BiomiX, a user-friendly bioinformatic tool for democratized analysis and integration of multiomics data.

Background: Interpreting biological system changes requires interpreting vast amounts of multi-omics data. While user-friendly tools exist for single-omics analysis, integrating multiple omics still requires bioinformatics expertise, limiting accessibility for the broader scientific community.

Results: BiomiX tackles the bottleneck in high-throughput omics data analysis, enabling efficient and integrated analysis of multiomics data obtained from two cohorts.

A templex-based study of the Atlantic Meridional Overturning Circulation dynamics in idealized chaotic models.

Significant changes in a system's dynamics can be understood through modifications in the topological structure of its flow in phase space. In the Earth's climate system, such changes are often referred to as tipping points. One of the large-scale components that may pass a tipping point is the Atlantic Meridional Overturning Circulation.

Multifactored accelerated marine corrosion of immersed steels influenced by washed ashore Sargassum rafts.

Since 2011, massive strandings of Sargassum (brown alga) have significantly affected Caribbean islands causing major health, environmental and economic problems. Amongst them, the degradation of algae releases corrosive gases, hydrogen sulphide (HS) and ammonia (NH) which causes an accelerated corrosion of the metallic structures of these coastal areas. The aim of this study was to quantify the impact of Sargassum strandings on the corrosion of three types of steels (DC01 carbon steel, 304L and 316L stainless steels) immersed for up to 120 days at various sites in Martinique which were gradually impacted by Sargassum.

Mitigating oxidative stress in oyster larvae: Curcumin promotes enhanced redox balance, antioxidant capacity, development, and resistance to antifouling compounds.

Curcumin (CUR) is a natural compound recognized for stimulating the expression of antioxidant genes. This characteristic has been used to promote animal health and production in aquaculture settings. We hypothesized that supplementing embryos of Crassostrea gigas oysters with CUR would improve their antioxidant capacity, development, and resilience to stress.

Communication between DNA polymerases and Replication Protein A within the archaeal replisome.

Replication Protein A (RPA) plays a pivotal role in DNA replication by coating and protecting exposed single-stranded DNA, and acting as a molecular hub that recruits additional replication factors. We demonstrate that archaeal RPA hosts a winged-helix domain (WH) that interacts with two key actors of the replisome: the DNA primase (PriSL) and the replicative DNA polymerase (PolD). Using an integrative structural biology approach, combining nuclear magnetic resonance, X-ray crystallography and cryo-electron microscopy, we unveil how RPA interacts with PriSL and PolD through two distinct surfaces of the WH domain: an evolutionarily conserved interface and a novel binding site.

Vibrio harveyi uses both type III secretion system and quorum sensing for the colonization of the European abalone.

The vibriosis of the European abalone, Haliotis tuberculata, is characterized by the rapidity of the infection by the pathogen Vibrio harveyi ORM4, leading to death of animals only after two days. The lethality of the pathogen is linked to the production of the type III secretion system (T3SS) and to genes regulated by quorum sensing (QS). The aim of this study was to investigate the colonization of the European abalone by both virulent and avirulent V.

- a large-scale dataset of 3D medical shapes for computer vision.

Objectives: The shape is commonly used to describe the objects. State-of-the-art algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from the growing popularity of ShapeNet (51,300 models) and Princeton ModelNet (127,915 models).

Carboxyl ester lipase hybrid 1 (CEL-HYB1) haplotypes confer varying risk for chronic pancreatitis.

The CEL-HYB1 hybrid allele of the carboxyl ester lipase (CEL) gene and its pseudogene (CELP) has been associated with chronic pancreatitis (CP). Recent work indicated that amino acid positions 488 and 548 in CEL-HYB1 determined pathogenicity. Haplotype Thr488-Ile548 was associated with CP while haplotypes Thr488-Thr548 and Ile488-Thr548 were benign.

Energy-Resolved Mass Spectrometry and Mid-Infrared Spectroscopy for Purity Assessment of a Synthetic Peptide Cyclised by Intramolecular Huisgen Click Chemistry.

Cyclic peptides have higher stability and better properties as therapeutic agents than their linear peptide analogues. Consequently, intramolecular click chemistry is becoming an increasingly popular method for the synthesis of cyclic peptides from their isomeric linear peptides. However, assessing the purity of these cyclic peptides by mass spectrometry is a significant challenge, as the linear and cyclic peptides have identical masses.

Identification and Characterization of Two Aryl Sulfotransferases from Deep-Sea Marine Fungi and Their Implications in the Sulfation of Secondary Metabolites.

Sulfation plays a critical role in the biosynthesis of small molecules, regulatory mechanisms such as hormone signaling, and detoxification processes (phase II enzymes). The sulfation reaction is catalyzed by a broad family of enzymes known as sulfotransferases (SULTs), which have been extensively studied in animals due to their medical importance, but also in plant key processes. Despite the identification of some sulfated metabolites in fungi, the mechanisms underlying fungal sulfation remain largely unknown.

Phenylobacterium ferrooxidans sp. nov., isolated from a sub-surface geothermal aquifer in Iceland.

A novel bacterial strain, HK31-G, was isolated from a subsurface geothermal aquifer (Hellisheidi, SW-Iceland) and was characterized using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA gene along with phylogenomic position indicated that the novel strain belongs to the genus Phenylobacterium. Cells are motile Gram-negative thin rods.

Are ultrasound salivary parenchymal lesions more severe in primary Sjögren patients with a longer disease duration? A cross-sectional study.

Objectives: Salivary gland ultrasound (SGUS) has an interest in primary Sjögren's disease (pSD) for diagnosis, but the evolution of parenchymal lesions over time is unknown. The objective of this study was to assess the severity of ultrasound abnormalities in relation to pSD duration from the time of buccal dryness onset.

Methods: In this cross-sectional international multicentre study, patients with pSD according to the 2002 or 2016 ACR/EULAR classification criteria were included.

L-MAE: Longitudinal masked auto-encoder with time and severity-aware encoding for diabetic retinopathy progression prediction.

Pre-training strategies based on self-supervised learning (SSL) have demonstrated success as pretext tasks for downstream tasks in computer vision. However, while SSL methods are often domain-agnostic, their direct application to medical imaging is challenging due to the distinct nature of medical images, including specific anatomical and temporal patterns relevant to disease progression. Additionally, traditional SSL pretext tasks often lack the contextual knowledge that is essential for clinical decision support.

Genomic Landscape of Thrombosis Recurrence Risk Across Venous Thromboembolism Subtypes.

Venous thromboembolism (VT) is a frequent (annual incidence of 1 to 2 per 1,000) and potentially life-threatening (case-fatality rate up to 10%) disease. VT is associated with serious short-term and long-term complications including a recurrence rate of approximately 20% within five years. Anticoagulant therapy, the mainstay of VT treatment, drastically reduces the risk of early VT recurrence, but it exposes patients to a substantial risk of bleeding.

Polystyrene nanoplastics impact the bioenergetics of developing zebrafish and limit molecular and physiological adaptive responses to acute temperature stress.

Plastic pollution is a growing environmental concern due to its ubiquitous impact on aquatic ecosystems. Nanoplastics can be generated from the breakdown of plastic waste and interact with organisms at the cellular level, potentially disrupting cellular physiology. We investigated the effects of 44 nm polystyrene nanoparticles (44 nm NanoPS) on the development and physiology of zebrafish (Danio rerio) in the presence of sublethal heat stress (32 °C vs control, 28 °C).

[Becoming an occupational health nurse].

Since March 2023, occupational health nurses have been required to have a professional license, a master's degree or an inter-university diploma. They are required to take over 200 hours of theoretical courses, and to complete one or more internships equivalent to over 100 hours.

Comprehensive analysis of supervised learning methods for electrical source imaging.

Electroencephalography source imaging (ESI) is an ill-posed inverse problem: an additional constraint is needed to find a unique solution. The choice of this constraint, or prior, remains a challenge for most ESI methods. This work explores the application of supervised learning methods for spatio-temporal ESI, where the relationship between measurements and sources is learned directly from the data.

Radiological anatomical measurements of the superficial temporal artery: an interobserver reproducibility study.

Purpose: Numerous studies have already reported on the anatomy of the superficial temporal artery (STA) on dissection or imaging, and more specifically on CT angiography. However, few studies have reported on the possible variations that exist between readers in the assessment of certain anatomical parameters. The aim of this study was to investigate the reproducibility of different anatomical measurements of the superficial temporal artery with CT angiography.

Harnessing the spatial and transcriptional regulation of monoterpenoid indole alkaloid metabolism in Alstonia scholaris leads to the identification of broad geissoschizine cyclase activities.

Monoterpene indole alkaloids (MIAs) are valuable metabolites produced in numerous medicinal plants from the Apocynaceae family such as Alstonia scholaris, which synthesizes strictamine, a MIA displaying neuropharmacological properties of a potential importance. To get insights into the MIA metabolism in A. scholaris, we studied here both the spatial and transcriptional regulations of MIA genes by performing a robust transcriptomics analysis of the main plant organs, leaf epidermis but also by sequencing RNA from leaves transiently overexpressing the master transcriptional regulator MYC2.

Gonyaulax montresoriae sp. nov. (Dinophyceae) from the Adriatic Sea produces predominantly yessotoxin.

Yessotoxin is one of the shellfish toxins leading to mussel farm closures in the Adriatic Sea of Italy. Two putative Gonyaulax spinifera strains GSA0501 and GSA0602 are known as yessotoxins producers, but their identities have remained elusive since 2005. To address this gap, we established five Gonyaulax strains by incubating sediments from the Adriatic Sea and subsequently isolating single cells.

Dissemination of antibiotic-resistant bacteria associated with microplastics collected from Monastir and Mahdia coasts (Tunisia).

The exponential use of plastics and their recalcitrant nature leads to their significant accumulation in the environment. The occurrence of plastic wastes is considered as a serious environmental problem. Additionally, plastic wastes can break down into smaller pieces called microplastics (MPs), leading to further interactions with the environment and living organisms.

Trace element uptake by macroalgae: Organic colloids as a source of metals, including Fe and rare earth elements.

We determined the concentrations of trace elements including Fe, Al, rare earth elements and Y (REY), in Ascophyllum nodosum, one of the most abundant brown macroalgae in the North Atlantic. Samples were collected in the Bay of Brest (Brittany, France) and in the estuary of its main contributing river. The Y/Ho, Al/Ga, and Zr/Hf ratios display values distinctive from seawater, but similar to the continental crust; an observation which we show cannot be explained by the incorporation of terrigenous particles, nor inorganic colloids.