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The DrugPattern tool for drug set enrichment analysis and its prediction for beneficial effects of oxLDL on type 2 diabetes

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Journal of Genetics and Genomics 2018年第7期45卷 389-397页

作者： Chuanbo Huang Weili Yang Junpei wang Yuan Zhou Bin Geng Georgios Kararigas Jichun Yang Qinghua Cui Department of Biomedical Informatics Department of Physiology and Pathophysiology MOE Key Lab of Cardiovascular Sciences School of Basic Medical Sciences Center for Non-Coding RNA Medicine Peking UniversityBeijing 100191China School of Mathematics Sciences Huaqiao University Quanzhou 362021 China Hypertension Center Fuwai Hospital Chinese Academy of Medical Sciences and Peking Union Medical CollegeState Key Laboratory of Cardiovascular Disease National Center for Cardiovascular Diseases Beijing 100037 China Charit-Universitatsmedizin Berlin. Corporate Member of Freie Universitat Berlin Humboldt-Universitat zu Berlin Berlin Institute of Health Institute of Gender in Medicine and Center for Cardiovascular Research. DZHK (German Centre for Cardiovascular Research) 10115 Berlin Germany Center of Bioinformatics Key Laboratory for Neuro-lnformation of Ministry of Education School of Life Science and Technology University of Electronic Science and Technology of China Chengdu 610054 China

Enrichment analysis methods, e.g., gene set enrichment analysis, represent one class of important bio- informatical resources for mining patterns in biomedical datasets. However, tools for inferring patterns and rules of a list of drugs are limited. In this study, we developed a web-based tool, DrugPattern, for drug set enrichment analysis. We first collected and curated 7019 drug sets, including indications, adverse reactions, targets, pathways, etc. from public databases. For a list of interested drugs, DrugPat- tern then evaluates the significance of the enrichment of these drugs in each of the 7019 drug sets. To validate DrugPattern, we employed it for the prediction of the effects of oxidized low-density lipoprotein （oxLDL）, a factor expected to be deleterious. We predicted that oxLDL has beneficial effects on some diseases, most of which were supported by evidence in the literature. Because DrugPattern predicted the potential beneficial effects of oxLDL in type 2 diabetes （T2D）, animal experiments were then performed to further verify this prediction. As a result, the experimental evidences validated the DrugPattern prediction that oxLDL indeed has beneficial effects on T2D in the case of energy restriction. These data confirmed the prediction accuracy of our approach and revealed unexpected protective roles for oxLDL in various diseases. This study provides a tool to infer patterns and rules in biomedical datasets based on drug set enrichment analysis.

关键词： Enrichment analysis Drug Data mining oxLDL Type 2 diabetes

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TISSUES 2.0: an integrative web resource on mammalian tissue expression (vol 2018, 2018)

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DATABASE-THE JOUrnaL OF BIOLOGICAL DATABASES AND CURATION 2018年第2018期2018卷 1-N.PAG页

作者： Palasca, Oana Santos, Alberto Stolte, Christian Gorodkin, Jan Jensen, Lars Juhl Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen DenmarkCenter for non-coding RNA in Technology and Health Faculty of Health and Medical Sciences University of Copenhagen Copenhagen DenmarkDepartment of Veterinary and Animal Sciences Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark New York Genome Center New York NY USA Center for non-coding RNA in Technology and Health Faculty of Health and Medical Sciences University of Copenhagen Copenhagen DenmarkDepartment of Veterinary and Animal Sciences Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Correspondence may also be addressed to Jan Gorodkin. Email: gorodkin@rth.dk Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen DenmarkCenter for non-coding RNA in Technology and Health Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Corresponding author: Tel: +45 35325025 Email: lars.juhl.jensen@cpr.ku.dk

Physiological and molecular similarities between organisms make it possible to translate findings from simpler experimental systems—model organisms—into more complex ones, such as human. This translation facilitates the understanding of biological processes under normal or disease conditions. Researchers aiming to identify the similarities and differences between organisms at the molecular level need resources collecting multi-organism tissue expression data. We have developed a database of gene-tissue associations in human, mouse, rat and pig by integrating multiple sources of evidence: transcriptomics covering all four species and proteomics (human only), manually curated and mined from the scientific literature. Through a scoring scheme, these associations are made comparable across all sources of evidence and across organisms. Furthermore, the scoring produces a confidence score assigned to each of the associations. The TISSUES database (version 2.0) is publicly accessible through a user-friendly web interface and as part of the STRING app for Cytoscape. In addition, we analyzed the agreement between datasets, across and within organisms, and identified that the agreement is mainly affected by the quality of the datasets rather than by the technologies used or organisms *** URL: http://***/

关键词： DATABASES TRANSCRIPTOMES PROTEOMICS

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Mapping geographical inequalities in childhood diarrhoeal morbidity and mortality in low-income and middle-income countries, 2000-17: analysis for the Global Burden of Disease Study 2017 (vol 395, pg 1779, 2020)

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LANCET 2020年第10239期395卷 1762-1762页

作者： Reiner, R. C., Jr. Hay, S., I Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Global Health School of Medicine University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States College of Health and Medical Sciences Haramaya University Harar Ethiopia Department of Epidemiology and Biostatistics Haramaya University Harar Ethiopia Department of Medical Laboratory Sciences Haramaya University Harar Ethiopia School of Nursing and Midwifery Haramaya University Harar Ethiopia School of Pharmacy Haramaya University Harar Ethiopia School of Public Health Haramaya University Harar Ethiopia Haramaya University Harar Ethiopia Advanced Diagnostic and Interventional Radiology Research Center Tehran University of Medical Sciences Tehran Iran Cancer Biology Research Center Tehran University of Medical Sciences Tehran Iran Cancer Research Institute Tehran University of Medical Sciences Tehran Iran Department of Economics and Management Sciences for Health Tehran University of Medical Sciences Tehran Iran Department of Environmental Health Engineering Tehran University of Medical Sciences Tehran Iran Department of Epidemiology and Biostatistics Tehran University of Medical Sciences Tehran Iran Department of Health Management and Economics Tehran University of Medical Sciences Tehran Iran Department of Microbiology Tehran University of Medical Sciences Tehran Iran Department of Pharmacology Tehran University of Medical Sciences Tehran Iran Digestive Diseases Research Institute Tehran University of Medical Sciences Tehran Iran Endocrinology and Metabolism Research Center Tehran University of Medical Sciences Tehran Iran Hematology-Oncology and Stem Cell Transplantation Research Center Tehran University of Medical Sciences Tehran Iran Iran National Institute of Health Research Tehran University of Medical Sciences Tehran Iran Metabolomics and

Summary Background Across low-income and middle-income countries (LMICs), one in ten deaths in children younger than 5 years is attributable to diarrhoea. The substantial between-country variation in both diarrhoea incidence and mortality is attributable to interventions that protect children, prevent infection, and treat disease. Identifying subnational regions with the highest burden and mapping associated risk factors can aid in reducing preventable childhood *** We used Bayesian model-based geostatistics and a geolocated dataset comprising 15 072 746 children younger than 5 years from 466 surveys in 94 LMICs, in combination with findings of the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017, to estimate posterior distributions of diarrhoea prevalence, incidence, and mortality from 2000 to 2017. From these data, we estimated the burden of diarrhoea at varying subnational levels (termed units) by spatially aggregating draws, and we investigated the drivers of subnational patterns by creating aggregated risk factor *** The greatest declines in diarrhoeal mortality were seen in south and southeast Asia and South America, where 54·0% (95% uncertainty interval [UI] 38·1-65·8), 17·4% (7·7-28·4), and 59·5% (34·2-86·9) of units, respectively, recorded decreases in deaths from diarrhoea greater than 10%. Although children in much of Africa remain at high risk of death due to diarrhoea, regions with the most deaths were outside Africa, with the highest mortality units located in Pakistan. Indonesia showed the greatest within-country geographical inequality; some regions had mortality rates nearly four times the average country rate. Reductions in mortality were correlated to improvements in water, sanitation, and hygiene (WASH) or reductions in child growth failure (CGF). Similarly, most high-risk areas had poor WASH, high CGF, or low oral rehydration therapy *** By co-analysing geospatial trends in d

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Global burden of 369 diseases and injuries in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019

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The Lancet 2020年第10258期396卷 1204-1222页

作者： Abbafati, Cristiana Abbas, Kaja M. Abbasi, Mohammad Abbasifard, Mitra Abbasi-Kangevari, Mohsen Abbastabar, Hedayat Abd-Allah, Foad Abdelalim, Ahmed Abdollahi, Mohammad Abdollahpour, Ibrahim Abedi, Aidin Abedi, Parisa Abegaz, Kedir Hussein Abolhassani, Hassan Abosetugn, Akine Eshete Aboyans, Victor Abrams, Elissa M. Abreu, Lucas Guimarães Abrigo, Michael R.M. Abu Haimed, Abdulaziz Khalid Abualhasan, Ahmed Abu-Gharbieh, Eman Abu-Raddad, Laith Jamal Abushouk, Abdelrahman I. Acebedo, Alyssa Ackerman, Ilana N. Adabi, Maryam Adair, Tim Adamu, Abdu A. Adebayo, Oladimeji M. Adedeji, Isaac Akinkunmi Adekanmbi, Victor Adelson, Jaimie D. Adeoye, Abiodun Moshood Adetokunboh, Olatunji O. Adham, Davoud Advani, Shailesh M. Afarideh, Mohsen Afshari, Mahdi Afshin, Ashkan Agardh, Emilie E. Agarwal, Gina Agasthi, Pradyumna Agesa, Kareha M. Aghaali, Mohammad Aghamir, Seyed Mohammad Kazem Agrawal, Anurag Ahmad, Tauseef Ahmadi, Alireza Ahmadi, Keivan Ahmadi, Mehdi Ahmadieh, Hamid Ahmadpour, Ehsan Ahmed, Muktar Beshir Aji, Budi Akalu, Temesgen Yihunie Akinyemi, Rufus Olusola Akinyemiju, Tomi Akombi, Blessing Akunna, Chisom Joyqueenet Alahdab, Fares Al-Aly, Ziyad Alam, Khurshid Alam, Noore Alam, Samiah Alam, Tahiya Alanezi, Fahad Mashhour Alanzi, Turki M. Albertson, Samuel B. Alcalde-Rabanal, Jacqueline Elizabeth Alema, Niguse Meles Alemu, Biresaw Wassihun Alemu, Yihun Mulugeta Alhabib, Khalid F. Alhassan, Robert Kaba Ali, Muhammad Ali, Saqib Alicandro, Gianfranco Alijanzadeh, Mehran Alinia, Cyrus Alipour, Vahid Alizade, Hesam Aljunid, Syed Mohamed Alla, François Allebeck, Peter Almadi, Majid Abdulrahman Hamad Almasi, Ali Almasi-Hashiani, Amir Almasri, Nihad A. Al-Mekhlafi, Hesham M. Almulhim, Abdulaziz M. Alonso, Jordi Al-Raddadi, Rajaa M. Altirkawi, Khalid A. Alumran, Arwa Khalid Alvis-Guzman, Nelson Alvis-Zakzuk, Nelson J. Amare, Azmeraw T. Amare, Bekalu Amini, Saeed Amini-Rarani, Mostafa Aminorroaya, Arya Amiri, Fatemeh Amit, Arianna Maever L. Amugsi, Dickson A. Amul, Gianna Gayle Herrera Anbesu, Etsay Woldu Ancuceanu, Robert Anderl Department of Juridical and Economic Studies La Sapienza University Rome Italy Department of Infectious Disease Epidemiology London School of Hygiene and Tropical Medicine London United Kingdom Social Determinants of Health Research Center Tehran Iran Department of Neurology Cairo University Cairo Egypt School of Pharmacy Tehran Iran The Institute of Pharmaceutical Sciences (TIPS) Tehran Iran Neuroscience Research Center Isfahan University of Medical Sciences Isfahan Iran Biostatistics Department Near East University Nicosia Cyprus Biostatistics and Health Informatics Madda Walabu University Bale Robe Ethiopia Research Center for Immunodeficiencies Tehran Iran Karolinska University Hospital Huddinge Sweden Department of Cardiology Dupuytren University Hospital Limoges France University of Limoges Limoges France Department of Pediatric Dentistry Federal University of Minas Gerais Belo Horizonte Brazil Department of Research Philippine Institute for Development Studies Quezon City Philippines Department of Healthcare Policy and Research Weill Cornell Medical College in Qatar Doha Qatar Harvard Medical School Boston MA United States Department of Medicine Ain Shams University Cairo Egypt Hamadan University of Medical Sciences Hamadan Iran School of Medicine Cardiff University Cardiff United Kingdom School of Laboratory Medicine and Science University College Hospital Ibadan Ibadan Nigeria Institute of Cardiovascular Diseases University of Ibadan Ibadan Nigeria Centre of Excellence for Epidemiological Modelling and Analysis Stellenbosch University Cape Town South Africa Department of Global Health Stellenbosch University Cape Town South Africa School of Health Ardabil University of Medical Science Ardabil Iran Social Behavioral Research Branch National Institute of Health Bethesda MD United States Department of Oncology Georgetown University Washington DC DC United States Department of Health Metrics Sciences School of Medicine Seattle WA

Background: In an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries. Methods: GBD estimates incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. Input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. Cause-specific death rates and cause fractions were calculated using the Cause of Death Ensemble model and spatiotemporal Gaussian process regression. Cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the GBD population, fertility, and mortality estimates. Deaths were multiplied by standard life expectancy at each age to calculate YLLs. A Bayesian meta-regression modelling tool, DisMod-MR 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate YLDs. We considered results in the context of the Socio-demographic Index (SDI), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. Uncertainty intervals (UIs) were generated for every metric using the 25th and 975th ordered 1000 draw value

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Prevalence and attributable health burden of chronic respiratory diseases, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017

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The Lancet Respiratory Medicine 2020年第6期8卷 585-596页

作者： Soriano, Joan B Kendrick, Parkes J Paulson, Katherine R Gupta, Vinay Abrams, Elissa M Adedoyin, Rufus Adesoji Adhikari, Tara Ballav Advani, Shailesh M Agrawal, Anurag Ahmadian, Elham Alahdab, Fares Aljunid, Syed Mohamed Altirkawi, Khalid A Alvis-Guzman, Nelson Anber, Nahla Hamed Andrei, Catalina Liliana Anjomshoa, Mina Ansari, Fereshteh Antó, Josep M Arabloo, Jalal Athari, Seyyede Masoume Athari, Seyyed Shamsadin Awoke, Nefsu Badawi, Alaa Banoub, Joseph Adel Mattar Bennett, Derrick A Bensenor, Isabela M Berfield, Kathleen S Sachiko Bernstein, Robert S Bhattacharyya, Krittika Bijani, Ali Brauer, Michael Bukhman, Gene Butt, Zahid A Cámera, Luis Alberto Car, Josip Carrero, Juan J Carvalho, Felix Castañeda-Orjuela, Carlos A Choi, Jee-Young Jasmine Christopher, Devasahayam J Cohen, Aaron J Dandona, Lalit Dandona, Rakhi Dang, Anh Kim Daryani, Ahmad de Courten, Barbora Demeke, Feleke Mekonnen Demoz, Gebre Teklemariam De Neve, Jan-Walter Desai, Rupak Dharmaratne, Samath Dhamminda Diaz, Daniel Douiri, Abdel Driscoll, Tim Robert Duken, Eyasu Ejeta Eftekhari, Aziz Elkout, Hajer Endries, Aman Yesuf Fadhil, Ibtihal Faro, Andre Farzadfar, Farshad Fernandes, Eduarda Filip, Irina Fischer, Florian Foroutan, Masoud Garcia-Gordillo, M.A. Gebre, Abadi Kahsu Gebremedhin, Ketema Bizuwork Gebremeskel, Gebreamlak Gebremedhn Gezae, Kebede Embaye Ghoshal, Aloke Gopal Gill, Paramjit Singh Gillum, Richard F Goudarzi, Houman Guo, Yuming Gupta, Rajeev Hailu, Gessessew Bugssa Hasanzadeh, Amir Hassen, Hamid Yimam Hay, Simon I Hoang, Chi Linh Hole, Michael K Horita, Nobuyuki Hosgood, H Dean Hostiuc, Mihaela Househ, Mowafa Ilesanmi, Olayinka Stephen Ilic, Milena D Irvani, Seyed Sina Naghibi Islam, Sheikh Mohammed Shariful Jakovljevic, Mihajlo Jamal, Amr A Jha, Ravi Prakash Jonas, Jost B Kabir, Zubair Kasaeian, Amir Kasahun, Gebremicheal Gebreslassie Kassa, Getachew Mullu Kefale, Adane Teshome Kengne, Andre Pascal Khader, Yousef Saleh Khafaie, Morteza Abdullatif Khan, Ejaz Ahmad Khan, Junaid Khubchandani, Jagdish Kim, Young-Eun Kim, Yun Jin Kisa, Hospital Universitario de La Princesa (Princess University Hospital) Madrid Spain Autonomous University of Madrid Madrid Spain Centro de Investigación Biomédica en Red Enfermedades Respiratorias (CIBERES) (Center for Biomedical Research in Respiratory Diseases Network) Madrid Spain Institute for Health Metrics and Evaluation Seattle WA United States Department of Surgery University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States Department of Global Health University of Washington Seattle WA United States Department of Medicine University of Washington Seattle WA United States University of Washington Seattle WA United States Section of Allergy and Clinical Immunology University of Manitoba Winnipeg MB Canada Ophthalmology Department University of Manitoba Winnipeg MB Canada Department of Paediatrics University of British Columbia Vancouver BC Canada School of Population and Public Health University of British Columbia Vancouver BC Canada Department of Medical Rehabilitation Obafemi Awolowo University Ile-Ife Nigeria Department of Public Health Aarhus University Aarhus Denmark Nepal Health Frontiers University of Southern Denmark Kathmandu Nepal Social Behavioral Research Branch National Institute of Health Bethesda MD United States Department of Oncology Georgetown University Washington DC United States Institute of Genomics and Integrative Biology Council of Scientific & Industrial Research Delhi India Internal Medicine Baylor College of Medicine Houston TX United States Research Center for Chronic Kidney Disease Tabriz University of Medical Sciences Tabriz Iran Research Center for Evidence Based Medicine Tabriz University of Medical Sciences Tabriz Iran Joint Ukraine-Azerbaijan International Research and Education Center of Nanobiotechnology and Functional Nanosystems Baku Azerbaijan Mayo Evidence-based Practice Center Mayo Clinic Foundat

Background: Previous attempts to characterise the burden of chronic respiratory diseases have focused only on specific disease conditions, such as chronic obstructive pulmonary disease (COPD) or asthma. In this study, we aimed to characterise the burden of chronic respiratory diseases globally, providing a comprehensive and up-to-date analysis on geographical and time trends from 1990 to 2017. Methods: Using data from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017, we estimated the prevalence, morbidity, and mortality attributable to chronic respiratory diseases through an analysis of deaths, disability-adjusted life-years (DALYs), and years of life lost (YLL) by GBD super-region, from 1990 to 2017, stratified by age and sex. Specific diseases analysed included asthma, COPD, interstitial lung disease and pulmonary sarcoidosis, pneumoconiosis, and other chronic respiratory diseases. We also assessed the contribution of risk factors (smoking, second-hand smoke, ambient particulate matter and ozone pollution, household air pollution from solid fuels, and occupational risks) to chronic respiratory disease-attributable DALYs. Findings: In 2017, 544·9 million people (95% uncertainty interval [UI] 506·9–584·8) worldwide had a chronic respiratory disease, representing an increase of 39·8% compared with 1990. Chronic respiratory disease prevalence showed wide variability across GBD super-regions, with the highest prevalence among both males and females in high-income regions, and the lowest prevalence in sub-Saharan Africa and south Asia. The age-sex-specific prevalence of each chronic respiratory disease in 2017 was also highly variable geographically. Chronic respiratory diseases were the third leading cause of death in 2017 (7·0% [95% UI 6·8–7·2] of all deaths), behind cardiovascular diseases and neoplasms. Deaths due to chronic respiratory diseases numbered 3 914 196 (95% UI 3 790 578–4 044 819) in 2017, an increase of 18·0% since 1990, while

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Proceedings of the EuBIC-MS 2020 Developers’ Meeting

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EuPA Open Proteomics 2020年 24卷 1-6页

作者： Christopher Ashwood Wout Bittremieux Eric W. Deutsch Nadezhda T. Doncheva Viktoria Dorfer Ralf Gabriels Vladimir Gorshkov Surya Gupta Andrew R. Jones Lukas Käll Dominik Kopczynski Lydie Lane Ludwig Lautenbacher Marc Legeay Marie Locard-Paulet Bart Mesuere Yasset Perez-Riverol Eugen Netz Sander Willems European Bioinformatics Community for Mass Spectrometry (info@***) Denmark Department of Cellular and Integrative Physiology University of Nebraska Medical Center Omaha USA Department of Computer Science University of Antwerp Antwerp Belgium Institute for Systems Biology Seattle WA 98109 USA Novo Nordisk Foundation Center for Protein Research University of Copenhagen Denmark Bioinformatics Research Group University of Applied Sciences Upper Austria Hagenberg Austria VIB-UGent Center for Medical Biotechnology VIB Ghent Belgium Department of Biochemistry and Molecular Biology University of Southern Denmark Denmark Institute of Systems Molecular and Integrative Biology University of Liverpool UK Science for Life Laboratory KTH - Royal Institute of Technology Solna Stockholm Sweden Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. Dortmund Germany SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine Faculty of Medicine Geneva University Geneva Switzerland Technical University of Munich Chair for Proteomics and Bioanalytics Freising Germany European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Applied Bioinformatics Dept. of Computer Science University of Tübingen Tübingen Germany Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA 92093 USA Center for non-coding RNA in Technology and Health Department of Veterinary and Animal Sciences University of Copenhagen Denmark Department of Biomolecular Medicine Ghent University Ghent Belgium Department of Applied Mathematics Computer Science and Statistics Ghent University Ghent Belgium Biomolecular Interactions Max Planck Institute for Developmental Biology Tübingen Germany

The 2020 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers’ meeting was held from January 13 th to January 17 th 2020 in Nyborg, Denmark. Among the participants were scientists as well as developers working in the field of computational mass spectrometry (MS) and proteomics. The 4-day program was split between introductory keynote lectures and parallel hackathon sessions. During the latter, the participants developed bioinformatics tools and resources addressing outstanding needs in the community. The hackathons allowed less experienced participants to learn from more advanced computational MS experts, and to actively contribute to highly relevant research projects. We successfully produced several new tools that will be useful to the proteomics community by improving data analysis as well as facilitating future research. All keynote recordings are available on https://***/10.5281/zenodo.3890181 .

关键词： Computational mass spectrometry Mass spectrometry Proteomics Bioinformatics Spectrum clustering Phosphoproteomics XIC extraction Proteomics graph networks Predicted spectra Metaproteomics Functional annotations Benchmark development

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Clinical and genetic delineation of autosomal recessive and dominant ACTL6B-related developmental brain disorders

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Genetics in Medicine 2025年第4期27卷 101251页

作者： Cali, Elisa Quirin, Tania Rocca, Clarissa Efthymiou, Stephanie Riva, Antonella Marafi, Dana Zaki, Maha S. Suri, Mohnish Dominguez, Roberto Elbendary, Hasnaa M. Alavi, Shahryar Abdel-Hamid, Mohamed S. Morsy, Heba Mau-Them, Frederic Tran Nizon, Mathilde Tesner, Pavel Ryba, Lukáš Zafar, Faisal Rana, Nuzhat Saadi, Nebal W. Firoozfar, Zahra Gencpinar, Pinar Unay, Bulent Ustun, Canan Bruel, Ange-Line Coubes, Christine Stefanich, Jennifer Sezer, Ozlem Agolini, Emanuele Novelli, Antonio Vasco, Gessica Lettori, Donatella Milh, Mathieu Villard, Laurent Zeidler, Shimriet Opperman, Henry Strehlow, Vincent Issa, Mahmoud Y. El Khassab, Hebatallah Chand, Prem Ibrahim, Shahnaz Rashidi-Nezhad, Ali Miryounesi, Mohammad Larki, Pegah Morrison, Jennifer Cristian, Ingrid Thiffault, Isabelle Bertsch, Nicole L. Noh, Grace J. Pappas, John Moran, Ellen Marinakis, Nikolaos M. Traeger-Synodinos, Joanne Hosseini, Susan Abbaszadegan, Mohammad Reza Caumes, Roseline Vissers, Lisenka E.L.M. Neshatdoust, Maedeh Montazer Zohour, Mostafa El Fahime, Elmostafa Canavati, Christina Kamal, Lara Kanaan, Moien Askander, Omar Voinova, Victoria Levchenko, Olga Haider, Shahzhad Halbach, Sara S. Elias Maia, Rayana Mansoor, Salehi Jain, Vivek Tawde, Sanjukta Challa, Viveka Santhosh R. Gowda, Vykuntaraju K. Srinivasan, Varunvenkat M. Victor, Lucas Alves Pinero-Banos, Benito Hague, Jennifer ElAwady, Heba Ahmed Maria de Miranda Henriques-Souza, Adelia Cheema, Huma Arshad Anjum, Muhammad Nadeem Idkaidak, Sara Alqarajeh, Firas Atawneh, Osama Mor-Shaked, Hagar Harel, Tamar Zifarelli, Giovanni Bauer, Peter Kok, Fernando Kitajima, Joao Paulo Monteiro, Fabiola Josahkian, Juliana Lesca, Gaetan Chatron, Nicolas Ville, Dorothe Murphy, David Neul, Jeffrey L. Mullegama, Sureni V. Begtrup, Amber Herman, Isabella Mitani, Tadahiro Posey, Jennifer E. Tay, Chee Geap Javed, Iram Carr, Lucinda Kanani, Farah Beecroft, Fiona Hane, Lee Abdelkreem, Elsayed Macek, Milan Bispo, Luciana Elmaksoud, Marwa Abd Hashemi-Gorji, Farzad Pehlivan, Davut Amor, David J. Jamra, Rami Abou Chung, Wend Department of Neuromuscular Diseases University College London Queen Square Institute of Neurology London United Kingdom RNA Molecular Biology Fonds de la Recherche Scientifique (F.R.S./FNRS) Université libre de Bruxelles (ULB) Biopark campus Gosselies Belgium Department of Neurosciences Rehabilitation Ophthalmology Genetics Maternal and Child Health University of Genoa Genoa Italy Department of Molecular and Human Genetics Baylor College of Medicine Houston TX United States Department of Pediatrics Faculty of Medicine Kuwait University Safat Kuwait Clinical Genetics Department Human Genetics and Genome Research Institute National Research Centre Cairo Egypt UK National Paediatric Ataxia Telangiectasia Clinic Nottingham University Hospitals NHS Trust Nottingham United Kingdom Nottingham Clinical Genetics Service Nottingham University Hospitals NHS Trust Nottingham United Kingdom Department of Physiology Perelman School of Medicine University of Pennsylvania Philadelphia PA United States Palindrome Isfahan Iran Medical Molecular Genetics Department Human Genetics and Genome Research Institute National Research Centre Cairo Egypt Human Genetics Department Medical Research Institute Alexandria University Egypt Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares Pôle de Biologie CHU Dijon Bourgogne Dijon France INSERM UMR1231 GAD Dijon France Service de génétique médicale CHU de Nantes Nantes France Institut du thorax INSERM CNRS UNIV Nantes Nantes France Department of Biology and Medical Genetics 2nd Faculty of Medicine Charles University and Motol University Hospital Prague Czech Republic Department of Paediatric Neurology Children's Hospital and Institute of Child Health Multan Pakistan College of Medicine/University of Baghdad Unit of Pediatric Neurology Children Welfare Teaching Hospital Baghdad Iraq İzmir Katip Çelebi University Tepecik Training and Research Department of Pediatric Neurology Izmir Türkiye U

Purpose: This study aims to comprehensively delineate the phenotypic spectrum of ACTL6B-related disorders, previously associated with both autosomal recessive and autosomal dominant neurodevelopmental disorders. Molecularly, the role of the nucleolar protein ACTL6B in contributing to the disease has remained unclear. Methods: We identified 105 affected individuals, including 39 previously reported cases, and systematically analyzed detailed clinical and genetic data for all individuals. Additionally, we conducted knockdown experiments in neuronal cells to investigate the role of ACTL6B in ribosome biogenesis. Results: Biallelic variants in ACTL6B are associated with severe-to-profound global developmental delay/intellectual disability, infantile intractable seizures, absent speech, autistic features, dystonia, and increased lethality. De novo monoallelic variants result in moderate-to-severe global developmental delay/intellectual disability, absent speech, and autistic features, whereas seizures and dystonia were less frequently observed. Dysmorphic facial features and brain abnormalities, including hypoplastic corpus callosum, and parenchymal volume loss/atrophy, are common findings in both groups. We reveal that in the nucleolus, ACTL6B plays a crucial role in ribosome biogenesis, particularly in pre-rrna processing. Conclusion: This study provides a comprehensive characterization of the clinical spectrum of both autosomal recessive and dominant forms of ACTL6B-associated disorders. It offers a comparative analysis of their respective phenotypes provides a plausible molecular explanation and suggests their inclusion within the expanding category of “ribosomopathies.” © 2024 The Authors

关键词： ACTL6B Autism BAFopathies Epileptic-dyskinetic encephalopathy Ribosomopathies

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Characterising acute and chronic care needs: insights from the Global Burden of Disease Study 2019

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Nature communications 2025年第1期16卷 4235-4235页

作者： Cecilia Anza-Ramirez J. Jaime Miranda Benedetta Armocida Jorge César Correia Harriette Gillian Christine Van Spall David Beran Amirali Aali Kalkidan Hassen Abate Semagn Mekonnen Abate Cristiana Abbafati Mohsen Abbasi-Kangevari Zeinab Abbasi-Kangevari Zahra Aryan Sina Azadnajafabad Mohammadreza Azangou-Khyavy Seyyed-Hadi Ghamari Mohammad Keykhaei Javad Khanali Sara Momtazmanesh Fateme Montazeri Shayan Rahmani Mohammad-Mahdi Rashidi Nazila Rezaei Negar Rezaei Sahar Saeedi Moghaddam Hossein Hassanian-Moghaddam Ali-Asghar Kolahi Ali Nikoobar Hedayat Abbastabar Ahmed M. Abdel-Azeem Michael Abdelmasseh Juan Sanabria Sherief Abd-Elsalam Ahmed Abdelwahab Gholamreza Abdoli Mohammad Abdollahi Meriem Abdoun Deldar Morad Abdulah Abu Yousuf Md Abdullah Ame Mehadi Abdurehman Getachew Abebe Aidin Abedi Chirag P. Doshi Vida Abedi Hassan Abidi Richard Gyan Aboagye Hassan Abolhassani Nima Rezaei Lucas Guimarães Abreu Michael R. M. Abrigo Yonas Derso Abtew Hiwa Abubaker Ali Eman Abu-Gharbieh Hiba Jawdat Barqawi Rabih Halwani Maha Mohamed Saber-Ayad Iman M. Talaat Ahmed Abu-Zaid Manfred Mario Kokou Accrombessi Juan Manuel Acuna Denberu Eshetie Adane Tigist Demssew Adane Isaac Yeboah Addo Giovanni Addolorato Oluwafemi Atanda Adeagbo Victor Adekanmbi Miracle Ayomikun Adesina Isaac Iyinoluwa Olufadewa Olatunji O. Adetokunboh Daniel Adedayo Adeyinka Qorinah Estiningtyas Sakilah Adnani Aanuoluwapo Adeyimika Afolabi Olayinka Stephen Ilesanmi Muhammad Sohail Afzal Saira Afzal Gina Agarwal Prerna Agarwal Pradyumna Agasthi Anurag Agrawal Marcela Agudelo-Botero Adolfo Martinez-Valle Bright Opoku Ahinkorah Aqeel Ahmad Sajjad Ahmad Sohail Ahmad Tauseef Ahmad Ali Ahmadi Siamak Sabour Keivan Ahmadi Sanjay Basu Sepideh Ahmadi Ali Ahmed Shaun Wen Huey Lee Ayman Ahmed Haroon Ahmed Jivan Qasim Ahmed Gahin Abdulraheem Tayib Yahya Yahya Luai A. Ahmed Iffat Elbarazi Syed Mahboob Shah Janardhana P. Aithala Marjan Ajami Budi Aji Hossein Akbarialiabad Yibeltal Akelew Meisam Akhlaghdoust Elham Jamshidi Addis Aklilu Azene Tesfaye Melat Woldemariam Maxwell Ak CRONICAS Center of Excellence in Chronic Diseases Universidad Peruana Cayetano Heredia Lima Peru School of Medicine Universidad Peruana Cayetano Heredia Lima Peru Sydney School of Public Health Faculty of Medicine and Health University of Sydney Sydney NSW Australia Faculty of Epidemiology and Population Health London School of Hygiene & Tropical Medicine London UK Division of Tropical and Humanitarian Medicine University of Geneva Geneva Switzerland Department of Cardiovascular Endocrine-metabolic Diseases and Aging Istituto Superiore di Sanità Rome Italy Division of Endocrinology Diabetology Nutrition and Therapeutic Patient Education Department of Medicine Geneva University Hospitals Geneva Switzerland Department of Medicine and Department of Health Research Evidence and Impact McMaster University Hamilton ON Canada Research Institute of St. Joe’s Hamilton ON Canada Population Health Research Institute Hamilton Canada Geneva University Hospitals Geneva Switzerland Faculty of Medicine Mashhad University of Medical Sciences Mashhad Iran Department of Nutrition and Dietetics Jimma University Jimma Ethiopia Anesthesiology Department Dilla University Addis Ababa Ethiopia Department of Juridical and Economic Studies La Sapienza University Rome Italy Non-Communicable Diseases Research Center Tehran University of Medical Sciences Tehran Iran Social Determinants of Health Research Center Shahid Beheshti University of Medical Sciences Tehran Iran Brigham and Women’s Hospital Harvard University Boston MA USA Students’ Scientific Research Center (SSRC) Tehran University of Medical Sciences Tehran Iran School of Medicine Tehran University of Medical Sciences Tehran Iran School of Medicine Shahid Beheshti University of Medical Sciences Tehran Iran Endocrinology and Metabolism Research Institute Tehran University of Medical Sciences Tehran Iran Chapter of Addiction Medicine University of Sydney Sydney NSW Australia Advanced Diagnostic and Intervent

Chronic care manages long-term, progressive conditions, while acute care addresses short-term conditions. Chronic conditions increasingly strain health systems, which are often unprepared for these demands. This study examines the burden of conditions requiring acute versus chronic care, including sequelae. Conditions and sequelae from the Global Burden of Diseases Study 2019 were classified into acute or chronic care categories. Data were analysed by age, sex, and socio-demographic index, presenting total numbers and contributions to burden metrics such as Disability-Adjusted Life Years (DALYs), Years Lived with Disability (YLD), and Years of Life Lost (YLL). Approximately 68% of DALYs were attributed to chronic care, while 27% were due to acute care. Chronic care needs increased with age, representing 86% of YLDs and 71% of YLLs, and accounting for 93% of YLDs from sequelae. These findings highlight that chronic care needs far exceed acute care needs globally, necessitating health systems to adapt accordingly. © 2025. The Author(s).

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Regulation of cellular sterol homeostasis by the oxygen responsive noncoding rna lincNORS (vol 1, 4755, 2020)

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NATURE COMMUNICATIONS 2020年第1期11卷 4755-4755页

作者： Wu, Xue Niculite, Cristina M. Preda, Mihai Bogdan Rossi, Annalisa Tebaldi, Toma Butoi, Elena White, Mattie K. Tudoran, Oana M. Petrusca, Daniela N. Jannasch, Amber S. Bone, William P. Zong, Xingyue Fang, Fang Burlacu, Alexandrina Paulsen, Michelle T. Hancock, Brad A. Sandusky, George E. Mitra, Sumegha Fishel, Melissa L. Buechlein, Aaron Ivan, Cristina Oikonomopoulos, Spyros Gorospe, Myriam Mosley, Amber Radovich, Milan Dave, Utpal P. Ragoussis, Jiannis Nephew, Kenneth P. Mari, Bernard McIntyre, Alan Konig, Heiko Ljungman, Mats Cousminer, Diana L. Macchi, Paolo Ivan, Mircea Department of Microbiology and Immunology Indiana University School of Medicine Indianapolis IN 46202 USA Department of Medicine Indiana University School of Medicine Indianapolis IN 46202 USA “Victor Babes” National Institute of Pathology Bucharest Romania Institute of Cellular Biology and Pathology “Nicolae Simionescu” Bucharest Romania Laboratory of Molecular and Cellular Neurobiology Department of Cellular Computational and Integrative Biology - CIBIO University of Trento Trento Italy Laboratory of Translational Genomics Department of Cellular Computational and Integrative Biology - CIBIO University of Trento Trento Italy Yale Cancer Center Yale University School of Medicine New Haven CT 06520 USA The Oncology Institute “Prof Dr. Ion Chiricuta” Cluj-Napoca Romania Metabolite Profiling Facility Bindley Bioscience Center Purdue University West Lafayette IN 47907 USA Department of Genetics Department of Systems Pharmacology and Translational Therapeutics Institute of Translational Medicine and Therapeutics Perelman School of Medicine University of Pennsylvania Philadelphia PA 19104 USA Department of Cellular and Integrative Physiology Indiana University School of Medicine Indianapolis IN USA Departments of Radiation Oncology and Environmental Health Sciences Center for RNA Biomedicine University of Michigan Ann Arbor MI 48109 USA Department of Surgery Indiana University School of Medicine Indianapolis IN 46202 USA Department of Pathology and Laboratory Medicine Indiana University School of Medicine Indianapolis IN 46202 USA Melvin and Bren Simon Cancer Center Indiana University Indianapolis IN USA Department of Obstetrics and Gynecology Indiana University School of Medicine Indianapolis IN 46202 USA Department of Pharmacology and Toxicology Department of Pediatrics Wells Center for Pediatric Research Indiana University School of Medicine Indianapolis IN 46202 USA Indiana University Center for Genomics and Bioinformatics Bloomington IN 47405 USA Center

We hereby provide the initial portrait of lincNORS, a spliced lincrna generated by the MIR193BHG locus, entirely distinct from the previously described miR-193b-365a tandem. While inducible by low O2 in a variety of cells and associated with hypoxia in vivo, our studies show that lincNORS is subject to multiple regulatory inputs, including estrogen signals. Biochemically, this lincrna fine-tunes cellular sterol/steroid biosynthesis by repressing the expression of multiple pathway components. Mechanistically, the function of lincNORS requires the presence of RALY, an rna-binding protein recently found to be implicated in cholesterol homeostasis. We also noticed the proximity between this locus and naturally occurring genetic variations highly significant for sterol/steroid-related phenotypes, in particular the age of sexual maturation. An integrative analysis of these variants provided a more formal link between these phenotypes and lincNORS, further strengthening the case for its biological relevance. noncoding transcripts contribute to the adaptation of cellular processes to oxygen levels. Here the authors characterize a hypoxia responsive lncrna lincNORS and show that it has a role in cellular sterol homeostasis.

关键词： Long non-coding rnas Long non-coding rnas Homeostasis Homeostasis

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Association between nonalcoholic Fatty Liver Disease and Carotid Artery Disease in a Community-Based Chinese Population： A Cross-Sectional Study

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Chinese Medical Journal 2018年第19期131卷 2269-2276页

作者： Yu-Chen Guo Yong Zhou Xing Gao Yan Yao Bin Geng Qing-Hua Cui Ji-Chun Yang Hong-Pu Hu Department of Health Information Management Institute of Medical Information Peking Union Medical College & Chinese Academy of Medical Sciences Beijing 100020 China Beijing Institute of Heart Lung and Blood Vessel Diseases Beijing Anzhen Hospital Capital Medical University Beijing 100029 China Department of Cardiology Beijing Anzhen Hospital Capital Medical University Beijing 100029 China Hypertension Center Fuwai Hospital Chinese Academy of Medical Sciences and Peking Union Medical College State Key Laboratory of Cardiovascular Disease Beijing 100037 China Department of Biomedical Informatics School of Basic Medical Sciences Key Laboratory of Molecular Cardiovascular Science of the Ministry of Education Center for Non-coding RNA Medicine Peking University Health Science Center Beijing 100191 China Department of Physiology and Pathophysiology School of Basic Medical Sciences Peking University Health Science Center Beijing 100191 China

Background： nonalcoholic fatty liver disease （NAFLD） is one of the most common chronic liver diseases with a high prevalence in the general population. The association between NAFLD and cardiovascular disease has been well addressed in previous studies. However, whether NAFLD is associated with carotid artery disease in a community-based Chinese population remained unclear. The aim of this study was to investigate the association between NAFLD and carotid artery disease. Methods： A total of 2612 participants （1091 men and 1521 women） aged 40 years and older from Jidong of Tangshan city （China） were selected for this study. NAFLD was diagnosed by abdominal ultrasonography. The presence of carotid stenosis or plaque was evaluated by carotid artery ultrasonography. Logistic regression was used to analyze the association between NAFLD and carotid artery disease. Results： Participants with NAFLD have a higher prevalence of carotid stenosis （12.9% vs. 4.6%） and carotid plaque （21.9% vs. 15.0%） than those without NAFLD. After adjusting for age, gender, smoking status, income, physical activity, diabetes, hypertension, triglyceride, waist-hip ratio, and high-density lipoprotein, NAFLD is significantly associated with carotid stenosis （odds ratio [OR]： 2.06, 95% confidence interval [CI]： 1.45-2.91）, but the association between NAFLD and carotid plaque is not statistically significant （OR： 1. 10, 95% CI： 0.86-1.40）. Conclusion： A significant association between NAFLD and carotid stenosis is found in a Chinese population.

关键词： Association Carotid Artery Disease Carotid Stenosis nonalcoholic Fatty Liver Disease

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