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arXiv 2022年

作者： Lobentanzer, Sebastian Aloy, Patrick Baumbach, Jan Bohar, Balazs Charoentong, Pornpimol Danhauser, Katharina Doğan, Tunca Dreo, Johann Dunham, Ian Fernandez-Torras, Adrià Gyori, Benjamin M. Hartung, Michael Hoyt, Charles Tapley Klein, Christoph Korcsmaros, Tamas Maier, Andreas Mann, Matthias Ochoa, David Pareja-Lorente, Elena Popp, Ferdinand Preusse, Martin Probul, Niklas Schwikowski, Benno Sen, Bünyamin Strauss, Maximilian T. Turei, Denes Ulusoy, Erva Heidrun Wodke, Judith Andrea Saez-Rodriguez, Julio Heidelberg University Faculty of Medicine Heidelberg University Hospital Institute for Computational Biomedicine Bioquant Heidelberg Germany The Barcelona Institute of Science and Technology Catalonia Barcelona Spain Catalonia Barcelona Spain Institute for Computational Systems Biology University of Hamburg Germany Earlham Institute Norwich United Kingdom Biological Research Centre Szeged Hungary Heidelberg University Im Neuenheimer Feld 267 Heidelberg69120 Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Department of Pediatrics Dr. von Hauner Children’s Hospital University Hospital LMU Munich Germany Biological Data Science Lab Department of Computer Engineering Hacettepe University Ankara Turkey Department of Bioinformatics Graduate School of Health Sciences Hacettepe University Ankara Turkey Computational Systems Biomedicine Lab Department of Computational Biology Institut Pasteur Université Paris Cité Paris France Bioinformatics and Biostatistics Hub Institut Pasteur Université Paris Cité Paris France Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Open Targets Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Laboratory of Systems Pharmacology Harvard Medical School Boston United States Imperial College London London United Kingdom Quadram Institute Bioscience Norwich United Kingdom Proteomics Program Novo Nordisk Foundation Centre for Protein Research University of Copenhagen Copenhagen Denmark Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Neuherberg Germany Medical Informatics Laboratory University Medicine Greifswald Germany

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to nonspecialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://***) frees up valuable developer time;we encourage further development and usage by the community. © 2022, CC BY-NC-ND.

关键词： Ontology

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Author Correction: Disrupting cellular memory to overcome drug resistance

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Nature communications 2024年第1期15卷 4264页

作者： Guillaume Harmange Raúl A Reyes Hueros Dylan L Schaff Benjamin Emert Michael Saint-Antoine Laura C Kim Zijian Niu Shivani Nellore Mitchell E Fane Gretchen M Alicea Ashani T Weeraratna M Celeste Simon Abhyudai Singh Sydney M Shaffer Cellular and Molecular Biology Graduate Group Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Biochemistry and Molecular Biophysics Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Bioengineering School of Engineering and Applied Sciences University of Pennsylvania Philadelphia PA USA. Division of Biology and Biological Engineering California Institute of Technology Pasadena CA 91125 USA. Department of Electrical and Computer Engineering University of Delaware Newark DE 19716 USA. Abramson Family Cancer Research Institute Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Chemistry College of the Arts and Sciences University of Pennsylvania Philadelphia PA USA. Department of Physics College of the Arts and Sciences University of Pennsylvania Philadelphia PA USA. Department of Biology College of the Arts and Sciences University of Pennsylvania Philadelphia PA USA. The Wharton School University of Pennsylvania Philadelphia PA USA. Cancer Signaling and Microenvironment Research Program Fox Chase Cancer Center Philadelphia PA USA. Department of Biochemistry and Molecular Biology Johns Hopkins School of Public Health Baltimore MD USA. Sidney Kimmel Cancer Center Johns Hopkins School of Medicine Baltimore MD USA. Department of Cell and Developmental Biology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Bioengineering School of Engineering and Applied Sciences University of Pennsylvania Philadelphia PA USA. sydshaffer@***. Department of Pathology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. sydshaffer@***.

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The generation challenge programme platform: Semantic standards and workbench for crop science

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International Journal of Plant Genomics 2008年第1期2008卷 369601页

作者： Bruskiewich, Richard Senger, Martin Davenport, Guy Ruiz, Manuel Rouard, Mathieu Hazekamp, Tom Takeya, Masaru Doi, Koji Satoh, Kouji Costa, Marcos Simon, Reinhard Balaji, Jayashree Akintunde, Akinnola Mauleon, Ramil Wanchana, Samart Shah, Trushar Anacleto, Mylah Portugal, Arllet Ulat, Victor Jun Thongjuea, Supat Braak, Kyle Ritter, Sebastian Dereeper, Alexis Skofic, Milko Rojas, Edwin Martins, Natalia Pappas, Georgios Alamban, Ryan Almodiel, Roque Barboza, Lord Hendrix Detras, Jeffrey Manansala, Kevin Mendoza, Michael Jonathan Morales, Jeffrey Peralta, Barry Valerio, Rowena Zhang, Yi Gregorio, Sergio Hermocilla, Joseph Echavez, Michael Yap, Jan Michael Farmer, Andrew Schiltz, Gary Lee, Jennifer Casstevens, Terry Jaiswal, Pankaj Meintjes, Ayton Wilkinson, Mark Good, Benjamin Wagner, James Morris, Jane Marshall, David Collins, Anthony Kikuchi, Shoshi Metz, Thomas McLaren, Graham Van Hintum, Theo Crop Research Informatics Laboratory International Rice Research Institute (IRRI) DAPO Box 7777 Metro Manila Philippines Crop Research Informatics Laboratory International Maize and Wheat Improvement Center (CIMMYT) DF 06600 Mexico Apdo. Postal 6-641 Mexico Centre International de Recherche Agronomique Pour le Développement (CIRAD) 34398 Montpellier Cedex 5 Avenue Agropolis France Bioversity International 00057 Maccarese (Fiumicino) Rome Via dei Tre Denari 472/a Italy National Institute for Agrobiological Sciences (NIAS) Tsukuba Ibaraki 305-8602 Kannondai 2-1-2 Japan Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA) Brasilia DF 70770-900 Parque Estaçao Biologia Final W5 Norte Brazil Centro Internacional de la Papa (CIP) Lima 12 Avenida La Molina 1895 La Molina Peru International Crops Research Institute for the Semi-Arid Tropics Patancheru Andhra Pradesh 502324 India International Center for Agricultural Research in the Dry Areas Aleppo P.O. Box 5466 Syrian Arab Republic National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Klong Luang Pathumthani 12120 Phahonyothin Road Klong 1 Thailand Institute of Computer Science College of Arts and Sciences University of the Philippines Los Banos Laguna 4031 Philippines Department of Computer Science University of the Philippines Melchor Hall Diliman Quezon City 1101 Philippines National Center for Genome Resources Santa Fe NM 87505 2935 Rodeo Park Drive East United States Scottish Crop Research Institute Invergowrie Dundee DD2 5DA United Kingdom Department of Plant Breeding Cornell University Ithaca NY 14853 United States African Centre for Gene Technologies Lynnwood Ridge 0040 P.O. Box 75011 South Africa Department of Medical Genetics Faculty of Medicine University of British Columbia Vancouver BC V6T 1Z3 Canada School of Computing Science Simon Fraser Universtiy Burnaby BC V5A 1S6 8888 University Drive Canada Bioinformatics Graduate Program Genome Sciences Centre BC

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform;(ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data;(iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making.

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Erratum for Wang et al., "Clinically Applicable System for Rapidly Predicting Enterococcus faecium Susceptibility to Vancomycin"

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Microbiology spectrum 2022年第1期10卷 e0261021页

作者： Hsin-Yao Wang Chia-Ru Chung Chao-Jung Chen Ko-Pei Lu Yi-Ju Tseng Tzu-Hao Chang Min-Hsien Wu Wan-Ting Huang Ting-Wei Lin Tsui-Ping Liu Tzong-Yi Lee Jorng-Tzong Horng Jang-Jih Lu Department of Laboratory Medicine Chang Gung Memorial Hospitalgrid.413801.f at Linkou Taoyuan City Taiwan. Ph.D. Program in Biomedical Engineering Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Computer Science and Information Engineering National Central Universitygrid.37589.30 Taoyuan City Taiwan. Graduate Institute of Integrated Medicine China Medical Universitygrid.254145.3 Taichung Taiwan. Proteomics Core Laboratory China Medical Universitygrid.254145.3 Hospital Taichung Taiwan. Graduate Program in Biomedical Information Yuan-Ze University Taoyuan City Taiwan. Department of Information Management Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Graduate Institute of Biomedical Informatics Taipei Medical University Taipei City Taiwan. Clinical Big Data Research Center Taipei Medical University Hospital Taipei City Taiwan. Graduate Institute of Biomedical Engineering Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Division of Haematology/Oncology Department of Internal Medicine Chang Gung Memorial Hospitalgrid.413801.f at Linkou Taoyuan City Taiwan. Biosensor Group Biomedical Engineering Research Center Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Pathology Kaohsiung Chang Gung Memorial Hospitalgrid.413801.f and Chang Gung University College of Medicine Kaohsiung Taiwan. School of Life and Health Sciences The Chinese University of Hong Kong Shenzhen China. Warshel Institute for Computational Biology The Chinese University of Hong Kong Shenzhen China. Department of Bioinformatics and Medical Engineering Asia University Taichung City Taiwan. School of Medicine Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Medical Biotechnology and Laboratory Science Chang Gung Universitygrid.145695.a Taoyuan City Taiwan.

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Global investments in pandemic preparedness and COVID-19: development assistance and domestic spending on health between 1990 and 2026

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The Lancet Global Health 2023年第3期11卷 e385-e413页

作者： Micah, Angela E. Bhangdia, Kayleigh Cogswell, Ian E. Lasher, Dylan Lidral-Porter, Brendan Maddison, Emilie R. Nguyen, Trang Nhu Ngoc Patel, Nishali Pedroza, Paola Solorio, Juan Stutzman, Hayley Tsakalos, Golsum Wang, Yifeng Warriner, Wesley Zhao, Yingxi Zlavog, Bianca S. Abbafati, Cristiana Abbas, Jaffar Abbasi-Kangevari, Mohsen Abbasi-Kangevari, Zeinab Abdelmasseh, Michael Abdulah, Deldar Morad Abedi, Aidin Abegaz, Kedir Hussein Abhilash, E.S. Aboagye, Richard Gyan Abolhassani, Hassan Abrigo, Michael R.M. Abubaker Ali, Hiwa Abu-Gharbieh, Eman Adem, Mohammed Hussien Afzal, Muhammad Sohail Ahmadi, Ali Ahmed, Haroon Ahmed Rashid, Tarik Aji, Budi Akbarialiabad, Hossein Akelew, Yibeltal Al Hamad, Hanadi Alam, Khurshid Alanezi, Fahad Mashhour Alanzi, Turki M. Al-Hanawi, Mohammed Khaled Alhassan, Robert Kaba Aljunid, Syed Mohamed Almustanyir, Sami Al-Raddadi, Rajaa M. Alvis-Guzman, Nelson Alvis-Zakzuk, Nelson J. Amare, Azmeraw T. Ameyaw, Edward Kwabena Amini-Rarani, Mostafa Amu, Hubert Ancuceanu, Robert Andrei, Tudorel Anwar, Sumadi Lukman Appiah, Francis Aqeel, Muhammad Arabloo, Jalal Arab-Zozani, Morteza Aravkin, Aleksandr Y. Aremu, Olatunde Aruleba, Raphael Taiwo Athari, Seyyed Shamsadin Avila-Burgos, Leticia Ayanore, Martin Amogre Azari, Samad Baig, Atif Amin Bantie, Abere Tilahun Barrow, Amadou Baskaran, Pritish Basu, Sanjay Batiha, Abdul-Monim Mohammad Baune, Bernhard T. Berezvai, Zombor Bhardwaj, Nikha Bhardwaj, Pankaj Bhaskar, Sonu Boachie, Micheal Kofi Bodolica, Virginia Botelho, João Silva Botelho Braithwaite, Dejana Breitborde, Nicholas J.K. Busse, Reinhard Cahuana-Hurtado, Lucero Catalá-López, Ferrán Chansa, Collins Charan, Jaykaran Chattu, Vijay Kumar Chen, Simiao Chukwu, Isaac Sunday Dadras, Omid Dandona, Lalit Dandona, Rakhi Dargahi, Abdollah Debela, Sisay Abebe Denova-Gutiérrez, Edgar Desye, Belay Dharmaratne, Samath Dhamminda Diao, Nancy Doan, Linh Phuong Dodangeh, Milad dos Santos, Wendel Mombaque Doshmangir, Leila Dube, John Eini, Ebrahim El Sayed Zaki, Maysaa El Tantawi, Maha Enyew, Daniel Berhanie Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Applied Mathematics University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States Nuffield Department of Medicine University of Oxford Oxford United Kingdom Department of Juridical and Economic Studies La Sapienza University Rome Italy Antai College of Economics Shanghai Jiao Tong University Shanghai China Non-communicable Diseases Research Center Tehran University of Medical Sciences Tehran Iran Research Center for Immunodeficiencies Tehran University of Medical Sciences Tehran Iran Multiple Sclerosis Research Center Tehran University of Medical Sciences Tehran Iran Children’s Medical Center Tehran University of Medical Sciences Tehran Iran Department of Epidemiology and Biostatistics Tehran University of Medical Sciences Tehran Iran Tehran Heart Center Tehran University of Medical Sciences Tehran Iran Faculty of Medicine Tehran University of Medical Sciences Tehran Iran National Institute for Health Research Tehran University of Medical Sciences Tehran Iran Department of Pharmacology Tehran University of Medical Sciences Tehran Iran Department of Cardiology Tehran University of Medical Sciences Tehran Iran Sina Trauma and Surgery Research Center Tehran University of Medical Sciences Tehran Iran Digestive Diseases Research Institute Tehran University of Medical Sciences Tehran Iran Department of Neurology Tehran University of Medical Sciences Tehran Iran Social Determinants of Health Research Center Shahid Beheshti University of Medical Sciences Tehran Iran Department of Epidemiology Shahid Beheshti University of Medical Sciences Tehran Iran Department of Health Economics and Statistics Shahid Beheshti University of Medical Sciences Tehran Iran Department of Neurosurgery Shahid Beheshti University of Medical Sciences Tehran Iran Ophthalmic R

Background: The COVID-19 pandemic highlighted gaps in health surveillance systems, disease prevention, and treatment globally. Among the many factors that might have led to these gaps is the issue of the financing of national health systems, especially in low-income and middle-income countries (LMICs), as well as a robust global system for pandemic preparedness. We aimed to provide a comparative assessment of global health spending at the onset of the pandemic;characterise the amount of development assistance for pandemic preparedness and response disbursed in the first 2 years of the COVID-19 pandemic;and examine expectations for future health spending and put into context the expected need for investment in pandemic preparedness. Methods: In this analysis of global health spending between 1990 and 2021, and prediction from 2021 to 2026, we estimated four sources of health spending: development assistance for health (DAH), government spending, out-of-pocket spending, and prepaid private spending across 204 countries and territories. We used the Organisation for Economic Co-operation and Development (OECD)'s Creditor Reporting System (CRS) and the WHO Global Health Expenditure Database (GHED) to estimate spending. We estimated development assistance for general health, COVID-19 response, and pandemic preparedness and response using a keyword search. Health spending estimates were combined with estimates of resources needed for pandemic prevention and preparedness to analyse future health spending patterns, relative to need. Findings: In 2019, at the onset of the COVID-19 pandemic, US$9·2 trillion (95% uncertainty interval [UI] 9·1–9·3) was spent on health worldwide. We found great disparities in the amount of resources devoted to health, with high-income countries spending $7·3 trillion (95% UI 7·2–7·4) in 2019;293·7 times the $24·8 billion (95% UI 24·3–25·3) spent by low-income countries in 2019. That same year, $43·1 billion in development assistance was provided

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Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements

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Nature protocols 2021年第7期16卷 3736页

作者： M Grace Gordon Fumitaka Inoue Beth Martin Max Schubach Vikram Agarwal Sean Whalen Shiyun Feng Jingjing Zhao Tal Ashuach Ryan Ziffra Anat Kreimer Ilias Georgakopoulos-Soares Nir Yosef Chun Jimmie Ye Katherine S Pollard Jay Shendure Martin Kircher Nadav Ahituv Department of Bioengineering and Therapeutic Sciences University of California San Francisco San Francisco CA USA. Institute for Human Genetics University of California San Francisco San Francisco CA USA. Biological and Medical Informatics Graduate Program University of California San Francisco San Francisco CA USA. Department of Bioengineering and Therapeutic Sciences University of California San Francisco San Francisco CA USA. fumitaka.inoue@ucsf.edu. Institute for Human Genetics University of California San Francisco San Francisco CA USA. fumitaka.inoue@ucsf.edu. Berlin Institute of Health (BIH) Berlin Germany. Department of Genome Sciences University of Washington Seattle WA USA. Calico Life Sciences LLC South San Francisco CA USA. Gladstone Institutes San Francisco CA USA. Department of Electrical Engineering and Computer Sciences and Center for Computational Biology University of California Berkeley Berkeley CA USA. Chan-Zuckerberg Biohub San Francisco CA USA. Division of Rheumatology Department of Medicine University of California San Francisco San Francisco CA USA. Institute for Computational Health Sciences University of California San Francisco San Francisco California USA. Department of Epidemiology and Biostatistics and Institute of Computational Health Sciences University of California San Francisco San Francisco CA USA. Department of Genome Sciences University of Washington Seattle WA USA. shendure@uw.edu. Howard Hughes Medical Institute Seattle WA USA. shendure@uw.edu. Brotman Baty Institute for Precision Medicine University of Washington Seattle WA USA. shendure@uw.edu. Berlin Institute of Health (BIH) Berlin Germany. martin.kircher@bihealth.de. Charité-Universitätsmedizin Berlin Berlin Germany. martin.kircher@bihealth.de. Department of Bioengineering and Therapeutic Sciences University of California San Francisco San Francisco CA USA. nadav.ahituv@ucsf.edu. Institute for Human Genetics University of California San

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A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3 (vol 111, pg 96, 2024)

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AMERICAN JOURNAL OF HUMAN GENETICS 2024年第4期11卷 805-805页

作者： Paul, Maimuna S. Michener, Sydney L. Pan, Hongling Chan, Hiuling Pfliger, Jessica M. Rosenfeld, Jill A. Lerma, Vanesa C. Tran, Alyssa Longley, Megan A. Lewis, Richard A. Weisz-Hubshman, Monika Bekheirnia, Mir Reza Bekheirnia, Nasim Massingham, Lauren Zech, Michael Wagner, Matias Engels, Hartmut Cremer, Kirsten Mangold, Elisabeth Peters, Sophia Trautmann, Jessica Perne, Claudia Mester, Jessica L. Sacoto, Maria J. Guillen Person, Richard McDonnell, Pamela P. Cohen, Stacey R. Lusk, Laina Cohen, Ana S. A. Le Pichon, Jean-Baptiste Pastinen, Tomi Zhou, Dihong Engleman, Kendra Racine, Caroline Faivre, Laurence Moutton, Sebastien Denomme-Pichon, Anne-Sophie Koh, Hyun Yong Poduri, Annapurna Bolton, Jeffrey Knopp, Cordula Suh, Dong Sun Julia Maier, Andrea Toosi, Mehran Beiraghi Karimiani, Ehsan Ghayoor Maroofian, Reza Schaefer, Gerald Bradley Ramakumaran, Vijayalakshmi Vasudevan, Pradeep Banos-Pinero, Benito Pagnamenta, Alistair T. Prasad, Chitra Osmond, Matthew Schuhmann, Sarah Vasileiou, Georgia Russ-Hall, Sophie Scheffer, Ingrid E. Carvill, Gemma L. Mefford, Heather Bacino, Carlos A. Lee, Brendan H. Chao, Hsiao-Tuan Department of Pediatrics Section of Neurology and Developmental Neuroscience Baylor College of Medicine Houston TX USA Jan and Dan Duncan Neurological Research Institute Texas Children’s Hospital Houston TX USA Cain Pediatric Neurology Research Foundation Laboratories Jan and Dan Duncan Neurological Research Institute Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Augustana College Rock Island IL USA Summer Undergraduate Research Training (SMART) Program Baylor College of Medicine Houston TX USA Graduate Program in Electrical and Computer Engineering Rice University Houston TX USA Department of Psychology University of Houston Houston TX USA Department of Ophthalmology Baylor College of Medicine Houston TX USA Renal Genetics Clinic Baylor College of Medicine Houston TX USA Rhode Island Hospital and Hasbro Children’s Hospital Providence RI USA Institute of Neurogenomics Helmholtz Zentrum München Munich Germany Institute of Human Genetics School of Medicine Technical University Munich Germany Institute for Advanced Study Technical University of Munich Garching Germany Division of Pediatric Neurology Developmental Neurology and Social Pediatrics Dr. von Hauner Children’s Hospital Munich Germany Institute of Human Genetics School of Medicine University Hospital Bonn University of Bonn Bonn Germany GeneDx Gaithersburg MD USA Epilepsy NeuroGenetics Initiative (ENGIN) Division of Neurology Children’s Hospital of Philadelphia Philadelphia PA USA Department of Neurology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Children’s Mercy Kansas City Genomic Medicine Center The University of Missouri-Kansas City (UMKC) School of Medicine Kansas City MO USA Department of Pediatrics Children’s Mercy Kansas City Kansas City MO USA Children’s Mercy Research Institute Kansas City MO USA Children’s Mercy Hospital Kansas City MO USA University Hospital Dijon Franc

PPFIA3 encodes the protein-tyrosine phosphatase, receptor-type, F-polypeptide-interacting-protein-alpha-3 (PPFIA3), which is a member of the LAR-protein-tyrosine phosphatase-interacting-protein (liprin) family involved in synapse formation and function, synaptic vesicle transport, and presynaptic active zone assembly. The protein structure and function are evolutionarily well conserved, but human diseases related to PPFIA3 dysfunction are not yet reported in OMIM. Here, we report 20 individuals with rare PPFIA3 variants (19 heterozygous and 1 compound heterozygous) presenting with developmental delay, intellectual disability, hypotonia, dysmorphisms, microcephaly or macrocephaly, autistic features, and epilepsy with reduced penetrance. Seventeen unique PPFIA3 variants were detected in 18 families. To determine the pathogenicity of PPFIA3 variants in vivo, we generated transgenic fruit flies producing either human wild-type (WT) PPFIA3 or five missense variants using GAL4-UAS targeted gene expression systems. In the fly overexpression assays, we found that the PPFIA3 variants in the region encoding the N-terminal coiled-coil domain exhibited stronger phenotypes compared to those affecting the C-terminal region. In the loss-of-function fly assay, we show that the homozygous loss of fly Liprin-α leads to embryonic lethality. This lethality is partially rescued by the expression of human PPFIA3 WT, suggesting human PPFIA3 function is partially conserved in the fly. However, two of the tested variants failed to rescue the lethality at the larval stage and one variant failed to rescue lethality at the adult stage. Altogether, the human and fruit fly data reveal that the rare PPFIA3 variants are dominant-negative loss-of-function alleles that perturb multiple developmental processes and synapse formation.

关键词： neurodevelopmental disorder synaptic protein active zone protein Mendelian phenotypes fruit flies

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A large-scale ENIGMA multisite replication study of brain age in depression

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Neuroimage: Reports 2022年第4期2卷 100149-100149页

作者： Han, Laura K.M. Dinga, Richard Leenings, Ramona Hahn, Tim Cole, James H. Aftanas, Lyubomir I. Amod, Alyssa R. Besteher, Bianca Colle, Romain Corruble, Emmanuelle Couvy-Duchesne, Baptiste Danilenko, Konstantin V. Fuentes-Claramonte, Paola Gonul, Ali Saffet Gotlib, Ian H. Goya-Maldonado, Roberto Groenewold, Nynke A. Hamilton, Paul Ichikawa, Naho Ipser, Jonathan C. Itai, Eri Koopowitz, Sheri-Michelle Li, Meng Okada, Go Okamoto, Yasumasa Churikova, Olga S. Osipov, Evgeny A. Penninx, Brenda W.J.H. Pomarol-Clotet, Edith Rodríguez-Cano, Elena Sacchet, Matthew D. Shinzato, Hotaka Sim, Kang Stein, Dan J. Uyar-Demir, Aslihan Veltman, Dick J. Schmaal, Lianne Centre for Youth Mental Health The University of Melbourne Parkville VIC Australia Orygen Parkville VIC Australia Department of Cognitive Science & Artificial Intelligence Tilburg University Tilburg Netherlands Institute for Translational Psychiatry University of Münster Münster Germany Faculty of Mathematics and Computer Science University of Münster Münster Germany Centre for Medical Image Computing Department of Computer Science University College London United Kingdom Dementia Research Centre Queen Square Institute of Neurology University College London United Kingdom Scientific Research Institute of Neuroscience and Medicine Novosibirsk Russian Federation Novosibirsk State University Novosibirsk Russian Federation Department of Psychiatry & Mental Health Neuroscience Institute University of Cape Town South Africa Department of Psychiatry and Psychotherapy Jena University Hospital Jena Germany Service Hospitalo-Universitaire de Psychiatrie de Bicêtre Mood Center Paris Saclay Assistance Publique-Hôpitaux de Paris Hôpitaux Universitaires Paris-Saclay Hôpital de Bicêtre Le Kremlin Bicêtre F-94275 France MOODS Team INSERM 1018 CESP (Centre de Recherche en Epidémiologie et Santé des Populations) Université Paris-Saclay Faculté de Médecine Paris-Saclay Le Kremlin Bicêtre F-94275 France Sorbonne Université Institut du Cerveau - Paris Brain Institute - ICM CNRS Inria Inserm AP-HP Hôpital de La Pitié Salpêtrière Paris F-75013 France Institute for Molecular Bioscience The University of Queensland St Lucia 4072 QLD Australia FIDMAG Hermanas Hospitalarias Research Foundation Barcelona Spain CIBERSAM Barcelona Spain SoCAT Lab Department of Psychiatry School of Medicine Ege University Izmir Turkey Department of Psychology Stanford University Stanford CA United States Laboratory of Systems Neuroscience and Imaging in Psychiatry (SNIP-Lab) University Medical Center Göttingen Göttingen Germany Center for Social and Affective Neuroscience Department o

Background: Several studies have evaluated whether depressed persons have older appearing brains than their nondepressed peers. However, the estimated neuroimaging-derived “brain age gap” has varied from study to study, likely driven by differences in training and testing sample (size), age range, and used modality/features. To validate our previously developed ENIGMA brain age model and the identified brain age gap, we aim to replicate the presence and effect size estimate previously found in the largest study in depression to date (N = 2126 controls & N = 2675 cases;+1.08 years [SE 0.22], Cohen's d = 0.14, 95% CI: 0.08–0.20), in independent cohorts that were not part of the original study. Methods: A previously trained brain age model (***/enigma_brainage) based on 77 FreeSurfer brain regions of interest was used to obtain unbiased brain age predictions in 751 controls and 766 persons with depression (18–75 years) from 13 new cohorts collected from 20 different scanners. Meta-regressions were used to examine potential moderating effects of basic cohort characteristics (e.g., clinical and scan technical) on the brain age gap. Results: Our ENIGMA MDD brain age model generalized reasonably well to controls from the new cohorts (predicted age vs. age: r = 0.73, R² = 0.47, MAE = 7.50 years), although the performance varied from cohort to cohort. In these new cohorts, on average, depressed persons showed a significantly higher brain age gap of +1 year (SE 0.35) (Cohen's d = 0.15, 95% CI: 0.05–0.25) compared with controls, highly similar to our previous finding. Significant moderating effects of FreeSurfer version 6.0 (d = 0.41, p = 0.007) and Philips scanner vendor (d = 0.50, p < 0.0001) were found, leading to more positive effect size estimates. Conclusions: This study further validates our previously developed ENIGMA brain age algorithm. Importantly, we replicated the brain age gap in depression with a comparable effect size. Thus, two large-s

关键词： Biological aging Brain age Depression ENIGMA consortium Replication study

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Global, regional, and national sex-specific burden and control of the HIV epidemic, 1990–2019, for 204 countries and territories: the Global Burden of Diseases Study 2019

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The Lancet HIV 2021年第10期8卷 e633-e651页

作者： Jahagirdar, Deepa Walters, Magdalene K. Novotney, Amanda Brewer, Edmond D. Frank, Tahvi D. Carter, Austin Biehl, Molly H. Abbastabar, Hedayat Abhilash, E.S. Abu-Gharbieh, Eman Abu-Raddad, Laith Jamal Adekanmbi, Victor Adeyinka, Daniel Adedayo Adnani, Qorinah Estiningtyas Sakilah Afzal, Saira Aghababaei, Soodabeh Ahinkorah, Bright Opoku Ahmad, Sajjad Ahmadi, Keivan Ahmadi, Sepideh Ahmadpour, Ehsan Ahmed, Muktar Beshir Rashid, Tarik Ahmed Salih, Yusra Ahmed Aklilu, Addis Akram, Tayyaba Akunna, Chisom Joyqueenet Al Hamad, Hanadi Alahdab, Fares Alanezi, Fahad Mashhour Aleksandrova, Ekaterina A. Alene, Kefyalew Addis Ali, Liaqat Alipour, Vahid Almustanyir, Sami Alvis-Guzman, Nelson Ameyaw, Edward Kwabena Amu, Hubert Andrei, Catalina Liliana Andrei, Tudorel Anvari, Davood Arabloo, Jalal Aremu, Olatunde Arulappan, Judie Atnafu, Desta Debalkie Quintanilla, Beatriz Paulina Ayala Ayza, Muluken Altaye Azari, Samad Darshan, B.B. Banach, Maciej Bärnighausen, Till Winfried Barra, Fabio Barrow, Amadou Basu, Sanjay Bazargan-Hejazi, Shahrzad Belay, Habtamu Gebrehana Berheto, Tezera Moshago Bezabhe, Woldesellassie Mequanint Bezabih, Yihienew Mequanint Bhagavathula, Akshaya Srikanth Bhardwaj, Nikha Bhardwaj, Pankaj Bhattacharyya, Krittika Bibi, Sadia Bijani, Ali Bisignano, Catherine Bolarinwa, Obasanjo Afolabi Boloor, Archith Boltaev, Azizbek A. Briko, Nikolay Ivanovich Buonsenso, Danilo Burkart, Katrin Butt, Zahid A. Cao, Chao Charan, Jaykaran Chatterjee, Souranshu Chattu, Soosanna Kumary Chattu, Vijay Kumar Choudhari, Sonali Gajanan Chu, Dinh-Toi Couto, Rosa A.S. Cowden, Richard G. Dachew, Berihun Assefa Dadras, Omid Dagnew, Amare Belachew Dahlawi, Saad M.A. Dai, Xiaochen Dandona, Lalit Dandona, Rakhi das Neves, José Degenhardt, Louisa Demeke, Feleke Mekonnen Desta, Abebaw Alemayehu Deuba, Keshab Dhamnetiya, Deepak Dhungana, Govinda Prasad Dianatinasab, Mostafa Diaz, Daniel Djalalinia, Shirin Doan, Linh Phuong Dorostkar, Fariba Edinur, Hisham Atan Effiong, Andem Eftekharzadeh, Sahar El Sayed Zaki, Maysaa Elayedath, Rajesh Elhadi, Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States Division of Allergy and Infectious Diseases University of Washington Seattle WA United States Department of Global Health University of Washington Seattle WA United States School of Social Work University of Washington Seattle WA United States Department of Medicine University of Washington Seattle WA United States Vagelos College of Physicians and Surgeones Columbia University Medical Center New York NY United States Division of Data Analytics and Delivery for Impact WHO Geneva Switzerland Advanced Diagnostic and Interventional Radiology Research Centre Tehran University of Medical Sciences Tehran Iran Multiple Sclerosis Research Centre Tehran University of Medical Sciences Tehran Iran School of Public Health Tehran University of Medical Sciences Tehran Iran Department of Epidemiology and Biostatistics Tehran University of Medical Sciences Tehran Iran Paediatric Chronic Kidney Disease Research Centre Tehran University of Medical Sciences Tehran Iran Department of Psychiatry Tehran University of Medical Sciences Tehran Iran Metabolomics and Genomics Research Centre Tehran University of Medical Sciences Tehran Iran Sina Trauma and Surgery Research Centre Tehran University of Medical Sciences Tehran Iran Research Centre for Immunodeficiencies Tehran University of Medical Sciences Tehran Iran Non-Communicable Diseases Research Centre Tehran University of Medical Sciences Tehran Iran Department of Botany Sree Narayana Guru College Chelannur Kozhikode India Clinical Sciences Department University of Sharjah Sharjah United Arab Emirates Mass Communication Department University of Sharjah Sharjah United Arab Emirates Department of Health-Care Policy and Research Weill Cornell Medical College in Qatar Doha Qatar Department of Population Medicine Ca

Background: The sustainable development goals (SDGs) aim to end HIV/AIDS as a public health threat by 2030. Understanding the current state of the HIV epidemic and its change over time is essential to this effort. This study assesses the current sex-specific HIV burden in 204 countries and territories and measures progress in the control of the epidemic. Methods: To estimate age-specific and sex-specific trends in 48 of 204 countries, we extended the Estimation and Projection Package Age-Sex Model to also implement the spectrum paediatric model. We used this model in cases where age and sex specific HIV-seroprevalence surveys and antenatal care-clinic sentinel surveillance data were available. For the remaining 156 of 204 locations, we developed a cohort-incidence bias adjustment to derive incidence as a function of cause-of-death data from vital registration systems. The incidence was input to a custom Spectrum model. To assess progress, we measured the percentage change in incident cases and deaths between 2010 and 2019 (threshold >75% decline), the ratio of incident cases to number of people living with HIV (incidence-to-prevalence ratio threshold <0·03), and the ratio of incident cases to deaths (incidence-to-mortality ratio threshold <1·0). Findings: In 2019, there were 36·8 million (95% uncertainty interval [UI] 35·1–38·9) people living with HIV worldwide. There were 0·84 males (95% UI 0·78–0·91) per female living with HIV in 2019, 0·99 male infections (0·91–1·10) for every female infection, and 1·02 male deaths (0·95–1·10) per female death. Global progress in incident cases and deaths between 2010 and 2019 was driven by sub-Saharan Africa (with a 28·52% decrease in incident cases, 95% UI 19·58–35·43, and a 39·66% decrease in deaths, 36·49–42·36). Elsewhere, the incidence remained stable or increased, whereas deaths generally decreased. In 2019, the global incidence-to-prevalence ratio was 0·05 (95% UI 0·05–0·06) and the global incidence-to-mortality ratio was

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Author Correction: The interrelation of sleep and mental and physical health is anchored in grey-matter neuroanatomy and under genetic control

Communications biology

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Communications biology 2020年第1期3卷 290页

作者： Masoud Tahmasian Fateme Samea Habibolah Khazaie Mojtaba Zarei Shahrzad Kharabian Masouleh Felix Hoffstaedter Julia Camilleri Peter Kochunov B T Thomas Yeo Simon Bodo Eickhoff Sofie Louise Valk Institute of Medical Science and Technology Shahid Beheshti University Tehran Iran. Sleep Disorders Research Center Kermanshah University of Medical Sciences Kermanshah Iran. Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour) Research Centre Jülich 52425 Jülich Germany. Institute of Systems Neuroscience Heinrich Heine University Düsseldorf 40225 Düsseldorf Germany. Maryland Psychiatric Research Center University of Maryland School of Medicine Baltimore MD 21201 USA. Department of Electrical and Computer Engineering Clinical Imaging Research Centre N.1 Institute for Health and Memory Networks Program National University of Singapore Singapore 119077 Singapore. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown MA 02114 USA. Centre for Sleep and Cognition National University of Singapore Singapore 119077 Singapore. NUS Graduate School for Integrative Sciences and Engineering National University of Singapore Singapore 119077 Singapore. Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour) Research Centre Jülich 52425 Jülich Germany. svalk@fz-juelich.de. Institute of Systems Neuroscience Heinrich Heine University Düsseldorf 40225 Düsseldorf Germany. svalk@fz-juelich.de.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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