%0 Journal Article %J Health Informatics J %D 2022 %T Open-source electronic health record systems: A systematic review of most recent advances. %A Shaikh, Mohsin %A Vayani, Arshad Hm %A Akram, Sabina %A Qamar, Nafees %K electronic health records %K Humans %K Medical Informatics %K Publications %K Software %X

Open-source Electronic Health Records (OS-EHRs) are of pivotal importance in the management, operations, and administration of any healthcare organization. With the advancement of health informatics, researchers and healthcare practitioners have proposed various frameworks to assess the maturation of Open-source EHRs. The significance of OS-EHRs stems from the fact that vendor-based EHR implementations are becoming financially burdensome, with some vendors raking in more than $1 billion with one contract. Contrarily, the adoption of OS-EHRs suffers from a lack of systematic evaluation from the standpoint of a standard reference model. To this end, the Healthcare Information and Management Systems Society (HIMSS) has presented a strategic road map called EMR Adoption and Maturity (EMRAM). The HIMSS-EMRAM model proposes a stage-wise model approach that is globally recognized and can be essentially applied as a benchmark evaluation criteria for open-source EHRs. This paper offers an applied descriptive methodology over the frequently studied open-source EHRs currently operational worldwide or has the potential of adoption in healthcare settings. Besides, we also present profiling (User Support, Developer' Support, Customization Support, Technical details, and Diagnostic help) of studied OS-EHRs from developer's and user's perspectives using updated standard metrics. We carried out multi-aspect objective analysis of studied systems covering EHR functions, software based features and implementation. This review portrays systematic aspects of electronic medical record standards for open-source software implementations. As we observed in the literature, prevalent research and working prototypes lack systematic review of the HIMSS-EMRAM model and do not present evolving software features. Therefore, after the application of our assessment measures, the results obtained indicate that OS-EHRs are yet to acquire standard compliance and implementation. The findings in this paper can be beneficial in the planning and implementation of OS-EHRs projects in the future.

%B Health Informatics J %V 28 %P 14604582221099828 %8 2022 Apr-Jun %G eng %N 2 %R 10.1177/14604582221099828 %0 Journal Article %J PLoS One %D 2019 %T The impact of PEPFAR transition on HIV service delivery at health facilities in Uganda. %A Wilhelm, Jess Alan %A Qiu, Mary %A Paina, Ligia %A Colantuoni, Elizabeth %A Mukuru, Moses %A Ssengooba, Freddie %A Bennett, Sara %X

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

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

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

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

%B PLoS One %V 14 %P e0223426 %8 2019 %G eng %N 10 %R 10.1371/journal.pone.0223426 %0 Journal Article %J PLoS Pathog %D 2016 %T Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. %A Van Voorhis, Wesley C %A Adams, John H %A Adelfio, Roberto %A Ahyong, Vida %A Akabas, Myles H %A Alano, Pietro %A Alday, Aintzane %A Alemán Resto, Yesmalie %A Alsibaee, Aishah %A Alzualde, Ainhoa %A Andrews, Katherine T %A Avery, Simon V %A Avery, Vicky M %A Ayong, Lawrence %A Baker, Mark %A Baker, Stephen %A Ben Mamoun, Choukri %A Bhatia, Sangeeta %A Bickle, Quentin %A Bounaadja, Lotfi %A Bowling, Tana %A Bosch, Jürgen %A Boucher, Lauren E %A Boyom, Fabrice F %A Brea, Jose %A Brennan, Marian %A Burton, Audrey %A Caffrey, Conor R %A Camarda, Grazia %A Carrasquilla, Manuela %A Carter, Dee %A Belen Cassera, Maria %A Chih-Chien Cheng, Ken %A Chindaudomsate, Worathad %A Chubb, Anthony %A Colon, Beatrice L %A Colón-López, Daisy D %A Corbett, Yolanda %A Crowther, Gregory J %A Cowan, Noemi %A D'Alessandro, Sarah %A Le Dang, Na %A Delves, Michael %A DeRisi, Joseph L %A Du, Alan Y %A Duffy, Sandra %A Abd El-Salam El-Sayed, Shimaa %A Ferdig, Michael T %A Fernández Robledo, José A %A Fidock, David A %A Florent, Isabelle %A Fokou, Patrick V T %A Galstian, Ani %A Gamo, Francisco Javier %A Gokool, Suzanne %A Gold, Ben %A Golub, Todd %A Goldgof, Gregory M %A Guha, Rajarshi %A Guiguemde, W Armand %A Gural, Nil %A Guy, R Kiplin %A Hansen, Michael A E %A Hanson, Kirsten K %A Hemphill, Andrew %A Hooft van Huijsduijnen, Rob %A Horii, Takaaki %A Horrocks, Paul %A Hughes, Tyler B %A Huston, Christopher %A Igarashi, Ikuo %A Ingram-Sieber, Katrin %A Itoe, Maurice A %A Jadhav, Ajit %A Naranuntarat Jensen, Amornrat %A Jensen, Laran T %A Jiang, Rays H Y %A Kaiser, Annette %A Keiser, Jennifer %A Ketas, Thomas %A Kicka, Sebastien %A Kim, Sunyoung %A Kirk, Kiaran %A Kumar, Vidya P %A Kyle, Dennis E %A Lafuente, Maria Jose %A Landfear, Scott %A Lee, Nathan %A Lee, Sukjun %A Lehane, Adele M %A Li, Fengwu %A Little, David %A Liu, Liqiong %A Llinás, Manuel %A Loza, Maria I %A Lubar, Aristea %A Lucantoni, Leonardo %A Lucet, Isabelle %A Maes, Louis %A Mancama, Dalu %A Mansour, Nuha R %A March, Sandra %A McGowan, Sheena %A Medina Vera, Iset %A Meister, Stephan %A Mercer, Luke %A Mestres, Jordi %A Mfopa, Alvine N %A Misra, Raj N %A Moon, Seunghyun %A Moore, John P %A Morais Rodrigues da Costa, Francielly %A Müller, Joachim %A Muriana, Arantza %A Nakazawa Hewitt, Stephen %A Nare, Bakela %A Nathan, Carl %A Narraidoo, Nathalie %A Nawaratna, Sujeevi %A Ojo, Kayode K %A Ortiz, Diana %A Panic, Gordana %A Papadatos, George %A Parapini, Silvia %A Patra, Kailash %A Pham, Ngoc %A Prats, Sarah %A Plouffe, David M %A Poulsen, Sally-Ann %A Pradhan, Anupam %A Quevedo, Celia %A Quinn, Ronald J %A Rice, Christopher A %A Abdo Rizk, Mohamed %A Ruecker, Andrea %A St Onge, Robert %A Salgado Ferreira, Rafaela %A Samra, Jasmeet %A Robinett, Natalie G %A Schlecht, Ulrich %A Schmitt, Marjorie %A Silva Villela, Filipe %A Silvestrini, Francesco %A Sinden, Robert %A Smith, Dennis A %A Soldati, Thierry %A Spitzmüller, Andreas %A Stamm, Serge Maximilian %A Sullivan, David J %A Sullivan, William %A Suresh, Sundari %A Suzuki, Brian M %A Suzuki, Yo %A Swamidass, S Joshua %A Taramelli, Donatella %A Tchokouaha, Lauve R Y %A Theron, Anjo %A Thomas, David %A Tonissen, Kathryn F %A Townson, Simon %A Tripathi, Abhai K %A Trofimov, Valentin %A Udenze, Kenneth O %A Ullah, Imran %A Vallieres, Cindy %A Vigil, Edgar %A Vinetz, Joseph M %A Voong Vinh, Phat %A Vu, Hoan %A Watanabe, Nao-Aki %A Weatherby, Kate %A White, Pamela M %A Wilks, Andrew F %A Winzeler, Elizabeth A %A Wojcik, Edward %A Wree, Melanie %A Wu, Wesley %A Yokoyama, Naoaki %A Zollo, Paul H A %A Abla, Nada %A Blasco, Benjamin %A Burrows, Jeremy %A Laleu, Benoît %A Leroy, Didier %A Spangenberg, Thomas %A Wells, Timothy %A Willis, Paul A %X

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.

%B PLoS Pathog %V 12 %P e1005763 %8 2016 Jul %G eng %N 7 %R 10.1371/journal.ppat.1005763 %0 Journal Article %J J Am Med Inform Assoc %D 2015 %T A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management. %A Neinstein, Aaron %A Wong, Jenise %A Look, Howard %A Arbiter, Brandon %A Quirk, Kent %A McCanne, Steve %A Sun, Yao %A Blum, Michael %A Adi, Saleh %X

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

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

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

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

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

%B J Am Med Inform Assoc %8 2015 Sep 2 %G eng %R 10.1093/jamia/ocv104 %0 Journal Article %J PLoS ONE %D 2011 %T An Open Environment CT-US Fusion for Tissue Segmentation during Interventional Guidance %A Caskey, , Charles F. %A Hlawitschka, , Mario %A Qin, , Shengping %A Mahakian, , Lisa M. %A Cardiff, , Robert D. %A Boone, , John M. %A Ferrara, , Katherine W. %X

Therapeutic ultrasound (US) can be noninvasively focused to activate drugs, ablate tumors and deliver drugs beyond the blood brain barrier. However, well-controlled guidance of US therapy requires fusion with a navigational modality, such as magnetic resonance imaging (MRI) or X-ray computed tomography (CT). Here, we developed and validated tissue characterization using a fusion between US and CT. The performance of the CT/US fusion was quantified by the calibration error, target registration error and fiducial registration error. Met-1 tumors in the fat pads of 12 female FVB mice provided a model of developing breast cancer with which to evaluate CT-based tissue segmentation. Hounsfield units (HU) within the tumor and surrounding fat pad were quantified, validated with histology and segmented for parametric analysis (fat: −300 to 0 HU, protein-rich: 1 to 300 HU, and bone: HU>300). Our open source CT/US fusion system differentiated soft tissue, bone and fat with a spatial accuracy of ∼1 mm. Region of interest (ROI) analysis of the tumor and surrounding fat pad using a 1 mm2 ROI resulted in mean HU of 68±44 within the tumor and −97±52 within the fat pad adjacent to the tumor (p<0.005). The tumor area measured by CT and histology was correlated (r2 = 0.92), while the area designated as fat decreased with increasing tumor size (r2 = 0.51). Analysis of CT and histology images of the tumor and surrounding fat pad revealed an average percentage of fat of 65.3% vs. 75.2%, 36.5% vs. 48.4%, and 31.6% vs. 38.5% for tumors <75 mm3, 75–150 mm3 and >150 mm3, respectively. Further, CT mapped bone-soft tissue interfaces near the acoustic beam during real-time imaging. Combined CT/US is a feasible method for guiding interventions by tracking the acoustic focus within a pre-acquired CT image volume and characterizing tissues proximal to and surrounding the acoustic focus.

%B PLoS ONE %I Public Library of Science %V 6 %P e27372 %8 11 %U http://dx.doi.org/10.1371%2Fjournal.pone.0027372 %R 10.1371/journal.pone.0027372 %0 Journal Article %J The American journal of tropical medicine and hygiene %D 2011 %T Use of an innovative, affordable, and open-source short message service-based tool to monitor malaria in remote areas of Uganda. %A Asiimwe, Caroline %A Gelvin, David %A Lee, Evan %A Ben Amor, Yanis %A Quinto, Ebony %A Katureebe, Charles %A Sundaram, Lakshmi %A Bell, David %A Berg, Matt %X 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. %B The American journal of tropical medicine and hygiene %V 85 %P 26-33 %8 2011 Jul %G eng %N 1 %1 http://www.ncbi.nlm.nih.gov/pubmed/21734120?dopt=Abstract %0 Journal Article %J Technology in cancer research & treatment %D 2007 %T RT_Image: an open-source tool for investigating PET in radiation oncology. %A Graves, Edward E %A Quon, Andrew %A Loo, Billy W %X 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. %B Technology in cancer research & treatment %V 6 %P 111-21 %8 2007 Apr %N 2 %1 http://www.ncbi.nlm.nih.gov/pubmed/17375973?dopt=Abstract