Effects of Syntactic Complexity on the Comprehension of Passive Clauses and wh-questions in Children with Developmental Language Disorder and Autism Plus Language Impairment.

There is considerable debate over the similarities and differences between developmental language disorder (DLD) and autism spectrum disorder plus language impairment (ALI). Few studies have compared these in terms of complex syntactic operations. This study aimed to explore the similarities and differences between children with DLD and children with ALI via investigating the effects of syntactic complexity operationalized in terms of movement and intervention in Mandarin passives and wh-questions.

Cryo-EM structure of human telomerase dimer reveals H/ACA RNP-mediated dimerization.

Telomerase ribonucleoprotein (RNP) synthesizes telomeric repeats at chromosome ends using a telomerase reverse transcriptase (TERT) and a telomerase RNA (hTR in humans). Previous structural work showed that human telomerase is typically monomeric, containing a single copy of TERT and hTR. Evidence for dimeric complexes exists, although the composition, high-resolution structure, and function remain elusive.

A risk score system including CT features for predicting early recurrence of resectable pancreatic ductal adenocarcinoma after radical resection: a dual-center retrospective study.

Purpose: To develop a score system including CT features for predicting postoperative early (≤ 1 year) recurrence-free survival (RFS) in resectable pancreatic ductal adenocarcinoma (PDAC) patients who underwent radical resection and assess its performance.

Materials And Methods: This dual-center, retrospective study included patients with resectable PDAC who underwent radical resection from September 2016 to April 2023. All CT features were independently evaluated by two blinded radiologists.

Investigate the Regulatory Role of Parathyroid Hormone on Condylar Fibrocartilage Homeostasis.

Introduction: Condylar fibrocartilage regeneration after injury has been hindered by its poor self-repair capacity. Injection of parathyroid hormone (PTH) has been proven to effectively delay cartilage damage in osteoarthritis. In this study, we investigated the regulatory effect of PTH on the homeostasis of condylar fibrocartilage.

A CT-based radiomics nomogram for the preoperative prediction of perineural invasion in pancreatic ductal adenocarcinoma.

Purpose: To develop a nomogram based on CT radiomics features for preoperative prediction of perineural invasion (PNI) in pancreatic ductal adenocarcinoma (PDAC) patients.

Methods: A total of 217 patients with histologically confirmed PDAC were enrolled in this retrospective study. Radiomics features were extracted from the whole tumor.

Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types.

The relationship between the oral microbiome and oral squamous cell carcinoma (OSCC) has been extensively investigated. Nonetheless, most previous studies were single-center, resulting in the absence of systematic evaluations. To address this gap, we performed a comprehensive meta-analysis on 1,255 samples from OSCC-related 16S rRNA gene data sets, representing a diverse range of OSCC phenotypes.

Transcription factor ATF3 aggravates kidney fibrosis by maintaining the state of histone H3 lysine 27 acetylation.

Background: Chronic kidney disease (CKD) is a global health issue, with renal fibrosis being a common pathway in CKD development. Histone modification plays crucial roles in transcriptional regulation, but their pathological functions and mechanisms in CKD are not well understood.

Methods: We utilized chromatin immunoprecipitation with next-generation DNA sequencing (ChIP-seq) and RNA-seq to evaluate the states and functions of H3 lysine 27 acetylation (H3K27ac) and H3 lysine 4 trimethylation (H3K4me3) in kidney of CKD mice.

An interpretable RNA foundation model for exploring functional RNA motifs in plants.

The complex 'language' of plant RNA encodes a vast array of biological regulatory elements that orchestrate crucial aspects of plant growth, development and adaptation to environmental stresses. Recent advancements in foundation models (FMs) have demonstrated their unprecedented potential to decipher complex 'language' in biology. In this study, we introduced PlantRNA-FM, a high-performance and interpretable RNA FM specifically designed for plants.

Bioinformatic approaches of liquid-liquid phase separation in human disease.

Biomolecular aggregation within cellular environments via liquid-liquid phase separation (LLPS) spontaneously forms droplet-like structures, which play pivotal roles in diverse biological processes. These structures are closely associated with a range of diseases, including neurodegenerative disorders, cancer and infectious diseases, highlighting the significance of understanding LLPS mechanisms for elucidating disease pathogenesis, and exploring potential therapeutic interventions. In this review, we delineate recent advancements in LLPS research, emphasizing its pathological relevance, therapeutic considerations, and the pivotal role of bioinformatic tools and databases in facilitating LLPS investigations.

Molecular and transcriptional basis of bidirectional CD4 T cell exhaustion in oropharyngeal squamous cell carcinoma.

Tumor-infiltrating CD4 T cells orchestrate the adaptive immune response through remarkable plasticity, and the expression patterns of exhaustion-related inhibitory receptors in these cells differ significantly from those of CD8 T cells. Thus, a better understanding of the molecular basis of CD4 T cell exhaustion and their responses to immune checkpoint blockade (ICB) is required. Here, we integrated multiomics approaches to define the phenotypic and molecular profiles of exhausted CD4 T cells in oropharyngeal squamous cell carcinoma (OPSCC).

iM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning.

DNA, beyond its canonical B-form double helix, adopts various alternative conformations, among which the i-motif, emerging in cytosine-rich sequences under acidic conditions, holds significant biological implications in transcription modulation and telomere biology. Despite recognizing the crucial role of i-motifs, predictive software for i-motif forming sequences has been limited. Addressing this gap, we introduce 'iM-Seeker', an innovative computational platform designed for the prediction and evaluation of i-motifs.

The diversity of inhibitory receptor co-expression patterns of exhausted CD8 T cells in oropharyngeal carcinoma.

Exhausted CD8 T cells (Texs) are characterized by the expression of various inhibitory receptors (IRs), whereas the functional attributes of these co-expressed IRs remain limited. Here, we systematically characterized the diversity of IR co-expression patterns in Texs from both human oropharyngeal squamous cell carcinoma (OPSCC) tissues and syngeneic OPSCC model. Nearly 60% of the Texs population co-expressed two or more IRs, and the number of co-expressed IRs was positively associated with superior exhaustion and cytotoxicity phenotypes.

Bacterial interactome disturbance in chronic obstructive pulmonary disease clinical stability and exacerbations.

Rationale: Our understanding of airway dysbiosis in chronic obstructive pulmonary disease (COPD) remains incomplete, which may be improved by unraveling the complexity in microbial interactome.

Objectives: To characterize reproducible features of airway bacterial interactome in COPD at clinical stability and during exacerbation, and evaluate their associations with disease phenotypes.

Methods: We performed weighted ensemble-based co-occurrence network analysis of 1742 sputum microbiomes from published and new microbiome datasets, comprising two case-control studies of stable COPD versus healthy control, two studies of COPD stability versus exacerbation, and one study with exacerbation-recovery time series data.

A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics.

Plants, as sessile organisms, deploy transcriptional dynamics for adapting to extreme growth conditions such as cold stress. Emerging evidence suggests that chromatin architecture contributes to transcriptional regulation. However, the relationship between chromatin architectural dynamics and transcriptional reprogramming in response to cold stress remains unclear.

The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation.

CCCTC-binding factor (CTCF), a ubiquitously expressed and highly conserved protein, is known to play a critical role in chromatin structure. Post-translational modifications (PTMs) diversify the functions of protein to regulate numerous cellular processes. However, the effects of PTMs on the genome-wide binding of CTCF and the organization of three-dimensional (3D) chromatin structure have not been fully understood.

Precise prediction of phase-separation key residues by machine learning.

Understanding intracellular phase separation is crucial for deciphering transcriptional control, cell fate transitions, and disease mechanisms. However, the key residues, which impact phase separation the most for protein phase separation function have remained elusive. We develop PSPHunter, which can precisely predict these key residues based on machine learning scheme.

Prediction of DNA i-motifs via machine learning.

i-Motifs (iMs), are secondary structures formed in cytosine-rich DNA sequences and are involved in multiple functions in the genome. Although putative iM forming sequences are widely distributed in the human genome, the folding status and strength of putative iMs vary dramatically. Much previous research on iM has focused on assessing the iM folding properties using biophysical experiments.

Genetic characteristics of common variable immunodeficiency patients with autoimmunity.

The pathogenesis of common variable immunodeficiency disorder (CVID) is complex, especially when combined with autoimmunity. Genetic factors may be potential explanations for this complex situation, and whole genome sequencing (WGS) provide the basis for this potential. Genetic information of patients with CVID with autoimmunity, together with their first-degree relatives, was collected through WGS.

DASES: a database of alternative splicing for esophageal squamous cell carcinoma.

Esophageal carcinoma ranks as the sixth leading cause of cancer-related mortality globally, with esophageal squamous cell carcinoma (ESCC) being particularly prevalent among Asian populations. Alternative splicing (AS) plays a pivotal role in ESCC development and progression by generating diverse transcript isoforms. However, the current landscape lacks a specialized database focusing on alternative splicing events (ASEs) derived from a large number of ESCC cases.

[Role of Liquid-Liquid Phase Separation in Cell Fate Transition and Diseases].

Liquid-liquid phase separation (LLPS), a novel mechanism of the organization and formation of cellular structures, plays a vital role in regulating cell fate transitions and disease pathogenesis and is gaining widespread attention. LLPS may lead to the assemblage of cellular structures with liquid-like fluidity, such as germ granules, stress granules, and nucleoli, which are classic membraneless organelles. These structures are typically formed through the high-concentration liquid aggregation of biomacromolecules driven by weak multivalent interactions.

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline.

Background: The gut microbiome and fecal metabolites have been found to influence sarcopenia, but whether there are potential bacteria that can alleviate sarcopenia has been under-investigated, and the molecular mechanism remains unclear.

Methods: To investigate the relationships between the gut microbiome, fecal metabolites and sarcopenia, subjects were selected from observational multi-ethnic study conducted in Western China. Sarcopenia was diagnosed according to the criteria of the Asian Working Group for Sarcopenia 2014.

Simultaneous profiling of chromatin architecture and transcription in single cells.

The three-dimensional structure of chromatin plays a crucial role in development and disease, both of which are associated with transcriptional changes. However, given the heterogeneity in single-cell chromatin architecture and transcription, the regulatory relationship between the three-dimensional chromatin structure and gene expression is difficult to explain based on bulk cell populations. Here we develop a single-cell, multimodal, omics method allowing the simultaneous detection of chromatin architecture and messenger RNA expression by sequencing (single-cell transcriptome sequencing (scCARE-seq)).