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AVM:A Manually Curated Database of Aerosol-transmitted Virus Mutations,Human Diseases,and Drugs

Genomics, Proteomics & bioinformatics 2024年第3期22卷 133-138页

作者： Lan Mei Yaopan Hou Jiajun Zhou Yetong Chang Yuwei Liu Di Wang Yunpeng Zhang Shangwei Ning Xia Li College of Bioinformatics Science and Technology Harbin Medical UniversityHarbin 150081China

Aerosol-transmitted viruses possess strong infectivity and can spread over long distances,earning the difficult-to-control *** cause various human diseases and pose serious threats to human *** can increase the transmissibility and virulence of the strains,reducing the protection provided by vaccines and weakening the efficacy of antiviral *** this study,we established a manually curated database(termed AVM)to store information on aerosol-transmitted viral mutations(VMs).The current version of the AVM contains 42,041 VMs(including 2613 immune escape mutations),45 clinical information datasets,and 407 drugs/antibodies/***,we recorded 88 human diseases associated with viruses and found that the same virus can target multiple organs in the body,leading to diverse ***,the AVM database offers a straightforward user interface for browsing,retrieving,and downloading *** database is a comprehensive resource that can provide timely and valuable information on the transmission,treatment,and diseases caused by aerosol-transmitted viruses(http://***/AVM).

关键词： Aerosol Viral mutation Immune escape mutation Human disease Drug

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NON UNIFORM EXPANSION AND ADDITIVE NOISE IMPLY RANDOM HORSESHOES AND RANDOM TOWER

arXiv

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arXiv 2025年

作者： Lamb, Jeroen S.W. Tenaglia, Giuseppe Turaev, Dmitry International Research Center for Neurointelligence The University of Tokyo Tokyo113-0033 Japan Centre for Applied Mathematics and Bioinformatics Department of Mathematics and Natural Sciences Gulf University for Science and Technology Halwally 32093 Kuwait Department of Mathematics Imperial College London LondonSW7 2AZ United Kingdom

We propose a notion of random horseshoe and prove density of random horseshoes and existence of a random young tower with exponential tail for non uniformly expanding random dynamical systems with additive noiseMSC Co... 详细信息

关键词： Lyapunov methods

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N-Heterocyclic Carbenes: Novel Derivatization Reagents for LC-MS Analysis of Aliphatic Aldehydes

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Analytical Chemistry 2025年 2025 May 2页

作者： Wang, Yan-Zhen Xiao, Hua-Ming Bai, Pei-Rong Liu, Xiang Liu, Xin Zhu, Quan-Fei Feng, Yu-Qi School of Bioengineering and Health Wuhan Textile University Wuhan430200 China Department of Chemistry Wuhan University Wuhan430072 China Frontier Science Center for Immunology and Metabolism Wuhan University Wuhan430072 China Department of Laboratory Medicine Wuhan Children’s Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan430016 China The Key Laboratory for Biomedical Photonics of MOE Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics Molecular Imaging Key Laboratory Systems Biology Theme Department of Biomedical Engineering College of Life Science and Technology Huazhong University of Science and Technology Wuhan430074 China

N-heterocyclic carbenes (NHCs) are versatile catalysts for organic reactions, characterized by their unique electron-donating properties and high activity. This study introduces NHCs as innovative derivatization reagents for liquid chromatography-mass spectrometry (LC-MS) analysis of aliphatic aldehydes. Five distinct NHC reagents were evaluated, and 2-mesityl-2,5,6,7-tetrahydropyrrolo[2,1-c][1,2,4]triazol-4-ium chloride (MTPTC) was identified as the most promising candidate due to its rapid reaction kinetics, high selectivity, and excellent product stability. The MTPTC-based derivatization reaction effectively addressed the issue of stereoisomeric products, resulting in well-resolved single peaks in the LC separation. Additionally, the derivatized products exhibited high stability, facilitating accurate and reliable quantitative analysis. Using MTPTC as the derivatization reagent, an LC-MS quantitative analysis strategy was developed for the determination of eight aliphatic aldehydes in human sera. The method demonstrated a broad linear range, low limits of detection and quantification, and satisfactory reproducibility and accuracy. The applicability of this method was further validated through the quantification of aliphatic aldehydes in the serum of sepsis patients. This work extends NHCs’ utility to analytical chemistry and introduces a novel derivatization reagent for the analysis of carbonyl compounds by LC-MS. © 2025 American Chemical Society.

关键词： Liquid chromatography

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Clinician-artificial intelligence collaboration: A win-win solution for efficiency and reliability in atrial fibrillation diagnosis

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Med 2025年 100668页

作者： Zhang, Peng Lin, Fan Ma, Fei Chen, Yuting Liu, Yuhang Feng, Xiaoli Fang, Siyi Zhang, Haowei Xiao, Shuna Yang, Xiangli Li, Dun Wang, Dao Wen Yang, Xiaoyun Li, Qiang Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory Department of Biomedical Engineering College of Life Science and Technology Huazhong University of Science and Technology Hubei Wuhan 430074 China MoE Key Laboratory for Biomedical Photonics Collaborative Innovation Center for Biomedical Engineering School of Engineering Sciences Huazhong University of Science and Technology Hubei Wuhan 430074 China Division of Cardiology Department of Internal Medicine Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Hubei Wuhan 430030 China Cardiovascular Center Liyuan Hospital Affiliated to Tongji Medical College Huazhong University of Science and Technology Hubei Wuhan 430077 China United Imaging Surgical Healthcare Co. Ltd. Hubei Wuhan 430206 China

Background: Given the biases and ethical concerns of AI models, the fully automatic diagnosis of diseases in clinical settings is challenging. In contrast, clinician-AI collaboration is considered essential to ensure the validity and reliability of utilizing AI models in clinical practice. However, effective strategies for clinician-AI collaboration remain largely unexplored. Methods: This study proposed a three-step general clinician-AI collaboration pipeline aimed at improving disease diagnosis efficiency: first, utilizing large real-world clinical datasets to evaluate and clarify clinicians’ diagnostic strengths/weaknesses;second, developing an AI model to complement clinicians’ weakness in disease diagnosis;and finally, proposing a clinician-AI collaboration strategy to leverage the strengths of both AI and clinicians. The effectiveness of this pipeline was validated through a study focusing on clinical paroxysmal atrial fibrillation (PAF) detection, utilizing 24-h Holter recordings from over 30,000 patients. Findings: In PAF detection, clinicians alone required a significant amount of time to identify the data and still overlooked 13.7% of PAF patients but successfully identified all non-atrial fibrillation (AF) patients. Conversely, AI alone rarely missed PAF patients but misidentified 23.3% of non-AF patients as having PAF. After implementing the proposed clinician-AI collaboration strategy, all patients were correctly identified, and clinicians’ workload was reduced by 76.7%. Conclusions: This study improves both the efficiency and reliability of PAF detection, bridging the gap between AI model development and its clinical application, thereby effectively promoting the application of AI models in clinical AF screening. Funding: This study was supported in part by the National Natural science Foundation of China. © 2025 The Author(s)

关键词： artificial intelligence in medicine atrial fibrillation atrial fibrillation detection atrial fibrillation screening clinician-AI collaboration deep learning diagnostic AI model electrocardiogram Holter monitoring segmentation model Translation to patients

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Multi-dimensional characterization of cellular states reveals clinically relevant immunological subtypes and therapeutic vulnerabilities in ovarian cancer

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Journal of Translational Medicine 2025年第1期23卷 1-18页

作者： Zhang, Can Li, Si Guo, Jiyu Pan, Tao Zhang, Ya Gao, Yueying Pan, Jiwei Liu, Meng Yang, Qingyi Yu, Jinyang Xu, Juan Li, Yongsheng Li, Xia College of Biomedical Information and Engineering Hainan Medical University Haikou 571199 China School of Interdisciplinary Medicine and Engineering Harbin Medical University Harbin 150081 China College of Bioinformatics Science and Technology Harbin Medical University Heilongjiang Province Harbin 150081 China Department of Radiation Oncology Harbin Medical University Cancer Hospital 150 Haping Road Nangang District Heilongjiang Harbin 150040 China Department of Anesthesiology The First Affiliated Hospital of Harbin Medical University Heilongjiang Harbin China

Background: Diverse cell types and cellular states in the tumor microenvironment (TME) are drivers of biological and therapeutic heterogeneity in ovarian cancer (OV). Characterization of the diverse malignant and immunology cellular states that make up the TME and their associations with clinical outcomes are critical for cancer therapy. However, we are still lack of knowledge about the cellular states and their clinical relevance in OV. Methods: We manually collected the comprehensive transcriptomes of OV samples and characterized the cellular states and ecotypes based on a machine-learning framework. The robustness of the cellular states was validated in independent cohorts and single-cell transcriptomes. The functions and regulators of cellular states were investigated. Meanwhile, we thoroughly examined the associations between cellular states and various clinical factors, including clinical prognosis and drug responses. Results: We depicted and characterized an immunophenotypic landscape of 3,099 OV samples and 80,044 cells based on a machine learning framework. We identified and validated 32 distinct transcriptionally defined cellular states from 12 cell types and three cellular communities or ecotypes, extending the current immunological subtypes in OV. Functional enrichment and upstream transcriptional regulator analyses revealed cancer hallmark-related pathways and potential immunological biomarkers. We further investigated the spatial patterns of identified cellular states by integrating the spatially resolved transcriptomes. Moreover, prognostic landscape and drug sensitivity analysis exhibited clinically relevant immunological subtypes and therapeutic vulnerabilities. Conclusion: Our comprehensive analysis of TME helps leveraging various immunological subtypes to highlight new directions and targets for the treatment of cancer. © The Author(s) 2025.

关键词： Cellular States Clinical prognosis Drug response Immunotherapy Tumor microenvironment

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Stereotypes About Enterotype: the Old and New Ideas

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Genomics, Proteomics & bioinformatics 2019年第1期17卷 4-12页

作者： Mingyue Cheng Kang Ning Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular-imaging Department of Bioinformatics and Systems Biology College of Life Science and TechnologyHuazhong University of Science and Technology

In 2011, the term ‘‘enterotype" first appeared to the general public in Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of *** firstly illustrated the definition of the enterotype and various factors influencing enterotypes,such as diet, administration of antibiotics, and age. Then we summarized lines of evidence that pose the concept against the enterotype, and described the current methods for enterotype ***, we showed that the concept of enterotype has been extended to other ecological *** on current studies on enterotypes, it has been clear that more studies with larger sample sizes are needed to characterize the enterotypes. Improved computational methods are also required to build sophisticated models, reflecting the dynamics and resilience of enterotypes.

关键词： Enterotype Gut microbiome Biomarker Continuity Computational methods

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Genome-wide DNA methylome analysis reveals a critical role of methylation-dysregulated lncRNAs in autophagy regulation in glioblastoma

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Genes & Diseases 2024年第5期11卷 51-54页

作者： Hongying Zhao Ying Liu Meiting Fei Lin Bo Lixia Wang Yaopeng Shu Peiqi Ben Li Wang College of Bioinformatics Science and Technology Harbin Medical UniversityHarbinHeilongjiang 150081China

Glioblastoma(GBM)is the most common primary malignant intracranial tumor with a very poor *** this study,we systematically analyzed the DNA methylation alterations of autophagy-related lncRNAs and their association with drug therapies in *** identified 9 DNA methylation-dysregulated lncRNA regulators of autophagy-related genes as autophagy-related lncRNAs.A dysregulated regulatory network consisting of 9 autophagy-related lncRNAs and 237 differentially expressed autophagy-related genes was *** of small molecule drug candidates that may affect DNA methylation dysregulated lncRNA activity,including 45 drug lncRNA pairs,involving 7 DNA methylation dysregulated lncRNAs and 43 ***,we identified a DNA methylation-dysregulated autophagy-related lncRNA MIR155HG as an independent prognostic indicator for GBM.

关键词： regulated alterations drugs

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Edge detection of wood image with rot based on gray transformation enhancement

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Advances in Information sciences and Service sciences 2012年第18期4卷 306-313页

作者： Mu, Hongbo Qi, Dawei Zhang, Mingming Northeast Forestry University China College of Bioinformatics science and technology Harbin Medicine University China

X-ray is selected to be the testing source for nondestructive testing. Wood rot image obtained by testing was done gray transformation. The contrast of the images after gray transformation can be enhanced obviously and the position of rot can be highlighted. Binary processing was adopted for the image after gray transformation. Then the edge of the binary image was extracted and the smooth edge curve of rot defect was obtained. The position and the size of defects can be known by scanning the edge of wood defects. The experiment results show that this method is feasible and effective. These features provide reliable evidences for feature extraction and processing of wood defect with rot.

关键词： Edge detection

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Strategies for enhancing interfacial built-in electric field strength in S-scheme heterojunction photocatalysts: A review

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Journal of Industrial and Engineering Chemistry 2025年

作者： Ahmad, Irshad Lama Tamang, Tensangmu Ali, Ijaz Alanazi, Abdullah K. Farahim, Farha Ali, Talat Ahmad Khasawneh, Mohammad Rauf, Abdur Department of Physics University of Agriculture Faisalabad38040 Pakistan Department of Biotechnology Yeungnam University Gyeongbuk Gyeongsan38541 Cuba Centre for Applied Mathematics and Bioinformatics Gulf University for Science and Technology Hawally32093 Kuwait Department of Chemistry College of Science Taif University Taif Saudi Arabia Department of Community Psychiatric and Mental Health Nursing King Khalid University Abha61413 Saudi Arabia Department of Basic Medical Sciences King Khalid University Abha61413 Saudi Arabia Department of Chemistry College of Science U.A.E. University Al-AinP.O. Box 15551 United Arab Emirates Institute of Physics Bahauddin Zakariya University Multan Pakistan

S-scheme heterojunctions, regarded as high-performance photocatalysts, have gained increasing attention in various applications due to their effective charge separation and migration, enhanced visible light absorption, high redox capacity, and remarkable stability. However, despite achieving effective charge separation, the built-in electric field (BIEF) driving charge separation process often lacks the desired strength. The BIEF strength is influenced by the Fermi level difference between the constituent semiconductors in an S-scheme heterojunction. Several emerging strategies have been explored to increase charge separation by enhancing the BIEF, particularly through modulation of band structure and Fermi levels. Despite significant progress in strengthening the BIEF, a review addressing these strategies is still lacking. This review consolidates recent advances in strategies to increase BIEF strength in S-scheme photocatalysts. Finally, the challenges and future perspectives for increasing BIEF strength through these strategies are discussed. This review provides valuable insights for researchers aiming to optimize charge separation and overall photocatalytic performance in S-scheme photocatalysts. © 2024 The Korean Society of Industrial and Engineering Chemistry

关键词： Fermi level

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Identification of Novel and Differentially Expressed MicroRNAs in the Ovaries of Laying and Non-Laying Ducks

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Journal of Integrative Agriculture 2013年第1期12卷 136-146页

作者： YU De-bing JIANG Bao-chun GONG Jing DONG Fu-lu LU Ying-lin YUE Hui-jie WANG Zheng-chao DU Wen-xing GUO An-yuan Department of Animal Science and Technology College of Animal Science and Technology Nanjing Agricultural University Bioinformatics & Molecular Imaging Key Laboratory Department of Systems Biology College of Life Science and Technology Huazhong University of Science and Technology Provincial Key Laboratory for Developmental Biology and Neurobiology College of Life Science Fujian Normal University

MicroRNAs （miRNAs）, which post-transcriptionally regulate gene expression by binding to the 3′untranslated region of mRNAs to either inhibit or enhance translation, are involved in diverse biological processes. The use of high-throughput Solexa sequencing plays important roles in the discovery of miRNAs. In this study, we used high-throughput Solexa sequencing to identify novel duck miRNAs and compare the miRNA expression profiles in laying and non-laying duck ovaries. Using a bioinformatic analysis, we discovered 86 potential duck miRNAs similar to known chicken miRNAs and 43 unique sequences that matched known miRNAs of other species. We also found that miRNA variations and isoforms were widespread in our two RNA libraries, with most of the variations occurring in the 3′region of the miRNAs. Furthermore, we detected 55 miRNAs that exhibited significant expression differences between laying and non-laying ducks. Gene ontology （GO） and kyoto encyclopedia of genes and genomes （KEGG） enrichment analyses of the potential targets of the differentially expressed miRNAs indicated these miRNAs may play key roles in the egg laying process. Finally, we confirmed the differential expression of 5 miRNAs in the laying and non-laying samples by qRT-PCR. Cumulatively, our work provides the first look at the miRNA expression profile of the duck ovary and provides novel insight into the roles of miRNAs in egg laying and reproduction.

关键词： microRNA Solexa sequencing duck ovary

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