Keeping it in the family: using protein family templates to rescue low confidence AlphaFold2 models.

Motivation: High confidence structure prediction models have become available for nearly all protein sequences. More than 200 million AlphaFold2 models are now publicly available. We observe that there can be significant variability in the prediction confidence as judged by plDDT scores across a protein family.

Update from 2010 (standard operating procedure): protocol for the 2024 British Society of Gastroenterology Guidelines on colorectal surveillance in inflammatory bowel disease.

Introduction: The evolving landscape of inflammatory bowel disease (IBD) necessitates refining colonoscopic surveillance guidelines. This study outlines methodology adopted by the British Society of Gastroenterology (BSG) Guideline Development Group (GDG) for updating IBD colorectal surveillance guidelines.

Methods And Analysis: The 'Grading of Recommendations, Assessment, Development and Evaluation' (GRADE) approach, as outlined in the GRADE handbook, was employed.

InterPro: the protein sequence classification resource in 2025.

InterPro (https://www.ebi.ac.

ECOD: integrating classifications of protein domains from experimental and predicted structures.

The evolutionary classification of protein domains (ECOD) classifies protein domains using a combination of sequence and structural data (http://prodata.swmed.edu/ecod).

The Pfam protein families database: embracing AI/ML.

The Pfam protein families database is a comprehensive collection of protein domains and families used for genome annotation and protein structure and function analysis (https://www.ebi.ac.

Rfam 15: RNA families database in 2025.

The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26 106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes.

: Self-esteem and body dissatisfaction in the drive for muscularity among Jamaican weight lifters.

This study examined a model of the associations among self-esteem, body dissatisfaction, and the drive for muscularity among Jamaican male weight lifters, and compared model relationships between weight lifters from rural and urban areas of residence. Using a purposive sampling approach, cross-sectional data were collected from 225 male weight lifters, ages 18-67 years ( = 28.16,  = 9.

Considerations for Severe Acute Respiratory Syndrome Coronavirus 2 Genomic Surveillance: A Joint Consensus Recommendation of the Association for Molecular Pathology and Association of Public Health Laboratories.

Next-generation sequencing (NGS) has applications in research, epidemiology, oncology, and infectious disease diagnostics. Wide variability exists in NGS wet laboratory techniques and dry laboratory analytical considerations. Thus, many questions remain unanswered when NGS methods are implemented in laboratories for infectious disease testing.

Computational Fluid Dynamic Simulation of the Cerebral Venous System in Multiple Sclerosis and Control Patients: Are Hemodynamic Variances Evident in Multiple Sclerosis?

Objective: An investigation was performed to determine the relevant hemodynamic parameters which could help assess vascular pathology in human diseases. Using these parameters, this study aims to assess if there are any hemodynamic differences in the cerebral veins of multiple sclerosis (MS) patients and controls which could impact the etiology of MS.

Methods: 40 MS participants and 20 controls were recruited for this study.

A lumped parameter modelling study of cerebral autoregulation in normal pressure hydrocephalus suggests the brain chooses to be ischemic.

Normal pressure hydrocephalus (NPH) is associated with a reduction in cerebral blood flow and an ischemic metabolic state. Ischemia should exhaust the available autoregulation in an attempt to correct the metabolic imbalance. There is evidence of some retained autoregulation reserve in NPH.

Investigation of protein family relationships with deep learning.

Motivation: In this article, we propose a method for finding similarities between Pfam families based on the pre-trained neural network ProtENN2. We use the model ProtENN2 per-residue embeddings to produce new high-dimensional per-family embeddings and develop an approach for calculating inter-family similarity scores based on these embeddings, and evaluate its predictions using structure comparison.

Results: We apply our method to Pfam annotation by refining clan membership for Pfam families, suggesting both new members of existing clans and potential new clans for future Pfam releases.

Rfam 15: RNA families database in 2025.

The Rfam database, a widely-used repository of non-coding RNA (ncRNA) families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26,106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes.

Mentalizing individuals, families and systems: Towards a translational socioecological approach.

Mentalization-based treatment (MBT) is a spectrum of interventions that share a central focus on improving the capacity for mentalizing. Although MBT was originally developed as a treatment for individuals with borderline personality disorder, its scope and focus have been broadened to become a socioecological approach that stresses the role of broader sociocultural factors in determining the closely related capacities for mentalizing and epistemic trust. This special issue brings together some of the newest developments in MBT that illustrate this shift.

Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models.

Classification of protein domains based on homology and structural similarity serves as a fundamental tool to gain biological insights into protein function. Recent advancements in protein structure prediction, exemplified by AlphaFold, have revolutionized the availability of protein structural data. We focus on classifying about 9000 Pfam families into ECOD (Evolutionary Classification of Domains) by using predicted AlphaFold models and the DPAM (Domain Parser for AlphaFold Models) tool.

Baseline self-efficacy predicts subsequent engagement behavior in an online physical activity intervention.

Background: The purported benefits of online physical activity interventions, in terms of reduced costs, high reach, and easy access, may not be fully realized if participants do not engage with the programs. However, there is a lack of research on modifiable predictors (e.g.

Exploring Nurse Responses to Spontaneous Breastfeeding Episodes During Routine Infant Health Checks in Finland: A Multimodal Conversation Analytic Approach.

Support for mothers' uptake and longevity in breastfeeding is a global health priority. The benefits of breastfeeding are well documented, ranging from immediate health benefits for the infant that include provision of the best nutrition, to longer-term impacts such as reducing the risk of future digestive complications and obesity in adulthood. We analyze how impromptu breastfeeding might be supported by health-care nurses in Finnish maternity and child health clinics during routine infant health checks.

Infant embodied requests and teacher-practitioner offers during early childhood education mealtimes.

The importance of building healthy relationships with food in children's early years is of paramount importance. Building on prior work exploring the social and linguistic practices in infant eating interaction experiences, this research uses a multimodal conversation analysis approach to explore how mealtime interactions are managed as a co-constructed activity between infants (0-2 years) and early childhood teacher-practitioners. Here we will explore video data recorded during mealtimes in an early childhood setting in Mid-Wales, where infants orient to recruitments for assistance and teachers provide offers of help with food items throughout the data.