Systematic analysis of biomolecular conformational ensembles with PENSA.

Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions-for example, with various mutations or bound ligands-in order to identify differences between the molecular conformations adopted under these conditions. However, the large amount of data produced by simulations of ever larger and more complex systems often renders it difficult to identify the structural features that are relevant to a particular biochemical phenomenon.

Enhancing lesion detection in liver and kidney CT scans via lesion mask selection from two models: A main model and a model focused on small lesions.

Automated segmentation and detection of tumors in CT scans of the liver and kidney have a significant potential in assisting clinicians with cancer diagnosis and treatment planning. However, current approaches, including state-of-the-art deep learning ones, still face many challenges. Many tumors are not detected by these approaches when tested on public datasets for tumor detection and segmentation such as the Kidney Tumor Segmentation Challenge (KiTS) and the Liver tumor segmentation challenge (LiTS).

Comprehensive genome analysis and variant detection at scale using DRAGEN.

Research and medical genomics require comprehensive, scalable methods for the discovery of novel disease targets, evolutionary drivers and genetic markers with clinical significance. This necessitates a framework to identify all types of variants independent of their size or location. Here we present DRAGEN, which uses multigenome mapping with pangenome references, hardware acceleration and machine learning-based variant detection to provide insights into individual genomes, with ~30 min of computation time from raw reads to variant detection.

On your terms or mine: pigs' response to imposed gentle tactile contact vs. free form interaction with a familiar human.

Positive human-animal interactions (HAIs) can be intrinsically rewarding and facilitate positive human-animal relationships. However, HAI paradigms vary across studies, and the influence of different interaction paradigms on the animal's response has been overlooked. We compared the behavioural responses of pigs (n = 28) individually tested with two types of gentle tactile interactions with a familiar human: 'free form (FF)' where the pig could voluntarily approach and interact as they normally would, and 'imposed contact (IC)' where the human imposed tactile contact on the pig according to a standardised protocol.

Transient CAR T cells with specificity to oncofetal glycosaminoglycans in solid tumors.

Glycosaminoglycans are often deprioritized as targets for synthetic immunotherapy due to the complexity of glyco-epitopes and limited options for obtaining specific subtype binding. Solid tumors express proteoglycans that are modified with oncofetal chondroitin sulfate (CS), a modification normally restricted to the placenta. Here, we report the design and functionality of transient chimeric antigen receptor (CAR) T cells with selectivity to oncofetal CS.

Incidence and factors associated with mitral valve reoperation in patients undergoing surgery for mitral regurgitation: A nationwide cohort study.

Background: When patients undergo surgery for mitral regurgitation, risk of reoperation is of concern.

Aims: To examine the incidence and factors associated with mitral reoperation following surgery for mitral regurgitation according to type of surgery.

Methods: Patients undergoing first-time surgery for mitral regurgitation, 1996-2021, were identified from nationwide registries.

Synthesis of alpha-Gal C-disaccharides.

The synthesis of C-disaccharides of α-d-galactopyranosyl-(1 → 3)-d-galactopyranose (α-Gal), potential tools for studying the biology of α-Gal glycans, is described. The synthetic strategy, centers on the reaction of two easily available precursors 1,2-O-isopropylidene-d-glyceraldehyde and an α-C-glactosyl-E-crotylboronate, which affords a mixture of two diastereomeric anti-crotylation products. The stereoselectivity of this reaction was controlled with (R)- and (S)-TRIP catalysts, and the appropriate diastereomer was transformed to C-linked disaccharides of α-Gal, in which the aglycone segment comprised O-, C- and S-glycoside entities that can enable glycoconjugate synthesis.

Use of frozen native feces for fecal microbiota transplantation in recurrent infection: a simple way to improve the efficiency of donor feces preparation.

Preparing fecal microbiota transplants immediately after donation is resource-intensive, and a proportion are destroyed following abnormal screening results. We retrospectively compared two processes, frozen fecal preparation (FFP) and fresh native frozen preparation (FNFP), for clinical efficacy in the treatment of recurrent infection (rCDI). FFP and FNFP were similarly effective with clinical success rates of 76.

PTER is a N-acetyltaurine hydrolase that regulates feeding and obesity.

Taurine is a conditionally essential micronutrient and one of the most abundant amino acids in humans. In endogenous taurine metabolism, dedicated enzymes are involved in the biosynthesis of taurine from cysteine and in the downstream metabolism of secondary taurine metabolites. One taurine metabolite is N-acetyltaurine.

Genome-wide association and polygenic risk score estimation of type 2 diabetes mellitus in Kinh Vietnamese-A pilot study.

A genome-wide association study (GWAS) is a powerful tool in investigating genetic contribution, which is a crucial factor in the development of complex multifactorial diseases, such as type 2 diabetes mellitus. Type 2 diabetes mellitus is a major healthcare burden in the Western Pacific region; however, there is limited availability of genetic-associated data for type 2 diabetes in Southeast Asia, especially among the Kinh Vietnamese population. This lack of information exacerbates global healthcare disparities.

CarcassFormer: an end-to-end transformer-based framework for simultaneous localization, segmentation and classification of poultry carcass defect.

In the food industry, assessing the quality of poultry carcasses during processing is a crucial step. This study proposes an effective approach for automating the assessment of carcass quality without requiring skilled labor or inspector involvement. The proposed system is based on machine learning (ML) and computer vision (CV) techniques, enabling automated defect detection and carcass quality assessment.

Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome.

Background: Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study, we benchmark the performance of cancer CNV calling by six most recent and commonly used software tools on their detection accuracy, sensitivity, and reproducibility. In comparison to other orthogonal methods, such as microarray and Bionano, we also explore the consistency of CNV calling across different technologies on a challenging genome.

Temporal changes in the number of European and American guideline recommendations and underlying evidence base for the management of infective: An update of previous published data.

This report aimed to examine temporal changes in the number of recommendations on management of infective endocarditis in the European and American guidelines. The number of recommendations has increased since 2004 without an increment in evidence base in the European iteration. American guidelines have reduced the number of recommendations with a main evidence base of level B.

A PTER-dependent pathway of taurine metabolism linked to energy balance.

Taurine is a conditionally essential micronutrient and one of the most abundant amino acids in humans. In endogenous taurine metabolism, dedicated enzymes are involved in biosynthesis of taurine from cysteine as well as the downstream derivatization of taurine into secondary taurine metabolites. One such taurine metabolite is N-acetyltaurine.

European soybean to benefit people and the environment.

Europe imports large amounts of soybean that are predominantly used for livestock feed, mainly sourced from Brazil, USA and Argentina. In addition, the demand for GM-free soybean for human consumption is project to increase. Soybean has higher protein quality and digestibility than other legumes, along with high concentrations of isoflavones, phytosterols and minerals that enhance the nutritional value as a human food ingredient.

Respectful Maternity Care in the United States-Characterizing Inequities Experienced by Birthing People.

Objective:  The purpose of this study is to understand experiences of respectful maternity care (RMC) from the perspective of birthing people in the United States from 2013 to 2018.

Methods:  We conducted an online cross-sectional survey of United States birthing people ages 18-50 in April 2018 using SurveyMonkey Audience. Quantitative survey data consisted of demographics and responses to RMC indicators.

Adverse childhood experiences among California student pharmacists.

Introduction: Adverse childhood experiences (ACEs) are associated with higher mental and physical illness and substance use disorders in adulthood. However, little is known about the prevalence of ACEs among student pharmacists and the factors associated with exposure. Our objective was to determine the prevalence of ACEs, resilience, and maladaptive coping strategies among student pharmacists in California.

Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms.

Research and medical genomics require comprehensive and scalable solutions to drive the discovery of novel disease targets, evolutionary drivers, and genetic markers with clinical significance. This necessitates a framework to identify all types of variants independent of their size (e.g.

The Relationship Between Choroidal Abnormalities and Visual Outcomes in Pediatric Patients With NF1-Associated Optic Pathway Gliomas.

Background: Choroidal abnormalities (CAs) visualized on near-infrared reflectance (NIR) imaging are a new diagnostic criterion for neurofibromatosis type 1 (NF1), but the association between the presence of CAs and visual function remains unknown. This study evaluated the relationship between visual acuity (VA) with the presence, number, or total area of CAs visualized by NIR in children with NF1-associated optic pathway gliomas (NF1-OPGs).

Methods: Patients (<18 years) enrolled in a prospective longitudinal study of children with NF1-associated OPGs from 3 institutions were eligible if they had optical coherence tomography (OCT) of the macula (Heidelberg Spectralis) with ≥1 year of follow-up.

[Collaborative narrative coaching in medicine: a case study with a resident physician and a practicing emergency physician].

In recent years, many postgraduate medical institutions are transitioning to a competency based medical education (CBME). This paradigm shift offers many advantages but has also been criticized for its potentially reductionist approach of targeting competency as the end goal. In this context, coaching may be an interesting intervention as it has been employed with success in other professional settings to go beyond achieving competency with a focus on continuous development.

Contrasting leaf-scale photosynthetic low-light response and its temperature dependency are key to differences in crop-scale radiation use efficiency.

Radiation use efficiency (RUE) is a key crop adaptation trait that quantifies the potential amount of aboveground biomass produced by the crop per unit of solar energy intercepted. But it is unclear why elite maize and grain sorghum hybrids differ in their RUE at the crop level. Here, we used a non-traditional top-down approach via canopy photosynthesis modelling to identify leaf-level photosynthetic traits that are key to differences in crop-level RUE.

Microplastic leachates inhibit small-scale self-organization in mussel beds.

Self-organized spatial patterns are increasingly recognized for their contribution to ecosystem functioning. They can improve the ecosystem's ability to respond to perturbation and thus increase its resilience to environmental stress. Plastic pollution has now emerged as major threat to aquatic and terrestrial biota.

The antibacterial effectiveness of lavender essential oil against methicillin-resistant : a systematic review.

With the overuse and misuse of antibiotics, multi-drug resistant organisms have become a prominent issue in healthcare, increasing morbidity and mortality in affected patients. One such organism of concern is methicillin-resistant (MRSA) which is a leading cause of a variety of clinical infections. Therefore, in the interest of finding alternate substances to antibiotics, there has been increased interest in the antibacterial properties of lavender essential oil (LEO).