Developing foundations for biomedical knowledgebases from literature using large language models - A systematic assessment.

While large language models (LLMs) have shown promising capabilities in biomedical applications, measuring their reliability in knowledge extraction remains a challenge. We developed a benchmark to compare LLMs in 11 literature knowledge extraction tasks that are foundational to automatic knowledgebase development, with or without task-specific examples supplied. We found large variation across the LLMs' performance, depending on the level of technical specialization, difficulty of tasks, scattering of original information, and format and terminology standardization requirements.

Revealing the Diverse Allergenic Protein Repertoire of Six Widely Consumed Crab Species: A Species-Specific Allergen in King Crab.

Background: Shellfish allergy poses a significant health risk affecting up to 2% of the global population. Comprehensive allergen profiling across species is crucial for improving diagnostics and therapies, given the challenges posed by cross-reactivity. This study aims to identify and compare the allergen profiles of six widely consumed edible crab species.

Oncogenic Activity and Sorafenib Sensitivity of p.S214C Mutation in Lung Cancer.

: RAF pathway aberrations are one of the hallmarks of lung cancer. Sorafenib is a multi-kinase inhibitor targeting the RAF pathway and is FDA-approved for several cancers, yet its efficacy in lung cancer is controversial. Previous clinical research showed that a p.

A cross-sectional study on the effects of intravesical BCG on urinary microbiota in bladder cancer patients.

Background: Urinary bladder cancer is among the most common malignancy worldwide. Despite surgical interventions and regular surveillance, recurrence and progression to advanced disease are observed in patients. Intravesical administration of Bacillus Calmette-Guérin (BCG) could reduce bladder cancer recurrence and progression in patients with intermediate- and high-risk non-muscle-invasive bladder cancer (NMIBC).

Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps.

Background: Ctenopharyngodon idella (grass carp), Mylopharyngodon piceus (black carp), Hypophthalmichthys nobilis (bighead carp), and Hypophthalmichthys molitrix (silver carp), collectively known as the four major domesticated Asian carp, are freshwater fish species from the family Cyprinidae and are widely consumed in China. Current studies on these species primarily focus on immune system regulation and the growth and development of individual species. However, in-depth genomic investigations and comprehensive comparative analysis remained limited.

The haplotype-resolved T2T genome for Bauhinia × blakeana sheds light on the genetic basis of flower heterosis.

Background: The Hong Kong orchid tree Bauhinia × blakeana Dunn has long been proposed to be a sterile interspecific hybrid exhibiting flower heterosis when compared to its likely parental species, Bauhinia purpurea L. and Bauhinia variegata L. Here, we report comparative genomic and transcriptomic analyses of the 3 Bauhinia species.

Deciphering the Cross-Reactivity of Tropomyosin across Three Molluscan Species: Insights into the Role of Conserved T-Cell and B-Cell Epitopes.

tropomyosin (HTM), tropomyosin (ATM), and tropomyosin (MTM) were reported as significant seafood allergens capable of eliciting severe allergic reactions. However, studies of cross-reactivity and epitope mapping among them are notably limited. This study discovered their cross-reactivity property through inhibition of IgG/IgE binding capacity and promotion of specific CD4T-cell proliferation.

-Amplified and -A159V Hotspot-Mutated Head and Neck Cancer Sensitive to the Rac Inhibitor EHop-016 In Vivo: A Proof-of-Concept Study.

aberrations in head and neck squamous cell carcinoma (HNSCC) remain clinically inactionable today. Here, we investigated the clinical significance and potential druggability of genomic aberrations in HNSCC. Notably, HPV(-)HNSCC patients bearing the unique HNSCC-prevalent -A159V hotspot mutation, P29S hotspot and G-box domain mutations, and copy number increases all displayed dismal overall survival (TCGA-HNSCC).

Genome-Wide Identification and Comparative Analysis of Allergens in .

Purpose: Crustacean shellfish is one of the eight most common food allergens, and crayfish is a highly valued shellfish species for consumption in China. However, the detailed allergen profile of crayfish remains unknown, with only four allergen groups reported in the WHO/IUIS allergen nomenclature database. In this study we aimed to identify novel allergens based on the genome and to reveal its allergen profile for developing better diagnostic tools and treatments.

Ginkgolide B increases healthspan and lifespan of female mice.

Various anti-aging interventions show promise in extending lifespan, but many are ineffective or even harmful to healthspan. Ginkgolide B (GB), derived from Ginkgo biloba, reduces aging-related morbidities such as osteoporosis, yet its effects on healthspan and longevity have not been fully understood. In this study, we found that continuous oral administration of GB to female mice beginning at 20 months of age extended median survival and median lifespan by 30% and 8.

Chinese expert consensus on allergen component resolved diagnosis.

Background: Allergen component resolved diagnosis (CRD) is a method for identifying specific protein molecules that cause hypersensitivity. Unlike traditional methods that use crude allergen extracts containing multiple component species, CRD focuses on individual allergen protein molecules for more precise diagnosis. The World Allergy Organization (WAO) recommends CRD as a supplement to clinical history and allergen extract testing, and in some cases, it can replace crude extract tests.

sRNAdeep: a novel tool for bacterial sRNA prediction based on DistilBERT encoding mode and deep learning algorithms.

Background: Bacterial small regulatory RNA (sRNA) plays a crucial role in cell metabolism and could be used as a new potential drug target in the treatment of pathogen-induced disease. However, experimental methods for identifying sRNAs still require a large investment of human and material resources.

Methods: In this study, we propose a novel sRNA prediction model called sRNAdeep based on the DistilBERT feature extraction and TextCNN methods.

Transcriptome-Optimized Hydrogel Design of a Stem Cell Niche for Enhanced Tendon Regeneration.

Bioactive hydrogels have emerged as promising artificial niches for enhancing stem cell-mediated tendon repair. However, a substantial knowledge gap remains regarding the optimal combination of niche features for targeted cellular responses, which often leads to lengthy development cycles and uncontrolled healing outcomes. To address this critical gap, an innovative, data-driven materiomics strategy is developed.

Single-cell RNA sequencing reveals heterogeneity of ALI model and epithelial cell alterations after exposure to electronic cigarette aerosol.

Electronic cigarettes (e-cigarettes) have been advertised as a healthier alternative to traditional cigarettes; however, their exact effects on the bronchial epithelium are poorly understood. Air-liquid interface culture human bronchial epithelium (ALI-HBE) contains various cell types, including basal cell, ciliated cell and secretory cell, providing an model that simulates the biological characteristics of normal bronchial epithelium. Multiplex single-cell RNA sequencing of ALI-HBE was used to reveal previously unrecognized transcriptional heterogeneity within the human bronchial epithelium and cell type-specific responses to acute exposure to e-cigarette aerosol (e-aerosol) containing distinct components (nicotine and/or flavoring).

PE/PPE Proteome and ESX-5 Substrate Spectrum in .

PE/PPE proteins secreted by the ESX-5 type VII secretion system constitute a major protein repertoire in pathogenic mycobacteria and are essential for bacterial survival, pathogenicity, and host-pathogen interaction; however, little is known about their expression and secretion. The scarcity of arginine and lysine residues in PE/PPE protein sequences and the high homology of their N-terminal domains limit protein identification using classical trypsin-based proteomic methods. This study used endoproteinase AspN and trypsin to characterize the proteome of Twenty-seven PE/PPE proteins were uniquely identified in AspN digests, especially PE_PGRS proteins.

Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis.

Background: Tuberculosis (TB) represents a major global health challenge. Drug resistance in Mycobacterium tuberculosis (MTB) poses a substantial obstacle to effective TB treatment. Identifying genomic mutations in MTB isolates holds promise for unraveling the underlying mechanisms of drug resistance in this bacterium.

Commonly used software tools produce conflicting and overly-optimistic AUPRC values.

The precision-recall curve (PRC) and the area under the precision-recall curve (AUPRC) are useful for quantifying classification performance. They are commonly used in situations with imbalanced classes, such as cancer diagnosis and cell type annotation. We evaluate 10 popular tools for plotting PRC and computing AUPRC, which were collectively used in more than 3000 published studies.

Comparative analysis of asian carps parvalbumin reveals the divergence pattern of major fish allergen.

Background: Asian carps, a popular freshwater fish globally, are valued for their flavor and serve as a crucial protein source, especially for infants. However, grass carp parvalbumin is highly allergenic, surpassing the allergenicity of fish like salmon and cod. The allergenic potential of parvalbumin in other Asian carps remains unknown, underscoring the need for allergen identification to improve the precision of fish allergy diagnosis and treatment.

Commonly used software tools produce conflicting and overly-optimistic AUPRC values.

The precision-recall curve (PRC) and the area under it (AUPRC) are useful for quantifying classification performance. They are commonly used in situations with imbalanced classes, such as cancer diagnosis and cell type annotation. We evaluated 10 popular tools for plotting PRC and computing AUPRC, which were collectively used in >3,000 published studies.

A Novel Multi-Strain E3 Probiotic Formula Improved the Gastrointestinal Symptoms and Quality of Life in Chinese Psoriasis Patients.

Psoriasis is a chronic immune-mediated inflammatory disease affecting the skin and other systems. Gastrointestinal disease was found to be correlated with psoriasis in previous studies and it can significantly affect the quality of life of psoriasis patients. Despite the importance of the gut microbiome in gut and skin health having already been demonstrated in many research studies, the potential effect of probiotics on GI comorbidities in psoriasis patients is unclear.

Novel Multi-Strain E3 Probiotic Formulation Improved Mental Health Symptoms and Sleep Quality in Hong Kong Chinese.

Mental health issues have emerged as a significant concern in public health, given their association with physical and psychological comorbidities and the resultant socioeconomic burdens. Recent studies have highlighted the interplay between gut microbes and brain functions through the gut-brain axis. To investigate this further, we conducted a targeted 16S rRNA sequencing and comprehensive bioinformatic analysis among Southern Chinese individuals to explore the role of the gut microbiome in depression, anxiety, and sleep disturbance.