SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis.

With the increasing volume of biomedical experimental data, standardizing, sharing, and integrating heterogeneous experimental data across domains has become a major challenge. To address this challenge, we have developed an ontology-supported Study-Experiment-Assay (SEA) common data model (CDM), which includes 10 core and 3 auxiliary classes based on object-oriented modeling. SEA CDM uses interoperable ontologies for data standardization and knowledge inference.

VO: The Vaccine Ontology.

With the widespread use of vaccines in research and clinical settings, there is an urgent need to standardize vaccine representation, integrate information across diverse vaccine types, and support computer-assisted reasoning. Accordingly, we have since 2007 developed the community-based Vaccine Ontology (VO), which aligns with the Basic Formal Ontology and adheres to OBO Foundry principles. VO models ontologically vaccines, vaccine components, vaccine immune responses, vaccine investigation studies and other vaccine-related topics.

Metabolomics and nutrient intake reveal metabolite-nutrient interactions in metabolic syndrome: insights from the Korean Genome and Epidemiology Study.

Background: Despite advances in metabolomics, the complex relationship between metabolites and nutrient intake in metabolic syndrome (MetS) remains poorly understood in the Korean population.

Objective: This study aimed to characterize the metabolomic profiles and nutrient intake associated with MetS and to examine their relationships in the Ansan-Ansung cohort of the Korean Genome and Epidemiology Study (KoGES).

Methods: Data from 2,306 middle-aged adults (1,109 men and 1,197 women) in the KoGES Ansan-Ansung cohort were analyzed.

Loss of pulmonary tissue protection and neutrophil microbicidal defects promote severe infection during influenza A virus infection.

Invasive pulmonary aspergillosis (IPA) is a severe fungal disease caused by () that may spread hematogenously to extrapulmonary organs. IPA is typically associated with a broad spectrum of immunocompromised conditions and constitutes a high mortality rate. While the association of influenza as a risk for secondary bacterial infections is well appreciated, emerging evidence indicates that influenza-hospitalized patients demonstrate increased susceptibility to severe aspergillosis infection.

Interneuron transcriptomics reveals pathologic markers of Alzheimer's disease progression.

Alzheimer's disease (AD) exhibits imbalance between neuronal excitation and inhibition, likely secondary to interneuron dysfunction. To reveal underlying mediators, we spatially profiled the transcriptome of neuronal subtypes in 5XFAD versus control mice at early- and late-stage disease. Pooled analysis of neuron types showed expected pathways at early-stage (RNA and protein processing pathways) versus late-stage (neurodegenerative pathways) disease.

Adverse childhood experiences and chronic health outcomes: evidence from 33 US states in the Behavioral Risk Factor Surveillance System, 2019-2023.

Background: Recent evidence suggests a significant association between adverse childhood experience (ACE) and chronic health outcomes among U.S. adults.

Impact of climate change on vaccine responses and inequity.

Climate change poses a substantial threat to global health by altering environmental conditions and impacting vaccine effectiveness. We explore how climate change impacts vaccines and worsens inequities, highlighting the need for further research and targeted interventions.

Cancer Vaccine Adjuvant Name Recognition from Biomedical Literature using Large Language Models.

Motivation: An adjuvant is a chemical incorporated into vaccines that enhances their efficacy by improving the immune response. Identifying adjuvant names from cancer vaccine studies is essential for furthering research and enhancing immunotherapies. However, the manual curation from the constantly expanding biomedical literature poses significant challenges.

Metabolic stress and age drive inflammation and cognitive decline in mice and humans.

Introduction: Metabolic stressors (obesity, metabolic syndrome, prediabetes, and type 2 diabetes [T2D]) increase the risk of cognitive impairment (CI), including Alzheimer's disease (AD). Immune system dysregulation and inflammation, particularly microglial mediated, may underlie this risk, but mechanisms remain unclear.

Methods: Using a high-fat diet-fed (HFD) model, we assessed longitudinal metabolism and cognition, and terminal inflammation and brain spatial transcriptomics.

Deciphering motor dysfunction and microglial activation in mThy1--synuclein mice: a comprehensive study of behavioral, gene expression, and methylation changes.

Introduction: Growing recognition of microglia's role in neurodegenerative disorders has accentuated the need to characterize microglia profiles and their influence on pathogenesis. To understand changes observed in the microglial profile during the progression of synucleinopathies, microglial gene expression and DNA methylation were examined in the mThy1--synuclein mouse model.

Methods: Disease progression was determined using behavioral tests evaluating locomotor deficits before DNA and RNA extraction at 7 and 10 months from isolated microglia for enzymatic methyl-sequencing and RNA-sequencing.

Longitudinal Metabolomics in Amyotrophic Lateral Sclerosis Implicates Impaired Lipid Metabolism.

Objective: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by altered metabolome and energy homeostasis, manifesting with body mass index changes and hypermetabolism-both prognostic of disease progression and survival. The cross-sectional ALS metabolome has been characterized, but longitudinal correlations to functional decline are lacking.

Methods: We longitudinally evaluated metabolomes from ALS plasma and terminal postmortem spinal cord and brain motor cortex tissue.

Evaluating GPT and BERT models for protein-protein interaction identification in biomedical text.

Motivation: Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. As biomedical literature continues to grow rapidly, there is an increasing need for automated and accurate extraction of these interactions to facilitate scientific discovery. Pretrained language models, such as generative pretrained transformers and bidirectional encoder representations from transformers, have shown promising results in natural language processing tasks.

Mitochondrial Oxidative Stress Regulates FOXP3+ T-Cell Activity and CD4-Mediated Inflammation in Older Adults with Frailty.

In healthy older adults, the immune system generally preserves its response and contributes to a long, healthy lifespan. However, rapid deterioration in immune regulation can lead to chronic inflammation, termed inflammaging, which accelerates pathological aging and diminishes the quality of life in older adults with frailty. A significant limitation in current aging research is the predominant focus on comparisons between young and older populations, often overlooking the differences between healthy older adults and those experiencing pathological aging.

Evaluation of GPT and BERT-based models on identifying proteinprotein interactions in biomedical text.

Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and accurate extraction of PPIs to facilitate scientific knowledge discovery. Pre-trained language models, such as generative pre-trained transformers (GPT) and bidirectional encoder representations from transformers (BERT), have shown promising results in natural language processing (NLP) tasks.

Transcriptomic profiling of sciatic nerves and dorsal root ganglia reveals site-specific effects of prediabetic neuropathy.

Peripheral neuropathy (PN) is a severe and frequent complication of obesity, prediabetes, and type 2 diabetes characterized by progressive distal-to-proximal peripheral nerve degeneration. However, a comprehensive understanding of the mechanisms underlying PN, and whether these mechanisms change during PN progression, is currently lacking. Here, gene expression data were obtained from distal (sciatic nerve; SCN) and proximal (dorsal root ganglia; DRG) injury sites of a high-fat diet (HFD)-induced mouse model of obesity/prediabetes at early and late disease stages.

Age-related dysregulation of intestinal epithelium fucosylation is linked to an increased risk of colon cancer.

Colon cancer affects people of all ages. However, its frequency, as well as the related morbidity and mortality, are high among older adults. The complex physiological changes in the aging gut substantially limit the development of cancer therapies.

A novel approach to quantifying individual's biological aging using Korea's national health screening program toward precision public health.

Accurate prediction of biological age can inform public health measures to extend healthy lifespans and reduce chronic conditions. Multiple theoretical models and methods have been developed; however, their applicability and accuracy are still not extensive. Here, we report Differential Aging and Health Index (DAnHI), a novel measure of age deviation, developed using physical and serum biomarkers from four million individuals in Korea's National Health Screening Program.

The chemokine receptor CXCR3 promotes CD8 T cell-dependent lung pathology during influenza pathogenesis.

The dual role of CD8 T cells in influenza control and lung pathology is increasingly appreciated. To explore whether protective and pathological functions can be linked to specific subsets, we dissected CD8 T responses in influenza-infected murine lungs. Our single-cell RNA-sequencing (scRNA-seq) analysis revealed notable diversity in CD8 T subpopulations during peak viral load and infection-resolved state.

IL-17RA promotes pathologic epithelial inflammation in a mouse model of upper respiratory influenza infection.

The upper respiratory tract (nasopharynx or NP) is the first site of influenza replication, allowing the virus to disseminate to the lower respiratory tract or promoting community transmission. The host response in the NP regulates an intricate balance between viral control and tissue pathology. The hyper-inflammatory responses promote epithelial injury, allowing for increased viral dissemination and susceptibility to secondary bacterial infections.

Non-invasive in vivo measurements of metabolic alterations in the type 2 diabetic brain by H magnetic resonance spectroscopy.

Type 2 diabetes (T2D) is a complex chronic metabolic disorder characterized by hyperglycemia because of insulin resistance. Diabetes with chronic hyperglycemia may alter brain metabolism, including brain glucose and neurotransmitter levels; however, detailed, longitudinal studies of metabolic alterations in T2D are lacking. To shed insight, here, we characterized the consequences of poorly controlled hyperglycemia on neurochemical profiles that reflect metabolic alterations of the brain in both humans and animal models of T2D.

Transcriptomic analysis of diabetic kidney disease and neuropathy in mouse models of type 1 and type 2 diabetes.

Diabetic kidney disease (DKD) and diabetic peripheral neuropathy (DPN) are common complications of type 1 (T1D) and type 2 (T2D) diabetes. However, the mechanisms underlying pathogenesis of these complications are unclear. In this study, we optimized a streptozotocin-induced db/+ murine model of T1D and compared it to our established db/db T2D mouse model of the same C57BLKS/J background.

Gut microbiome correlates with plasma lipids in amyotrophic lateral sclerosis.

Amyotrophic lateral sclerosis (ALS) is a complex, fatal neurodegenerative disease. Disease pathophysiology is incompletely understood but evidence suggests gut dysbiosis occurs in ALS, linked to impaired gastrointestinal integrity, immune system dysregulation and altered metabolism. Gut microbiome and plasma metabolome have been separately investigated in ALS, but little is known about gut microbe-plasma metabolite correlations, which could identify robust disease biomarkers and potentially shed mechanistic insight.

The amyotrophic lateral sclerosis exposome: recent advances and future directions.

Amyotrophic lateral sclerosis (ALS) is a fatal disease of motor neuron degeneration with typical survival of only 2-5 years from diagnosis. The causes of ALS are multifactorial: known genetic mutations account for only around 70% of cases of familial ALS and 15% of sporadic cases, and heritability estimates range from 8% to 61%, indicating additional causes beyond genetics. Consequently, interest has grown in environmental contributions to ALS risk and progression.

Corrigendum: Tox21Enricher-Shiny: an R Shiny application for toxicity functional annotation analysis.

[This corrects the article DOI: 10.3389/ftox.2023.