Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data.

High-throughput sequencing (HTS) technologies have been instrumental in investigating biological questions at the bulk and single-cell levels. Comparative analysis of two HTS data sets often relies on testing the statistical significance for the difference of two negative binomial distributions (DOTNB). Although negative binomial distributions are well studied, the theoretical results for DOTNB remain largely unexplored.

Highly sensitive ECL detection of miRNA based on self-generated coreactant and target-induced catalyzed hairpin assembly.

Background: Recently, various techniques have been developed to accurately and sensitively detect tumor biomarkers for the early diagnosis and effective therapy of cancer. The electrochemiluminescence (ECL) method holding outstanding features including high sensitivity, ease of operation, and spatiotemporal controllability exhibited great potential for DNA/RNA detection, immunoassay, cancer cell detection, and environmental analysis. However, a glaring problem of ECL approaches is that the layer-by-layer modification on the electrode leads to poor stability and sensitivity of the sensors.

DeepIMAGER: Deeply Analyzing Gene Regulatory Networks from scRNA-seq Data.

Understanding the dynamics of gene regulatory networks (GRNs) across diverse cell types poses a challenge yet holds immense value in unraveling the molecular mechanisms governing cellular processes. Current computational methods, which rely solely on expression changes from bulk RNA-seq and/or scRNA-seq data, often result in high rates of false positives and low precision. Here, we introduce an advanced computational tool, DeepIMAGER, for inferring cell-specific GRNs through deep learning and data integration.

Targeting NG2 relieves the resistance of BRAF-mutant thyroid cancer cells to BRAF inhibitors.

BRAF represents a constitutively active onco-kinase and stands as the most prevalent genetic alteration in thyroid cancer. However, the clinical efficacy of small-molecule inhibitors targeting BRAF is often limited by acquired resistance. Here, we find that nerve/glial antigen 2 (NG2), also known as chondroitin sulfate proteoglycan 4 (CSPG4), is up-regulated in thyroid cancers, and its expression is increased with tumor progression in a BRAF-driven thyroid cancer mouse model.

Deep Batch Integration and Denoise of Single-Cell RNA-Seq Data.

Numerous single-cell transcriptomic datasets from identical tissues or cell lines are generated from different laboratories or single-cell RNA sequencing (scRNA-seq) protocols. The denoising of these datasets to eliminate batch effects is crucial for data integration, ensuring accurate interpretation and comprehensive analysis of biological questions. Although many scRNA-seq data integration methods exist, most are inefficient and/or not conducive to downstream analysis.

RNF115 aggravates tumor progression through regulation of CDK10 degradation in thyroid carcinoma.

Background: RING Finger Protein 115 (RNF115), a notable E3 ligase, is known to modulate tumorigenesis and metastasis. In our investigation, we endeavor to unravel the putative function and inherent mechanism through which RNF115 influences the evolution of thyroid carcinoma (THCA).

Methods: We analyzed RNF115 expression in THCA using the Cancer Genome Atlas (TCGA) database.

MYO5A overexpression promotes invasion and correlates with low lymphocyte infiltration in head and neck squamous carcinoma.

Head and neck squamous carcinoma (HNSC) poses a significant public health challenge due to its substantial morbidity. Nevertheless, despite advances in current treatments, the prognosis for HNSC remains unsatisfactory. To address this, single-cell RNA sequencing (RNA-seq) and bulk RNA-seq data combined with in vitro studies were conducted to examine the role of MYO5A (Myosin VA) in HNSC.

Self-supervised deep clustering of single-cell RNA-seq data to hierarchically detect rare cell populations.

Single-cell RNA sequencing (scRNA-seq) is a widely used technique for characterizing individual cells and studying gene expression at the single-cell level. Clustering plays a vital role in grouping similar cells together for various downstream analyses. However, the high sparsity and dimensionality of large scRNA-seq data pose challenges to clustering performance.

scTIGER: A Deep-Learning Method for Inferring Gene Regulatory Networks from Case versus Control scRNA-seq Datasets.

Inferring gene regulatory networks (GRNs) from single-cell RNA-seq (scRNA-seq) data is an important computational question to find regulatory mechanisms involved in fundamental cellular processes. Although many computational methods have been designed to predict GRNs from scRNA-seq data, they usually have high false positive rates and none infer GRNs by directly using the paired datasets of case-versus-control experiments. Here we present a novel deep-learning-based method, named scTIGER, for GRN detection by using the co-differential relationships of gene expression profiles in paired scRNA-seq datasets.

A Feedback Loop Involving Exosomal miR-146a and NG2 to Propel the Development and Progression of Hypothyroidism.

Thyrotropin receptor (TSHR) plays a central role in maintaining thyroid function and TSHR impairment causes hypothyroidism, which is often associated with metabolic disarrangement. The most common type of hypothyroidism is autoimmune disease-related and the mechanism, particularly with respect to the role of microRNAs (miRNAs), has not been delineated. Serum from 30 patients with subclinical hypothyroidism (SCH) and 30 healthy individuals were collected and exosomal miR-146a (exo-miR-146a) was examined, followed by extensive mechanistic investigation using various molecular and cellular experimental approaches and genetic-knockout mouse models.

Efficacy and safety of Artemisia annua sublingual immunotherapy in patients with seasonal allergic rhinoconjunctivitis over two pollen seasons.

Objective: This study investigates the efficacy and safety of sublingual immunotherapy (SLIT) with A. annua allergens in patients with seasonal allergic rhinoconjunctivitis over two pollen seasons.

Methods: Seventy patients with moderate-severe seasonal allergic rhinoconjunctivitis were divided evenly into the SLIT and control groups.

The Feasibility Study of Intraoperative RLN Monitoring Using Cricothyroid Membrane-Inserted Needle Electrodes During Thyroid Surgery.

Objective: This study evaluated the feasibility, stability, safety, and economy of cricothyroid membrane (CM)-inserted needle electrodes for recurrent laryngeal nerve monitoring.

Study Design: Parallel and controlled study.

Setting: Clinical research center for thyroid diseases of Shaanxi province.

[The influence of additional roll test on the repositioning procedure by SRM-vertigo diagnosis system for horizontal canal benign paroxysmal positional vertigo].

To evaluate the influence of an additional roll test on the repositioning procedure by SRM-vertigo diagnosis system for horizontal canal benign paroxysmal positional vertigo（HC-BPPV）. A total of 713 patients diagnosed with HC-BPPV in Department of Otolaryngology Head and Neck Surgery，the First Affiliated Hospital of Xi'an Jiaotong University from Jan 2020 to Feb 2022 were enrolled. The patients were divided into two groups by hospital card numbers, in which the number is odd were considered as group A, and the number is even were considered as group B.

Frizzled-3 suppression overcomes multidrug chemoresistance by Wnt/β-catenin signaling pathway inhibition in hepatocellular carcinoma cells.

Multidrug resistance (MDR) is a major obstacle to the efficacy of hepatocellular carcinoma (HCC) chemotherapy. Previous studies have identified that low FZD3 predicted decreased survival after intraperitoneal versus intravenous-only chemotherapy in ovarian cancer. This study aimed to identify a potential target in HCC chemotherapy.

[Progress in active surveillance for adult low-risk papillary thyroid microcarcinoma].

The incidence of papillary thyroid microcarcinoma （PTMC） increases rapidly. However, epidemiological and autopsy studies show that the prevalence of low-risk papillary thyroid microcarcinoma （LR-PTMC） is very high, but the mortality is very low. There is over-diagnosis and over-treatment for LR-PTMC.

SKP2 Contributes to AKT Activation by Ubiquitination Degradation of PHLPP1, Impedes Autophagy, and Facilitates the Survival of Thyroid Carcinoma.

Papillary thyroid carcinoma (PTC) is the most common subtype of thyroid carcinoma. Despite a good prognosis, approximately a quarter of PTC patients are likely to relapse. Previous reports suggest an association between S-phase kinase-associated protein 2 (SKP2) and the prognosis of thyroid cancer.

Investigation of Volumetric Block Proportion (VBP) Effect on Excavation-Induced Ground Response of Talus-like Rock Mass Based on DEM Simulations.

Due to the complexity of the talus-like rock mass with different values of volumetric block proportion (VPB), it is thus crucial to explore the VBP effect on the excavation-induced ground responses. We conduct a series of 2D DEM (discrete element method) simulations on a common circular tunnel excavation in the talus-like rock mass with different VBPs (0%, 15%, 50%, 85% and 100%). For each VBP, two support scenarios, i.

Decoding brain memory formation by single-cell RNA sequencing.

To understand how distinct memories are formed and stored in the brain is an important and fundamental question in neuroscience and computational biology. A population of neurons, termed engram cells, represents the physiological manifestation of a specific memory trace and is characterized by dynamic changes in gene expression, which in turn alters the synaptic connectivity and excitability of these cells. Recent applications of single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) are promising approaches for delineating the dynamic expression profiles in these subsets of neurons, and thus understanding memory-specific genes, their combinatorial patterns and regulatory networks.

Supervised Contrastive Learning and Intra-Dataset Adversarial Adaptation for Iris Segmentation.

Precise iris segmentation is a very important part of accurate iris recognition. Traditional iris segmentation methods require complex prior knowledge and pre- and post-processing and have limited accuracy under non-ideal conditions. Deep learning approaches outperform traditional methods.

Combining Phenotypes of Nucleotide Excision Repair Pathway to Predict the Risk of Head and Neck Squamous Cell Carcinomas in a Chinese Population.

Background: Nucleotide excision repair (NER) is pivotal in the development of smoking-related malignancies. Nine core genes (, , , , , , , , and ) are highly involved in the NER process. We combined two phenotypes of NER pathway (NER protein and NER gene mRNA expression) and evaluated their associations with the risks of the head and neck squamous cell carcinomas (HNSCCs) in a Chinese population.

Detecting Fear-Memory-Related Genes from Neuronal scRNA-seq Data by Diverse Distributions and Bhattacharyya Distance.

The detection of differentially expressed genes (DEGs) is one of most important computational challenges in the analysis of single-cell RNA sequencing (scRNA-seq) data. However, due to the high heterogeneity and dropout noise inherent in scRNAseq data, challenges in detecting DEGs exist when using a single distribution of gene expression levels, leaving much room to improve the precision and robustness of current DEG detection methods. Here, we propose the use of a new method, DEGman, which utilizes several possible diverse distributions in combination with Bhattacharyya distance.

Mechanisms of Xiong-Pi-Fang in treating coronary heart disease associated with depression: A systematic pharmacology strategy and in vivo pharmacological validation.

Background: Coronary heart disease (CHD) and depression are very common and often co-existing disorders. Xiong-Pi-Fang (XPF), a therapeutic classical traditional Chinese medicine (TCM) formula, has shown satisfactory efficacy in treating CHD associated with depression. However, its mechanism of action is still unknown.

Gut microbiome in modulating immune checkpoint inhibitors.

Gut microbiome has been increasingly recognized for its influence on a diverse array of human diseases including cancer, and may also influence the outcome of cancer therapies. A prime example is seen in immunotherapy, for which gut microbes determine the therapeutic responses associated with immune checkpoint inhibitors (ICIs) in preclinical models and patient cohorts. This evidence hints that inter-individual variations in the gut microbiota may account for the significant heterogeneity in immunotherapeutic responses to ICIs.

[Significance of rapid axial roll test in determining the responsible semicircular canal for horizontal canal benign paroxysmal positional vertigo].

To compare the diagnostic performance of the rapid axial roll test（RART） and the traditional roll test（SRT）in determining the responsible semicircular canal for horizontal canal benign paroxysmal positional vertigo（HC-BPPV）. A total of 400 patients diagnosed with HC-BPPV from January 2020 to December 2020 were collected and randomly divided into two groups. Among them, there were 202 cases in the RART group and 198 cases in the SRT group.

Novel recombinant human thyroid-stimulating hormone in aiding postoperative assessment of patients with differentiated thyroid cancer-phase I/II study.

Purpose: Thyroid hormone withdrawal (THW) inevitably induced hypothyroidism in patients with differentiated thyroid cancer (DTC), and we aimed to evaluate the safety and efficacy of a novel recombinant human thyroid-stimulating hormone (rhTSH, ZGrhTSH) as an alternative of THW in China.

Methods: Totally, 64 DTC patients were enrolled with 24 in the dose-escalation cohort equally grouped into 0.9 mg × 1 day, 0.