Performance comparison of germline variant calling tools in sporadic disease cohorts.

Accurate variant calling is essential for next-generation sequencing (NGS)-based diagnosis of rare diseases, yet most benchmarking studies have focused on standard cell lines or trio-based samples, with limited relevance to sporadic cases. Here, we systematically compared the performance of DeepVariant and GATK HaplotypeCaller in two Chinese cohorts of patients with sporadic epilepsy (EP) and autism spectrum disorder (ASD). DeepVariant exhibited higher precision and sensitivity in detecting single nucleotide variants (SNVs), while GATK showed a distinct advantage in identifying rare variants, which are often key to understanding the genetic basis of rare diseases.

Effects of immune checkpoint inhibitors on the pulmonary circulation in lung cancer patients.

Immune checkpoint inhibitors (ICIs) are effective anti-tumor agents, but new immune-related side effects (irAEs) are emerging. This retrospective cohort study investigated 461 lung cancer patients treated with ICIs over 2 years, analyzing changes in pulmonary artery diameter (PAD), aortic diameter (AoD), and the pulmonary artery/aortic diameter (PAD/AoD) ratio through chest computed tomography (CT) at baseline, 3 months, 6 months, 1 year, and 2 years post-treatment. The PAD increased from 25.

A Sinonasal Paranasal Mesenchymal Tumor Associated With Tumor-Induced Osteomalacia: A Case Report and Literature Review.

Introduction: Tumor-induced osteomalacia (TIO) is a rare paraneoplastic syndrome that is characterized by hypophosphatemia resulting from the leakage of renal phosphate. Due to its diverse and nonspecific clinical manifestations, the diagnosis is often delayed.

Case Report: We present the rare case of a 33-year-old man with TIO who was presented with chronic bilateral hip joint pain and was initially misdiagnosed with osteonecrosis of the femoral head.

Microbiome data integration via shared dictionary learning.

Data integration is a powerful tool for facilitating a comprehensive and generalizable understanding of microbial communities and their association with outcomes of interest. However, integrating data sets from different studies remains a challenging problem because of severe batch effects, unobserved confounding variables, and high heterogeneity across data sets. We propose a new data integration method called MetaDICT, which initially estimates the batch effects by weighting methods in causal inference literature and then refines the estimation via novel shared dictionary learning.

Behavioural response and physiological adaptation of captive sub-adult giant pandas in response to a short-term social environment.

During ex-situ conservation, giant pandas inevitably transition from their natural wild habitats to captive environments. The living conditions of captive giant pandas differ significantly from those in the wild. For instance, during the sub-adult stage, solitary giant pandas are human-reared in groups.

Effects of Parasitism and Venom from the Endoparasitoid on Immunity of the Host .

The pupal endoparasitoid injects venom into its host during oviposition, yet knowledge about the venom remains limited. This study explores how parasitism and venom from impair the host's cellular and humoral immunity. At 12-24 h post-parasitization, parasitized pupae had significantly lower total hemocyte counts and also exhibited higher mortality than non-parasitized controls.

Applications of Tissue-Inducing Biomaterials in Nonosseous Tissues: Evidence Map of Animal Studies.

Tissue-inducing biomaterials, which promote tissue regeneration without the addition of exogenous cells and/or bioactive factors, have recently attracted increasing interest in the repair of nonosseous tissues. As a key strategy for transforming data into actionable evidence, evidence-based biomaterials research plays a critical role in guiding material development. In this study, evidence mapping method was employed to systematically analyze and visualize animal study designs, material characteristics, outcome indicators, and evaluation methods, aiming to identify current research trends and emerging focal areas.

Electrically driven lasing from a dual-cavity perovskite device.

Solution-processed semiconductor lasers promise lightweight, wearable and scalable optoelectronic applications. Among the gain media for solution-processed lasers, metal halide perovskites stand out as an exceptional class because of their ability to achieve wavelength-adjustable, low-threshold lasing under optical pumping. Despite the progress in this field, electrically driven lasing from perovskite semiconductors remains a critical challenge.

Analysis of key parameters influencing performance for assembled aluminum alloy buckling-restrained braces.

Buckling-restrained braces (BRBs) are widely used in engineering practice as both load-bearing and energy-dissipating components. However, the application of traditional BRBs is often limited by their self-weight, particularly in long-span structures. To address this limitation, this study proposes a novel BRB configuration that combines a redesigned structural form with lightweight aluminum alloy material.

Complete genome of the sp. f15 isolated from Daihai Lake in Inner Mongolia.

We isolated a strain of the genus from Daihai Lake in Inner Mongolia. The complete genome size is 2,614,554 bp, with a genomic DNA G + C content of 39.3%.

The atlantoaxial distance ratio (AADR): proposal and validation of a novel radiographic parameter for the evaluation vertical atlantoaxial dislocation in a preliminary descriptive study.

Objectives: Vertical atlantoaxial dislocation (VAAD) is a clinically significant but often overlooked component of atlantoaxial instability, yet a reliable, universally applicable radiographic parameter for its quantification is lacking. This preliminary study proposes and validates a novel metric, the atlantoaxial distance ratio (AADR), for the radiographic assessment of VAAD.

Materials And Methods: The AADR is calculated on lateral cervical radiographs as the ratio of the mean vertical distance from the C1 superior tubercles to the C2 inferior endplate, divided by the anteroposterior diameter of the C2 inferior endplate.

Quantifying heavy metal concentrations in industrial-transitional zone soils via integrated XRF and VIS-NIR spectroscopy.

Some suburbs urgently need to investigate soil heavy metal contamination to ensure a clean environment. Compared to traditional monitoring methods, XRF and VIS-NIR spectroscopy offer advantages such as rapid, non-destructive, cost-effective, and environmentally friendly analysis. In this study, we developed multiple estimation models for Cd and As content, evaluated the impact of different spectral preprocessing methods on model accuracy, and analyzed the distribution characteristics and for the feature wavelengths selected by competitive adaptive reweighted sampling (CARS).

A 17.1 kb duplication downstream GATA6 is strongly associated with egg weight in chicken.

Egg weight (EW) is one of the most economically important traits in chickens. Recent statistics show that the EWs of most yellow-feathered chickens in China fall within the 40 ~ 50 g range, while, Danzhou (DZH) chickens exhibit significantly lower EW compared to this range. Here, we aim to identify candidate genes and regulatory variants involved in EW control by conducting a genome-wide association study (GWAS) with high-density SNPs obtained from whole-genome sequencing (WGS).

Community-Driven Copy Number Variant Discovery at Scale: Results from a Rare Disease Genomics Hackathon.

Purpose: Copy number variants (CNVs) are a major contributor to rare genetic diseases, but their detection and interpretation from short-read genome sequencing (srGS) data remain challenging, especially at scale. Large amounts of existing srGS data remain under-analyzed for clinically relevant CNVs.

Methods: During a collaborative Hackathon, we developed and applied scalable CNV analysis workflows to srGS data from three unsolved, exome-negative, rare disease cohorts: Primary Immunodeficiency (N = 39), Turkish developmental disorders (N = 31), and data from the Genomics Research to Elucidate the Genetics of Rare diseases (GREGoR) (N = 1437).

Patient journey and Quality of Life for Patients with Idiopathic Pulmonary Fibrosis (IPFLife) in China: a sequential exploratory mixed methods research protocol.

Introduction: Idiopathic pulmonary fibrosis (IPF) is a rare, chronic and progressive lung disease with a significant impact on patients' quality of life. While much research has focused on disease mechanisms and treatment efficacy, limited attention has been paid to the landscape, unmet needs, patient experiences and quality of life. Understanding these aspects through the patient journey is essential for developing patient-centred therapeutic strategies.

Towards the Flatter Landscape and Better Generalization in Federated Learning under Client-level Differential Privacy.

To defend the inference attacks and mitigate the sensitive information leakages in Federated Learning (FL), client-level Differentially Private FL (DPFL) is the de-facto standard for privacy protection by clipping local updates and adding random noise. However, existing DPFL methods tend to make a sharp loss landscape and have poor weight perturbation robustness, resulting in severe performance degradation. To alleviate these issues, we propose a novel DPFL algorithm named DP-FedSAM, which leverages gradient perturbation to mitigate the negative impact of DP.

Impact Factors for Trajectories of Medication and Healthy Lifestyle Adherence in Young Adults With Hypertension: A Mixed Methods Study.

Treatment adherence is a cornerstone of effective hypertension management. However, the dynamic patterns of adherence and their influencing factors among young Chinese adults with hypertension remain insufficiently understood. This study aimed to explore the trajectories of medication adherence and healthy lifestyle behaviors, as well as the associated influencing factors, in this population.

Determination of Mn Valence States in Nanocatalysts During Sustainable Syngas Conversion.

Constructing structure-activity relationships (SAR) between nanocatalysts under reactive atmospheres makes them indispensable for chemical synthesis, energy transformation, and environmental remediation. However, this structure sensitivity remains ambiguous for metals/metal oxides due to dynamic changes in metal valences under a reductive atmosphere. Herein, this study delves into the complexities of Mn-based nanocatalysts, focusing on the impact of the Mn valence state in a test reaction converting sustainable syngas to aromatics-a process highly sensitive to the catalyst's redox environment and active site characteristics.

Administration of Ascorbic Acid Alleviates Neuronal Damage After Cerebral Ischemia in ODS Rats.

Reactive oxygen species (ROS) contribute to cerebral damage in transient cerebral ischemia, making their elimination a key therapeutic target. Osteogenic disorder Shionogi (ODS) rats, which lack endogenous L-ascorbic acid (AA) synthesis, serve as a useful model for investigating AA's protective effects against ischemic brain injury. ODS rats were given an AA-free diet (0% AA), 0.

QComp: A QSAR-Based Imputation Framework for Drug Discovery.

In drug discovery, in vitro and in vivo experiments generate biochemical activity data that are crucial for evaluating the efficacy and toxicity of compounds. These data sets are massive, sparse, and ever-evolving. Quantitative structure-activity relationship (QSAR) models, which predict biochemical activities from compound structures, face challenges in integrating the evolving experimental data agilely as studies progress.

Mapping pea seed composition through strategic selection of accessions from the Nordic gene bank.

This study aims to utilise natural variation in pea seed composition from NordGen collections to identify key traits for optimized plant-based ingredients functionality while minimizing refined extraction processes. Given the impracticality of chemically analysing 1942 accessions, an algorithm-assisted approach was employed, using image-derived features and datasets to pre-select 51 accessions. Protein content, thousand kernel weight, perimeter, and G-value were determined as primary criteria via PCA, capturing variations in protein composition and other key components.

Survey and improvement strategies for gene prioritization with large language models.

Motivation: Rare diseases remain difficult to diagnose due to limited patient data and genetic diversity, with many cases remaining undiagnosed despite advances in variant prioritization tools. While large language models have shown promise in medical applications, their optimal application for trustworthy and accurate gene prioritization downstream of modern prioritization tools has not been systematically evaluated.

Results: We benchmarked various language models for gene prioritization using multi-agent and Human Phenotype Ontology classification approaches to categorize patient cases by phenotype-based solvability levels.

Regulation of Molecular Solar Thermal Energy Storage Capacity of Azobenzene and Acrylic Ester Copolymers through Hydrogen Bonding and Application in Solar Thermal Cells.

Azobenzene photoactive molecules are capable of undergoing reversible E-to-Z isomerization upon excitation with light of specific wavelengths, allowing for stable storage and controllable release of photochemical energy. This makes them an effective approach for harnessing solar energy. Azobenzene polymers, in particular, show great potential for molecular solar thermal energy storage systems (MOST) owing to their excellent film-forming performance on various substrates.

Transfersome enhances nail penetration of antifungal drug and photosensitizer for chemo-photodynamic therapy of onychomycosis in a novel rat model.

Onychomycosis is a prevalent nail infection caused by fungi, presenting significant treatment challenges due to poor drug penetration and high recurrence rates. Current treatments, including oral and topical antifungals, often have limited efficacy and can lead to resistance. Transfersomes are lipid vesicles that can penetrate skin for transdermal drug delivery.

Discovery of novel covalent PI3Kδ inhibitors bearing alaninamide moiety by lysine-targeted covalent strategy.

PI3Kδ is involved in a wide range of cellular processes, including cell growth, proliferation and differentiation, making it as one of the most valuable targets for the treatment of hematologic tumors. Herein, we developed a series of novel covalent PI3Kδ inhibitors bearing alaninamide moiety by lysine-targeted covalent strategic design. The optimal compound M7, containing the phenolic ester warhead, demonstrated excellent in vitro strong bioactivity and selectivity for PI3Kδ.