@article {1312, title = {The case for free and open source software in research and scholarship.}, journal = {Philos Trans A Math Phys Eng Sci}, volume = {379}, year = {2021}, month = {2021 May 17}, pages = {20200079}, abstract = {

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other {\textquoteright}open{\textquoteright} initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability-including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of {\textquoteright}open source{\textquoteright} as {\textquoteright}open code{\textquoteright} is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today. This article is part of the theme issue {\textquoteright}Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification {\textquoteright}.

}, issn = {1471-2962}, doi = {10.1098/rsta.2020.0079}, author = {Fortunato, Laura and Galassi, Mark} } @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 {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 {1278, title = {Large care gaps in primary care management of asthma: a longitudinal practice audit.}, journal = {BMJ Open}, volume = {9}, year = {2019}, month = {2019 01 29}, pages = {e022506}, abstract = {

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

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

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

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

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

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

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

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

TRIAL REGISTRATION NUMBER: NCT01070095; Pre-results.

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

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

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

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

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

}, issn = {2473-4276}, doi = {10.1200/CCI.18.00132}, author = {Isoviita, Veli-Matti and Salminen, Liina and Azar, Jimmy and Lehtonen, Rainer and Roering, Pia and Carp{\'e}n, Olli and Hietanen, Sakari and Gr{\'e}nman, Seija and Hynninen, Johanna and F{\"a}rkkil{\"a}, Anniina and Hautaniemi, Sampsa} } @article {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 {1217, title = {STEM: An Open Source Tool for Disease Modeling.}, journal = {Health Secur}, volume = {17}, year = {2019}, month = {2019 Jul/Aug}, pages = {291-306}, abstract = {

The Spatiotemporal Epidemiologic Modeler (STEM) is an open source software project supported by the Eclipse Foundation and used by a global community of researchers and public health officials working to track and, when possible, control outbreaks of infectious disease in human and animal populations. STEM is not a model or a tool designed for a specific disease; it is a flexible, modular framework supporting exchange and integration of community models, reusable plug-in components, and denominator data, available to researchers worldwide at www.eclipse.org/stem. A review of multiple projects illustrates its capabilities. STEM has been used to study variations in transmission of seasonal influenza in Israel by strains; evaluate social distancing measures taken to curb the H1N1 epidemic in Mexico City; study measles outbreaks in part of London and inform local policy on immunization; and gain insights into H7N9 avian influenza transmission in China. A multistrain dengue fever model explored the roles of the mosquito vector, cross-strain immunity, and antibody response in the frequency of dengue outbreaks. STEM has also been used to study the impact of variations in climate on malaria incidence. During the Ebola epidemic, a weekly conference call supported the global modeling community; subsequent work modeled the impact of behavioral change and tested disease reintroduction via animal reservoirs. Work in Germany tracked salmonella in pork from farm to fork; and a recent doctoral dissertation used the air travel feature to compare the potential threats posed by weaponizing infectious diseases. Current projects include work in Great Britain to evaluate control strategies for parasitic disease in sheep, and in Germany and Hungary, to validate the model and inform policy decisions for African swine fever. STEM Version 4.0.0, released in early 2019, includes tools used in these projects and updates technical aspects of the framework to ease its use and re-use.

}, issn = {2326-5108}, doi = {10.1089/hs.2019.0018}, author = {Douglas, Judith V and Bianco, Simone and Edlund, Stefan and Engelhardt, Tekla and Filter, Matthias and G{\"u}nther, Taras and Hu, Kun Maggie and Nixon, Emily J and Sevilla, Nereyda L and Swaid, Ahmad and Kaufman, James H} } @article {1216, title = {Transforming Two Decades of ePR Data to OMOP CDM for Clinical Research.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {233-237}, abstract = {

This paper presents the extract-transform-and-load (ETL) process from the Electronic Patient Records (ePR) at the Heart Institute (InCor) to the OMOP Common Data Model (CDM) format. We describe the initial database characterization, relational source mappings, selection filters, data transformations and patient de-identification using the open-source OHDSI tools and SQL scripts. We evaluate the resulting InCor-CDM database by recreating the same patient cohort from a previous reference study (over the original data source) and comparing the cohorts{\textquoteright} descriptive statistics and inclusion reports. The results exhibit that up to 91\% of the reference patients were retrieved by our method from the ePR through InCor-CDM, with AUC=0.938. The results indicate that the method that we employed was able to produce a new database that was both consistent with the original data and in accordance to the OMOP CDM standard.

}, issn = {1879-8365}, doi = {10.3233/SHTI190218}, author = {Lima, Daniel M and Rodrigues-Jr, Jose F and Traina, Agma J M and Pires, Fabio A and Gutierrez, Marco A} } @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 {1204, title = {The mobile sleep lab app: {An} open-source framework for mobile sleep assessment based on consumer-grade wearable devices}, journal = {Computers in Biology and Medicine}, volume = {103}, year = {2018}, pages = {8{\textendash}16}, abstract = {BACKGROUND: Sleep disorders have a prevalence of up to 50\% and are commonly diagnosed using polysomnography. However, polysomnography requires trained staff and specific equipment in a laboratory setting, which are expensive and limited resources are available. Mobile and wearable devices such as fitness wristbands can perform limited sleep monitoring but are not evaluated well. Here, the development and evaluation of a mobile application to record and synchronize data from consumer-grade sensors suitable for sleep monitoring is presented and evaluated for data collection capability in a clinical trial. METHODS: Wearable and ambient consumer-grade sensors were selected to mimic the functionalities of clinical sleep laboratories. Then, a modular application was developed for recording, processing and visualizing the sensor data. A validation was performed in three phases: (1) sensor functionalities were evaluated, (2) self-experiments were performed in full-night experiments, and (3) the application was tested for usability in a clinical trial on primary snoring. RESULTS: The evaluation of the sensors indicated their suitability for assessing basic sleep characteristics. Additionally, the application successfully recorded full-night sleep. The collected data was of sufficient quality to detect and measure body movements, cardiac activity, snoring and brightness. The ongoing clinical trial phase showed the successful deployment of the application by medical professionals. CONCLUSION: The proposed software demonstrated a strong potential for medical usage. With low costs, it can be proposed for screening, long-term monitoring or in resource-austere environments. However, further validations are needed, in particular the comparison to a clinical sleep laboratory.}, keywords = {Mobile sleep laboratory, Sleep screening, Smartphone, Telemedicine, Wearable technology}, issn = {1879-0534}, doi = {10.1016/j.compbiomed.2018.09.025}, author = {Burgdorf, Andreas and G{\"u}the, Inga and Jovanovi{\'c}, Marko and Kutafina, Ekaterina and Kohlschein, Christian and Bitsch, J{\'o} {\'A}gila and Jonas, Stephan M.} } @article {1235, title = {A Platform for Innovation and Standards Evaluation: a Case Study from the OpenMRS Open-Source Radiology Information System.}, journal = {J Digit Imaging}, volume = {31}, year = {2018}, month = {2018 06}, pages = {361-370}, abstract = {

Open-source development can provide a platform for innovation by seeking feedback from community members as well as providing tools and infrastructure to test new standards. Vendors of proprietary systems may delay adoption of new standards until there are sufficient incentives such as legal mandates or financial incentives to encourage/mandate adoption. Moreover, open-source systems in healthcare have been widely adopted in low- and middle-income countries and can be used to bridge gaps that exist in global health radiology. Since 2011, the authors, along with a community of open-source contributors, have worked on developing an open-source radiology information system (RIS) across two communities-OpenMRS and LibreHealth. The main purpose of the RIS is to implement core radiology workflows, on which others can build and test new radiology standards. This work has resulted in three major releases of the system, with current architectural changes driven by changing technology, development of new standards in health and imaging informatics, and changing user needs. At their core, both these communities are focused on building general-purpose EHR systems, but based on user contributions from the fringes, we have been able to create an innovative system that has been used by hospitals and clinics in four different countries. We provide an overview of the history of the LibreHealth RIS, the architecture of the system, overview of standards integration, describe challenges of developing an open-source product, and future directions. Our goal is to attract more participation and involvement to further develop the LibreHealth RIS into an Enterprise Imaging System that can be used in other clinical imaging including pathology and dermatology.

}, keywords = {Diagnostic Imaging, Humans, Radiology Information Systems, Software, Systems Integration, Workflow}, issn = {1618-727X}, doi = {10.1007/s10278-018-0088-5}, author = {Gichoya, Judy W and Kohli, Marc and Ivange, Larry and Schmidt, Teri S and Purkayastha, Saptarshi} } @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 {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 {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 {1192, title = {{OpenICE} medical device interoperability platform overview and requirement analysis}, journal = {Biomedizinische Technik. Biomedical Engineering}, year = {2017}, abstract = {We give an overview of OpenICE, an open source implementation of the ASTM standard F2761 for the Integrated Clinical Environment (ICE) that leverages medical device interoperability, together with an analysis of the clinical and non-functional requirements and community process that inspired its design.}, keywords = {Interoperability, medical applications, patient safety, platform, requirements engineering}, issn = {1862-278X}, doi = {10.1515/bmt-2017-0040}, author = {Arney, David and Plourde, Jeffrey and Goldman, Julian M.} } @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 {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} } @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 {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 {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 {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 {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 {1149, title = {Open Source Platform for Collaborative Construction of Wearable Sensor Datasets for Human Motion Analysis and an Application for Gait Analysis.}, journal = {J Biomed Inform}, year = {2016}, month = {2016 Sep 1}, abstract = {

Nearly every practical improvement in modelling human motion is well founded in a properly designed collection of data or datasets. These datasets must be made publicly available for the community could validate and accept them. It is reasonable to concede that a collective, guided enterprise could serve to devise solid and substantial datasets, as a result of a collaborative effort, in the same sense as the open software community does. In this way datasets could be complemented, extended and expanded in size with, for example, more individuals, samples and human actions. For this to be possible some commitments must be made by the collaborators, being one of them sharing the same data acquisition platform. In this paper, we offer an affordable open source hardware and software platform based on inertial wearable sensors in a way that several groups could cooperate in the construction of datasets through common software suitable for collaboration. Some experimental results about the throughput of the overall system are reported showing the feasibility of acquiring data from up to 6 sensors with a sampling frequency no less than 118Hz. Also, a proof-of-concept dataset is provided comprising sampled data from 12 subjects suitable for gait analysis.

}, issn = {1532-0480}, doi = {10.1016/j.jbi.2016.08.025}, author = {Llamas, C{\'e}sar and Gonz{\'a}lez, Manuel A and Hern{\'a}ndez, C{\'a}rmen and Vegas, Jes{\'u}s} } @article {1148, title = {Open-source, small-animal magnetic resonance-guided focused ultrasound system.}, journal = {J Ther Ultrasound}, volume = {4}, year = {2016}, month = {2016}, pages = {22}, abstract = {

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

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

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

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

}, issn = {2050-5736}, doi = {10.1186/s40349-016-0066-7}, author = {Poorman, Megan E and Chaplin, Vandiver L and Wilkens, Ken and Dockery, Mary D and Giorgio, Todd D and Grissom, William A and Caskey, Charles F} } @article {1122, title = {PACS for Bhutan: a cost effective open source architecture for emerging countries.}, journal = {Insights Imaging}, year = {2016}, month = {2016 Jul 28}, abstract = {

This paper reports the design and implementation of an innovative and cost-effective imaging management infrastructure suitable for radiology centres in emerging countries. It was implemented in the main referring hospital of Bhutan equipped with a CT, an MRI, digital radiology, and a suite of several ultrasound units. They lacked the necessary informatics infrastructure for image archiving and interpretation and needed a system for distribution of images to clinical wards. The solution developed for this project combines several open source software platforms in a robust and versatile archiving and communication system connected to analysis workstations equipped with a FDA-certified version of the highly popular Open-Source software. The whole system was implemented on standard off-the-shelf hardware. The system was installed in three~days, and training of the radiologists as well as the technical and IT staff was provided onsite to ensure full ownership of the system by the local team. Radiologists were rapidly capable of reading and interpreting studies on the diagnostic workstations, which had a significant benefit on their workflow and ability to perform diagnostic tasks more efficiently. Furthermore, images were also made available to several clinical units on standard desktop computers through a web-based viewer.

MESSAGES/TEACHING POINTS: {\textbullet} Open source imaging informatics platforms can provide cost-effective alternatives for PACS {\textbullet} Robust and cost-effective open architecture can provide adequate solutions for emerging countries {\textbullet} Imaging informatics is often lacking in hospitals equipped with digital modalities.

}, issn = {1869-4101}, doi = {10.1007/s13244-016-0512-7}, author = {Ratib, Osman and Roduit, Nicolas and Nidup, Dechen and De Geer, Gerard and Rosset, Antoine and Geissbuhler, Antoine} } @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 {1112, title = {TACIT: An open-source text analysis, crawling, and interpretation tool.}, journal = {Behav Res Methods}, year = {2016}, month = {2016 Mar 4}, abstract = {

As human activity and interaction increasingly take place online, the digital residues of these activities provide a valuable window into a range of psychological and social processes. A great deal of progress has been made toward utilizing these opportunities; however, the complexity of managing and analyzing the quantities of data currently available has limited both the types of analysis used and the number of researchers able to make use of these data. Although fields such as computer science have developed a range of techniques and methods for handling these difficulties, making use of those tools has often required specialized knowledge and programming experience. The Text Analysis, Crawling, and Interpretation Tool (TACIT) is designed to bridge this gap by providing an intuitive tool and interface for making use of state-of-the-art methods in text analysis and large-scale data management. Furthermore, TACIT is implemented as an open, extensible, plugin-driven architecture, which will allow other researchers to extend and expand these capabilities as new methods become available.

}, issn = {1554-3528}, doi = {10.3758/s13428-016-0722-4}, author = {Dehghani, Morteza and Johnson, Kate M and Garten, Justin and Boghrati, Reihane and Hoover, Joe and Balasubramanian, Vijayan and Singh, Anurag and Shankar, Yuvarani and Pulickal, Linda and Rajkumar, Aswin and Parmar, Niki Jitendra} } @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 {1032, title = {Anterior loop of the inferior alveolar nerve: Averages and prevalence based on CT scans.}, journal = {J Prosthet Dent}, year = {2015}, month = {2015 Oct 9}, abstract = {

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

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

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

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

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

}, issn = {1097-6841}, doi = {10.1016/j.prosdent.2015.06.025}, author = {Juan, Del Valle Lovato and Grageda, Edgar and Crespo, Salvador G{\'o}mez} } @article {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 {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 {1279, title = {Identifying patients with asthma in primary care electronic medical record systems Chart analysis-based electronic algorithm validation study.}, journal = {Can Fam Physician}, volume = {61}, year = {2015}, month = {2015 Oct}, pages = {e474-83}, abstract = {

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

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

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

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

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

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

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

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

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

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

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

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

}, issn = {1826-6983}, doi = {10.1007/s11547-015-0560-y}, author = {Valeri, Gianluca and Zuccaccia, Matteo and Badaloni, Andrea and Ciriaci, Damiano and La Riccia, Luigi and Mazzoni, Giovanni and Maggi, Stefania and Giovagnoni, Andrea} } @article {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 {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 {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 {994, title = {Towards the Implementation of an openEHR-based Open Source EHR Platform (a vision paper).}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {45-9}, abstract = {

Healthcare Information Systems are a big business. Currently there is an explosion of EHR/EMR products available on the market, and the best tools are really expensive. Many developing countries and healthcare providers cannot access such tools, and for those who can, there is not a clear strategy for the evolution, scaling, and cost of these electronic health products. The lack of standard-based implementations conduct to the creation of isolated information silos that cannot be exploited (i.e. shared between providers to promote a holistic view of each patient{\textquoteright}s medical history). This paper exposes the main elements behind a Standard-based Open Source EHR Platform that is future-proof and allows to evolve and scale with minimal cost. The proposed EHR Architecture is based on openEHR specifications, adding elements emerged from research and development experiences, leading to a design that can be implemented in any modern technology. Different implementations will be interoperable by design. This Platform will leverage contexts of scarce resources, reusing clinical knowledge, a common set of software components and services.

}, issn = {0926-9630}, author = {Pazos Guti{\'e}rrez, Pablo} } @article {1051, title = {High dimensional biological data retrieval optimization with NoSQL technology.}, journal = {BMC Genomics}, volume = {15 Suppl 8}, year = {2014}, month = {2014}, pages = {S3}, abstract = {

BACKGROUND: High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies. Although microarray data is supported in data warehouses such as tranSMART, when querying relational databases for hundreds of different patient gene expression records queries are slow due to poor performance. Non-relational data models, such as the key-value model implemented in NoSQL databases, hold promise to be more performant solutions. Our motivation is to improve the performance of the tranSMART data warehouse with a view to supporting Next Generation Sequencing data.

RESULTS: In this paper we introduce a new data model better suited for high-dimensional data storage and querying, optimized for database scalability and performance. We have designed a key-value pair data model to support faster queries over large-scale microarray data and implemented the model using HBase, an implementation of Google{\textquoteright}s BigTable storage system. An experimental performance comparison was carried out against the traditional relational data model implemented in both MySQL Cluster and MongoDB, using a large publicly available transcriptomic data set taken from NCBI GEO concerning Multiple Myeloma. Our new key-value data model implemented on HBase exhibits an average 5.24-fold increase in high-dimensional biological data query performance compared to the relational model implemented on MySQL Cluster, and an average 6.47-fold increase on query performance on MongoDB.

CONCLUSIONS: The performance evaluation found that the new key-value data model, in particular its implementation in HBase, outperforms the relational model currently implemented in tranSMART. We propose that NoSQL technology holds great promise for large-scale data management, in particular for high-dimensional biological data such as that demonstrated in the performance evaluation described in this paper. We aim to use this new data model as a basis for migrating tranSMART{\textquoteright}s implementation to a more scalable solution for Big Data.

}, keywords = {Database Management Systems, Databases, Genetic, High-Throughput Nucleotide Sequencing, Humans, Information Storage and Retrieval, Medical Informatics, Multiple Myeloma, Oligonucleotide Array Sequence Analysis, Transcriptome}, issn = {1471-2164}, doi = {10.1186/1471-2164-15-S8-S3}, author = {Wang, Shicai and Pandis, Ioannis and Wu, Chao and He, Sijin and Johnson, David and Emam, Ibrahim and Guitton, Florian and Guo, Yike} } @article {1033, title = {Making cytological diagnoses on digital images using the iPath network.}, journal = {Acta Cytol}, volume = {58}, year = {2014}, month = {2014}, pages = {453-60}, abstract = {

BACKGROUND: The iPath telemedicine platform Basel is mainly used for histological and cytological consultations, but also serves as a valuable learning tool.

AIM: To study the level of accuracy in making diagnoses based on still images achieved by experienced cytopathologists, to identify limiting factors, and to provide a cytological image series as a learning set.

METHOD: Images from 167 consecutive cytological specimens of different origin were uploaded on the iPath platform and evaluated by four cytopathologists. Only wet-fixed and well-stained specimens were used. The consultants made specific diagnoses and categorized each as benign, suspicious or malignant.

RESULTS: For all consultants, specificity and sensitivity regarding categorized diagnoses were 83-92 and 85-93\%, respectively; the overall accuracy was 88-90\%. The interobserver agreement was substantial (κ = 0.791). The lowest rate of concordance was achieved in urine and bladder washings and in the identification of benign lesions.

CONCLUSION: Using a digital image set for diagnostic purposes implies that even under optimal conditions the accuracy rate will not exceed to 80-90\%, mainly because of lacking supportive immunocytochemical or molecular tests. This limitation does not disqualify digital images for teleconsulting or as a learning aid. The series of images used for the study are open to the public at http://pathorama.wordpress.com/extragenital-cytology-2013/.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, Computers, Handheld, Cytodiagnosis, Diagnosis, Differential, Female, Humans, Hyperplasia, Infant, Male, Metaplasia, Middle Aged, Neoplasms, Observer Variation, Reproducibility of Results, Sensitivity and Specificity, Telemedicine}, issn = {0001-5547}, doi = {10.1159/000369241}, author = {Dalquen, Peter and Savic Prince, Spasenija and Spieler, Peter and Kunze, Dietmar and Neumann, Heinrich and Eppenberger-Castori, Serenella and Adams, Heiner and Glatz, Katharina and Bubendorf, Lukas} } @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 {1026, title = {Simplifying electronic data capture in clinical trials: workflow embedded image and biosignal file integration and analysis via web services.}, journal = {J Digit Imaging}, volume = {27}, year = {2014}, month = {2014 Oct}, pages = {571-80}, abstract = {

To improve data quality and save cost, clinical trials are nowadays performed using electronic data capture systems (EDCS) providing electronic case report forms (eCRF) instead of paper-based CRFs. However, such EDCS are insufficiently integrated into the medical workflow and lack in interfacing with other study-related systems. In addition, most EDCS are unable to handle image and biosignal data, although electrocardiography (EGC, as example for one-dimensional (1D) data), ultrasound (2D data), or magnetic resonance imaging (3D data) have been established as surrogate endpoints in clinical trials. In this paper, an integrated workflow based on OpenClinica, one of the world{\textquoteright}s largest EDCS, is presented. Our approach consists of three components for (i) sharing of study metadata, (ii) integration of large volume data into eCRFs, and (iii) automatic image and biosignal analysis. In all components, metadata is transferred between systems using web services and JavaScript, and binary large objects (BLOBs) are sent via the secure file transfer protocol and hypertext transfer protocol. We applied the close-looped workflow in a multicenter study, where long term (7~days/24~h) Holter ECG monitoring is acquired on subjects with diabetes. Study metadata is automatically transferred into OpenClinica, the 4~GB BLOBs are seamlessly integrated into the eCRF, automatically processed, and the results of signal analysis are written back into the eCRF immediately.

}, keywords = {Algorithms, Automatic Data Processing, Clinical Trials as Topic, Database Management Systems, Humans, Image Processing, Computer-Assisted, Information Storage and Retrieval, Internet, Medical Records Systems, Computerized, Systems Integration, Workflow}, issn = {1618-727X}, doi = {10.1007/s10278-014-9694-z}, author = {Haak, Daniel and Samsel, Christian and Gehlen, Johan and Jonas, Stephan and Deserno, Thomas M} } @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 {947, title = {A user-friendly, open-source tool to project impact and cost of diagnostic tests for tuberculosis.}, journal = {Elife}, year = {2014}, month = {2014 Jun 4}, pages = {e02565}, abstract = {

Most existing models of infectious diseases, including tuberculosis (TB), do not allow end-users to customize results to local conditions. We created a dynamic transmission model to project TB incidence, TB mortality, multidrug-resistant (MDR) TB prevalence, and incremental costs over five years after scale-up of nine alternative diagnostic strategies including combinations of sputum smear microscopy, Xpert MTB/RIF, microcolony-based culture, and same-day diagnosis. We developed a corresponding web-based interface that allows users to specify local costs and epidemiology. Full model code - including the ability to change any input parameter - is also included. The impact of improved diagnostic testing was greater for mortality and MDR-TB prevalence than TB incidence, and was maximized in high-incidence, low-HIV settings. More costly interventions generally had greater impact. In settings with little capacity for up-front investment, same-day microscopy had greatest impact on TB incidence and became cost-saving within five years if feasible to deliver at $10/test. In settings where more initial investment was possible, population-level scale-up of either Xpert MTB/RIF or microcolony-based culture offered substantially greater benefits, often averting ten times more TB cases than narrowly-targeted diagnostic strategies at minimal incremental long-term cost. Where containing MDR-TB is the overriding concern, Xpert for smear-positives has reasonable impact on MDR-TB incidence, but at substantial price and little impact on overall TB incidence and mortality. This novel, user-friendly modeling framework improves decision-makers{\textquoteright} ability to evaluate the impact of TB diagnostic strategies, accounting for local conditions.

}, issn = {2050-084X}, doi = {10.7554/eLife.02565}, author = {Dowdy, David W and Andrews, Jason R and Dodd, Peter J and Gilman, Robert H} } @article {1009, title = {AccessMRS: integrating OpenMRS with smart forms on Android.}, journal = {Stud Health Technol Inform}, volume = {192}, year = {2013}, month = {2013}, pages = {866-70}, abstract = {

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

}, keywords = {electronic health records, Forms and Records Control, Information Storage and Retrieval, Medical Record Linkage, Mobile Applications, Programming Languages, Software Design, Systems Integration, User-Computer Interface}, issn = {0926-9630}, author = {Fazen, Louis E and Chemwolo, Benjamin T and Songok, Julia J and Ruhl, Laura J and Kipkoech, Carolyne and Green, James M and Ikemeri, Justus E and Christoffersen-Deb, Astrid} } @article {1010, title = {E-health systems for management of MDR-TB in resource-poor environments: a decade of experience and recommendations for future work.}, journal = {Stud Health Technol Inform}, volume = {192}, year = {2013}, month = {2013}, pages = {627-31}, abstract = {

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

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

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

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

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

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

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Cambodia, Child, Child, Preschool, Female, Humans, Internet, Male, Middle Aged, Remote Consultation, Retrospective Studies, Surgical Procedures, Operative, telepathology, Videoconferencing, Young Adult}, issn = {1758-1109}, doi = {10.1177/1357633X13512071}, author = {Kadaba, Varsha and Ly, Tho and Noor, Saqib and Chhut, Serey V and Hinsch, Nora and Stauch, Gerhard and Gollogly, James} } @article {894, title = {Novel open-source electronic medical records system for palliative care in low-resource settings.}, journal = {BMC Palliat Care}, volume = {12}, year = {2013}, month = {2013}, pages = {31}, abstract = {

BACKGROUND: The need for palliative care in sub-Saharan Africa is staggering: this region shoulders over 67\% of the global burden of HIV/AIDS and cancer. However, provisions for these essential services remain limited and poorly integrated with national health systems in most nations. Moreover, the evidence base for palliative care in the region remains scarce. This study chronicles the development and evaluation of DataPall, an open-source electronic medical records system that can be used to track patients, manage data, and generate reports for palliative care providers in these settings.DataPall was developed using design criteria encompassing both functional and technical objectives articulated by hospital leaders and palliative care staff at a leading palliative care center in Malawi. The database can be used with computers that run Windows XP SP 2 or newer, and does not require an internet connection for use. Subsequent to its development and implementation in two hospitals, DataPall was tested among both trained and untrained hospital staff populations on the basis of its usability with comparison to existing paper records systems as well as on the speed at which users could perform basic database functions. Additionally, all participants evaluated this program on a standard system usability scale.

RESULTS: In a study of health professionals in a Malawian hospital, DataPall enabled palliative care providers to find patients{\textquoteright} appointments, on average, in less than half the time required to locate the same record in current paper records. Moreover, participants generated customizable reports documenting patient records and comprehensive reports on providers{\textquoteright} activities with little training necessary. Participants affirmed this ease of use on the system usability scale.

CONCLUSIONS: DataPall is a simple, effective electronic medical records system that can assist in developing an evidence base of clinical data for palliative care in low resource settings. The system is available at no cost, is specifically designed to chronicle care in the region, and is catered to meet the technical needs and user specifications of such facilities.

}, issn = {1472-684X}, doi = {10.1186/1472-684X-12-31}, author = {Shah, Kamal G and Slough, Tara Lyn and Yeh, Ping Teresa and Gombwa, Suave and Kiromera, Athanase and Oden, Z Maria and Richards-Kortum, Rebecca R} } @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 {1053, title = {tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research.}, journal = {AMIA Jt Summits Transl Sci Proc}, volume = {2013}, year = {2013}, month = {2013}, pages = {6-8}, abstract = {

tranSMART is an emerging global open source public private partnership community developing a comprehensive informatics-based analysis and data-sharing cloud platform for clinical and translational research. The tranSMART consortium includes pharmaceutical and other companies, not-for-profits, academic entities, patient advocacy groups, and government stakeholders. The tranSMART value proposition relies on the concept that the global community of users, developers, and stakeholders are the best source of innovation for applications and for useful data. Continued development and use of the tranSMART platform will create a means to enable "pre-competitive" data sharing broadly, saving money and, potentially accelerating research translation to cures. Significant transformative effects of tranSMART includes 1) allowing for all its user community to benefit from experts globally, 2) capturing the best of innovation in analytic tools, 3) a growing {\textquoteright}big data{\textquoteright} resource, 4) convergent standards, and 5) new informatics-enabled translational science in the pharma, academic, and not-for-profit sectors.

}, issn = {2153-4063}, author = {Athey, Brian D and Braxenthaler, Michael and Haas, Magali and Guo, Yike} } @article {859, title = {The use of open source electronic health records within the federal safety net.}, journal = {J Am Med Inform Assoc}, year = {2013}, month = {2013 Jun 6}, abstract = {

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

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

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

}, issn = {1437-160X}, doi = {10.1007/s00296-013-2845-6}, author = {Ariani, Alarico and Carotti, Marina and Gutierrez, Marwin and Bichisecchi, Elisabetta and Grassi, Walter and Giuseppetti, Gian Marco and Salaffi, Fausto} } @article {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 {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} } @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 {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} } @article {1050, title = {S2DIA: a diagnostic system for Diabetes mellitus using SANA platform.}, journal = {Conf Proc IEEE Eng Med Biol Soc}, volume = {2012}, year = {2012}, month = {2012}, pages = {6078-81}, abstract = {

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

}, keywords = {Diabetes Mellitus, Type 2, Diagnosis, Computer-Assisted, Humans, Risk Factors}, issn = {1557-170X}, doi = {10.1109/EMBC.2012.6347380}, author = {Costa, Clayton M and Gondim, Dikson D and Gondim, Dibson D and Soares, Heliana B and Ribeiro, Anna G C D and Silva, Ikaro and Winkler, Erick and Celi, Leo and Guerreiro, Ana M G and Leite, Cic{\'\i}lia R M} } @inbook {789, title = {SOFA: A Multi-Model Framework for Interactive Physical Simulation}, booktitle = {Soft Tissue Biomechanical Modeling for Computer Assisted Surgery}, series = {Studies in Mechanobiology, Tissue Engineering and Biomaterials}, volume = {11}, year = {2012}, pages = {283-321}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Simulation Open Framework Architecture (SOFA) is an open-source C++ library primarily targeted at interactive computational medical simulation. SOFA facilitates collaborations between specialists from various domains, by decomposing complex simulators into components designed independently and organized in a scenegraph data structure. Each component encapsulates one of the aspects of a simulation, such as the degrees of freedom, the forces and constraints, the differential equations, the main loop algorithms, the linear solvers, the collision detection algorithms or the interaction devices. The simulated objects can be represented using several models, each of them optimized for a different task such as the computation of internal forces, collision detection, haptics or visual display. These models are synchronized during the simulation using a mapping mechanism. CPU and GPU implementations can be transparently combined to exploit the computational power of modern hardware architectures. Thanks to this flexible yet efficient architecture, SOFA can be used as a test-bed to compare models and algorithms, or as a basis for the development of complex, high-performance simulators.}, isbn = {978-3-642-29013-8}, doi = {10.1007/8415_2012_125}, url = {http://dx.doi.org/10.1007/8415_2012_125}, author = {Faure, Fran{\c c}ois and Duriez, Christian and Delingette, Herv{\'e} and Allard, J{\'e}r{\'e}mie and Gilles, Benjamin and Marchesseau, St{\'e}phanie and Talbot, Hugo and Courtecuisse, Hadrien and Bousquet, Guillaume and Peterlik, Igor and Cotin, St{\'e}phane}, editor = {Payan, Yohan} } @conference {829, title = {A Standards-Based Open Source Application to Gather Health Assessment Data in Developing Countries}, booktitle = {Global Humanitarian Technology Conference (GHTC), 2012 IEEE}, year = {2012}, month = {oct.}, abstract = {Many organizations are working in developing coun- tries to support local health care organizations and infrastructure to provide sustainable, community-based health care. This requires not only the influx of medical staff and supplies, but also requires maintaining individual health care records and enabling the ability to collect, analyze and aggregate data in the field to customize care to the local needs of the community, and to provide continuity of care to its citizens. The recent rise of adoption of standards for electronic health records(EHR) provides an alternative to using paper forms in mobile health clinics that often serve these countries. In this paper, we describe an open-source, standards-based health assessment software application developed by the non-profit organization Health Records For Everyone (HR4E) and field tested in a mobile health clinic in rural Ethiopia in the fall of 2011. The application allows mobile health clinic staff to quickly deploy medical clinics and collect patient data electronically in the face of various environmental challenges. In addition to producing electronic patient records which are validated in-field using HL7{\textquoteright}s Clinical Document Architecture standard, the application allows medical practitioners to view and summarize patient data for in-field analysis.}, keywords = {and Telemedicine, Ash, Communities, Computers, Health, Medical services, Medical Technology, Mobile communication, Software, Standards}, doi = {10.1109/GHTC.2012.78}, author = {Gainer, Alex and Roth, Mary and Strong, Phil and Davis, James} } @article {1036, title = {A static-image telepathology system for dermatopathology consultation in East Africa: the Massachusetts General Hospital Experience.}, journal = {J Am Acad Dermatol}, volume = {67}, year = {2012}, month = {2012 Nov}, pages = {997-1007}, abstract = {

BACKGROUND: The histologic diagnosis of skin lesions in the developing world is complicated by the shortage of pathologists with subspecialty training in dermatopathology, limited access to ancillary diagnostic testing, and costly referrals for expert glass slide consultation in challenging cases.

OBJECTIVE: In this study we evaluate the feasibility of a static-image telepathology platform in Africa for performing accurate dermatopathology consultations.

METHODS: A static-image telepathology platform using the iPath server was utilized by referring pathologists in 4 African hospitals. Diagnostic interpretations were provided by Massachusetts General Hospital dermatopathologists at no cost. The diagnostic accuracy and interobserver correlation was evaluated.

RESULTS: The static histopathologic images were diagnostic in 22 of 29 (76\%) cases. Diagnostic accuracy between static image and glass slide diagnosis in 22 cases was 91\%, ranging from 86\% to 95\% according to years of dermatopathology subspecialty expertise. Comparison with the glass slides showed that the telepathology diagnosis was limited by inappropriate field selection in only one case. Interobserver concordance between two pathologists was high (K = 0.86) suggesting that this platform is easy to use with minimal training of both referring and consulting pathologists.

LIMITATIONS: Concordance between conventional microscopy and static image telepathology was performed in 22 of 29 cases for which glass slides were received. Interobserver concordance was performed for two pathologists.

CONCLUSION: Static-image telepathology is a feasible means of rendering diagnoses on dermatopathology cases and is a cost-effective technology for obtaining much-needed second opinions in resource-poor settings.

}, keywords = {Africa, Eastern, Cost-Benefit Analysis, Feasibility Studies, Hospitals, General, Humans, Massachusetts, Microscopy, Observer Variation, Pathology, Clinical, Remote Consultation, Skin Diseases, Skin Neoplasms, telepathology}, issn = {1097-6787}, doi = {10.1016/j.jaad.2011.12.036}, author = {Gimbel, Devon C and Sohani, Aliyah R and Prasad Busarla, Satya Vara and Kirimi, Jesca Muthoni and Sayed, Shahin and Okiro, Patricia and Nazarian, Rosalynn M} } @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 {868, title = {The caBIG{\textregistered} Life Science Business Architecture Model.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 May 15}, pages = {1429-35}, abstract = {

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

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

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

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

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

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

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

}, keywords = {Data Compression, Female, Germany, Guideline Adherence, Humans, Image Processing, Computer-Assisted, Mammography, Mass Screening, Online Systems, Phantoms, Imaging, Quality Assurance, Health Care, Radiology Information Systems, Reference Standards, Software}, issn = {1438-9010}, doi = {10.1055/s-0031-1281599}, author = {Czwoydzinski, J and Girnus, R and Sommer, A and Heindel, W and Lenzen, H} } @article {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 {597, title = {Forward field computation with OpenMEEG.}, journal = {Computational intelligence and neuroscience}, volume = {2011}, year = {2011}, month = {2011}, pages = {923703}, abstract = {To recover the sources giving rise to electro- and magnetoencephalography in individual measurements, realistic physiological modeling is required, and accurate numerical solutions must be computed. We present OpenMEEG, which solves the electromagnetic forward problem in the quasistatic regime, for head models with piecewise constant conductivity. The core of OpenMEEG consists of the symmetric Boundary Element Method, which is based on an extended Green Representation theorem. OpenMEEG is able to provide lead fields for four different electromagnetic forward problems: Electroencephalography (EEG), Magnetoencephalography (MEG), Electrical Impedance Tomography (EIT), and intracranial electric potentials (IPs). OpenMEEG is open source and multiplatform. It can be used from Python and Matlab in conjunction with toolboxes that solve the inverse problem; its integration within FieldTrip is operational since release 2.0.}, issn = {1687-5273}, author = {Gramfort, Alexandre and Papadopoulo, Th{\'e}odore and Olivi, Emmanuel and Clerc, Maureen} } @article {594, title = {Implementation of the Zambia electronic perinatal record system for comprehensive prenatal and delivery care.}, journal = {International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics}, volume = {113}, year = {2011}, month = {2011 May}, pages = {131-6}, abstract = {OBJECTIVE: To characterize prenatal and delivery care in an urban African setting. METHODS: The Zambia Electronic Perinatal Record System (ZEPRS) was implemented to record demographic characteristics, past medical and obstetric history, prenatal care, and delivery and newborn care for pregnant women across 25 facilities in the Lusaka public health sector. RESULTS: From June 1, 2007, to January 31, 2010, 115552 pregnant women had prenatal and delivery information recorded in ZEPRS. Median gestation age at first prenatal visit was 23weeks (interquartile range [IQR] 19-26). Syphilis screening was documented in 95663 (83\%) pregnancies: 2449 (2.6\%) women tested positive, of whom 1589 (64.9\%) were treated appropriately. 111108 (96\%) women agreed to HIV testing, of whom 22\% were diagnosed with HIV. Overall, 112813 (98\%) of recorded pregnancies resulted in a live birth, and 2739 (2\%) in a stillbirth. The median gestational age was 38weeks (IQR 35-40) at delivery; the median birth weight of newborns was 3000g (IQR 2700-3300g). CONCLUSION: The results demonstrate the feasibility of using a comprehensive electronic medical record in an urban African setting, and highlight its important role in ongoing efforts to improve clinical care.}, issn = {1879-3479}, author = {Chi, Benjamin H and Vwalika, Bellington and Killam, William P and Wamalume, Chibesa and Giganti, Mark J and Mbewe, Reuben and Stringer, Elizabeth M and Chintu, Namwinga T and Putta, Nande B and Liu, Katherine C and Chibwesha, Carla J and Rouse, Dwight J and Stringer, Jeffrey S A} } @article {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 {1029, title = {A partnership approach for Electronic Data Capture in small-scale clinical trials.}, journal = {J Biomed Inform}, volume = {44 Suppl 1}, year = {2011}, month = {2011 Dec}, pages = {S103-8}, abstract = {

Amid researchers{\textquoteright} growing need for study data management, the CTSA-funded Institute for Translational Health Sciences developed an approach to combine technical and scientific resources with small-scale clinical trials researchers in order to make Electronic Data Capture more efficient. In a 2-year qualitative evaluation we found that the importance of ease of use and training materials outweighed number of features and functionality. EDC systems we evaluated were Catalyst Web Tools, OpenClinica and REDCap. We also found that two other systems, Caisis and LabKey, did not meet the specific user needs of the study group.

}, keywords = {Clinical Trials as Topic, Data Collection, Humans, Internet, Medical Informatics}, issn = {1532-0480}, doi = {10.1016/j.jbi.2011.05.008}, author = {Franklin, Joshua D and Guidry, Alicia and Brinkley, James F} } @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} } @article {606, title = {Use of an innovative, affordable, and open-source short message service-based tool to monitor malaria in remote areas of Uganda.}, journal = {The American journal of tropical medicine and hygiene}, volume = {85}, year = {2011}, month = {2011 Jul}, pages = {26-33}, abstract = {Abstract. Quality health management requires timely and accurate data, and paper-based reporting does not fill this role adequately. The introduction of malaria rapid diagnostic tests and the availability of wireless communications present an opportunity to open direct data transmission and feedback between peripheral health workers and central managers. In November 2009, the Uganda Ministry of Health deployed a short message service-based reporting system in two districts. At a set-up cost of $100/health facility, local technician support of $ 400 per month, and a cost of $0.53/week/clinic, the SMS reporting system was started at more than 140 clinics. Positivity rates for rapid diagnostic tests and artemisinin combination therapy stock outs were 48\% and 54\% in Kabale and 71\% and 54\% in Gulu, among other reports, at more than 85\% health facilities reporting weekly and without monetary incentives or additional supervision. The SMS-based reporting systems have potential to improve timeliness in reporting of specific, time-sensitive metrics at modest cost, while by-passing current bottlenecks in the flow of data. With the development of specific capacity to manage stock data at district level, the availability of timely data offers potential to address commodity distribution problems and reduce stock-outs.}, issn = {1476-1645}, author = {Asiimwe, Caroline and Gelvin, David and Lee, Evan and Ben Amor, Yanis and Quinto, Ebony and Katureebe, Charles and Sundaram, Lakshmi and Bell, David and Berg, Matt} } @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 {849, title = {The Yale cTAKES extensions for document classification: architecture and application.}, journal = {J Am Med Inform Assoc}, volume = {18}, year = {2011}, month = {2011 Sep-Oct}, pages = {614-20}, abstract = {

BACKGROUND: Open-source clinical natural-language-processing (NLP) systems have lowered the barrier to the development of effective clinical document classification systems. Clinical natural-language-processing systems annotate the syntax and semantics of clinical text; however, feature extraction and representation for document classification pose technical challenges.

METHODS: The authors developed extensions to the clinical Text Analysis and Knowledge Extraction System (cTAKES) that simplify feature extraction, experimentation with various feature representations, and the development of both rule and machine-learning based document classifiers. The authors describe and evaluate their system, the Yale cTAKES Extensions (YTEX), on the classification of radiology reports that contain findings suggestive of hepatic decompensation.

RESULTS AND DISCUSSION: The F(1)-Score of the system for the retrieval of abdominal radiology reports was 96\%, and was 79\%, 91\%, and 95\% for the presence of liver masses, ascites, and varices, respectively. The authors released YTEX as open source, available at http://code.google.com/p/ytex.

}, keywords = {Connecticut, Data Mining, Decision Support Systems, Clinical, electronic health records, Humans, Liver Failure, Natural Language Processing, Pattern Recognition, Automated, Radiology Information Systems}, issn = {1527-974X}, doi = {10.1136/amiajnl-2011-000093}, author = {Garla, Vijay and Lo Re, Vincent and Dorey-Stein, Zachariah and Kidwai, Farah and Scotch, Matthew and Womack, Julie and Justice, Amy and Brandt, Cynthia} } @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 {20226035, title = {CASE: a framework for computer supported outbreak detection.}, journal = {BMC medical informatics and decision making}, volume = {10}, year = {2010}, month = {2010}, pages = {14}, abstract = {BACKGROUND: In computer supported outbreak detection, a statistical method is applied to a collection of cases to detect any excess cases for a particular disease. Whether a detected aberration is a true outbreak is decided by a human expert. We present a technical framework designed and implemented at the Swedish Institute for Infectious Disease Control for computer supported outbreak detection, where a database of case reports for a large number of infectious diseases can be processed using one or more statistical methods selected by the user. RESULTS: Based on case information, such as diagnosis and date, different statistical algorithms for detecting outbreaks can be applied, both on the disease level and the subtype level. The parameter settings for the algorithms can be configured independently for different diagnoses using the provided graphical interface. Input generators and output parsers are also provided for all supported algorithms. If an outbreak signal is detected, an email notification is sent to the persons listed as receivers for that particular disease. CONCLUSIONS: The framework is available as open source software, licensed under GNU General Public License Version 3. By making the code open source, we wish to encourage others to contribute to the future development of computer supported outbreak detection systems, and in particular to the development of the CASE framework.}, author = {Cakici, Baki and Hebing, Kenneth and Gr{\"u}newald, Maria and Saretok, Paul and Hulth, Anette} } @article {1046, title = {Facilitating secondary use of medical data by using openEHR archetypes.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {1117-21}, abstract = {

Clinical trials are of high importance for medical progress. But even though more and more clinical data is available in electronic patient records (EPRs) and more and more electronic data capture (EDC) systems are used in trials, there is still a gap which makes EPR / EDC interoperability difficult and hampers secondary use of medical routine data. The openEHR architecture for Electronic Health Records is based on a two level modeling approach which makes use of {\textquoteright}archetypes{\textquoteright}. We want to analyze whether archetypes can help to bridge this gap by building an integrated EPR / EDC system based on openEHR archetypes. We used the {\textquoteright}openEHR Reference Framework and Application{\textquoteright} (Opereffa) and existing archetypes for medical data. Furthermore, we developed dedicated archetypes to document study meta data. We developed a first prototype implementation of an archetype based integrated EPR / EDC system. Next steps will be the evaluation of an extended prototype in a real clinical trial scenario. Opereffa was a good starting point for our work. OpenEHR archetypes proved useful for secondary use of health data.

}, keywords = {Clinical Trials as Topic, Feasibility Studies, Humans, Medical Record Linkage, Medical Records Systems, Computerized, Semantics, Systems Integration}, issn = {0926-9630}, author = {Kohl, Christian D and Garde, Sebastian and Knaup, Petra} } @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 {20646816, title = {Mandibular reconstruction with fibula free flap. Experience of virtual reconstruction using Osirix((R)), a free and open source software for medical imagery.}, journal = {Annales de chirurgie plastique et esthetique}, year = {2010}, month = {2010 Jun 18}, abstract = {The techniques of free tissue transfers are mainly used for mandibular reconstruction by specialized surgical teams. This type of reconstruction is mostly realized in matters of head and neck cancers affecting mandibular bone and requiring a wide surgical resection and interruption of the mandible. To decrease the duration of the operation, surgical procedure involves generally two teams, one devoted to cancer resection and the other one to raise the fibular flap and making the reconstruction. For a better preparation of this surgical procedure, we propose here the use of a medical imaging software enabling mandibular reconstructions in three dimensions using the CT-scan done during the initial disease-staging checkup. The software used is Osirix((R)), developed since 2004 by a team of radiologists from Geneva and UCLA, working on Apple((R)) computers and downloadable free of charge in its basic version. We report here our experience of this software in 17 patients, with a preoperative modelling in three dimensions of the mandible, of the segment of mandible to be removed. It also forecasts the numbers of fragments of fibula needed and the location of osteotomies.}, author = {Albert, S and Cristofari, J-P and Cox, A and Bensimon, J-L and Guedon, C and Barry, B} } @article {596, title = {OpenMEEG: opensource software for quasistatic bioelectromagnetics.}, journal = {Biomedical engineering online}, volume = {9}, year = {2010}, month = {2010}, pages = {45}, abstract = {Interpreting and controlling bioelectromagnetic phenomena require realistic physiological models and accurate numerical solvers. A semi-realistic model often used in practise is the piecewise constant conductivity model, for which only the interfaces have to be meshed. This simplified model makes it possible to use Boundary Element Methods. Unfortunately, most Boundary Element solutions are confronted with accuracy issues when the conductivity ratio between neighboring tissues is high, as for instance the scalp/skull conductivity ratio in electro-encephalography. To overcome this difficulty, we proposed a new method called the symmetric BEM, which is implemented in the OpenMEEG software. The aim of this paper is to present OpenMEEG, both from the theoretical and the practical point of view, and to compare its performances with other competing software packages.}, keywords = {Benchmarking, Computers, Electric Impedance, Electricity, Electroencephalography, Electromagnetic Phenomena, Licensure, Magnetics, Magnetoencephalography, Models, Theoretical, Quality Control, Software, Time Factors, Tomography}, issn = {1475-925X}, author = {Gramfort, Alexandre and Papadopoulo, Th{\'e}odore and Olivi, Emmanuel and Clerc, Maureen} } @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 {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 {19056288, title = {Dimensional error of selective laser sintering, three-dimensional printing and PolyJet models in the reproduction of mandibular anatomy.}, journal = {Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery}, volume = {37}, year = {2009}, month = {2009 Apr}, pages = {167-73}, abstract = {BACKGROUND: Selective laser sintering (SLS), three-dimensional printing (3DP) and PolyJet are rapid prototyping (RP) techniques to fabricate prototypes from virtual biomedical images. To be used in maxillofacial surgery, these models must accurately reproduce the craniofacial skeleton. PURPOSE: To analyze the capacity of SLS, 3DP and PolyJet models to reproduce mandibular anatomy and their dimensional error. MATERIAL: Dry mandible, helical CT images, SLS, 3DP and PolyJet prototypes, and digital electronic caliper. METHODS: Helical CT images were acquired from a dry mandible (criterion standard) and manipulated with the InVesalius software. Prototypes were produced using SLS, 3DP and PolyJet techniques. Thirteen linear measurements of each prototype were made and compared with the dry mandible measurements. RESULTS: The results showed a dimensional error of 1.79\%, 3.14\% and 2.14\% for SLS, 3DP and PolyJet models, respectively. The models satisfactorily reproduced anatomic details and the SLS and PolyJet prototypes showed greater dimensional precision and reproduced mandibular anatomy more accurately than the 3DP model. CONCLUSIONS: The SLS prototype had a greater dimensional accuracy than the PolyJet and 3DP models. The PolyJet technique reproduced anatomic details of the mandible more accurately.}, author = {Ibrahim, Danilo and Broilo, Tiago Leonardo and Heitz, Claiton and Gerhardt de Oliveira, Mar{\'\i}lia and de Oliveira, Helena Willhelm and Nobre, Stella Maris Wanderlei and Dos Santos Filho, Jos{\'e} Henrique Gomes and Silva, Daniela Nascimento} } @conference {1087, title = {Open Source: A Lever for Enhancing Opportunities of Healthcare Information Systems - An Italian Case Study}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001828700280037}, author = {Emanuele Baj and Paolo Locatelli and Stefano Gatti and Nicola Restifo and Gianni Origgi and Silvia Bragagia} } @conference {903, title = {PESCA: Developing an open source platform to bring eHealth to latin america and the caribbean}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe, OSEHC 2009 In Conjunction with BIOSTEC 2009 and the EFMI LIFOSS WG}, year = {2009}, abstract = {Nowadays the society needs to communicate and the technologies are revolutionizing the information systems, especially for the health; where an effective use of the technologies is used to favor the needs of the persons. These technologies can contribute to the development of the local economies. Open source software (OSS) can be an useful strategy to bring information and communication technologies to developing countries. However, specially in Latin America and the Caribbean, there are some barriers in adopting OSS for health: the need for open standards, heterogeneous OSS developed without normalization and metrics, English predominance as top OSS language, lack of initiatives to evaluate existing health OSS and needs for quality control and functional validation. The Open Source Platform for eHealth (PESCA) has been designed as a set of interoperable modules that can solve either: simple problems on health management and communication in primary care or complex problems in healthcare systems, including telehealth communications between heterogeneous institutions.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-67650527704\&partnerID=40\&md5=cb5a91f3ccf525ed19857b1e3354a61d}, author = {Orcero, D.S.a}, editor = {L{\'o}pez, D.L.b} } @article {19321384, title = {The state and profile of open source software projects in health and medical informatics.}, journal = {International journal of medical informatics}, volume = {78}, year = {2009}, month = {2009 Jul}, pages = {457-72}, abstract = {PURPOSE: Little has been published about the application profiles and development patterns of open source software (OSS) in health and medical informatics. This study explores these issues with an analysis of health and medical informatics related OSS projects on SourceForge, a large repository of open source projects. METHODOLOGY: A search was conducted on the SourceForge website during the period from May 1 to 15, 2007, to identify health and medical informatics OSS projects. This search resulted in a sample of 174 projects. A Java-based parser was written to extract data for several of the key variables of each project. Several visually descriptive statistics were generated to analyze the profiles of the OSS projects. RESULTS: Many of the projects have sponsors, implying a growing interest in OSS among organizations. Sponsorship, we discovered, has a significant impact on project success metrics. Nearly two-thirds of the projects have a restrictive license type. Restrictive licensing may indicate tighter control over the development process. Our sample includes a wide range of projects that are at various stages of development (status). Projects targeted towards the advanced end user are primarily focused on bio-informatics, data formats, database and medical science applications. CONCLUSION: We conclude that there exists an active and thriving OSS development community that is focusing on health and medical informatics. A wide range of OSS applications are in development, from bio-informatics to hospital information systems. A profile of OSS in health and medical informatics emerges that is distinct and unique to the health care field. Future research can focus on OSS acceptance and diffusion and impact on cost, efficiency and quality of health care.}, author = {Janamanchi, Balaji and Katsamakas, Evangelos and Raghupathi, Wullianallur and Gao, Wei} } @article {18999296, title = {caBIG compatibility review system: software to support the evaluation of applications using defined interoperability criteria.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2008}, month = {2008}, pages = {197-201}, abstract = {The caBIG Compatibility Review System (CRS) is a web-based application to support compatibility reviews, which certify that software applications that pass the review meet a specific set of criteria that allow them to interoperate. The CRS contains workflows that support both semantic and syntactic reviews, which are performed by the caBIG Vocabularies and Common Data Elements (VCDE) and Architecture workspaces, respectively. The CRS increases the efficiency of compatibility reviews by reducing administrative overhead and it improves uniformity by ensuring that each review is conducted according to a standard process. The CRS provides metrics that allow the review team to evaluate the level of data element reuse in an application, a first step towards quantifying the extent of harmonization between applications. Finally, functionality is being added that will provide automated validation of checklist criteria, which will further simplify the review process.}, author = {Freimuth, Robert R and Schauer, Michael W and Lodha, Preeti and Govindrao, Poornima and Nagarajan, Rakesh and Chute, Christopher G} } @article {803, title = {Designing Tracking Software for Image-Guided Surgery Applications: IGSTK Experience.}, journal = {Int J Comput Assist Radiol Surg}, volume = {3}, year = {2008}, month = {2008 Nov 1}, pages = {395-403}, abstract = {OBJECTIVE: Many image-guided surgery applications require tracking devices as part of their core functionality. The Image-Guided Surgery Toolkit (IGSTK) was designed and developed to interface tracking devices with software applications incorporating medical images. METHODS: IGSTK was designed as an open source C++ library that provides the basic components needed for fast prototyping and development of image-guided surgery applications. This library follows a component-based architecture with several components designed for specific sets of image-guided surgery functions. At the core of the toolkit is the tracker component that handles communication between a control computer and navigation device to gather pose measurements of surgical instruments present in the surgical scene. The representations of the tracked instruments are superimposed on anatomical images to provide visual feedback to the clinician during surgical procedures. RESULTS: The initial version of the IGSTK toolkit has been released in the public domain and several trackers are supported. The toolkit and related information are available at www.igstk.org. CONCLUSION: With the increased popularity of minimally invasive procedures in health care, several tracking devices have been developed for medical applications. Designing and implementing high-quality and safe software to handle these different types of trackers in a common framework is a challenging task. It requires establishing key software design principles that emphasize abstraction, extensibility, reusability, fault-tolerance, and portability. IGSTK is an open source library that satisfies these needs for the image-guided surgery community.}, issn = {1861-6429}, doi = {10.1007/s11548-008-0243-4}, author = {Enquobahrie, Andinet and Gobbi, David and Turek, Matt and Cheng, Patrick and Yaniv, Ziv and Lindseth, Frank and Cleary, Kevin} } @article {19068935, title = {Implementation of the Veterans Health Administration VistA clinical information system around the world.}, journal = {Healthcare quarterly (Toronto, Ont.)}, volume = {11}, year = {2008}, month = {2008}, pages = {83-9}, abstract = {The success story of the Veterans Health Administration (VHA) within the US Department of Veterans Affairs has been well documented and is generally well known. What is generally not known is that the VHA{\textquoteright}s clinical information system, known as VistA, and the computerized patient record system clinical user interface front end have been successfully transported and implemented to a number of non-VHA healthcare organizations across the United States. Moreover, VistA software modules have been installed, or are being considered for installation, in healthcare institutions around the world in countries such as Mexico, Finland, Jordan, Germany, Nigeria, Egypt, Malaysia, India, Brazil, Pakistan and Samoa.}, author = {Protti, Denis and Groen, Peter} } @article {18366760, title = {OpenMS - an open-source software framework for mass spectrometry.}, journal = {BMC bioinformatics}, volume = {9}, year = {2008}, month = {2008}, pages = {163}, abstract = {BACKGROUND: Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever increasing amounts of data. Consequently, analysis of the data is currently often the bottleneck for experimental studies. Although software tools for many data analysis tasks are available today, they are often hard to combine with each other or not flexible enough to allow for rapid prototyping of a new analysis workflow. RESULTS: We present OpenMS, a software framework for rapid application development in mass spectrometry. OpenMS has been designed to be portable, easy-to-use and robust while offering a rich functionality ranging from basic data structures to sophisticated algorithms for data analysis. This has already been demonstrated in several studies. CONCLUSION: OpenMS is available under the Lesser GNU Public License (LGPL) from the project website at http://www.openms.de.}, url = {http://www.biomedcentral.com/1471-2105/9/163}, author = {Sturm, Marc and Bertsch, Andreas and Gr{\"o}pl, Clemens and Hildebrandt, Andreas and Hussong, Rene and Lange, Eva and Pfeifer, Nico and Schulz-Trieglaff, Ole and Zerck, Alexandra and Reinert, Knut and Kohlbacher, Oliver} } @article {802, title = {The image-guided surgery toolkit IGSTK: an open source C++ software toolkit.}, journal = {J Digit Imaging}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {21-33}, abstract = {This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers{\textquoteright} mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences.}, keywords = {Computer Systems, Data Display, Database Management Systems, Humans, Information Dissemination, Information Storage and Retrieval, Safety, Software, Software Design, Software Validation, Surgery, Computer-Assisted, Systems Integration, User-Computer Interface}, issn = {0897-1889}, doi = {10.1007/s10278-007-9054-3}, author = {Enquobahrie, Andinet and Cheng, Patrick and Gary, Kevin and Ibanez, Luis and Gobbi, David and Lindseth, Frank and Yaniv, Ziv and Aylward, Stephen and Jomier, Julien and Cleary, Kevin} } @article {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 {18183912, title = {PyEPL: a cross-platform experiment-programming library.}, journal = {Behavior research methods}, volume = {39}, year = {2007}, month = {2007 Nov}, pages = {950-8}, abstract = {PyEPL (the Python Experiment-Programming Library) is a Python library which allows cross-platform and object-oriented coding of behavioral experiments. It provides functions for displaying text and images onscreen, as well as playing and recording sound, and is capable of rendering 3-D virtual environments forspatial-navigation tasks. It is currently tested for Mac OS X and Linux. It interfaces with Activewire USB cards (on Mac OS X) and the parallel port (on Linux) for synchronization of experimental events with physiological recordings. In this article, we first present two sample programs which illustrate core PyEPL features. The examples demonstrate visual stimulus presentation, keyboard input, and simulation and exploration of a simple 3-D environment. We then describe the components and strategies used in implementing PyEPL.}, author = {Geller, Aaron S and Schlefer, Ian K and Sederberg, Per B and Jacobs, Joshua and Kahana, Michael J} } @article {1040, title = {The RAFT network: 5 years of distance continuing medical education and tele-consultations over the Internet in French-speaking Africa.}, journal = {Int J Med Inform}, volume = {76}, year = {2007}, month = {2007 May-Jun}, pages = {351-6}, abstract = {

Continuing education of healthcare professionals is a key element for the quality and efficiency of a health system. In developing countries, this activity is usually limited to capitals, and delocalized professionals do not have access to such opportunities, or to didactic material adapted to their needs. This limits the interest of such professionals to remain active in the periphery, where they are most needed to implement effective strategies for prevention and first-line healthcare. Telemedicine tools enable the communication and sharing of medical information in electronic form, and thus facilitate access to remote expertise. A physician located far from a reference center can consult its colleagues remotely in order to resolve a difficult case, follow a continuous education course over the Internet, or access medical information from digital libraries or knowledge bases. These same tools can also be used to facilitate exchanges between centers of medical expertise: health institutions of a same country as well as across borders. Since 2000, the Geneva University Hospitals have been involved in coordinating the development of a network for eHealth in Africa (the RAFT, R{\'e}seau en Afrique Francophone pour la T{\'e}l{\'e}m{\'e}decine), first in Mali, and now extending to 10 French-speaking African countries. The core activity of the RAFT is the webcasting of interactive courses. These sessions put the emphasis on knowledge sharing across care professionals, usually in the form of presentations and dialogs between experts in different countries. The technology used for the webcasting works with a slow (25 kbits/s) internet connection. Other activities of the RAFT network include visioconferences, teleconsultations based on the iPath system, collaborative knowledge bases development, support for medical laboratories quality control, and the evaluation of the use of telemedicine in rural areas (via satellite connections) in the context of multisectorial development. Finally, a strong emphasis is put on the development of capacities for the creation, maintenance, and publication of quality medical didactic contents. Specific courses are organized for the national coordinators of the network to develop these competencies, with the help of the Health-On-the-Net Foundation. The richness of the plurality of knowledge and know-how must be steered towards emulation and sharing, respectful of each partner{\textquoteright}s identity and culture. Collaborations with UNESCO and WHO have been initiated to address these challenges.

}, keywords = {Africa, Computer Simulation, Computer-Assisted Instruction, Curriculum, Education, Distance, Education, Medical, Continuing, Educational Technology, Humans, Internationality, Language, Referral and Consultation, Remote Consultation}, issn = {1386-5056}, doi = {10.1016/j.ijmedinf.2007.01.012}, author = {Geissbuhler, Antoine and Bagayoko, Cheick Oumar and Ly, Ousmane} } @article {17375973, title = {RT_Image: an open-source tool for investigating PET in radiation oncology.}, journal = {Technology in cancer research \& treatment}, volume = {6}, year = {2007}, month = {2007 Apr}, pages = {111-21}, abstract = {Positron emission tomography (PET) has emerged as a valuable imaging modality for the diagnosis and staging of cancer. However, despite evidence that PET may be useful for defining target volumes for radiation therapy, no standardized methodology for accomplishing this task exists. To facilitate the investigation of the utility of PET imaging in radiotherapy treatment planning and accelerate its integration into clinical radiation oncology, we have developed software for exploratory analysis and segmentation of functional imaging datasets. The application, RT_Image, allows display of multiple imaging datasets and associated three-dimensional regions-of-interest (ROIs) at arbitrary view angles and fields of view. It also includes semi-automated image segmentation tools for defining metabolically active tumor volumes that may aid creation of target volumes for treatment planning. RT_Image is DICOM compliant, permitting the transfer of imaging data and DICOM-RT structure sets between the application and treatment planning software. RT_Image has been used by radiation oncologists, nuclear medicine physicians, and radiation physicists to analyze over 200 PET datasets. Novel segmentation techniques have been implemented within this programming framework for therapy planning and for evaluation of molecular imaging-derived parameters as prognostic indicators. RT_Image represents a freely-available software base on which further investigations of the utlity of PET and molecular imaging in radiation oncology may be built. The development of tools such as this is critical in order to realize the potential of molecular imaging-guided radiation therapy.}, author = {Graves, Edward E and Quon, Andrew and Loo, Billy W} } @conference {SOFA07, title = {SOFA - an Open Source Framework for Medical Simulation}, booktitle = {Medicine Meets Virtual Reality (MMVR{\textquoteright}15)}, year = {2007}, month = {February}, address = {Long Beach, USA}, url = {http://www.sofa-framework.org/docs/SOFA_MMVR07.pdf}, author = {Allard, J{\'e}r{\'e}mie and Cotin, St{\'e}phane and Faure, Fran{\c c}ois and Bensoussan, Pierre-Jean and Poyer, Fran{\c c}ois and Duriez, Christian and Delingette, Herv{\'e} and Grisoni, Laurent} } @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 {1041, title = {Static telepathology in cancer institute of Tehran university: report of the first academic experience in Iran.}, journal = {Diagn Pathol}, volume = {1}, year = {2006}, month = {2006}, pages = {33}, abstract = {

Telepathology is the practice of pathology, which allows quick and timely access to an expert opinion at a distance. We analyzed our new experience in cancer Institute of Tehran University of Medical Sciences with the iPath telepathology server of Basel University. One hundred sixty one cases in a period of 32 months were consulted. These cases received for second evaluation but the definite diagnosis could not be made in this centre. The number of images per case ranged from 3 to 32 (mean: 8). Except one case all cases were evaluated by consultants. Definite final diagnosis was achieved in 88/160 (54.7\%). Recommendations for further evaluation were offered in 42/160 cases (26\%). Major discrepancies were encountered in 30/160 cases (19\%). Thirty-nine of the cases (24.3\%) were reported within 1 day. The rate of achieving final diagnosis was higher in histological group rather than cytological ones. Increase in number of H\&E images had no significant effect on achieving a definite final diagnosis. The rate of achieving final diagnosis in this study is much lower than other similar studies, which could be due to inappropriate sampling images, a potential cause of misdiagnosis in static telepathology. The other possible reason is that all of the cases in this study were problematic cases that a definite diagnosis could not be made for them even in primary consultation. The mean time for achieving a final diagnosis was also more than other studies, which could be for the reasons mentioned above.

}, issn = {1746-1596}, doi = {10.1186/1746-1596-1-33}, author = {Abdirad, Afshin and Sarrafpour, Babak and Ghaderi-Sohi, Siavash} } @article {16545965, title = {User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability.}, journal = {NeuroImage}, volume = {31}, year = {2006}, month = {2006 Jul 1}, pages = {1116-28}, abstract = {Active contour segmentation and its robust implementation using level set methods are well-established theoretical approaches that have been studied thoroughly in the image analysis literature. Despite the existence of these powerful segmentation methods, the needs of clinical research continue to be fulfilled, to a large extent, using slice-by-slice manual tracing. To bridge the gap between methodological advances and clinical routine, we developed an open source application called ITK-SNAP, which is intended to make level set segmentation easily accessible to a wide range of users, including those with little or no mathematical expertise. This paper describes the methods and software engineering philosophy behind this new tool and provides the results of validation experiments performed in the context of an ongoing child autism neuroimaging study. The validation establishes SNAP intrarater and interrater reliability and overlap error statistics for the caudate nucleus and finds that SNAP is a highly reliable and efficient alternative to manual tracing. Analogous results for lateral ventricle segmentation are provided.}, author = {Yushkevich, Paul A and Piven, Joseph and Hazlett, Heather Cody and Smith, Rachel Gimpel and Ho, Sean and Gee, James C and Gerig, Guido} } @article {781, title = {ParaView : An End-User Tool for Large Data Visualization}, journal = {Energy}, volume = {836}, year = {2005}, pages = {717{\textendash}732}, url = {http://scholar.google.com/scholar?hl=en\&btnG=Search\&q=intitle:ParaView:+An+end-user+tool+for+large+data+visualization$\#$0}, author = {Ahrens, James and Geveci, Berk and Law, Charles}, editor = {Hansen, C R and Johnson, C DEditors} } @article {850, title = {SQL Clinic: the open-source alternative for electronic medical records.}, journal = {Psychiatr Serv}, volume = {56}, year = {2005}, month = {2005 Mar}, pages = {269-71}, keywords = {Humans, Medical Records Systems, Computerized, Psychiatry, Software}, issn = {1075-2730}, doi = {10.1176/appi.ps.56.3.269}, author = {Good, Thomas and DiTommaso, Marianne} } @article {12807803, title = {Technical description of RODS: a real-time public health surveillance system.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {10}, year = {2003}, month = {2003 Sep-Oct}, pages = {399-408}, abstract = {This report describes the design and implementation of the Real-time Outbreak and Disease Surveillance (RODS) system, a computer-based public health surveillance system for early detection of disease outbreaks. Hospitals send RODS data from clinical encounters over virtual private networks and leased lines using the Health Level 7 (HL7) message protocol. The data are sent in real time. RODS automatically classifies the registration chief complaint from the visit into one of seven syndrome categories using Bayesian classifiers. It stores the data in a relational database, aggregates the data for analysis using data warehousing techniques, applies univariate and multivariate statistical detection algorithms to the data, and alerts users of when the algorithms identify anomalous patterns in the syndrome counts. RODS also has a Web-based user interface that supports temporal and spatial analyses. RODS processes sales of over-the-counter health care products in a similar manner but receives such data in batch mode on a daily basis. RODS was used during the 2002 Winter Olympics and currently operates in two states-Pennsylvania and Utah. It has been and continues to be a resource for implementing, evaluating, and applying new methods of public health surveillance.}, author = {Tsui, Fu-Chiang and Espino, Jeremy U and Dato, Virginia M and Gesteland, Per H and Hutman, Judith and Wagner, Michael M} }