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At least 19 recordsLinked to original sources
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

Pithos - a scalable and secure data container for FAIR-compliant research data management in life sciences.

Modern research techniques have led to exponential growth in the volume and complexity of scientific data. Consequently, managing these volumes securely and efficiently has become a major challenge. While all research domains face these challenges, life science research is particularly affected because current approaches often rely on a large set of different file formats, with metadata stored in separated databases or spreadsheets. This leads to fragmented datasets, orphaned data, and compromised research reproducibility. Traditional solutions also force researchers to choose between security and accessibility, with encrypted files preventing selective access and indexed formats lacking adequate security for sensitive data. These limitations are particularly problematic in large-scale genomic studies where researchers must decompress multi-gigabyte files to access specific regions, creating computational bottlenecks and inefficient network usage when working with cloud-stored datasets. We introduce Pithos, a next-generation file format specifically designed for scientific data management in distributed cloud environments. The format uses content-defined chunking to enable efficient deduplication across distributed storage systems, thereby reducing storage costs and bandwidth requirements. The append-only structure ensures data immutability and allows for incremental updates without compromising content. Benchmark results show that Pithos outperforms existing solutions in read and write performance, with comparable or improved storage efficiency.

Biological Science Disciplines↗
PubMed1991

AIDS-related health behavior: coping, protection motivation, and previous behavior.

The purpose of this study was to examine Rogers' protection motivation theory and aspects of Janis and Mann's conflict theory in the context of AIDS-related health behavior. Subjects were 84 heterosexual men and women and 147 homosexual men with multiple sexual partners; LISREL's path-analysis techniques were used to evaluate the goodness of fit of the structural equation models. Protection motivation theory did fit the data but had considerably more explanatory power for heterosexual than for homosexual subjects (49 vs. 22%, respectively). When coping styles were added, different patterns of findings were found among both groups. Adding variables such as social norms and previous behavior increased the explained variance to 73% for heterosexual subjects and to 44% for homosexual subjects. It was concluded that although protection motivation theory did fit the data fairly adequately, expanding the theory with other variables--especially those related to previous behavior--could improve our understanding of AIDS-related health behavior.

Acquired Immunodeficiency Syndrome↗
PubMed1991

The development of traffic and traffic safety in six developed countries.

Two models are presented, describing the development of traffic and traffic safety. Traffic volumes, measured by the total amount of vehicle kilometers per year, are expected to follow a sigmoid saturation curve over time. The logistic function is used to model this development. The fatality rate, the number of fatalities per vehicle kilometer, is chosen to measure safety. The (negative) exponential function is selected to model the fatality rates over time. It is argued that these two aspects of the traffic system are fundamental and that the development of the number of fatalities results by multiplication. Given this assumption, the fall in the number of fatalities, noticed in almost all developed countries after a steady increase until 1970, does not need a special explanation. It follows from the combination of the monotonically increasing traffic volumes and the monotonically decreasing fatality rates. The two parsimonious models fit the data fairly well for six developed countries. The parameters differ substantially between countries, but also show common features. It is found from the parameters of the logistic function, that for all countries the points of maximum increase in traffic volume coincide just after 1970, the moment of the energy crisis. It is concluded from this finding that the energy crisis was caused by the cumulating demands of the oil-consuming countries, resulting in a reaction of the oil-producing countries. From the parameters of the exponential function, it is found that there also is a common point of intersection for fatality rates around 1980. It is shown that the development of safety is directly related to the development of traffic. The ten-year delay is interpreted as the time necessary for planning and implementation of safety measures. Finally, a striking relation is found between the volume parameters and the fatality-rate parameters, suggesting that the number of fatalities is a function of the derivative of the amount of traffic in the mathematical sense.

Accidents, Traffic↗
PubMed2026

Genetics of sensory nutrition.

Sensory nutrition is an emerging research area that examines how chemosensory perception, particularly taste and smell, shapes dietary behaviours, nutritional status, and disease risk. Variation in how individuals perceive the same foods may help explain differences in diet quality and responsiveness to behavioural dietary interventions, yet chemosensory phenotypes are rarely measured at the population level. Genetic variation contributes to this perceptual diversity and provides a framework for investigating sensory determinants of diet using genomic approaches. This review summarises evidence linking chemosensory genetics to perception and dietary behaviours, and discusses applications for causal inference and for precision and personalised nutrition. Twin studies reveal moderate to high heritability for bitter taste traits, with more modest and phenotype-dependent estimates for sweetness, sourness, saltiness, fat-related traits, and olfactory measures. Genome-wide association studies have identified loci in taste and olfactory receptor genes associated with specific chemosensory traits as well as liking and intake of various foods, although the evidence remains concentrated on bitter taste and populations of European ancestry. These genetic variants have been used in Mendelian randomisation, a genetics-based approach that strengthens causal inference, to test whether sensory traits influence dietary behaviour. For precision nutrition, evidence for taste genotype-stratified interventions remains limited and mixed. Realising the promise of sensory nutrition will require scalable and standardised chemosensory phenotyping, Findable, Accessible, Interoperable, and Reusable (FAIR) data infrastructure, expanded research in diverse populations, and integration with broader biological and sociocultural determinants of dietary intake.

Genetics↗
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↗
PubMed1987

Influence of perfusate oncotic pressure on the transcapillary clearance of albumin in maximally vasodilated rat skeletal muscle.

An external detection technique was developed for repetitive and reliable measurements of clearance (Cl) of 99mTc-albumin during alterations of serum colloid osmotic pressure (pi p). Isolated, maximally vasodilated rat hindquarters were perfused with serum of two pi ps (20 mmHg and 45 mmHg) at four or five different filtration rates (Fv) for each pi p in each animal. The recorded accumulation rates of 99mTc-albumin (AR) were converted into dimensions of albumin clearance, setting the isogravimetric Cl at normal vascular pressures (pi p = 20 mmHg) at 0.0246 +/- 0.0012 ml min-1 per 100 g, which was obtained in defined muscle samples in 11 separate experiments. Serum perfusion with higher colloid osmotic pressure (45 mmHg) shifted the albumin clearance values upwards, without affecting the slope of the Cl vs. Fv relationship. Thus, the reflection coefficient (sigma) for albumin did not seem to be affected by the changes in pi p, while the isogravimetric albumin clearance was increased to roughly 0.058 ml min-1 per 100 g. Explicit two-pore equations were found to describe the experimental data fairly well, yielding an average sigma for albumin of 0.92 and a minor contribution of diffusion to overall transport even at low Fvs. Moreover, a coupling of macromolecular clearance to pi p may serve to minimize alterations in plasma protein concentration.

Animals↗
PubMed1992

Dynamic response of the isolated passive rat diaphragm strip.

To further our understanding of the mechanisms underlying chest wall mechanics, we investigated the dynamic response of the isolated passive rat diaphragm strip. Stress adaptation of the tissue was measured from 0.05 to 60 s after subjecting the strips to strain steps of normalized strain amplitudes from 0.005 to 0.04. The tissue resistance (R), elastance (E), and hysteresivity (eta) were measured in the same range of amplitudes by sinusoidally straining the strip at frequencies from 0.03125 to 10 Hz. The stress (T) depended exponentially on the strain (epsilon) and relaxed and recovered linearly with the logarithm of time. E increased linearly with the logarithm of frequency and decreased with increasing amplitude. R fell hyperbolically with frequency and showed an amplitude dependence similar to that of E. To interpret the strong nonlinear behavior, we extended the viscoelastic model of Hildebrandt (J. Appl. Physiol. 28: 365-372, 1970) to include an exponential stress-strain relationship. Accordingly, the step response was described by T - Tr = Tr(e alpha delta epsilon - 1)(1 - gamma log t), where delta epsilon is the strain amplitude, Tr is the initial operating stress, alpha is a measure of the stress-strain nonlinearity, and gamma is the rate of stress adaptation. The oscillatory response of the model was computed by applying Fung's quasi-linear viscoelastic theory. This quasi-linear viscoelastic model fitted the step and oscillatory data fairly well but only if alpha depended negatively on delta epsilon, as might be expected in a plastic material.

Animals↗
PubMed1988

Dose-response relationships in rodents of promoter carcinogens: a tentative interpretation of some downward trends.

This study analyzes a set of dose-response curves relative to promoter carcinogens administered to experimental animals with or without initiator pretreatment. In the case of initiator plus promoter treatment, as well as for low experimental doses, the experimental data and their mathematical fitting indicate a downward shape of the dose-response curves as a general feature. In this study, the following hypothesis, according to the two-stage carcinogenic action of initiator plus promoter treatment, is presented to interpret this downward shape: (i) an initiating action, involving a subset of available "targets" (the number of "initiated" targets is assumed to depend on initiating treatment level), and (ii) a subsequent dose-dependent promoting process, mainly involving the initiated targets. This process reaches a saturation level when all the initiated targets have been promoted. This kind of process may be quantitatively described by a saturated exponential model: P(d) = K(1 - exp(-K0 + K1d)] which fits the experimental data fairly well. No indication supporting the hypothesis of a threshold for the chemicals examined resulted from the analysis. In the specific case of sodium saccharin, experimental dose-response relationships were available with or without initiator pretreatment (BBN and MNU). While in the first case the shape of the dose-response curve is downward, in the second case, it is upward and significantly different.

Animals↗
PubMed1986

Regional deposition of particles in human lung after induced bronchoconstriction.

The percentage 24-hr lung retention (Ret24), a measure of penetration to the aveoli, of 4 micron monodispersed Teflon particles, aerodynamic diameter 6 micron, was studied in 8 healthy nonsmokers. The particles were inhaled at 0.2 1/sec with maximally deep breaths. Bronchoconstriction was induced by inhalation of a methacholinebromide aerosol for one exposure before and for one exposure after inhalation of the Teflon particles. Airway resistance (Raw) was measured using a whole body pletysmograph before and after the induction of bronchoconstriction and increased on an average by a factor 2-3. Ret24 was significantly lower when the Teflon particles were inhaled during bronchoconstriction than when bronchoconstriction was induced after inhalation of the Teflon particles, 26 +/- 12% and 48 +/- 6% (mean +/- SD), respectively. These experimental data agree fairly well with data on deposition due to impaction and sedimentation using a lung model where the diameters of the airways were varied so that an increase in airway resistance occurs similar to that produced in our experimental subjects. However, the experimental data tended to be lower than the theoretical ones when the particles were inhaled during the induced bronchoconstriction. In this study, where the mucociliary transport system was stimulated by methacholinebromide, the percentage 3-hr retention (Ret3) was highly correlated with Ret24, r = 0.97, i.e., Ret3 can be used instead of the Ret24. This implies that radionuclides with shorter half-lives which give lower radiation doses, can be used, and that subjects can be studied within shorter periods of time.

Adult↗
PubMed2025

Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.

The explosion of microbial omics data has outpaced the ability of many researchers to analyze it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab: a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbial science. The Microbiology Galaxy Lab enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community (microbiology.usegalaxy.org, .eu, .org.au, .fr).

Journal Article↗
PubMed1978

An evaluation of the utility of high blood pressure detection fairs.

Our data indicate that voluntary casual screenings in essentially middle class locations may be of limited value in attracting the young, the black, and the male relative to the target population. Our screens attracted a large proportion of individuals who where already aware of their high blood pressure. Nevertheless, these screens can be useful in getting and keeping individuals under medical care: newly detected hypertensives, those who knew they have it and even some of those under treatment for it.

Evaluation Studies as Topic↗
PubMed2026

Community-driven advances in computational mass spectrometry: The perspective of EuBIC-MS members.

Advances in data acquisition, artificial intelligence, and integrative bioinformatics are driving the rapid evolution of computational mass spectrometry, and in turn, transforming modern proteomics, metabolomics, and lipidomics. These developments have greatly increased the scale and complexity of mass spectrometry data, underscoring the importance of evolving accurate, transparent, efficient and reproducible data processing workflows. Addressing these challenges requires collaborative innovation that brings together expertise in software engineering, statistics, and biology. The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS), an initiative of the European Proteomics Association (EuPA), fosters a culture of open, community-driven development through its biennial Developers Meetings and Winter Schools. This commentary summarizes the scientific background and outcomes of the EuBIC-MS Developers Meeting 2025, which took place in Novacella, Italy. Three keynote presentations highlighted major frontiers in the field: deep proteome and phosphoproteome profiling, text mining for protein-protein interaction extraction, and scalable proteomics for AI-driven drug discovery. Seven community-selected hackathons addressed emerging challenges such as single-cell proteomics data analysis, FAIR metadata extraction, deep learning frameworks, R-Python interoperability, and DIA validation. Together, these efforts demonstrate the potential for scientific and technical innovation to arise from open collaboration, and highlight how community-driven initiatives can accelerate progress in computational mass spectrometry. SIGNIFICANCE: Modern proteomics increasingly depends on computational advances to translate complex, high-dimensional data into biological knowledge. The EuBIC-MS Developers Meeting 2025 exemplifies how community-driven collaboration can directly accelerate this process by bringing together experts from bioinformatics, statistics, and experimental proteomics to co-develop open, interoperable, and reproducible analytical tools. By fostering shared software frameworks, transparent benchmarking, and collaborative problem solving, the EuBIC-MS community helps ensure that technological innovation translates into reliable biological insights. This collaborative model strengthens the foundation for quantitative, system-level understanding of proteomes and establishes a sustainable path for integrating artificial intelligence and next-generation data acquisition into routine biological discovery. This commentary shows some current highlights in the field of computational mass spectrometry and community-based approaches undertaken during the most recent Developers Meeting to solve these challenges. The approaches discussed and initiated during the meeting - ranging from deep proteome profiling and phosphosite mapping to text mining, single-cell data analysis, and FAIR metadata extraction - address key bottlenecks that currently limit the biological interpretability and comparability of proteomics data.

Mass Spectrometry↗
PubMed1992

Clinical assessment of fetal blood flow velocimetry.

A statistical procedure is presented to analyze the relation between Doppler indices (DIs) such as pulsatility index (PI), resistance index (RI), A/B and clinical data of pregnancy and fetal outcome of three groups: (1) uncomplicated pregnancy, eutrophic fetus (NF), (2) pregnancy-induced hypertension (PIH), and (3) pregnancy and delivery of a dystrophic fetus (IUGR), and the acidity classes according to Saling, respectively. Proceeding and mathematical requirements as well as the possibilities to validate the methodology are introduced, and an application to previously published data is presented. By multivariate analysis of the data a fair prognosis of NF, PIH and IUGR was possible. The variability inherent to the data sampling requires a mathematical postprocessing in the framework of an adequate model before any clinical conclusions can be derived from DIs.

Blood Flow Velocity↗
PubMed1990

[Prececal crude protein digestion and amino acid absorption during the use of ileorectostomy and fistula technic in swine].

Described in this paper are ileocecal cannulation and ileorectostomy, two methods used for quantitative collection of chyme in the context of protein assessment on the basis of prececally absorbable amino acids. Reference is made to the manufacture of new, flexible intestinal cannulas of biocompatible material and to the surgical approaches in connection with either method. Determination of prececal digestibility of crude nutrients and absorption of amino acids in three rations fed to pigs with ileorectal anastomoses and ileocecal cannulas gave identical data or fair agreement with the extension of two amino acids. The conclusion was drawn that data recorded by means of the two methods can be used in the preparation of tabulated values.

Absorption↗
PubMed1992

Comparison of cardiac output measured by intrapulmonary artery Doppler, thermodilution, and electromagnetometry.

A Doppler pulmonary artery catheter system (Doppler cardiac output monitor or DOPCOM) that continuously measures instantaneous and mean cardiac output was recently introduced. Because thermodilution (TD) flow measurements may not represent an adequate standard, the present study was designed to compare TD and DOPCOM cardiac output measurements with aortic electromagnetic (EM) flow in cardiac surgical patients. Twenty-one patients scheduled for elective coronary artery bypass grafting were enrolled in the study. Simultaneous measurement of cardiac output by all three methods was performed before cardiopulmonary bypass, after cardiopulmonary bypass with the aorta cannulated and volume intermittently infused, and after decannulation. Analysis of all data demonstrated fair TD and EM correlation (r = 0.80), with minimal bias (0.03 +/- 1.21 L/min) and a median absolute error of 0.53 L/min; DOPCOM and EM data showed moderate correlation (r = 0.64), a bias of -0.61 +/- 1.50 L/min, and a median absolute error the same as TD (0.51 L/min). However, distribution of DOPCOM values was heavily skewed by 3 patients in whom flow measurements immediately after cardiopulmonary bypass were markedly different between the DOPCOM and electromagnetometry, probably because of malposition of the Doppler transducers secondary to partial catheter withdrawal during bypass. Consistent with this theory was the finding that before CPB, the DOPCOM was significantly better than TD in predicting EM flow (median absolute error: DOPCOM, 0.12 L/min, and TD, 0.48 L/min; p = 0.04). Our data suggest that, in general, the DOPCOM shows similar precision to TD for predicting EM flow measurements, although the DOPCOM may underestimate actual flow.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMedDate not supplied

Time sequence of coagulation data in patients with decompensated liver cirrhosis and suspected disseminated intravascular coagulation.

In patients with liver cirrhosis, especially in the advanced stage, the coexistence of low clotting factor levels, hypofibrinogenemia, thrombocytopenia and elevated fibrin(ogen) degradation product (FDP) and D-dimer levels may suggest the presence of disseminated intravascular coagulation (DIC). In this study we evaluated, in 21 patients with decompensated liver cirrhosis and elevated FDP and D-dimer levels, the time sequence of their coagulation data during a follow-up period of 15 days after the first observation; our aim was to clarify if these patients tend to develop during this time interval a severe consumption coagulopathy as an expression of overt DIC. We evaluated serum fibrinogen, platelet count, prothrombin activity, serum FDP and plasma D-dimer levels at days 1, 3, 6, 10 and 15. The coagulation data were fairly stable during the study period in all patients, even in the two patients who had upper digestive tract bleeding during the study time. Only two patients affected by infectious diseases showed a decrease of D-dimer and FDP levels after healing. Our data suggest that in decompensated liver cirrhosis the detection of elevated FDP and D-dimer levels is seldom related to the occurrence of an overt DIC, at least during a short time interval; in this condition heparin therapy seems therefore not advisable and even potentially dangerous.

Aged↗