Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection.

The influx of whole genome sequencing (WGS) data in the public health and clinical diagnostic sectors has created a need for data analysis methods and bioinformatics expertise, which can be a bottleneck for many laboratories. At Sciensano, the Belgian national public health institute, an intuitive and user-friendly bioinformatics tool portal was implemented using Galaxy, an open-source platform for data analysis and workflow creation. The Galaxy @Sciensano instance is available to both internal and external scientists and offers a wide range of tools provided by the community, complemented by over 50 custom tools and pipelines developed in-house.

Evaluation of clinical risk stratification to determine benefit from long-term versus short-term androgen deprivation in high-risk localized prostate cancer.

Background: Patients treated with RT and long-term androgen deprivation therapy (ltADT) for high-risk localized prostate cancer (HRLPC) with 1 high-risk factor (any of Gleason ≥8, PSA > 20 ng/mL, ≥cT3; "high-risk") have better outcomes than those with 2-3 factors and/or cN1 disease ("very high risk"). We evaluated whether this risk stratification could determine benefit from ltADT versus short-term (stADT).

Methods: The Intermediate Clinical Endpoints in Cancer of the Prostate (ICECaP) repository of randomized trials was queried to identify eligible patients and trials.

Rehabilitation of human hearing with a totally implantable cochlear implant: a feasibility study.

Background: Cochlear implants (CIs) are neuroprosthetic devices which restore hearing in severe-to-profound hearing loss through electrical stimulation of the auditory nerve. Current CIs use an externally worn audio processor. A long-term goal in the field has been to develop a device in which all components are contained within a single implant.

One-quarter of freshwater fauna threatened with extinction.

Freshwater ecosystems are highly biodiverse and important for livelihoods and economic development, but are under substantial stress. To date, comprehensive global assessments of extinction risk have not included any speciose groups primarily living in freshwaters. Consequently, data from predominantly terrestrial tetrapods are used to guide environmental policy and conservation prioritization, whereas recent proposals for target setting in freshwaters use abiotic factors.

Endothelial tip-cell position, filopodia formation and biomechanics require BMPR2 expression and signaling.

Blood vessel formation relies on biochemical and mechanical signals, particularly during sprouting angiogenesis when endothelial tip cells (TCs) guide sprouting through filopodia formation. The contribution of BMP receptors in defining tip-cell characteristics is poorly understood. Our study combines genetic, biochemical, and molecular methods together with 3D traction force microscopy, which reveals an essential role of BMPR2 for actin-driven filopodia formation and mechanical properties of endothelial cells (ECs).

Dual-targeting CRISPR-CasRx reduces C9orf72 ALS/FTD sense and antisense repeat RNAs in vitro and in vivo.

The most common genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) is an intronic GC repeat expansion in C9orf72. The repeats undergo bidirectional transcription to produce sense and antisense repeat RNA species, which are translated into dipeptide repeat proteins (DPRs). As toxicity has been associated with both sense and antisense repeat-derived RNA and DPRs, targeting both strands may provide the most effective therapeutic strategy.

Dynamic transitions of initiator binding coordinate the replication of the two chromosomes in Vibrio cholerae.

The replication of the two chromosomes in the pathogenic bacterium Vibrio cholerae is coordinated by the binding of initiator protein RctB to a checkpoint sequence, crtS. Replication of crtS on the primary chromosome (Chr1) triggers replication of the secondary chromosome (Chr2), but the details are poorly understood. Here, we analyze RctB binding patterns in the V.

Early life factors and later metabolic syndrome in European children and adolescents.

Background And Aims: Early life factors have been suggested to be associated with later cardiometabolic risk in children, adolescents and adults. Our study aimed to investigate the associations between early life factors and metabolic syndrome (MetS) in children and adolescents.

Methods And Results: Our analysis sample comprised of 8852 children aged 2-9 years at baseline that participated in up to three examination waves of the pan-European IDEFICS/I.

Diagnostic Testing for Laryngopharyngeal Reflux Disease: The Role of 24-hour Hypopharyngeal-Esophageal Multichannel Intraluminal Impedance-pH Monitoring.

Laryngopharyngeal reflux disease (LPRD) presents as a constellation of nonspecific upper aerodigestive tract symptoms and signs. Among many objective tools available on the market, hypopharyngeal-esophageal multichannel intraluminal impedance and pH monitoring (HEMII-pH) is considered to date the gold standard technique for diagnosing LPRD, as well as tailoring treatment according to the different LPR profiles. More studies are needed to further validate and standardize diagnostic criteria and evaluate long-term outcomes of patients diagnosed and treated for LPRD using HEMII-pH.

Divergent destinies: insights into the molecular mechanisms underlying EPI and PE fate determination.

Mammalian pre-implantation development is entirely devoted to the specification of extra-embryonic lineages, which are fundamental for embryo morphogenesis and support. The second fate decision is taken just before implantation, as defined by the epiblast (EPI) and the primitive endoderm (PE) specification. Later, EPI forms the embryo proper and PE contributes to the formation of the yolk sac.

Society for Immunotherapy of Cancer: updates and best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) image analysis and data sharing.

Objectives: Multiplex immunohistochemistry and immunofluorescence (mIHC/IF) are emerging technologies that can be used to help define complex immunophenotypes in tissue, quantify immune cell subsets, and assess the spatial arrangement of marker expression. mIHC/IF assays require concerted efforts to optimize and validate the multiplex staining protocols prior to their application on slides. The best practice guidelines for staining and validation of mIHC/IF assays across platforms were previously published by this task force.

Risk ranking of mycotoxins in plant-based meat and dairy alternatives under protein transition scenarios.

While reducing the consumption of animal-source foods is recommended for planetary and human health, potential emerging food safety risks associated with the transition to dietary patterns featuring plant-based meat (PBMA) and dairy alternatives (PBDA) remain unexplored. We assessed the exposure to mycotoxins and ranked the associated health risks related to the consumption of PBMA and PBDA. We simulated diets by replacing animal-source proteins with their plant-based alternatives.

How thawing and salting affects the post-cooked quality of frozen beef: New insights into the mechanism of fiber morphology evolution and water migration.

To get insight into the thawing and salting in recovery and protection mechanisms on quality in frozen meat after subsequent cooking. The myofiber morphological-water evolution and quality changes in beef during freezing-thawing-cooking and freezing-cooking treatments were investigated. The cooking losses of fresh-cooked, frozen-cooked, and frozen-thawed-cooked samples were 27.

Microbial production of food lipids using the oleaginous yeast Apiotrichum brassicae.

Oleaginous yeasts offer a promising sustainable alternative for producing edible lipids, potentially replacing animal and unsustainable plant fats and oils. In this study, we screened 11 oleaginous yeast species for their lipid profiles and identified Apiotrichum brassicae as the most promising candidate due to its versatility across different growth media. A.

Cardiovascular events observed among patients in the etrasimod clinical programme: an integrated safety analysis of patients with moderately to severely active ulcerative colitis.

Objective: Etrasimod is an oral, once-daily, selective sphingosine 1-phosphate (S1P) receptor modulator for the treatment of moderately to severely active ulcerative colitis (UC). S1P receptor expression on cardiac cells is involved in cardiac conduction. We report cardiovascular treatment-emergent adverse events (TEAEs) associated with S1P receptor modulators and other cardiovascular events in the etrasimod UC clinical programme.

First pass effect in patients with large core infarcts undergoing mechanical thrombectomy: subgroup analysis of the prospective international ASSIST registry.

Background: Studies have described a first pass effect (FPE) where patients with successful recanalization after one pass experience better outcomes. Few studies have evaluated this in patients with large core infarctions.

Objective: To determine whether patients with large core infarcts undergoing mechanical thrombectomy in which first pass reperfusion is achieved experience improved outcomes compared with those who undergo more than one pass.

Low apolipoprotein A1 and high apolipoprotein B levels indicate specific lipid changes in treatment naïve early psoriatic arthritis.

Objectives: To investigate serum lipid profile in early, treatment-naïve psoriatic arthritis (PsA) and to determine whether changes in classical lipids or apolipoproteins are specific to PsA.

Methods: Total cholesterol, non-high-density lipoprotein cholesterol (non-HDL-c), low-density lipoprotein cholesterol (LDL-c), HDL-c, triglycerides, apolipoprotein B (ApoB) and apolipoprotein A1 (ApoA1) were compared in newly diagnosed untreated PsA patients (n=75) to sex- and age-matched controls (healthy control (HC)) (n=61) and early untreated rheumatoid arthritis (RA) patients (n=50).

Results: Among classical lipid measurements, HDL-c levels were lower in PsA than in HC and RA (df 2, χ10, p=0.

The microalgal sector in Europe: towards a sustainable bioeconomy.

Microalgae are a diverse group of photosynthetic microorganisms that can be exploited to produce sustainable food and feed products, alleviate environmental pollution, or sequester CO to mitigate climate change, among other uses. To optimize resource use and integrate industrial waste streams, it is essential to consider factors such as the biology and cultivation parameters of the microalgal species and strains, as well as the cultivation system and processing technologies employed. This paper reviews the main commercial applications of microalgae (including cyanobacteria) and examines the biological and biotechnological aspects critical to the sustainable processing of microalgal biomass and its derived compounds.

Chromic Electrospun Polymer Nanofibers: Preparation, Applications, and the Future.

Physical understanding and determination of different analytes without the need for advanced and additional equipment are highly important, which can be achieved by using stimuli-induced chromic materials. Physical and chemical incorporation of responsive chromophores into different polymers results in the fabrication of chromic polymers. Chromic electrospun nanofibers are prepared using the electrospinning technique, and their stimuli-responsivity is improved due to their high surface-to-volume ratio.

Innovations in primary healthcare in Slovenia 2011-2020: Exploring the stepwise process behind effective implementation.

Countries worldwide seek to strengthen their primary healthcare systems often through introducing health promotion and disease prevention, multidisciplinary teams, group practices and community approaches to advance universal health coverage. These strategies are underpinned by scientific evidence and international standards. Slovenia's primary healthcare system reflects many of these features, with universally accessible, multidisciplinary, and integrated health services, emphasizing health promotion, disease prevention, and equity.