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Anatomical Record (Hoboken, N.J. : 2007) Apr 2022Human fetal and embryos collections (FECs) peaked in the late 19th century, an era before informed consent, and hence have unclear provenance. These collections are not... (Review)
Review
Human fetal and embryos collections (FECs) peaked in the late 19th century, an era before informed consent, and hence have unclear provenance. These collections are not only historical artifacts, but prized resources for education and research. This study aimed to determine, via a narrative review, the present location, status, and profile of reported human fetal and embryonic collections. Twenty-seven articles that reported on collections appropriate to the study were selected from an initial search pool of 120 articles. The reported collections were in: Australia (n = 1), Germany (n = 6), Japan (n = 1), Spain (n = 1), and the United States (n = 5). The largest collection is reported to contain 45,000 prenatal remains and the smallest, three remains. The purpose of establishing majority of the collections was for education and research. Eight collections contain both embryos and fetuses, one collection contained embryos, exclusively. Another collection contained only fetuses and one neonatal cadaver. The provenance, where mentioned, specified gynecologists and obstetricians as the main source of remains (n = 5). Except for the Kyoto Collection, information regarding informed consent from the next-of-kin was lacking. This paper draws upon the three themes of purpose, provenance, and profile and highlights the need to establish agreed international guidelines for the most appropriate ethical and sustainable practice with respect to establishment, procurement of remains, access, and maintenance of these collections. Nine domains for these guidelines are recommended: consent, privacy, commercial gain, digital and emerging technologies, commemorations and memorials, destruction and disposal, dignity of donors, global database and collaboration, and sustainability.
Topics: Cadaver; Female; Fetus; Germany; Humans; Infant, Newborn; Informed Consent; Pregnancy; Spain; United States
PubMed: 35099840
DOI: 10.1002/ar.24863 -
Reviews in Fish Biology and Fisheries 2023Seafood is an important source of protein and micronutrients, but fishery stocks are increasingly under pressure from both legitimate and illegitimate fishing practices....
Seafood is an important source of protein and micronutrients, but fishery stocks are increasingly under pressure from both legitimate and illegitimate fishing practices. Sustainable management of our oceans is a global responsibility, aligning with United Nations Sustainable Development Goal 14, . In a post-COVID-19 world, there is an opportunity to build back better, where locally sourced food via transparent supply chains are ever-more important. This article summarises emerging research of two innovative case studies in detecting and validating seafood provenance; and using alternative supply chains to minimise the opportunity for seafood fraud in a post-COVID-19 world.
PubMed: 36593873
DOI: 10.1007/s11160-022-09747-2 -
Journal of Hand and Microsurgery Jan 2021We have all heard the old aphorism, "Necessity is the mother of invention." While the provenance of the proverb is uncertain, its truth is not in doubt. This is true for... (Review)
Review
We have all heard the old aphorism, "Necessity is the mother of invention." While the provenance of the proverb is uncertain, its truth is not in doubt. This is true for the development of hand surgery in Malaysia. As part of the management for leprosy, patients with high ulnar nerve palsies were managed by the pioneers of hand surgery in Malaysia. They did tendon transfers to improve the quality of life of these patients. Since then, hand surgery in Malaysia have grown leaps and bounds. From a small humble beginning in the suburb of Sungai Buloh to organizing the 10th Congress of Asian Pacific Federation of Societies for Surgery of the Hand, hand surgery in Malaysia will only get better with time.
PubMed: 33707919
DOI: 10.1055/s-0040-1721942 -
Patterns (New York, N.Y.) Sep 2021Reproducible computational research (RCR) is the keystone of the scientific method for analyses, packaging the transformation of raw data to published results. In... (Review)
Review
Reproducible computational research (RCR) is the keystone of the scientific method for analyses, packaging the transformation of raw data to published results. In addition to its role in research integrity, improving the reproducibility of scientific studies can accelerate evaluation and reuse. This potential and wide support for the FAIR principles have motivated interest in metadata standards supporting reproducibility. Metadata provide context and provenance to raw data and methods and are essential to both discovery and validation. Despite this shared connection with scientific data, few studies have explicitly described how metadata enable reproducible computational research. This review employs a functional content analysis to identify metadata standards that support reproducibility across an analytic stack consisting of input data, tools, notebooks, pipelines, and publications. Our review provides background context, explores gaps, and discovers component trends of embeddedness and methodology weight from which we derive recommendations for future work.
PubMed: 34553169
DOI: 10.1016/j.patter.2021.100322 -
BMJ (Clinical Research Ed.) Aug 2022
Topics: Alcohol Drinking; Ethanol; Humans
PubMed: 35948355
DOI: 10.1136/bmj.o1979 -
MSphere Jun 2022The availability of public genomics data has become essential for modern life sciences research, yet the quality, traceability, and curation of these data have...
The availability of public genomics data has become essential for modern life sciences research, yet the quality, traceability, and curation of these data have significant impacts on a broad range of microbial genomics research. While microbial genome databases such as NCBI's RefSeq database leverage the scalability of crowd sourcing for growth, genomics data provenance and authenticity of the source materials used to produce data are not strict requirements. Here, we describe the assembly of 1,113 bacterial genome references produced from authenticated materials sourced from the American Type Culture Collection (ATCC), each with full genomics data provenance relating to bioinformatics methods, quality control, and passage history. Comparative genomics analysis of ATCC standard reference genomes (ASRGs) revealed significant issues with regard to NCBI's RefSeq bacterial genome assemblies related to completeness, mutations, structure, strain metadata, and gaps in traceability to the original biological source materials. Nearly half of RefSeq assemblies lack details on sample source information, sequencing technology, or bioinformatics methods. Deep curation of these records is not within the scope of NCBI's core mission in supporting open science, which aims to collect sequence records that are submitted by the public. Nonetheless, we propose that gaps in metadata accuracy and data provenance represent an "elephant in the room" for microbial genomics research. Effectively addressing these issues will require raising the level of accountability for data depositors and acknowledging the need for higher expectations of quality among the researchers whose research depends on accurate and attributable reference genome data. The traceability of microbial genomics data to authenticated physical biological materials is not a requirement for depositing these data into public genome databases. This creates significant risks for the reliability and data provenance of these important genomics research resources, the impact of which is not well understood. We sought to investigate this by carrying out a comparative genomics study of 1,113 ATCC standard reference genomes (ASRGs) produced by ATCC from authenticated and traceable materials using the latest sequencing technologies. We found widespread discrepancies in genome assembly quality, genetic variability, and the quality and completeness of the associated metadata among hundreds of reference genomes for ATCC strains found in NCBI's RefSeq database. We present a comparative analysis of -assembled ASRGs, their respective metadata, and variant analysis using RefSeq genomes as a reference. Although assembly quality in RefSeq has generally improved over time, we found that significant quality issues remain, especially as related to genomic data and metadata provenance. Our work highlights the importance of data authentication and provenance for the microbial genomics community, and underscores the risks of ignoring this issue in the future.
Topics: Databases, Genetic; Genome, Bacterial; Genome, Microbial; Genomics; Reproducibility of Results
PubMed: 35491842
DOI: 10.1128/msphere.00077-22 -
Science Advances Aug 2021The centrality of the Krebs cycle in metabolism has long been interpreted as evidence of its antiquity, and consequently, questions regarding its provenance, and whether...
The centrality of the Krebs cycle in metabolism has long been interpreted as evidence of its antiquity, and consequently, questions regarding its provenance, and whether it initially functioned as a cycle or not, have received much attention. The present report shows that prebiotic oxidation of α-hydroxy carboxylates can be achieved by UV photolysis of a simple geochemical species (HS), which leads to α-oxo carboxylates that feature in the Krebs cycle and glyoxylate shunt. Further reaction of these products leads to almost all intermediates of the Krebs cycle proper, succinate semialdehyde bypass, and glyoxylate shunt. Fumarate, the missing Krebs cycle component, and the required α-hydroxy carboxylates can be provided by a highly related hydrogen cyanide chemistry, which also provides precursors for amino acids, nucleotides, and phospholipids.
PubMed: 34389542
DOI: 10.1126/sciadv.abh3981 -
Hellenic Journal of Nuclear Medicine 2022It could be argued that the first medical historian in the Western Medical Tradition, is the author of the treatise On Ancient Medicine, included in the Hippocratic...
It could be argued that the first medical historian in the Western Medical Tradition, is the author of the treatise On Ancient Medicine, included in the Hippocratic Corpus, in all probability, Hippocrates himself. In our time, the domain of the history of medicine is inhabited by two factions, often indifferent towards each other's contributions, if not occasionally confrontational. One faction is represented by medical practitioners who, usually upon retirement from clinical care, research and seek to understand the practice and evolution of their craft in the recent and distant past. They are the medical historians. The other, by academic historians with a background in humanities who view and research the history of medicine from a different perspective. Historiography, the philosophy of science, philological concerns, the provenance of manuscripts, textual scrutiny, the cultural and social parameters relevant to their historical subject, are the focus of the work of these historians of medicine. Rarely, researchers of the history of medicine combine optimally humanities with a medical background. Many will recognize Sir William Osler (1849-1919) as the best representative of this happy cohabitation. The opportunity now arises for a fruitful collaboration between medical historians and historians of medicine in recording the unprecedented times and the global challenges of the COVID-19 pandemic. Now is the time for truce.
Topics: COVID-19; Historiography; History, 20th Century; Humans; Nuclear Medicine; Pandemics; Philosophy
PubMed: 35503555
DOI: 10.1967/s002449912442 -
Patterns (New York, N.Y.) May 2020Data provenance is a machine-readable summary of the collection and computational history of a dataset. Data provenance confers or adds value to a dataset, helps...
Data provenance is a machine-readable summary of the collection and computational history of a dataset. Data provenance confers or adds value to a dataset, helps reproduce computational analyses, or validates scientific conclusions. The people of the End-to-End Provenance Project are a community of professionals who have developed software tools to collect and use data provenance.
PubMed: 33205093
DOI: 10.1016/j.patter.2020.100016 -
JMIR Research Protocols Nov 2021Provenance supports the understanding of data genesis, and it is a key factor to ensure the trustworthiness of digital objects containing (sensitive) scientific data....
BACKGROUND
Provenance supports the understanding of data genesis, and it is a key factor to ensure the trustworthiness of digital objects containing (sensitive) scientific data. Provenance information contributes to a better understanding of scientific results and fosters collaboration on existing data as well as data sharing. This encompasses defining comprehensive concepts and standards for transparency and traceability, reproducibility, validity, and quality assurance during clinical and scientific data workflows and research.
OBJECTIVE
The aim of this scoping review is to investigate existing evidence regarding approaches and criteria for provenance tracking as well as disclosing current knowledge gaps in the biomedical domain. This review covers modeling aspects as well as metadata frameworks for meaningful and usable provenance information during creation, collection, and processing of (sensitive) scientific biomedical data. This review also covers the examination of quality aspects of provenance criteria.
METHODS
This scoping review will follow the methodological framework by Arksey and O'Malley. Relevant publications will be obtained by querying PubMed and Web of Science. All papers in English language will be included, published between January 1, 2006 and March 23, 2021. Data retrieval will be accompanied by manual search for grey literature. Potential publications will then be exported into a reference management software, and duplicates will be removed. Afterwards, the obtained set of papers will be transferred into a systematic review management tool. All publications will be screened, extracted, and analyzed: title and abstract screening will be carried out by 4 independent reviewers. Majority vote is required for consent to eligibility of papers based on the defined inclusion and exclusion criteria. Full-text reading will be performed independently by 2 reviewers and in the last step, key information will be extracted on a pretested template. If agreement cannot be reached, the conflict will be resolved by a domain expert. Charted data will be analyzed by categorizing and summarizing the individual data items based on the research questions. Tabular or graphical overviews will be given, if applicable.
RESULTS
The reporting follows the extension of the Preferred Reporting Items for Systematic reviews and Meta-Analyses statements for Scoping Reviews. Electronic database searches in PubMed and Web of Science resulted in 469 matches after deduplication. As of September 2021, the scoping review is in the full-text screening stage. The data extraction using the pretested charting template will follow the full-text screening stage. We expect the scoping review report to be completed by February 2022.
CONCLUSIONS
Information about the origin of healthcare data has a major impact on the quality and the reusability of scientific results as well as follow-up activities. This protocol outlines plans for a scoping review that will provide information about current approaches, challenges, or knowledge gaps with provenance tracking in biomedical sciences.
INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)
DERR1-10.2196/31750.
PubMed: 34813494
DOI: 10.2196/31750