@article {1304, title = {iBEX: Modular Open-Source Software for Digital Radiography.}, journal = {J Digit Imaging}, volume = {33}, year = {2020}, month = {2020 06}, pages = {708-721}, abstract = {

A device-independent software package, named iBEX, is developed to accelerate the research and development efforts for X-ray imaging setups such as chest radiography, linear and multidirectional tomography, and dental and skeletal radiography. Its extension mechanism makes the software adaptable for a wide range of digital X-ray imaging hardware combinations and provides capabilities for researchers to develop image processing plug-ins. Independent of the X-ray sensor technology, iBEX could integrate with heterogeneous communication channels of digital detectors. iBEX is a freeware option for preclinical and early clinical testing of radiography devices. It provides tools to calibrate the device, integrate to health information infrastructure, acquire image, store studies on local storage, and send them to Picture Archiving and Communication System (PACS). iBEX is a unique open-source project bringing X-ray imaging devices{\textquoteright} software into the scope of the open-source community to reduce the X-ray scanners{\textquoteright} research effort, potentially increase the image quality, and cut down the production and testing costs of radiography devices.

}, keywords = {Humans, Image Processing, Computer-Assisted, Radiographic Image Enhancement, Radiology Information Systems, Software, Tomography, X-Ray Computed}, issn = {1618-727X}, doi = {10.1007/s10278-019-00304-1}, author = {Brusan, Altay and Durmaz, F Ayta{\c c} and Yaman, Alper and {\"O}zt{\"u}rk, Cengizhan} } @article {1220, title = {CODE STROKE ALERT-Concept and Development of a Novel Open-Source Platform to Streamline Acute Stroke Management.}, journal = {Front Neurol}, volume = {10}, year = {2019}, month = {2019}, pages = {725}, abstract = {

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

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

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

}, issn = {1879-8365}, doi = {10.3233/SHTI190175}, author = {Baskaya, Mert and Yuksel, Mustafa and Erturkmen, Gokce Banu Laleci and Cunningham, Miriam and Cunningham, Paul} } @article {1293, title = {Designing mHealth for maternity services in primary health facilities in a low-income setting - lessons from a partially successful implementation.}, journal = {BMC Med Inform Decis Mak}, volume = {18}, year = {2018}, month = {2018 11 12}, pages = {96}, abstract = {

BACKGROUND: Increasing mobile phone ownership, functionality and access to mobile-broad band internet services has triggered growing interest to harness the potential of mobile phone technology to improve health services in low-income settings. The present project aimed at designing an mHealth system that assists midlevel health workers to provide better maternal health care services by automating the data collection and decision-making process. This paper describes the development process and technical aspects of the system considered critical for possible replication. It also highlights key lessons learned and challenges during implementation.

METHODS: The mHealth system had front-end and back-end components. The front-end component was implemented as a mobile based application while the back-end component was implemented as a web-based application that ran on a central server for data aggregation and report generation. The current mHealth system had four applications; namely, data collection/reporting, electronic health records, decision support, and provider education along the continuum of care including antenatal, delivery and postnatal care. The system was pilot-tested and deployed in selected health centers of North Shewa Zone, Amhara region, Ethiopia.

RESULTS: The system was used in 5 health centers since Jan 2014 and later expanded to additional 10 health centers in June 2016 with a total of 5927 electronic forms submitted to the back-end system. The submissions through the mHealth system were slightly lower compared to the actual number of clients who visited those facilities as verified by record reviews. Regarding timeliness, only 11\% of the electronic forms were submitted on the day of the client visit, while an additional 17\% of the forms were submitted within 10~days of clients{\textquoteright} visit. On average forms were submitted 39~days after the day of clients visit with a range of 0 to 150~days.

CONCLUSIONS: In conclusion, the study illustrated that an effective mHealth intervention can be developed using an open source platform and local resources. The system impacted key health outcomes and contributed to timely and complete data submission. Lessons learned through the process including success factors and challenges are discussed.

}, keywords = {Cell Phone, Delivery of Health Care, electronic health records, Ethiopia, Female, Health Facilities, Humans, Maternal Health Services, Mobile Applications, Poverty, Pregnancy, Telemedicine}, issn = {1472-6947}, doi = {10.1186/s12911-018-0704-9}, author = {Shiferaw, Solomon and Workneh, Andualem and Yirgu, Robel and Dinant, Geert-Jan and Spigt, Mark} } @article {1282, title = {Effect of glycosylated hemoglobin on response to ranibizumab therapy in diabetic macular edema: real-world outcomes in 312 patients.}, journal = {Can J Ophthalmol}, volume = {53}, year = {2018}, month = {2018 08}, pages = {415-419}, abstract = {

OBJECTIVE: To investigate the effect of serum glycosylated hemoglobin (HbA1c) on the outcomes of ranibizumab therapy for diabetic macular edema (DME).

DESIGN: Retrospective cohort study.

PARTICIPANTS: Patients receiving ranibizumab injections for centre-involving DME in a National Health Service setting.

METHODS: The Moorfields OpenEyes database was used to study eyes with DME treated with ranibizumab from October 2013 to November 2015 at the Moorfields City Road, Ealing, Northwick Park, and St George{\textquoteright}s Hospital sites. Only eyes receiving a minimum of 3 injections and completing 12 months of follow-up were included. If both eyes received treatment, the first eye treated was analyzed. When both eyes received initial treatment simultaneously, random number tables were used to select the eye for analysis. HbA1c was tested at the initiation of ranibizumab treatment. Multivariate regression analysis was used to identify relationships between HbA1c and the outcome measures.

OUTCOMES: The primary outcome was change in visual acuity (VA) Early Treatment of Diabetic Retinopathy study (ETDRS) letters. The secondary outcomes were change in central subfield thickness (CSFT) and macular volume (MV), as well as number of injections in year 1.

RESULTS: Three hundred and twelve eyes of 312 patients were included in the analysis. HbA1c was not related to change in VA (p = 0.577), change in CSFT (p = 0.099), change in MV (p = 0.082), or number of injections in year 1 (p = 0.859).

CONCLUSIONS: HbA1c is not related to functional or anatomical outcomes at 1 year in DME treated with ranibizumab.

}, keywords = {Aged, Angiogenesis Inhibitors, Biomarkers, Diabetic Retinopathy, Female, Follow-Up Studies, Glycated Hemoglobin A, Humans, Intravitreal Injections, Macula Lutea, Macular Edema, Male, Middle Aged, Ranibizumab, Retrospective Studies, Tomography, Optical Coherence, Treatment Outcome, Vascular Endothelial Growth Factor A, Visual Acuity}, issn = {1715-3360}, doi = {10.1016/j.jcjo.2017.10.008}, author = {Shalchi, Zaid and Okada, Mali and Bruynseels, Alice and Palethorpe, David and Yusuf, Ammar and Hussain, Rohan and Herrspiegel, Christina and Scazzarriello, Antonio and Habib, Abubakar and Amin, Razia and Rajendram, Ranjan} } @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 {1276, title = {A Mobile-Based Community Health Management Information System for Community Health Workers and Their Supervisors in 2 Districts of Zambia.}, journal = {Glob Health Sci Pract}, volume = {5}, year = {2017}, month = {2017 09 27}, pages = {486-494}, abstract = {

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

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

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

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

}, keywords = {Community Health Services, Community Health Workers, Delivery of Health Care, Health information systems, Humans, Mobile Applications, Referral and Consultation, Zambia}, issn = {2169-575X}, doi = {10.9745/GHSP-D-16-00275}, author = {Biemba, Godfrey and Chiluba, Boniface and Yeboah-Antwi, Kojo and Silavwe, Vichaels and Lunze, Karsten and Mwale, Rodgers K and Russpatrick, Scott and Hamer, Davidson H} } @article {1263, title = {The State of Open Source Electronic Health Record Projects: A Software Anthropology Study.}, journal = {JMIR Med Inform}, volume = {5}, year = {2017}, month = {2017 Feb 24}, pages = {e6}, abstract = {

BACKGROUND: Electronic health records (EHR) are a key tool in managing and storing patients{\textquoteright} information. Currently, there are over 50 open source EHR systems available. Functionality and usability are important factors for determining the success of any system. These factors are often a direct reflection of the domain knowledge and developers{\textquoteright} motivations. However, few published studies have focused on the characteristics of free and open source software (F/OSS) EHR systems and none to date have discussed the motivation, knowledge background, and demographic characteristics of the developers involved in open source EHR projects.

OBJECTIVE: This study analyzed the characteristics of prevailing F/OSS EHR systems and aimed to provide an understanding of the motivation, knowledge background, and characteristics of the developers.

METHODS: This study identified F/OSS EHR projects on SourceForge and other websites from May to July 2014. Projects were classified and characterized by license type, downloads, programming languages, spoken languages, project age, development status, supporting materials, top downloads by country, and whether they were "certified" EHRs. Health care F/OSS developers were also surveyed using an online survey.

RESULTS: At the time of the assessment, we uncovered 54 open source EHR projects, but only four of them had been successfully certified under the Office of the National Coordinator for Health Information Technology (ONC Health IT) Certification Program. In the majority of cases, the open source EHR software was downloaded by users in the United States (64.07\%, 148,666/232,034), underscoring that there is a significant interest in EHR open source applications in the United States. A survey of EHR open source developers was conducted and a total of 103 developers responded to the online questionnaire. The majority of EHR F/OSS developers (65.3\%, 66/101) are participating in F/OSS projects as part of a paid activity and only 25.7\% (26/101) of EHR F/OSS developers are, or have been, health care providers in their careers. In addition, 45\% (45/99) of developers do not work in the health care field.

CONCLUSION: The research presented in this study highlights some challenges that may be hindering the future of health care F/OSS. A minority of developers have been health care professionals, and only 55\% (54/99) work in the health care field. This undoubtedly limits the ability of functional design of F/OSS EHR systems from being a competitive advantage over prevailing commercial EHR systems. Open source software seems to be a significant interest to many; however, given that only four F/OSS EHR systems are ONC-certified, this interest is unlikely to yield significant adoption of these systems in the United States. Although the Health Information Technology for Economic and Clinical Health (HITECH) act was responsible for a substantial infusion of capital into the EHR marketplace, the lack of a corporate entity in most F/OSS EHR projects translates to a marginal capacity to market the respective F/OSS system and to navigate certification. This likely has further disadvantaged F/OSS EHR adoption in the United States.

}, issn = {2291-9694}, doi = {10.2196/medinform.5783}, author = {Alsaffar, Mona and Yellowlees, Peter and Odor, Alberto and Hogarth, Michael} } @article {1176, title = {Three-dimensional image reconstruction with free open-source {OsiriX} software in video-assisted thoracoscopic lobectomy and segmentectomy}, journal = {International Journal of Surgery (London, England)}, year = {2017}, abstract = {OBJECTIVE: The aim of this retrospective study was to evaluate the practice and the feasibility of Osirix, a free and open-source medical imaging software, in performing accurate video-assisted thoracoscopic lobectomy and segmentectomy. METHODS: From July 2014 to April 2016, 63 patients received anatomical video-assisted thoracoscopic surgery (VATS), either lobectomy or segmentectomy, in our department. Three-dimensional (3D) reconstruction images of 61 (96.8\%) patients were preoperatively obtained with contrast-enhanced computed tomography (CT). Preoperative resection simulations were accomplished with patient-individual reconstructed 3D images. For lobectomy, pulmonary lobar veins, arteries and bronchi were identified meticulously by carefully reviewing the 3D images on the display. For segmentectomy, the intrasegmental veins in the affected segment for division and the intersegmental veins to be preserved were identified on the 3D images. Patient preoperative characteristics, surgical outcomes and postoperative data were reviewed from a prospective database. RESULTS: The study cohort of 63 patients included 33 (52.4\%) men and 30 (47.6\%) women, of whom 46 (73.0\%) underwent VATS lobectomy and 17 (37.0\%) underwent VATS segmentectomy. There was 1 conversion from VATS lobectomy to open thoracotomy because of fibrocalcified lymph nodes. A VATS lobectomy was performed in 1 case after completing the segmentectomy because invasive adenocarcinoma was detected by intraoperative frozen-section analysis. There were no 30-day or 90-day operative mortalities CONCLUSIONS: The free, simple, and user-friendly software program Osirix can provide a 3D anatomic structure of pulmonary vessels and a clear vision into the space between the lesion and adjacent tissues, which allows surgeons to make preoperative simulations and improve the accuracy and safety of actual surgery.}, keywords = {Lobectomy, Segmentectomy, Three-dimensional reconstruction technique, Video-assisted thoracoscopic surgery}, issn = {1743-9159}, doi = {10.1016/j.ijsu.2017.01.079}, author = {Yao, Fei and Wang, Jian and Yao, Ju and Hang, Fangrong and Lei, Xu and Cao, Yongke} } @inbook {1119, title = {BiobankCloud: A Platform for the Secure Storage, Sharing, and Processing of Large Biomedical Data Sets}, booktitle = {Biomedical Data Management and Graph Online Querying: VLDB 2015 Workshops, Big-O(Q) and DMAH, Waikoloa, HI, USA, August 31 {\textendash} September 4, 2015, Revised Selected Papers}, year = {2016}, pages = {89{\textendash}105}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {Biobanks store and catalog human biological material that is increasingly being digitized using next-generation sequencing (NGS). There is, however, a computational bottleneck, as existing software systems are not scalable and secure enough to store and process the incoming wave of genomic data from NGS machines. In the BiobankCloud project, we are building a Hadoop-based platform for the secure storage, sharing, and parallel processing of genomic data. We extended Hadoop to include support for multi-tenant studies, reduced storage requirements with erasure coding, and added support for extensible and consistent metadata. On top of Hadoop, we built a scalable scientific workflow engine featuring a proper workflow definition language focusing on simple integration and chaining of existing tools, adaptive scheduling on Apache Yarn, and support for iterative dataflows. Our platform also supports the secure sharing of data across different, distributed Hadoop clusters. The software is easily installed and comes with a user-friendly web interface for running, managing, and accessing data sets behind a secure 2-factor authentication. Initial tests have shown that the engine scales well to dozens of nodes. The entire system is open-source and includes pre-defined workflows for popular tasks in biomedical data analysis, such as variant identification, differential transcriptome analysis using RNA-Seq, and analysis of miRNA-Seq and ChIP-Seq data.}, isbn = {978-3-319-41576-5}, doi = {10.1007/978-3-319-41576-5_7}, url = {http://dx.doi.org/10.1007/978-3-319-41576-5_7}, author = {Bessani, Alysson and Brandt, J{\"o}rgen and Bux, Marc and Cogo, Vinicius and Dimitrova, Lora and Dowling, Jim and Gholami, Ali and Hakimzadeh, Kamal and Hummel, Micheal and Ismail, Mahmoud and Laure, Erwin and Leser, Ulf and Litton, Jan-Eric and Martinez, Roxanna and Niazi, Salman and Reichel, Jane and Zimmermann, Karin}, editor = {Wang, Fusheng and Luo, Gang and Weng, Chunhua and Khan, Arijit and Mitra, Prasenjit and Yu, Cong} } @article {1137, title = {How open science helps researchers succeed.}, journal = {Elife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

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

}, issn = {2050-084X}, doi = {10.7554/eLife.16800}, author = {McKiernan, Erin C and Bourne, Philip E and Brown, C Titus and Buck, Stuart and Kenall, Amye and Lin, Jennifer and McDougall, Damon and Nosek, Brian A and Ram, Karthik and Soderberg, Courtney K and Spies, Jeffrey R and Thaney, Kaitlin and Updegrove, Andrew and Woo, Kara H and Yarkoni, Tal} } @article {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 {1067, title = {Open-Source Radiation Exposure Extraction Engine (RE3) with Patient-Specific Outlier Detection.}, journal = {J Digit Imaging}, year = {2015}, month = {2015 Dec 7}, abstract = {

We present an open-source, picture archiving and communication system (PACS)-integrated radiation exposure extraction engine (RE3) that provides study-, series-, and slice-specific data for automated monitoring of computed tomography (CT) radiation exposure. RE3 was built using open-source components and seamlessly integrates with the PACS. RE3 calculations of dose length product (DLP) from the Digital imaging and communications in medicine (DICOM) headers showed high agreement (R (2) = 0.99) with the vendor dose pages. For study-specific outlier detection, RE3 constructs robust, automatically updating multivariable regression models to predict DLP in the context of patient gender and age, scan length, water-equivalent diameter (D w), and scanned body volume (SBV). As proof of concept, the model was trained on 811 CT chest, abdomen + pelvis (CAP) exams and 29 outliers were detected. The continuous variables used in the outlier detection model were scan length (R (2) = 0.45), D w (R (2) = 0.70), SBV (R (2) = 0.80), and age (R (2) = 0.01). The categorical variables were gender (male average 1182.7 {\textpm} 26.3 and female 1047.1 {\textpm} 26.9~mGy~cm) and pediatric status (pediatric average 710.7 {\textpm} 73.6~mGy~cm and adult 1134.5 {\textpm} 19.3~mGy~cm).

}, issn = {1618-727X}, doi = {10.1007/s10278-015-9852-y}, author = {Weisenthal, Samuel J and Folio, Les and Kovacs, William and Seff, Ari and Derderian, Vana and Summers, Ronald M and Yao, Jianhua} } @article {1031, title = {Evaluation of software maintain ability with open EHR - a comparison of architectures.}, journal = {Int J Med Inform}, volume = {83}, year = {2014}, month = {2014 Nov}, pages = {849-59}, abstract = {

PURPOSE: To assess whether it is easier to maintain a clinical information system developed using open EHR model driven development versus mainstream methods.

METHODS: A new open source application (GastrOS) has been developed following open EHR{\textquoteright}s multi-level modelling approach using .Net/C$\#$ based on the same requirements of an existing clinically used application developed using Microsoft Visual Basic and Access database. Almost all the domain knowledge was embedded into the software code and data model in the latter. The same domain knowledge has been expressed as a set of open EHR Archetypes in GastrOS. We then introduced eight real-world change requests that had accumulated during live clinical usage, and implemented these in both systems while measuring time for various development tasks and change in software size for each change request.

RESULTS: Overall it took half the time to implement changes in GastrOS. However it was the more difficult application to modify for one change request, suggesting the nature of change is also important. It was not possible to implement changes by modelling only. Comparison of relative measures of time and software size change within each application highlights how architectural differences affected maintain ability across change requests.

CONCLUSIONS: The use of open EHR model driven development can result in better software maintain ability. The degree to which open EHR affects software maintain ability depends on the extent and nature of domain knowledge involved in changes. Although we used relative measures for time and software size, confounding factors could not be totally excluded as a controlled study design was not feasible.

}, keywords = {Data Curation, electronic health records, Information Dissemination, Information Storage and Retrieval, Meaningful Use, Software, Software Design}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2014.07.006}, author = {Atalag, Koray and Yang, Hong Yul and Tempero, Ewan and Warren, James R} } @article {945, title = {ExpertEyes: Open-source, high-definition eyetracking.}, journal = {Behav Res Methods}, year = {2014}, month = {2014 Jun 17}, abstract = {

ExpertEyes is a low-cost, open-source package of hardware and software that is designed to provide portable high-definition eyetracking. The project involves several technological innovations, including portability, high-definition video recording, and multiplatform software support. It was designed for challenging recording environments, and all processing is done offline to allow for optimization of parameter estimation. The pupil and corneal reflection are estimated using a novel forward eye model that simultaneously fits both the pupil and the corneal reflection with full ellipses, addressing a common situation in which the corneal reflection sits at the edge of the pupil and therefore breaks the contour of the ellipse. The accuracy and precision of the system are comparable to or better than what is available in commercial eyetracking systems, with a typical accuracy of less than 0.4{\textdegree} and best accuracy below 0.3{\textdegree}, and with a typical precision (SD method) around 0.3{\textdegree} and best precision below 0.2{\textdegree}. Part of the success of the system comes from a high-resolution eye image. The high image quality results from uncasing common digital camcorders and recording directly to SD cards, which avoids the limitations of the analog NTSC format. The software is freely downloadable, and complete hardware plans are available, along with sources for custom parts.

}, issn = {1554-3528}, doi = {10.3758/s13428-014-0465-z}, author = {Parada, Francisco J and Wyatte, Dean and Yu, Chen and Akavipat, Ruj and Emerick, Brandi and Busey, Thomas} } @article {943, title = {Open-source electronic data capture system offered increased accuracy and cost-effectiveness compared with paper methods in Africa.}, journal = {J Clin Epidemiol}, year = {2014}, month = {2014 Aug 15}, abstract = {

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

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

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

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

}, issn = {1878-5921}, doi = {10.1016/j.jclinepi.2014.06.012}, author = {Dillon, David G and Pirie, Fraser and Pomilla, Cristina and Sandhu, Manjinder S and Motala, Ayesha A and Young, Elizabeth H} } @article {949, title = {Surgical planning of Isshiki type I thyroplasty using an open-source Digital Imaging and Communication in Medicine viewer OsiriX.}, journal = {Acta Otolaryngol}, volume = {134}, year = {2014}, month = {2014 Jun}, pages = {620-5}, abstract = {

CONCLUSION: Preoperative surgical planning of Isshiki type I thyroplasty with the Digital Imaging and Communication in Medicine (DICOM) viewer OsiriX can be used for strategic and predictable type I thyroplasty.

OBJECTIVES: The aim of this study was to determine the efficacy of the preoperative planning of type I thyroplasty using the DICOM viewer OsiriX.

METHODS: Five patients with unilateral vocal cord paralysis and severe breathy dysphonia were included in this study. Multidetector computed tomography (CT) DICOM data were obtained and breath holding was performed during image acquisition. Using three-dimensional multiplanar reconstruction, we outlined the optimal location for a window. Type I thyroplasty was performed using Isshiki{\textquoteright}s original method, and only the placement of the window was decided according to the preoperative simulation point. To verify the advantages of this method, we compared our data with the previous data for total operation time and voice quality at 3 months after the operation without the DICOM viewer planning.

RESULTS: All patients are free from dysphonia and their glottic closures have resolved satisfactorily. Postoperative CT revealed that appropriate implant positioning resulted in successful surgical intervention. The comparison of total operation time showed that with the new method, operation duration was shortened by 12 min.

}, issn = {1651-2251}, doi = {10.3109/00016489.2014.880796}, author = {Hara, Hirotaka and Hori, Takeshi and Sugahara, Kazuma and Yamashita, Hiroshi} } @article {864, title = {Integration of PACS and CAD systems using DICOMDIR and open-source tools}, year = {2013}, pages = {86740V-86740V-6}, abstract = {The advancements of the last 30 years have made picture archiving and communication system (PACS) an indispensable technology to improve the delivery and management of clinical imaging services. Similarly, the maturation of algorithms and computer aided detection (CAD) systems has enhanced the interpretation and diagnosis of radiographical images. However, the lack of integration between the two systems inhibits the rate of development and application of these recent innovations in reaching the clinical users of PACS. We aim to enhance the clinical efficiency of CAD systems by developing an accessible, fully automated, user-friendly, and integrated linkage of CAD and PACS systems. This is the first integration initiative to take advantage of DICOMDIR file and its ability to index DICOM files, allowing images outside of PACS to be viewed within PACS. In this demonstration, the CAD system evaluates CT chest exams to detect lesions in the ribs and produces whole rib map images, screenshots, and detection report. A script executes the rib CAD system and creates a DICOMDIR file using {\quotedblbase}DCMTK", an open-source DICOM toolkit. We evaluated our system on thirty 5mm slice thickness and thirty 2mm slice thickness image studies and demonstrated a time saving efficiency of 93s{\textpm}14s and 221s{\textpm}17s per exam, respectively, compared to the current non-integrated workflow of using CAD systems. The advantages of this system are that it is easy to implement, requires no additional workstation and training, and allows CAD results to be viewed in PACS without disrupting radiology workflow, while maintaining the independence of both technologies. {\textcopyright} (2013) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).}, doi = {10.1117/12.2001560}, url = {+ http://dx.doi.org/10.1117/12.2001560}, author = {Huang, Jiaxin and Ling, Alexander and Summers, Ronald M. and Yao, Jianhua} } @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 {1280, title = {What do electronic health record vendors reveal about their products: an analysis of vendor websites.}, journal = {J Med Internet Res}, volume = {15}, year = {2013}, month = {2013 Feb 19}, pages = {e36}, abstract = {

BACKGROUND: Purchasing electronic health records (EHRs) typically follows a process in which potential adopters actively seek information, compare alternatives, and form attitudes towards the product. A potential source of information on EHRs that can be used in the process is vendor websites. It is unclear how much product information is presented on EHR vendor websites or the extent of its value during EHR purchasing decisions.

OBJECTIVE: To explore what features of EHR systems are presented by vendors in Ontario, Canada, on their websites, and the persuasive means they use to market such systems; to compare the online information available about primary care EHR systems with that about hospital EHR systems, and with data compiled by OntarioMD, a regional certifying agency.

METHODS: A list of EHR systems available in Ontario was created. The contents of vendor websites were analyzed. A template for data collection and organization was developed and used to collect and organize information on the vendor, website content, and EHR features. First, we mapped information on system features to categories based on a framework from the Institute of Medicine (IOM). Second, we used a grounded theory-like approach to explore information for building consumer confidence in the vendor and product, and the various persuasive strategies employed on vendor websites. All data were first coded by one researcher. A peer reviewer independently analyzed a randomly chosen subset of the websites (10 of 21; 48\%) and provided feedback towards a unified coding scheme. All data were then re-coded and categorized into themes. Finally, we compared information from vendor websites and data gathered by OntarioMD.

RESULTS: Vendors provided little specific product information on their websites. Only two of five acute care EHR websites (40\%) and nine of 16 websites for primary care systems (56\%) featured seven or all eight of the IOM components. Several vendor websites included system interface demonstrations: screenshots (six websites), public videos or slideshows (four websites), or for registered viewers only (three websites). Persuasive means used by vendors included testimonials on 14/21 (67\%) websites, and directional language. Except for one free system, trial EHR versions were not available. OntarioMD provided more comprehensive information about primary care systems than the vendors{\textquoteright} websites. Of 14 points of comparison, only the inclusion of templates and bilingual interfaces were fully represented in both data sources. For all other categories, the vendor websites were less complete than the OntarioMD site.

CONCLUSIONS: EHR vendor websites employ various persuasive means, but lack product-specific information and do not provide options for trying systems on a limited basis. This may impede the ability of potential adopters to form perceptions and compare various offerings. Both vendors and clients could benefit from greater transparency and more specific product information on the Web.

TRIAL REGISTRATION: N/A.

}, keywords = {Commerce, electronic health records, Humans, Internet, Marketing of Health Services, Ontario, Telemedicine}, issn = {1438-8871}, doi = {10.2196/jmir.2312}, author = {Yeung, Natalie K and Jadad, Alejandro R and Shachak, Aviv} } @article {793, title = {Integrating clinical practice and public health surveillance using electronic medical record systems.}, journal = {Am J Prev Med}, volume = {42}, year = {2012}, month = {2012 Jun}, pages = {S154-62}, abstract = {Electronic medical record (EMR) systems have rich potential to improve integration between primary care and the public health system at the point of care. EMRs make it possible for clinicians to contribute timely, clinically detailed surveillance data to public health practitioners without changing their existing workflows or incurring extra work. New surveillance systems can extract raw data from providers{\textquoteright} EMRs, analyze them for conditions of public health interest, and automatically communicate results to health departments. The current paper describes a model EMR-based public health surveillance platform called Electronic Medical Record Support for Public Health (ESP). The ESP platform provides live, automated surveillance for notifiable diseases, influenza-like illness, and diabetes prevalence, care, and complications. Results are automatically transmitted to state health departments.}, issn = {1873-2607}, doi = {10.1016/j.amepre.2012.04.005}, author = {Klompas, Michael and McVetta, Jason and Lazarus, Ross and Eggleston, Emma and Haney, Gillian and Kruskal, Benjamin A and Yih, W Katherine and Daly, Patricia and Oppedisano, Paul and Beagan, Brianne and Lee, Michael and Kirby, Chaim and Heisey-Grove, Dawn and DeMaria, Alfred and Platt, Richard} } @conference {774, title = {Research and implementation of Electronic Medical Records Editing System based on CDA}, booktitle = {Consumer Electronics, Communications and Networks (CECNet), 2012 2nd International Conference on}, year = {2012}, month = {april}, abstract = {It is difficult to exchange information between heterogeneous Hospital Information Systems (HIS). It becomes the obstacle of regional medical system establishment. The coming forth of HL7 (Health Level 7) CDA (Clinical Document Architecture) standard provides the technical basic conditions. This paper describes CDA standards and CDA document structure. Through a complete analysis of Electronic Medical Record (EMR), the model of Electronic Medical Records Editing Subsystem is given. Based on this model, functional modules of Electronic Medical Records Editing Subsystem are designed and implemented. Through Electronic Medical Records Editing Subsystem, clinical documents can effectively produce, parse, validate and view. It provides a technical support for exchanges of medical and health information.}, keywords = {CDA document structure, CDA standards, clinical document architecture, document handling, electronic medical records editing system, EMR, health level 7, HIS, HL7, hospital information systems, information exchange, medical information systems, regional medical system establishment}, doi = {10.1109/CECNet.2012.6201451}, url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=\&arnumber=6201451\&contentType=Conference+Publications\&queryText\%3DResearch+and+implementation+of+Electronic+Medical+Records+Editing+System+based+on+CDA}, author = {Lu Xiaoqi and Yu Ning and Gu Yu and Jia Weitao} } @inbook {786, title = {VURTIGO: Visualization Platform for Real-Time, MRI-Guided Cardiac Electroanatomic Mapping}, booktitle = {Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges}, series = {Lecture Notes in Computer Science}, volume = {7085}, year = {2012}, pages = {244-253}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Guidance of electrophysiological (EP) procedures by magnetic resonance imaging (MRI) has significant advantages over x-ray fluoroscopy. Display of electroanatomic mapping (EAM) during an intervention fused with a prior MR volume and DE-MRI derived tissue classification should improve the accuracy of cardiac resynchronization therapy (CRT) for ventricular arrhythmias. Improved accuracy in the spatial localization of recorded EP points will produce an EAM to constrain and customize patient-specific cardiac electroanatomic models being developed for understanding the patterns of arrhythmogenic slow conduction zones causing reentry circuits and treatment planning. The Vurtigo software presented here is a four dimensional (3D+time) real-time visualization application for guiding interventions capable of displaying prior volumes, real-time MRI scan planes, EAM (voltage or activation times), segmented models, and tracked catheters. This paper will describe the architecture and features of Vurtigo followed by the application example of guiding percutaneous cardiac electroanatomic mapping in porcine models.}, isbn = {978-3-642-28325-3}, url = {http://dx.doi.org/10.1007/978-3-642-28326-0_25}, author = {Radau, Perry and Pintilie, Stefan and Flor, Roey and Biswas, Labonny and Oduneye, Samuel and Ramanan, Venkat and Anderson, Kevan and Wright, Graham}, editor = {Camara, Oscar and Konukoglu, Ender and Pop, Mihaela and Rhode, Kawal and Sermesant, Maxime and Young, Alistair} } @article {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 {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} } @conference {1086, title = {Commercial Open Source RIS/PACS: The ClearCanvas Experience}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001827400220027}, author = {Norman Young and Clinton Chau and John Adziovsky} } @article {20124747, title = {Fundamental of medical image processing with personal computer system--Image processing of computed tomography with imageJ}, journal = {Nippon Hoshasen Gijutsu Gakkai zasshi}, volume = {65}, year = {2009}, month = {2009 Dec 20}, pages = {1680-2}, author = {Yamamoto, Shuji} } @article {19157968, title = {The OpenMRS Implementers Network.}, journal = {International journal of medical informatics}, volume = {78}, year = {2009}, month = {2009 Nov}, pages = {711-20}, abstract = {OBJECTIVE: OpenMRS (www.openmrs.org) is a configurable open source electronic medical record application developed and maintained by a large network of open source developers coordinated by the Regenstrief Institute and Partners in Health and mainly used for HIV patient and treatment information management in Africa. Our objective is to develop an open Implementers Network for OpenMRS to provide regional support for the growing number of OpenMRS implementations in Africa and to include African developers and implementers in the future growth of OpenMRS. METHODS: We have developed the OpenMRS Implementers Network using a dedicated Wiki site and e-mail server. We have also organized annual meetings in South Africa and regional training courses at African locations where OpenMRS is being implemented. An OpenMRS Internship program has been initiated and we have started collaborating with similar networks and projects working in Africa. To evaluate its potential, OpenMRS was implemented initially at one site in South Africa by a single implementer using a downloadable OpenMRS application and only the OpenMRS Implementers Network for support. RESULTS: The OpenMRS Implementers Network Wiki and list server have grown into effective means of providing implementation support and forums for exchange of implementation experiences. The annual OpenMRS Implementers meeting has been held in South Africa for the past three years and is attracting successively larger numbers of participants with almost 200 implementers and developers attending the 2008 meeting in Durban, South Africa. Six African developers are presently registered on the first intake of the OpenMRS Internship program. Successful collaborations have been started with several African developer groups and projects initiated to develop interoperability between OpenMRS and various applications. The South African OpenMRS Implementer group successfully configured, installed and maintained an integrated HIV/TB OpenMRS application without significant programming support. Since then, this model has been replicated in several other African sites. The OpenMRS Implementers Network has contributed substantially to the growth and sustainability of OpenMRS in Africa and has become a useful way of including Africans in the development and implementation of OpenMRS in developing countries. The Network provides valuable support and enables a basic OpenMRS application to be implemented in the absence of onsite programmers.}, url = {http://www.healthware.org/openmrs/openmrs.pdf}, author = {Seebregts, Christopher J and Mamlin, Burke W and Biondich, Paul G and Fraser, Hamish S F and Wolfe, Benjamin A and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Baker, Elaine and Musinguzi, Nicholas and Kayiwa, Daniel and Fourie, Carl and Lesh, Neal and Kanter, Andrew and Yiannoutsos, Constantin T and Bailey, Christopher} } @article {19745435, title = {Reversible anonymization of DICOM images using automatically generated policies.}, journal = {Studies in health technology and informatics}, volume = {150}, year = {2009}, month = {2009}, pages = {861-5}, abstract = {Many real-world applications in the area of medical imaging like case study databases require separation of identifying (IDATA) and non-identifying (MDATA) data, specifically those offering Internet-based data access. These kinds of projects also must provide a role-based access system, controlling, how patient data must be organized and how it can be accessed. On DICOM image level, different image types support different kind of information, intermixing IDATA and MDATA in a single object. To separate them, it is possible to reversibly anonymize DICOM objects by substituting IDATA by a unique anonymous token. In case that later an authenticated user needs full access to an image, this token can be used for re-linking formerly separated IDATA and MDATA, thus resulting in a dynamically generated, exact copy of the original image. The approach described in this paper is based on the automatic generation of anonymization policies from the DICOM standard text, providing specific support for all kinds of DICOM images. The policies are executed by a newly developed framework based on the DICOM toolkit DCMTK and offer a reliable approach to reversible anonymization. The implementation is evaluated in a German BMBF-supported expert network in the area of skeletal dysplasias, SKELNET, but may generally be applicable to related projects, enormously improving quality and integrity of diagnostics in a field focused on images. It performs effectively and efficiently on real-world test images from the project and other kind of DICOM images.}, author = {Onken, Michael and Riesmeier, J{\"o}rg and Engel, Marcel and Yabanci, Adem and Zabel, Bernhard and Despr{\'e}s, Stefan} } @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 {18276143, title = {iPath: interactive exploration of biochemical pathways and networks.}, journal = {Trends in biochemical sciences}, volume = {33}, year = {2008}, month = {2008 Mar}, pages = {101-3}, abstract = {iPath is an open-access online tool (http://pathways.embl.de) for visualizing and analyzing metabolic pathways. An interactive viewer provides straightforward navigation through various pathways and enables easy access to the underlying chemicals and enzymes. Customized pathway maps can be generated and annotated using various external data. For example, by merging human genome data with two important gut commensals, iPath can pinpoint the complementarity of the host-symbiont metabolic capacities.}, author = {Letunic, Ivica and Yamada, Takuji and Kanehisa, Minoru and Bork, Peer} } @article {18570554, title = {Standards-based, open-source electronic health record systems: a desirable future for the U.S. health industry.}, journal = {Telemedicine journal and e-health : the official journal of the American Telemedicine Association}, volume = {14}, year = {2008}, month = {2008 Apr}, pages = {284-8}, abstract = {Many healthcare systems are moving toward a fully electronic health record (EHR) in order to better manage patient care. Unfortunately, in the United States, many current EHR systems leave much to be desired. Among well-documented criticisms are that they tend to be inflexible, proprietary, nonintuitive, expensive, difficult to maintain and rarely interoperable across health systems. From the clinician{\textquoteright}s perspective, these flaws sometimes make having an EHR system seem no better than retaining a paper-based system. Open-source software, a great success in other information-intensive industries, is one possible solution to these problems, and may help integrate a functional EHR system into, and across, more health systems and clinics because of the greater potential for local customization. We believe that the advantages of an open-source EHR system outweigh the costs of a more traditional, proprietary EHR system, and recommend that more work be done to advance an interoperable open-source EHR system in the United States. Open-source EHR systems have the potential to improve healthcare in the United States as they have done in many other areas around the world.}, author = {Yellowlees, Peter M and Marks, Shayna L and Hogarth, Michael and Turner, Stuart} } @article {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 {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 {15924271, title = {Establishing a Web-based DICOM teaching file authoring tool using open-source public software.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {18}, year = {2005}, month = {2005 Sep}, pages = {169-75}, abstract = {Online teaching files are an important source of educational and referential materials in the radiology community. The commonly used Digital Imaging and Communications in Medicine (DICOM) file format of the radiology community is not natively supported by common Web browsers. The ability of the Web server to convert and parse DICOM is important when the DICOM-converting tools are not available. In this paper, we describe our approach to develop a Web-based teaching file authoring tool. Our server is built using Apache Web server running on FreeBSD operating system. The dynamic page content is produced by Hypertext Preprocessor (PHP). Digital Imaging and Communications in Medicine images are converted by ImageMagick into Joint Photographic Experts Group (JPEG) format. Digital Imaging and Communications in Medicine attributes are parsed by dicom3tools and stored in PostgreSQL database. Using free software available from the Internet, we build a Web service that allows radiologists to create their own online teaching file cases with a common Web browser.}, author = {Lee, Wen-Jeng and Yang, Chung-Yi and Liu, Kao-Lang and Liu, Hon-Man and Ching, Yu-Tai and Chen, Shyh-Jye} } @article {18238234, title = {BioSig: an imaging bioinformatics system for phenotypic analysis.}, journal = {IEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society}, volume = {33}, year = {2003}, month = {2003}, pages = {814-24}, abstract = {Organisms express their genomes in a cell-specific manner, resulting in a variety of cellular phenotypes or phenomes. Mapping cell phenomes under a variety of experimental conditions is necessary in order to understand the responses of organisms to stimuli. Representing such data requires an integrated view of experimental and informatic protocols. The proposed system, named BioSig, provides the foundation for cataloging cellular responses as a function of specific conditioning, treatment, staining, etc., for either fixed tissue or living cell studies. A data model has been developed to capture experimental variables and map them to image collections and their computed representation. This representation is hierarchical and spans across sample tissues, cells, and organelles, which are imaged with light microscopy. At each layer, content is represented with an attributed graph, which contains information about cellular morphology, protein localization, and cellular organization in tissue or cell culture. The Web-based multilayer informatics architecture uses the data model to provide guided workflow access for content exploration.}, author = {Parvin, B and Yang, Qing and Fontenay, G and Barcellos-Hoff, M H} }