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  1. 11561
    “…The implementation is open-source and available on https://bioinformatics.fh-hagenberg.at/immunoanalyzer/.…”
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    ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data
  2. 11562
    “…METHODS: Clinical information and transcriptome profiling of patients with LUAD were retrieved and downloaded from open-source databases. Autophagy-dependent ferroptosis-related genes were screened by published articles. …”
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    Comprehensive analysis of the autophagy-dependent ferroptosis-related gene FANCD2 in lung adenocarcinoma
  3. 11563
    “…RESULTS: Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and microdiversity levels. …”
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    MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations
  4. 11564
    “…We implemented simulation models using Hyperledger Fabric, an open source blockchain framework. RESULTS: We performed a simulation of the EMR-sharing process and compared it with previous works on blockchain-based medical systems to check the proposed system’s performance. …”
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    Privacy Preservation in Patient Information Exchange Systems Based on Blockchain: System Design Study
  5. 11565
    “…CONCLUSIONS: The proposed aims will collectively demonstrate a precision feedback service developed using an open-source technical infrastructure for computable knowledge management. …”
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    A Scalable Service to Improve Health Care Quality Through Precision Audit and Feedback: Proposal for a Randomized Controlled Trial
  6. 11566
    “…METHODS: We developed a tool to analyze the public opinion on COVID-19 vaccines from Twitter, exploiting, among other techniques, a state-of-the-art system for the identification of adverse drug events on social media; natural language processing models for sentiment analysis; statistical tools; and open-source databases to visualize the trending hashtags, news articles, and their factuality. …”
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    Monitoring User Opinions and Side Effects on COVID-19 Vaccines in the Twittersphere: Infodemiology Study of Tweets
  7. 11567
    “…We outline the process for training and validating discrete-time prediction models, and demonstrate its application using the open-source R statistical programming environment. RESULTS: Using publicly available data sets, we show that some discrete-time prediction models achieve better prediction performance than the continuous-time Cox proportional hazards model. …”
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    Survival prediction models: an introduction to discrete-time modeling
  8. 11568
    “…We calculated these measures using open-source packages in R. Pearson correlations between activity count and each measure were quantified both marginally and conditionally on age, sex, and BMI. …”
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    Comparison of Accelerometry-Based Measures of Physical Activity: Retrospective Observational Data Analysis Study
  9. 11569
    “…Image segmentation of the contrast enhancing parts of the tumor was performed semi-automatically using the open-source software platform 3D Slicer. A total of 107 radiomic features were extracted by hand-delineated regions of interest from the pre-treatment MRI images of each patient. …”
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    Testing the applicability and performance of Auto ML for potential applications in diagnostic neuroradiology
  10. 11570
    “…METHODS: We developed and evaluated a step-counting app for older adults on an open-source wrist-worn device (Amulet). The app includes algorithms to infer the level of physical activity and to count steps. …”
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    A Smartwatch Step-Counting App for Older Adults: Development and Evaluation Study
  11. 11571
    por Espinoza, Josh L., Dupont, Chris L.
    Publicado 2022
    “…RESULTS: In this study, we introduce the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite developed to recover genomes from all domains. …”
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    VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
  12. 11572
    “…OCTA images of the macula (10°x10°, 15°x15°, or 20°x20° centered on the fovea) and peripapillary area (15 × 15º centered on optic nerve head) were exported from the device and processed using the open-source software Fiji. The mSVC, mDVC, and pSVC were automatically analyzed regarding vascular density in the total area and four sectors (superior, inferior, nasal, and temporal). …”
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    A standardized method to quantitatively analyze optical coherence tomography angiography images of the macular and peripapillary vessels
  13. 11573
    “…Threshold-based segmentation of involved lung was implemented using an open-source tool for whole-lung segmentation under the presence of severe pathologies (R231CovidWeb, Hofmanninger et al., 2020) and consecutive quantitative assessment of lung attenuation. …”
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    Assessment of COVID-19 lung involvement on computed tomography by deep-learning-, threshold-, and human reader-based approaches—an international, multi-center comparative study
  14. 11574
    por Spitzer, Hannah, Ripart, Mathilde, Whitaker, Kirstie, D’Arco, Felice, Mankad, Kshitij, Chen, Andrew A, Napolitano, Antonio, De Palma, Luca, De Benedictis, Alessandro, Foldes, Stephen, Humphreys, Zachary, Zhang, Kai, Hu, Wenhan, Mo, Jiajie, Likeman, Marcus, Davies, Shirin, Güttler, Christopher, Lenge, Matteo, Cohen, Nathan T, Tang, Yingying, Wang, Shan, Chari, Aswin, Tisdall, Martin, Bargallo, Nuria, Conde-Blanco, Estefanía, Pariente, Jose Carlos, Pascual-Diaz, Saül, Delgado-Martínez, Ignacio, Pérez-Enríquez, Carmen, Lagorio, Ilaria, Abela, Eugenio, Mullatti, Nandini, O’Muircheartaigh, Jonathan, Vecchiato, Katy, Liu, Yawu, Caligiuri, Maria Eugenia, Sinclair, Ben, Vivash, Lucy, Willard, Anna, Kandasamy, Jothy, McLellan, Ailsa, Sokol, Drahoslav, Semmelroch, Mira, Kloster, Ane G, Opheim, Giske, Ribeiro, Letícia, Yasuda, Clarissa, Rossi-Espagnet, Camilla, Hamandi, Khalid, Tietze, Anna, Barba, Carmen, Guerrini, Renzo, Gaillard, William Davis, You, Xiaozhen, Wang, Irene, González-Ortiz, Sofía, Severino, Mariasavina, Striano, Pasquale, Tortora, Domenico, Kälviäinen, Reetta, Gambardella, Antonio, Labate, Angelo, Desmond, Patricia, Lui, Elaine, O’Brien, Terence, Shetty, Jay, Jackson, Graeme, Duncan, John S, Winston, Gavin P, Pinborg, Lars H, Cendes, Fernando, Theis, Fabian J, Shinohara, Russell T, Cross, J Helen, Baldeweg, Torsten, Adler, Sophie, Wagstyl, Konrad
    Publicado 2022
    “…We aimed to develop an open-source, interpretable, surface-based machine-learning algorithm to automatically identify FCDs on heterogeneous structural MRI data from epilepsy surgery centres worldwide. …”
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    Interpretable surface-based detection of focal cortical dysplasias: a Multi-centre Epilepsy Lesion Detection study
  15. 11575
    “…We used logistic regression models to estimate unadjusted and adjusted odds ratios (aOR) and their 95% confidence intervals (CI) for the associations between independent variables (e.g., demographic variables, neighborhood safety, COVID Stay-at-Home order and length of time) and physical activity levels that did not meet (i.e., < 600 metabolic equivalents of task [MET]-minutes/week) or met guidelines (i.e., ≥ 600 MET-minutes/week). We used R-Studio open-source edition to clean and code data and SAS V9.4 for analyses. …”
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    Factors associated with meeting physical activity guidelines during the COVID-19 pandemic
  16. 11576
    “…Muscle sodium content over 40 min was measured using a dedicated plugin in the open-source DICOM viewer Horos. Handgrip strength was measured and correlated with sodium content. …”
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    Muscle sodium content in patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome
  17. 11577
    “…AMR genes from both approaches were identified using the open-source AMR database, ResFinder. The AMR gene data obtained from plasmids utilizing each approach were compared based on information from whole genome sequencing (WGS) data. …”
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    135. Comparing the Bioinformatic and Experimental Approaches for Identifying Antibiotic Resistance Genes on Plasmids of Acinetobacter baumannii
  18. 11578
    “…TMAs were processed to histological slides, stained, digitized and assessed for the applicability of machine learning strategies and open–source tools in diagnosis of prostate cancer. We applied the software QuPath to extract features for shape, stain intensity, and texture of TMA cores for three stainings, H&E, ERG, and PIN-4. …”
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    Evaluation of automatic discrimination between benign and malignant prostate tissue in the era of high precision digital pathology
  19. 11579
    “…METHODS: mRNA expression of genes involved in glucose metabolism and PSMA regulation obtained from primary PCa specimens were retrieved from open-source databases and analyzed using an integrative bioinformatics approach. …”
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    Gene’s expression underpinning the divergent predictive value of [18F]F-fluorodeoxyglucose and prostate-specific membrane antigen positron emission tomography in primary prostate cancer: a bioinformatic and experimental study
  20. 11580
    “…At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software (https://sourceforge.net/projects/calis-p/). …”
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    Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes
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