Acceptability, feasibility, and impact of the MyGut digital health platform in the monitoring and management of inflammatory bowel disease.

Background: Digital health monitoring may help facilitate self-management strategies when caring for patients with inflammatory bowel disease (IBD).

Aims: This study investigated the feasibility of implementing the MyGut health application when caring for patients with IBD and evaluated whether its use improved health outcomes.

Methods: We conducted a prospective trial in 2 Canadian hospitals from 2020 to 2023.

A Comprehensive and Robust Multiplex-DIA Workflow Profiles Protein Turnover Regulations Associated with Cisplatin Resistance.

Measuring protein turnover is essential for understanding cellular biological processes and advancing drug discovery. The multiplex DIA mass spectrometry (DIA-MS) approach, combined with dynamic SILAC labeling (pulse-SILAC, or pSILAC), has proven to be a reliable method for analyzing protein turnover and degradation kinetics. Previous multiplex DIA-MS workflows have employed various strategies, including leveraging the highest isotopic labeling channels of peptides to enhance the detection of isotopic MS signal pairs or clusters.

Segmentation-Free Estimation of Left Ventricular Ejection Fraction Using 3D CNN Is Reliable and Improves as Multiple Cardiac MRI Cine Orientations Are Combined.

Objectives: We aimed to study classical, publicly available convolutional neural networks (3D-CNNs) using a combination of several cine-MR orientation planes for the estimation of left ventricular ejection fraction (LVEF) without contour tracing.

Methods: Cine-MR examinations carried out on 1082 patients from our institution were analysed by comparing the LVEF provided by the CVI42 software (V5.9.

On the identification of differentially-active transcription factors from ATAC-seq data.

ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations.

Clinical and economic impact of pharmacist interventions to identify drug-related problems in multidisciplinary cancer care: a prospective trial.

Background: The prescription of antitumor drugs has often been associated with drug-related problems. Pretherapeutic multidisciplinary risk assessment programs including pharmaceutical care have been established to secure the initiation of injectable and oral antitumor therapies. This prospective cross-sectional double-center study evaluated the clinical and economic impact of the pharmacist in detecting drug-related problems in patients initiating antitumor therapies.

Benchmarking computational methods for single-cell chromatin data analysis.

Background: Single-cell chromatin accessibility assays, such as scATAC-seq, are increasingly employed in individual and joint multi-omic profiling of single cells. As the accumulation of scATAC-seq and multi-omics datasets continue, challenges in analyzing such sparse, noisy, and high-dimensional data become pressing. Specifically, one challenge relates to optimizing the processing of chromatin-level measurements and efficiently extracting information to discern cellular heterogeneity.

Multiscale modeling uncovers 7q11.23 copy number variation-dependent changes in ribosomal biogenesis and neuronal maturation and excitability.

Copy number variation (CNV) at 7q11.23 causes Williams-Beuren syndrome (WBS) and 7q microduplication syndrome (7Dup), neurodevelopmental disorders (NDDs) featuring intellectual disability accompanied by symmetrically opposite neurocognitive features. Although significant progress has been made in understanding the molecular mechanisms underlying 7q11.

miRNA-mediated inhibition of an actomyosin network in hippocampal pyramidal neurons restricts sociability in adult male mice.

Social deficits are frequently observed in patients suffering from neurodevelopmental disorders, but the molecular mechanisms regulating sociability are still poorly understood. We recently reported that the loss of the microRNA (miRNA) cluster miR-379-410 leads to hypersocial behavior and anxiety in mice. Here, we show that ablating miR-379-410 in excitatory neurons of the postnatal mouse hippocampus recapitulates hypersociability, but not anxiety.

Ten simple rules for computational biologists collaborating with wet lab researchers.

Computational biologists are frequently engaged in collaborative data analysis with wet lab researchers. These interdisciplinary projects, as necessary as they are to the scientific endeavor, can be surprisingly challenging due to cultural differences in operations and values. In this Ten Simple Rules guide, we aim to help dry lab researchers identify sources of friction and provide actionable tools to facilitate respectful, open, transparent, and rewarding collaborations.

On the identification of differentially-active transcription factors from ATAC-seq data.

ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations.

Noradrenaline release from the locus coeruleus shapes stress-induced hippocampal gene expression.

Exposure to an acute stressor triggers a complex cascade of neurochemical events in the brain. However, deciphering their individual impact on stress-induced molecular changes remains a major challenge. Here, we combine RNA sequencing with selective pharmacological, chemogenetic, and optogenetic manipulations to isolate the contribution of the locus coeruleus-noradrenaline (LC-NA) system to the acute stress response in mice.

Evaluation of plasma canine C-reactive protein concentrations in dogs with otitis media, healthy dogs and dogs with chronic otitis externa.

Background: Otitis is characterised by inflammation of one or more of the structures of the ear. At present, to confirm or exclude otitis media (OM), it is most often necessary to perform a computed tomography (CT) scan or magnetic resonance imaging. Inflammation is an immune defence response found in many conditions that can be detected and tracked by measuring biological markers of inflammation as the Canine C-reactive protein (CRP).

Bounds for spectral projectors on generic tori.

We investigate norms of spectral projectors on thin spherical shells for the Laplacian on generic tori, including generic rectangular tori. We state a conjecture and partially prove it, improving on previous results concerning arbitrary tori.

Harnessing PROTAC technology to combat stress hormone receptor activation.

Counteracting the overactivation of glucocorticoid receptors (GR) is an important therapeutic goal in stress-related psychiatry and beyond. The only clinically approved GR antagonist lacks selectivity and induces unwanted side effects. To complement existing tools of small-molecule-based inhibitors, we present a highly potent, catalytically-driven GR degrader, KH-103, based on proteolysis-targeting chimera technology.

Sperm chromatin accessibility's involvement in the intergenerational effects of stress hormone receptor activation.

Dexamethasone is a stress hormone receptor agonist used widely in clinics. We and others previously showed that paternal administration of dexamethasone in mice affects the phenotype of their offspring. The substrate of intergenerational transmission of environmentally induced effects often involves changes in sperm RNA, yet other epigenetic modifications in the germline can be affected and are also plausible candidates.

A dataset of physico-chemical properties, extractable organic N, N mineralization and physical organic matter fractionation of soils developed on loess silts, crystalline rocks and sedimentary rocks.

A network of 137 cultivated fields covering the wide diversity of soils, crop rotations and cropping practices throughout the region of Brittany (France) was monitored to collect data on soil organic nitrogen (SON) mineralization and to identify the factors that explain the observed variability. The dataset presented in this article contains all of the information about the soils, which were subjected to pedological description and in-depth analysis of their topsoil properties. The topsoil (0-30 cm) was sampled by mixing 30 samples to obtain one composite per field, which was divided into one sub-sample sieved at 5 mm to analyze soil microbial biomass (SMB) and SON mineralization via anaerobic incubation, and one subsample dried at 40 °C and sieved at 2 mm.

Comparative effects of various running exercise modalities on femoral bone quality in rats.

Background: It is now well established that physical exercise is an effective preventive method to reduce and treat certain chronic diseases, particularly musculoskeletal disorders. At the bone level, running exercise is well known for its positive effects on various parameters of bone quality. There is, however, no consensus regarding the effects of different running exercise modalities on bone quality.

A COnsensus-based Standards for the selection of health Measurement INstruments systematic review of orthognathic patient-reported outcome measures.

Introduction: This systematic review aimed to identify and appraise the validity studies of patient-reported outcome measures (PROMs) reporting the outcomes of combined orthodontic-orthognathic surgery in treating dentofacial deformity.

Methods: The search strategy was conducted using the COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) Systematic Review methodology. The following databases were searched for original studies outlining the development and/or validation of PROMs produced to measure the outcomes of combined orthognathic-orthodontic treatment: EMBASE, MEDLINE, PsycInfo and Scopus.

Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.

Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines, formally assess performance across common situations as well as edge cases, and ultimately guide users on what tools to use. Benchmarking can also be important for community building and advancing methods in a principled way.

Reuniting philosophy and science to advance cancer research.

Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer.

Retinoic Acid and Retinoid X Receptors.

One of the most fundamental discoveries in human biology was that of the existence of essential micronutrients that the body cannot synthesize but nonetheless requires for proper functioning [...

The vascular gene Apold1 is dispensable for normal development but controls angiogenesis under pathological conditions.

The molecular mechanisms of angiogenesis have been intensely studied, but many genes that control endothelial behavior and fate still need to be described. Here, we characterize the role of Apold1 (Apolipoprotein L domain containing 1) in angiogenesis in vivo and in vitro. Single-cell analyses reveal that - across tissues - the expression of Apold1 is restricted to the vasculature and that Apold1 expression in endothelial cells (ECs) is highly sensitive to environmental factors.

Deep Learning to Classify AL versus ATTR Cardiac Amyloidosis MR Images.

The aim of this work was to compare the classification of cardiac MR-images of AL versus ATTR amyloidosis by neural networks and by experienced human readers. Cine-MR images and late gadolinium enhancement (LGE) images of 120 patients were studied (70 AL and 50 TTR). A VGG16 convolutional neural network (CNN) was trained with a 5-fold cross validation process, taking care to strictly distribute images of a given patient in either the training group or the test group.

Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex.

The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates a broad spectrum of (patho)physiological processes in response to numerous substances including pollutants, natural products and metabolites. However, the scarcity of structural data precludes understanding of how AHR is activated by such diverse compounds. Our 2.

Efficacy of Intravenous Ustekinumab Reinduction in Patients With Crohn's Disease With a Loss of Response.

Background/aims: In patients receiving ustekinumab (UST) for treatment of Crohn's disease, there is no proven strategy to enhance or re-capture response. We assessed the utility of UST intravenous (IV) reinduction (~6 mg/kg) to achieve clinical, biochemical and endoscopic response or remission, in patients with partial or loss of response to UST maintenance therapy.

Methods: A multicentre, retrospective cohort study was performed.