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BMJ (Clinical Research Ed.) May 2024
Topics: Humans; Social Media; Smartphone; Adolescent; Mental Health; Mental Disorders; Adolescent Health
PubMed: 38806185
DOI: 10.1136/bmj-2024-079828 -
Scientific Data Sep 2023The Ontology for Avida (OntoAvida) aims to develop an integrated vocabulary for the description of Avida, the most widely used computational approach for performing...
The Ontology for Avida (OntoAvida) aims to develop an integrated vocabulary for the description of Avida, the most widely used computational approach for performing experimental evolution using digital organisms-self-replicating computer programs that evolve within a user-defined computational environment. The lack of a clearly defined vocabulary makes some biologists feel reluctant to embrace the field of digital evolution. This integrated framework empowers biologists by equipping them with the necessary tools to explore and analyze the field of digital evolution more effectively. By leveraging the vocabulary of Avida, researchers can gain deeper insights into the evolutionary processes and dynamics of digital organisms. In addition, OntoAvida allows researchers to make inference based on certain rules and constraints, facilitate the reproducibility of in silico evolution experiments and trace the provenance of the data stored in avidaDB-an RDF database containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms. OntoAvida is part of the Open Biological and Biomedical Ontologies (OBO Foundry) and is available at http://www.obofoundry.org/ontology/ontoavida.html .
PubMed: 37689762
DOI: 10.1038/s41597-023-02514-3 -
New Biotechnology Dec 2023AI development in biotechnology relies on high-quality data to train and validate algorithms. The FAIR principles (Findable, Accessible, Interoperable, and Reusable) and...
AI development in biotechnology relies on high-quality data to train and validate algorithms. The FAIR principles (Findable, Accessible, Interoperable, and Reusable) and regulatory frameworks such as the In Vitro Diagnostic Regulation (IVDR) and the Medical Device Regulation (MDR) specify requirements on specimen and data provenance to ensure the quality and traceability of data used in AI development. In this paper, a framework is presented for recording and publishing provenance information to meet these requirements. The framework is based on the use of standardized models and protocols, such as the W3C PROV model and the ISO 23494 series, to capture and record provenance information at various stages of the data generation and analysis process. The framework and use case illustrate the role of provenance information in supporting the development of high-quality AI algorithms in biotechnology. Finally, the principles of the framework are illustrated in a simple computational pathology use case, showing how specimen and data provenance can be used in the development and documentation of an AI algorithm. The use case demonstrates the importance of managing and integrating distributed provenance information and highlights the complex task of considering factors such as semantic interoperability, confidentiality, and the verification of authenticity and integrity.
Topics: Algorithms; Biotechnology; Artificial Intelligence
PubMed: 37758054
DOI: 10.1016/j.nbt.2023.09.006 -
Journal of the Science of Food and... Mar 2024Provenance is becoming increasingly important in meat supply chains as it lends products higher perceived quality. However, its precise definition and interpretation... (Review)
Review
Provenance is becoming increasingly important in meat supply chains as it lends products higher perceived quality. However, its precise definition and interpretation along with its associated characteristics factors have remained somewhat elusive. This review meticulously defines meat provenance while dissecting the essential factors and associated quality attributes that constitute its essence and are subsequently employed to establish pertinent markers for provenance. Meat provenance emerges as a multi-dimensional construct stemming from the adept management of a constellation of factors relating to geographical origin, farm production system, traceability, and authenticity. Through intricate interactions, these factors unveil innate originality that not only forges a distinct reputation but also imparts a unique typicity to the meat product. Gaining insights into a meat product's provenance becomes attainable by scrutinizing its pertinent composition and organoleptic quality traits. Trace elements and stable isotopes stand out as provenance markers, forging a direct connection to both geographical origin and dietary sources. While somewhat less direct in linkage, other markers such as plant biomarkers, fatty acid composition, pH levels, flavour and aromatic compounds along with organoleptic characteristics contribute to the overall understanding of provenance. Additionally, the identification of animal species and breeds serves as key markers, particularly in the context of protected geographical indications. The study findings are useful for the various stakeholders of how the information for meat provenance can be linked with intrinsic and extrinsic factors for meat quality and protecting the integrity of the supply chain with special reference to traceability and authenticity. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
PubMed: 38545907
DOI: 10.1002/jsfa.13492 -
BMJ (Clinical Research Ed.) Mar 2024
Topics: Humans; Health Care Sector; State Medicine; England
PubMed: 38503446
DOI: 10.1136/bmj-2024-079261 -
BMJ (Clinical Research Ed.) Mar 2024
Topics: Humans; Leadership; Trust
PubMed: 38503456
DOI: 10.1136/bmj.q692 -
BMJ (Clinical Research Ed.) Apr 2024
Topics: Humans; Latin America; Global Health
PubMed: 38569718
DOI: 10.1136/bmj.q716 -
Global Change Biology Sep 2023Intraspecific variation plays a critical role in extant and future forest responses to climate change. Forest tree species with wide climatic niches rely on the... (Review)
Review
Intraspecific variation plays a critical role in extant and future forest responses to climate change. Forest tree species with wide climatic niches rely on the intraspecific variation resulting from genetic adaptation and phenotypic plasticity to accommodate spatial and temporal climate variability. A centuries-old legacy of forest ecological genetics and provenance trials has provided a strong foundation upon which to continue building on this knowledge, which is critical to maintain climate-adapted forests. Our overall objective is to understand forest trees intraspecific responses to climate across species and biomes, while our specific objectives are to describe ecological genetics models used to build our foundational knowledge, summarize modeling approaches that have expanded the traditional toolset, and extensively review the literature from 1994 to 2021 to highlight the main contributions of this legacy and the new analyzes of provenance trials. We reviewed 103 studies comprising at least three common gardens, which covered 58 forest tree species, 28 of them with range-wide studies. Although studies using provenance trial data cover mostly commercially important forest tree species from temperate and boreal biomes, this synthesis provides a global overview of forest tree species adaptation to climate. We found that evidence for genetic adaptation to local climate is commonly present in the species studied (79%), being more common in conifers (87.5%) than in broadleaf species (67%). In 57% of the species, clines in fitness-related traits were associated with temperature variables, in 14% of the species with precipitation, and in 25% of the species with both. Evidence of adaptation lags was found in 50% of the species with range-wide studies. We conclude that ecological genetics models and analysis of provenance trial data provide excellent insights on intraspecific genetic variation, whereas the role and limits of phenotypic plasticity, which will likely determine the fate of extant forests, is vastly understudied.
Topics: Trees; Climate Change; Forests; Adaptation, Physiological; Ecosystem
PubMed: 37029765
DOI: 10.1111/gcb.16711 -
A Road Map for Peer Review of Real-World Evidence Studies on Safety and Effectiveness of Treatments.Diabetes Care Aug 2023The growing acceptance of real-world evidence (RWE) in clinical and regulatory decision-making, coupled with increasing availability of health care data and advances in... (Review)
Review
The growing acceptance of real-world evidence (RWE) in clinical and regulatory decision-making, coupled with increasing availability of health care data and advances in automated analytic approaches, has contributed to a marked expansion of RWE studies of diabetes and other diseases. However, a recent spate of high-profile retractions highlights the need for improvements in the conduct of RWE research as well as in the associated peer review and editorial processes. We review best pharmacoepidemiologic practices and common pitfalls regarding design, measurement, analysis, data validity, appropriateness, and generalizability of RWE studies. To enhance RWE study assessments, we propose that journal editors require 1) study authors to complete RECORD-PE, a reporting guideline for pharmacoepidemiological studies on routinely collected data, 2) availability of predetermined study protocols and analysis plans, 3) inclusion of pharmacoepidemiologists on the peer review team, and 4) provision of detail on data provenance, characterization, and custodianship to facilitate assessment of the data source. We recognize that none of these steps guarantees a high-quality research study. Collectively, however, they permit an informed assessment of whether the study was adequately designed and conducted and whether the data source used was fit for purpose.
Topics: Humans; Peer Review; Delivery of Health Care
PubMed: 37471605
DOI: 10.2337/dc22-2037 -
Frontiers in Plant Science 2023Tree height (H) and stem diameter at breast height (DBH) (H-D) relationship is correlated with timber yield and quality as well as stability of forest and is crucial in...
Tree height (H) and stem diameter at breast height (DBH) (H-D) relationship is correlated with timber yield and quality as well as stability of forest and is crucial in forest management and genetic breeding. It is influenced by not only environmental factors such as site quality and climate factors but also genetic control that is mostly neglected. A dataset of H and DBH of 25 provenances of Buch.-Ham. ex D. Don at four sites was used to model the H-D relationship. The dummy variable nonliner mixed-effect equations were applied to evaluate the effects of sites and provenances on variations of the H-D relationship and to select superior provenances of . Weibull equation was selected as the base model for the H-D relationship. The sites affected asymptotes of the H-D curves, and the provenance effect on asymptotes of the H-D curves varied across sites. Taking above-average DBH and lower asymptote of the H-D curves as indicators, five excellent provenances were screened out at each site with a rate of 20%. Their selection gains of individual volume ranged from 1.99% to 29.81%, and their asymptote parameter () and H-D ratio were 7.17%-486.05% and 3.07-4.72% lower than the relevant total means at four sites, respectively. Genetic selection based on the H-D relationship could promote selection efficiency of excellent germplasms and was beneficial for the large-sized timber production of .
PubMed: 37849846
DOI: 10.3389/fpls.2023.1248278