Dataset Information

The Placental Atlas Tool (PAT): A collaborative research and discovery platform for the placental research community.

ABSTRACT: INTRODUCTION:The placenta is one of the least understood, yet arguably one of the most important organs for human health and development. While there have been numerous research efforts dedicated to understanding the placenta's critical role, these studies and the data they produced remain separated and largely disparate. In order to facilitate placental research, the Eunice Kennedy Shriver National Institute of Child and Human Development (NICHD) released in October 2018 the Placental Atlas Tool (PAT) (https://pat.nichd.nih.gov/), an internet-based platform offering users a centralized placental database of molecular datasets, analytic tools, and images. METHODS:PAT is a cloud-based system developed by the business requirements defined by NICHD leadership and extramural placental researchers. PAT employs a metadata-driven web interface to provide curated placental datasets and images, enriched with structured, descriptive metadata to enhance data discoverability. PAT also incorporates open source molecular data analytical tools to provide a flexible analytics workflow for placental researchers. RESULTS:PAT launched with 426 analyzable molecular placental datasets consisting of over 12,500 samples from 10 distinct species, all systematically annotated and processed for enhanced research utility. 828 placental images, consisting of 7 imaging modalities across 47 species, and nearly 300 annotated linked publications supplement the datasets to facilitate knowledge integration and hypothesis generation across disparate molecular studies. DISCUSSION:PAT will maximize the NICHD's investment in placental research by reinforcing open scientific inquiry, facilitating reuse of datasets, promoting novel research and testing of new hypotheses and analytic methods, and facilitating education of new researchers.

SUBMITTER: Ilekis JV

PROVIDER: S-EPMC6527124 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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The Placental Atlas Tool (PAT): A collaborative research and discovery platform for the placental research community.

Ilekis John V JV Keller Michael M Shlionskaya Alexandra A Ferguson Christopher H CH Patel Bianca B Meitiv Alexander Lobkovsky AL Gorman Bryan B Mohale Archana A

Placenta 20190401

<h4>Introduction</h4>The placenta is one of the least understood, yet arguably one of the most important organs for human health and development. While there have been numerous research efforts dedicated to understanding the placenta's critical role, these studies and the data they produced remain separated and largely disparate. In order to facilitate placental research, the Eunice Kennedy Shriver National Institute of Child and Human Development (NICHD) released in October 2018 the Placental A ...[more]

PMID: 31103066

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Project description:IntroductionFuture digital health research hinges on methodologies to conduct remote clinical assessments and in-home monitoring. The Collaborative Aging Research Using Technology (CART) initiative was introduced to establish a digital technology research platform that could widely assess activity in the homes of diverse cohorts of older adults and detect meaningful change longitudinally. This paper reports on the built end-to-end design of the CART platform, its functionality, and the resulting research capabilities.MethodsCART platform development followed a principled design process aiming for scalability, use case flexibility, longevity, and data privacy protection while allowing sharability. The platform, comprising ambient technology, wearables, and other sensors, was deployed in participants' homes to provide continuous, long-term (months to years), and ecologically valid data. Data gathered from CART homes were sent securely to a research server for analysis and future data sharing.ResultsThe CART system was created, iteratively tested, and deployed to 232 homes representing four diverse cohorts (African American, Latinx, low-income, and predominantly rural-residing veterans) of older adults (n = 301) across the USA. Multiple measurements of wellness such as cognition (e.g., mean daily computer use time = 160-169 min), physical mobility (e.g., mean daily transitions between rooms = 96-155), sleep (e.g., mean nightly sleep duration = 6.3-7.4 h), and level of social engagement (e.g., reports of overnight visitors = 15-45%) were collected across cohorts.ConclusionThe CART initiative resulted in a minimally obtrusive digital health-enabled system that met the design principles while allowing for data capture over extended periods and can be widely used by the research community. The ability to monitor and manage health digitally within the homes of older adults is an important alternative to in-person assessments in many research contexts. Further advances will come with wider, shared use of the CART system in additional settings, within different disease contexts, and by diverse research teams.

Project description:Soft tissue sarcoma (STS) is a heterogeneous family of rare mesenchymal tumors, characterized by histopathological and molecular diversity. Tissue microarray (TMA) is a tool that allows performing research in orphan diseases in a more efficient and cost-effective way. TMAs are paraffin blocks consisting of multiple small representative tissue cores from biological samples, for example, from multiple donors, diverse sites of disease, or multiple different diseases. In 2015, we began constructing TMAs using archival tumor material from STS patients. Specimens were well annotated in terms of histopathological diagnosis, treatment, and clinical follow-up of the tissue donors. Each TMA block contains duplicate or triplicate 1.0-1.5 mm tissue cores from representative tumor areas selected by sarcoma pathologists. The construction of TMAs was performed with TMA Grand Master (3DHistech). So far, we have established disease-specific TMAs from 7 STS subtypes: gastrointestinal stromal tumor (72 cases included in the array), alveolar soft part sarcoma (n = 12 + 47), clear cell sarcoma (n = 22 + 32), leiomyosarcoma (n = 55), liposarcoma (n = 42), inflammatory myofibroblastic tumor (n = 12 + 21), and alveolar rhabdomyosarcoma (n = 24). We also constructed a multisarcoma TMA covering a representative number of important histopathological subtypes on arrays for screening purposes, namely, angiosarcoma, dedifferentiated liposarcoma, pleomorphic liposarcoma, and myxoid liposarcoma, leiomyosarcoma, malignant peripheral nerve sheath tumor, myxofibrosarcoma, rhabdomyosarcoma, synovial sarcoma, and undifferentiated pleomorphic sarcoma, with 7-11 individual cases per subtype. We are currently expanding the list of TMAs with additional sarcoma entities, considering the heterogeneity of this family of tumors. Our extensive STS TMA platform is suitable for rapid and cost-effective morphological, immunohistochemical, and molecular characterization of the tumor as well as for the identification of potential novel diagnostic markers and drug targets. It is readily available for collaborative projects with research partners.

Dataset Information

The Placental Atlas Tool (PAT): A collaborative research and discovery platform for the placental research community.

Publications

The Placental Atlas Tool (PAT): A collaborative research and discovery platform for the placental research community.

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