Earth's longest preserved linear volcanic ridge generated by a moving Kerguelen hotspot.

Recent seismic tomography unveiled complex mantle plume structures diverging from the originally proposed single, narrow, and vertically-oriented plume conduits, which necessitates new perspectives on the mechanism of hotspot motion. While several recent endeavours have focused on Pacific hotspots' motion, knowledge of others remains limited. Here we constrain the motions of the Kerguelen hotspot within the Indian Ocean by obtaining robust Ar/Ar ages for the Ninetyeast Ridge, Earth's longest linear volcanic ridge.

PhysioFit: a software to quantify cell growth parameters and extracellular fluxes.

Summary: Quantification of growth parameters and extracellular uptake and production fluxes is central in systems and synthetic biology. Fluxes can be estimated using various mathematical models by fitting time-course measurements of the concentration of cells and extracellular substrates and products. A single tool is available to non-computational biologists to calculate extracellular fluxes, but it is hardly interoperable and is limited to a single hard-coded growth model.

A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques.

Background: The growing abundance of in vitro omics data, coupled with the necessity to reduce animal testing in the safety assessment of chemical compounds and even eliminate it in the evaluation of cosmetics, highlights the need for adequate computational methodologies. Data from omics technologies allow the exploration of a wide range of biological processes, therefore providing a better understanding of mechanisms of action (MoA) related to chemical exposure in biological systems. However, the analysis of these large datasets remains difficult due to the complexity of modulations spanning multiple biological processes.

PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.

As terabytes of multi-omics data are being generated, there is an ever-increasing need for methods facilitating the integration and interpretation of such data. Current multi-omics integration methods typically output lists, clusters, or subnetworks of molecules related to an outcome. Even with expert domain knowledge, discerning the biological processes involved is a time-consuming activity.

Genome scale metabolic network modelling for metabolic profile predictions.

Metabolic profiling (metabolomics) aims at measuring small molecules (metabolites) in complex samples like blood or urine for human health studies. While biomarker-based assessment often relies on a single molecule, metabolic profiling combines several metabolites to create a more complex and more specific fingerprint of the disease. However, in contrast to genomics, there is no unique metabolomics setup able to measure the entire metabolome.

Challenges and perspectives for naming lipids in the context of lipidomics.

Introduction: Lipids are key compounds in the study of metabolism and are increasingly studied in biology projects. It is a very broad family that encompasses many compounds, and the name of the same compound may vary depending on the community where they are studied.

Objectives: In addition, their structures are varied and complex, which complicates their analysis.

PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.

As terabytes of multi-omics data are being generated, there is an ever-increasing need for methods facilitating the integration and interpretation of such data. Current multi-omics integration methods typically output lists, clusters, or subnetworks of molecules related to an outcome. Even with expert domain knowledge, discerning the biological processes involved is a time-consuming activity.

APEX: an Annotation Propagation Workflow through Multiple Experimental Networks to Improve the Annotation of New Metabolite Classes in .

Spectral similarity networks, also known as molecular networks, are crucial in non-targeted metabolomics to aid identification of unknowns aiming to establish a potential structural relation between different metabolite features. However, too extensive differences in compound structures can lead to separate clusters, complicating annotation. To address this challenge, we developed an automated Annotation Propagation through multiple EXperimental Networks (APEX) workflow, which integrates spectral similarity networks with mass difference networks and homologous series.

Finite element analysis in the optimization of posterior-stabilized total knee arthroplasty.

Posterior-stabilized total knee arthroplasty (PS-TKA) is associated with high rates of satisfaction and functional recovery. This is notably attributed to implant optimization in terms of design, choice of materials, positioning and understanding of biomechanics. Finite elements analysis (FEA) is an assessment technique that contributed to this optimization by ensuring mechanical results based on numerical simulation.

Definition of thermal indicators for the study of thermoregulation alterations in the foot of people living within diabetic peripheral neuropathy: A proof of concept.

Aims: This study investigates how diabetic peripheral neuropathy is linked to impairment of thermoregulatory mechanisms using a thermal camera, spectral thermal analysis and a physical test.

Methods: The plantar skin temperature of all participants was measured using a thermal camera following a 6-min walking exercise. The data were subjected to frequency decomposition, resulting in two frequency ranges corresponding to endothelial and neurogenic mechanisms.

ELIXIR and Toxicology: a community in development.

Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine.

Suggesting disease associations for overlooked metabolites using literature from metabolic neighbors.

In human health research, metabolic signatures extracted from metabolomics data have a strong added value for stratifying patients and identifying biomarkers. Nevertheless, one of the main challenges is to interpret and relate these lists of discriminant metabolites to pathological mechanisms. This task requires experts to combine their knowledge with information extracted from databases and the scientific literature.

Rubble pile asteroids are forever.

Rubble piles asteroids consist of reassembled fragments from shattered monolithic asteroids and are much more abundant than previously thought in the solar system. Although monolithic asteroids that are a kilometer in diameter have been predicted to have a lifespan of few 100 million years, it is currently not known how durable rubble pile asteroids are. Here, we show that rubble pile asteroids can survive ambient solar system bombardment processes for extremely long periods and potentially 10 times longer than their monolith counterparts.

Validation of a novel finite-element model for evaluating patellofemoral forces and stress during squatting after posterior-stabilized total knee arthroplasty.

Introduction: Several studies have documented the relationship between patellofemoral pain and patient dissatisfaction after total knee arthroplasty (TKA). However, few computer simulations have been designed to evaluate the patellofemoral joint during flexion. The aim of this study was to validate a new computational simulation, driven by forces and moments, and to analyze patellofemoral reaction forces and stress under squat loading conditions after TKA implantation.

Volume and rate of volcanic CO emissions governed the severity of past environmental crises.

The emplacement of large igneous provinces (LIPs) has been linked to catastrophic mass extinctions in Earth's history, but some LIPs are only associated with less severe oceanic anoxic events, and others have negligible environmental effects. Although it is widely accepted that massive magma outpouring can affect the environment through volatile degassing, it remains debated what controls the severity of environmental crises. Here, we demonstrate that the second-most-voluminous Phanerozoic LIP, the Kerguelen LIP, may have contributed to the early Aptian oceanic anoxic event 1a, a global event previously believed to have been caused by the Ontong Java LIP.

Gestational exposure to bisphenol A induces region-specific changes in brain metabolomic fingerprints in sheep.

Fetal brain development depends on maternofetal thyroid function. In rodents and sheep, perinatal BPA exposure is associated with maternal and/or fetal thyroid disruption and alterations in central nervous system development as demonstrated by metabolic modulations in the encephala of mice. We hypothesized that a gestational exposure to a low dose of BPA affects maternofetal thyroid function and fetal brain development in a region-specific manner.

PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management.

Introduction: Accuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However, the annotation process is often hampered by the lack of spectral reference data in experimental conditions, as well as logistical difficulties in the spectral data management and exchange of annotations between laboratories.

Objectives: To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with an ergonomic Web interface and Web services to support metabolite annotation and laboratory data management.

Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation.

Both targeted and untargeted mass spectrometry-based metabolomics approaches are used to understand the metabolic processes taking place in various organisms, from prokaryotes, plants, fungi to animals and humans. Untargeted approaches allow to detect as many metabolites as possible at once, identify unexpected metabolic changes, and characterize novel metabolites in biological samples. However, the identification of metabolites and the biological interpretation of such large and complex datasets remain challenging.

Age and composition of young basalts on the Moon, measured from samples returned by Chang'e-5.

Orbital data indicate that the youngest volcanic units on the Moon are basalt lavas in Oceanus Procellarum, a region with high levels of the heat-producing elements potassium, thorium, and uranium. The Chang’e-5 mission collected samples of these young lunar basalts and returned them to Earth for laboratory analysis. We measure an age of 1963 ± 57 million years for these lavas and determine their chemical and mineralogical compositions.

Milk metabolome reveals variations on enteric methane emissions from dairy cows fed a specific inhibitor of the methanogenesis pathway.

Metabolome profiling in biological fluids is an interesting approach for exploring markers of methane emissions in ruminants. In this study, a multiplatform metabolomics approach was used for investigating changes in milk metabolic profiles related to methanogenesis in dairy cows. For this purpose, 25 primiparous Holstein cows at similar lactation stage were fed the same diet supplemented with (treated, n = 12) or without (control, n = 13) a specific antimethanogenic additive that reduced enteric methane production by 23% with no changes in intake, milk production, and health status.

Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis.

Over-representation analysis (ORA) is one of the commonest pathway analysis approaches used for the functional interpretation of metabolomics datasets. Despite the widespread use of ORA in metabolomics, the community lacks guidelines detailing its best-practice use. Many factors have a pronounced impact on the results, but to date their effects have received little systematic attention.

FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases.

Motivation: Metabolomics studies aim at reporting a metabolic signature (list of metabolites) related to a particular experimental condition. These signatures are instrumental in the identification of biomarkers or classification of individuals, however their biological and physiological interpretation remains a challenge. To support this task, we introduce FORUM: a Knowledge Graph (KG) providing a semantic representation of relations between chemicals and biomedical concepts, built from a federation of life science databases and scientific literature repositories.

Impact glasses from Belize represent tektites from the Pleistocene Pantasma impact crater in Nicaragua.

Tektites are terrestrial impact-generated glasses that are ejected long distance (up to 11,000 km), share unique characteristics and have a poorly understood formation process. Only four tektite strewn-fields are known, and three of them are sourced from known impact craters. Here we show that the recently discovered Pantasma impact crater (14 km diameter) in Nicaragua is the source of an impact glass strewn-field documented in Belize 530 km away.

Multiplatform metabolomics for an integrative exploration of metabolic syndrome in older men.

Background: Metabolic syndrome (MetS), a cluster of factors associated with risks of developing cardiovascular diseases, is a public health concern because of its growing prevalence. Considering the combination of concomitant components, their development and severity, MetS phenotypes are largely heterogeneous, inducing disparity in diagnosis.

Methods: A case/control study was designed within the NuAge longitudinal cohort on aging.