Browsing by Author "Ray, Jessica"

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    FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology
    (bioRxiv, 2024-08-22) Border, Samuel; Ferreira, Ricardo Melo; Lucarelli, Nicholas; Manthey, David; Kumar, Suhas; Paul, Anindya; Mimar, Sayat; Naglah, Ahmed; Cheng, Ying-Hua; Barisoni, Laura; Ray, Jessica; Strekalova, Yulia; Rosenberg, Avi Z.; Tomaszewski, John E.; Hodgin, Jeffrey B.; HuBMAP consortium; El-Achkar, Tarek M.; Jain, Sanjay; Eadon, Michael T.; Sarder, Pinaki; Medicine, School of Medicine
    Spatial -OMICS technologies facilitate the interrogation of molecular profiles in the context of the underlying histopathology and tissue microenvironment. Paired analysis of histopathology and molecular data can provide pathologists with otherwise unobtainable insights into biological mechanisms. To connect the disparate molecular and histopathologic features into a single workspace, we developed FUSION (Functional Unit State IdentificatiON in WSIs [Whole Slide Images]), a web-based tool that provides users with a broad array of visualization and analytical tools including deep learning-based algorithms for in-depth interrogation of spatial -OMICS datasets and their associated high-resolution histology images. FUSION enables end-to-end analysis of functional tissue units (FTUs), automatically aggregating underlying molecular data to provide a histopathology-based medium for analyzing healthy and altered cell states and driving new discoveries using "pathomic" features. We demonstrate FUSION using 10x Visium spatial transcriptomics (ST) data from both formalin-fixed paraffin embedded (FFPE) and frozen prepared datasets consisting of healthy and diseased tissue. Through several use-cases, we demonstrate how users can identify spatial linkages between quantitative pathomics, qualitative image characteristics, and spatial --omics.
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    User-Centered Framework for Implementation of Technology (UFIT): Development of an Integrated Framework for Designing Clinical Decision Support Tools Packaged With Tailored Implementation Strategies
    (JMIR, 2024-05-21) Ray, Jessica; Benjamin Finn, Emily; Tyrrell, Hollyce; Aloe, Carlin F.; Perrin, Eliana M.; Wood, Charles T.; Miner, Dean S.; Grout, Randall; Michel, Jeremy J.; Damschroder, Laura J.; Sharifi, Mona; Pediatrics, School of Medicine
    Background: Electronic health record-based clinical decision support (CDS) tools can facilitate the adoption of evidence into practice. Yet, the impact of CDS beyond single-site implementation is often limited by dissemination and implementation barriers related to site- and user-specific variation in workflows and behaviors. The translation of evidence-based CDS from initial development to implementation in heterogeneous environments requires a framework that assures careful balancing of fidelity to core functional elements with adaptations to ensure compatibility with new contexts. Objective: This study aims to develop and apply a framework to guide tailoring and implementing CDS across diverse clinical settings. Methods: In preparation for a multisite trial implementing CDS for pediatric overweight or obesity in primary care, we developed the User-Centered Framework for Implementation of Technology (UFIT), a framework that integrates principles from user-centered design (UCD), human factors/ergonomics theories, and implementation science to guide both CDS adaptation and tailoring of related implementation strategies. Our transdisciplinary study team conducted semistructured interviews with pediatric primary care clinicians and a diverse group of stakeholders from 3 health systems in the northeastern, midwestern, and southeastern United States to inform and apply the framework for our formative evaluation. Results: We conducted 41 qualitative interviews with primary care clinicians (n=21) and other stakeholders (n=20). Our workflow analysis found 3 primary ways in which clinicians interact with the electronic health record during primary care well-child visits identifying opportunities for decision support. Additionally, we identified differences in practice patterns across contexts necessitating a multiprong design approach to support a variety of workflows, user needs, preferences, and implementation strategies. Conclusions: UFIT integrates theories and guidance from UCD, human factors/ergonomics, and implementation science to promote fit with local contexts for optimal outcomes. The components of UFIT were used to guide the development of Improving Pediatric Obesity Practice Using Prompts, an integrated package comprising CDS for obesity or overweight treatment with tailored implementation strategies.