data Collection, Epidemiological Monitoring, Farmers, Female, Humans, Kenya, Male, Mobile Applications, Pilot Projects, Proof of Concept Study, Trypanosomiasis, African}, issn = {1756-0500}, doi = {10.1186/s13104-019-4198-z}, author = {Wamwenje, Sarah A O and Wangwe, Ibrahim I and Masila, Nicodemus and Mirieri, Caroline K and Wambua, Lillian and Kulohoma, Benard W} } @article {1226, title = {Comparison of Open-Source Electronic Health Record Systems Based on Functional and User Performance Criteria.}, journal = {Healthc Inform Res}, volume = {25}, year = {2019}, month = {2019 Apr}, pages = {89-98}, abstract = {

Objectives: Open-source Electronic Health Record (EHR) systems have gained importance. The main aim of our research is to guide organizational choice by comparing the features, functionality, and user-facing system performance of the five most popular open-source EHR systems.

Methods: We performed qualitative content analysis with a directed approach on recently published literature (2012-2017) to develop an integrated set of criteria to compare the EHR systems. The functional criteria are an integration of the literature, meaningful use criteria, and the Institute of Medicine{\textquoteright}s functional requirements of EHR, whereas the user-facing system performance is based on the time required to perform basic tasks within the EHR system.

Results: Based on the Alexa web ranking and Google Trends, the five most popular EHR systems at the time of our study were OSHERA VistA, GNU Health, the Open Medical Record System (OpenMRS), Open Electronic Medical Record (OpenEMR), and OpenEHR. We also found the trends in popularity of the EHR systems and the locations where they were more popular than others. OpenEMR met all the 32 functional criteria, OSHERA VistA met 28, OpenMRS met 12 fully and 11 partially, OpenEHR-based EHR met 10 fully and 3 partially, and GNU Health met the least with only 10 criteria fully and 2 partially.

Conclusions: Based on our functional criteria, OpenEMR is the most promising EHR system, closely followed by VistA. With regards to user-facing system performance, OpenMRS has superior performance in comparison to OpenEMR.

}, issn = {2093-3681}, doi = {10.4258/hir.2019.25.2.89}, author = {Purkayastha, Saptarshi and Allam, Roshini and Maity, Pallavi and Gichoya, Judy W} } @article {1286, title = {Cytomine: Toward an Open and Collaborative Software Platform for Digital Pathology Bridged to Molecular Investigations.}, journal = {Proteomics Clin Appl}, volume = {13}, year = {2019}, month = {2019 01}, pages = {e1800057}, abstract = {

PURPOSE: Digital histology is being increasingly used in research and clinical applications. In parallel, new tissue imaging methods (e.g., imaging mass spectrometry) are currently regarded as very promising approaches for better molecular diagnosis in pathology. However, these new data sources are still often underexploited because of the lack of collaborative software to share and correlate information for multimodal analysis.

EXPERIMENTAL DESIGN: The open science paradigm is followed to develop new features in the web-based Cytomine software to support next-generation digital pathology bridged to molecular investigations.

RESULTS: New open-source developments allow to explore whole-slide classical histology with Matrix Assisted Laser Desorption Ionisation (MALDI) imaging and to support preprocessing for biomarker discovery using laser microdissection-based microproteomics.

CONCLUSIONS AND CLINICAL RELEVANCE: The updated version of Cytomine is the first open and web-based tool to enable sharing data from classical histology, molecular imaging, and cell counting for proteomics preprocessing. It holds good promise to fulfill imminent needs in molecular histopathology.

}, keywords = {Intersectoral Collaboration, Multimodal Imaging, Pathology, Proteomics, Software, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization}, issn = {1862-8354}, doi = {10.1002/prca.201800057}, author = {Rubens, Ulysse and Hoyoux, Renaud and Vanosmael, Laurent and Ouras, Mehdy and Tasset, Maxime and Hamilton, Christopher and Longuesp{\'e}e, R{\'e}mi and Mar{\'e}e, Rapha{\"e}l} } @article {1229, title = {Data model harmonization for the All Of Us Research Program: Transforming i2b2 data into the OMOP common data model.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0212463}, abstract = {

BACKGROUND: The All Of Us Research Program (AOU) is building a nationwide cohort of one million patients{\textquoteright} EHR and genomic data. Data interoperability is paramount to the program{\textquoteright}s success. AOU is standardizing its EHR data around the Observational Medical Outcomes Partnership (OMOP) data model. OMOP is one of several standard data models presently used in national-scale initiatives. Each model is unique enough to make interoperability difficult. The i2b2 data warehousing and analytics platform is used at over 200 sites worldwide, which uses a flexible ontology-driven approach for data storage. We previously demonstrated this ontology system can drive data reconfiguration, to transform data into new formats without site-specific programming. We previously implemented this on our 12-site Accessible Research Commons for Health (ARCH) network to transform i2b2 into the Patient Centered Outcomes Research Network model.

METHODS AND RESULTS: Here, we leverage our investment in i2b2 high-performance transformations to support the AOU OMOP data pipeline. Because the ARCH ontology has gained widespread national interest (through the Accrual to Clinical Trials network, other PCORnet networks, and the Nebraska Lexicon), we leveraged sites{\textquoteright} existing investments into this standard ontology. We developed an i2b2-to-OMOP transformation, driven by the ARCH-OMOP ontology and the OMOP concept mapping dictionary. We demonstrated and validated our approach in the AOU New England HPO (NEHPO). First, we transformed into OMOP a fake patient dataset in i2b2 and verified through AOU tools that the data was structurally compliant with OMOP. We then transformed a subset of data in the Partners Healthcare data warehouse into OMOP. We developed a checklist of assessments to ensure the transformed data had self-integrity (e.g., the distributions have an expected shape and required fields are populated), using OMOP{\textquoteright}s visual Achilles data quality tool. This i2b2-to-OMOP transformation is being used to send NEHPO production data to AOU. It is open-source and ready for use by other research projects.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0212463}, author = {Klann, Jeffrey G and Joss, Matthew A H and Embree, Kevin and Murphy, Shawn N} } @article {1222, title = {Data on security requirements in open-source software projects.}, journal = {Data Brief}, volume = {25}, year = {2019}, month = {2019 Aug}, pages = {103590}, abstract = {

The datasets presented in this article are related the research paper entitled "A Linear Classifier Approach for Identifying Security Requirements in Open Source Software Development" Wang et al. (2018) [1]. This article describes requirements collected from three open-source software (OSS) projects and labels of security requirements. The datasets are made available to support automated security requirements analyzing tools development as well as tools{\textquoteright} evaluation.

}, issn = {2352-3409}, doi = {10.1016/j.dib.2018.12.029}, author = {Wang, Wentao and Mahakala, Kavya Reddy and Gupta, Arushi and Hussein, Nesrin and Wang, Yinglin} } @article {1266, title = {From paper maps to digital maps: enhancing routine immunisation microplanning in Northern Nigeria.}, journal = {BMJ Glob Health}, volume = {4}, year = {2019}, month = {2019}, pages = {e001606}, abstract = {

Geographical information systems (GIS) can be effective decision-support tools. In this paper, we detail a GIS approach implemented by the Bauchi and Sokoto state primary healthcare development agencies in Nigeria to generate and convert routine immunisation (RI) paper maps to digital maps for microplanning. The process involved three stages: primary and secondary data collection and reconciliation, geospatial data processing and analysis, and production and validation of maps. The data collection and reconciliation stage identified a number of challenges with secondary data sources, including the need to standardise and reconcile health facility and settlement names. The study team was unable to apply population estimates generated from the Global Polio Eradication Initiative to RI planning because operational boundaries for polio activities are defined differently from RI activities. Application of open-source GIS software enabled the combination of multiple datasets and analysis of geospatial data to calculate catchment areas for primary health centres (PHCs) and assign vaccination strategies to communities. The activity resulted in the development of PHC catchment area digital maps, and captured next steps and lessons learnt for RI microplanning in the two states. While the digital maps provided input into the microplanning process, more work is needed to build capacity, standardise processes and ensure the quality of data used to generate the maps. RI service providers and communities must be engaged in the process to validate, understand the data, the contextual factors that influence decisions about which vaccination strategies RI microplans include and how resources are allocated.

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2019-001606}, author = {Dougherty, Leanne and Abdulkarim, Masduq and Mikailu, Fiyidi and Tijani, Usman and Owolabi, Kazeem and Gilroy, Kate and Naiya, Ahmed and Abdullahi, Adamu and Bodinga, Hadiza and Olayinka, Folake and Moise, Imelda} } @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 {1211, title = {Open source software security vulnerability detection based on dynamic behavior features.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0221530}, abstract = {

Open source software has been widely used in various industries due to its openness and flexibility, but it also brings potential security problems. Therefore, security analysis is required before using open source software. The current mainstream open source software vulnerability analysis technology is based on source code, and there are problems such as false positives, false negatives and restatements. In order to solve the problems, based on the further study of behavior feature extraction and vulnerability detection technology, a method of using dynamic behavior features to detect open source software vulnerabilities is proposed. Firstly, the relationship between open source software vulnerability and API call sequence is studied. Then, the behavioral risk vulnerability database of open source software is proposed as a support for vulnerability detection. In addition, the CNN-IndRNN classification model is constructed by improving the Independently Recurrent Neural Net-work (IndRNN) algorithm and applies to open source software security vulnerability detection. The experimental results verify the effectiveness of the proposed open source software security vulnerability detection method based on dynamic behavior features.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0221530}, author = {Li, Yuancheng and Ma, Longqiang and Shen, Liang and Lv, Junfeng and Zhang, Pan} } @article {1228, title = {PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model Title.}, journal = {Bioinformatics}, year = {2019}, month = {2019 Jun 19}, abstract = {

MOTIVATION: Electronic Health Records (EHR) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.

RESULTS: We present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership Common Data Model (CDM) format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open-source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.

AVAILABILITY: PatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btz409}, author = {Glicksberg, Benjamin S and Oskotsky, Boris and Thangaraj, Phyllis M and Giangreco, Nicholas and Badgeley, Marcus A and Johnson, Kipp W and Datta, Debajyoti and Rudrapatna, Vivek and Rappoport, Nadav and Shervey, Mark M and Miotto, Riccardo and Goldstein, Theodore C and Rutenberg, Eugenia and Frazier, Remi and Lee, Nelson and Israni, Sharat and Larsen, Rick and Percha, Bethany and Li, Li and Dudley, Joel T and Tatonetti, Nicholas P and Butte, Atul J} } @article {1269, title = {Quality of routine facility data for monitoring priority maternal and newborn indicators in DHIS2: A case study from Gombe State, Nigeria.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0211265}, abstract = {

INTRODUCTION: Routine health information systems are critical for monitoring service delivery. District Heath Information System, version 2 (DHIS2) is an open source software platform used in more than 60 countries, on which global initiatives increasingly rely for such monitoring. We used facility-reported data in DHIS2 for Gombe State, north-eastern Nigeria, to present a case study of data quality to monitor priority maternal and neonatal health indicators.

METHODS: For all health facilities in DHIS2 offering antenatal and postnatal care services (n = 497) and labor and delivery services (n = 486), we assessed the quality of data for July 2016-June 2017 according to the World Health Organization data quality review guidance. Using data from DHIS2 as well as external facility-level and population-level household surveys, we reviewed three data quality dimensions-completeness and timeliness, internal consistency, and external consistency-and considered the opportunities for improvement.

RESULTS: Of 14 priority maternal and neonatal health indicators that could be tracked through facility-based data, 12 were included in Gombe{\textquoteright}s DHIS2. During July 2016-June 2017, facility-reported data in DHIS2 were incomplete at least 40\% of the time, under-reported 10\%-60\% of the events documented in facility registers, and showed inconsistencies over time, between related indicators, and with an external data source. The best quality data elements were those that aligned with Gombe{\textquoteright}s health program priorities, particularly older health programs, and those that reflected contact indicators rather than indicators related to the provision of commodities or content of care.

CONCLUSION: This case study from Gombe State, Nigeria, demonstrates the high potential for effective monitoring of maternal and neonatal health using DHIS2. However, coordinated action at multiple levels of the health system is needed to maximize reporting of existing data; rationalize data flow; routinize data quality review, feedback, and supervision; and ensure ongoing maintenance of DHIS2.

}, keywords = {Adolescent, Adult, Female, Guidelines as Topic, Health information systems, Humans, Infant Health, Infant, Newborn, Maternal Health, Middle Aged, Nigeria, Pregnancy, Quality Indicators, Health Care, Young Adult}, issn = {1932-6203}, doi = {10.1371/journal.pone.0211265}, author = {Bhattacharya, Antoinette Alas and Umar, Nasir and Audu, Ahmed and Felix, Habila and Allen, Elizabeth and Schellenberg, Joanna R M and Marchant, Tanya} } @article {1234, title = {Secondary Data Use in Rwanda: Leveraging OpenMRS for Global HIV Research.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {1732}, abstract = {

The Rwandan Ministry of Health supports a countrywide installation of the Open Medical Record System (OpenMRS) to improve clinical recordkeeping and patient care. However, electronic medical records also can be a valuable source of data for observational and experimental studies. We describe the challenges and lessons learned when reusing OpenMRS data in Rwanda for global HIV epidemiology research.

}, keywords = {Biomedical Research, electronic health records, Epidemiologic Studies, HIV, Humans, Rwanda}, issn = {1879-8365}, doi = {10.3233/SHTI190620}, author = {Muhoza, Benjamin and Remera, Eric and Shi, Qiuhu and Kabahizi, Jules and Brazier, Ellen and Sinayobye, Jean d{\textquoteright}Amour and Duda, Stephany N} } @article {1268, title = {Census-independent population mapping in northern Nigeria.}, journal = {Remote Sens Environ}, volume = {204}, year = {2018}, month = {2018 Jan}, pages = {786-798}, abstract = {

Although remote sensing has long been used to aid in the estimation of population, it has usually been in the context of spatial disaggregation of national census data, with the census counts serving both as observational data for specifying models and as constraints on model outputs. Here we present a framework for estimating populations from the bottom up, entirely independently of national census data, a critical need in areas without recent and reliable census data. To make observations of population density, we replace national census data with a microcensus, in which we enumerate population for a sample of small areas within the states of Kano and Kaduna in northern Nigeria. Using supervised texture-based classifiers with very high resolution satellite imagery, we produce a binary map of human settlement at 8-meter resolution across the two states and then a more refined classification consisting of 7 residential types and 1 non-residential type. Using the residential types and a model linking them to the population density observations, we produce population estimates across the two states in a gridded raster format, at approximately 90-meter resolution. We also demonstrate a simulation framework for capturing uncertainty and presenting estimates as prediction intervals for any region of interest of any size and composition within the study region. Used in concert with previously published demographic estimates, our population estimates allowed for predictions of the population under 5 in ten administrative wards that fit strongly with reference data collected during polio vaccination campaigns.

}, issn = {0034-4257}, doi = {10.1016/j.rse.2017.09.024}, author = {Weber, Eric M and Seaman, Vincent Y and Stewart, Robert N and Bird, Tomas J and Tatem, Andrew J and McKee, Jacob J and Bhaduri, Budhendra L and Moehl, Jessica J and Reith, Andrew E} } @article {1203, title = {The {District} {Health} {Information} {System} ({DHIS}2): {A} literature review and meta-synthesis of its strengths and operational challenges based on the experiences of 11 countries}, journal = {Health Information Management: Journal of the Health Information Management Association of Australia}, year = {2018}, pages = {1833358318777713}, abstract = {BACKGROUND: Health information systems offer many potential benefits for healthcare, including financial benefits and for improving the quality of patient care. The purpose of District Health Information Systems (DHIS) is to document data that are routinely collected in all public health facilities in a country using the system. OBJECTIVE: The aim of this study was to examine the strengths and operational challenges of DHIS2, with a goal to enable decision makers in different counties to more accurately evaluate the outcomes of introducing DHIS2 into their particular country. METHOD: A review of the literature combined with the method of meta-synthesis was used to source information and interpret results relating to the strengths and operational challenges of DHIS2. Databases (Embase, PubMed, Scopus and Google Scholar) were searched for documents related to strengths and operational challenges of DHIS2, with no time limit up to 8 April 2017. The review and evaluation of selected studies was conducted in three stages: title, abstract and full text. Each of the selected studies was reviewed carefully and key concepts extracted. These key concepts were divided into two categories of strengths and operational challenges of DHIS2. Then, each category was grouped based on conceptual similarity to achieve the main themes and sub-themes. Content analysis was used to analyse extracted data. RESULTS: Of 766 identified citations, 20 studies from 11 countries were included and analysed in this study. Identified strengths in the DHIS were represented in seven themes (with 21 categories): technical features of software, proper management of data, application flexibility, networking and increasing the satisfaction of stakeholders, development of data management, increasing access to information and economic benefits. Operational challenges were identified and captured in 11 themes (with 18 categories): funds; appropriate communication infrastructure; the need for the existence of appropriate data; political, cultural, social and structural infrastructure; manpower; senior managers; training; using academic potentials; definition and standardising the deployment processes; neglect to application of criteria and clinical guidelines in the use of system; data security; stakeholder communications challenges and the necessity to establish a pilot system. CONCLUSION: This study highlighted specific strengths in the technical and functional aspects of DHIS2 and also drew attention to particular challenges and concerns. These results provide a sound evidence base for decision makers and policymakers to enable them to make more accurate decisions about whether or not to use the DHIS2 in the health system of their country.}, keywords = {content analysis, District Health Information System, health information system, health information technology, information technology, meta-synthesis, qualitative research}, issn = {1322-4913}, doi = {10.1177/1833358318777713}, author = {Dehnavieh, Reza and Haghdoost, AliAkbar and Khosravi, Ardeshir and Hoseinabadi, Fahime and Rahimi, Hamed and Poursheikhali, Atousa and Khajehpour, Nahid and Khajeh, Zahra and Mirshekari, Nadia and Hasani, Marziyeh and Radmerikhi, Samera and Haghighi, Hajar and Mehrolhassani, Mohammad Hossain and Kazemi, Elaheh and Aghamohamadi, Saeide} } @article {1283, title = {How do paper and electronic records compare for completeness? A three centre study.}, journal = {Eye (Lond)}, volume = {32}, year = {2018}, month = {2018 07}, pages = {1232-1236}, abstract = {

OBJECTIVES: Medical records are legal documentation of patients{\textquoteright} care hence must be accurate and complete for both medical and legal purposes. Electronic patient record (EPR) systems aim to improve the accuracy of documentation, provide better organisation and access of data. This study compares the completeness of traditional note records and EPR in glaucoma patients.

METHODS: Using criteria from the April 2009 National Institute for Health and Care Excellence (NICE) guidelines completeness of data entry was compared between EPR and paper notes in three units. Moorfields Eye Hospital (City Road) uses the Openeyes EPR. Bedford Hospital (Moorfields Eye Centre) and Western Eye Hospital use the Medisoft EPR. The standard was set at 100\% compliance for predetermined parameters.

RESULTS: One hundred seventy paper notes and 270 electronic records were analysed. With the exception of central corneal thickness (p = 0.31), all other key parameters were more consistently recorded in the paper records than in the EPR. Intraocular pressure (p = 0.004), anterior chamber configuration and depth assessments using gonioscopy (p < 0.001), fundus examination (p = 0.015), past medical history (p < 0.001), medication including glaucoma medication (p < 0.001) and drug allergies (p < 0.001).

CONCLUSIONS: Our results show that paper records are significantly more complete than EPR. This is the case for two different EPRs and three separate sites. We propose additional training to aid data-collection; improving the design of EPRs by investigating factors such as layout and use of forced choice fields.

}, keywords = {electronic health records, Glaucoma, Humans, Medical Records, Ophthalmology}, issn = {1476-5454}, doi = {10.1038/s41433-018-0065-8}, author = {Wu, Clara Hoi Ka and Luk, Sheila M H and Holder, Richard L and Rodrigues, Zena and Ahmed, Faisal and Murdoch, Ian} } @article {1287, title = {Landmark detection in 2D bioimages for geometric morphometrics: a multi-resolution tree-based approach.}, journal = {Sci Rep}, volume = {8}, year = {2018}, month = {2018 01 11}, pages = {538}, abstract = {

The detection of anatomical landmarks in bioimages is a necessary but tedious step for geometric morphometrics studies in many research domains. We propose variants of a multi-resolution tree-based approach to speed-up the detection of landmarks in bioimages. We extensively evaluate our method variants on three different datasets (cephalometric, zebrafish, and drosophila images). We identify the key method parameters (notably the multi-resolution) and report results with respect to human ground truths and existing methods. Our method achieves recognition performances competitive with current existing approaches while being generic and fast. The algorithms are integrated in the open-source Cytomine software and we provide parameter configuration guidelines so that they can be easily exploited by end-users. Finally, datasets are readily available through a Cytomine server to foster future research.

}, keywords = {Algorithms, Animals, Body Weights and Measures, Drosophila, Humans, Image Processing, Computer-Assisted, Software, Zebrafish}, issn = {2045-2322}, doi = {10.1038/s41598-017-18993-5}, author = {Vandaele, R{\'e}my and Aceto, Jessica and Muller, Marc and P{\'e}ronnet, Fr{\'e}d{\'e}rique and Debat, Vincent and Wang, Ching-Wei and Huang, Cheng-Ta and Jodogne, S{\'e}bastien and Martinive, Philippe and Geurts, Pierre and Mar{\'e}e, Rapha{\"e}l} } @article {1290, title = {mLearning in the Democratic Republic of the Congo: A Mixed-Methods Feasibility and Pilot Cluster Randomized Trial Using the Safe Delivery App.}, journal = {Glob Health Sci Pract}, volume = {6}, year = {2018}, month = {2018 12 27}, pages = {693-710}, abstract = {

BACKGROUND: Substandard delivery care has been widely documented as a major cause of maternal mortality in health facilities globally. Health worker learning via mobile devices is increasing rapidly; however, there is little evidence of mLearning effectiveness. This study sought to determine the feasibility, acceptability, and potential effect of the Safe Delivery App (SDA) on health workers{\textquoteright} practices in basic emergency obstetric and newborn care (BEmONC) in the Democratic Republic of the Congo (DRC). The Theoretical Domains Framework was used to guide this research.

METHODS: Eight BEmONC facilities in central DRC were randomized to either an mLearning intervention or to standard practice (control). Maternal and newborn health workers in intervention facilities (n=64) were trained on the use of smartphones and the French version of the SDA. The SDA is an evidence-based BEmONC training resource with visual guidance using animated videos and clinical management instructions developed by the Maternity Foundation and the Universities of Copenhagen and Southern Denmark. Knowledge on postpartum hemorrhage (PPH) and neonatal resuscitation (NR) and self-confidence in performing 12 BEmONC procedures were assessed at baseline and at 3 months post-intervention. Eighteen qualitative interviews were conducted with app users and key stakeholders to assess feasibility and acceptability of mLearning and the use of the SDA. Maternal mortality was compared in intervention and control facilities using a smartphone-based Open Data Kit (ODK) data application. One smartphone with SDA and ODK was entrusted to intervention facilities for the study period, whereas control facilities received smartphones with ODK only.

RESULTS: The analysis included 62 heath workers. Knowledge scores on postpartum hemorrhage and neonatal resuscitation increased significantly from baseline among intervention participants compared with controls at 3 months post-intervention (mean difference for PPH knowledge, 17.4 out of 100; 95\% confidence interval [CI]=10.7 to 24.0 and 19.4 for NR knowledge; 95\% CI=11.4 to 27.4), as did self-confidence scores on 12 essential BEmONC procedures (mean difference, 4.2 out of 48; CI=0.7 to 7.7). Increases were unaffected by health worker cadre and previous smartphone use. Qualitative interviews supported the feasibility and acceptability of the SDA and mLearning, and the potential for it to impact maternal and neonatal mortality in the DRC.

CONCLUSION: Use of the Safe Delivery App supported increased health worker knowledge and self-confidence in the management of obstetric and newborn emergencies after 3 months. SDA and mLearning were found to be feasible and acceptable to health workers and key stakeholders in the DRC.

}, keywords = {Congo, Feasibility Studies, Female, Humans, Infant Care, Infant, Newborn, Interviews as Topic, Male, Maternal Mortality, Mobile Applications, Obstetrics, Pilot Projects, qualitative research, Quality of Health Care}, issn = {2169-575X}, doi = {10.9745/GHSP-D-18-00275}, author = {Bolan, Nancy E and Sthreshley, Larry and Ngoy, Bernard and Ledy, Faustin and Ntayingi, Mano and Makasy, Davis and Mbuyi, Marie-Claude and Lowa, Gisele and Nemeth, Lynne and Newman, Susan} } @article {1224, title = {Towards Implementation of OMOP in a German University Hospital Consortium.}, journal = {Appl Clin Inform}, volume = {9}, year = {2018}, month = {2018 01}, pages = {54-61}, abstract = {

BACKGROUND: In 2015, the German Federal Ministry of Education and Research initiated a large data integration and data sharing research initiative to improve the reuse of data from patient care and translational research. The Observational Medical Outcomes Partnership (OMOP) common data model and the Observational Health Data Sciences and Informatics (OHDSI) tools could be used as a core element in this initiative for harmonizing the terminologies used as well as facilitating the federation of research analyses across institutions.

OBJECTIVE: To realize an OMOP/OHDSI-based pilot implementation within a consortium of eight German university hospitals, evaluate the applicability to support data harmonization and sharing among them, and identify potential enhancement requirements.

METHODS: The vocabularies and terminological mapping required for importing the fact data were prepared, and the process for importing the data from the source files was designed. For eight German university hospitals, a virtual machine preconfigured with the OMOP database and the OHDSI tools as well as the jobs to import the data and conduct the analysis was provided. Last, a federated/distributed query to test the approach was executed.

RESULTS: While the mapping of ICD-10 German Modification succeeded with a rate of 98.8\% of all terms for diagnoses, the procedures could not be mapped and hence an extension to the OMOP standard terminologies had to be made.Overall, the data of 3 million inpatients with approximately 26 million conditions, 21 million procedures, and 23 million observations have been imported.A federated query to identify a cohort of colorectal cancer patients was successfully executed and yielded 16,701 patient cases visualized in a Sunburst plot.

CONCLUSION: OMOP/OHDSI is a viable open source solution for data integration in a German research consortium. Once the terminology problems can be solved, researchers can build on an active community for further development.

}, keywords = {Cooperative Behavior, Germany, Health Plan Implementation, Hospitals, University, Humans, Outcome Assessment (Health Care), Surveys and Questionnaires, Vocabulary}, issn = {1869-0327}, doi = {10.1055/s-0037-1617452}, author = {Maier, C and Lang, L and Storf, H and Vormstein, P and Bieber, R and Bernarding, J and Herrmann, T and Haverkamp, C and Horki, P and Laufer, J and Berger, F and H{\"o}ning, G and Fritsch, H W and Sch{\"u}ttler, J and Ganslandt, T and Prokosch, H U and Sedlmayr, M} } @article {1277, title = {Barriers and facilitators to Electronic Medical Records usage in the Emergency Centre at Komfo Anokye Teaching Hospital, Kumasi-Ghana.}, journal = {Afr J Emerg Med}, volume = {7}, year = {2017}, month = {2017 Dec}, pages = {177-182}, abstract = {

Introduction: The use of paper for record keeping (or a manual system) has been the order of the day in almost all health care facilities in resource poor countries. This system has presented numerous challenges, which the use of Electronic Medical Records (EMR) seeks to address. The objectives of the study were to identify the facilitators and barriers to EMR implementation in Komfo Anokye Teaching Hospital{\textquoteright}s (KATH) Emergency Centre (EC) and to identify lessons learned. These will help in implementation of EMR in ECs in similar settings.

Methods: This was a non-interventional, descriptive cross-sectional and purely qualitative study using a semi-structured interview guide for a study population of 24. The interviews were manually recorded and analysed thematically. EMR implementation was piloted in the EC. Some of the EC staff doubled as EMR personnel. An open source EMR was freely downloaded and customised to meet the needs of the EC. The EMR database created was a hybrid one comprising of digital bio-data of patients and scanned copies of their paper EC records.

Results: The facilitators for utilising the system included providing training to staff, the availability of some logistics, and the commitment of staff. The project barriers were funding, full-time information technology expertise, and automatic data and power backups. It was observed that with the provision of adequate human and financial resources, the challenges were overcome and the adoption of the EMR improved.

Discussion: The EMR has been a partial success. The facilitators identified in this study, namely training, provision of logistics, and staff commitment represent foundations to work from. The barriers identified could be addressed with additional funding, provision of information technology expertise, and data and power back up. It is acknowledged that lack of funding could substantially limit EMR implementation.

}, issn = {2211-4203}, doi = {10.1016/j.afjem.2017.05.002}, author = {Gyamfi, Adwoa and Mensah, Kofi A and Oduro, George and Donkor, Peter and Mock, Charles N} } @article {1270, title = {Coverage of routine reporting on malaria parasitological testing in Kenya, 2015-2016.}, journal = {Glob Health Action}, volume = {10}, year = {2017}, month = {2017}, pages = {1413266}, abstract = {

BACKGROUND: Following the launch of District Health Information System 2 across facilities in Kenya, more health facilities are now capable of carrying out malaria parasitological testing and reporting data as part of routine health information systems, improving the potential value of routine data for accurate and timely tracking of rapidly changing disease epidemiology at fine spatial resolutions.

OBJECTIVES: This study evaluates the current coverage and completeness of reported malaria parasitological testing data in DHIS2 specifically looking at patterns in geographic coverage of public health facilities in Kenya.

METHODS: Monthly facility level data on malaria parasitological testing were extracted from Kenya DHIS2 between November 2015 and October 2016. DHIS2 public facilities were matched to a geo-coded master facility list to obtain coordinates. Coverage was defined as the geographic distribution of facilities reporting any data by region. Completeness of reporting was defined as the percentage of facilities reporting any data for the whole 12-month period or for 3, 6 and 9 months.

RESULTS: Public health facilities were 5,933 (59\%) of 10,090 extracted. Fifty-nine per Cent of the public facilities did not report any data while 36, 29 and 22\% facilities had data reported at least 3, 6 and 9 months, respectively. Only 8\% of public facilities had data reported for every month. There were proportionately more hospitals (86\%) than health centres (76\%) and dispensaries/clinics (30\%) reporting. There were significant geographic variations in reporting rates. Counties along the malaria endemic coast had the lowest reporting rate with only 1\% of facilities reporting consistently for 12 months.

CONCLUSION: Current coverage and completeness of reporting of malaria parasitological diagnosis across Kenya{\textquoteright}s public health system remains poor. The usefulness of routine data to improve our understanding of sub-national heterogeneity across Kenya would require significant improvements to the consistency and coverage of data captured by DHIS2.

}, keywords = {Health Facilities, Health information systems, Humans, Kenya, Malaria, Mandatory Reporting, Public Health Surveillance}, issn = {1654-9880}, doi = {10.1080/16549716.2017.1413266}, author = {Maina, Joseph K and Macharia, Peter M and Ouma, Paul O and Snow, Robert W and Okiro, Emelda A} } @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 {1160, title = {Donor{\textquoteright}s support tool: {Enabling} informed secondary use of patient{\textquoteright}s biomaterial and personal data}, journal = {International Journal of Medical Informatics}, volume = {97}, year = {2017}, pages = {282{\textendash}292}, abstract = {PURPOSE: Biomedical research is being catalyzed by the vast amount of data rapidly collected through the application of information technologies (IT). Despite IT advances, the methods for involving patients and citizens in biomedical research remain static, paper-based and organized around national boundaries and anachronistic legal frameworks. The purpose of this paper is to study the current practices for obtaining consent for biobanking and the legal requirements for reusing the available biomaterial and data in EU and finally to present a novel tool to this direction enabling the secondary use of data and biomaterial. METHOD: We review existing European legislation for secondary use of patient{\textquoteright}s biomaterial and data for research, identify types and scopes of consent, formal requirements for consent, and consider their implications for implementing electronic consent tools. To this direction, we proceed further to develop a modular tool, named Donor{\textquoteright}s Support Tool (DST), designed to connect researchers with participants, and to promote engagement, informed participation and individual decision making. RESULTS: To identify the advantages of our solution we compare our tool with six other relevant approaches. The results show that our tool scores higher than the other tools in functionality, security and intelligence whereas it is the only one free and open-source. In addition, the potential of our solution is shown by a proof of concept deployment in an existing clinical setting, where it was really appreciated, as streamlining the relevant workflow.}, keywords = {Biobank, Dynamic consent, Electronic consent, Secondary use of biomaterial and personal data}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.10.019}, author = {Kondylakis, Haridimos and Koumakis, Lefteris and H{\"a}nold, Stephanie and Nwankwo, Iheanyi and Forg{\'o}, Nikolaus and Marias, Kostas and Tsiknakis, Manolis and Graf, Norbert} } @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 {1206, title = {Health care consumer{\textquoteright}s perception of the {Electronic} {Medical} {Record} ({EMR}) system within a referral hospital in {Kigali}, {Rwanda}}, journal = {Rwanda Journal}, volume = {4}, year = {2017}, pages = {48{\textendash}53{\textendash}53}, abstract = {Background: Worldwide Electronic Medical Records (EMR) when compared to a paper-based system has been proven to improve service delivering numerous health care facilities. However, no research has been described in the literature regarding the user{\textquoteright}s perception of the clinical electronic medical record (EMR) system in Rwanda. The objective of this study is to evaluate the health care consumer{\textquoteright}s perception of the Electronic Medical Record (EMR) OpenClinic regarding improving the quality of health care delivery within the hospital setting. How does the OpenClinic system affect the patients{\textquoteright} waiting time? How complete is the information obtained from OpenClinic as compared to paper medical records, and the level of satisfaction of the users of OpenClinic.Method: A structured questionnaire was developed, validated and utilized in this quantitative research project. Quantitative data were collected from 170 participants while an interview guide was used to collect qualitative data from 6 key informants at a referral hospital in Kigali. The SPSS version 20.0 was used to analyze the quantitative data. The interviews transcribed verbatim; the data were thematically analyzed and categorized by pre-determined themes. Permission to conduct the study was approved from the ethics committee of the University of Rwanda, College of Health Sciences and the hospital.Results: The majority of the participants were satisfied with OpenClinic, (90\%), while only a few (10\%) did not perceive any advantage of a computer-based EMR and preferred paper based records.Conclusion: Openclinc EMR was seen to be an improvement in the data collection involving health care delivery in Kigali, Rwanda.Keywords: Electronic Medical Records, OpenClinic and Perceptions}, keywords = {Electronic medical records, OpenClinic and Perceptions}, issn = {2305-2678}, doi = {10.4314/rj.v4i1.7F}, url = {https://www.ajol.info/index.php/rj/article/view/156412}, author = {Uwambaye, Peace and Njunwa, Kato and Nuhu, Assouman and Kumurenzi, Anne and Isyagi, Moses and Murererehe, Julienne and Ngarambe, Donart} } @article {1294, title = {How the introduction of a human resources information system helped the Democratic Republic of Congo to mobilise domestic resources for an improved health workforce.}, journal = {Health Policy Plan}, volume = {32}, year = {2017}, month = {2017 Nov 01}, pages = {iii25-iii31}, abstract = {

The Democratic Republic of Congo has flagged health workforce management and compensation as issues requiring attention, including the problem of ghost workers (individuals on payroll who do not exist and/or show up at work). Recognising the need for reliable health workforce information, the government has worked to implement iHRIS, an open source human resources information system that facilitates health workforce management. In Kasa{\"\i} Central and Kasa{\"\i} Provinces, health workers brought relevant documentation to data collection points, where trained teams interviewed them and entered contact information, identification, photo, current job, and employment and education history into iHRIS on laptops. After uploading the data, the Ministry of Public Health used the database of over 11 500 verified health worker records to analyse health worker characteristics, density, compensation, and payroll. Both provinces had less than one physician per 10 000 population and a higher urban versus rural health worker density. Most iHRIS-registered health workers (57\% in Kasa{\"\i} Central and 73\% in Kasa{\"\i}) reported receiving no regular government pay of any kind (salaries or risk allowances). Payroll analysis showed that 27\% of the health workers listed as salary recipients in the electronic payroll system were ghost workers, as were 42\% of risk allowance recipients. As a result, the Ministries of Public Health, Public Service, and Finance reallocated funds away from ghost workers to cover salaries (n = 781) and risk allowances (n = 2613) for thousands of health workers who were previously under- or uncompensated due to lack of funds. The reallocation prioritised previously under- or uncompensated mid-level health workers, with 49\% of those receiving salaries and 68\% of those receiving risk allowances representing cadres such as nurses, laboratory technicians, and midwifery cadres. Assembling accurate health worker records can help governments understand health workforce characteristics and use data to direct scarce domestic resources to where they are most needed.

}, keywords = {Democratic Republic of the Congo, Health Personnel, Health Workforce, Humans, Management Information Systems, Personnel Management, Remuneration}, issn = {1460-2237}, doi = {10.1093/heapol/czx113}, author = {Likofata Esanga, Jean-Robert and Viadro, Claire and McManus, Leah and Wesson, Jennifer and Matoko, Nicaise and Ngumbu, Epiphane and Gilroy, Kate E and Trudeau, Daren} } @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 {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 {1174, title = {A national standards-based assessment on functionality of electronic medical records systems used in {Kenyan} public-{Sector} health facilities}, journal = {International Journal of Medical Informatics}, volume = {97}, year = {2017}, pages = {68{\textendash}75}, abstract = {BACKGROUND: Variations in the functionality, content and form of electronic medical record systems (EMRs) challenge national roll-out of these systems as part of a national strategy to monitor HIV response. To enforce the EMRs minimum requirements for delivery of quality HIV services, the Kenya Ministry of Health (MoH) developed EMRs standards and guidelines. The standards guided the recommendation of EMRs that met a preset threshold for national roll-out. METHODS: Using a standards-based checklist, six review teams formed by the MoH EMRs Technical Working Group rated a total of 17 unique EMRs in 28 heath facilities selected by individual owners for their optimal EMR implementation. EMRs with an aggregate score of >=60\% against checklist criteria were identified by the MoH as suitable for upgrading and rollout to Kenyan public health facilities. RESULTS: In Kenya, existing EMRs scored highly in health information and reporting (mean score=71.8\%), followed by security, system features, core clinical information, and order entry criteria (mean score=58.1\%-55.9\%), and lowest against clinical decision support (mean score=17.6\%) and interoperability criteria (mean score=14.3\%). Four EMRs met the 60.0\% threshold: OpenMRS, IQ-Care, C-PAD and Funsoft. On the basis of the review, the MoH provided EMRs upgrade plans to owners of all the 17 systems reviewed. CONCLUSION: The standards-based review in Kenya represents an effort to determine level of conformance to the EMRs standards and prioritize EMRs for enhancement and rollout. The results support concentrated use of resources towards development of the four recommended EMRs. Further review should be conducted to determine the effect of the EMR-specific upgrade plans on the other 13 EMRs that participated in the review exercise.}, keywords = {Checklist, EMRs, Review, Standards}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.09.013}, author = {Kang{\textquoteright}a, Samuel and Puttkammer, Nancy and Wanyee, Steven and Kimanga, Davies and Madrano, Jason and Muthee, Veronica and Odawo, Patrick and Sharma, Anjali and Oluoch, Tom and Robinson, Katherine and Kwach, James and Lober, William B.} } @article {1205, title = {Open-{Source} {Electronic} {Health} {Record} {Systems} for {Low}-{Resource} {Settings}: {Systematic} {Review}}, journal = {JMIR Medical Informatics}, volume = {5}, year = {2017}, abstract = {Background Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas. Objective The aim of this study was to conduct a systematic review of open-source EHR systems based on the requirements and limitations of low-resource settings. Methods First, we reviewed existing literature on the comparison of available open-source solutions. In close collaboration with the University of Gondar Hospital, Ethiopia, we identified common limitations in poor resource environments and also the main requirements that EHRs should support. Then, we extensively evaluated the current open-source EHR solutions, discussing their strengths and weaknesses, and their appropriateness to fulfill a predefined set of features relevant for low-resource settings. Results The evaluation methodology allowed assessment of several key aspects of available solutions that are as follows: (1) integrated applications, (2) configurable reports, (3) custom reports, (4) custom forms, (5) interoperability, (6) coding systems, (7) authentication methods, (8) patient portal, (9) access control model, (10) cryptographic features, (11) flexible data model, (12) offline support, (13) native client, (14) Web client,(15) other clients, (16) code-based language, (17) development activity, (18) modularity, (19) user interface, (20) community support, and (21) customization. The quality of each feature is discussed for each of the evaluated solutions and a final comparison is presented. Conclusions There is a clear demand for open-source, reliable, and flexible EHR systems in low-resource settings. In this study, we have evaluated and compared five open-source EHR systems following a multidimensional methodology that can provide informed recommendations to other implementers, developers, and health care professionals. We hope that the results of this comparison can guide decision making when needing to adopt, install, and maintain an open-source EHR solution in low-resource settings.}, issn = {2291-9694}, doi = {10.2196/medinform.8131}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703976/}, author = {Syzdykova, Assel and Malta, Andr{\'e} and Zolfo, Maria and Diro, Ermias and Oliveira, Jos{\'e} Lu{\'\i}s} } @article {1202, title = {Open-source mobile digital platform for clinical trial data collection in low-resource settings}, journal = {BMJ innovations}, volume = {3}, year = {2017}, pages = {26{\textendash}31}, abstract = {BACKGROUND: Governments, universities and pan-African research networks are building durable infrastructure and capabilities for biomedical research in Africa. This offers the opportunity to adopt from the outset innovative approaches and technologies that would be challenging to retrofit into fully established research infrastructures such as those regularly found in high-income countries. In this context we piloted the use of a novel mobile digital health platform, designed specifically for low-resource environments, to support high-quality data collection in a clinical research study. OBJECTIVE: Our primary aim was to assess the feasibility of a using a mobile digital platform for clinical trial data collection in a low-resource setting. Secondarily, we sought to explore the potential benefits of such an approach. METHODS: The investigative site was a research institute in Nairobi, Kenya. We integrated an open-source platform for mobile data collection commonly used in the developing world with an open-source, standard platform for electronic data capture in clinical trials. The integration was developed using common data standards (Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model), maximising the potential to extend the approach to other platforms. The system was deployed in a pharmacokinetic study involving healthy human volunteers. RESULTS: The electronic data collection platform successfully supported conduct of the study. Multidisciplinary users reported high levels of satisfaction with the mobile application and highlighted substantial advantages when compared with traditional paper record systems. The new system also demonstrated a potential for expediting data quality review. DISCUSSION AND CONCLUSIONS: This pilot study demonstrated the feasibility of using a mobile digital platform for clinical research data collection in low-resource settings. Sustainable scientific capabilities and infrastructure are essential to attract and support clinical research studies. Since many research structures in Africa are being developed anew, stakeholders should consider implementing innovative technologies and approaches.}, keywords = {clinical research, eSource, Global Health, mHealth, Reverse Innovations}, issn = {2055-642X}, doi = {10.1136/bmjinnov-2016-000164}, author = {van Dam, Joris and Omondi Onyango, Kevin and Midamba, Brian and Groosman, Nele and Hooper, Norman and Spector, Jonathan and Pillai, Goonaseelan Colin and Ogutu, Bernhards} } @article {1189, title = {Orchestrating differential data access for translational research: a pilot implementation}, journal = {BMC Medical Informatics and Decision Making}, volume = {17}, year = {2017}, month = {2017}, pages = {30}, abstract = {BACKGROUND: Translational researchers need robust IT solutions to access a range of data types, varying from public data sets to pseudonymised patient information with restricted access, provided on a case by case basis. The reason for this complication is that managing access policies to sensitive human data must consider issues of data confidentiality, identifiability, extent of consent, and data usage agreements. All these ethical, social and legal aspects must be incorporated into a differential management of restricted access to sensitive data. METHODS: In this paper we present a pilot system that uses several common open source software components in a novel combination to coordinate access to heterogeneous biomedical data repositories containing open data (open access) as well as sensitive data (restricted access) in the domain of biobanking and biosample research. Our approach is based on a digital identity federation and software to manage resource access entitlements. RESULTS: Open source software components were assembled and configured in such a way that they allow for different ways of restricted access according to the protection needs of the data. We have tested the resulting pilot infrastructure and assessed its performance, feasibility and reproducibility. CONCLUSIONS: Common open source software components are sufficient to allow for the creation of a secure system for differential access to sensitive data. The implementation of this system is exemplary for researchers facing similar requirements for restricted access data. Here we report experience and lessons learnt of our pilot implementation, which may be useful for similar use cases. Furthermore, we discuss possible extensions for more complex scenarios.}, isbn = {1472-6947}, doi = {10.1186/s12911-017-0424-6}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5363029/}, author = {Brandizi, Marco and Melnichuk, Olga and Bild, Raffael and Kohlmayer, Florian and Rodriguez-Castro, Benedicto and Spengler, Helmut and Kuhn, Klaus A and Kuchinke, Wolfgang and Ohmann, Christian and Mustonen, Timo and Linden, Mikael and Nyr{\"o}nen, Tommi and Lappalainen, Ilkka and Brazma, Alvis and Sarkans, Ugis} } @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 {1291, title = {Using Android and Open Data Kit Technology in Data Management for Research in Resource-Limited Settings in the Niger Delta Region of Nigeria: Cross-Sectional Household Survey.}, journal = {JMIR Mhealth Uhealth}, volume = {5}, year = {2017}, month = {2017 Nov 30}, pages = {e171}, abstract = {

BACKGROUND: Data collection in Sub-Saharan Africa has traditionally been paper-based. However, the popularization of Android mobile devices and data capture software has brought paperless data management within reach. We used Open Data Kit (ODK) technology on Android mobile devices during a household survey in the Niger Delta region of Nigeria.

OBJECTIVE: The aim of this study was to describe the pros and cons of deploying ODK for data management.

METHODS: A descriptive cross-sectional household survey was carried out by 6 data collectors between April and May 2016. Data were obtained from 1706 persons in 601 households across 6 communities in 3 states in the Niger Delta. The use of Android mobile devices and ODK technology involved form building, testing, collection, aggregation, and download for data analysis. The median duration for data collection per household and per individual was 25.7 and 9.3 min, respectively.

RESULTS: Data entries per device ranged from 33 (33/1706, 1.93\%) to 482 (482/1706, 28.25\%) individuals between 9 (9/601, 1.5\%) and 122 (122/601, 20.3\%) households. The most entries (470) were made by data collector 5. Only 2 respondents had data entry errors (2/1706, 0.12\%). However, 73 (73/601, 12.1\%) households had inaccurate date and time entries for when data collection started and ended. The cost of deploying ODK was estimated at US $206.7 in comparison with the estimated cost of US $466.7 for paper-based data management.

CONCLUSIONS: We found the use of mobile data capture technology to be efficient and cost-effective. As Internet services improve in Africa, we advocate their use as effective tools for health information management.

}, issn = {2291-5222}, doi = {10.2196/mhealth.7827}, author = {Maduka, Omosivie and Akpan, Godwin and Maleghemi, Sylvester} } @article {1134, title = {Assessment of four common underfive children illnesses Routine Health Management Information System data for decision making at Ilemela Municipal Council, Northwest Tanzania: A case series analysis.}, journal = {Int J Med Inform}, volume = {93}, year = {2016}, month = {2016 Sep}, pages = {85-91}, abstract = {

BACKGROUND: In 2012, The Tanzania Ministry Of Health introduced the revised Routine Health Management Information System (RHMIS) modules and registers, and introduced the open source software for data collection at the district council level. Despite a series of data collection tools revisions, the quality of data collated from both public and private primary health care facilities has not been investigated.

METHODS: A case series study design was conducted on underfive children outpatient registers and monthly reports on malaria, acute respiratory infections, acute diarrhoea and pneumonia from 10 randomly selected health facilities. The data was entered into excel software and exported to stata version 11 for analysis. The data was analyzed for completeness, timely report submission and reporting accuracy.

RESULTS: The Study found that 62\% of the expected data was complete. Around 40\% of the facilities submitted reports on time. Private health facilities submitted monthly reports late compared to the public facilities (p-value=0.039). There was 26\% over-reporting of diagnosis. Health centres tended to over-report more diagnoses by 11 times higher than the dispensaries. In addition, private owned health facilities tended to over-report more diagnoses by 6 times higher than public owned health facilities.

CONCLUSION: The RHMIS data collected through out patients department (OPD) registers on four common underfive children{\textquoteright}s illnesses at ilemela municipality were of unsatisfactory quality in light of allocation of resource allocations in the comprehensive council health plan.

}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.06.003}, author = {Kabakama, Severin and Ngallaba, Sospatro and Musto, Richard and Montesanti, Stephanie and Konje, Eveline and Kishamawe, Coleman} } @article {1172, title = {Automated population of an i2b2 clinical data warehouse from an {openEHR}-based data repository}, journal = {Journal of Biomedical Informatics}, volume = {63}, year = {2016}, pages = {277{\textendash}294}, abstract = {BACKGROUND: Detailed Clinical Model (DCM) approaches have recently seen wider adoption. More specifically, openEHR-based application systems are now used in production in several countries, serving diverse fields of application such as health information exchange, clinical registries and electronic medical record systems. However, approaches to efficiently provide openEHR data to researchers for secondary use have not yet been investigated or established. METHODS: We developed an approach to automatically load openEHR data instances into the open source clinical data warehouse i2b2. We evaluated query capabilities and the performance of this approach in the context of the Hanover Medical School Translational Research Framework (HaMSTR), an openEHR-based data repository. RESULTS: Automated creation of i2b2 ontologies from archetypes and templates and the integration of openEHR data instances from 903 patients of a paediatric intensive care unit has been achieved. In total, it took an average of \~{}2527s to create 2.311.624 facts from 141.917 XML documents. Using the imported data, we conducted sample queries to compare the performance with two openEHR systems and to investigate if this representation of data is feasible to support cohort identification and record level data extraction. DISCUSSION: We found the automated population of an i2b2 clinical data warehouse to be a feasible approach to make openEHR data instances available for secondary use. Such an approach can facilitate timely provision of clinical data to researchers. It complements analytics based on the Archetype Query Language by allowing querying on both, legacy clinical data sources and openEHR data instances at the same time and by providing an easy-to-use query interface. However, due to different levels of expressiveness in the data models, not all semantics could be preserved during the ETL process.}, keywords = {Archetypes, Clinical data repository, clinical information systems, Data warehouse, Detailed clinical models, Healthcare analytics, i2b2, openEHR, Secondary use}, issn = {1532-0480}, doi = {10.1016/j.jbi.2016.08.007}, author = {Haarbrandt, Birger and Tute, Erik and Marschollek, Michael} } @article {1237, title = {Automating indicator data reporting from health facility EMR to a national aggregate data system in Kenya: An Interoperability field-test using OpenMRS and DHIS2.}, journal = {Online J Public Health Inform}, volume = {8}, year = {2016}, month = {2016}, pages = {e188}, abstract = {

Developing countries are increasingly strengthening national health information systems (HIS) for evidence-based decision-making. However, the inability to report indicator data automatically from electronic medical record systems (EMR) hinders this process. Data are often printed and manually re-entered into aggregate reporting systems. This affects data completeness, accuracy, reporting timeliness, and burdens staff who support routine indicator reporting from patient-level data. After conducting a feasibility test to exchange indicator data from Open Medical Records System (OpenMRS) to District Health Information System version 2 (DHIS2), we conducted a field test at a health facility in Kenya. We configured a field-test DHIS2 instance, similar to the Kenya Ministry of Health (MOH) DHIS2, to receive HIV care and treatment indicator data and the KenyaEMR, a customized version of OpenMRS, to generate and transmit the data from a health facility. After training facility staff how to send data using DHIS2 reporting module, we compared completeness, accuracy and timeliness of automated indicator reporting with facility monthly reports manually entered into MOH DHIS2. All 45 data values in the automated reporting process were 100\% complete and accurate while in manual entry process, data completeness ranged from 66.7\% to 100\% and accuracy ranged from 33.3\% to 95.6\% for seven months (July 2013-January 2014). Manual tally and entry process required at least one person to perform each of the five reporting activities, generating data from EMR and manual entry required at least one person to perform each of the three reporting activities, while automated reporting process had one activity performed by one person. Manual tally and entry observed in October 2013 took 375 minutes. Average time to generate data and manually enter into DHIS2 was over half an hour (M=32.35 mins, SD=0.29) compared to less than a minute for automated submission (M=0.19 mins, SD=0.15). The results indicate that indicator data sent electronically from OpenMRS-based EMR at a health facility to DHIS2 improves data completeness, eliminates transcription errors and delays in reporting, and reduces the reporting burden on human resources. This increases availability of quality indicator data using available resources to facilitate monitoring service delivery and measuring progress towards set goals.

}, issn = {1947-2579}, doi = {10.5210/ojphi.v8i2.6722}, author = {Kariuki, James M and Manders, Eric-Jan and Richards, Janise and Oluoch, Tom and Kimanga, Davies and Wanyee, Steve and Kwach, James O and Santas, Xenophon} } @article {1157, title = {Benefits, {Challenges} and {Potential} {Strategies} of {Open} {Source} {Health} {Economic} {Models}}, journal = {PharmacoEconomics}, year = {2016}, issn = {1179-2027}, doi = {10.1007/s40273-016-0479-8}, author = {Dunlop, William C. N. and Mason, Nicola and Kenworthy, James and Akehurst, Ron L.} } @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 {1288, title = {Collaborative analysis of multi-gigapixel imaging data using Cytomine.}, journal = {Bioinformatics}, volume = {32}, year = {2016}, month = {2016 05 01}, pages = {1395-401}, abstract = {

MOTIVATION: Collaborative analysis of massive imaging datasets is essential to enable scientific discoveries.

RESULTS: We developed Cytomine to foster active and distributed collaboration of multidisciplinary teams for large-scale image-based studies. It uses web development methodologies and machine learning in order to readily organize, explore, share and analyze (semantically and quantitatively) multi-gigapixel imaging data over the internet. We illustrate how it has been used in several biomedical applications.

AVAILABILITY AND IMPLEMENTATION: Cytomine (http://www.cytomine.be/) is freely available under an open-source license from http://github.com/cytomine/ A documentation wiki (http://doc.cytomine.be) and a demo server (http://demo.cytomine.be) are also available.

CONTACT: info@cytomine.be

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

}, keywords = {Image Interpretation, Computer-Assisted, Internet, Software, Statistics as Topic}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btw013}, author = {Mar{\'e}e, Rapha{\"e}l and Rollus, Lo{\"\i}c and St{\'e}vens, Benjamin and Hoyoux, Renaud and Louppe, Gilles and Vandaele, R{\'e}my and Begon, Jean-Michel and Kainz, Philipp and Geurts, Pierre and Wehenkel, Louis} } @article {1167, title = {{ConoSurf}: {Open}-source 3D scanning system based on a conoscopic holography device for acquiring surgical surfaces}, journal = {The international journal of medical robotics + computer assisted surgery: MRCAS}, year = {2016}, abstract = {BACKGROUND: A difficulty in computer-assisted interventions is acquiring the patient{\textquoteright}s anatomy intraoperatively. Standard modalities have several limitations: low image quality (ultrasound), radiation exposure (computed tomography) or high costs (magnetic resonance imaging). An alternative approach uses a tracked pointer; however, the pointer causes tissue deformation and requires sterilizing. Recent proposals, utilizing a tracked conoscopic holography device, have shown promising results without the previously mentioned drawbacks. METHODS: We have developed an open-source software system that enables real-time surface scanning using a conoscopic holography device and a wide variety of tracking systems, integrated into pre-existing and well-supported software solutions. RESULTS: The mean target registration error of point measurements was 1.46~mm. For a quick guidance scan, surface reconstruction improved the surface registration error compared with point-set registration. CONCLUSIONS: We have presented a system enabling real-time surface scanning using a tracked conoscopic holography device. Results show that it can be useful for acquiring the patient{\textquoteright}s anatomy during surgery.}, issn = {1478-596X}, doi = {10.1002/rcs.1788}, author = {Brudfors, Mikael and Garc{\'\i}a-V{\'a}zquez, Ver{\'o}nica and Ses{\'e}-Lucio, Bego{\~n}a and Marinetto, Eugenio and Desco, Manuel and Pascau, Javier} } @article {1129, title = {Development of an Open Source Educational Resource: "Clinical Procedures for Safer Patient Care".}, journal = {Stud Health Technol Inform}, volume = {225}, year = {2016}, month = {2016}, pages = {979-80}, abstract = {

An Open Education Resource (OER) has been developed by two nurse educators to address inconsistencies in how clinical health care skills are taught and practiced in the clinical setting, and to ensure best practice and quality care based on the latest evidence. A checklist approach aims to provide clear steps and rationale for procedures, standardized processes for clinical skills and to assist nursing schools and clinical practice partners in teaching clinical skills, and keeping procedural practice current. The format is logical, organized and focused on patient safety, and will provide information retrieval opportunities at the point of care to support decisions and plan patient care. This poster discusses the development of this resource, the framework used, and the process from conception to distribution.

}, issn = {0926-9630}, author = {Doyle, Glynda and McCutcheon, Jodie} } @article {1130, title = {Development of an open technology sensor suite for assisted living: a student-led research project.}, journal = {Interface Focus}, volume = {6}, year = {2016}, month = {2016 Aug 6}, pages = {20160018}, abstract = {

Many countries have a rapidly ageing population, placing strain on health services and creating a growing market for assistive technology for older people. We have, through a student-led, 12-week project for 10 students from a variety of science and engineering backgrounds, developed an integrated sensor system to enable older people, or those at risk, to live independently in their own homes for longer, while providing reassurance for their family and carers. We provide details on the design procedure and performance of our sensor system and the management and execution of a short-term, student-led research project. Detailed information on the design and use of our devices, including a door sensor, power monitor, fall detector, general in-house sensor unit and easy-to-use location-aware communications device, is given, with our open designs being contrasted with closed proprietary systems. A case study is presented for the use of our devices in a real-world context, along with a comparison with commercially available systems. We discuss how the system could lead to improvements in the quality of life of older users and increase the effectiveness of their associated care network. We reflect on how recent developments in open source technology and rapid prototyping increase the scope and potential for the development of powerful sensor systems and, finally, conclude with a student perspective on this team effort and highlight learning outcomes, arguing that open technologies will revolutionize the way in which technology will be deployed in academic research in the future.

}, issn = {2042-8898}, doi = {10.1098/rsfs.2016.0018}, author = {Manton, James D and Hughes, Josephine A E and Bonner, Oliver and Amjad, Omar A and Mair, Philip and Miele, Isabella and Wang, Tiesheng and Levdik, Vitaly and Hall, Richard D and Baekelandt, G{\'e}raldine and Vasconcellos, Fernando da Cruz and Hadeler, Oliver and Hutter, Tanya and Kaminski, Clemens F} } @article {1120, title = {Development of an open-source web-based intervention for Brazilian smokers - Viva sem Tabaco.}, journal = {BMC Med Inform Decis Mak}, volume = {16}, year = {2016}, month = {2016}, pages = {103}, abstract = {

BACKGROUND: Web-based interventions for smoking cessation available in Portuguese do not adhere to evidence-based treatment guidelines. Besides, all existing web-based interventions are built on proprietary platforms that developing countries often cannot afford. We aimed to describe the development of "Viva sem Tabaco", an open-source web-based intervention.

RESULTS: The development of the intervention included the selection of content from evidence-based guidelines for smoking cessation, the design of the first layout, conduction of 2 focus groups to identify potential features, refinement of the layout based on focus groups and correction of content based on feedback provided by specialists on smoking cessation. At the end, we released the source-code and intervention on the Internet and translated it into Spanish and English.

CONCLUSIONS: The intervention developed fills gaps in the information available in Portuguese and the lack of open-source interventions for smoking cessation. The open-source licensing format and its translation system may help researchers from different countries deploying evidence-based interventions for smoking cessation.

}, issn = {1472-6947}, doi = {10.1186/s12911-016-0339-7}, author = {Gomide, H P and Bernardino, H S and Richter, K and Martins, L F and Ronzani, T M} } @article {1169, title = {dot-app: a {Graphviz}-{Cytoscape} conversion plug-in}, journal = {F1000Research}, volume = {5}, year = {2016}, pages = {2543}, abstract = {dot-app is a Cytoscape 3 app that allows Cytoscape to import and export Graphviz (*.dot, *.gv) files, also known as DOT files due to the *.dot extension and their conformance to the DOT language syntax. The DOT format was originally created in the early 2000s to represent graph topologies, layouts and formatting. DOT-encoded files are produced and consumed by a number of open-source graph applications, including GraphViz, Gephi, neato, smyrna, and others. While DOT-based graph applications are popular, they emphasize general graph layout and styling over the topological and semantic analysis functions available in domain-focused applications such as Cytoscape. While domain-focused applications have easy access to large networks (10,000 to 100,000 nodes) and advanced analysis and formatting, they do not offer all of the styling options that DOT-based applications (particularly GraphViz) do. dot-app enables the interchange of networks between Cytoscape and DOT-based applications so that users can benefit from the features of both. dot-app was first deployed to the Cytoscape App Store in August 2015, has since registered more than 1,200 downloads, and has been highly rated by more than 20 users.}, keywords = {attribute conversion, Cytoscape, Data visualization, DOT, export, format conversion, GraphViz, import, Network}, doi = {10.12688/f1000research.9751.1}, author = {Fitts, Braxton and Zhang, Ziran and Maher, Massoud and Demchak, Barry} } @article {1137, title = {How open science helps researchers succeed.}, journal = {Elife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Open access, open data, open source and other open scholarship practices are growing in popularity and necessity. However, widespread adoption of these practices has not yet been achieved. One reason is that researchers are uncertain about how sharing their work will affect their careers. We review literature demonstrating that open research is associated with increases in citations, media attention, potential collaborators, job opportunities and funding opportunities. These findings are evidence that open research practices bring significant benefits to researchers relative to more traditional closed practices.

}, issn = {2050-084X}, doi = {10.7554/eLife.16800}, author = {McKiernan, Erin C and Bourne, Philip E and Brown, C Titus and Buck, Stuart and Kenall, Amye and Lin, Jennifer and McDougall, Damon and Nosek, Brian A and Ram, Karthik and Soderberg, Courtney K and Spies, Jeffrey R and Thaney, Kaitlin and Updegrove, Andrew and Woo, Kara H and Yarkoni, Tal} } @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 {1135, title = {Improving documentation of clinical care within a clinical information network: an essential initial step in efforts to understand and improve care in Kenyan hospitals.}, journal = {BMJ Glob Health}, volume = {1}, year = {2016}, month = {2016 May 24}, pages = {e000028}, abstract = {

In many low income countries health information systems are poorly equipped to provide detailed information on hospital care and outcomes. Information is thus rarely used to support practice improvement. We describe efforts to tackle this challenge and to foster learning concerning collection and use of information. This could improve hospital services in Kenya. We are developing a Clinical Information Network, a collaboration spanning 14 hospitals, policy makers and researchers with the goal of improving information available on the quality of inpatient paediatric care across common childhood illnesses in Kenya. Standardised data from hospitals{\textquoteright} paediatric wards are collected using non-commercial and open source tools. We have implemented procedures for promoting data quality which are performed prior to a process of semi-automated analysis and routine report generation for hospitals in the network. In the first phase of the Clinical Information Network, we collected data on over 65 000 admission episodes. Despite clinicians{\textquoteright} initial unfamiliarity with routine performance reporting, we found that, as an initial focus, both engaging with each hospital and providing them information helped improve the quality of data and therefore reports. The process has involved mutual learning and building of trust in the data and should provide the basis for collaborative efforts to improve care, to understand patient outcome, and to evaluate interventions through shared learning. We have found that hospitals are willing to support the development of a clinically focused but geographically dispersed Clinical Information Network in a low-income setting. Such networks show considerable promise as platforms for collaborative efforts to improve care, to provide better information for decision making, and to enable locally relevant research.

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2016-000028}, author = {Tuti, Timothy and Bitok, Michael and Malla, Lucas and Paton, Chris and Muinga, Naomi and Gathara, David and Gachau, Susan and Mbevi, George and Nyachiro, Wycliffe and Ogero, Morris and Julius, Thomas and Irimu, Grace and English, Mike} } @article {1131, title = {Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.}, journal = {Med Image Anal}, year = {2016}, month = {2016 Jul 7}, abstract = {

The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision.

}, issn = {1361-8423}, doi = {10.1016/j.media.2016.06.035}, author = {Kapur, Tina and Pieper, Steve and Fedorov, Andriy and Fillion-Robin, J-C and Halle, Michael and O{\textquoteright}Donnell, Lauren and Lasso, Andras and Ungi, Tamas and Pinter, Csaba and Finet, Julien and Pujol, Sonia and Jagadeesan, Jayender and Tokuda, Junichi and Norton, Isaiah and Estepar, Raul San Jose and Gering, David and Aerts, Hugo J W L and Jakab, Marianna and Hata, Nobuhiko and Ibanez, Luiz and Blezek, Daniel and Miller, Jim and Aylward, Stephen and Grimson, W Eric L and Fichtinger, Gabor and Wells, William M and Lorensen, William E and Schroeder, Will and Kikinis, Ron} } @article {1162, title = {Jenkins-{CI}, an {Open}-{Source} {Continuous} {Integration} {System}, as a {Scientific} {Data} and {Image}-{Processing} {Platform}}, journal = {Journal of Biomolecular Screening}, year = {2016}, abstract = {High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.}, keywords = {CellProfiler, continuous integration, high-content screening, high-performance computing}, issn = {1552-454X}, doi = {10.1177/1087057116679993}, author = {Moutsatsos, Ioannis K. and Hossain, Imtiaz and Agarinis, Claudia and Harbinski, Fred and Abraham, Yann and Dobler, Luc and Zhang, Xian and Wilson, Christopher J. and Jenkins, Jeremy L. and Holway, Nicholas and Tallarico, John and Parker, Christian N.} } @article {1151, title = {A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD).}, journal = {J Am Med Inform Assoc}, year = {2016}, month = {2016 Aug 18}, abstract = {

OBJECTIVE: The goal of this study was to develop a practical framework for recognizing and disambiguating clinical abbreviations, thereby improving current clinical natural language processing (NLP) systems{\textquoteright} capability to handle abbreviations in clinical narratives.

METHODS: We developed an open-source framework for clinical abbreviation recognition and disambiguation (CARD) that leverages our previously developed methods, including: (1) machine learning based approaches to recognize abbreviations from a clinical corpus, (2) clustering-based semiautomated methods to generate possible senses of abbreviations, and (3) profile-based word sense disambiguation methods for clinical abbreviations. We applied CARD to clinical corpora from Vanderbilt University Medical Center (VUMC) and generated 2 comprehensive sense inventories for abbreviations in discharge summaries and clinic visit notes. Furthermore, we developed a wrapper that integrates CARD with MetaMap, a widely used general clinical NLP system.Results and Conclusion CARD detected 27 317 and 107 303 distinct abbreviations from discharge summaries and clinic visit notes, respectively. Two sense inventories were constructed for the 1000 most frequent abbreviations in these 2 corpora. Using the sense inventories created from discharge summaries, CARD achieved an F1 score of 0.755 for identifying and disambiguating all abbreviations in a corpus from the VUMC discharge summaries, which is superior to MetaMap and Apache{\textquoteright}s clinical Text Analysis Knowledge Extraction System (cTAKES). Using additional external corpora, we also demonstrated that the MetaMap-CARD wrapper improved MetaMap{\textquoteright}s performance in recognizing disorder entities in clinical notes. The CARD framework, 2 sense inventories, and the wrapper for MetaMap are publicly available at https://sbmi.uth.edu/ccb/resources/abbreviation.htm We believe the CARD framework can be a valuable resource for improving abbreviation identification in clinical NLP systems.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocw109}, author = {Wu, Yonghui and Denny, Joshua C and Rosenbloom, S Trent and Miller, Randolph A and Giuse, Dario A and Wang, Lulu and Blanquicett, Carmelo and Soysal, Ergin and Xu, Jun and Xu, Hua} } @article {1128, title = {A Low Cost/Low Power Open Source Sensor System for Automated Tuberculosis Drug Susceptibility Testing.}, journal = {Sensors (Basel)}, volume = {16}, year = {2016}, month = {2016}, abstract = {

In this research an open source, low power sensor node was developed to check the growth of mycobacteria in a culture bottle with a nitrate reductase assay method for a drug susceptibility test. The sensor system reports the temperature and color sensor output frequency change of the culture bottle when the device is triggered. After the culture process is finished, a nitrite ion detecting solution based on a commercial nitrite ion detection kit is injected into the culture bottle by a syringe pump to check bacterial growth by the formation of a pigment by the reaction between the solution and the color sensor. Sensor status and NRA results are broadcasted via a Bluetooth low energy beacon. An Android application was developed to collect the broadcasted data, classify the status of cultured samples from multiple devices, and visualize the data for the end users, circumventing the need to examine each culture bottle manually during a long culture period. The authors expect that usage of the developed sensor will decrease the cost and required labor for handling large amounts of patient samples in local health centers in developing countries. All 3D-printerable hardware parts, a circuit diagram, and software are available online.

}, issn = {1424-8220}, doi = {10.3390/s16060942}, author = {Kim, Kyukwang and Kim, Hyeong Keun and Lim, Hwijoon and Myung, Hyun} } @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 {1147, title = {An open source solution for an in-house built dynamic platform for the validation of stereotactic ablative body radiotherapy for VMAT and IMRT.}, journal = {Australas Phys Eng Sci Med}, year = {2016}, month = {2016 Sep 15}, abstract = {

An in-house solution for the verification of dose delivered to a moving phantom as required for the clinical implementation of lung stereotactic ablative body radiation therapy was developed. The superior-inferior movement required to simulate tumour motion during a normal breathing cycle was achieved via the novel use of an Arduino Uno{\texttrademark}, a low-cost open-source microcontroller board connected to a high torque servo motor. Slow CT imaging was used to acquire the image set and a 4D cone beam CT (4D-CBCT) verified the efficacy of contoured margins before treatment on the moving phantom. Treatment fields were delivered to a section of a CIRS{\texttrademark} anthropomorphic phantom. Dose verification to the dynamic phantom with Gafchromic EBT3 film using 3~\%-1~mm gamma analysis acceptance criteria registered an absolute dose pass rate for IMRT and VMAT of 98 and 96.6~\%, respectively. It was verified that 100~\% of the PTV received the prescribed dose of 12~Gy per fraction using the dynamic phantom, and no major discrepancy between planned and measured results due to interplay between multileaf collimator sequences and target motion was observed. This study confirmed that the use of an in-house solution using open source hardware and software with existing quality assurance equipment was appropriate in validating a new treatment technique.

}, issn = {1879-5447}, doi = {10.1007/s13246-016-0484-4}, author = {Munoz, Luis and Ziebell, Amy and Morton, Jason and Bhat, Madhava} } @article {1124, title = {Open-source LIMS in Vietnam: The path toward sustainability and host country ownership.}, journal = {Int J Med Inform}, volume = {93}, year = {2016}, month = {2016 Sep}, pages = {92-102}, abstract = {

OBJECTIVE: The objectives of this case report are as follows: to describe the process of establishing a national laboratory information management system (LIMS) program for clinical and public health laboratories in Vietnam; to evaluate the outcomes and lessons learned; and to present a model for sustainability based on the program outcomes that could be applied to diverse laboratory programs.

METHODS: This case report comprises a review of program documentation and records, including planning and budgetary records of the donor, monthly reports from the implementer, direct observation, and ad-hoc field reports from technical advisors and governmental agencies. Additional data on program efficacy and user acceptance were collected from routine monitoring of laboratory policies and operational practices.

RESULTS: LIMS software was implemented at 38 hospital, public health and HIV testing laboratories in Vietnam. This LIMS was accepted by users and program managers as a useful tool to support laboratory processes. Implementation cost per laboratory and average duration of deployment decreased over time, and project stakeholders initiated transition of financing (from the donor to local institutions) and of system maintenance functions (from the implementer to governmental and site-level staff). Collaboration between the implementer in Vietnam and the global LIMS user community was strongly established, and knowledge was successfully transferred to staff within Vietnam.

CONCLUSION: Implementing open-sourced LIMS with local development and support was a feasible approach towards establishing a sustainable laboratory informatics program that met the needs of health laboratories in Vietnam. Further effort to institutionalize IT support capacity within key government agencies is ongoing.

}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.06.010}, author = {Landgraf, Kenneth M and Kakkar, Reshma and Meigs, Michelle and Jankauskas, Paul T and Phan, Thi Thu Huong and Nguyen, Viet Nga and Nguyen, Duy Thai and Duong, Thanh Tung and Nguyen, Thi Hoa and Bond, Kyle B} } @article {1113, title = {Open-sourced coding expands UMN{\textquoteright}s StudyFinder to additional CTSA institutions}, year = {2016}, publisher = { AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE}, address = {Washington}, abstract = {Research tool connects patients, healthy participants to translational research.}, url = {http://www.eurekalert.org/pub_releases/2016-04/uoma-oce042616.php}, author = {Erin McHenry} } @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 {1156, title = {{SimVascular}: {An} {Open} {Source} {Pipeline} for {Cardiovascular} {Simulation}}, journal = {Annals of Biomedical Engineering}, year = {2016}, abstract = {Patient-specific cardiovascular simulation has become a paradigm in cardiovascular research and is emerging as a powerful tool in basic, translational and clinical research. In this paper we discuss the recent development of a fully open-source SimVascular software package, which provides a complete pipeline from medical image data segmentation to patient-specific blood flow simulation and analysis. This package serves as a research tool for cardiovascular modeling and simulation, and has contributed to numerous advances in personalized medicine, surgical planning and medical device design. The SimVascular software has recently been refactored and expanded to enhance functionality, usability, efficiency and accuracy of image-based patient-specific modeling tools. Moreover, SimVascular previously required several licensed components that hindered new user adoption and code management and our recent developments have replaced these commercial components to create a fully open source pipeline. These developments foster advances in cardiovascular modeling research, increased collaboration, standardization of methods, and a growing developer community.}, keywords = {Hemodynamics, Image-based CFD, open-source, Patient-specific modeling}, issn = {1573-9686}, doi = {10.1007/s10439-016-1762-8}, author = {Updegrove, Adam and Wilson, Nathan M. and Merkow, Jameson and Lan, Hongzhi and Marsden, Alison L. and Shadden, Shawn C.} } @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 {1139, title = {VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy.}, journal = {Sci Rep}, volume = {6}, year = {2016}, month = {2016}, pages = {29132}, abstract = {

The nanoscale molecular assembly of mammalian viruses during their infectious life cycle remains poorly understood. Their small dimensions, generally bellow the 300nm diffraction limit of light microscopes, has limited most imaging studies to electron microscopy. The recent development of super-resolution (SR) light microscopy now allows the visualisation of viral structures at resolutions of tens of nanometers. In addition, these techniques provide the added benefit of molecular specific labelling and the capacity to investigate viral structural dynamics using live-cell microscopy. However, there is a lack of robust analytical tools that allow for precise mapping of viral structure within the setting of infection. Here we present an open-source analytical framework that combines super-resolution imaging and na{\"\i}ve single-particle analysis to generate unbiased molecular models. This tool, VirusMapper, is a high-throughput, user-friendly, ImageJ-based software package allowing for automatic statistical mapping of conserved multi-molecular structures, such as viral substructures or intact viruses. We demonstrate the usability of VirusMapper by applying it to SIM and STED images of vaccinia virus in isolation and when engaged with host cells. VirusMapper allows for the generation of accurate, high-content, molecular specific virion models and detection of nanoscale changes in viral architecture.

}, issn = {2045-2322}, doi = {10.1038/srep29132}, author = {Gray, Robert D M and Beerli, Corina and Pereira, Pedro Matos and Scherer, Kathrin Maria and Samolej, Jerzy and Bleck, Christopher Karl Ernst and Mercer, Jason and Henriques, Ricardo} } @article {1062, title = {Archetype relational mapping - a practical openEHR persistence solution.}, journal = {BMC Med Inform Decis Mak}, volume = {15}, year = {2015}, month = {2015}, pages = {88}, abstract = {

BACKGROUND: One of the primary obstacles to the widespread adoption of openEHR methodology is the lack of practical persistence solutions for future-proof electronic health record (EHR) systems as described by the openEHR specifications. This paper presents an archetype relational mapping (ARM) persistence solution for the archetype-based EHR systems to support healthcare delivery in the clinical environment.

METHODS: First, the data requirements of the EHR systems are analysed and organized into archetype-friendly concepts. The Clinical Knowledge Manager (CKM) is queried for matching archetypes; when necessary, new archetypes are developed to reflect concepts that are not encompassed by existing archetypes. Next, a template is designed for each archetype to apply constraints related to the local EHR context. Finally, a set of rules is designed to map the archetypes to data tables and provide data persistence based on the relational database.

RESULTS: A comparison study was conducted to investigate the differences among the conventional database of an EHR system from a tertiary Class A hospital in China, the generated ARM database, and the Node + Path database. Five data-retrieving tests were designed based on clinical workflow to retrieve exams and laboratory tests. Additionally, two patient-searching tests were designed to identify patients who satisfy certain criteria. The ARM database achieved better performance than the conventional database in three of the five data-retrieving tests, but was less efficient in the remaining two tests. The time difference of query executions conducted by the ARM database and the conventional database is less than 130~\%. The ARM database was approximately 6-50 times more efficient than the conventional database in the patient-searching tests, while the Node + Path database requires far more time than the other two databases to execute both the data-retrieving and the patient-searching tests.

CONCLUSIONS: The ARM approach is capable of generating relational databases using archetypes and templates for archetype-based EHR systems, thus successfully adapting to changes in data requirements. ARM performance is similar to that of conventionally-designed EHR systems, and can be applied in a practical clinical environment. System components such as ARM can greatly facilitate the adoption of openEHR architecture within EHR systems.

}, issn = {1472-6947}, doi = {10.1186/s12911-015-0212-0}, author = {Wang, Li and Min, Lingtong and Wang, Rui and Lu, Xudong and Duan, Huilong} } @article {992, title = {A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Sep 2}, abstract = {

OBJECTIVE: Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management.

MATERIALS AND METHODS: An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software.

RESULTS: Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application ("app"), Blip, to visualize the data. Tidepool{\textquoteright}s software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security.

DISCUSSION: By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use.

CONCLUSION: The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool{\textquoteright}s open source, cloud model for health data interoperability is applicable to other healthcare use cases.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv104}, author = {Neinstein, Aaron and Wong, Jenise and Look, Howard and Arbiter, Brandon and Quirk, Kent and McCanne, Steve and Sun, Yao and Blum, Michael and Adi, Saleh} } @article {1190, title = {caTissue Suite to OpenSpecimen: developing an extensible, open source, web-based biobanking management system}, journal = {Journal of biomedical informatics}, volume = {57}, year = {2015}, month = {2015/10/}, pages = {456 - 464}, abstract = {The National Cancer Institute (NCI) Cancer Biomedical Informatics Grid({\textregistered}) (caBIG({\textregistered})) program established standards and best practices for biorepository data management by creating an infrastructure to propagate biospecimen resource sharing while maintaining data integrity and security. caTissue suite, a biospecimen data management software tool, has evolved from this effort. More recently, the caTissue suite continues to evolve as an open source initiative known as OpenSpecimen. The essential functionality of OpenSpecimen includes the capture and representation of highly granular, hierarchically-structured data for biospecimen processing, quality assurance, tracking, and annotation. Ideal for multi-user and multi-site biorepository environments, OpenSpecimen permits role-based access to specific sets of data operations through a user-interface designed to accommodate varying workflows and unique user needs. The software is interoperable, both syntactically and semantically, with an array of other bioinformatics tools given its integration of standard vocabularies thus enabling research involving biospecimens. End-users are encouraged to share their day-to-day experiences in working with the application, thus providing to the community board insight into the needs and limitations which need be addressed. Users are also requested to review and validate new features through group testing environments and mock screens. Through this user interaction, application flexibility and interoperability have been recognized as necessary developmental focuses essential for accommodating diverse adoption scenarios and biobanking workflows to catalyze advances in biomedical research and operations. Given the diversity of biobanking practices and workforce roles, efforts have been made consistently to maintain robust data granularity while aiding user accessibility, data discoverability, and security within and across applications by providing a lower learning curve in using OpenSpecimen. Iterative development and testing cycles provide continuous maintenance and up-to-date capabilities for this freely available, open-access, web-based software application that is globally-adopted at over 25 institutions.}, isbn = {1532-04641532-0480}, doi = {10.1016/j.jbi.2015.08.020}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772150/}, author = {McIntosh, Leslie D and Sharma, Mukesh K and Mulvihill, David and Gupta, Snehil and Juehne, Anthony and George, Bijoy and Khot, Suhas B and Kaushal, Atul and Watson, Mark A and Nagarajan, Rakesh} } @article {1030, title = {Do interoperable national information systems enhance availability of data to assess the effect of scale-up of HIV services on health workforce deployment in resource-limited countries?}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {677-81}, abstract = {

Sub-Saharan Africa (SSA) bears the heaviest burden of the HIV epidemic. Health workers play a critical role in the scale-up of HIV programs. SSA also has the weakest information and communication technology (ICT) infrastructure globally. Implementing interoperable national health information systems (HIS) is a challenge, even in developed countries. Countries in resource-limited settings have yet to demonstrate that interoperable systems can be achieved, and can improve quality of healthcare through enhanced data availability and use in the deployment of the health workforce. We established interoperable HIS integrating a Master Facility List (MFL), District Health Information Software (DHIS2), and Human Resources Information Systems (HRIS) through application programmers interfaces (API). We abstracted data on HIV care, health workers deployment, and health facilities geo-coordinates. Over 95\% of data elements were exchanged between the MFL-DHIS and HRIS-DHIS. The correlation between the number of HIV-positive clients and nurses and clinical officers in 2013 was R2=0.251 and R2=0.261 respectively. Wrong MFL codes, data type mis-match and hyphens in legacy data were key causes of data transmission errors. Lack of information exchange standards for aggregate data made programming time-consuming.

}, issn = {0926-9630}, author = {Oluoch, Tom and Muturi, David and Kiriinya, Rose and Waruru, Anthony and Lanyo, Kevin and Nguni, Robert and Ojwang, James and Waters, Keith P and Richards, Janise} } @article {1006, title = {Enabling Better Interoperability for HealthCare: Lessons in Developing a Standards Based Application Programing Interface for Electronic Medical Record Systems.}, journal = {J Med Syst}, volume = {39}, year = {2015}, month = {2015 Nov}, pages = {182}, abstract = {

We sought to enable better interoperability and easy adoption of healthcare applications by developing a standardized domain independent Application Programming Interface (API) for an Electronic Medical Record (EMR) system. We leveraged the modular architecture of the Open Medical Record System (OpenMRS) to build a Fast Healthcare Interoperability Resources (FHIR) based add-on module that could consume FHIR resources and requests made on OpenMRS. The OpenMRS FHIR module supports a subset of FHIR resources that could be used to interact with clinical data persisted in OpenMRS. We demonstrate the ease of connecting healthcare applications using the FHIR API by integrating a third party Substitutable Medical Apps \& Reusable Technology (SMART) application with OpenMRS via FHIR. The OpenMRS FHIR module is an optional component of the OpenMRS platform. The FHIR API significantly reduces the effort required to implement OpenMRS by preventing developers from having to learn or work with a domain specific OpenMRS API. We propose an integration pathway where the domain specific legacy OpenMRS API is gradually retired in favor of the new FHIR API, which would be integrated into the core OpenMRS platform. Our efforts indicate that a domain independent API is a reality for any EMR system. These efforts demonstrate the adoption of an emerging FHIR standard that is seen as a replacement for both Health Level 7 (HL7) Version 2 and Version 3. We propose a gradual integration approach where our FHIR API becomes the preferred method for communicating with the OpenMRS platform.

}, issn = {1573-689X}, doi = {10.1007/s10916-015-0356-6}, author = {Kasthurirathne, Suranga N and Mamlin, Burke and Kumara, Harsha and Grieve, Grahame and Biondich, Paul} } @article {1145, title = {A Generic Data Harmonization Process for Cross-linked Research and Network Interaction. Construction and Application for the Lung Cancer Phenotype Database of the German Center for Lung Research.}, journal = {Methods Inf Med}, volume = {54}, year = {2015}, month = {2015}, pages = {455-60}, abstract = {

OBJECTIVE: Joint data analysis is a key requirement in medical research networks. Data are available in heterogeneous formats at each network partner and their harmonization is often rather complex. The objective of our paper is to provide a generic approach for the harmonization process in research networks. We applied the process when harmonizing data from three sites for the Lung Cancer Phenotype Database within the German Center for Lung Research.

METHODS: We developed a spreadsheet-based solution as tool to support the harmonization process for lung cancer data and a data integration procedure based on Talend Open Studio.

RESULTS: The harmonization process consists of eight steps describing a systematic approach for defining and reviewing source data elements and standardizing common data elements. The steps for defining common data elements and harmonizing them with local data definitions are repeated until consensus is reached. Application of this process for building the phenotype database led to a common basic data set on lung cancer with 285 structured parameters. The Lung Cancer Phenotype Database was realized as an i2b2 research data warehouse.

CONCLUSION: Data harmonization is a challenging task requiring informatics skills as well as domain knowledge. Our approach facilitates data harmonization by providing guidance through a uniform process that can be applied in a wide range of projects.

}, issn = {0026-1270}, doi = {10.3414/ME14-02-0030}, author = {Firnkorn, D and Ganzinger, M and Muley, T and Thomas, M and Knaup, P} } @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 {997, title = {Innovating to enhance clinical data management using non-commercial and open source solutions across a multi-center network supporting inpatient pediatric care and research in Kenya.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Jun 10}, abstract = {

OBJECTIVE: To share approaches and innovations adopted to deliver a relatively inexpensive clinical data management (CDM) framework within a low-income setting that aims to deliver quality pediatric data useful for supporting research, strengthening the information culture and informing improvement efforts in local clinical practice.

MATERIALS AND METHODS: The authors implemented a CDM framework to support a Clinical Information Network (CIN) using Research Electronic Data Capture (REDCap), a noncommercial software solution designed for rapid development and deployment of electronic data capture tools. It was used for collection of standardized data from case records of multiple hospitals{\textquoteright} pediatric wards. R, an open-source statistical language, was used for data quality enhancement, analysis, and report generation for the hospitals.

RESULTS: In the first year of CIN, the authors have developed innovative solutions to support the implementation of a secure, rapid pediatric data collection system spanning 14 hospital sites with stringent data quality checks. Data have been collated on over 37 000 admission episodes, with considerable improvement in clinical documentation of admissions observed. Using meta-programming techniques in R, coupled with branching logic, randomization, data lookup, and Application Programming Interface (API) features offered by REDCap, CDM tasks were configured and automated to ensure quality data was delivered for clinical improvement and research use.

CONCLUSION: A low-cost clinically focused but geographically dispersed quality CDM (Clinical Data Management) in a long-term, multi-site, and real world context can be achieved and sustained and challenges can be overcome through thoughtful design and implementation of open-source tools for handling data and supporting research.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv028}, author = {Tuti, Timothy and Bitok, Michael and Paton, Chris and Makone, Boniface and Malla, Lucas and Muinga, Naomi and Gathara, David and English, Mike} } @article {972, title = {MzJava: An open source library for mass spectrometry data processing.}, journal = {J Proteomics}, year = {2015}, month = {2015 Jun 30}, abstract = {

Mass spectrometry (MS) is a widely used and evolving technique for the high-throughput identification of molecules in biological samples. The need for sharing and reuse of code among bioinformaticians working with MS data prompted the design and implementation of MzJava, an open-source Java Application Programming Interface (API) for MS related data processing. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce (hadoop.apache.org) and Apache Spark (spark.apache.org) frameworks for cluster computing was implemented. The library has been developed applying best practices of software engineering. To ensure that MzJava contains code that is correct and easy to use the library{\textquoteright}s API was carefully designed and thoroughly tested. MzJava is an open-source project distributed under the AGPL v3.0 licence. MzJava requires Java 1.7 or higher. Binaries, source code and documentation can be downloaded from http://mzjava.expasy.org and https://bitbucket.org/sib-pig/mzjava.

}, issn = {1876-7737}, doi = {10.1016/j.jprot.2015.06.013}, author = {Horlacher, Oliver and Nikitin, Frederic and Alocci, Davide and Mariethoz, Julien and M{\"u}ller, Markus and Lisacek, Frederique} } @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 {987, title = {Open source software in a practical approach for post processing of radiologic images.}, journal = {Radiol Med}, volume = {120}, year = {2015}, month = {2015 Mar}, pages = {309-23}, abstract = {

PURPOSE: The purpose of this paper is to evaluate the use of open source software (OSS) to process DICOM images.

MATERIALS AND METHODS: We selected 23 programs for Windows and 20 programs for Mac from 150 possible OSS programs including DICOM viewers and various tools (converters, DICOM header editors, etc.). The programs selected all meet the basic requirements such as free availability, stand-alone application, presence of graphical user interface, ease of installation and advanced features beyond simple display monitor. Capabilities of data import, data export, metadata, 2D viewer, 3D viewer, support platform and usability of each selected program were evaluated on a scale ranging from 1 to 10 points.

RESULTS: Twelve programs received a score higher than or equal to eight. Among them, five obtained a score of 9: 3D Slicer, MedINRIA, MITK 3M3, VolView, VR Render; while OsiriX received 10.

CONCLUSIONS: OsiriX appears to be the only program able to perform all the operations taken into consideration, similar to a workstation equipped with proprietary software, allowing the analysis and interpretation of images in a simple and intuitive way. OsiriX is a DICOM PACS workstation for medical imaging and software for image processing for medical research, functional imaging, 3D imaging, confocal microscopy and molecular imaging. This application is also a good tool for teaching activities because it facilitates the attainment of learning objectives among students and other specialists.

}, keywords = {Diagnostic Imaging, Humans, Image Interpretation, Computer-Assisted, Image Processing, Computer-Assisted, Radiology Information Systems, Reproducibility of Results, Sensitivity and Specificity, Software, Software Validation, User-Computer Interface}, issn = {1826-6983}, doi = {10.1007/s11547-014-0437-5}, author = {Valeri, Gianluca and Mazza, Francesco Antonino and Maggi, Stefania and Aramini, Daniele and La Riccia, Luigi and Mazzoni, Giovanni and Giovagnoni, Andrea} } @article {1065, title = {OpenFDA: an innovative platform providing access to a wealth of FDA{\textquoteright}s publicly available data.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Dec 7}, abstract = {

OBJECTIVE: The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs).

MATERIALS AND METHODS: Using cutting-edge technologies deployed on FDA{\textquoteright}s new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges.

RESULTS: Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event.

CONCLUSION: With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv153}, author = {Kass-Hout, Taha A and Xu, Zhiheng and Mohebbi, Matthew and Nelsen, Hans and Baker, Adam and Levine, Jonathan and Johanson, Elaine and Bright, Roselie A} } @article {995, title = {OpenHELP (Heidelberg laparoscopy phantom): development of an open-source surgical evaluation and training tool.}, journal = {Surg Endosc}, year = {2015}, month = {2015 Feb 12}, abstract = {

BACKGROUND: Apart from animal testing and clinical trials, surgical research and laparoscopic training mainly rely on phantoms. The aim of this project was to design a phantom with realistic anatomy and haptic characteristics, modular design and easy reproducibility. The phantom was named open-source Heidelberg laparoscopic phantom (OpenHELP) and serves as an open-source platform.

METHODS: The phantom was based on an anonymized CT scan of a male patient. The anatomical structures were segmented to obtain digital three-dimensional models of the torso and the organs. The digital models were materialized via rapid prototyping. One flexible, using an elastic abdominal wall, and one rigid method, using a plastic shell, to simulate pneumoperitoneum were developed. Artificial organ production was carried out sequentially starting from raw gypsum models to silicone molds to final silicone casts. The reproduction accuracy was exemplarily evaluated for ten silicone rectum models by comparing the digital 3D surface of the original rectum with CT scan by calculating the root mean square error of surface variations. Haptic realism was also evaluated to find the most realistic silicone compositions on a visual analog scale (VAS, 0-10).

RESULTS: The rigid and durable plastic torso and soft silicone organs of the abdominal cavity were successfully produced. A simulation of pneumoperitoneum could be created successfully by both methods. The reproduction accuracy of ten silicone rectum models showed an average root mean square error of 2.26 (0-11.48) mm. Haptic realism revealed an average value on a VAS of 7.25 (5.2-9.6) for the most realistic rectum.

CONCLUSION: The OpenHELP phantom proved to be feasible and accurate. The phantom was consecutively applied frequently in the field of computer-assisted surgery at our institutions and is accessible as an open-source project at www.open-cas.org for the academic community.

}, issn = {1432-2218}, doi = {10.1007/s00464-015-4094-0}, author = {Kenngott, H G and W{\"u}nscher, J J and Wagner, M and Preukschas, A and Wekerle, A L and Neher, P and Suwelack, S and Speidel, S and Nickel, F and Oladokun, D and Maier-Hein, L and Dillmann, R and Meinzer, H P and M{\"u}ller-Stich, B P} } @article {1005, title = {A Standards-Based Architecture Proposal for Integrating Patient mHealth Apps to Electronic Health Record Systems.}, journal = {Appl Clin Inform}, volume = {6}, year = {2015}, month = {2015}, pages = {488-505}, abstract = {

BACKGROUND: Mobile health Applications (mHealth Apps) are opening the way to patients{\textquoteright} responsible and active involvement with their own healthcare management. However, apart from Apps allowing patient{\textquoteright}s access to their electronic health records (EHRs), mHealth Apps are currently developed as dedicated "island systems".

OBJECTIVE: Although much work has been done on patient{\textquoteright}s access to EHRs, transfer of information from mHealth Apps to EHR systems is still low. This study proposes a standards-based architecture that can be adopted by mHealth Apps to exchange information with EHRs to support better quality of care.

METHODS: Following the definition of requirements for the EHR/mHealth App information exchange recently proposed, and after reviewing current standards, we designed the architecture for EHR/mHealth App integration. Then, as a case study, we modeled a system based on the proposed architecture aimed to support home monitoring for congestive heart failure patients. We simulated such process using, on the EHR side, OpenMRS, an open source longitudinal EHR and, on the mHealth App side, the iOS platform.

RESULTS: The integration architecture was based on the bi-directional exchange of standard documents (clinical document architecture rel2 - CDA2). In the process, the clinician "prescribes" the home monitoring procedures by creating a CDA2 prescription in the EHR that is sent, encrypted and de-identified, to the mHealth App to create the monitoring calendar. At the scheduled time, the App alerts the patient to start the monitoring. After the measurements are done, the App generates a structured CDA2-compliant monitoring report and sends it to the EHR, thus avoiding local storage.

CONCLUSIONS: The proposed architecture, even if validated only in a simulation environment, represents a step forward in the integration of personal mHealth Apps into the larger health-IT ecosystem, allowing the bi-directional data exchange between patients and healthcare professionals, supporting the patient{\textquoteright}s engagement in self-management and self-care.

}, issn = {1869-0327}, doi = {10.4338/ACI-2014-12-RA-0115}, author = {Marceglia, S and Fontelo, P and Rossi, E and Ackerman, M J} } @article {986, title = {Taking advantage of continuity of care documents to populate a research repository.}, journal = {J Am Med Inform Assoc}, volume = {22}, year = {2015}, month = {2015 Mar}, pages = {370-9}, abstract = {

OBJECTIVE: Clinical data warehouses have accelerated clinical research, but even with available open source tools, there is a high barrier to entry due to the complexity of normalizing and importing data. The Office of the National Coordinator for Health Information Technology{\textquoteright}s Meaningful Use Incentive Program now requires that electronic health record systems produce standardized consolidated clinical document architecture (C-CDA) documents. Here, we leverage this data source to create a low volume standards based import pipeline for the Informatics for Integrating Biology and the Bedside (i2b2) clinical research platform. We validate this approach by creating a small repository at Partners Healthcare automatically from C-CDA documents.

MATERIALS AND METHODS: We designed an i2b2 extension to import C-CDAs into i2b2. It is extensible to other sites with variances in C-CDA format without requiring custom code. We also designed new ontology structures for querying the imported data.

RESULTS: We implemented our methodology at Partners Healthcare, where we developed an adapter to retrieve C-CDAs from Enterprise Services. Our current implementation supports demographics, encounters, problems, and medications. We imported approximately 17 000 clinical observations on 145 patients into i2b2 in about 24 min. We were able to perform i2b2 cohort finding queries and view patient information through SMART apps on the imported data.

DISCUSSION: This low volume import approach can serve small practices with local access to C-CDAs and will allow patient registries to import patient supplied C-CDAs. These components will soon be available open source on the i2b2 wiki.

CONCLUSIONS: Our approach will lower barriers to entry in implementing i2b2 where informatics expertise or data access are limited.

}, keywords = {Biomedical Research, Continuity of Patient Care, Database Management Systems, Databases as Topic, Humans, Information Storage and Retrieval, Meaningful Use, Systems Integration}, issn = {1527-974X}, doi = {10.1136/amiajnl-2014-003040}, author = {Klann, Jeffrey G and Mendis, Michael and Phillips, Lori C and Goodson, Alyssa P and Rocha, Beatriz H and Goldberg, Howard S and Wattanasin, Nich and Murphy, Shawn N} } @article {1007, title = {Towards Standardized Patient Data Exchange: Integrating a FHIR Based API for the Open Medical Record System.}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {932}, abstract = {

Interoperability is essential to address limitations caused by the ad hoc implementation of clinical information systems and the distributed nature of modern medical care. The HL7 V2 and V3 standards have played a significant role in ensuring interoperability for healthcare. FHIR is a next generation standard created to address fundamental limitations in HL7 V2 and V3. FHIR is particularly relevant to OpenMRS, an Open Source Medical Record System widely used across emerging economies. FHIR has the potential to allow OpenMRS to move away from a bespoke, application specific API to a standards based API. We describe efforts to design and implement a FHIR based API for the OpenMRS platform. Lessons learned from this effort were used to define long term plans to transition from the legacy OpenMRS API to a FHIR based API that greatly reduces the learning curve for developers and helps enhance adhernce to standards.

}, issn = {0926-9630}, author = {Kasthurirathne, Suranga N and Mamlin, Burke and Grieve, Grahame and Biondich, Paul} } @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 {971, title = {XNAT Central: Open sourcing imaging research data.}, journal = {Neuroimage}, year = {2015}, month = {2015 Jul 2}, abstract = {

XNAT Central is a publicly accessible medical imaging data repository based on the XNAT open-source imaging informatics platform. It hosts a wide variety of research imaging data sets. The primary motivation for creating XNAT Central was to provide a central repository to host and provide access to a wide variety of neuroimaging data. In this capacity, XNAT Central hosts a number of data sets from research labs and investigative efforts from around the world, including the OASIS Brains imaging studies, the NUSDAST study of schizophrenia, and more. Over time, XNAT Central has expanded to include imaging data from many different fields of research, including oncology, orthopedics, cardiology, and animal studies, but continues to emphasize neuroimaging data. Through the use of XNAT{\textquoteright}S DICOM metadata extraction capabilities, XNAT Central provides a searchable repository of imaging data that can be referenced by groups, labs, or individuals working in many different areas of research. The future development of XNAT Central will be geared towards greater ease of use as a reference library of heterogeneous neuroimaging data and associated synthetic data. It will also become a tool for making data available supporting published research and academic articles.

}, issn = {1095-9572}, doi = {10.1016/j.neuroimage.2015.06.076}, author = {Herrick, Rick and Horton, William and Olsen, Timothy and McKay, Michael and Archie, Kevin A and Marcus, Daniel S} } @article {946, title = {An Albanian open source telemedicine platform.}, journal = {Telemed J E Health}, volume = {20}, year = {2014}, month = {2014 Jul}, pages = {673-7}, abstract = {

INTRODUCTION: The use of open source technologies to create collaboration platforms can produce huge advantages with small investment.

MATERIALS AND METHODS: We set up a telemedicine network for a healthcare district with typical centralization issues of developing countries. Our network was built using broadband Internet connection, and the digital divide in rural areas was reduced by means of wireless Internet connection. A software infrastructure was deployed on the network to implement the collaboration platform among different healthcare facilities.

RESULTS: We obtained an integrated platform with modest investment in hardware and operating systems and no costs for application software. Messaging, content management, information sharing, and videoconferencing are among the available services of the infrastructure. Furthermore, open source software is managed and continuously updated by active communities, making it possible to obtain systems similar to commercial ones in terms of quality and reliability.

CONCLUSIONS: As the use of free software in public administration is being widely promoted across the European Union, our experience may provide an example to implement similar infrastructures in the field of healthcare and welfare.

}, issn = {1556-3669}, doi = {10.1089/tmj.2013.0239}, author = {Zangara, Gianluca and Valentino, Francesca and Spinelli, Gaetano and Valenza, Mario and Marcheggiani, Angelo and Di Blasi, Francesco} } @article {941, title = {Computational Pathology and Telepathology: SY05-1 TELECYTOLOGY TC AND TELEPATHOLOGY TP IN UNDERSERVED COUNTRIES TOY OR TOOL?}, journal = {Pathology}, volume = {46 Suppl 2}, year = {2014}, month = {2014 Oct}, pages = {S7}, abstract = {

BACKGROUND: Pathologic anatomic practice is an essential part of medical practice even in low-income countries. It is an extraordinarily helpful tool in finding therapeutic decisions, monitoring therapeutic processes and in academic teaching students and residents in understanding aetiology and morphology of infectious and neoplastic diseases. However, all countries worldwide are suffering from a shortage of experienced surgical pathologists providing an adequate service to the clinics. Training pathologists is a time-consuming procedure and it takes more than one decade. Therefore new techniques have to be utilized to overcome the gap of human resources in medical fields in these countries. Telepathology and telecytology may be effective tools to transfer both knowledge and experience to any place in the world with simple technical equipment using the Internet. We evaluate the benefit of TP and TC on three projects, with different educational levels of the local pathologists.

MATERIAL AND APPROACH: In 2002 Cambodian pathologists started off with telepathology using iPath Network as an open-source system. Up to now more than 5600 cases have been submitted to experts. In 2007 a Tanzanian hospital started telepathology and solved more than 3600 cases. In 2010 an Afghan group of medical experts started using TP and submitted more than 1600 cases. The latest 100 cases of each group were analysed with respect to (1) the organs concerned; (2) the diagnostic techniques used such as histology vs cytology; (3) complexity of the diagnostic question; (4) information quality and quantity; (5) diagnostic concordance between primary diagnosis and the experts opinion; and (6) diagnostic accuracy of the experts diagnoses in order to evaluate the benefit of the projects.

RESULTS AND CONCLUSION: Telepathology services are ranging from a triage of diagnostic assessment of benign vs malignant to academic-scientific services including teaching and research facilities. Breast pathology is predominant in Afghanistan, whereas cervix pathology is the leading issue in Tanzania, and in Cambodia soft tissue/bone pathology plays the major role. In more than 50\% cytology was applied in Afghanistan and only 10\% and 5\% in Cambodia and Tanzania respectively. The complexity of diagnostic questions differs from Cambodia using TP for confirmation in most cases, to Tanzania and Afghanistan using TP mostly for primary diagnosis. Diagnostic concordance depending on both the experience of local pathologists and the technical facilities of the laboratory was high in Cambodia, followed by Tanzania and Afghanistan. Diagnostic accuracy corresponding with the quantity and quality of information followed the same pattern. The success of TP projects can be measured by the number of TP sessions and by the sustainability of projects. Our TP/TC projects in those countries with limited resources are effective tools in improving medical health care.

}, keywords = {iPath, open source software, telepathology}, issn = {1465-3931}, doi = {10.1097/01.PAT.0000454068.32934.09}, author = {Stauch, Gerhard and Miringa, Angelica and Raoufi, Rokai and Vathana, Cchut Serey and Hetzmann, Sophia and Hinsch, Nora and Dalquen, Peter and Voelker, Ullrich and Kunze, Dietmar} } @article {1003, title = {Innovative approaches to clinical data management in resource limited settings using open-source technologies.}, journal = {PLoS Negl Trop Dis}, volume = {8}, year = {2014}, month = {2014 Sep}, pages = {e3134}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0003134}, author = {Omollo, Raymond and Ochieng, Michael and Mutinda, Brian and Omollo, Truphosa and Owiti, Rhoda and Okeyo, Seth and Wasunna, Monique and Edwards, Tansy} } @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 {1096, title = {Medical Subject Headings (MeSH) for indexing and retrieving open-source healthcare data.}, journal = {Stud Health Technol Inform}, volume = {202}, year = {2014}, month = {2014}, pages = {157-60}, abstract = {

The US federal government initiated the Open Government Directive where federal agencies are required to publish high value datasets so that they are available to the public. Data.gov and the community site Healthdata.gov were initiated to disperse such datasets. However, data searches and retrieval for these sites are keyword driven and severely limited in performance. The purpose of this paper is to address the issue of extracting relevant open-source data by proposing a method of adopting the MeSH framework for indexing and data retrieval. A pilot study was conducted to compare the performance of traditional keywords to MeSH terms for retrieving relevant open-source datasets related to "mortality". The MeSH framework resulted in greater sensitivity with comparable specificity to the keyword search. MeSH showed promise as a method for indexing and retrieving data, yet future research should conduct a larger scale evaluation of the performance of the MeSH framework for retrieving relevant open-source healthcare datasets.

}, issn = {0926-9630}, author = {Marc, David T and Khairat, Saif S} } @article {943, title = {Open-source electronic data capture system offered increased accuracy and cost-effectiveness compared with paper methods in Africa.}, journal = {J Clin Epidemiol}, year = {2014}, month = {2014 Aug 15}, abstract = {

OBJECTIVES: Existing electronic data capture options are often financially unfeasible in resource-poor settings or difficult to support technically in the field. To help facilitate large-scale multicenter studies in sub-Saharan Africa, the African Partnership for Chronic Disease Research (APCDR) has developed an open-source electronic questionnaire (EQ).

STUDY DESIGN AND SETTING: To assess its relative validity, we compared the EQ against traditional pen-and-paper methods using 200 randomized interviews conducted in an ongoing type 2 diabetes case-control study in South Africa.

RESULTS: During its 3-month validation, the EQ had a lower frequency of errors (EQ, 0.17 errors per 100 questions; paper, 0.73 errors per 100 questions; P-value <=0.001), and a lower monetary cost per correctly entered question, compared with the pen-and-paper method. We found no marked difference in the average duration of the interview between methods (EQ, 5.4~minutes; paper, 5.6~minutes).

CONCLUSION: This validation study suggests that the EQ may offer increased accuracy, similar interview duration, and increased cost-effectiveness compared with paper-based data collection methods. The APCDR EQ software is freely available (https://github.com/apcdr/questionnaire).

}, issn = {1878-5921}, doi = {10.1016/j.jclinepi.2014.06.012}, author = {Dillon, David G and Pirie, Fraser and Pomilla, Cristina and Sandhu, Manjinder S and Motala, Ayesha A and Young, Elizabeth H} } @article {1019, title = {Strengthening district-based health reporting through the district health management information software system: the Ugandan experience.}, journal = {BMC Med Inform Decis Mak}, volume = {14}, year = {2014}, month = {2014}, pages = {40}, abstract = {

BACKGROUND: Untimely, incomplete and inaccurate data are common challenges in planning, monitoring and evaluation of health sector performance, and health service delivery in many sub-Saharan African settings. We document Uganda{\textquoteright}s experience in strengthening routine health data reporting through the roll-out of the District Health Management Information Software System version 2 (DHIS2).

METHODS: DHIS2 was adopted at the national level in January 2011. The system was initially piloted in 4 districts, before it was rolled out to all the 112 districts by July 2012. As part of the roll-out process, 35 training workshops targeting 972 users were conducted throughout the country. Those trained included Records Assistants (168, 17.3\%), District Health Officers (112, 11.5\%), Health Management Information System Focal Persons (HMIS-FPs) (112, 11.5\%), District Biostatisticians (107, 11\%) and other health workers (473, 48.7\%). To assess improvements in health reporting, we compared data on completeness and timeliness of outpatient and inpatient reporting for the period before (2011/12) and after (2012/13) the introduction of DHIS2. We reviewed data on the reporting of selected health service coverage indicators as a proxy for improved health reporting, and documented implementation challenges and lessons learned during the DHIS2 roll-out process.

RESULTS: Completeness of outpatient reporting increased from 36.3\% in 2011/12 to 85.3\% in 2012/13 while timeliness of outpatient reporting increased from 22.4\% to 77.6\%. Similarly, completeness of inpatient reporting increased from 20.6\% to 57.9\% while timeliness of inpatient reporting increased from 22.5\% to 75.6\%. There was increased reporting on selected health coverage indicators (e.g. the reporting of one-year old children who were immunized with three doses of pentavelent vaccine increased from 57\% in 2011/12 to 87\% in 2012/13). Implementation challenges included limited access to computers and internet (34\%), inadequate technical support (23\%) and limited worker force (18\%).

CONCLUSION: Implementation of DHIS2 resulted in improved timeliness and completeness in reporting of routine outpatient, inpatient and health service usage data from the district to the national level. Continued onsite support supervision and mentorship and additional system/infrastructure enhancements, including internet connectivity, are needed to further enhance the performance of DHIS2.

}, keywords = {Health Information Management, Health information systems, Health Services, Humans, Inpatients, Outpatients, Uganda}, issn = {1472-6947}, doi = {10.1186/1472-6947-14-40}, author = {Kiberu, Vincent Micheal and Matovu, Joseph K B and Makumbi, Fredrick and Kyozira, Carol and Mukooyo, Eddie and Wanyenze, Rhoda K} } @article {1034, title = {Telecytological diagnosis of space-occupying lesions of the liver.}, journal = {Acta Cytol}, volume = {58}, year = {2014}, month = {2014}, pages = {174-81}, abstract = {

OBJECTIVE: In this study, the efficiency of telemedical consulting with regard to fine needle aspirates from space-occupying lesions (SOLs) of the liver is investigated for the first time.

STUDY DESIGN: The study includes fine needle aspirations from 62 patients, 33 with hepatocellular carcinoma (HCC) and 29 with non-hepatic tumors. Using the Internet-based iPath system, the initial pathologist submitted 1-8 images from smears and cell block sections. One consultant assessed the cytological and another one the histological images. Both made their diagnoses independent of each other. A final diagnosis was made by immunochemistry of cell block sections. The cytological images were analyzed retrospectively for the occurrence of the most typical HCC indicators. The number of these indicators was related to the initial diagnoses of the three pathologists, and possible reasons for diagnostic errors were analyzed based on this analysis.

RESULTS: The accuracy of the preliminary telemedical diagnoses regarding HCC was 82.0\% for the cytological images and 87.7\% for the histological images. Most of the false diagnoses occurred in tumors with unusual cytological and histological patterns.

CONCLUSIONS: Telemedical consulting is a valuable tool to obtain a second opinion. However, for improvement of the diagnosis of HCC, supplementary immunochemical tests are necessary.

}, keywords = {Adult, Aged, Aged, 80 and over, Carcinoma, Hepatocellular, Female, Humans, Image-Guided Biopsy, Liver, Liver Neoplasms, Male, Middle Aged, Retrospective Studies, Telemedicine}, issn = {0001-5547}, doi = {10.1159/000357195}, author = {Mostafa, Mohammad Golam and Dalquen, Peter and Kunze, Dietmar and Terracciano, Luigi} } @article {1020, title = {Towards an intelligent decision support system for public health surveillance - a qualitative analysis of information needs.}, journal = {Stud Health Technol Inform}, volume = {202}, year = {2014}, month = {2014}, pages = {44-7}, abstract = {

Public health information systems are often implemented considering the functionalities and requirements established by administrative staff or researchers, but sometimes ignoring the particular needs of decision makers. This paper describes a proposal to support the design of a Decision Support System for Public Health Surveillance in Colombia, by conducting a qualitative study to identify the real needs of people involved in decision making processes. Based on the study results, an intelligent computational component that supports Data Analysis Automation, Prediction of future scenarios and the identification of new Behavioral Patterns is proposed. The component will be implemented using the Case Based Reasoning methodology, which will be integrated as a new component of the Open Source DHIS2 Platform, enabling public health decision-making.

}, issn = {0926-9630}, author = {Mera, Maritza and Gonz{\'a}lez, Carolina and L{\'o}pez, Diego M} } @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} } @conference {1081, title = {Analyzing open-source and commercial EHR solutions from an international perspective}, booktitle = {e-Health Networking, Applications Services (Healthcom), 2013 IEEE 15th International Conference on}, year = {2013}, month = {Oct}, keywords = {African continent, Allscripts Professional, Asia, CareTracker, commercial, commercial EHR solutions, commercial electronic health records, Companies, eclinicalworks, economic resources, EHR, electronic health records systems market, Electronic medical records, healthcare systems, Hospitals, HOSxp, implementation, international barrier, international perspective, interoperable EHR platform, Latin America, medical information systems, open source software, open systems, open-source, open-source EHR systems, open-source electronic health records, open-source solutions, OpenEMR, OpenVistA, public domain software, search engines, US companies, wealthiest countries}, doi = {10.1109/HealthCom.2013.6720708}, author = {de la Torre, I. and Martinez, B. and Lopez-Coronado, M.} } @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 {874, title = {Customising DHIS2 for Maternal and Child Health Information Management in Sri Lanka}, journal = {Sri Lanka Journal of Bio-Medical Informatics}, volume = {3}, year = {2013}, abstract = {Maternal and Child Health (MCH) is an important component of the primary health care system. MCH systems are developed incorporated with health information systems. Electronic MCH Information Management Systems are emerging and they have proven to improve the quality, efficiency and the cost of medical care. Vendor neutral open source software, such as DHIS2, provides the resources to develop most of the Health Information Management systems. By following open standards; quality, productivity, cost management and data safety can be improved.DOi: http://dx.doi.org/10.4038/sljbmi.v3i2.2496 Sri Lanka Journal of Biomedical Informatics 2012; 3:47-54}, keywords = {DHIS2, Information Systems, Maternal and Child Health, open source}, url = {http://www.sljol.info/index.php/SLJBMI/article/view/2496}, author = {M. Manoj} } @article {891, title = {Fundus image diagnostic agreement in uveitis utilizing free and open source software.}, journal = {Can J Ophthalmol}, volume = {48}, year = {2013}, month = {2013 Aug}, pages = {227-34}, abstract = {

OBJECTIVE: To assess the adequacy of image agreement regarding uveitis based on color fundus and fluorescein angiography images alone, and to use free and open source applications to conduct an image agreement study.

DESIGN: Cross-sectional agreement study.

PARTICIPANTS: Baseline fundus and fluorescein images of patients with panuveitis, posterior, or intermediate uveitis enrolled in the Multi-center Uveitis Steroid Treatment (MUST) trial.

METHODS: Three fellowship-trained specialists in uveitis independently reviewed patient images using ClearCanvas{\texttrademark} and responded using Epi Info{\texttrademark}. The diagnoses of the 3 reviewers were compared with the MUST clinician as a gold standard. A rank transformation adjusted for the possible variation in number of responses per patient. Chance-corrected interobserver agreement among the 3 reviewers was estimated with the ι coefficient. Confidence interval (CI) and SE were bootstrapped.

RESULTS: Agreement between the diagnoses of the respondents and the baseline MUST clinician{\textquoteright}s diagnosis was poor across all diagnostic categories, ι = 0.09 (95\% CI, 0.07-0.11). The agreement among respondents alone also was poor, ι = 0.11 {\textpm} 0.02 (95\% CI, 0.08-0.13). The specialists requested more patient historical and clinical information to make a diagnosis on all patients.

CONCLUSIONS: The role in distinguishing the multiple conditions in uveitis appears to be limited when based on fundus imaging alone. Future studies should investigate different categories of clinical data to supplement image data. Freely available applications have excellent utility in ophthalmic imaging agreement studies.

}, issn = {0008-4182}, doi = {10.1016/j.jcjo.2013.02.010}, author = {Hsieh, Jane and Honda, Andrea F and Su{\'a}rez-Fari{\~n}as, Mayte and Samson, C Michael and Kedhar, Sanjay and Mauro, John and Francis, Jasmine and Badamo, Jason and Diaz, Vicente A and Kempen, John H and Latkany, Paul A} } @article {865, title = {GBM volumetry using the 3D Slicer medical image computing platform.}, journal = {Sci Rep}, volume = {3}, year = {2013}, month = {2013}, pages = {1364}, abstract = {

Volumetric change in glioblastoma multiforme (GBM) over time is a critical factor in treatment decisions. Typically, the tumor volume is computed on a slice-by-slice basis using MRI scans obtained at regular intervals. (3D)Slicer - a free platform for biomedical research - provides an alternative to this manual slice-by-slice segmentation process, which is significantly faster and requires less user interaction. In this study, 4 physicians segmented GBMs in 10 patients, once using the competitive region-growing based GrowCut segmentation module of Slicer, and once purely by drawing boundaries completely manually on a slice-by-slice basis. Furthermore, we provide a variability analysis for three physicians for 12 GBMs. The time required for GrowCut segmentation was on an average 61\% of the time required for a pure manual segmentation. A comparison of Slicer-based segmentation with manual slice-by-slice segmentation resulted in a Dice Similarity Coefficient of 88.43 {\textpm} 5.23\% and a Hausdorff Distance of 2.32 {\textpm} 5.23 mm.

}, issn = {2045-2322}, doi = {10.1038/srep01364}, author = {Egger, Jan and Kapur, Tina and Fedorov, Andriy and Pieper, Steve and Miller, James V and Veeraraghavan, Harini and Freisleben, Bernd and Golby, Alexandra J and Nimsky, Christopher and Kikinis, Ron} } @article {855, title = {Health care transformation through collaboration on open-source informatics projects: integrating a medical applications platform, research data repository, and patient summarization.}, journal = {Interact J Med Res}, volume = {2}, year = {2013}, month = {2013}, pages = {e11}, abstract = {

BACKGROUND: The Strategic Health IT Advanced Research Projects (SHARP) program seeks to conquer well-understood challenges in medical informatics through breakthrough research. Two SHARP centers have found alignment in their methodological needs: (1) members of the National Center for Cognitive Informatics and Decision-making (NCCD) have developed knowledge bases to support problem-oriented summarizations of patient data, and (2) Substitutable Medical Apps, Reusable Technologies (SMART), which is a platform for reusable medical apps that can run on participating platforms connected to various electronic health records (EHR). Combining the work of these two centers will ensure wide dissemination of new methods for synthesized views of patient data. Informatics for Integrating Biology and the Bedside (i2b2) is an NIH-funded clinical research data repository platform in use at over 100 sites worldwide. By also working with a co-occurring initiative to SMART-enabling i2b2, we can confidently write one app that can be used extremely broadly.

OBJECTIVE: Our goal was to facilitate development of intuitive, problem-oriented views of the patient record using NCCD knowledge bases that would run in any EHR. To do this, we developed a collaboration between the two SHARPs and an NIH center, i2b2.

METHODS: First, we implemented collaborative tools to connect researchers at three institutions. Next, we developed a patient summarization app using the SMART platform and a previously validated NCCD problem-medication linkage knowledge base derived from the National Drug File-Reference Terminology (NDF-RT). Finally, to SMART-enable i2b2, we implemented two new Web service "cells" that expose the SMART application programming interface (API), and we made changes to the Web interface of i2b2 to host a "carousel" of SMART apps.

RESULTS: We deployed our SMART-based, NDF-RT-derived patient summarization app in this SMART-i2b2 container. It displays a problem-oriented view of medications and presents a line-graph display of laboratory results.

CONCLUSIONS: This summarization app can be run in any EHR environment that either supports SMART or runs SMART-enabled i2b2. This i2b2 "clinical bridge" demonstrates a pathway for reusable app development that does not require EHR vendors to immediately adopt the SMART API. Apps can be developed in SMART and run by clinicians in the i2b2 repository, reusing clinical data extracted from EHRs. This may encourage the adoption of SMART by supporting SMART app development until EHRs adopt the platform. It also allows a new variety of clinical SMART apps, fueled by the broad aggregation of data types available in research repositories. The app (including its knowledge base) and SMART-i2b2 are open-source and freely available for download.

}, issn = {1929-073X}, doi = {10.2196/ijmr.2454}, author = {Klann, Jeffrey G and McCoy, Allison B and Wright, Adam and Wattanasin, Nich and Sittig, Dean F and Murphy, Shawn N} } @article {933, title = {International data-sharing for radiotherapy research: An open-source based infrastructure for multicentric clinical data mining.}, journal = {Radiother Oncol}, year = {2013}, month = {2013 Dec 2}, abstract = {

Extensive, multifactorial data sharing is a crucial prerequisite for current and future (radiotherapy) research. However, the cost, time and effort to achieve this are often a roadblock. We present an open-source based data-sharing infrastructure between two radiotherapy departments, allowing seamless exchange of de-identified, automatically translated clinical and biomedical treatment data.

}, issn = {1879-0887}, doi = {10.1016/j.radonc.2013.11.001}, author = {Roelofs, Erik and Dekker, Andr{\'e} and Meldolesi, Elisa and van Stiphout, Ruud G P M and Valentini, Vincenzo and Lambin, Philippe} } @article {852, title = {The Medical Imaging Interaction Toolkit: challenges and advances : 10 years of open-source development.}, journal = {Int J Comput Assist Radiol Surg}, year = {2013}, month = {2013 Apr 16}, abstract = {

PURPOSE: ~~~The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. METHODS: ~~~MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. RESULTS: ~~~MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. CONCLUSIONS: ~~~MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today{\textquoteright}s and tomorrow{\textquoteright}s clinically motivated research.

}, issn = {1861-6429}, doi = {10.1007/s11548-013-0840-8}, author = {Nolden, Marco and Zelzer, Sascha and Seitel, Alexander and Wald, Diana and M{\"u}ller, Michael and Franz, Alfred M and Maleike, Daniel and Fangerau, Markus and Baumhauer, Matthias and Maier-Hein, Lena and Maier-Hein, Klaus H and Meinzer, Hans -Peter and Wolf, Ivo} } @inbook {866, title = {MITK-US: Echtzeitverarbeitung von Ultraschallbildern in MITK}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2013}, series = {Informatik aktuell}, year = {2013}, pages = {302-307}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Ultraschall (US) als bildgebendes Verfahren in der Medizin ist nicht invasiv, schnell, vielerorts verf{\"u}gbar, kommt ohne Strahlenbelastung aus und liefert kontinuierlich Daten in Echtzeit. Die Nutzung von US f{\"u}r computerassistierte Interventionen (CAI) stellt jedoch nicht nur extrem hohe Anforderungen an die Methoden zur Bildverarbeitung aufgrund der beschr{\"a}nkten Bildqualit{\"a}t, sondern bedeutet auch einen betr{\"a}chtlichen Integrationsaufwand wenn die Daten in Echtzeit weiterverarbeitet werden sollen. Mit MITK-US stellen wir in dieser Arbeit ein neues Modul f{\"u}r das Open Source verf{\"u}gbare Medical Imaging Interaction Toolkit (MITK) vor, welches die einheitliche Einbindung und Weiterverarbeitung von Echtzeitultraschalldaten erm{\"o}glicht und somit den Aufwand f{\"u}r die Integration von US in CAI Systeme verringert. Da die Verwendung von Echtzeitdaten insbesondere im Bereich der CAI zahlreiche neue M{\"o}glichkeiten bietet, erwarten wir einen hohen Nutzen dieses Moduls f{\"u}r k{\"u}nftige Projekte.}, isbn = {978-3-642-36479-2}, doi = {10.1007/978-3-642-36480-8_53}, url = {http://dx.doi.org/10.1007/978-3-642-36480-8_53}, author = {Franz, AlfredMichael and M{\"a}rz, Keno and Seitel, Alexander and M{\"u}ller, Michael and Zelzer, Sascha and Nodeln, Marco and Meinzer, Hans-Peter and Maier-Hein, Lena}, editor = {Meinzer, Hans-Peter and Deserno, Thomas Martin and Handels, Heinz and Tolxdorff, Thomas} } @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 {919, title = {Physiological states and functional relation between thyrotropin and free thyroxine in thyroid health and disease: in vivo and in silico data suggest a hierarchical model.}, journal = {J Clin Pathol}, volume = {66}, year = {2013}, month = {2013 Apr}, pages = {335-42}, abstract = {

AIMS: Understanding the exact relationship between serum thyrotropin/thyroid stimulating hormone (TSH) and free thyroxine (FT(4)) is a prerequisite for improving diagnostic reliability and clinical decision making.

METHODS: We (1) retrospectively studied the relationship between TSH and FT(4) in a large unselected clinical sample (n=6641) of primary hypothyroid, euthyroid and hyperthyroid subjects, and (2) applied a mathematical model of thyroid hormone feedback control to assess the relation between structural parameters and TSH levels in the different functional states.

RESULTS: When separately analysing total sample and untreated subjects, the correlation slope for logTSH versus FT(4) for hypothyroid subjects was significantly different from that of the euthyroid panel and hyperthyroid subjects (the latter being compromised by reaching the TSH assay{\textquoteright}s lower detection limit). As trends between functional states changed, each functional segment appeared to become differently regulated. Theoretical modelling and sensitivity analysis revealed that the influence of various structural parameters on TSH levels also depends on the overall function of the feedback loop.

CONCLUSIONS: Our data suggest that the states of hypothyroidism, euthyroidism and hyperthyroidism can be regarded as differently regulated entities. The apparent complexity could be replicated by mathematical modelling suggesting a hierarchical type of feedback regulation involving patterns of operative mechanisms unique to each condition. For clinical purposes and assay evaluation, neither the standard model relating logTSH with FT(4), nor an alternative model based on non-competitive inhibition can be reliably represented by a single correlation comparing all samples for both hormones in one all-inclusive group.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Autoantibodies, Autoantigens, Biological Markers, Computer Simulation, Feedback, Physiological, Humans, Hyperthyroidism, Hypothyroidism, Iodide Peroxidase, Iron-Binding Proteins, Linear Models, Middle Aged, Models, Biological, Multivariate Analysis, Nonlinear Dynamics, Predictive Value of Tests, Retrospective Studies, Thyroid Diseases, Thyroid Function Tests, Thyroid Gland, Thyrotropin, Thyroxine, Young Adult}, issn = {1472-4146}, doi = {10.1136/jclinpath-2012-201213}, author = {Midgley, John E M and Hoermann, Rudolf and Larisch, Rolf and Dietrich, Johannes W} } @article {918, title = {Is pituitary TSH an adequate measure of thyroid hormone-controlled homoeostasis during thyroxine treatment?}, journal = {Eur J Endocrinol}, volume = {168}, year = {2013}, month = {2013 Feb}, pages = {271-80}, abstract = {

OBJECTIVE: In recognition of its primary role in pituitary-thyroid feedback, TSH determination has become a key parameter for clinical decision-making. This study examines the value of TSH as a measure of thyroid hormone homoeostasis under thyroxine (T(4)) therapy.

DESIGN AND METHODS: We have examined the interrelationships between free triiodothyronine (FT(3)), free T(4) (FT(4)) and pituitary TSH by means of i) a retrospective analysis of a large clinical sample comprising 1994 patients either untreated or on varying doses of l-T(4) and ii) independent mathematical simulation applying a model of thyroid homoeostasis, together with a sensitivity analysis.

RESULTS: Over a euthyroid to mildly hyperthyroid functional range, we found markedly different correlation slopes of log TSH vs FT(3) and FT(4) between untreated patients and l-T(4) groups. Total deiodinase activity (G(D)) was positively correlated with TSH in untreated subjects. However, G(D) was significantly altered and the correlation was lost under increasing l-T(4) doses. Ninety-five per cent confidence intervals for FT(3) and FT(4), when assessed in defined TSH concentration bands, differed significantly for l-T(4)-treated compared with untreated patients. Higher doses were often needed to restore FT(3) levels within its reference range. Sensitivity analysis revealed the influence of various structural parameters on pituitary TSH secretion including an important role of pituitary deiodinase type 2.

CONCLUSION: The data reveal disjoints between FT(4)-TSH feedback and T(3) production that persist even when sufficient T(4) apparently restores euthyroidism. T(4) treatment displays a compensatory adaptation but does not completely re-enact normal euthyroid physiology. This invites a study of the clinical consequences of this disparity.

}, keywords = {Adult, Female, Homeostasis, Humans, Hypothyroidism, Male, Pituitary Gland, Retrospective Studies, Thyrotropin, Thyroxine, Triiodothyronine}, issn = {1479-683X}, doi = {10.1530/EJE-12-0819}, author = {Hoermann, Rudolf and Midgley, John E M and Larisch, Rolf and Dietrich, Johannes W} } @article {875, title = {Three-dimensional volumetric rendition of cannon ball pulmonary metastases by the use of 3D Slicer, an open source free software package.}, journal = {BMJ Case Rep}, volume = {2013}, year = {2013}, month = {2013}, issn = {1757-790X}, doi = {10.1136/bcr-2012-008248}, author = {Revannasiddaiah, Swaroop and Susheela, Sridhar Papaiah and Madhusudhan, N and Mallarajapatna, Govindarajan 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 {837, title = {Adaptation of a web-based, open source electronic medical record system platform to support a large study of tuberculosis epidemiology.}, journal = {BMC Med Inform Decis Mak}, volume = {12}, year = {2012}, month = {2012}, pages = {125}, abstract = {UNLABELLED: ABSTRACT: BACKGROUND: In 2006, we were funded by the US National Institutes of Health to implement a study of tuberculosis epidemiology in Peru. The study required a secure information system to manage data from a target goal of 16,000 subjects who needed to be followed for at least one year. With previous experience in the development and deployment of web-based medical record systems for TB treatment in Peru, we chose to use the OpenMRS open source electronic medical record system platform to develop the study information system. Supported by a core technical and management team and a large and growing worldwide community, OpenMRS is now being used in more than 40 developing countries. We adapted the OpenMRS platform to better support foreign languages. We added a new module to support double data entry, linkage to an existing laboratory information system, automatic upload of GPS data from handheld devices, and better security and auditing of data changes. We added new reports for study managers, and developed data extraction tools for research staff and statisticians. Further adaptation to handle direct entry of laboratory data occurred after the study was launched. RESULTS: Data collection in the OpenMRS system began in September 2009. By August 2011 a total of 9,256 participants had been enrolled, 102,274 forms and 13,829 laboratory results had been entered, and there were 208 users. The system is now entirely supported by the Peruvian study staff and programmers. CONCLUSIONS: The information system served the study objectives well despite requiring some significant adaptations mid-stream. OpenMRS has more tools and capabilities than it did in 2008, and requires less adaptations for future projects. OpenMRS can be an effective research data system in resource poor environments, especially for organizations using or considering it for clinical care as well as research.}, issn = {1472-6947}, doi = {10.1186/1472-6947-12-125}, author = {Fraser, Hamish S F and Thomas, David and Tomaylla, Juan and Garcia, Nadia and Lecca, Leonid and Murray, Megan and Becerra, Mercedes C} } @article {1021, title = {ARDEN2BYTECODE: a one-pass Arden Syntax compiler for service-oriented decision support systems based on the OSGi platform.}, journal = {Comput Methods Programs Biomed}, volume = {106}, year = {2012}, month = {2012 May}, pages = {114-25}, abstract = {

Patient empowerment might be one key to reduce the pressure on health care systems challenged by the expected demographic changes. Knowledge based systems can, in combination with automated sensor measurements, improve the patients{\textquoteright} ability to review their state of health and make informed decisions. The Arden Syntax as a standardized language to represent medical knowledge can be used to express the corresponding decision rules. In this paper we introduce ARDEN2BYTECODE, a newly developed open source compiler for the Arden Syntax. ARDEN2BYTECODE runs on Java Virtual Machines (JVM) and translates Arden Syntax directly to Java Bytecode (JBC) executable on JVMs. ARDEN2BYTECODE easily integrates into service oriented architectures, like the Open Services Gateway Initiative (OSGi) platform. Apart from an evaluation of compilation performance and execution times, ARDEN2BYTECODE was integrated into an existing knowledge supported exercise training system and recorded training sessions have been used to check the implementation.

}, keywords = {Decision Support Systems, Management, Programming Languages}, issn = {1872-7565}, doi = {10.1016/j.cmpb.2011.11.003}, author = {Gietzelt, Matthias and Goltz, Ursula and Grunwald, Daniel and Lochau, Malte and Marschollek, Michael and Song, Bianying and Wolf, Klaus-Hendrik} } @article {795, title = {BioImageXD: an open, general-purpose and high-throughput image-processing platform.}, journal = {Nat Methods}, volume = {9}, year = {2012}, month = {2012}, pages = {683-9}, abstract = {BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.}, issn = {1548-7105}, doi = {10.1038/nmeth.2047}, author = {Kankaanp{\"a}{\"a}, Pasi and Paavolainen, Lassi and Tiitta, Silja and Karjalainen, Mikko and P{\"a}iv{\"a}rinne, Joacim and Nieminen, Jonna and Marjom{\"a}ki, Varpu and Heino, Jyrki and White, Daniel J} } @article {1049, title = {Designing and Implementing an Innovative SMS-based alert system (RapidSMS-MCH) to monitor pregnancy and reduce maternal and child deaths in Rwanda.}, journal = {Pan Afr Med J}, volume = {13}, year = {2012}, month = {2012}, pages = {31}, abstract = {

INTRODUCTION: With the continuous growth of mobile network coverage and unprecedented penetration of mobile devices in the developing world, several mHealth initiatives are being implemented in developing countries. This paper aims to describe requirements for designing and implementing a mobile phone-based communication system aiming at monitoring pregnancy and reducing bottlenecks in communication associated with maternal and newborn deaths; and document challenges and lessons learned.

METHODS: An SMS-based system was developed to improve maternal and child health (MCH) using RapidSMS({\textregistered}), a free and open-sourced software development framework. To achieve the expected results, the RapidSMS-MCH system was customized to allow interactive communication between a community health worker (CHW)following mother-infant pairs in their community, a national centralized database, the health facility and in case of an emergency alert, the ambulance driver. The RapidSMS-MCH system was piloted in Musanze district, Nothern province of Rwanda over a 12-month period.

RESULTS: A total of 432 CHW were trained and equipped with mobile phones. A total of 35,734 SMS were sent by 432 CHW from May 2010 to April 2011. A total of 11,502 pregnancies were monitored. A total of 362 SMS alerts for urgent and life threatening events were registered. We registered a 27\% increase in facility based delivery from 72\% twelve months before to 92\% at the end of the twelve months pilot phase. Major challenges were telephone maintenance and replacement. Disctrict heath team capacity to manage and supervise the system was strengthened by the end of pilot phase. Highly committed CHWs and effective coordination by the District health team were critical enablers.

CONCLUSION: We successully designed and implemented a mobile phone SMS-based system to track pregnancy and maternal and child outcomes in limited resources setting. Implementation of mobile-phone systems at community level could contribute to improving emergency obstetric and neonatal care, yet it requires a well-organized community health structure in limited resource settings.

}, keywords = {Cell Phones, Child Mortality, Child, Preschool, Emergency Medical Services, Female, Fetal Death, Health Plan Implementation, Humans, Infant, Newborn, Maternal Death, Maternal Health Services, Maternal-Child Health Centers, Monitoring, Physiologic, Pregnancy, Prenatal Care, Program Development, Rwanda, Telemedicine}, issn = {1937-8688}, author = {Ngabo, Fidele and Nguimfack, Judith and Nwaigwe, Friday and Mugeni, Catherine and Muhoza, Denis and Wilson, David R and Kalach, John and Gakuba, Richard and Karema, Corrine and Binagwaho, Agnes} } @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 {784, title = {DicomBrowser: Software for Viewing and Modifying DICOM Metadata.}, journal = {J Digit Imaging}, year = {2012}, month = {2012 Feb 15}, abstract = {Digital Imaging and Communications in Medicine (DICOM) is the dominant standard for medical imaging data. DICOM-compliant devices and the data they produce are generally designed for clinical use and often do not match the needs of users in research or clinical trial settings. DicomBrowser is software designed to ease the transition between clinically oriented DICOM tools and the specialized workflows of research imaging. It supports interactive loading and viewing of DICOM images and metadata across multiple studies and provides a rich and flexible system for modifying DICOM metadata. Users can make ad hoc changes in a graphical user interface, write metadata modification scripts for batch operations, use partly automated methods that guide users to modify specific attributes, or combine any of these approaches. DicomBrowser can save modified objects as local files or send them to a DICOM storage service using the C-STORE network protocol. DicomBrowser is open-source software, available for download at http://nrg.wustl.edu/software/dicom-browser .}, issn = {1618-727X}, doi = {10.1007/s10278-012-9462-x}, author = {Archie, Kevin A and Marcus, Daniel S} } @article {815, title = {Free and open-source software application for the evaluation of coronary computed tomography angiography images.}, journal = {Arq Bras Cardiol}, year = {2012}, month = {2012 Oct 2}, abstract = {BACKGROUND: The standardization of images used in Medicine in 1993 was performed using the DICOM (Digital Imaging and Communications in Medicine) standard. Several tests use this standard and it is increasingly necessary to design software applications capable of handling this type of image; however, these software applications are not usually free and open-source, and this fact hinders their adjustment to most diverse interests. OBJECTIVE: To develop and validate a free and open-source software application capable of handling DICOM coronary computed tomography angiography images. METHODS: We developed and tested the ImageLab software in the evaluation of 100 tests randomly selected from a database. We carried out 600 tests divided between two observers using ImageLab and another software sold with Philips Brilliance computed tomography appliances in the evaluation of coronary lesions and plaques around the left main coronary artery (LMCA) and the anterior descending artery (ADA). To evaluate intraobserver, interobserver and intersoftware agreements, we used simple and kappa statistics agreements. RESULTS: The agreements observed between software applications were generally classified as substantial or almost perfect in most comparisons. CONCLUSION: The ImageLab software agreed with the Philips software in the evaluation of coronary computed tomography angiography tests, especially in patients without lesions, with lesions < 50\% in the LMCA and < 70\% in the ADA. The agreement for lesions > 70\% in the ADA was lower, but this is also observed when the anatomical reference standard is used.}, issn = {1678-4170}, author = {Hadlich, Marcelo Souza and Oliveira, Gl{\'a}ucia Maria Moraes and Feij{\'o}o, Ra{\'u}l A and Azevedo, Clerio F and Tura, Bernardo Rangel and Ziemer, Paulo Gustavo Portela and Blanco, Pablo Javier and Pina, Gustavo and Meira, M{\'a}rcio and Souza E Silva, Nelson Albuquerque de} } @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} } @article {793, title = {Integrating clinical practice and public health surveillance using electronic medical record systems.}, journal = {Am J Prev Med}, volume = {42}, year = {2012}, month = {2012 Jun}, pages = {S154-62}, abstract = {Electronic medical record (EMR) systems have rich potential to improve integration between primary care and the public health system at the point of care. EMRs make it possible for clinicians to contribute timely, clinically detailed surveillance data to public health practitioners without changing their existing workflows or incurring extra work. New surveillance systems can extract raw data from providers{\textquoteright} EMRs, analyze them for conditions of public health interest, and automatically communicate results to health departments. The current paper describes a model EMR-based public health surveillance platform called Electronic Medical Record Support for Public Health (ESP). The ESP platform provides live, automated surveillance for notifiable diseases, influenza-like illness, and diabetes prevalence, care, and complications. Results are automatically transmitted to state health departments.}, issn = {1873-2607}, doi = {10.1016/j.amepre.2012.04.005}, author = {Klompas, Michael and McVetta, Jason and Lazarus, Ross and Eggleston, Emma and Haney, Gillian and Kruskal, Benjamin A and Yih, W Katherine and Daly, Patricia and Oppedisano, Paul and Beagan, Brianne and Lee, Michael and Kirby, Chaim and Heisey-Grove, Dawn and DeMaria, Alfred and Platt, Richard} } @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}} } @article {820, title = {MITK Diffusion Imaging.}, journal = {Methods Inf Med}, volume = {51}, year = {2012}, month = {2012 Oct 11}, pages = {441-8}, abstract = {Background: Diffusion-MRI provides a unique window on brain anatomy and insights into aspects of tissue structure in living humans that could not be studied previously. There is a major effort in this rapidly evolving field of research to develop the algorithmic tools necessary to cope with the complexity of the datasets. Objectives: This work illustrates our strategy that encompasses the development of a modularized and open software tool for data processing, visualization and interactive exploration in diffusion imaging research and aims at reinforcing sustainable evaluation and progress in the field. Methods: In this paper, the usability and capabilities of a new application and toolkit component of the Medical Imaging and Interaction Toolkit (MITK, www.mitk.org), MITK-DI, are demonstrated using in-vivo datasets. Results: MITK-DI provides a comprehensive software framework for high-performance data processing, analysis and interactive data exploration, which is designed in a modular, extensible fashion (using CTK) and in adherence to widely accepted coding standards (e.g. ITK, VTK). MITK-DI is available both as an open source software development toolkit and as a ready-to-use installable application. Conclusions: The open source release of the modular MITK-DI tools will increase verifiability and comparability within the research community and will also be an important step towards bringing many of the current techniques towards clinical application.}, issn = {0026-1270}, doi = {10.3414/ME11-02-0031}, author = {Fritzsche, K H and Neher, P F and Reicht, I and van Bruggen, T and Goch, C and Reisert, M and Nolden, M and Zelzer, S and Meinzer, H-P and Stieltjes, B} } @conference {785, title = {MITK global tractography}, booktitle = {Medical Imaging 2012: Image Processing}, year = {2012}, publisher = {SPIE}, organization = {SPIE}, abstract = {Fiber tracking algorithms yield valuable information for neurosurgery as well as automated diagnostic approaches. However, they have not yet arrived in the daily clinical practice. In this paper we present an open source integration of the global tractography algorithm proposed by Reisert et.al.1 into the open source Medical Imaging Interaction Toolkit (MITK) developed and maintained by the Division of Medical and Biological Informatics at the German Cancer Research Center (DKFZ). The integration of this algorithm into a standardized and open development environment like MITK enriches accessibility of tractography algorithms for the science community and is an important step towards bringing neuronal tractography closer to a clinical application. The MITK diffusion imaging application, downloadable from www.mitk.org, combines all the steps necessary for a successful tractography: preprocessing, reconstruction of the images, the actual tracking, live monitoring of intermediate results, postprocessing and visualization of the final tracking results. This paper presents typical tracking results and demonstrates the steps for pre- and post-processing of the images.}, doi = {10.1117/12.911215}, url = {http://link.aip.org/link/?PSI/8314/83144D/1}, author = {Peter F. Neher and Bram Stieltjes and Marco Reisert and Ignaz Reicht and Meinzer, Hans-Peter and Klaus H. Fritzsche}, editor = {David R. Haynor and Sebastien Ourselin} } @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 {817, title = {Open-source point-of-care electronic medical records for use in resource-limited settings: systematic review and questionnaire surveys.}, journal = {BMJ Open}, volume = {2}, year = {2012}, month = {2012}, abstract = {BACKGROUND: Point-of-care electronic medical records (EMRs) are a key tool to manage chronic illness. Several EMRs have been developed for use in treating HIV and tuberculosis, but their applicability to primary care, technical requirements and clinical functionalities are largely unknown. OBJECTIVES: This study aimed to address the needs of clinicians from resource-limited settings without reliable internet access who are considering adopting an open-source EMR. STUDY ELIGIBILITY CRITERIA: Open-source point-of-care EMRs suitable for use in areas without reliable internet access. STUDY APPRAISAL AND SYNTHESIS METHODS: The authors conducted a comprehensive search of all open-source EMRs suitable for sites without reliable internet access. The authors surveyed clinician users and technical implementers from a single site and technical developers of each software product. The authors evaluated availability, cost and technical requirements. RESULTS: The hardware and software for all six systems is easily available, but they vary considerably in proprietary components, installation requirements and customisability. LIMITATIONS: This study relied solely on self-report from informants who developed and who actively use the included products. CONCLUSIONS AND IMPLICATIONS OF KEY FINDINGS: Clinical functionalities vary greatly among the systems, and none of the systems yet meet minimum requirements for effective implementation in a primary care resource-limited setting. The safe prescribing of medications is a particular concern with current tools. The dearth of fully functional EMR systems indicates a need for a greater emphasis by global funding agencies to move beyond disease-specific EMR systems and develop a universal open-source health informatics platform.}, issn = {2044-6055}, doi = {10.1136/bmjopen-2011-000690}, author = {Millard, Peter S and Bru, Juan and Berger, Christopher A} } @article {828, title = {A quick guide to software licensing for the scientist-programmer.}, journal = {PLoS Comput Biol}, volume = {8}, year = {2012}, month = {2012}, pages = {e1002598}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002598}, author = {Morin, Andrew and Urban, Jennifer and Sliz, Piotr} } @article {788, title = {The SMART Platform: early experience enabling substitutable applications for electronic health records.}, journal = {J Am Med Inform Assoc}, year = {2012}, month = {2012 Mar 17}, abstract = {ObjectiveThe Substitutable Medical Applications, Reusable Technologies (SMART) Platforms project seeks to develop a health information technology platform with substitutable applications (apps) constructed around core services. The authors believe this is a promising approach to driving down healthcare costs, supporting standards evolution, accommodating differences in care workflow, fostering competition in the market, and accelerating innovation.Materials and methodsThe Office of the National Coordinator for Health Information Technology, through the Strategic Health IT Advanced Research Projects (SHARP) Program, funds the project. The SMART team has focused on enabling the property of substitutability through an app programming interface leveraging web standards, presenting predictable data payloads, and abstracting away many details of enterprise health information technology systems. Containers-health information technology systems, such as electronic health records (EHR), personally controlled health records, and health information exchanges that use the SMART app programming interface or a portion of it-marshal data sources and present data simply, reliably, and consistently to apps.ResultsThe SMART team has completed the first phase of the project (a) defining an app programming interface, (b) developing containers, and (c) producing a set of charter apps that showcase the system capabilities. A focal point of this phase was the SMART Apps Challenge, publicized by the White House, using http://www.challenge.gov website, and generating 15 app submissions with diverse functionality.ConclusionKey strategic decisions must be made about the most effective market for further disseminating SMART: existing market-leading EHR vendors, new entrants into the EHR market, or other stakeholders such as health information exchanges.}, issn = {1527-974X}, doi = {10.1136/amiajnl-2011-000622}, author = {Mandl, Kenneth D and Mandel, Joshua C and Murphy, Shawn N and Bernstam, Elmer Victor and Ramoni, Rachel L and Kreda, David A and McCoy, J Michael and Adida, Ben and Kohane, Isaac S.} } @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} } @article {779, title = {STIR: software for tomographic image reconstruction release 2.}, journal = {Phys Med Biol}, volume = {57}, year = {2012}, month = {2012 Feb 21}, pages = {867-83}, abstract = {We present a new version of STIR (Software for Tomographic Image Reconstruction), an open source object-oriented library implemented in C++~for 3D positron emission tomography reconstruction. This library has been designed such that it can be used for many algorithms and scanner geometries, while being portable to various computing platforms. This second release enhances its flexibility and modular design and includes additional features such as Compton scatter simulation, an additional iterative reconstruction algorithm and parametric image reconstruction (both indirect and direct). We discuss the new features in this release and present example results. STIR can be downloaded from http://stir.sourceforge.net.}, keywords = {Algorithms, Animals, Computers, Image Processing, Computer-Assisted, Mice, Software, Tomography}, issn = {1361-6560}, doi = {10.1088/0031-9155/57/4/867}, author = {Thielemans, Kris and Tsoumpas, Charalampos and Mustafovic, Sanida and Beisel, Tobias and Aguiar, Pablo and Dikaios, Nikolaos and Jacobson, Matthew W} } @article {775, title = {Towards the Adoption of Open Source and Open Access Electronic Health Record Systems}, journal = {Journal of Healthcare Engineering}, volume = {3}, year = {2012}, month = {03}, pages = {141{\textendash}162}, abstract = {As the Electronic Health Record (EHR) systems constantly expand to support more clinical activities and their implementations in healthcare organizations become more widespread, several communities have been working intensively for several years to develop open access and open source EHR software, aiming at reducing the costs of EHR deployment and maintenance. In this paper, we describe and evaluate the most popular open source electronic medical records such as openEMR, openMRS and patientOS, providing their technical features and potentials. These systems are considered quite important due to their prevalence. The article presents the key features of each system and outlines the advantages and problems of Open Source Software (OSS) Systems through a review of the literature, in order to demonstrate the possibility of their adoption in modern electronic healthcare systems. Also discussed are the future trends of OS EHRs in the context of the Personal Health Records and mobile computing paradigm.}, doi = {10.1260/2040-2295.3.1.141}, url = {http://dx.doi.org/10.1260/2040-2295.3.1.141}, author = {Maglogiannis, Ilias} } @article {810, title = {Arden2ByteCode: A one-pass Arden Syntax compiler for service-oriented decision support systems based on the OSGi platform.}, journal = {Comput Methods Programs Biomed}, year = {2011}, doi = {10.1016/j.cmpb.2011.11.003}, url = {http://dx.doi.org/10.1016/j.cmpb.2011.11.003} note = {Epub ahead of print}, author = {Gietzelt, Matthias and Goltz, Ursula and Grunwald, Daniel and Lochau, Malte and Marschollek, Michael and Song, Bianying and Wolf, Klaus-Hendrik} } @article {696, title = {ATOM - an OMERO add-on for automated import of image data.}, journal = {BMC research notes}, volume = {4}, year = {2011}, month = {2011}, pages = {382}, abstract = {UNLABELLED: ABSTRACT: BACKGROUND: Modern microscope platforms are able to generate multiple gigabytes of image data in a single experimental session. In a routine research laboratory workflow, these data are initially stored on the local acquisition computer from which files need to be transferred to the experimenter{\textquoteright}s (remote) image repository (e.g., DVDs, portable hard discs or server-based storage) because of limited local data storage. Although manual solutions for this migration, such as OMERO - a client-server software for visualising and managing large amounts of image data - exist, this import process may be a time-consuming and tedious task. FINDINGS: We have developed ATOM, a Java-based and thus platform-independent add-on for OMERO enabling automated transfer of image data from a wide variety of acquisition software packages into OMERO. ATOM provides a graphical user interface and allows pre-organisation of experimental data for the transfer. CONCLUSIONS: ATOM is a convenient extension of the OMERO software system. An automated interface to OMERO will be a useful tool for scientists working with file formats supported by the Bio-Formats file format library, a platform-independent library for reading the most common file formats of microscope images.}, issn = {1756-0500}, doi = {10.1186/1756-0500-4-382}, author = {M{\"u}ller, Oliver and Lipp, Peter and Kaestner, Lars} } @article {575, title = {Brainstorm: A User-Friendly Application for MEG/EEG Analysis}, journal = {Computational Intelligence and Neuroscience}, volume = {2011}, year = {2011}, month = {01/2011}, abstract = {Brainstorm is a collaborative open-source application dedicated to magnetoencephalography (MEG) and electroencephalography (EEG) data visualization and processing, with an emphasis on cortical source estimation techniques and their integration with anatomical magnetic resonance imaging (MRI) data. The primary objective of the software is to connect MEG/EEG neuroscience investigators with both the best-established and cutting-edge methods through a simple and intuitive graphical user interface (GUI).}, doi = {10.1155/2011/879716}, url = {http://www.hindawi.com/journals/cin/2011/879716/}, author = {Fran{\c c}ois Tadel and Sylvain Baillet and John C. Mosher and Dimitrios Pantazis} } @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 {Ferranti23092011, title = {The design and implementation of an open-source, data-driven cohort recruitment system: the Duke Integrated Subject Cohort and Enrollment Research Network (DISCERN)}, journal = {Journal of the American Medical Informatics Association}, year = {2011}, abstract = {Objective Failure to reach research subject recruitment goals is a significant impediment to the success of many clinical trials. Implementation of health-information technology has allowed retrospective analysis of data for cohort identification and recruitment, but few institutions have also leveraged real-time streams to support such activities.Design Duke Medicine has deployed a hybrid solution, The Duke Integrated Subject Cohort and Enrollment Research Network (DISCERN), that combines both retrospective warehouse data and clinical events contained in prospective Health Level 7 (HL7) messages to immediately alert study personnel of potential recruits as they become eligible.Results DISCERN analyzes more than 500{\quotesinglbase}{\"A}{\`a}000 messages daily in service of 12 projects. Users may receive results via email, text pages, or on-demand reports. Preliminary results suggest DISCERN{\textquoteright}s unique ability to reason over both retrospective and real-time data increases study enrollment rates while reducing the time required to complete recruitment-related tasks. The authors have introduced a preconfigured DISCERN function as a self-service feature for users.Limitations The DISCERN framework is adoptable primarily by organizations using both HL7 message streams and a data warehouse. More efficient recruitment may exacerbate competition for research subjects, and investigators uncomfortable with new technology may find themselves at a competitive disadvantage in recruitment.Conclusion DISCERN{\textquoteright}s hybrid framework for identifying real-time clinical events housed in HL7 messages complements the traditional approach of using retrospective warehoused data. DISCERN is helpful in instances when the required clinical data may not be loaded into the warehouse and thus must be captured contemporaneously during patient care. Use of an open-source tool supports generalizability to other institutions at minimal cost.}, doi = {10.1136/amiajnl-2011-000115}, url = {http://jamia.bmj.com/content/early/2011/09/23/amiajnl-2011-000115.abstract}, author = {Ferranti, Jeffrey M and Gilbert, William and McCall, Jonathan and Shang, Howard and Barros, Tanya and Horvath, Monica M} } @article {589, title = {FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data.}, journal = {Computational intelligence and neuroscience}, volume = {2011}, year = {2011}, month = {2011}, pages = {156869}, abstract = {This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.}, keywords = {Electroencephalography, Electrophysiological Phenomena, Humans, Magnetoencephalography, Numerical Analysis, Computer-Assisted, Software, User-Computer Interface}, issn = {1687-5273}, author = {Oostenveld, Robert and Fries, Pascal and Maris, Eric and Schoffelen, Jan-Mathijs} } @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} } @conference {MEJIA:2011:INRIA-00567598:1, title = {Invasive composition for the evolution of a health information system}, booktitle = {Variability \& Composition (VariComp)}, year = {2011}, note = {{ACM} 978-1-4503-0646-1/11/03 {D}.: {S}oftware/{D}.3: {PROGRAMMING} {LANGUAGES}/{D}.3.3: {L}anguage {C}onstructs and {F}eatures}, month = {03}, address = {Pernambuco Brazil}, abstract = {{I}n this paper we show that some of the evolution tasks in {O}pen{MRS}, a health information system, may require the invasive modification of interfaces and implementations in order to offer an appropriate modularization. {W}e introduce a new composition framework in {J}ava that supports the definition of expressive pattern-based invasive compositions. {F}ur thermore, we show that the composition framework allows us to concisely define an evolution scenario of {O}pen{MRS} that supports the consolidation of patient data from differ- ent remote instances.}, keywords = {Aspect-oriented programming, Distributed systems, Health information systems, Invasive software composition}, url = {http://hal.inria.fr/inria-00567598/PDF/mejia-sudholt-benavides_varicomp-AOSD2011.pdf}, author = {Mejia, Ismael and S{\"u}dholt, Mario and Benavides Navarro, Luis Daniel} } @inbook {springerlink:10.1007/978-3-642-24418-6_15, title = {Libre Software as an Innovation Enabler in India Experiences of a Bangalorian Software SME}, 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_15}, pages = {220-232}, publisher = {Springer Boston}, organization = {Springer Boston}, abstract = {Free/Libre and open source software (FLOSS) has been advocated for its presumed capacity to support native software industries in developing countries. It is said to create new spaces for exploration and to lower entry barriers to mature software markets, for example. However, little empirical research has been conducted concerning FLOSS business in a developing country setting and, thus, there is not much evidence to support or refute these claims. This paper presents a business case study conducted in India, a country branded as a {\textquoteright}software powerhouse{\textquoteright} of the developing world. The findings show how FLOSS has opened up significant opportunities for the case company, especially in terms of improving its innovative capability and upgrading in the software value chain. On the other hand, they also highlight some challenges to FLOSS involvement that rise specifically from the Indian context.}, isbn = {978-3-642-24417-9}, url = {http://dx.doi.org/10.1007/978-3-642-24418-6_15}, author = {Henttonen, Katja}, editor = {Hissam, Scott and Russo, Barbara and de Mendon{\c c}a Neto, Manoel and Kon, Fabio} } @article {573, title = {mantisGRID: A Grid Platform for DICOM Medical Images Management in Colombia and Latin America.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {24}, year = {2011}, month = {2011 Apr}, pages = {271-83}, abstract = {This paper presents the mantisGRID project, an interinstitutional initiative from Colombian medical and academic centers aiming to provide medical grid services for Colombia and Latin America. The mantisGRID is a GRID platform, based on open source grid infrastructure that provides the necessary services to access and exchange medical images and associated information following digital imaging and communications in medicine (DICOM) and health level 7 standards. The paper focuses first on the data abstraction architecture, which is achieved via Open Grid Services Architecture Data Access and Integration (OGSA-DAI) services and supported by the Globus Toolkit. The grid currently uses a 30-Mb bandwidth of the Colombian High Technology Academic Network, RENATA, connected to Internet 2. It also includes a discussion on the relational database created to handle the DICOM objects that were represented using Extensible Markup Language Schema documents, as well as other features implemented such as data security, user authentication, and patient confidentiality. Grid performance was tested using the three current operative nodes and the results demonstrated comparable query times between the mantisGRID (OGSA-DAI) and Distributed mySQL databases, especially for a large number of records.}, issn = {1618-727X}, author = {Garcia Ruiz, Manuel and Garcia Chaves, Alvin and Ruiz Iba{\~n}ez, Carlos and Gutierrez Mazo, Jorge Mario and Ramirez Giraldo, Juan Carlos and Pelaez Echavarria, Alejandro and Valencia Diaz, Edison and Pelaez Restrepo, Gustavo and Montoya Munera, Edwin Nelson and Garcia Loaiza, Bernardo and Gomez Gonzalez, Sebastian} } @article {591, title = {MITK-ToF-Range data within MITK.}, journal = {International journal of computer assisted radiology and surgery}, year = {2011}, month = {2011 May 31}, abstract = {PURPOSE: The time-of-flight (ToF) technique is an emerging technique for rapidly acquiring distance information and is becoming increasingly popular for intra-operative surface acquisition. Using the ToF technique as an intra-operative imaging modality requires seamless integration into the clinical workflow. We thus aim to integrate ToF support in an existing framework for medical image processing. METHODS: MITK-ToF was implemented as an extension of the open-source C++ Medical Imaging Interaction Toolkit (MITK) and provides the basic functionality needed for rapid prototyping and development of image-guided therapy (IGT) applications that utilize range data for intra-operative surface acquisition. This framework was designed with a module-based architecture separating the hardware-dependent image acquisition task from the processing of the range data. RESULTS: The first version of MITK-ToF has been released as an open-source toolkit and supports several ToF cameras and basic processing algorithms. The toolkit, a sample application, and a tutorial are available from http://mitk.org . CONCLUSIONS: With the increased popularity of time-of-flight cameras for intra-operative surface acquisition, integration of range data supports into medical image processing toolkits such as MITK is a necessary step. Handling acquisition of range data from different cameras and processing of the data requires the establishment and use of software design principles that emphasize flexibility, extendibility, robustness, performance, and portability. The open-source toolkit MITK-ToF satisfies these requirements for the image-guided therapy community and was already used in several research projects.}, issn = {1861-6429}, author = {Seitel, Alexander and Yung, Kwong and Mersmann, Sven and Kilgus, Thomas and Groch, Anja and Dos Santos, Thiago R and Franz, Alfred M and Nolden, Marco and Meinzer, Hans-Peter and Maier-Hein, Lena} } @article {doi:10.3109/17538157.2011.590257, title = {A novel open-source web-based platform promoting collaboration of healthcare professionals and biostatisticians: A design science approach}, journal = {Informatics for Health and Social Care}, year = {2011}, pages = {1-15}, abstract = {Collaboration among clinicians and statisticians is relatively poor, with many cases leading to poor quality research, reflected by low level of evidence studies published in the literature, thus affecting the overall quality of healthcare. We have developed a novel open-source web-based platform aiming in reinforcing the clinician{\textendash}statistician relationship, using an iterative design research process by involving all end-users. Evaluation of this platform by healthcare professionals and biostatisticians was highly positive, as we first identified the pitfalls of their relationship and overcame them through the use of this platform. We are hoping that this will strengthen the clinician{\textendash}statistician relationship in the short term and ultimately improve the quality of research and hence the quality of healthcare in the long term.}, keywords = {clinician, collaboration, design science research, open source, quality of research, relationship, statisticians, user-centred}, doi = {10.3109/17538157.2011.590257}, url = {http://informahealthcare.com/doi/abs/10.3109/17538157.2011.590257}, author = {Raptis, Dimitri A. and Mettler, Tobias and Tzanas, Kostas and Graf, Rolf} } @article {1038, title = {An online method for diagnosis of difficult TB cases for developing countries.}, journal = {Stud Health Technol Inform}, volume = {164}, year = {2011}, month = {2011}, pages = {168-73}, abstract = {

Optimal use of limited human, technical and financial resources is a major concern for tuberculosis (TB) control in developing nations. Further impediments include a lack of trained physicians, and logistical difficulties in arranging face-to-face (f-2-f) TB Diagnostic Committee (TBDC) consultations. Use of e-Health for virtual TBDCs (Internet and "iPath"), to address such issues is being studied in the Philippines and Pakistan. In Pakistan, radiological diagnosis of 88 sputum smear negative but suspected TB patients has been compared with the {\textquoteright}gold standards{\textquoteright} (TB culture, and 2-month clinical follow up). Of 88 diagnostic decisions made by primary physicians at the spoke site and electronic TBDC (e-TBDC) at hub site, there was agreement in 71 cases and disagreement on 17 cases. The turn-around time (TAT; patient registration at spoke site for f-2-f diagnosis to receiving the electronic diagnosis), averaged 34.6 hours; ranging 9 minutes to 289.2 hours. Average TAT at the rural site (59.15 hours) was more than the urban site (15.9 hours). Comparison of e-TBDC and f-2-f diagnosis with the gold standards showed only slight differences. Using culture as the gold standard, e-TBDC decisions showed greater accuracy (sensitivity - 32.4\%) as compared to f-2-f (27.6\%); using 2-month clinical follow-up as the gold standard, f-2-f diagnosis showed slightly better improvement in patient symptoms and weight as compared to e-TBDC. In Philippines "iPath" was trialed and demonstrated that e-TBDCs have potential. Such groups could review cases, diagnose, and write comments remotely, reducing the diagnosis and treatment delay compared to usual care.

}, keywords = {Adult, Developing Countries, Diagnostic Techniques and Procedures, Female, Humans, Internet, Male, Middle Aged, Mycobacterium Infections, Nontuberculous, Pakistan, Philippines, Telemedicine, Tuberculosis, Pulmonary}, issn = {0926-9630}, author = {Marcelo, Alvin and Fatmi, Zafar and Firaza, Paul Nimrod and Shaikh, Shiraz and Dandan, Alvin Joseph and Irfan, Muhammad and Bari, Vaqar and Scott, Richard E} } @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 {720, title = {OpenMRS, A Global Medical Records System Collaborative: Factors Influencing Successful Implementation.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, volume = {2011}, year = {2011}, month = {2011}, pages = {960-968}, abstract = {OpenMRS is an open-source, robust electronic health record (EHR) platform that is supported by a large global network and used in over forty countries. We explored what factors lead to successful implementation of OpenMRS in resource constrained settings. Data sources included in-person and telephone key informant interviews, focus groups and responses to an electronic survey from 10 sites in 7 countries. Qualitative data was coded through independent coding, discussion and consensus. The most common perceived benefits of implementation were for providing clinical care, reporting to funders, managing operations and research. Successful implementation factors include securing adequate infrastructure, and sociotechnical system factors, particularly adequate staffing, computers, and ability to use software. Strategic and tactical planning were successful strategies, including understanding and addressing the infrastructure and human costs involved, training or hiring personnel technically capable of modifying the software and integrating it into the daily work flow to meet clinicians{\textquoteright} needs.}, issn = {1942-597X}, author = {Mohammed-Rajput, Nareesa A and Smith, Dawn C and Mamlin, Burke and Biondich, Paul and Doebbeling, Brad N} } @article {1028, title = {On selecting a clinical trial management system for large scale, multi-centre, multi-modal clinical research study.}, journal = {Stud Health Technol Inform}, volume = {168}, year = {2011}, month = {2011}, pages = {89-95}, abstract = {

Clinical research studies offer many challenges for their supporting information systems. AIBL assembled 1112 participants who volunteered crucial information for a comprehensive study on neurodegenerative diseases. This paper discusses the shortcomings of the clinical trial management system chosen to record the results of the study. A set of guidelines was devised and a critique of five systems ensued. OpenClinica was selected as the most appropriate option. The main contribution of this paper is: (i) proposing a set of guidelines to determine the appropriateness of Clinical Trial Management Systems (CTMS) solution; (ii) providing a brief critique of existing commercial and open-sourced CTMS; and (iii) alluding to some data migration issues and providing cues on how to address them. We conclude that open-source CTMS are viable alternatives to the more expensive commercial systems to conduct, record and manage clinical studies.

}, keywords = {Australia, Checklist, Choice Behavior, Clinical Trials as Topic, Decision Support Systems, Clinical, Medical Informatics, Multicenter Studies as Topic}, issn = {0926-9630}, author = {Leroux, Hugo and McBride, Simon and Gibson, Simon} } @booklet {10.1118/1.3611983, title = {SU-E-T-33: Pydicom: An Open Source DICOM Library}, volume = {38}, number = {6}, year = {2011}, pages = {3493-3493}, publisher = {AAPM}, issn = {00942405}, doi = {DOI:10.1118/1.3611983}, url = {http://dx.doi.org/doi/10.1118/1.3611983}, author = {D Mason} } @article {640, title = {Towards Open Collaborative Health Informatics - The Role of Free/Libre Open Source Principles. Contribution of the IMIA Open Source Health Informatics Working Group.}, journal = {Yearbook of medical informatics}, volume = {6}, year = {2011}, month = {2011}, pages = {63-72}, abstract = {OBJECTIVES: : To analyze the contribution of Free/Libre Open Source Software in health care (FLOSS-HC) and to give perspectives for future developments. METHODS: The paper summarizes FLOSS-related trends in health care as anticipated by members of the IMIA Open Source Working Group. Data were obtained through literature review and personal experience and observations of the authors in the last two decades. A status quo is given by a frequency analysis of the database of Medfloss.org, one of the world{\textquoteright}s largest platforms dedicated to FLOSS-HC. The authors discuss current problems in the field of health care and finally give a prospective roadmap, a projection of the potential influences of FLOSS in health care. RESULTS: FLOSS-HC already exists for more than 2 decades. Several projects have shown that FLOSS may produce highly competitive alternatives to proprietary solutions that are at least equivalent in usability and have a better total cost of ownership ratio. The Medfloss.org database currently lists 221 projects of diverse application types. CONCLUSIONS: FLOSS principles hold a great potential for addressing several of the most critical problems in health care IT. The authors argue that an ecosystem perspective is relevant and that FLOSS principles are best suited to create health IT systems that are able to evolve over time as medical knowledge, technologies, insights, workflows etc. continuously change. All these factors that inherently influence the development of health IT systems are changing at an ever growing pace. Traditional models of software engineering are not able to follow these changes and provide up-to-date systems for an acceptable cost/value ratio. To allow FLOSS to positively influence Health IT in the future a "FLOSS-friendly" environment has to be provided. Policy makers should resolve uncertainties in the legal framework that disfavor FLOSS. Certification procedures should be specified in a way that they do not raise additional barriers for FLOSS.}, issn = {0943-4747}, author = {Karopka, T and Schmuhl, H and Marcelo, A and Molin, J Dal and Wright, G} } @article {536, title = {Tracking and monitoring the health workforce: a new human resources information system (HRIS) in Uganda.}, journal = {Human resources for health}, volume = {9}, year = {2011}, month = {2011 Feb 17}, pages = {6}, abstract = {ABSTRACT: BACKGROUND: Health workforce planning is important in ensuring that the recruitment, training and deployment of health workers are conducted in the most efficient way possible. However, in many developing countries, human resources for health data are limited, inconsistent, out-dated, or unavailable. Consequently, policy-makers are unable to use reliable data to make informed decisions about the health workforce. Computerized human resources information systems (HRIS) enable countries to collect, maintain, and analyze health workforce data. METHODS: The purpose of this article is twofold. First, we describe Uganda{\textquoteright}s transition from a paper filing system to an electronic HRIS capable of providing information about country-specific health workforce questions. We examine the ongoing five-step HRIS strengthening process used to implement an HRIS that tracks health worker data at the Uganda Nurses and Midwives Council (UNMC). Secondly, we describe how HRIS data can be used to address workforce planning questions via an initial analysis of the UNMC training, licensure and registration records from 1970 through May 2009. RESULTS: The data indicate that, for the 25 482 nurses and midwives who entered training before 2006, 72\% graduated, 66\% obtained a council registration, and 28\% obtained a license to practice. Of the 17 405 nurses and midwives who obtained a council registration as of May 2009, 96\% are of Ugandan nationality and just 3\% received their training outside of the country. Thirteen per cent obtained a registration for more than one type of training. Most (34\%) trainings with a council registration are for the enrolled nurse training, followed by enrolled midwife (25\%), registered (more advanced) nurse (21\%), registered midwife (11\%), and more specialized trainings (9\%). CONCLUSION: The UNMC database is valuable in monitoring and reviewing information about nurses and midwives. However, information obtained from this system is also important in improving strategic planning for the greater health care system in Uganda. We hope that the use of a real-world example of HRIS strengthening provides guidance for the implementation of similar projects in other countries or contexts.}, issn = {1478-4491}, author = {Spero, Julie C and McQuide, Pamela A and Matte, Rita} } @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 {610, title = {Adaptive radiotherapy based on contrast enhanced cone beam CT imaging.}, journal = {Acta oncologica (Stockholm, Sweden)}, volume = {49}, year = {2010}, month = {2010 Oct}, pages = {972-7}, abstract = {Cone beam CT (CBCT) imaging has become an integral part of radiation therapy, with images typically used for offline or online patient setup corrections based on bony anatomy co-registration. Ideally, the co-registration should be based on tumor localization. However, soft tissue contrast in CBCT images may be limited. In the present work, contrast enhanced CBCT (CECBCT) images were used for tumor visualization and treatment adaptation. Material and methods. A spontaneous canine maxillary tumor was subjected to repeated cone beam CT imaging during fractionated radiotherapy (10 fractions in total). At five of the treatment fractions, CECBCT images, employing an iodinated contrast agent, were acquired, as well as pre-contrast CBCT images. The tumor was clearly visible in post-contrast minus pre-contrast subtraction images, and these contrast images were used to delineate gross tumor volumes. IMRT dose plans were subsequently generated. Four different strategies were explored: 1) fully adapted planning based on each CECBCT image series, 2) planning based on images acquired at the first treatment fraction and patient repositioning following bony anatomy co-registration, 3) as for 2), but with patient repositioning based on co-registering contrast images, and 4) a strategy with no patient repositioning or treatment adaptation. The equivalent uniform dose (EUD) and tumor control probability (TCP) calculations to estimate treatment outcome for each strategy. Results. Similar translation vectors were found when bony anatomy and contrast enhancement co-registration were compared. Strategy 1 gave EUDs closest to the prescription dose and the highest TCP. Strategies 2 and 3 gave EUDs and TCPs close to that of strategy 1, with strategy 3 being slightly better than strategy 2. Even greater benefits from strategies 1 and 3 are expected with increasing tumor movement or deformation during treatment. The non-adaptive strategy 4 was clearly inferior to all three adaptive strategies. Conclusion. CECBCT may prove useful for adaptive radiotherapy.}, keywords = {Animals, Carcinoma, Cone-Beam Computed Tomography, Contrast Media, Dog Diseases, Dogs, Female, Maxillary Neoplasms, Patient Positioning, Radiographic Image Enhancement, Radiotherapy Planning, Computer-Assisted}, issn = {1651-226X}, author = {S{\o}vik, Aste and R{\o}dal, Jan and Skogmo, Hege K and Lerv{\r a}g, Christoffer and Eilertsen, Karsten and Malinen, Eirik} } @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 {20118730, title = {Computer-aided volumetric comparison of reconstructed orbits for blow-out fractures with nonpreformed versus 3-dimensionally preformed titanium mesh plates: a preliminary study.}, journal = {Journal of computer assisted tomography}, volume = {34}, year = {2010}, month = {2010 Jan}, pages = {98-104}, abstract = {OBJECTIVES: To compare and evaluate, using computer-aided volumetric measurements, the accuracy and reliability of nonpreformed mesh plates (NPMPs) versus 3-dimensionally preformed titanium mesh plates (PMPs) in posttraumatic orbital volume restoration. PATIENTS AND METHODS: Facial coronal computed tomographic scan slices from 20 patients (10 in the NPMP and 10 in the PMP group) were used to measure bony orbital volume using OsiriX Medical Image software (version 3.3.2, www.osirix-viewer.com). The procedure was performed on both orbits; thereafter, the volume of the contralateral health orbit was used as a control for comparison in the 2 groups of patients. The difference in orbital volume between the 2 groups and between the reconstructed versus uninjured side in both groups have been statistically correlated. RESULTS: The mean orbital volume between the reconstructed (19.215 mL in NPMP and 21.791 mL in PMP) and the contralateral uninjured side (18.955 mL in NPMP and 21.710 mL in PMP) was not statistically significant (P > 0.05). The mean orbital volumes of the reconstructed orbits were 19.215 mL in the NPMP and 21.791 mL in the PMP group, with no statistically significant difference (P > 0.05). The volume data of the reconstructed orbit fitted that of the contralateral uninjured orbit with an accuracy of a maximum of 1.85 mL in the NPMP group and 2.5 mL in the PMP group. CONCLUSIONS: The current study demonstrated that there were no significant differences in the orbital volume restoration using either technique. In fact, both techniques allow for close reproduction of natural orbital volume and shape, and its use in posttraumatic orbital wall reconstruction was successful.}, author = {Scolozzi, Paolo and Momjian, Armen and Heuberger, Joris} } @article {20335647, title = {The development and design of an electronic patient record using open source web-based technology.}, journal = {The HIM journal}, volume = {39}, year = {2010}, month = {2010}, pages = {30-5}, abstract = {This paper describes the method used to develop the One Stop Crisis Centre (OSCC) Portal, an open source web-based electronic patient record system (EPR) for the One Stop Crisis Center, Hospital Universiti Sains Malaysia (HUSM) in Kelantan, Malaysia. Features and functionalities of the system are presented to demonstrate the workflow. Use of the OSCC Portal improved data integration and data communication and contributed to improvements in care management. With implementation of the OSCC portal, improved coordination between disciplines and standardisation of data in HUSM were noticed. It is expected that this will in turn result in improved data confidentiality and data integrity. The collected data will also be useful for quality assessment and research. Other low-resource centers with limited computer hardware and access to open-source software could benefit from this endeavour.}, author = {Syed-Mohamad, Sharifa Mastura and Ali, Siti Hawa and Mat-Husin, Mohd Nazri} } @article {904, title = {Electronic data capture for registries and clinical trials in orthopaedic surgery: Open source versus commercial systems}, journal = {Clinical Orthopaedics and Related Research}, volume = {468}, year = {2010}, pages = {2664{\textendash}2671}, abstract = {Background: Collection and analysis of clinical data can help orthopaedic surgeons to practice evidence based medicine. Spreadsheets and offline relational databases are prevalent, but not flexible, secure, workflow friendly and do not support the generation of standardized and interoperable data. Additionally these data collection applications usually do not follow a structured and planned approach which may result in failure to achieve the intended goal. Questions/purposes: Our purposes are (1) to provide a brief overview of EDC systems, their types, and related pros and cons as well as to describe commonly used EDC platforms and their features; and (2) describe simple steps involved in designing a registry/clinical study in DADOS P, an open source EDC system. Where are we now?: Electronic data capture systems aimed at addressing these issues are widely being adopted at an institutional/national/ international level but are lacking at an individual level. A wide array of features, relative pros and cons and different business models cause confusion and indecision among orthopaedic surgeons interested in implementing EDC systems. Where do we need to go?: To answer clinical questions and actively participate in clinical studies, orthopaedic surgeons should collect data in parallel to their clinical activities. Adopting a simple, user-friendly, and robust EDC system can facilitate the data collection process. How do we get there?: Conducting a balanced evaluation of available options and comparing them with intended goals and requirements can help orthopaedic surgeons to make an informed choice. {\textcopyright} 2010 The Association of Bone and Joint Surgeons{\textregistered}.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-77957336660\&partnerID=40\&md5=dec3706be86215e9656a06f82265cb28}, author = {Shah, J.a b and Rajgor, D.a b and Pradhan, S.a b and McCready, M.c and Zaveri, A.a d and Pietrobon, R.c} } @article {611, title = {Evaluation of adaptive radiotherapy of bladder cancer by image-based tumour control probability modelling.}, journal = {Acta oncologica (Stockholm, Sweden)}, volume = {49}, year = {2010}, month = {2010 Oct}, pages = {1045-51}, abstract = {Clinical implementation of adaptive radiotherapy strategies could benefit from extended tools for plan evaluation and selection. For this purpose we investigated the feasibility of image-based tumour control probability (TCP) modelling using the bladder as example of a tumour site with potential benefit from adaptive strategies.}, keywords = {Carcinoma, Computer Simulation, Humans, Image Processing, Computer-Assisted, Models, Statistical, Probability, Radiotherapy Dosage, Radiotherapy Planning, Computer-Assisted, Radiotherapy, Conformal, Tumor Burden, Urinary Bladder, Urinary Bladder Neoplasms}, issn = {1651-226X}, author = {Wright, Pauliina and Muren, Ludvig P and H{\o}yer, Morten and Malinen, Eirik} } @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 {586, title = {The extensible open-source rigid and affine image registration module of the Medical Imaging Interaction Toolkit (MITK).}, journal = {Computer methods and programs in biomedicine}, volume = {100}, year = {2010}, month = {2010 Oct}, pages = {79-86}, abstract = {Although non-rigid registration methods are available or under development for many specific problems in medicine, rigid and affine registration is an important task that is often performed for pre-aligning images before using non-rigid registration. In this paper, we present a free and open-source application for rigid and affine image registration, which is designed both for developers and for end-users. The application is based on the Medical Imaging Interaction Toolkit (MITK) and allows for inter-modality and intra-modality rigid 2D-2D and 3D-3D registration of medical images such as CT, MRI, or ultrasound. The framework as well as the application can be easily extended by adding new transforms, metrics and optimizers. Thus, developers of new algorithms are enabled to test and use their algorithms more quickly, spending less work on user interfaces. Additionally, the framework provides the possibility to use image masks to restrict the evaluation of metric values by the optimizer on certain areas of the images.}, keywords = {Computers, Diagnostic Imaging, Image Enhancement, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated, Software, User-Computer Interface}, issn = {1872-7565}, author = {Stein, D and Fritzsche, K H and Nolden, M and Meinzer, H P and Wolf, I} } @article {20409608, title = {The extensible open-source rigid and affine image registration module of the Medical Imaging Interaction Toolkit (MITK).}, journal = {Computer methods and programs in biomedicine}, year = {2010}, month = {2010 Apr 19}, abstract = {Although non-rigid registration methods are available or under development for many specific problems in medicine, rigid and affine registration is an important task that is often performed for pre-aligning images before using non-rigid registration. In this paper, we present a free and open-source application for rigid and affine image registration, which is designed both for developers and for end-users. The application is based on the Medical Imaging Interaction Toolkit (MITK) and allows for inter-modality and intra-modality rigid 2D-2D and 3D-3D registration of medical images such as CT, MRI, or ultrasound. The framework as well as the application can be easily extended by adding new transforms, metrics and optimizers. Thus, developers of new algorithms are enabled to test and use their algorithms more quickly, spending less work on user interfaces. Additionally, the framework provides the possibility to use image masks to restrict the evaluation of metric values by the optimizer on certain areas of the images.}, author = {Stein, D and Fritzsche, K H and Nolden, M and Meinzer, H P and Wolf, I} } @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 {1014, title = {Implementing OpenMRS for patient monitoring in an HIV/AIDS care and treatment program in rural Mozambique.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {411-5}, abstract = {

We have adopted the Open Medical Record System (OpenMRS) framework to implement an electronic patient monitoring system for an HIV care and treatment program in Mozambique. The program provides technical assistance to the Ministry of Health supporting the scale up of integrated HIV care and support services in health facilities in rural resource limited settings. The implementation is in use for adult and pediatric programs, with ongoing roll-out to cover all supported sites. We describe early experiences in adapting the system to the program needs, addressing infrastructure challenges, creating a regional support team, training data entry staff, migrating a legacy database, deployment, and current use. We find that OpenMRS offers excellent prospects for in-country development of health information systems, even in severely resource limited settings. However, it also requires considerable organizational infrastructure investment and technical capacity building to ensure continued local support.

}, keywords = {Database Management Systems, Delivery of Health Care, electronic health records, HIV Infections, Information Storage and Retrieval, Medical Record Linkage, Mozambique, Population Surveillance, Rural Health Services}, issn = {0926-9630}, author = {Manders, Eric-Jan and Jos{\'e}, Eurico and Solis, Manuel and Burlison, Janeen and Nhampossa, Jos{\'e} Leopoldo and Moon, Troy} } @proceedings {512, title = {Indivo X: Developing a Fully Substitutable Personally Controlled Health Record Platform}, year = {2010}, month = {11/2010}, abstract = {To support a rich ecosystem of third-party applications around a personally controlled health record (PCHR), we have redesigned Indivo, the original PCHR, as a web- based platform with feature-level substitutability. Core to this new release is the Indivo X Application Program- ming Interface (API), the contract between the PCHR platform and the end-user apps. Using rapid iterative de- velopment to build a minimal feature set from real-world requirements, the resulting Indivo X API, now in public stable beta, is enabling developers, including third-party contributors, to quickly create and integrate novel fea- tures into patients{\textquoteright} online records, ultimately building a fully customizable experience for diverse patient needs.}, url = {http://proceedings.amia.org/127eoo}, author = {Adida, Ben and Sanyal, Arjun and Zabak, Steve and Kohane, Isaac S. and Mandl, Kenneth D} } @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 {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 {19910667, title = {The medical exploration toolkit: an efficient support for visual computing in surgical planning and training.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {16}, year = {2010}, month = {2010 Jan-Feb}, pages = {133-46}, abstract = {Application development is often guided by the usage of software libraries and toolkits. For medical applications, the toolkits currently available focus on image analysis and volume rendering. Advance interactive visualizations and user interface issues are not adequately supported. Hence, we present a toolkit for application development in the field of medical intervention planning, training, and presentation--the MEDICALEXPLORATIONTOOLKIT (METK). The METK is based on the rapid prototyping platform MeVisLab and offers a large variety of facilities for an easy and efficient application development process. We present dedicated techniques for advanced medical visualizations, exploration, standardized documentation, adn interface widgets for common tasks. These include, e.g., advanced animation facilities, viewpoint selection, several illustrative rendering techniques, and new techniques for object selection in 3D surface models. No extended programming skills are needed for application building, since a graphical programming approach can be used. the toolkit is freely available and well documented to facilitate the use and extension of the toolkit.}, author = {M{\"u}hler, Konrad and Tietjen, Christian and Ritter, Felix and Preim, Bernhard} } @article {1043, title = {An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging.}, journal = {BMC Med Imaging}, volume = {10}, year = {2010}, month = {2010}, pages = {16}, abstract = {

BACKGROUND: In magnetic resonance (MR) imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization.

RESULTS: After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/TOMROP T1; modified Look-Locker (MOLLI) T1; single-echo T2/T2*; and multi-echo T2/T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data.

CONCLUSIONS: MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet.

}, keywords = {Algorithms, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Programming Languages, Reproducibility of Results, Sensitivity and Specificity, Software}, issn = {1471-2342}, doi = {10.1186/1471-2342-10-16}, author = {Messroghli, Daniel R and Rudolph, Andre and Abdel-Aty, Hassan and Wassmuth, Ralf and Kuhne, Titus and Dietz, Rainer and Schulz-Menger, Jeanette} } @article {1471-2342-10-16, title = {An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging}, journal = {BMC Medical Imaging}, volume = {10}, number = {1}, year = {2010}, pages = {16}, abstract = {BACKGROUND:In magnetic resonance (MR) imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization. RESULTS:After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/ TOMROP T1; modified Look-Locker inversion recovery (MOLLI) T1; single-echo T2/ T2*; and multi-echo T2/ T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data. CONCLUSIONS:MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet. }, issn = {1471-2342}, doi = {10.1186/1471-2342-10-16}, url = {http://www.biomedcentral.com/1471-2342/10/16}, author = {Messroghli, Daniel and Rudolph, Andre and Abdel-Aty, Hassan and Wassmuth, Ralf and Kuhne, Titus and Dietz, Rainer and Schulz-Menger, Jeanette} } @booklet {UCAM-CL-TR-768, title = {Report on existing open-source electronic medical records}, number = {UCAM-CL-TR-768}, year = {2010}, publisher = {University of Cambridge, Computer Laboratory}, abstract = {In this report we provide an overview of existing open-source electronic medical records and assess them against the criteria established by the EViDence group.}, issn = {1476-2986}, url = {http://www.cl.cam.ac.uk/techreports/UCAM-CL-TR-768.pdf}, author = {Morrison, Cecily and Iosif, Adona and Danka, Miklos} } @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 {20001786, title = {Using ImageJ for the quantitative analysis of flow-based adhesion assays in real-time under physiologic flow conditions.}, journal = {Platelets}, volume = {21}, year = {2010}, month = {2010 Feb}, pages = {60-6}, abstract = {This article intends to close the gap between the abundance of regular articles focusing on adhesive mechanisms of cells in a flow field and purely technical reports confined to the description of newly developed algorithms, not yet ready to be used by users without programming skills. A simple and robust method is presented for analysing raw videomicroscopic data of flow-based adhesion assays using the freely available public domain software ImageJ. We describe in detail the image processing routines used to rapidly and reliably evaluate the number of adherent and translocating platelets in videomicroscopic recordings. The depicted procedures were exemplified by analysing platelet interaction with immobilized von Willebrand factor and fibrinogen in flowing blood under physiological wall shear rates. Neutralizing GPIbalpha function reduced shear-dependent platelet translocation on von Willebrand factor and abolished firm platelet adhesion. Abciximab, Tirofiban and Eptifibatide completely inhibited GPIIb/IIIa-dependent stable platelet deposition on fibrinogen. The presented method to analyse videomicroscopic recordings from flow-based adhesion assays offers the advantage of providing a simple and reliable way to quantify flow-based adhesion assays, which is completely based on ImageJ and can easily be applied to study adhesion mechanisms of cells in non-fluorescent modes without the need to deviate from the presented protocol.}, author = {Meyer dos Santos, Sascha and Klinkhardt, Ute and Schneppenheim, Reinhard and Harder, Sebastian} } @article {19403467, title = {Acceptability of a personally controlled health record in a community-based setting: implications for policy and design.}, journal = {Journal of medical Internet research}, volume = {11}, year = {2009}, month = {2009}, pages = {e14}, abstract = {BACKGROUND: Consumer-centered health information systems that address problems related to fragmented health records and disengaged and disempowered patients are needed, as are information systems that support public health monitoring and research. Personally controlled health records (PCHRs) represent one response to these needs. PCHRs are a special class of personal health records (PHRs) distinguished by the extent to which users control record access and contents. Recently launched PCHR platforms include Google Health, Microsoft{\textquoteright}s HealthVault, and the Dossia platform, based on Indivo. OBJECTIVE: To understand the acceptability, early impacts, policy, and design requirements of PCHRs in a community-based setting. METHODS: Observational and narrative data relating to acceptability, adoption, and use of a personally controlled health record were collected and analyzed within a formative evaluation of a PCHR demonstration. Subjects were affiliates of a managed care organization run by an urban university in the northeastern United States. Data were collected using focus groups, semi-structured individual interviews, and content review of email communications. Subjects included: n = 20 administrators, clinicians, and institutional stakeholders who participated in pre-deployment group or individual interviews; n = 52 community members who participated in usability testing and/or pre-deployment piloting; and n = 250 subjects who participated in the full demonstration of which n = 81 initiated email communications to troubleshoot problems or provide feedback. All data were formatted as narrative text and coded thematically by two independent analysts using a shared rubric of a priori defined major codes. Sub-themes were identified by analysts using an iterative inductive process. Themes were reviewed within and across research activities (ie, focus group, usability testing, email content review) and triangulated to identify patterns. RESULTS: Low levels of familiarity with PCHRs were found as were high expectations for capabilities of nascent systems. Perceived value for PCHRs was highest around abilities to co-locate, view, update, and share health information with providers. Expectations were lowest for opportunities to participate in research. Early adopters perceived that PCHR benefits outweighed perceived risks, including those related to inadvertent or intentional information disclosure. Barriers and facilitators at institutional, interpersonal, and individual levels were identified. Endorsement of a dynamic platform model PCHR was evidenced by preferences for embedded searching, linking, and messaging capabilities in PCHRs; by high expectations for within-system tailored communications; and by expectation of linkages between self-report and clinical data. CONCLUSIONS: Low levels of awareness/preparedness and high expectations for PCHRs exist as a potentially problematic pairing. Educational and technical assistance for lay users and providers are critical to meet challenges related to: access to PCHRs, especially among older cohorts; workflow demands and resistance to change among providers; inadequate health and technology literacy; clarification of boundaries and responsibility for ensuring accuracy and integrity of health information across distributed data systems; and understanding confidentiality and privacy risks. Continued demonstration and evaluation of PCHRs is essential to advancing their use.}, author = {Weitzman, Elissa R and Kaci, Liljana and Mandl, Kenneth D} } @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 {19352444, title = {DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool.}, journal = {Frontiers in neuroinformatics}, volume = {3}, year = {2009}, month = {2009}, pages = {9}, abstract = {Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK{\textquoteright}s low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user{\textquoteright}s operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data.}, author = {Gouws, Andr{\'e} and Woods, Will and Millman, Rebecca and Morland, Antony and Green, Gary} } @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 {19439392, title = {Interactive segmentation framework of the Medical Imaging Interaction Toolkit.}, journal = {Computer methods and programs in biomedicine}, volume = {96}, year = {2009}, month = {2009 Oct}, pages = {72-83}, abstract = {Interactive methods are indispensable for real world applications of segmentation in medicine, at least to allow for convenient and fast verification and correction of automated techniques. Besides traditional interactive tasks such as adding or removing parts of a segmentation, adjustment of contours or the placement of seed points, the relatively recent Graph Cut and Random Walker segmentation methods demonstrate an interest in advanced interactive strategies for segmentation. Though the value of toolkits and extensible applications is generally accepted for the development of new segmentation algorithms, the topic of interactive segmentation applications is rarely addressed by current toolkits and applications. In this paper, we present the extension of the Medical Imaging Interaction Toolkit (MITK) with a framework for the development of interactive applications for image segmentation. The framework provides a clear structure for the development of new applications and offers a plugin mechanism to easily extend existing applications with additional segmentation tools. In addition, the framework supports shape-based interpolation and multi-level undo/redo of modifications to binary images. To demonstrate the value of the framework, we also present a free, open-source application named InteractiveSegmentation for manual segmentation of medical images (including 3D+t), which is built based on the extended MITK framework. The application includes several features to effectively support manual segmentation, which are not found in comparable freely available applications. InteractiveSegmentation is fully developed and successfully and regularly used in several projects. Using the plugin mechanism, the application enables developers of new algorithms to begin algorithmic work more quickly.}, author = {Maleike, D and Nolden, M and Meinzer, H-P and Wolf, I} } @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 {20351824, title = {Mychildren{\textquoteright}s: integration of a personally controlled health record with a tethered patient portal for a pediatric and adolescent population.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, volume = {2009}, year = {2009}, month = {2009}, pages = {65-9}, abstract = {Personally controlled health records (PCHRs) and patient portals are increasingly being offered by healthcare institutions, employers, insurance companies and commercial entities to allow patients access to their health information. Both applications offer unique services to provide patients with tools to manage their health. While PCHRs allow users ubiquitous, portable, patient controlled access to their health information, traditional patient portals provide provider-tethered applications allowing patients access, but not control of, certain healthcare information, as well as communication and administrative functions, such as secure messaging, appointment management and prescription refill requests, facilitating care at a specific healthcare facility.We describe our approach for the design, content creation, policy development, and implementation of MyChildren{\textquoteright}s, a unique web-based application leveraging the advantages of both a provider-tethered patient portal and a PCHR to allow patients and their guardians access to the functionality and convenience of a traditional patient portal, as well as the portability and flexibility of a PCHR.}, author = {Bourgeois, Fabienne C and Mandl, Kenneth D and Shaw, Danny and Flemming, Daisy and Nigrin, Daniel J} } @article {19745456, title = {Open source and healthcare in Europe - time to put leading edge ideas into practice.}, journal = {Studies in health technology and informatics}, volume = {150}, year = {2009}, month = {2009}, pages = {963-7}, abstract = {Free/Libre and Open Source Software (FLOSS) is a process of software development, a method of licensing and a philosophy. Although FLOSS plays a significant role in several market areas, the impact in the health care arena is still limited. FLOSS is promoted as one of the most effective means for overcoming fragmentation in the health care sector and providing a basis for more efficient, timely and cost effective health care provision. The 2008 European Federation for Medical Informatics (EFMI) Special Topic Conference (STC) explored a range of current and future issues related to FLOSS in healthcare (FLOSS-HC). In particular, there was a focus on health records, ubiquitous computing, knowledge sharing, and current and future applications. Discussions resulted in a list of main barriers and challenges for use of FLOSS-HC. Based on the outputs of this event, the 2004 Open Steps events and subsequent workshops at OSEHC2009 and Med-e-Tel 2009, a four-step strategy has been proposed for FLOSS-HC: 1) a FLOSS-HC inventory; 2) a FLOSS-HC collaboration platform, use case database and knowledge base; 3) a worldwide FLOSS-HC network; and 4) FLOSS-HC dissemination activities. The workshop will further refine this strategy and elaborate avenues for FLOSS-HC from scientific, business and end-user perspectives. To gain acceptance by different stakeholders in the health care industry, different activities have to be conducted in collaboration. The workshop will focus on the scientific challenges in developing methodologies and criteria to support FLOSS-HC in becoming a viable alternative to commercial and proprietary software development and deployment.}, author = {Murray, Peter J and Wright, Graham and Karopka, Thomas and Betts, Helen and Orel, Andrej} } @article {19157968, title = {The OpenMRS Implementers Network.}, journal = {International journal of medical informatics}, volume = {78}, year = {2009}, month = {2009 Nov}, pages = {711-20}, abstract = {OBJECTIVE: OpenMRS (www.openmrs.org) is a configurable open source electronic medical record application developed and maintained by a large network of open source developers coordinated by the Regenstrief Institute and Partners in Health and mainly used for HIV patient and treatment information management in Africa. Our objective is to develop an open Implementers Network for OpenMRS to provide regional support for the growing number of OpenMRS implementations in Africa and to include African developers and implementers in the future growth of OpenMRS. METHODS: We have developed the OpenMRS Implementers Network using a dedicated Wiki site and e-mail server. We have also organized annual meetings in South Africa and regional training courses at African locations where OpenMRS is being implemented. An OpenMRS Internship program has been initiated and we have started collaborating with similar networks and projects working in Africa. To evaluate its potential, OpenMRS was implemented initially at one site in South Africa by a single implementer using a downloadable OpenMRS application and only the OpenMRS Implementers Network for support. RESULTS: The OpenMRS Implementers Network Wiki and list server have grown into effective means of providing implementation support and forums for exchange of implementation experiences. The annual OpenMRS Implementers meeting has been held in South Africa for the past three years and is attracting successively larger numbers of participants with almost 200 implementers and developers attending the 2008 meeting in Durban, South Africa. Six African developers are presently registered on the first intake of the OpenMRS Internship program. Successful collaborations have been started with several African developer groups and projects initiated to develop interoperability between OpenMRS and various applications. The South African OpenMRS Implementer group successfully configured, installed and maintained an integrated HIV/TB OpenMRS application without significant programming support. Since then, this model has been replicated in several other African sites. The OpenMRS Implementers Network has contributed substantially to the growth and sustainability of OpenMRS in Africa and has become a useful way of including Africans in the development and implementation of OpenMRS in developing countries. The Network provides valuable support and enables a basic OpenMRS application to be implemented in the absence of onsite programmers.}, url = {http://www.healthware.org/openmrs/openmrs.pdf}, author = {Seebregts, Christopher J and Mamlin, Burke W and Biondich, Paul G and Fraser, Hamish S F and Wolfe, Benjamin A and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Baker, Elaine and Musinguzi, Nicholas and Kayiwa, Daniel and Fourie, Carl and Lesh, Neal and Kanter, Andrew and Yiannoutsos, Constantin T and Bailey, Christopher} } @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 {17947615, title = {Early experiences with personal health records.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {15}, year = {2008}, month = {2008 Jan-Feb}, pages = {1-7}, abstract = {Over the past year, several payers, employers, and commercial vendors have announced personal health record projects. Few of these are widely deployed and few are fully integrated into ambulatory or hospital-based electronic record systems. The earliest adopters of personal health records have many lessons learned that can inform these new initiatives. We present three case studies--MyChart at Palo Alto Medical Foundation, PatientSite at Beth Israel Deaconess Medical Center, and Indivo at Children{\textquoteright}s Hospital Boston. We describe our implementation challenges from 1999 to 2007 and postulate the evolving challenges we will face over the next five years.}, author = {Halamka, John D and Mandl, Kenneth D and Tang, Paul C} } @article {10.1109/HICSS.2008.26, title = {A Light-Weight Component for Adding Decision Support to Electronic Medical Records}, journal = {Hawaii International Conference on System Sciences}, year = {2008}, pages = {251}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, issn = {1530-1605}, doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.2008.26}, author = {Jens H. Weber-Jahnke and Glen McCallum} } @article {Jahnke-weber_makingavailable, title = {Making available Clinical Decision Support in Service-Oriented Architectures}, journal = {Journal on Information Technology in Healthcare}, volume = {6}, year = {2008}, pages = {54}, chapter = {42}, abstract = {Computer-based clinical decision support (CDS) has great potential for cost savings and for increasing patient safety and quality of care. The cost of owning and particularly maintaining CDS systems is significant. Therefore, it makes good economic sense to share a CDS service installation among a larger set of client systems. The emerging paradigm of serviceoriented architectures (SOAs) embraces the idea of sharing and interaction between loosely coupled, co-operative services. Canada has based its planned architecture for realizing the electronic medical record (EMR) on the SOA paradigm. While CDS components are currently not in the set of services to be constructed for Canada{\textquoteright}s health information infrastructure, they seems to be growing interest in adding them in the future, after the more essential services have been implemented. In this paper, we discuss the status of clinical decision support systems today and some challenges of making them available in SOA-based infrastructures. We report on design choices and solutions we have selected during the construction of the EGADSS (Electronic Guideline and Decision Support System) component. Our design decisions are based on domainspecific challenges such as knowledge, data and workflow interoperability as well as on technical considerations about construction high quality services for SOA-based infrastructures. EGADSS has been released under open-source license and is freely available.}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.88.5385\&rep=rep1\&type=pdf}, author = {Jens H. Jahnke-Weber and Morgan Price and Glen McCallum} } @article {18953134, title = {Open source electronic health record and patient data management system for intensive care.}, journal = {Studies in health technology and informatics}, volume = {141}, year = {2008}, month = {2008}, pages = {139-45}, abstract = {BACKGROUND AND OBJECTIVES: In Intensive Care Units, the amount of data to be processed for patients care, the turn over of the patients, the necessity for reliability and for review processes indicate the use of Patient Data Management Systems (PDMS) and electronic health records (EHR). To respond to the needs of an Intensive Care Unit and not to be locked with proprietary software, we developed a PDMS and EHR based on open source software and components. METHODS: The software was designed as a client-server architecture running on the Linux operating system and powered by the PostgreSQL data base system. The client software was developed in C using GTK interface library. The application offers to the users the following functions: medical notes captures, observations and treatments, nursing charts with administration of medications, scoring systems for classification, and possibilities to encode medical activities for billing processes. RESULTS: Since his deployment in February 2004, the PDMS was used to care more than three thousands patients with the expected software reliability and facilitated data management and review processes. Communications with other medical software were not developed from the start, and are realized by the use of the Mirth HL7 communication engine. Further upgrade of the system will include multi-platform support, use of typed language with static analysis, and configurable interface. CONCLUSION: The developed system based on open source software components was able to respond to the medical needs of the local ICU environment. The use of OSS for development allowed us to customize the software to the preexisting organization and contributed to the acceptability of the whole system.}, author = {Massaut, Jacques and Reper, Pascal} } @article {18570637, title = {OSPACS: Ultrasound image management system.}, journal = {Source code for biology and medicine}, volume = {3}, year = {2008}, month = {2008}, pages = {11}, abstract = {ABSTRACT: BACKGROUND: Ultrasound scanning uses the medical imaging format, DICOM, for electronically storing the images and data associated with a particular scan. Large health care facilities typically use a picture archiving and communication system (PACS) for storing and retrieving such images. However, these systems are usually not suitable for managing large collections of anonymized ultrasound images gathered during a clinical screening trial. RESULTS: We have developed a system enabling the accurate archiving and management of ultrasound images gathered during a clinical screening trial. It is based upon a Windows application utilizing an open-source DICOM image viewer and a relational database. The system automates the bulk import of DICOM files from removable media by cross-validating the patient information against an external database, anonymizing the data as well as the image, and then storing the contents of the file as a field in a database record. These image records may then be retrieved from the database and presented in a tree-view control so that the user can select particular images for display in a DICOM viewer or export them to external media. CONCLUSION: This system provides error-free automation of ultrasound image archiving and management, suitable for use in a clinical trial. An open-source project has been established to promote continued development of the system.}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442597/}, author = {Stott, Will and Ryan, Andy and Jacobs, Ian J and Menon, Usha and Bessant, Conrad and Jones, Christopher} } @article {18570554, title = {Standards-based, open-source electronic health record systems: a desirable future for the U.S. health industry.}, journal = {Telemedicine journal and e-health : the official journal of the American Telemedicine Association}, volume = {14}, year = {2008}, month = {2008 Apr}, pages = {284-8}, abstract = {Many healthcare systems are moving toward a fully electronic health record (EHR) in order to better manage patient care. Unfortunately, in the United States, many current EHR systems leave much to be desired. Among well-documented criticisms are that they tend to be inflexible, proprietary, nonintuitive, expensive, difficult to maintain and rarely interoperable across health systems. From the clinician{\textquoteright}s perspective, these flaws sometimes make having an EHR system seem no better than retaining a paper-based system. Open-source software, a great success in other information-intensive industries, is one possible solution to these problems, and may help integrate a functional EHR system into, and across, more health systems and clinics because of the greater potential for local customization. We believe that the advantages of an open-source EHR system outweigh the costs of a more traditional, proprietary EHR system, and recommend that more work be done to advance an interoperable open-source EHR system in the United States. Open-source EHR systems have the potential to improve healthcare in the United States as they have done in many other areas around the world.}, author = {Yellowlees, Peter M and Marks, Shayna L and Hogarth, Michael and Turner, Stuart} } @article {18755989, title = {Whose personal control? Creating private, personally controlled health records for pediatric and adolescent patients.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {15}, year = {2008}, month = {2008 Nov-Dec}, pages = {737-43}, abstract = {Personally controlled health records (PCHRs) enable patients to store, manage, and share their own health data, and promise unprecedented consumer access to medical information. To deploy a PCHR in the pediatric population requires crafting of access and security policies, tailored to a record that is not only under patient control, but one that may also be accessed by parents, guardians, and third-party entities. Such hybrid control of health information requires careful consideration of both the PCHR vendor{\textquoteright}s access policies, as well as institutional policies regulating data feeds to the PCHR, to ensure that the privacy and confidentiality of each user is preserved. Such policies must ensure compliance with legal mandates to prevent unintended disclosures and must preserve the complex interactions of the patient-provider relationship. Informed by our own operational involvement in the implementation of the Indivo PCHR, we provide a framework for understanding and addressing the challenges posed by child, adolescent, and family access to PCHRs.}, author = {Bourgeois, Fabienne C and Taylor, Patrick L and Emans, S Jean and Nigrin, Daniel J and Mandl, Kenneth D} } @mastersthesis {889, title = {An empirical investigation into the adoption of open source software in hospitals}, year = {2007}, school = {University of Maryland at Baltimore County}, type = {phd}, address = {Catonsville, MD, USA}, abstract = {Information technology holds great promise for reducing cost and improving quality in health care. Open source software (OSS) has emerged as a potential alternative to commercial and closed-source products in many domains. OSS has gained considerable attention recently in the health care arena, and proponents claim that it overcomes many of the obstacles to IT adoption that health care organizations face. Yet, how and why OSS is being adopted and implemented within hospitals in particular remains a poorly understood issue. This research attempts to further this understanding so that hospitals may make better informed decisions about adoption of IT, and OSS in particular, in the future. We use a qualitative grounded theory approach in order to explore the extent of OSS adoption in hospitals as well as the factors facilitating and inhibiting adoption. Surveys and interviews are used to acquire both breadth and depth of understanding. First, a survey was used to explore and characterize the types of OSS products adopted in hospitals and the extent to which they have been adopted. For methodological reasons, we focused on Baltimore, Washington and Northern Virginia area hospitals. Following the survey, semi-structured interviews were conducted with hospital IT managers in order to attain a deeper understanding of the factors that are facilitating and inhibiting the adoption of OSS in hospitals. The findings suggest a very limited adoption of OSS in hospitals. Adopters tend to be very large hospitals, with IT budgets of less than 3\% of the total budget and a large number of IT support staff. The results also show that hospitals tend to adopt general-purpose instead of domain-specific OSS. We also found that hospital software vendors are the critical factor facilitating the adoption of OSS in hospitals. Conversely, lack of in-house development, as well as a perceived lack of security, quality, and accountability of OSS products were factors found to be inhibiting adoption. An empirical model describing the adoption of OSS in hospitals, based upon our findings, is presented to illustrate the factors facilitating and inhibiting the adoption of OSS in hospitals.}, isbn = {978-0-549-35501-4}, author = {Munoz-Cornejo, Gilberto} } @article {17700908, title = {Free and open source enabling technologies for patient-centric, guideline-based clinical decision support: a survey.}, journal = {Yearbook of medical informatics}, year = {2007}, month = {2007}, pages = {74-86}, abstract = {OBJECTIVES: Guideline-based clinical decision support is an emerging paradigm to help reduce error, lower cost, and improve quality in evidence-based medicine. The free and open source (FOS) approach is a promising alternative for delivering cost-effective information technology (IT) solutions in health care. In this paper, we survey the current FOS enabling technologies for patient-centric, guideline-based care, and discuss the current trends and future directions of their role in clinical decision support. METHODS: We searched PubMed, major biomedical informatics websites, and the web in general for papers and links related to FOS health care IT systems. We also relied on our background and knowledge for specific subtopics. We focused on the functionalities of guideline modeling tools, and briefly examined the supporting technologies for terminology, data exchange and electronic health record (EHR) standards. RESULTS: To effectively support patient-centric, guideline-based care, the computerized guidelines and protocols need to be integrated with existing clinical information systems or EHRs. Technologies that enable such integration should be accessible, interoperable, and scalable. A plethora of FOS tools and techniques for supporting different knowledge management and quality assurance tasks involved are available. Many challenges, however, remain in their implementation. CONCLUSIONS: There are active and growing trends of deploying FOS enabling technologies for integrating clinical guidelines, protocols, and pathways into the main care processes. The continuing development and maturation of such technologies are likely to make increasingly significant contributions to patient-centric, guideline-based clinical decision support.}, author = {Leong, T Y and Kaiser, K and Miksch, S} } @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} } @inbook {springerlink:10.1007/978-3-540-73044-6_189, title = {O3-RWS: a Java-based, IHE-compliant open-source radiology workstation}, booktitle = {11th Mediterranean Conference on Medical and Biomedical Engineering and Computing 2007}, series = {IFMBE Proceedings}, volume = {16}, year = {2007}, note = {10.1007/978-3-540-73044-6_189}, pages = {727-731}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Within the Open Three Consortium (O3) an open source radiological reporting workstation, called O3- RWS, has been studied, developed and experimented in the routine of European and US hospitals. The O3 Consortium is an international open-source project constituted in 2005 by Higher Education in Clinical Engineering (HECE) of the University of Trieste; it deals with the multi-centric integration of hospitals, RHIOs and citizen (care at home and on the move, and ambient assisted living). O3-RWS has been studied and developed with the goal to give a solution for the needs of the physician, who wants to have an easy-to-use, light and complete solution for the radiology reporting and report creation. O3-RWS, a very versatile platform-independent radiology workstation, providing user authentication and being easy to use also for private users, is able to retrieve, visualize and manage medical images; in an universal version, it is going to be able to deal with vital signs like ECG, hemodynamical and pneumological data.}, isbn = {978-3-540-73044-6}, url = {http://dx.doi.org/10.1007/978-3-540-73044-6_189}, author = {Faustini, Giorgio and Inchingolo, P.}, editor = {Magjarevic, Ratko and Jarm, Tomaz and Kramar, Peter and Zupanic, Anze} } @article {18074196, title = {Open-source, low-cost, high-reliability solutions for digital imaging systems: example of a "dicom router".}, journal = {La Radiologia medica}, volume = {112}, year = {2007}, month = {2007 Dec}, pages = {1252-9}, abstract = {PURPOSE: The purpose of this article is to illustrate a case where acquisition of digital imaging know-how by a modern radiotherapy division has helped to solve a technical problem while allowing substantial savings through the use of free and open-source resources. The problem was related to the necessity to route, with complex policies, the images produced by different digital imaging and communications in medicine (DICOM) sources within the department or in other divisions and/or hospitals. MATERIALS AND METHODS: The problem was solved by using completely free, well-tested and stable technologies (PHP, Apache, MySQL, DCMTK OFFIS, Red Hat Linux 9A and Linux Fedora Core 4) and low-cost hardware to contain costs. In the development, we also considered integration of the routed images with the existing electronic clinical records. RESULTS: The system developed, called the dicom router, implemented two kinds of routing: manual and automatic, both oriented to link the images acquired with the existing electronic clinical records. System stability was enhanced in a second phase by using a low-cost hardware redundancy solution. The system has now been operating for 1 year and has proved the value of the technologies used. CONCLUSIONS: The need to operate with more than one provider creates a series of integration issues, so that it becomes economically appealing to acquire internally the knowledge needed to interact more precisely with providers of big information technology (IT) solutions. This need is well catered for by open-source technologies, which are well documented and available to everyone. By using them, in-house IT technicians are able to implement valuable technical solutions for small-to medium-sized informatization problems, which would otherwise remain unsolved except with great economic efforts.}, author = {Gatta, R and Abeni, F and Buglione, M and Peveri, A and Barbera, F and Tonoli, S and Fratta, P and Magrini, S M} } @article {17249408, title = {OpenSourcePACS: an extensible infrastructure for medical image management.}, journal = {IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society}, volume = {11}, year = {2007}, month = {2007 Jan}, pages = {94-109}, abstract = {The development of comprehensive picture archive and communication systems (PACS) has mainly been limited to proprietary developments by vendors, though a number of freely available software projects have addressed specific image management tasks. The openSourcePACS project aims to provide an open source, common foundation upon which not only can a basic PACS be readily implemented, but to also support the evolution of new PACS functionality through the development of novel imaging applications and services. openSourcePACS consists of four main software modules: 1) image order entry, which enables the ordering and tracking of structured image requisitions; 2) an agent-based image server framework that coordinates distributed image services including routing, image processing, and querying beyond the present digital image and communications in medicine (DICOM) capabilities; 3) an image viewer, supporting standard display and image manipulation tools, DICOM presentation states, and structured reporting; and 4) reporting and result dissemination, supplying web-based widgets for creating integrated reports. All components are implemented using Java to encourage cross-platform deployment. To demonstrate the usage of openSourcePACS, a preliminary application supporting primary care/specialist communication was developed and is described herein. Ultimately, the goal of openSourcePACS is to promote the wide-scale development and usage of PACS and imaging applications within academic and research communities.}, url = {http://escholarship.org/uc/item/186368fv}, author = {Bui, Alex A T and Morioka, Craig and Dionisio, John David N and Johnson, David B and Sinha, Usha and Ardekani, Siamak and Taira, Ricky K and Aberle, Denise R and El-Saden, Suzie and Kangarloo, Hooshang} } @article {17238397, title = {Cooking up an open source EMR for developing countries: OpenMRS - a recipe for successful collaboration.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2006}, month = {2006}, pages = {529-33}, abstract = {Millions of people are continue to die each year from HIV/AIDS. The majority of infected persons (>95\%) live in the developing world. A worthy response to this pandemic will require coordinated, scalable, and flexible information systems. We describe the OpenMRS system, an open source, collaborative effort that can serve as a foundation for EMR development in developing countries. We report our progress to date, lessons learned, and future directions.}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1839638}, author = {Mamlin, Burke W and Biondich, Paul G and Wolfe, Ben A and Fraser, Hamish and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Tierney, William M} } @article {17018156, title = {Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow.}, journal = {BMC bioinformatics}, volume = {7}, year = {2006}, month = {2006}, pages = {430}, abstract = {BACKGROUND: In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies. RESULTS: We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. CONCLUSION: Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved.}, author = {Morisawa, Hiraku and Hirota, Mikako and Toda, Tosifusa} } @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} } @article {17238765, title = {The OpenMRS system: collaborating toward an open source EMR for developing countries.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2006}, month = {2006}, pages = {1146}, abstract = {OpenMRS is an open source infrastructure for the creation of medical record systems in developing countries. Produced and maintained collaboratively across multiple institutions, this framework consists of an open source data model, a set of core application functions, and a default implementation. The goal of this implementation is to provide the beginnings of an EMR that is suitable for all groups involved with healthcare in developing countries.}, author = {Wolfe, Benjamin A and Mamlin, Burke W and Biondich, Paul G and Fraser, Hamish S F and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Tierney, William M} } @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 {16284146, title = {Informatics in radiology (infoRAD): an open source framework for modification and communication of DICOM objects.}, journal = {Radiographics : a review publication of the Radiological Society of North America, Inc}, volume = {25}, year = {2005}, month = {2005 Nov-Dec}, pages = {1709-21}, abstract = {A configurable framework has been developed that can receive, modify, and export images in different picture archiving and communication system scenarios. The framework has three main components: a receiver for Digital Imaging and Communications in Medicine (DICOM) objects, a processing pipeline to apply one or more modifications to these objects, and one or more senders to send the processed objects to predefined addresses. The toolbox programming was implemented as an open source project in Java. The processing pipeline uses the concept of configurable plug-ins. One plug-in is user programmable by means of extensible stylesheet language files and allows conversion of DICOM objects to extensible markup language documents or other file types. Input and output channels are the DICOM Storage service, DICOM compact disks-read-only memory (CD-ROMs), and the local file system. The toolbox has been successfully applied to different clinical scenarios, including the correction of DICOM objects from non-Integrating the Healthcare Enterprise (IHE) conform modalities, pseudonaming of DICOM images, and use of the IHE Portable Data for Imaging profile with import and export of CD-ROMs. The toolbox has proved reliability in the clinical routine. Because of the open programming interfaces, the functionality can easily be adapted to future applications.}, author = {Hackl{\"a}nder, Thomas and Martin, Jens and Kleber, Klaus} } @article {16160381, title = {Linking primary care information systems and public health information networks: lessons from the Philippines.}, journal = {Studies in health technology and informatics}, volume = {116}, year = {2005}, month = {2005}, pages = {955-60}, abstract = {Community-based primary care information systems are one of the building blocks for national health information systems. In the Philippines, after the devolution of health care to local governments, we observed "health information system islands" connected to national vertical programs being implemented in devolved health units. These structures lead to a huge amount of "information work" in the transformation of health information at the community level. This paper describes work done to develop and implement the open-source Community Based Health Information Tracking System (CHITS) Project, which was implemented to address this information management problem and its outcomes. Several lessons learned from the field as well as software development strategies are highlighted in building community level information systems that link to national level health information systems.}, author = {Tolentino, Herman and Marcelo, Alvin and Marcelo, Portia and Maramba, Inocencio} } @article {16779052, title = {Linking primary care information systems and public health vertical programs in the Philippines: an open-source experience.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2005}, month = {2005}, pages = {311-5}, abstract = {Community-based primary care information systems are one of the building blocks for national health information systems. In the Philippines, after the devolution of health care to local governments, we observed "health information system islands" connected to national vertical programs being implemented in devolved health units. These structures lead to a huge amount of "information work" in the transformation of health information at the community level. This paper describes work done to develop and implement the open-source Community Based Health Information Tracking System (CHITS) Project, which was implemented to address this information management problem and its outcomes. Several lessons learned from the field as well as software development strategies are highlighted in building community level information systems that link to national level health information systems.}, author = {Herman, Tolentino and Marcelo, Alvin and Marcelo, Portia and Maramba, Inocencio} } @article {587, title = {The medical imaging interaction toolkit.}, journal = {Medical image analysis}, volume = {9}, year = {2005}, month = {2005 Dec}, pages = {594-604}, abstract = {Thoroughly designed, open-source toolkits emerge to boost progress in medical imaging. The Insight Toolkit (ITK) provides this for the algorithmic scope of medical imaging, especially for segmentation and registration. But medical imaging algorithms have to be clinically applied to be useful, which additionally requires visualization and interaction. The Visualization Toolkit (VTK) has powerful visualization capabilities, but only low-level support for interaction. In this paper, we present the Medical Imaging Interaction Toolkit (MITK). The goal of MITK is to significantly reduce the effort required to construct specifically tailored, interactive applications for medical image analysis. MITK allows an easy combination of algorithms developed by ITK with visualizations created by VTK and extends these two toolkits with those features, which are outside the scope of both. MITK adds support for complex interactions with multiple states as well as undo-capabilities, a very important prerequisite for convenient user interfaces. Furthermore, MITK facilitates the realization of multiple, different views of the same data (as a multiplanar reconstruction and a 3D rendering) and supports the visualization of 3D+t data, whereas VTK is only designed to create one kind of view of 2D or 3D data. MITK reuses virtually everything from ITK and VTK. Thus, it is not at all a competitor to ITK or VTK, but an extension, which eases the combination of both and adds the features required for interactive, convenient to use medical imaging software. MITK is an open-source project (www.mitk.org).}, keywords = {Algorithms, Artificial Intelligence, Computer Graphics, Diagnostic Imaging, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Pattern Recognition, Automated, Software, User-Computer Interface}, issn = {1361-8415}, author = {Wolf, Ivo and Vetter, Marcus and Wegner, Ingmar and B{\"o}ttger, Thomas and Nolden, Marco and Sch{\"o}binger, Max and Hastenteufel, Mark and Kunert, Tobias and Meinzer, Hans-Peter} } @article {500, title = {Advances in functional and structural MR image analysis and implementation as FSL.}, journal = {NeuroImage}, volume = {23 Suppl 1}, year = {2004}, month = {2004}, pages = {S208-19}, abstract = {The techniques available for the interrogation and analysis of neuroimaging data have a large influence in determining the flexibility, sensitivity, and scope of neuroimaging experiments. The development of such methodologies has allowed investigators to address scientific questions that could not previously be answered and, as such, has become an important research area in its own right. In this paper, we present a review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB). This research has focussed on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data. The majority of the research laid out in this paper has been implemented as freely available software tools within FMRIB{\textquoteright}s Software Library (FSL).}, keywords = {Bayes Theorem, Brain, Databases, Factual, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Models, Neurological, Models, Statistical, Software}, issn = {1053-8119}, author = {Smith, Stephen M and Jenkinson, Mark and Woolrich, Mark W and Beckmann, Christian F and Behrens, Timothy E J and Johansen-Berg, Heidi and Bannister, Peter R and De Luca, Marilena and Drobnjak, Ivana and Flitney, David E and Niazy, Rami K and Saunders, James and Vickers, John and Zhang, Yongyue and De Stefano, Nicola and Brady, J Michael and Matthews, Paul M} } @article {762, title = {A flexible registration framework for multimodal image data.}, journal = {Conf Proc IEEE Eng Med Biol Soc}, volume = {3}, year = {2004}, month = {2004}, pages = {1755-8}, abstract = {This paper describes a registration framework based on the insight segmentation and registration toolkit (ITK) which can be used for matching multimodal image data. Different target groups with individual needs and precognition are addressed. The framework offers tools for supporting different matching tasks in a clinical environment. A setup editor defines specific rigid or non rigid matching approaches and the appropriate parameters. Different metrics including a correlation metric, a difference metric and mutual information based metrics are available. Furthermore, a test series editor can be used to evaluate the selected setup. The evaluation results, which are expressed in statistical figures, trends and performance measures, can be visualized and used for an optimal adapted setup configuration. Tests for matching precision, quality and parameter adjustments are offered. For export and import of image data, the most frequently used file formats of clinical environments like DICOM and ANALYZE are supported. We demonstrate some registration examples which frequently occur in the neurosurgical routine of a University Hospital.}, issn = {1557-170X}, doi = {10.1109/IEMBS.2004.1403526}, author = {Dickhaus, H and Floca, R and Eisenmann, U and Metzner, R and Wirtz, C R} } @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 {12810121, title = {Open Source software in medical informatics--why, how and what.}, journal = {International journal of medical informatics}, volume = {69}, year = {2003}, month = {2003 Mar}, pages = {175-84}, abstract = {{\textquoteright}Open Source{\textquoteright} is a 20-40 year old approach to licensing and distributing software that has recently burst into public view. Against conventional wisdom this approach has been wildly successful in the general software market--probably because the openness lets programmers the world over obtain, critique, use, and build upon the source code without licensing fees. Linux, a UNIX-like operating system, is the best known success. But computer scientists at the University of California, Berkeley began the tradition of software sharing in the mid 1970s with BSD UNIX and distributed the major internet network protocols as source code without a fee. Medical informatics has its own history of Open Source distribution: Massachusetts General{\textquoteright}s COSTAR and the Veterans Administration{\textquoteright}s VISTA software have been distributed as source code at no cost for decades. Bioinformatics, our sister field, has embraced the Open Source movement and developed rich libraries of open-source software. Open Source has now gained a tiny foothold in health care (OSCAR GEHR, OpenEMed). Medical informatics researchers and funding agencies should support and nurture this movement. In a world where open-source modules were integrated into operational health care systems, informatics researchers would have real world niches into which they could engraft and test their software inventions. This could produce a burst of innovation that would help solve the many problems of the health care system. We at the Regenstrief Institute are doing our part by moving all of our development to the open-source model.}, author = {McDonald, Clement J and Schadow, Gunther and Barnes, Michael and Dexter, Paul and Overhage, J Marc and Mamlin, Burke and McCoy, J Michael} } @article {12925540, title = {Open-source software and the primary care EMR.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {10}, year = {2003}, month = {2003 Nov-Dec}, pages = {616; author reply 617}, author = {Kantor, Gareth S and Wilson, Wayne D and Midgley, Adrian} } @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} }