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Nature aging 2024年第10期4卷 1508页

作者： Thomas R Austin Maria Nethander Howard A Fink Anna E Törnqvist Diana I Jalal Petra Buzkova Joshua I Barzilay Laura Carbone Maiken E Gabrielsen Louise Grahnemo Tianyuan Lu Kristian Hveem Christian Jonasson Jorge R Kizer Arnulf Langhammer Kenneth J Mukamal Robert E Gerszten Bruce M Psaty John A Robbins Yan V Sun Anne Heidi Skogholt John A Kanis Helena Johansson Bjørn Olav Åsvold Rodrigo J Valderrabano Jie Zheng J Brent Richards Eivind Coward Claes Ohlsson Cardiovascular Health Research Unit University of Washington Seattle WA US. Department of Internal Medicine and Clinical Nutrition Institute of Medicine Sahlgrenska Osteoporosis Centre Centre for Bone and Arthritis Research at the Sahlgrenska Academy University of Gothenburg Gothenburg Sweden. Bioinformatics and Data Center Sahlgrenska Academy University of Gothenburg Gothenburg Sweden. Geriatric Research Education and Clinical Center VA Health Care System Minneapolis MN US. Department of Medicine University of Minnesota Minneapolis MN US. Division of Nephrology Department of Internal Medicine Carver College of Medicine Iowa City IA US. Iowa City VA Medical Center Iowa City IA US. Department of Biostatistics University of Washington Seattle WA US. Division of Endocrinology Kaiser Permanente of Georgia Atlanta GA US. Charlie Norwood VAMC Augusta GA US. Division of Rheumatology Department of Medicine Medical College of Georgia Augusta University Augusta GA US. HUNT Center for Molecular and Clinical Epidemiology Department of Public Health and Nursing Norwegian University of Science and Technology Trondheim Norway. Lady Davis Institute for Medical Research Jewish General Hospital Montreal Quebec Canada. Quantitative Life Sciences Program McGill University Montreal Quebec Canada. 5 Prime Sciences Inc Montreal Quebec Canada. HUNT Research Centre NTNU Levanger Norway. Levanger Hospital Nord-Trøndelag Hospital Trust Levanger Norway. Cardiology Section San Francisco VA Health Care System San Francisco CA US. Department of Medicine Epidemiology and Biostatistics University of California San Francisco San Francisco CA US. Department of Medicine Beth Israel Deaconess Medical Center Brookline MA US. Departments of Medicine Epidemiology and Health Systems and Population Health University of Washington Seattle WA US. Department of Medicine University of California Davis CA US. Department of Epidemiology Rollins School of Public Health

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Leveraging implicit knowledge in neural networks for functional dissection and engineering of proteins (vol 1, pg 225, 2019)

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NATURE MACHINE INTELLIGENCE 2019年第6期1卷 290-290页

作者： zu Belzen, Julius Upmeier Buergel, Thore Holderbach, Stefan Bubeck, Felix Adam, Lukas Gandor, Catharina Klein, Marita Mathony, Jan Pfuderer, Pauline Platz, Lukas Przybilla, Moritz Schwendemann, Max Heid, Daniel Hoffmann, Mareike Daniela Jendrusch, Michael Schmelas, Carolin Waldhauer, Max Lehmann, Irina Niopek, Dominik Eils, Roland University of Heidelberg Synthetic Biology Group Institute for Pharmacy and Molecular Biotechnology and Center for Quantitative Analysis of Molecular and Cellular Biosystems Heidelberg Germany (GRID:grid.7700.0) (ISNI:0000 0001 2190 4373) Digital Health Center Berlin Institute of Health (BIH) and Charité University Medicine Berlin Germany (GRID:grid.6363.0) (ISNI:0000 0001 2218 4662) University of Heidelberg Synthetic Biology Group Institute for Pharmacy and Molecular Biotechnology and Center for Quantitative Analysis of Molecular and Cellular Biosystems Heidelberg Germany (GRID:grid.7700.0) (ISNI:0000 0001 2190 4373) University of Heidelberg Synthetic Biology Group Institute for Pharmacy and Molecular Biotechnology and Center for Quantitative Analysis of Molecular and Cellular Biosystems Heidelberg Germany (GRID:grid.7700.0) (ISNI:0000 0001 2190 4373) German Cancer Research Center (DKFZ) Department of Theoretical Bioinformatics Heidelberg Germany (GRID:grid.7497.d) (ISNI:0000 0004 0492 0584) University Hospital Heidelberg Department of Infectious Diseases Virology Heidelberg Germany (GRID:grid.5253.1) (ISNI:0000 0001 0328 4908) BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University Heidelberg Germany (GRID:grid.7700.0) (ISNI:0000 0001 2190 4373) Berlin Institute of Health (BIH) and Charité University Medicine Molecular Epidemiology Unit Berlin Germany (GRID:grid.484013.a) University of Heidelberg Synthetic Biology Group Institute for Pharmacy and Molecular Biotechnology and Center for Quantitative Analysis of Molecular and Cellular Biosystems Heidelberg Germany (GRID:grid.7700.0) (ISNI:0000 0001 2190 4373) University Hospital Heidelberg Health Data Science Unit Heidelberg Germany (GRID:grid.5253.1) (ISNI:0000 0001 0328 4908) Digital Health Center Berlin Institute of Health (BIH) and Charité University Medicine Berlin Germany (GRID:grid.6363.0) (ISNI:0000 0001 2218 4662) University Hospital Heidelberg Health Data Science Unit Heidelberg Germany (GRI

Proteins are nature’s most versatile molecular machines. Deep neural networks trained on large protein datasets have recently been used to tackle the unmet complexity of protein sequence–function relationships. The implicit knowledge contained in these networks represents a powerful, but thus far inaccessible, resource for understanding protein biology. Here, we show that occlusion-based sensitivity analysis can leverage the knowledge present in deep-neural-network-based protein sequence classifiers to identify functionally relevant parts of proteins. We first validated our approach by successfully predicting positions that mediate small molecule binding or catalytic activity across different protein classes. Next, we inferred the impact of point mutations on the activity of ERK and HRas, signalling factors frequently deregulated in cancer. Finally, we used our approach to identify engineering hotspots in CRISPR–Cas9 and anti-CRISPR protein AcrIIA4. Our work demonstrates how implicit knowledge in neural networks can be harnessed for protein functional dissection and protein *** neural networks are a powerful tool for predicting protein function, but identifying the specific parts of a protein sequence that are relevant to its functions remains a challenge. An occlusion-based sensitivity technique helps interpret these deep neural networks, and can guide protein engineering by locating functionally relevant protein positions.

关键词： Proteins

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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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A second update on mapping the human genetic architecture of COVID-19

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Nature 2023年第7977期621卷 E7-E26页

作者： Masahiro Kanai Christine Stevens Benjamin M. Neale Mark Daly Andrea Ganna Amy Trankiem Mary K. Balaconis Samuli Ripatti Lindo Nkambul Mark J. Daly Sam Bryant Matthew Solomonson Shea J. Andrews Mattia Cordioli Juha Karjalainen Juha Mehtonen Matti Pirinen Andrea Corbetta Bradley Jermy Kati Donner Katja Kivinen Aarno Palotie Mari Kaunisto Kumar Veerapen Konrad J. Karczewski Alicia R. Martin Elizabeth G. Atkinson Kristin Tsuo Nikolas Baya Rahul Gupta Raymond K. Walters Duncan S. Palmer Gopal Sarma Nathan Cheng Wenhan Lu Claire Churchhouse Jacqueline I. Goldstein Daniel King Wei Zhou Cotton Seed Hilary Finucane F. Kyle Satterstrom Gita A. Pathak Akiko Iwasaki Karolina Chwialkowska Karolina Chwiałkowska Brooke N. Wolford Hajar Fauzan Ahmad Shea Andrews Kathrin Aprile von Hohenstaufen Puoti Palwende R. Boua Guillaume Butler-Laporte Celia M. T. Greenwood Bartha M. Knoppers Mark Lathrop Carmen L. Cadilla Francesca Colombo Nicole Dueker Chloe Kirk Atanu Kumar Dutta Yasser M. El-Sherbiny Jehan J. El-Jawhari Doaa Shahin Ahmed Elzeiny Tamer A. Mansour Madonna M. Eltoukhy Attia A. S. Mohamed Sahar Esmaeeli Annika Faucon Israel Fernández Cadenas Israel Fernandez-Cadenas Laia Llucià-Carol Natalia Cullell Elena Muiño Jara Cárcel-Márquez Margherita Francescatto Laurent Francioli Lindokuhle Nkambule Jatin Arora Soumya Raychaudhuri Caroline Cusick Lude Franke Macarena Fuentes Macarena Fuentes-Guajardo David Gómez Cabrero Emi N. Harry Philip Jansen József L. Szentpéteri Réka Várnai Elżbieta Kaja Athanasios Kousathanas Dorote Pasko Mark J. Caulfield Alex Stuckey Christopher A. Odhams Susan Walker Daniel Rhodes Richard H. Scott Loukas Moutsianas Afshan Siddiq Peter Goddard Sally Donovan Tala Zainy Fiona Maleady-Crowe Linda Todd Shahla Salehi Greg Elgar Georgia Chan Prabhu Arumugam Christine Patch Augusto Rendon Tom A. Fowler Jose E. Krieger Sanjay K. Patel Audrey Lemaçon Sophie Limou Pietro Lió Eirini Marouli Charles Hinds Minttu M. Marttila Carolina Medina-Gómez Isabelle Migeotte Soumyajit Mondal Andrés Moreno-Estrada Leire Moya Tomok Broad Institute of MIT and Harvard Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Program in Bioinformatics and Integrative Genomics Harvard Medical School Boston MA USA Institute for Molecular Medicine Finland (FIMM) University of Helsinki Helsinki Finland Institute for Molecular Medicine Finland University of Helsinki Helsinki Finland Institute for Molecular Medicine Finland (FIMM) HiLIFE University of Helsinki Helsinki Finland Public Health Faculty of Medicine University of Helsinki Helsinki Finland Analytic & Translational Genetics Unit Massachusetts General Hospital Boston MA USA Stanley Center for Psychiatric Research & Program in Medical and Population Genetics Cambridge UK Institute for Molecular Medicine Finland (FIMM) Univerisity of Helsinki Helsinki Finland University of California San Francisco San Francisco CA USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA Department of Psychiatry School of Medicine Yale University New Haven CT USA Veteran Affairs Connecticut Healthcare System West Haven CT USA Yale University New Haven CT USA Centre for Bioinformatics and Data Analysis Medical University of Bialystok Bialystok Poland Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA Faculty of Industrial Sciences and Technology Universiti Malaysia Pahang Pahang Malaysia Icahn School of Medicine at Mount Sinai New York NY USA Genolier Innovation Network and Hub Swiss Medical Network Genolier Healthcare Campus Genolier Switzerland Immediate Independent Multidisciplinary Med & Biotech Research Association Milan Italy Clinical Research Unit of Nanor

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Authorship Correction: International Changes in COVID-19 Clinical Trajectories Across 315 Hospitals and 6 Countries: Retrospective Cohort Study

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Journal of medical Internet research 2021年第11期23卷 e34625页

作者： Griffin M Weber Harrison G Zhang Sehi L'Yi Clara-Lea Bonzel Chuan Hong Paul Avillach Alba Gutiérrez-Sacristán Nathan P Palmer Amelia Li Min Tan Xuan Wang William Yuan Nils Gehlenborg Anna Alloni Danilo F Amendola Antonio Bellasi Riccardo Bellazzi Michele Beraghi Mauro Bucalo Luca Chiovato Kelly Cho Arianna Dagliati Hossein Estiri Robert W Follett Noelia García Barrio David A Hanauer Darren W Henderson Yuk-Lam Ho John H Holmes Meghan R Hutch Ramakanth Kavuluru Katie Kirchoff Jeffrey G Klann Ashok K Krishnamurthy Trang T Le Molei Liu Ne Hooi Will Loh Sara Lozano-Zahonero Yuan Luo Sarah Maidlow Adeline Makoudjou Alberto Malovini Marcelo Roberto Martins Bertrand Moal Michele Morris Danielle L Mowery Shawn N Murphy Antoine Neuraz Kee Yuan Ngiam Marina P Okoshi Gilbert S Omenn Lav P Patel Miguel Pedrera Jiménez Robson A Prudente Malarkodi Jebathilagam Samayamuthu Fernando J Sanz Vidorreta Emily R Schriver Petra Schubert Pablo Serrano Balazote Byorn Wl Tan Suzana E Tanni Valentina Tibollo Shyam Visweswaran Kavishwar B Wagholikar Zongqi Xia Daniela Zöller Isaac S Kohane Tianxi Cai Andrew M South Gabriel A Brat Department of Biomedical Informatics Harvard Medical School Boston MA United States. BIOMERIS (BIOMedical Research Informatics Solutions) Pavia Italy. Clinical Research Unit Botucatu Medical School São Paulo State University Botucatu Brazil. Division of Nephrology Department of Medicine Ente Ospedaliero Cantonale Lugano Switzerland. Department of Electrical Computer and Biomedical Engineering University of Pavia Pavia Italy. Information Technology Department Azienda Socio-Sanitaria Territoriale di Pavia Pavia Italy. Unit of Internal Medicine and Endocrinology Istituti Clinici Scientifici Maugeri SpA SB IRCCS Pavia Italy. Massachusetts Veterans Epidemiology Research and Information Center Veterans Affairs Boston Healthcare System Boston MA United States. Department of Electrical Computer and Biomedical Engineering University of Pavia Pavia Italy. Department of Medicine Massachusetts General Hospital Boston MA United States. Department of Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles CA United States. Health Informatics Hospital Universitario 12 de Octubre Madrid Spain. Department of Learning Health Sciences University of Michigan Medical School Ann Arbor MI United States. Department of Biomedical Informatics University of Kentucky Lexington KY United States. Department of Biostatistics Epidemiology and Informatics University of Pennsylvania Perelman School of Medicine Philadelphia PA United States. Institute for Biomedical Informatics University of Pennsylvania Perelman School of Medicine Philadelphia PA United States. Department of Preventive Medicine Northwestern University Chicago IL United States. Institute for Biomedical Informatics University of Kentucky Lexington KY United States. Medical University of South Carolina Charleston SC United States. Department of Computer Science Renaissance Computing Institute University of North Carolina at Chapel Hill Chapel Hill NC United States. Departm

[This corrects the article DOI: 10.2196/31400.].

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Power aware scheme for water pipeline monitoring based on Wireless Sensor Networks

Power aware scheme for water pipeline monitoring based on Wi...

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International Conference on Intelligent Systems Design and Applications (ISDA)

作者： Manel Elleuchi Manel Boujelben Mohamed Abid Abdulfattah M. Obeid Mohammed S. BenSaleh Multimedia and Digital Data Processing (CETIC) National School of Engineers of Sfax ResearchCenter in Informatics Sfax Tunisia CES research unit National School of Engineers of Sfax Research Center in Informatics Multimedia and Digital Data Processing (CETIC) Technopark Sfax Tunisia National Center for Electronics Communications and Photonics King Abdulaziz City for Science and Technology Riyadh Kingdom of Saudi Arabi King Abdulaziz City for Science And Technology Riyadh Al Riyadh Province SA

ISBN: (纸本)9781467387101

Recently, using Wireless Sensor Networks (WSNs) is increasing in many areas, whether scientific, logistic, military, health and water monitoring. Water is among the vital material transported by pipeline systems. Any leakage in the pipe can cause major financial losses and possible environmental damages. Therefore, it is necessary to have a real time leak detection system. WSNs can play an important role to effectively detect the leak and minimize the water loss. Sensor size, however, is a significant limitation in terms of energy autonomy. In fact, the battery is very small and in general, it is not replaceable or rechargeable. Therefore, many studies are currently focusing on the management of the energy consumed by sensor nodes. In this paper, we propose a new energy efficient scheme for leak detection in water pipeline based on WSNs. The main goal of our proposal is to solve the problem of losing water and ameliorate network lifetime by reducing energy needs. The proposed scheme is composed of three tasks: deployment of sensors, routing and replacement of failed nodes. Simulations results validate the choice of the best cluster based routing protocol which will be executed in the second task of the proposed scheme.

关键词： Monitoring Routing Wireless sensor networks Logic gates Color Clustering algorithms Algorithm design and analysis

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