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At least 19 recordsLinked to original sources
PubMed2026

Q&A with Michèle Ramsay.

Michèle Ramsay, PhD, is Director of the Sydney Brenner Institute for Molecular Bioscience, Professor in Human Genetics, and South African Research Chair in Genomics and Bioinformatics of African Populations at the University of the Witwatersrand, Johannesburg. While promoting research excellence in Africa and contributing to research that accurately represents African populations in global science, she supports capacity strengthening in the fields of genomics and precision medicine. Michèle is a founding member of the Human Heredity and Health in Africa Consortium, co-chair of the International Health Cohorts Consortium, member of the WHO Technical Advisory Group for Genomics (TAG-G), and co-chair of the Lancet Commission on Precision Health. She contributes low- and middle-income countries' perspectives to global genomics, promoting ethical, equitable and fair principles and practices.

Humans↗
PubMed2025

MelanoDB: A dataset of clinical and molecular features of patients with advanced melanoma treated with MAPK inhibitors.

MAPK inhibitors (MAPKi) have revolutionized the treatment of patients with advanced melanoma. However, primary and acquired resistance mechanisms limit their efficacy. Predicting MAPKi response from the tumor baseline features remains challenging due to the limited size of patient cohorts. Therefore, we collected data from nine different patient cohorts (total n = 417 patients with advanced melanoma treated with MAPKi) to identify clinical and molecular features. Our curated dataset, named MelanoDB, includes whole or partial exome sequencing data for 191 patients, copy number alteration information for 66 patients, and gene expression data for 132 patients. We provide a web application to explore the integrated dataset and data distribution across the collected studies, and we share this dataset with the scientific community according to the Findable, Accessible, Interoperable, Reusable (FAIR) principles.

Humans↗
PubMed2026

The need for standardization and improved open (meta)data practices in metaproteomics.

Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices. Video Abstract.

Proteomics↗
PubMed2026

Programmatic access to ICTV virus taxonomy through a public ontology API.

BACKGROUND: The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. FINDINGS: To address this, we developed a public and sustainable solution leveraging ontology-based APIs. All available ICTV Master Species List (MSL) releases, from MSL1 to MSL41, were transformed into a unified, semantically structured ontology comprising more than 195,000 current and historical entities and deployed through the Ontology Lookup Service (OLS). The ontology is automatically rebuilt and republished whenever a new MSL release becomes available. Complementary ICTV-NCBI mappings and helper libraries support integration into downstream systems. CONCLUSIONS: Together, these resources enable, for the first time, public programmatic retrieval of current and historical ICTV taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints, including resolution of former taxonomic terms to their current accepted taxon or taxa and retrieval of taxon histories across releases. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗
PubMed2025

Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines.

As the biomedical data ecosystem increasingly embraces the findable, accessible, interoperable, and reusable (FAIR) data principles to publish multimodal datasets to the cloud, opportunities for cloud-based research continue to expand. Besides the potential for accelerated and diverse biomedical discovery that comes from a harmonized data ecosystem, the cloud also presents a shift away from the standard practice of duplicating data to computational clusters or local computers for analysis. However, despite these benefits, researcher migration to the cloud has lagged, in part due to insufficient educational resources to train biomedical scientists on cloud infrastructure. There exists a conceptual lack especially around the crafting of custom analytic pipelines that require software not pre-installed by cloud analysis platforms. We here present three fundamental concepts necessary for custom pipeline creation in the cloud. These overarching concepts are workflow and cloud provider agnostic, extending the utility of this education to serve as a foundation for any computational analysis running any dataset in any biomedical cloud platform. We illustrate these concepts using one of our own custom analyses, a study using the case-parent trio design to detect sex-specific genetic effects on orofacial cleft (OFC) risk, which we crafted in the biomedical cloud analysis platform CAVATICA.

Cloud Computing↗
PubMed2026

Programmatic access to ICTV virus taxonomy through a public ontology API.

The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. To address this, we developed a public and sustainable solution leveraging ontology-based APIs. Successive ICTV Master Species List (MSL) releases were transformed into a structured ontology and deployed as a unified representation through the Ontology Lookup Service (OLS). The framework also provides ICTV-NCBI mappings and helper libraries for integration into downstream systems. This enables, for the first time, public programmatic retrieval of current and historical virological taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗
PubMed2026

The Lipid Interactome: an interactive and open access platform for exploring cellular lipid-protein interactions.

SUMMARY: Lipid-protein interactions play essential roles in cellular signaling and membrane dynamics, yet their systematic characterization has long been hindered by the inherent biochemical properties of lipids. Recent advances in functionalized lipid probes-equipped with photoactivatable crosslinkers, affinity handles, and photocleavable protecting groups-have enabled proteomics-based identification of lipid interacting proteins with unprecedented specificity and resolution. Despite the growing number of published lipid interactomes, there remains no centralized effort to harmonize, compare, or integrate these datasets. The Lipid Interactome addresses this gap by providing a structured, interactive web portal that adheres to FAIR data principles-ensuring that lipid interactome studies are Findable, Accessible, Interoperable, and Reusable. Through standardized data formatting, interactive visualizations, and direct cross-study comparisons, this resource enables researchers to systematically explore the protein-binding partners of diverse bioactive lipids. By consolidating and curating lipid interactome proteomics data from multiple studies, the Lipid Interactome database serves as a critical tool for deciphering the biological functions of lipids in cellularsystems. AVAILABILITY AND IMPLEMENTATION: This site can be viewed at LipidInteractome.org. All data are available for download. No user information is collected or necessary for data navigation, interaction, or download.

Proteins↗
PubMed2025

"It just feels morally not right to Sell the data": Ethical and social perspectives on human genomic data sharing in Uganda-A phenomenological qualitative study.

While genomic data sharing enhances transparency and research efficiency, it also raises significant ethical and social challenges. This study explored stakeholders' perspectives on these issues, particularly around privacy, confidentiality, and equity in collaborative research. A phenomenological qualitative study was conducted between August and December 2023 at Makerere University College of Health Sciences, other research-intensive institutions, and national regulatory bodies. The study engaged 86 participants: 47 key informants (16 researchers, 14 ethics committee members, nine community advisory board members, and eight research regulators) and four deliberative focus group discussions with 39 participants. Interviews were transcribed verbatim, and thematic analysis was conducted using NVivo 14. Three major themes emerged: (1) stakeholders' experiences in genomic research, including their roles as participants, implementers, or overseers; (2) ethical concerns, such as informed consent, third-party data access, inequities between high-income and low- and middle-income country (LMIC) researchers and participants, and the lack of benefit-sharing frameworks; and (3) social implications, including stigma, discrimination, labeling, community perceptions of fairness, and the need for meaningful engagement. Participants emphasized the importance of protecting participant rights, promoting equity, and ensuring robust data governance and security. The theoretical frameworks of principlism and distributive justice provided a valuable lens for examining these concerns, particularly by highlighting the need to safeguard privacy and fairly distribute responsibilities and benefits in global collaborations. Participants also noted that perceptions of fairness are shaped by trust, local context, and past experiences with research factors that are critical for building equitable and respectful partnerships. This study underscores the urgent need to strengthen protections for research participants and promote fairness in genomic data sharing. Policies should, if adopted, emphasize culturally contextualized consent, active community engagement, restricted third-party data access, and strong data protection mechanisms to address existing inequities and prevent misuse.

LMICs↗
PubMed1978

[Carcinomas of the transverse colon. A series of 75 cases (author's transl)].

The authors report a series of 75 cases of carcinoma of the transverse colon, involving equally the right and left halves. They rarely arose from the middle segment (10% of the series). Usually the tumour was very large affecting the serous layer with lymph node invasion. Liver metastases were frequent. 50% of patients were aged over 70 years. Theoretically, wide removal attempting to cure the disease means removing both colonic angles and the areas supplied by both the superior and inferior mesenteric arteries. But fairly often the existence of vascular variations in the transverse mesocolon permits one to restrict the extent of the resection whilst saving the basic principles of radical removal. Furthermore, in 20% the treatment was purely palliative. The operative mortality was high (25%). The five year survival, in the whole series was about 50%.

Aged↗
PubMed1977

The physical basis of some urodynamic measurements.

This report concerns certain principles of physics that are relevant to the clinical practice of Urology as well as the research urodynamicist. Supplemental material is available in previous publications for the physiologist, cardiovascular, dynamicist, anesthesiologist and the like. The material is fairly recent only in its application to the lower urinary tract. Pressure-volume relationships were applied to be cardiovascular system more than 20 years age. Indeed, for those interested in urodynamic methods, there is a vast fund of useful pertinent information in the literature on vascular dynamics. The problems of steady and unsteady flow in flexible structures are common to both specialties. It would be unfortunate if urodynamicists were required to learn of the phenomena and their implications by the drudgery of repeated measurements rather than taking guidance from previous work. This report is intended to serve as an introduction to the approach and, hopefully, will stimulate those who are interested in urodynamic methods to seek out this information and to interpret their measurements in the light of fundamental physical phenomena that have been described and analyzed.

Biomechanical Phenomena↗
PubMed1975

New approach to management of intracranial aneurysms.

In six cases an attempt was made to relieve the tension on intracranial aneurysms by temporarily clamping the internal carotid artery in the neck, so as to increase the expansibility of the artery. This approach was based on the concept (or "A principle") that haemorrhage is caused by the aneurysm having to bear the full force of systolic pulse pressure when atherosclerosis prevents this pressure being taken up by the normally expansile arterial wall. Follow-up has been fairly short, but the preliminary findings in four of the six patients are encouraging. More attention must be paid in the future to the significance of atherosclerosis in the onset of bleeding from intracranial aneurysms and the incidence of postoperative problems. The argument that atherosclerosis permits the transmission of the systolic pulse directly to the aneurysm wall requires further investigation. The earlier pathological signs of atherosclerosis must receive greater attention, and post-mortem study of the walls of arteries in immediate juxtaposition to aneurysms with high-powered magnification is required.

Adult↗
PubMed1977

[Infarction of the right ventricle. 2. Prognostic and therapeutic aspects].

Infarctions of the right ventricle have a reputation for being innocuous which appears to be unjustified; in a group of 21 patients in whom the diagnosis has been based on the haemodynamic principles put forward in the previous paper, we have had 7 deaths. The prognosis appears to be determined by two types of complication: ruptures of the posterior septum (4 cases), which are very distinctive in their clinical and topographical picture; and haemodynamic complications (10 cases of decompensation) which are related fairly rarely with the lesion of the right ventricle (2 cases), but more often with an associated complication, especially hypovolaemia, in which state the involvement of the right ventricle seems to play a particularly major role in increasing the slowing of the circulation. The proposed treatment plan is aimed at the permanent establishment of an effective circulating volume in the uncomplicated cases; in cases with complications, the aims are twofold--filling of the vascular bed and vasodilators, either separately or simultaneously.

Aged↗
PubMed1975

Magnetorheography; calculation of blood flow from surface induced potentials.

This research is an attempt to measure blood flow without doing any hurt to the body. When the body is placed in a high magnetic field the blood-flow-induced electromotive force (EMF) can be detected with the surface electrodes using the same principle as an electromagnetic flow-meter. This blood flow measurement is named magnetorheography (its recording: MRG). A theoretical analysis of the potential in the tissue shows that blood flow can be calculated from the surface-induced EMF (MRG) without measuring the radius and the depth of the vessel from the skin surface, when the surface is fairly flat in the vicinity of the vessel. A model experiment verified the theory. In order to apply the theory to the measurement in an in situ situation, a structural coefficient was introduced which is related to the external shape, internal tissue compositions and their impedance of the body. Using such a coefficient the flow calculated from MRG, by an equation including the coefficient, agreed with the flow actually recorded. In experiments on the thighs of 8 dogs weighing 7 to 17 Kg, MRG proved to be proportional to arterial flow and the coefficients were approximately constant. These results indicate that blood flow may possibly be estimated by the calculation from MRG.

Animals↗
PubMed1976

Patient work under Fair Labor Standards: the issue in perspective.

The 1973 federal court ruling in Souder v. Brennan required that patient workers in institutions for the mentally ill and mentally retarded be paid in accordance with the minimum wage and other provisions of the Fair Labor Standards Act. The author believes that ruling, which ran contrary to widely accepted institutional practices, is more readily understandable when viewed in the broader context of wage-and-hour legislation. He presents a brief history of the legislation, discusses the provisions relating to the employment of handicapped workers included in the 1966 amendments, and emphasizes that one basic principle underlies all the regulations and procedures: a patient must be paid what he earns. He also urges increased attention to the clinical design of compensated work systems to promote therapeutic and rehabilitative objectives.

Persons with Disabilities↗
PubMed1977

The measurement of granulocyte kinetics.

Studies using 3H-TdR, DF32P or 51Cr have all contributed important information concerning neutrophil kinetics in normal and abnormal conditions. Recent evidence, however, suggests that DF32P underestimates, and 51Cr overestimates, the blood neutrophil T1/2 and that both isotopes overestimate the TBNP, compared with 3H-TdR-derived data. The differences are quantitative and not qualitative, and the principles of blood neutrophil kinetics defined by DF32P studies are still valid. 3H-TdR studies are impractical for general use, and clinical measurement of neutrophil kinetics will have to continue to rely on the use of either DF32P or 51Cr. Comparison of abnormal findings with normal values obtained using the same isotope is probably valid for either technique. Changes in neutrophil kinetics leading to a neutrophil leucocytosis in different situations are fairly predictable from published data. In neutropenias, however, kinetic studies might be needed to delineate the relative contributions of under-production, shortened survival and excessive margination in the individual patient.

Cell Division↗
PubMed2025

Simple scaling laws control the genetic architectures of human complex traits.

Genome-wide association studies have revealed that the genetic architectures of complex traits vary widely, including in terms of the numbers, effect sizes, and allele frequencies of significant hits. However, at present we lack a principled way of understanding the similarities and differences among traits. Here, we describe a probabilistic model that combines the effects of mutation, drift, and stabilizing selection at individual sites with a genome-scale model of phenotypic variation. In this model, the architecture of a trait arises from the distribution of selection coefficients of mutations and from two scaling parameters. We fit this model for 95 highly polygenic quantitative traits of different kinds from the UK Biobank. Notably, we infer that all these traits have fairly similar, though not identical, distributions of selection coefficients. This similarity suggests that differences in architectures of highly polygenic traits arise mainly from the two scaling parameters: the mutational target size and heritability per site, which vary by orders of magnitude among traits. When these two scale factors are accounted for, we find that the architectures of all 95 traits are very similar.

Humans↗
PubMed1978

[Enzymo-immunological estimations. Principles and applications (author's transl)].

Diagrams of the reactions of enzymo-immunological estimations are similar to those of radio-immunoassay. The only difference is that an enzymatic label is substituted on the antigen or the antibody for the isotopic label and that consequently a measurement of enzyme activity replaces isotopic counting. One must therefore add a further stage of substrate addition and a stage of enzyme reaction. There is however a technic which has no equivalent in radio-immunoassay, the EMIT system, where one measures the change in activity of a haptenised enzyme under the influence of the corresponding anti-haptene antibody. The author reviews the main problems raised by the first group of technics and gives a few examples of the results of estimation of alpha-foeto-protein obtained with 3 different reactions with fairly similar performances. The advantages and disadvantages of enzymo-immunologic technics are reviewed. The two major advantages seem to be the stability of the reagents and the fact that they avoid the administrative controls which restrict the use of isotopes.

Antibodies↗
PubMed2026

AI-driven diagnostic and prognostic models for metabolic dysfunction-associated steatotic liver disease: insights from clinical, imaging, and multi-omics studies-a scoping review.

Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as non-alcoholic fatty liver disease (NAFLD), is the most common chronic liver disease around the world, affecting 33.6% of the adult population (95% CI: 28.1%-39.5%; I 2 = 99.9%), or roughly one in three. The extent of the liver damage is variable, from simple steatosis to metabolic dysfunction-associated steatohepatitis (MASH, formerly NASH), cirrhosis and hepatocellular carcinoma (HCC). Early diagnosis is essential to prevent serious liver damage. Traditional diagnostic techniques such as liver biopsy, imaging, and biomarker testing are all invasive, costly, reduced sensitive to early-stage disease, and they also have variability among observers. Modern diagnostic and prognostic approaches based on the principles of Artificial Intelligence (AI) and specifically on machine learning (ML) and deep learning (DL) have enabled multimodal approaches integrating clinical, imaging and molecular data. This scoping review conducted per PRISMA-ScR guidelines, synthesizes findings from 73 studies (search window 2020-2026) across three dimensions: clinical data driven models, imaging-based classifiers (ultrasound, CT and MRI), and multi-omics (genomics, transcriptomics and proteomics) techniques. Moreover, emergence of models such as U-Net and LiverNet 2.x, classification models like DeepLiverNet and BiLSTM models, as well as transformer frameworks and the identification of biomarkers models are also described. This study also investigates challenges such as data heterogeneity, data interpretability, fairness and real-world clinical application. Finally, important areas of research opportunities and future directions are highlighted to present a developing clinically applicable, explainable and ethical AI solutions to manage MASLD.

MASLD↗