Qinghua Cui
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View article: Psychometric validation of the Chinese version of the PROMIS-29 profile in community-dwelling older adults with multimorbidities
Psychometric validation of the Chinese version of the PROMIS-29 profile in community-dwelling older adults with multimorbidities Open
Background The Patient-Reported Outcomes Measurement Information System 29-item (PROMIS-29) profile is commonly used to measure patients’ self-reported health status. This study examined the psychometric properties of the Chinese version o…
View article: Enhancing protein structure prediction accuracy by prioritizing important residues using protein language models
Enhancing protein structure prediction accuracy by prioritizing important residues using protein language models Open
Accurate prediction of protein tertiary structures from amino acid sequences remains a fundamental challenge in computational biology. Although AlphaFold2 represents a major advance, systematic discrepancies persist between its predictions…
View article: Enhancing mRNA translation efficiency with discriminative and generative artificial intelligence by optimizing 5′ UTR sequences
Enhancing mRNA translation efficiency with discriminative and generative artificial intelligence by optimizing 5′ UTR sequences Open
The mRNA-based therapeutics, notably mRNA vaccines, represent a new era of powerful tools to combat various diseases. However, the relatively low translation efficiency of exogenous mRNA often limits its wide application. Here, we propose …
View article: Nucleotide Metabolism and Immune Genes Can Predict the Prognostic Risk of Hepatocellular Carcinoma and the Immune Microenvironment
Nucleotide Metabolism and Immune Genes Can Predict the Prognostic Risk of Hepatocellular Carcinoma and the Immune Microenvironment Open
The overall survival of hepatocellular carcinoma (HCC) remains poor, highlighting the need for better prognostic tools. Nucleotide metabolism fuels tumor progression, while the immune microenvironment dictates therapy response, but integra…
View article: Life origin and evolution may be influenced by the dynamical Coupling between Earth’s magnetic field strength and atmospheric oxygen level
Life origin and evolution may be influenced by the dynamical Coupling between Earth’s magnetic field strength and atmospheric oxygen level Open
A recent study has revealed that Earth’s magnetic field strength and atmospheric oxygen level exhibit strongly correlated, linearly increasing trends (M-O relationship) over the past 540 million years. This discovery sheds new lights on th…
View article: Zearalenone at environmental levels promoted ER- positive breast cancer cell lines through the hedgehog pathway
Zearalenone at environmental levels promoted ER- positive breast cancer cell lines through the hedgehog pathway Open
Zearalenone (ZEA) has been recognized as a common exogenous nonsteroidal estrogen in environments which possessed a disruptive effect on organisms. Exposure to exogenous estrogen has been revealed to affect breast cancer development. Howev…
View article: MedImg: An Integrated Database for Public Medical Images
MedImg: An Integrated Database for Public Medical Images Open
The advancements in deep learning algorithms for medical image analysis have garnered significant attention in recent years. While several studies have shown promising results, with models achieving or even surpassing human performance, tr…
View article: CEMIP Maintains Vascular Contractility by Controlling PP1c-MLC20 Cascade in SMCs
CEMIP Maintains Vascular Contractility by Controlling PP1c-MLC20 Cascade in SMCs Open
BACKGROUND: The CEMIP (cell migration–inducing protein) exhibits extremely high expression levels in smooth muscle tissues. However, whether CEMIP modulates the contractile phenotype of vascular smooth muscle cells and confers blood pressu…
View article: A large-scale foundation model for bulk transcriptomes
A large-scale foundation model for bulk transcriptomes Open
Large language models (LLMs) have emerged as powerful foundation models leading to breakthroughs in transcriptome analysis. However, current RNA-seq foundation models are exclusively pretrained on sparse single-cell RNA-seq (scRNA-seq) dat…
View article: Timosaponin B-II suppresses gastric cancer cell proliferation and induces apoptosis via the Nrf2/miR-455-3p/KLF6 pathway
Timosaponin B-II suppresses gastric cancer cell proliferation and induces apoptosis via the Nrf2/miR-455-3p/KLF6 pathway Open
TB-II suppresses GC cell proliferation and induces apoptosis via the Nrf2/miR-455-3p/KLF6 pathway.
View article: Differential impact of spotted fever group rickettsia and anaplasmosis on tick microbial ecology: evidence from multi-species comparative microbiome analysis
Differential impact of spotted fever group rickettsia and anaplasmosis on tick microbial ecology: evidence from multi-species comparative microbiome analysis Open
Tick-borne diseases (TBDs) pose a significant public health challenge, as their incidence is increasing due to the effects of climate change and ecological shifts. The interplay between tick-borne pathogens and the host microbiome is an em…
View article: Risk model of nucleotide metabolism and immunity signature genes in predicting of hepatocellular carcinoma prognosis and immune microenvironment
Risk model of nucleotide metabolism and immunity signature genes in predicting of hepatocellular carcinoma prognosis and immune microenvironment Open
Background:Given the persistent poor prognosis of hepatocellular carcinoma (HCC), it is imperative to establish a multi-feature prognostic prediction model. Methods: LIHC patient data were obtained from TCGA, and LIHC patients were cluster…
View article: Comprehensive profiling of <i>N</i><sup>6</sup>-methyladnosine (m<sup>6</sup>A) readouts reveals novel m<sup>6</sup>A readers that regulate human embryonic stem cell differentiation
Comprehensive profiling of <i>N</i><sup>6</sup>-methyladnosine (m<sup>6</sup>A) readouts reveals novel m<sup>6</sup>A readers that regulate human embryonic stem cell differentiation Open
N 6 -methyladenosine (m 6 A) methylation has emerged as a prevalent RNA modification that extensively impacts various physiological and pathological processes via various post-transcriptional readout effects in mammals. High-throughput met…
View article: CHIEF: An Attention-based Ensemble Learning Framework for Functional Protein Design
CHIEF: An Attention-based Ensemble Learning Framework for Functional Protein Design Open
Protein de novo design is a longstanding challenge in biological field due to the multifaceted physicochemical properties and complexities of proteins. Several deep learning models have emerged for protein de novo design. However, each mod…
View article: Identification of Metabolism-Related Hub Genes in Heart Failure via Comprehensive Transcriptome Analysis
Identification of Metabolism-Related Hub Genes in Heart Failure via Comprehensive Transcriptome Analysis Open
Background: Metabolic dysfunction is a key driver of heart failure (HF) progression. Identifying metabolic hub genes in HF may reveal novel therapeutic targets. Methods: Transcriptomic datasets from HF patients (GEO database) and metabolis…
View article: Ovarian cancer cell cluster inhibits pancreatic cancer progression
Ovarian cancer cell cluster inhibits pancreatic cancer progression Open
Pancreatic cancer is the most lethal cancer and all of the current cancer treatment strategies fail at this disease. It is thus urgently important to explore novel therapeutics. We previously revealed that it can be significantly inhibited…
View article: Transcriptomic Profiling Reveals 17β‐Estradiol Treatment Represses Ubiquitin‐Proteasomal Mediators in Skeletal Muscle of Ovariectomized Mice
Transcriptomic Profiling Reveals 17β‐Estradiol Treatment Represses Ubiquitin‐Proteasomal Mediators in Skeletal Muscle of Ovariectomized Mice Open
Background With a decline of 17β‐estradiol (E2) at menopause, E2 has been implicated in the accompanied loss of skeletal muscle mass and strength. We aimed at characterizing transcriptomic responses of skeletal muscle to E2 in female mice,…
View article: Characteristics of Soil Microbial Community Structure in Different Land Use Types of the Huanghe Alluvial Plain
Characteristics of Soil Microbial Community Structure in Different Land Use Types of the Huanghe Alluvial Plain Open
The Huanghe alluvial plain plays a crucial role in biodiversity conservation. However, its ecosystem has become sensitive and fragile due to long-term human disturbances. Enhancing the resilience of this ecosystem and promoting the sustain…
View article: Metatranscriptomic Analysis Uncovers RNA Virus Diversity in Ticks From the China–Russia–North Korea Border Region
Metatranscriptomic Analysis Uncovers RNA Virus Diversity in Ticks From the China–Russia–North Korea Border Region Open
Ticks serve as critical viral vectors, and border regions, acting as convergence zones of complex ecosystems, provide diverse habitats for ticks and their hosts, thereby underscoring the need to investigate the tick‐borne virome compositio…
View article: Global, Regional, and National Burden of Atherosclerotic Cardiovascular Disease, Projections to 2035 and its Attributable Risk Factors from 1990 to 2021: A Systematic Analysis for the Global Burden of Disease Study 2021
Global, Regional, and National Burden of Atherosclerotic Cardiovascular Disease, Projections to 2035 and its Attributable Risk Factors from 1990 to 2021: A Systematic Analysis for the Global Burden of Disease Study 2021 Open
View article: Ambient Temperature Modulates Human Hematological Parameters
Ambient Temperature Modulates Human Hematological Parameters Open
View article: A combined deep learning framework for mammalian m6A site prediction
A combined deep learning framework for mammalian m6A site prediction Open
View article: TransmiR v3.0: an updated transcription factor-microRNA regulation database
TransmiR v3.0: an updated transcription factor-microRNA regulation database Open
microRNAs (miRNAs) are active in various biological processes by mediating gene expression, and the full investigation of miRNA transcription is crucial for understanding the mechanisms underlying miRNA deregulation in pathological conditi…
View article: Cell Death: Mechanisms and Potential Targets in Breast Cancer Therapy
Cell Death: Mechanisms and Potential Targets in Breast Cancer Therapy Open
Breast cancer (BC) has become the most life-threatening cancer to women worldwide, with multiple subtypes, poor prognosis, and rising mortality. The molecular heterogeneity of BC limits the efficacy and represents challenges for existing t…
View article: Pomegranate seeds: a comprehensive review of traditional uses, chemical composition, and pharmacological properties
Pomegranate seeds: a comprehensive review of traditional uses, chemical composition, and pharmacological properties Open
Pomegranate seeds (PS) are the dried seeds derived from pomegranate fruit, accounting for approximately 20% of the fruit’s total weight, and are a by-product of pomegranate juice extraction. These seeds hold significance in traditional med…
View article: A BSL-2 compliant mouse model of SARS-CoV-2 infection for efficient and convenient antiviral evaluation
A BSL-2 compliant mouse model of SARS-CoV-2 infection for efficient and convenient antiviral evaluation Open
Animal models of authentic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection require operation in biosafety level 3 (BSL-3) containment. In the present study, we established a mouse model employing a single-cycle infec…
View article: Comprehensive prediction and analysis of human protein essentiality based on a pre-trained protein large language model
Comprehensive prediction and analysis of human protein essentiality based on a pre-trained protein large language model Open
Human essential genes and their protein products are indispensable for the viability and development of the individuals. Thus, it is quite important to decipher the essential proteins and up to now numerous computational methods have been …
View article: MedImg: a database for public medical image integration
MedImg: a database for public medical image integration Open
The advancements of deep learning algorithms in medical image analysis has garnered tremendous attention in recent years. Several studies have reported that the models have achieved and even surpassed human performance, whereas the transla…
View article: Estimating the selection pressure and evolutionary rate of proteins on the non-neutral hypothesis of synonymous mutations
Estimating the selection pressure and evolutionary rate of proteins on the non-neutral hypothesis of synonymous mutations Open
The Nonsynonymous/Synonymous substitution rate ratio (Ka/Ks) is a commonly used metric to estimate the selection pressure and evolutionary rate of proteins in comparative genomics, which plays critical roles in molecular evolution in both …
View article: Gap-Δenergy, a New Metric of the Bond Energy State, Assisting to Predict Molecular Toxicity
Gap-Δenergy, a New Metric of the Bond Energy State, Assisting to Predict Molecular Toxicity Open
Molecular toxicity is a critical feature of drug development. It is thus very important to develop computational models to evaluate the toxicity of small molecules. The accuracy of toxicity prediction largely depends on the quality of mole…