AlphaFold2's training set powers its predictions of fold-switched conformations.

AlphaFold2 (AF2), a deep-learning based model that predicts protein structures from their amino acid sequences, has recently been used to predict multiple protein conformations. In some cases, AF2 has successfully predicted both dominant and alternative conformations of fold-switching proteins, which remodel their secondary and tertiary structures in response to cellular stimuli. Whether AF2 has learned enough protein folding principles to reliably predict alternative conformations outside of its training set is unclear.

Structural insights into SSNA1 self-assembly and its microtubule binding for centriole maintenance.

SSNA-1 is a fibrillar protein localized at the area where dynamic microtubule remodeling occurs including centrosomes. Despite the important activities of SSNA1 to microtubules such as nucleation, co-polymerization, and lattice sharing microtubule branching, the underlying molecular mechanism have remained unclear due to a lack of structural information. Here, we determined the cryo-EM structure of SSNA-1 at 4.

In a Canine Model of Septic Shock, Cardiomyopathy Occurs Independent of Catecholamine Surges and Cardiac Microvascular Ischemia.

Background: High levels of catecholamines are cardiotoxic and associated with stress-induced cardiomyopathies. Septic patients are routinely exposed to endogenously released and exogenously administered catecholamines, which may alter cardiac function and perfusion causing ischemia. Early during human septic shock, left ventricular ejection fraction (LVEF) decreases but normalizes in survivors over 7-10 days.

Myocardial Abnormalities Across the AHA/ACC Stages of Heart Failure in Patients With Diabetes.

Background: Cardiac magnetic resonance imaging (CMR) could serve as a robust tool for comprehensive evaluation of early changes across heart failure (HF) stages classified by the American Heart Association/American College of Cardiology guideline in diabetes mellitus (DM).

Objectives: The authors aimed to explore phenotypic imaging features characterizing DM participants at different HF stages by CMR.

Methods: DM participants with preserved ejection fraction who underwent CMR examination between January 2020 and December 2021 were evaluated.

Demographics, Epidemiology, Mortality, and Difficult-To-Treat Resistance Patterns of Bacterial Bloodstream Infections in the Global United States Military Health System from 2010-2019: A Retrospective Cohort Study.

Objective: To describe demographics, causative pathogens, hospitalization, mortality, and antimicrobial resistance of bacterial bloodstream infections (BSIs) among beneficiaries in the global U.S. Military Health System (MHS), a single-provider healthcare system with 10-year longitudinal follow-up.

TSLP acts on regulatory T cells to maintain their identity and limit allergic inflammation.

Thymic stromal lymphopoietin (TSLP) is a type I cytokine that promotes allergic responses and mediates type 2 immunity. A balance between effector T cells (T), which drive the immune response, and regulatory T cells (T), which suppress the response, is required for proper immune homeostasis. Here, we report that TSLP differentially acts on T versus T to balance type 2 immunity.

A new pipeline SPICE identifies novel JUN-IKZF1 composite elements.

Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. Using SPICE, we successfully identified known composite elements, such as AP1-IRF composite elements (AICEs) and STAT5 tetramers, and also uncovered several novel binding partners, including JUN-IKZF1 composite elements.

Factors associated with diabetes mellitus and hypertension among adults in the northern rural area, Afghanistan.

Afghanistan has an increasing trend of mortality due to non-communicable diseases but most studies were conducted in urban areas. This study aimed to assess the prevalence and factors associated with diabetes mellitus and hypertension in a rural area in Afghanistan. A cross-sectional study was conducted from September to October 2019 including 373 people who were 18-79 years old and lived in Andkhoy District, Afghanistan.

Transfusion-transmitted bacterial infection risk due to the proliferation of psychrotrophic bacterial species in RBCs and their difficulty in detection.

Background: Reports of cases of bacterial infection due to transfusion of red blood cell (RBC) components (RBC-TTBI) are relatively rare. Hence, the possibility of undetectable bacterial contamination in RBCs, especially by psychrotrophic bacteria, must be clarified.

Study Design And Methods: We assessed nine psychrotrophic bacterial species, including those implicated in bacteremia or RBC-TTBIs.

Satellite DNA shapes dictate pericentromere packaging in female meiosis.

The abundance and sequence of satellite DNA at and around centromeres is evolving rapidly despite the highly conserved and essential process through which the centromere directs chromosome inheritance. The impact of such rapid evolution is unclear. Here we find that sequence-dependent DNA shape dictates packaging of pericentromeric satellites in female meiosis through a conserved DNA-shape-recognizing chromatin architectural protein, high mobility group AT-hook 1 (HMGA1).

Potentiating CD20 monoclonal antibody therapy by targeting complement C3 fragment covalently deposited on lymphoma cells.

Monoclonal antibodies (mAbs) improve survival of patients with mature B-cell malignancies. Fcγ-receptor dependent effector mechanisms kill tumor cells but can promote antigen loss through trogocytosis, contributing to treatment failures. Cell-bound mAbs trigger the complement cascade to deposit C3 activation fragments and lyse cells.

Demographic-Based Personalized Left Ventricular Hypertrophy Thresholds for Hypertrophic Cardiomyopathy Diagnosis.

Background: Hypertrophic cardiomyopathy (HCM) is a leading cause of sudden cardiac death. Current diagnosis emphasizes the detection of left ventricular hypertrophy (LVH) using a fixed threshold of ≥15-mm maximum wall thickness (MWT). This study proposes a method that considers individual demographics to adjust LVH thresholds as an alternative to a 1-size-fits-all approach.

Refinement of a Published Gene-Physical Activity Interaction Impacting HDL-Cholesterol: Role of Sex and Lipoprotein Subfractions.

Large-scale gene-environment interaction (GxE) discovery efforts often involve analytical compromises for the sake of data harmonization and statistical power. Refinement of exposures, covariates, outcomes, and population subsets may be helpful to establish often-elusive replication and evaluate potential clinical utility. Here, we used additional datasets, an expanded set of statistical models, and interrogation of lipoprotein metabolism via nuclear magnetic resonance (NMR)-based lipoprotein subfractions to refine a previously discovered GxE modifying the relationship between physical activity (PA) and HDL-cholesterol (HDL-C).

The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods.

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, e.

A new pipeline SPICE identifies novel JUN-IKZF1 composite elements.

Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. Using SPICE, we successfully identified known composite elements, such as AP1-IRF composite elements (AICEs) and STAT5 tetramers, and also uncovered several novel binding partners, including JUN-IKZF1 composite elements.

The expected polygenic risk score (ePRS) framework: an equitable metric for quantifying polygenetic risk via modeling of ancestral makeup.

Polygenic risk scores (PRSs) depend on genetic ancestry due to differences in allele frequencies between ancestral populations. This leads to implementation challenges in diverse populations. We propose a framework to calibrate PRS based on ancestral makeup.

Critical Care Management of Acute Venous Thromboembolism: Integrating Pharmacotherapy, Thrombectomy, and Temporary Mechanical Support.

Venous thromboembolism (VTE), which includes pulmonary embolism and deep vein thrombosis, carries significant morbidity and mortality risks, and is conventionally managed with anticoagulation. In recent years, notable progress has been made in the therapeutic options available for the acute treatment of VTE. The heterogeneity within pulmonary embolism, spanning a wide spectrum of risks, underscores the critical need for precise risk stratification, particularly in identifying individuals prone to right heart failure and increased mortality.

Obesity and the development of Parkinson's disease within the Framingham Heart study cohort.

Objective: To determine the role of obesity in the development of Parkinson's disease (PD).

Background: Obesity has been reported to be both a risk factor for PD, as well as potentially protective. The Framingham Heart Study (FHS) is a multigenerational longitudinal cohort study that was started in 1948, which is well-known for its cardiovascular health studies.

A Scoping Review on Sex and Gender Differences in the Adverse Health Outcomes of Individuals with Sickle Cell Trait.

Although there is an emerging body of evidence that addresses the adverse health outcomes of individuals with sickle cell trait (SCT), it is not clear if the findings are generalizable from a sex and gender perspective. The purpose of this scoping review was to complete an assessment of main concepts, identify knowledge gaps, and determine the potential value of conducting an eventual systematic review. The research question guiding this scoping review is: In SCT individuals with adverse health outcomes, what is known about sex and gender differences? We conducted a scoping review of research on SCT from 2016 to 2022 across five databases, with 36 research studies included in the review.

Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction.

In recent years, advances in artificial intelligence (AI) have transformed structural biology, particularly protein structure prediction. Though AI-based methods, such as AlphaFold (AF), often predict single conformations of proteins with high accuracy and confidence, predictions of alternative folds are often inaccurate, low-confidence, or simply not predicted at all. Here, we review three blind spots that alternative conformations reveal about AF-based protein structure prediction.

Improved Patient-Reported Outcomes With Post-Transplant Cyclophosphamide: A Quality-of-Life Evaluation and 2-Year Outcomes of BMT CTN 1703.

The BMT CTN 1703 phase III trial confirmed that graft-versus-host disease (GVHD) prophylaxis with post-transplantation cyclophosphamide (PTCy), tacrolimus (Tac), and mycophenolate mofetil (MMF) results in superior GVHD-free, relapse-free survival (GRFS) compared with Tac/methotrexate (MTX) prophylaxis. This companion study assesses the effect of these regimens on patient-reported outcomes (PROs). Using the Lee Chronic GVHD Symptom Score and PROMIS subscales (physical function, GI symptoms, social role satisfaction) as primary end points and hemorrhagic cystitis symptoms and Lee subscales as secondary end points, responses from English and Spanish speakers were analyzed at baseline and days 100, 180, and 365 after transplant.

Endonuclease G promotes hepatic mitochondrial respiration by selectively increasing mitochondrial tRNA production.

Mitochondrial endonuclease G (EndoG) contributes to chromosomal degradation when it is released from mitochondria during apoptosis. It is presumed to also have a mitochondrial function because EndoG deficiency causes mitochondrial dysfunction. However, the mechanism by which EndoG regulates mitochondrial function is not known.

Association of Mycobacterium tuberculosis aerosolization and HIV coinfection in the index case with T cell responses in household contacts.

Exposure to pulmonary tuberculosis (PTB) culminates in heterogeneous outcomes, including variation in Mtb antigen-specific interferon-gamma (IFN-γ) T-cell responses. IFN-γ-independent cytokines, including tumor necrosis factor (TNF) and interleukin (IL-2), offer potential diagnostic improvements and insights into pathogenesis. We hypothesized that ESAT6/CFP10 TNF and IL-2 responses improve Mtb infection detection among exposed household contacts (HHCs) and are associated with index case Mtb aerosolization (i.

Effects of seven days' fasting on physical performance and metabolic adaptation during exercise in humans.

Humans have, throughout history, faced periods of starvation necessitating increased physical effort to gather food. To explore adaptations in muscle function, 13 participants (7 males and 6 females) fasted for seven days. They lost 4.