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BMJ (Clinical Research Ed.) Sep 2019The public must be engaged in AI innovations to ensure real benefits for health
The public must be engaged in AI innovations to ensure real benefits for health
PubMed: 31519553
DOI: 10.1136/bmj.l5434 -
Scientific Data Sep 2019The field of pharmacogenomics presents great challenges for researchers that are willing to make their studies reproducible and shareable. This is attributed to the...
The field of pharmacogenomics presents great challenges for researchers that are willing to make their studies reproducible and shareable. This is attributed to the generation of large volumes of high-throughput multimodal data, and the lack of standardized workflows that are robust, scalable, and flexible to perform large-scale analyses. To address this issue, we developed pharmacogenomic workflows in the Common Workflow Language to process two breast cancer datasets in a reproducible and transparent manner. Our pipelines combine both pharmacological and molecular profiles into a portable data object that can be used for future analyses in cancer research. Our data objects and workflows are shared on Harvard Dataverse and Code Ocean where they have been assigned a unique Digital Object Identifier, providing a level of data provenance and a persistent location to access and share our data with the community.
Topics: Computational Biology; Humans; Information Dissemination; Pharmacogenomic Testing; Software; Workflow
PubMed: 31481707
DOI: 10.1038/s41597-019-0174-7 -
The FEBS Journal Jan 2022The FEBS Journal, a leading multidisciplinary journal in the life sciences, publishes high-impact papers on diverse topics relating to molecular mechanisms underpinning...
The FEBS Journal, a leading multidisciplinary journal in the life sciences, publishes high-impact papers on diverse topics relating to molecular mechanisms underpinning biological processes. Here, Editor-in-Chief Seamus Martin discusses the critical importance of data provenance and data integrity to the scientific method and discusses some of the highlights from 2021 at The FEBS Journal.
PubMed: 34982855
DOI: 10.1111/febs.16332 -
Molecular Microbiology Jun 2022Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus and the leading cause of congenital disabilities as well as a significant cause of disease in immunocompromised... (Review)
Review
Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus and the leading cause of congenital disabilities as well as a significant cause of disease in immunocompromised patients. The envelopment and egress of HCMV particles is an essential step of the viral life cycle as it determines viral spread and potentially tropism. Here we review the current literature on HCMV envelopment and egress with a particular focus on the role of virus-containing multivesicular body-like vesicles for virus egress and spread. We discuss the difficulties of determining the cellular provenance of these structures in light of viral redistribution of cellular marker proteins and provide potential paths to illuminate their genesis. Finally, we discuss how divergent egress pathways could result in virions of different tropisms.
Topics: Cytomegalovirus; Humans; Proteins; Virion; Virus Assembly
PubMed: 35607767
DOI: 10.1111/mmi.14946 -
Patterns (New York, N.Y.) Aug 2020Deep learning, a set of approaches using artificial neural networks, has generated rapid recent advancements in machine learning. Deep learning does, however, have the...
Deep learning, a set of approaches using artificial neural networks, has generated rapid recent advancements in machine learning. Deep learning does, however, have the potential to reduce the reproducibility of scientific results. Model outputs are critically dependent on the data and processing approach used to initially generate the model, but this provenance information is usually lost during model training. To avoid a future reproducibility crisis, we need to improve our deep-learning model management. The FAIR principles for data stewardship and software/workflow implementation give excellent high-level guidance on ensuring effective reuse of data and software. We suggest some specific guidelines for the generation and use of deep-learning models in science and explain how these relate to the FAIR principles. We then present dtoolAI, a Python package that we have developed to implement these guidelines. The package implements automatic capture of provenance information during model training and simplifies model distribution.
PubMed: 33205122
DOI: 10.1016/j.patter.2020.100073 -
RoFo : Fortschritte Auf Dem Gebiete Der... May 2024Worldwide, the study and examination of human remains and the circumstances of their acquisition for anatomical collection have received great interest. As part of...
Worldwide, the study and examination of human remains and the circumstances of their acquisition for anatomical collection have received great interest. As part of provenance research projects, a large number of collections are being investigated to determine whether the human remains have been acquired in a correct or unlawful way because the people could have been killed in order to be used as "anthropological objects" for research purposes and to become so-called "specimens". These topics have also been addressed by the Institute of Anatomy at the University Medical Center Rostock. The role of radiology in this interdisciplinary project will be presented using selected examples.The anatomical collection at the University of Rostock includes 40 human skulls, 14 plaster casts, 6 Egyptian mummy heads, and 1 full-body mummy. In addition to the examination by a historian, an anthropologist, and forensic pathologists, additional computed tomography was carried out on nine skulls and the full-body mummy. Micro-computed tomography was also carried out on seven skulls in order to enable a look behind the mummification material and tissue remains.(Micro-)computed tomography was able to close diagnostic gaps and the results presented some rather unexpected findings.Due to interdisciplinary collaboration, individual fates could be determined, which provided information about the individual's life and death circumstances. None of the examined individuals showed evidence of colonial-era injustice or the use of violence that would have led to their inclusion in the collection. (Micro-)computed tomography was a valuable addition to this provenance research project. · Computed tomography enhances interdisciplinary provenance research projects.. · Computed tomography enables a non-destructive examination of human remains.. · The future of research and presentation of human remains will increasingly be virtual.. · Steinhagen I, Brinker U, Kolbe V et al. The role of radiology in provenance research - experiences from the collaboration between radiology and anatomy at the University of Rostock and future perspectives. Fortschr Röntgenstr 2024; DOI 10.1055/a-2303-0312.
PubMed: 38744319
DOI: 10.1055/a-2303-0312 -
Frontiers in Genetics 2022Fair and equitable benefit sharing of genetic resources is an expectation of the Nagoya Protocol. Although the Nagoya Protocol does not yet formally apply to Digital...
Fair and equitable benefit sharing of genetic resources is an expectation of the Nagoya Protocol. Although the Nagoya Protocol does not yet formally apply to Digital Sequence Information ("DSI"), discussions are currently underway regarding to include such data through ongoing Convention on Biological Diversity ("CBD") negotiations. While Indigenous Peoples and Local Communities ("IPLC") expect the value generated from genomic data to be subject to benefit sharing arrangements, a range of views are currently being expressed by Nation States, IPLC and other stakeholders. The use of DSI gives rise to unique considerations, creating a gray area as to how it should be considered under the Nagoya Protocol's Access and Benefit Sharing ("ABS") principles. One way for benefit sharing to be enhanced is through the connection of data to proper provenance information. A significant development is the use of digital labeling systems to ensure that the origin of samples is appropriately disclosed. The Traditional Knowledge and Biocultural Labels initiative offers a practical option for data provided to genomic databases. In particular, the BioCultural Labels ("BC Labels") are a mechanism for Indigenous communities to identify and maintain provenance, origin and authority over biocultural material and data generated from Indigenous land and waters held in research, cultural institutions and data repositories. This form of cultural metadata adds value to the research endeavor and the creation of Indigenous fields within databases adds transparency and accountability to the research environment.
PubMed: 36212139
DOI: 10.3389/fgene.2022.1014044 -
Frontiers in Cell and Developmental... 2022Lineage tracing experiments give dynamic information on the functional behaviour of dividing cells. These experiments therefore have become an important tool for... (Review)
Review
Lineage tracing experiments give dynamic information on the functional behaviour of dividing cells. These experiments therefore have become an important tool for studying stem and progenitor cell fate behavior . When cell proliferation is high or the frequency of induced clones cannot be precisely controlled, the merging and fragmentation of clones renders the retrospective interpretation of clonal fate data highly ambiguous, potentially leading to unguarded interpretations about lineage relationships and fate behaviour. Here, we discuss and generalize statistical strategies to detect, resolve and make use of clonal fragmentation and merging. We first explain how to detect the rates of clonal fragmentation and merging using simple statistical estimates. We then discuss ways to restore the clonal provenance of labelled cells algorithmically and statistically and elaborate on how the process of clonal fragmentation can indirectly inform about cell fate. We generalize and extend results from the context of their original publication.
PubMed: 36589749
DOI: 10.3389/fcell.2022.1054476 -
Journal of Grid Computing 2022In scientific collaboration, data sharing, the exchange of ideas and results are essential to knowledge construction and the development of science. Hence, we must...
In scientific collaboration, data sharing, the exchange of ideas and results are essential to knowledge construction and the development of science. Hence, we must guarantee interoperability, privacy, traceability (reinforcing transparency), and trust. Provenance has been widely recognized for providing a history of the steps taken in scientific experiments. Consequently, we must support traceability, assisting in scientific results' reproducibility. One of the technologies that can enhance trust in collaborative scientific experimentation is blockchain. This work proposes an architecture, named BlockFlow, based on blockchain, provenance, and cloud infrastructure to bring trust and traceability in the execution of collaborative scientific experiments. The proposed architecture is implemented on Hyperledger, and a scenario about the genomic sequencing of the SARS-CoV-2 coronavirus is used to evaluate the architecture, discussing the benefits of providing traceability and trust in collaborative scientific experimentation. Furthermore, the architecture addresses the heterogeneity of shared data, facilitating interpretation by geographically distributed researchers and analysis of such data. Through a blockchain-based architecture that provides support on provenance and blockchain, we can enhance data sharing, traceability, and trust in collaborative scientific experiments.
PubMed: 36246518
DOI: 10.1007/s10723-022-09626-x -
Health Services & Outcomes Research... Nov 2022The supply chain is a complex network in healthcare that crosses organizational and geographical borders. The inherent complexity of such structures can introduce...
The supply chain is a complex network in healthcare that crosses organizational and geographical borders. The inherent complexity of such structures can introduce impurities inclusive of erroneous facts, lack of transparency, and restricted records provenance. In the healthcare business, counterfeit pills are one of the major reasons for the harmful impact on human health and also for financial losses. Thus, pharmaceutical supply chains and end-to-end tracking systems are the recent research in healthcare. In this paper, we propose blockchain based traceability of counterfeited drugs (BBTCD) that implements tracking of counterfeited drugs using smart contracts on the Ethereum blockchain. We propose a solution to fully decentralize the tracking in healthcare by storing BBTCD on IPFS (Inter Planetary File System) to provide transparency, cost-effectiveness.
PubMed: 36438614
DOI: 10.1007/s10742-022-00292-w