scholarly journals An open source tool to compute measures of inpatient glycemic control: translating from healthcare analytics research to clinical quality improvement

JAMIA Open ◽  
2021 ◽  
Vol 4 (2) ◽  
Author(s):  
Ying Chen ◽  
Yilin Ning ◽  
Prem Thomas ◽  
Mark Salloway ◽  
Maudrene Luor Shyuan Tan ◽  
...  
Keyword(s):  
Glycemic Control ◽  
Open Source ◽  
Graphical Interface ◽  
Prior Work ◽  
Healthcare Analytics ◽  
Privacy Concerns ◽  
Open Source Tool ◽  
Extended Code ◽  
User Friendly

Abstract Objectives The objective of this study is to facilitate monitoring of the quality of inpatient glycemic control by providing an open-source tool to compute glucometrics. To allay regulatory and privacy concerns, the tool is usable locally; no data are uploaded to the internet. Materials and Methods We extended code, initially developed for healthcare analytics research, to serve the clinical need for quality monitoring of diabetes. We built an application, with a graphical interface, which can be run locally without any internet connection. Results We verified that our code produced results identical to prior work in glucometrics. We extended the prior work by including additional metrics and by providing user customizability. The software has been used at an academic healthcare institution. Conclusion We successfully translated code used for research methods into an open source, user-friendly tool which hospitals may use to expedite quality measure computation for the management of inpatients with diabetes.

scholarly journals QuickStitch for seamless stitching of confocal mosaics through high-pass filtering and recursive normalization

2016 ◽  
Author(s):  
Pavel A. Brodskiy ◽  
Paulina M. Eberts ◽  
Cody Narciso ◽  
Jochen Kursawe ◽  
Alexander Fletcher ◽  
...  
Keyword(s):  
Open Source ◽  
Large Scale ◽  
Imaging System ◽  
Tissue Level ◽  
Cellular Level ◽  
Specific Information ◽  
Open Source Tool ◽  
The Individual ◽  
User Friendly ◽  
High Pass

ABSTRACTFluorescence micrographs naturally exhibit darkening around their edges (vignetting), which makes seamless stitching challenging. If vignetting is not corrected for, a stitched image will have visible seams where the individual images (tiles) overlap, introducing a systematic error into any quantitative analysis of the image. Although multiple vignetting correction methods exist, there remains no open-source tool that robustly handles large 2D immunofluorescence-based mosaic images. Here, we develop and validate QuickStitch, a tool that applies a recursive normalization algorithm to stitch large-scale immunofluorescence-based mosaics without incurring vignetting seams. We demonstrate how the tool works successfully for tissues of differing size, morphology, and fluorescence intensity. QuickStitch requires no specific information about the imaging system. It is provided as an open-source tool that is both user friendly and extensible, allowing straightforward incorporation into existing image processing pipelines. This enables studies that require accurate segmentation and analysis of high-resolution datasets when parameters of interest include both cellular-level phenomena and larger tissue-level regions of interest.

Traffic Simulation with Open-Source and Commercial Traffic Microsimulators: A Case Study

2022 ◽  
Vol 24 (2) ◽  
pp. E49-E62
Author(s):  
Nelson Baza-Solares ◽  
Ruben Velasquez-Martínez ◽  
Cristian Torres-Bohórquez ◽  
Yerly Martínez-Estupiñán ◽  
Cristian Poliziani
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Transport Modeling ◽  
Graphical Interface ◽  
Urban Centers ◽  
Output Data ◽  
Computational Tools ◽  
Input And Output ◽  
User Friendly

The analysis of traffic problems in large urban centers often requires the use of computational tools, which give the possibility to make a more detailed analysis of the issue, suggest solutions, predict behaviors and, above all, support efficient decision-making. Transport microsimulation software programs are a handy set of tools for this type of analysis. This research paper shows a case study where functions and limitations of Aimsun version 8.2.0, a commercial-like European software and Sumo version 1.3.1, a European open-source software, are presented. The input and output data are similar in both software and the interpretation of results is quite intuitive for both, as well. However, Aimsun's graphical interface interprets results more user-friendly, because Sumo is an open-access software presented as an effective alternative tool for transport modeling.

scholarly journals DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence Micrographs

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 397
Author(s):  
Boyoung Kim
Keyword(s):  
Open Source ◽  
Three Dimensional ◽  
Graphical Interface ◽  
Matlab Toolbox ◽  
Function Generator ◽  
Point Spread ◽  
Spread Function ◽  
Asymmetric Shape ◽  
User Friendly ◽  
Imaging Conditions

To investigate the cellular structure, biomedical researchers often obtain three-dimensional images by combining two-dimensional images taken along the z axis. However, these images are blurry in all directions due to diffraction limitations. This blur becomes more severe when focusing further inside the specimen as photons in deeper focus must traverse a longer distance within the specimen. This type of blur is called depth-variance. Moreover, due to lens imperfection, the blur has asymmetric shape. Most deconvolution solutions for removing blur assume depth-invariant or x-y symmetric blur, and presently, there is no open-source for depth-variant asymmetric deconvolution. In addition, existing datasets for deconvolution microscopy also assume invariant or x-y symmetric blur, which are insufficient to reflect actual imaging conditions. DVDeconv, that is a set of MATLAB functions with a user-friendly graphical interface, has been developed to address depth-variant asymmetric blur. DVDeconv includes dataset, depth-variant asymmetric point spread function generator, and deconvolution algorithms. Experimental results using DVDeconv reveal that depth-variant asymmetric deconvolution using DVDeconv removes blurs accurately. Furthermore, the dataset in DVDeconv constructed can be used to evaluate the performance of microscopy deconvolution to be developed in the future.

scholarly journals Using the Data Quality Dashboard to Improve the EHDEN Network

2021 ◽  
Vol 11 (24) ◽  
pp. 11920
Author(s):  
Clair Blacketer ◽  
Erica A. Voss ◽  
Frank DeFalco ◽  
Nigel Hughes ◽  
Martijn J. Schuemie ◽  
...  
Keyword(s):  
Decision Making ◽  
Clinical Practice ◽  
Data Quality ◽  
Open Source ◽  
Baseline Level ◽  
Quality Of Data ◽  
Open Source Tool ◽  
Regulatory Decision ◽  
Standard Data

Federated networks of observational health databases have the potential to be a rich resource to inform clinical practice and regulatory decision making. However, the lack of standard data quality processes makes it difficult to know if these data are research ready. The EHDEN COVID-19 Rapid Collaboration Call presented the opportunity to assess how the newly developed open-source tool Data Quality Dashboard (DQD) informs the quality of data in a federated network. Fifteen Data Partners (DPs) from 10 different countries worked with the EHDEN taskforce to map their data to the OMOP CDM. Throughout the process at least two DQD results were collected and compared for each DP. All DPs showed an improvement in their data quality between the first and last run of the DQD. The DQD excelled at helping DPs identify and fix conformance issues but showed less of an impact on completeness and plausibility checks. This is the first study to apply the DQD on multiple, disparate databases across a network. While study-specific checks should still be run, we recommend that all data holders converting their data to the OMOP CDM use the DQD as it ensures conformance to the model specifications and that a database meets a baseline level of completeness and plausibility for use in research.

scholarly journals Conducting linguistic experiments online with OpenSesame and OSWeb

2021 ◽  
Author(s):  
Sebastiaan Mathot ◽  
Jennifer March
Keyword(s):  
Data Quality ◽  
Open Source ◽  
Viable Alternative ◽  
Graphical Interface ◽  
Technical Expertise ◽  
Behavioral Experiments ◽  
Online Experiments ◽  
Temporal Precision ◽  
Server Software ◽  
User Friendly

In this Methods Showcase, we outline a workflow for running behavioral experiments online, with a focus on linguistic experiments. The workflow that we describe here relies on three tools: OpenSesame/ OSWeb (open source) provides a user-friendly graphical interface for developing experiments; JATOS (open source) is server software for hosting experiments; and Prolific (commercial) is a platform for recruiting participants. These three tools integrate well with each other, and together they provide a workflow that requires little technical expertise. We discuss several challenges that are associated with running online experiments, including temporal precision, the ability to implement counterbalancing, and data quality. We conclude that these problems are real but surmountable, and that in many cases online experiments are a viable alternative to laboratory-based experiments.

Insulin Management for Type 1 Diabetic Patients During Social Alcohol Consumption: The SPRITZ Study

2020 ◽  
Vol 16 (6) ◽  
pp. 619-627
Author(s):  
Elisa Cipponeri ◽  
Cesare Blini ◽  
Christian Lamera ◽  
Valentina De Mori ◽  
Giovanni Veronesi ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Glycemic Control ◽  
Educational Program ◽  
Insulin Pump ◽  
Insulin Pump Therapy ◽  
Pump Therapy ◽  
Adult Type ◽  
Time To Peak

Background : There is no data available on the best insulin treatment to counteract the effects of glucose excursions due to a moderate alcohol intake associated with portions of slight fat and protein-containing food, as often the case during social happenings or “happy hours”. Introduction: This study analyzes the glycemic control and quality of life in 8 adult type 1 diabetic (T1D) patients on insulin-pump therapy which were invited to consume a traditional Italian aperitif (“Spritz” and chips). Introduction : This study analyzes the glycemic control and quality of life in 8 adult type 1 diabetic (T1D) patients on insulin-pump therapy which were invited to consume a traditional Italian aperitif (“Spritz” and chips). Methods: Patients consumed Spritz aperitif twice: using their habitual bolus, based on carbohydrates (CHO) counting (V1), or with a personalized, advanced bolus (V2) calculated from insulin/Kcal derived from Fats and Proteins (FPU). Post-prandial glucose was continuously monitored; glucose incremental areas (iAUC), glucose peak and time to peak, and estimated change from V1 to V2 from repeated- measures models were computed. Each patient fulfilled validated questionnaires on quality of life, knowledge about diabetes and CHO counting. Results : After the educational program, a reduced iAUC (0-80 min: -306, p=ns; 40-80 min: -400, p=0.07) due to greater (p=0.03) and prolonged double-wave insulin boluses was observed. Blood glucose peak and time to peak were also reduced. Moreover, improvements in the psycho-affective dimension, as well as in the alimentary knowledge were detected. Conclusion: Therefore, a personalized educational program on CHO + FPU counting together with insulin bolus management can improve glycemic control during social consumption of alcohol, with positive reflections on the psycho-affective dimension. Further studies are mandatory to confirm such preliminary results.

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