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1.
bioRxiv ; 2023 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-36945489

RESUMO

Selecting and implementing a tissue-clearing protocol is challenging. Established more than 100 years ago, tissue clearing is still a rapidly evolving field of research. There are currently many published protocols to choose from, and each performs better or worse across a range of key evaluation factors (e.g., speed, cost, tissue stability, fluorescence quenching). Additionally, tissue-clearing protocols are often optimized for specific experimental contexts, and applying an existing protocol to a new problem can require a lengthy period of adaptation by trial and error. Although the primary literature and review articles provide a useful starting point for optimization, there is growing recognition that many articles do not provide sufficient detail to replicate or reproduce experimental results. To help address this issue, we have developed a novel, freely available repository of tissue-clearing protocols named T-CLEARE (Tissue CLEAring protocol REpository; https://doryworkspace.org/doryviz). T-CLEARE incorporates community responses to an open survey designed to capture details not commonly found in the scientific literature, including modifications to published protocols required for specific use cases and instances when tissue-clearing protocols did not perform well (negative results). The goal of T-CLEARE is to provide a forum for the community to share evaluations and modifications of tissue-clearing protocols for various tissue types and potentially identify best-in-class methods for a given application.

2.
Am J Prev Med ; 65(3): 534-542, 2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-36935055

RESUMO

INTRODUCTION: Social determinants are structures and conditions in the biological, physical, built, and social environments that affect health, social and physical functioning, health risk, quality of life, and health outcomes. The adoption of recommended, standard measurement protocols for social determinants of health will advance the science of minority health and health disparities research and provide standard social determinants of health protocols for inclusion in all studies with human participants. METHODS: A PhenX (consensus measures for Phenotypes and eXposures) Working Group of social determinants of health experts was convened from October 2018 to May 2020 and followed a well-established consensus process to identify and recommend social determinants of health measurement protocols. The PhenX Toolkit contains data collection protocols suitable for inclusion in a wide range of research studies. The recommended social determinants of health protocols were shared with the broader scientific community to invite review and feedback before being added to the Toolkit. RESULTS: Nineteen social determinants of health protocols were released in the PhenX Toolkit (https://www.phenxtoolkit.org) in May 2020 to provide measures at the individual and structural levels for built and natural environments, structural racism, economic resources, employment status, occupational health and safety, education, environmental exposures, food environment, health and health care, and sociocultural community context. CONCLUSIONS: Promoting the adoption of well-established social determinants of health protocols can enable consistent data collection and facilitate comparing and combining studies, with the potential to increase their scientific impact.


Assuntos
Qualidade de Vida , Determinantes Sociais da Saúde , Humanos , Fenótipo , Coleta de Dados , Projetos de Pesquisa
3.
Sci Data ; 9(1): 449, 2022 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-35896564

RESUMO

Recent advances in fluorescence microscopy techniques and tissue clearing, labeling, and staining provide unprecedented opportunities to investigate brain structure and function. These experiments' images make it possible to catalog brain cell types and define their location, morphology, and connectivity in a native context, leading to a better understanding of normal development and disease etiology. Consistent annotation of metadata is needed to provide the context necessary to understand, reuse, and integrate these data. This report describes an effort to establish metadata standards for three-dimensional (3D) microscopy datasets for use by the Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative and the neuroscience research community. These standards were built on existing efforts and developed with input from the brain microscopy community to promote adoption. The resulting 3D Microscopy Metadata Standards (3D-MMS) includes 91 fields organized into seven categories: Contributors, Funders, Publication, Instrument, Dataset, Specimen, and Image. Adoption of these metadata standards will ensure that investigators receive credit for their work, promote data reuse, facilitate downstream analysis of shared data, and encourage collaboration.


Assuntos
Metadados , Microscopia , Encéfalo/anatomia & histologia , Encéfalo/diagnóstico por imagem , Conjuntos de Dados como Assunto , Humanos , Microscopia/métodos , Microscopia/normas
4.
Curr Protoc ; 1(4): e111, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33905618

RESUMO

The PhenX (consensus measures for Phenotypes and eXposures) Toolkit (https://www.phenxtoolkit.org/) is a publicly available, web-based catalog of recommended, well-established measurement protocols of phenotypes and exposures. The goal of PhenX is to facilitate the use of standard measures, enhance data interoperability, and promote collaborative and translational research. PhenX is driven by the scientific community and historically has depended on working groups of experts to recommend measures for release in the PhenX Toolkit. The urgent need for recommended, standard measures for COVID-19 research triggered the development of a "rapid release" process for releasing new content in the PhenX Toolkit. Initially, PhenX collaborated with the National Institutes of Health (NIH) Office of Behavioral and Social Sciences Research, the National Human Genome Research Institute, and the NIH Disaster Research Response (DR2) program to create a library of COVID-19 measurement protocols. With additional support from NIH, PhenX adapted crowdsourcing techniques to accelerate prioritization and recommendation of protocols for release in the PhenX Toolkit. Prioritized COVID-19-specific protocols were used to anchor and define specialty collections of protocols that were subject to review and approval by the PhenX Steering Committee. In addition to the COVID-19-specific protocols, the specialty collections include existing, well-established PhenX protocols, use of which will further enhance data interoperability and cross-study analysis. The COVID-19 specialty collections are Behaviors and Risks; Ethnicity, Race and Demographics; History, Treatment and Outcomes; Information Resources; Psychosocial and Mental Health; and Socioeconomic. The development and usage of PhenX COVID-19 specialty collections are described in this article. © 2021 The Authors. Basic Protocol: Selecting COVID-19 protocols.


Assuntos
Pesquisa Biomédica , COVID-19 , Bases de Dados Factuais , Software , COVID-19/epidemiologia , COVID-19/fisiopatologia , Humanos , Internet , SARS-CoV-2/isolamento & purificação , Pesquisa Translacional Biomédica , Estados Unidos
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