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Reconstructing positive and negative couplings in Ising spin networks by sorted local transfer entropy

Physical Review E 2019年第1期100卷 012121-012121页

作者： Felix Goetze Pik-Yin Lai Department of Physics and Center for Complex Systems National Central University Chung-Li District Taoyuan City 320 Taiwan Republic of China and Molecular Science and Technology Program Taiwan International Graduate Program Academia Sinica Taipei Taiwan Republic of China

We employ the sorted local transfer entropy (SLTE) to reconstruct the coupling strengths of Ising spin networks with positive and negative couplings (Jij), using only the time-series data of the spins. The SLTE method is model-free in the sense that no knowledge of the underlying dynamics of the spin system is required and is applicable to a broad class of systems. Contrary to the inference of coupling from pairwise transfer entropy, our method can reliably distinguish spin pair interactions with positive and negative couplings. The method is tested for the inverse Ising problem for different Jij distributions and various spin dynamics, including synchronous and asynchronous update Glauber dynamics and Kawasaki exchange dynamics. It is found that the pairwise SLTE is proportional to the pairwise coupling strength to a good extent for all cases studied. In addition, the reconstruction works well for both the equilibrium and nonequilibrium cases of the time-series data. Comparison to other inverse Ising problem approaches using mean-field equations is also discussed.

关键词： Information theory Ising model Time series analysis

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Adherence patterns of Escherichia coli in the intestine and its role in pathogenesis

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Medicine in Microecology 2020年 5卷

作者： Govindarajan, Deenadayalan Karaiyagowder Viswalingam, Nandhini Meganathan, Yogesan Kandaswamy, Kumaravel Laboratory of Molecular Biology and Genetic Engineering Department of Biotechnology Kumaraguru College of Technology Coimbatore 641049 Tamil Nadu India Singapore Centre for Environmental Life Sciences Engineering Nanyang Technological University 60 Nanyang Drive 637551 Singapore Food Science and Technology Program Department of Chemistry National University of Singapore 3 Science Drive 117543 Singapore

Gut microbiota plays an important role in maintaining a healthy intestine. Escherichia coli (***) is a commensal bacteria colonizes the mucous membranes of the gut, intestine, and urinary tract. However, these strains incorporate genetic elements to become pathotype and affected in hundreds of millions of people worldwide. Seven pathotypes have been categorized such as Entero-Hemorrhagic *** (EHEC), Entero-Aggregative *** (EAEC), Entero-Pathogenic *** (EPEC), Entero-Toxigenic *** (ETEC), Diffusely Adherent *** (DAEC), Entero-Invasive *** (EIEC) and Adherent-Invasive *** (AIEC), and each pathotype possess distinct virulence mechanism and virulence factors to disrupt the host intestinal epithelial cells that cause diarrhea and other intestinal inflammation. This review highlights the various fimbrial and afimbrial adherence mechanisms of *** pathovars, and how it competes with commensal bacteria in achieving pathogenicity in the host. Such adherence mechanisms are mediated by virulence proteins that have a significant impact on the outcome of intestinal inflammation. © 2020 The Author(s)

关键词： Adherence mechanism E.coli pathotypes Gut microbiota Inflammation

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Publisher Correction: Circadian regulation of cancer stem cells and the tumor microenvironment during metastasis

Nature cancer

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Nature cancer 2024年第5期5卷 809页

作者： Yu Wang Rajesh Narasimamurthy Meng Qu Nuolin Shi Haidong Guo Yuezhen Xue Nick Barker Institute of Molecular and Cell Biology Agency for Science Technology and Research (A*STAR) Singapore Singapore. Department of Neurology Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine Shanghai China. Academy of Integrative Medicine Shanghai University of Traditional Chinese Medicine Shanghai China. Program in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore. The Fourth Affiliated Hospital of School of Medicine and International School of Medicine International Institutes of Medicine Zhejiang University Yiwu China. Academy of Integrative Medicine Shanghai University of Traditional Chinese Medicine Shanghai China. hdguo@***. Institute of Molecular and Cell Biology Agency for Science Technology and Research (A*STAR) Singapore Singapore. yzxue@imcb.a-star.edu.sg. Institute of Molecular and Cell Biology Agency for Science Technology and Research (A*STAR) Singapore Singapore. nicholas_barker@imcb.a-star.edu.sg. Department of Physiology Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore. nicholas_barker@imcb.a-star.edu.sg.

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The cell surface marker CD36 selectively identifies matured,mitochondria-rich hPSC-cardiomyocytes

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细胞研究（英文版） 2020年第7期30卷 626-629页

作者： Ellen Ngar-Yun Poon Xiao-ling Luo Sarah E.Webb Bin Yan Rui Zhao Stanley Chun Ming Wu Yong Yang Peng Zhang Huajun Bai Jiaofang Shao Ching Man Chan Godfrey Chi-Fung Chan Suk Ying Tsang Rebekah L.Gundry Huang-Tian Yang Kenneth R.Boheler Department of Medicine and Therapeutics and Centre for Cardiovascular Genomics and Medicine The Chinese University of Hong Kong (CUHK) HKSAR China CAS Key Laboratory of Tissue Microenvironment and Tumor Laboratory of Molecular CardiologyShanghai Institute of Nutrition and Health University of Chinese Academy of Sciences (CAS) CAS Shanghai China Division of Life Science and State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology HKSAR China Department of Computer Science The University of Hong Kong (HKU) HKSAR China Intervention and Cell Therapy Center Peking University Shenzhen Hospital Shenzhen China School of Life Sciences CUHK HKSAR China Department of Paediatrics and Adolescent Medicine HKU HKSAR China School of Biomedical Sciences HKU HKSAR China SUSTech Academy for Advanced Interdisciplinary Studies Southern University of Science and Technology (SUSTech) Shenzhen China Department of Bioinformatics School of Biomedical Engineering and InformaticsNanjing Medical University Nanjing Jiangsu China State Key Laboratory of Agrobiotechnology CUHK HKSAR China Department of Biochemistry and Center for Biomedical Mass Spectrometry Research Medical College of Wisconsin Milwaukee WIUSA CardiOmics Program Center for Heart and Vascular Research Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology University of Nebraska Medical Center Omaha NE USA Institute for Stem Cell and Regeneration Medicine CASBeijing China Division of Cardiology Department of Medicineand Department of Biomedical Engineering The Johns Hopkins University Baltimore MD USA

Dear Editor,Human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) are of significant translational value to in vitro studies of human cardiac development, drug and cardiotoxicity testing and cardiac disease *** of hPSCs to CMs,however, yields mixed cultures of atrial-, ventricular-, and pacemaker-like cells as well as non-CMs in variable proportions.1

关键词： Stem-cell differentiation Stem cells

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MIFA: Metadata, Incentives, Formats, and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis

arXiv

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arXiv 2023年

作者： Zulueta-Coarasa, Teresa Jug, Florian Mathur, Aastha Moore, Josh Muñoz-Barrutia, Arrate Anita, Liviu Babalola, Kola Bankhead, Pete Gilloteaux, Perrine Gogoberidze, Nodar Jones, Martin Kleywegt, Gerard J. Korir, Paul Kreshuk, Anna Yoldaş, Aybüke Küpcü Marconato, Luca Narayan, Kedar Norlin, Nils Oezdemir, Bugra Riesterer, Jessica Rzepka, Norman Sarkans, Ugis Serrano, Beatriz Tischer, Christian Uhlmann, Virginie Ulman, Vladimír Hartley, Matthew European Molecular Biology Laboratory European Bioinformatics Institute Hinxton United Kingdom Human Technopole V.le Rita Levi-Montalcini 1 Milan20017 Italy Heidelberg Meyerhofstraße 1 Heidelberg69117 Germany German BioImaging Gesellschaft für Mikroskopie und Bildanalyse e.V. Konstanz Germany Universidad Carlos III de Madrid Leganés Madrid Spain Instituto de Investigación Sanitaria Gregorio Marañón Madrid Spain Edinburgh Pathology Centre for Genomic and Experimental Medicine CRUK Scotland Centre University of Edinburgh Edinburgh United Kingdom Nantes Université CHU Nantes CNRS Inserm BioCore US16 SFR Bonamy NantesF 44000 France Imaging Platform Broad Institute Cambridge United States Francis Crick Institute London United Kingdom Cell Biology and Biophysics Unit European Molecular Biology Laboratory Heidelberg69117 Germany Genome Biology Unit Heidelberg Germany Heidelberg Germany Collaboration for joint PhD degree between EMBL and Heidelberg University Faculty of Biosciences Germany Center for Molecular Microscopy Center for Cancer Research National Cancer Institute NIH BethesdaMD United States Cancer Research Technology Program Frederick National Laboratory for Cancer Research FrederickMD United States Lund University 221 00 Sweden Knight Cancer Institute Oregon Health & Science University PortlandOR United States Scalable Minds GmbH Potsdam Germany European Molecular Biology Laboratory Heidelberg Germany IT4Innovations VSB – Technical University of Ostrava Ostrava-Poruba Czech Republic

Artificial Intelligence methods are powerful tools for biological image analysis and processing. High-quality annotated images are key to training and developing new methods, but access to such data is often hindered by the lack of standards for sharing datasets. We brought together community experts in a workshop to develop guidelines to improve the reuse of bioimages and annotations for AI applications. These include standards on data formats, metadata, data presentation and sharing, and incentives to generate new datasets. We are positive that the MIFA (Metadata, Incentives, Formats, and Accessibility) recommendations will accelerate the development of AI tools for bioimage analysis by facilitating access to high quality training data. © 2023, CC BY.

关键词： Metadata

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Mercury in aquatic fauna contamination:A systematic review on its dynamics and potential health risks

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Journal of Environmental sciences 2019年第10期31卷 205-218页

作者： Paloma de Almeida Rodrigues Rafaela Gomes Ferrari Luciano Neves dos Santos Carlos Adam Conte Junior Molecular and Analytical Laboratory Center Department of Food TechnologyFaculty of VeterinaryUniversidade Federal FluminenseNiteróiBrazil Chemistry Institute Food Science ProgramUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil National Institute of Health Quality Control Fundacaeo Oswaldo CruzRio de JaneiroBrazil Laboratory of Theoretical and Applied Ichthyology Department of Ecology and Marine ResourcesUniversidade Federal do Estado do Rio de JaneiroRio de JaneiroBrazil

Mercury is an important pollutant,released into aquatic ecosystems both naturally and by anthropogenic *** element is transferred to aquatic organisms in different ways,causing potential health *** addition,mercury can be accumulated by humans,especially through the consumption of contaminated *** systematic review aims to present mercury pathways,the major routes through which this element reaches the aquatic environment and its transformations until becoming available to living animals,leading to bioaccumulation and biomagnification *** key biotic and abiotic factors affecting such processes,the impact of mercury on animal and human health and the issue of seafood consumption as a source of chronic mercury contamination are also addressed.A total of 101 articles were retrieved from a standardized search on three databases(PubMed,Emabse,and Web of science),in addition to 28 other studies not found on these databases but considered fundamental to this review(totaling 129 articles).Both biotic and abiotic factors display fundamental importance in mediating mercurial dynamics,i.e.,muscle tropism,and salinity,***,mercurial contamination in aquatic environments affects animal health,especially the risk of extinction species and also on human health,with methylmercury the main mercury species responsible for acute and chronic symptomatology.

关键词： Mercury levels Seafood Methylmercury Public health Aquatic environment

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Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk (vol 54, pg 804, 2022)

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NATURE GENETICS 2022年第8期54卷 1259-1259页

作者： Turner, Adam W. Hu, Shengen Shawn Mosquera, Jose Verdezoto Ma, Wei Feng Hodonsky, Chani J. Wong, Doris Auguste, Gaelle Song, Yipei Sol-Church, Katia Farber, Emily Kundu, Soumya Kundaje, Anshul Lopez, Nicolas G. Ma, Lijiang Ghosh, Saikat Kumar B. Onengut-Gumuscu, Suna Ashley, Euan A. Quertermous, Thomas Finn, Aloke V. Leeper, Nicholas J. Kovacic, Jason C. Bjorkegren, Johan L. M. Zang, Chongzhi Miller, Clint L. Center for Public Health Genomics University of Virginia Charlottesville VA USA Department of Biochemistry and Molecular Genetics University of Virginia Charlottesville VA USA Medical Scientist Training Program University of Virginia Charlottesville VA USA Department of Pathology University of Virginia Charlottesville VA USA Robert M. Berne Cardiovascular Research Center University of Virginia Charlottesville VA USA Genome Analysis & Technology Core University of Virginia Charlottesville VA USA Genome Sciences Laboratory University of Virginia Charlottesville VA USA Department of Genetics Stanford University School of Medicine Stanford CA USA Department of Computer Science Stanford University Stanford CA USA Division of Vascular Surgery Department of Surgery Stanford University Stanford CA USA Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology Icahn School of Medicine at Mount Sinai New York NY USA CVPath Institute Gaithersburg MD USA Department of Public Health Sciences University of Virginia Charlottesville VA USA Division of Cardiovascular Medicine Department of Medicine Stanford University Stanford CA USA Cardiovascular Research Institute Icahn School of Medicine at Mount Sinai New York NY USA Victor Chang Cardiac Research Institute Darlinghurst New South Wales Australia St. Vincent’s Clinical School University of New South Wales Sydney New South Wales Australia Integrated Cardio Metabolic Centre Department of Medicine Karolinska Institutet Huddinge Sweden

Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across cell types. Genome-wide association studies have identified over 200 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements. Here, we applied single-nucleus assay for transposase-accessible chromatin with sequencing to profile 28,316 nuclei across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell-type-specific elements and transcription factors, and prioritized functional CAD risk variants. We identified elements in smooth muscle cell transition states (for example, fibromyocytes) and functional variants predicted to alter smooth muscle cell- and macrophage-specific regulation of MRAS (3q22) and LIPA (10q23), respectively. We further nominated key driver transcription factors such as PRDM16 and TBX2. Together, this single-nucleus atlas provides a critical step towards interpreting regulatory mechanisms across the continuum of CAD risk.

关键词： Atherosclerosis Epigenomics Gene regulation

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Schizophrenia:Genetics,neurological mechanisms,and therapeutic approaches

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Neural Regeneration Research 2026年第3期 1089-1103页

作者： Debbie Xiu En Lim Shi Yun Yeo Zhen You Ashley Chia Aaron Zefrin Fernandis Jimmy Lee John Jia En Chua Department of Physiology Yong Loo Lin School of Medicine National University of Singapore LSI Neurobiology Programme National University of Singapore Healthy Longevity Translational Research Program Yong Loo Lin School of Medicine National University of Singapore Quantitative Biosciences MSD International GmbHSingapore Branch North Region Institute of Mental Health Lee Kong Chian School of Medicine Nanyang Technological University Institute of Molecular and Cell Biology Agency for Science Technology and Research (A*STAR)

Schizophrenia is a complex psychiatric disorder marked by positive and negative symptoms,leading to mood disturbances,cognitive impairments,and social *** anti-psychotic medications remain the cornerstone of treatment,they often fail to fully address certain ***,treatment-resistant schizophrenia,affecting 30%-40% of patients,remains a substantial clinical ***,negative symptoms and cognitive impairments have been linked to disruptions in the glutamatergic,serotonin,GABAergic,and muscarinic pathways in the *** advances using genome-wide association study and other approaches have uncovered a significant number of new schizophrenia risk genes that uncovered new,and reinforced prior,concepts on the genetic and neurological underpinnings of schizophrenia,including abnormalities in synaptic function,immune processes,and lipid ***,new therapeutics targeting different modalities,which are expected to address some of the limitations of anti-psychotic drugs currently being offered to patients,are currently being ***,these efforts provide new momentum for the next phase of schizophrenia research and treatment.

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Protein and lipid expansion microscopy with trypsin and tyramide signal amplification for 3D imaging

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Scientific reports 2023年第1期13卷 21922页

作者： Ueh-Ting Tim Wang Xuejiao Tian Yae-Huei Liou Sue-Ping Lee Hsiao-Tang Hu Chieh-Han Lu Po-Ting Lin Ya-Jen Cheng Peilin Chen Bi-Chang Chen Affiliated Senior High School of National Taiwan Normal University Taipei 106348 Taiwan. Research Center for Applied Sciences Academia Sinica Taipei 11529 Taiwan. Nano Science and Technology Program Taiwan International Graduate Program Academia Sinica and National Tsing Hua University Taipei 11529 Taiwan. Department of Engineering and System Science National Tsing Hua University Hsinchu 300 Taiwan. Institute of Molecular Biology Academia Sinica Taipei 11529 Taiwan. Institute and Undergraduate Program of Electro-Optical Engineering National Taiwan Normal University Taipei 116 Taiwan. Neuroscience Program NPAS Academia Sinica Taipei 11529 Taiwan ROC. Research Center for Applied Sciences Academia Sinica Taipei 11529 Taiwan. chenb10@gate.sinica.edu.tw.

Expansion microscopy, whereby the relative positions of biomolecules are physically increased via hydrogel expansion, can be used to reveal ultrafine structures of cells under a conventional microscope. Despite its utility for achieving super-resolution imaging, expansion microscopy suffers a major drawback, namely reduced fluorescence signals caused by excessive proteolysis and swelling effects. This caveat results in a lower photon budget and disfavors fluorescence imaging over a large field of view that can cover an entire expanded cell, especially in 3D. In addition, the complex procedures and specialized reagents of expansion microscopy hinder its popularization. Here, we modify expansion microscopy by deploying trypsin digestion to reduce protein loss and tyramide signal amplification to enhance fluorescence signal for point-scanning-based imaging. We name our new methodology TT-ExM to indicate dual trypsin and tyramide treatments. TT-ExM may be applied for both antibody and lipid staining. TT-ExM displayed enhanced protein retention for endoplasmic reticulum and mitochondrial markers in COS-7 cell cultures. Importantly, TT-ExM-based lipid staining clearly revealed the complex 3D membrane structures in entire expanded cells. Through combined lipid and DNA staining, our TT-ExM methodology highlighted mitochondria by revealing their DNA and membrane structures in cytoplasm, as well as the lipid-rich structures formed via phase separation in nuclei at interphase. We also observed lipid-rich chromosome matrices in the mitotic cells. These high-quality 3D images demonstrate the practicality of TT-ExM. Thus, readily available reagents can be deployed in TT-ExM to significantly enhance fluorescence signals and generate high-quality and ultrafine-resolution images under confocal microscopy.

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Author Correction: Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites

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Nature communications 2025年第1期16卷 527页

作者： Anna Delgado-Tejedor Rebeca Medina Oguzhan Begik Luca Cozzuto Judith López Sandra Blanco Julia Ponomarenko Eva Maria Novoa Centre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona Spain. Universitat Pompeu Fabra Barcelona Spain. Molecular Mechanisms Program Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca Salamanca Spain. Instituto de Investigación Biomédica de Salamanca (IBSAL) Hospital Universitario de Salamanca Salamanca Spain. Centre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona Spain. eva.novoa@crg.eu. Universitat Pompeu Fabra Barcelona Spain. eva.novoa@crg.eu. ICREA Pg. Lluís Companys 23 Barcelona Spain. eva.novoa@crg.eu.

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