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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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Cover Feature: Gas-Phase Transformation of Fluorinated Benzoporphyrins to Porphyrin-Embedded Conical Nanocarbons (Chem. Eur. J. 53/2020)

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Chemistry – A European Journal 2020年第53期26卷 12083-12083页

作者： Dr. Dominik Lungerich Dr. Jakob Felix Hitzenberger Michael Ruppel Dr. Tibor Döpper Dr. Matthias Witt Prof. Dr. Ivana Ivanović-Burmazović Prof. Dr. Andreas Görling Prof. Dr. Norbert Jux Prof. Dr. Thomas Drewello Department of Chemistry and Pharmacy & Interdisciplinary Center for Molecular Materials (ICMM) Organic Chemistry II Friedrich-Alexander-University Erlangen-Nuernberg Nikolaus-Fiebiger-Str. 10 91058 Erlangen Germany Center for Nanomedicine Institute for Basic Science (IBS) Seoul 03722 Republic of Korea Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul 03722 Republic of Korea Department of Chemistry and Pharmacy Physical Chemistry I Friedrich-Alexander-University Erlangen-Nuernberg Egerlandstrasse 3 91058 Erlangen Germany Department of Chemistry and Pharmacy Theoretical Chemistry Friedrich-Alexander-University Erlangen-Nuernberg Egerlandstrasse 3 91058 Erlangen Germany Bruker Daltonics GmbH Fahrenheitstrasse 4 28359 Bremen Germany Department of Chemistry and Pharmacy Bioinorganic Chemistry Friedrich-Alexander-University Erlangen-Nuernberg Egerlandstrasse 1 91058 Erlangen Germany

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Dark-Exciton-Mediated Fano Resonance from a Single Gold Nanostructure Deposited on Monolayer WS2 at Room Temperature

arXiv

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arXiv 2018年

作者： Wang, Mingsong Wu, Zilong Krasnok, Alex Zhang, Tianyi Liu, Mingzu Liu, He Scarabelli, Leonardo Fang, Jie Liz-Marzán, Luis M. Terrones, Mauricio Alù, Andrea Zheng, Yuebing Department of Mechanical Engineering Materials Science and Engineering Program Texas Materials Institute University of Texas at Austin AustinTX78712 United States Photonics Initiative Advanced Science Research Center Physics Program Graduate Center Department of Electrical Engineering City College of The City University of New York NY10031 United States Department of Materials Science and Engineering Department of Physics Center for 2-Dimensional and Layered Materials Department of Chemistry Pennsylvania State University Pennsylvania State University University ParkPA16802 United States Department of Chemistry and Biochemistry California NanoSystems Institute University of California Los Angeles Los AngelesCA90095 United States Bionanoplasmonics Laboratory CIC biomaGUNE Paseo de Miramón 182 Donostia-San Sebastián20014 Spain Ikerbasque Basque Foundation for Science Bilbao48013 Spain Biomedical Research Networking Center in Bioengineering Biomaterials and Nanomedicine CIBER-BBN Donostia- San Sebastián20014 Spain

Strong spatial confinement and highly reduced dielectric screening provide monolayer transition metal dichalcogenides (TMDCs) with strong many-body effects, thereby possessing optically forbidden excitonic states (i.e., dark excitons) at room temperature. Herein, we explore the interaction of surface plasmons with dark excitons in hybrid systems consisting of stacked gold nanotriangles (AuNTs) and monolayer WS2. We observe a narrow Fano resonance when the hybrid system is surrounded by water, and we attribute the narrowing of the spectral Fano linewidth to the plasmon-enhanced decay of dark K-K excitons. Our results reveal that dark excitons in monolayer WS2 can strongly modify Fano resonances in hybrid plasmon-exciton systems and can be harnessed for novel optical sensors and active nanophotonic devices. Copyright © 2018, The Authors. All rights reserved.

关键词： Gold nanoparticles

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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Enhancing cell infiltration of electrospun fibrous scaffolds in tissue regeneration

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Bioactive Materials 2016年第1期1卷 56-64页

作者： Jinglei Wu Yi Hong Department of Bioengineering University of Texas at ArlingtonArlingtonTX 76019USA Joint Graduate Program in Biomedical Engineering University of Texas Southwestern Medical CenterDallasTX 75390USA

Electrospinning is one of the most effective approaches to fabricate tissue-engineered scaffolds composed of nano-to sub-microscale fibers that simulate a native extracellular ***,one major concern about electrospun scaffolds for tissue repair and regeneration is that their small pores defined by densely compacted fibers markedly hinder cell infiltration and tissue *** address this problem,researchers have developed and investigated various methods of manipulating scaffold structures to increase pore size or loosen the *** methods involve the use of physical treatments,such as salt leaching,gas foaming and custom-made collectors,and combined techniques to obtain electrospun scaffolds with loose fibrous structures and large *** article provides a summary of these motivating electrospinning techniques to enhance cell infiltration of electrospun scaffolds,which may inspire new electrospinning techniques and their new biomedical applications.

关键词： Electrospinning Scaffolds Porosity control Cell infiltration Tissue regeneration

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Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales

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Drug Discovery Today: Disease Models 2018年 28卷 105-115页

作者： Williams, Candace L. Caraballo-Rodríguez, Andrés Mauricio Allaband, Celeste Zarrinpar, Amir Knight, Rob Gauglitz, Julia M. Institute for Conservation Research San Diego Zoo Global United States Collaborative Mass Spectrometry Innovation Center Skaggs School of Pharmacy and Pharmaceutical Sciences University of California La Jolla San Diego 92307 CA United States Biomedical Sciences Graduate Program University of California La Jolla San Diego 92307 CA United States Department of Medicine University of California La Jolla San Diego 92307 CA United States Veterans Affairs San Diego Healthcare System San Diego California University of California La Jolla San Diego 92307 CA United States Department of Pediatrics University of California La Jolla San Diego 92037 CA United States Department of Bioengineering University of California La Jolla San Diego 92093 CA United States Department of Computer Science and Engineering University of California La Jolla San Diego 92093 CA United States Center for Microbiome Innovation University of California La Jolla San Diego 92307 CA United States

Captive wildlife are a unique set of animals, whose diverse host–microbe symbioses are underexplored. Compared to their wild counterparts they are particularly susceptible to a variety of diseases, many of which have explicit or purported links to the microbiome. In this perspective, we will examine how the microbiome influences gastrointestinal disorders, metabolic dysregulation, reproduction, and disease susceptibility in captive wildlife. Investigation of wildlife, and specifically captive wildlife, affords a unique opportunity to gain understanding of the broad diversity of the associated microbiota and learn from nature's molecular and microbial responses to disease. Studies like these could lead to the discovery of new interventions, ranging from dietary changes to the use of microbes or their natural products as treatment. Intervention strategies can lead to the discovery of medically relevant small molecules and the development of a novel platform for N-of-1 targeted medical investigations. © 2019 Elsevier Ltd

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The role of traction in membrane curvature generation

arXiv

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arXiv 2017年

作者： Alimohamadi, Haleh Vasan, Ritvik Hassinger, Julian E. Stachowiak, Jeanne C. Rangamani, Padmini Department of Mechanical and Aerospace Engineering University of California San Diego San DiegoCA92093 United States Biophysics Graduate Program University of California BerkeleyCA94720 United States Department of Biomedical Engineering University of Texas at Austin AustinTX78712 United States

Curvature in biological membranes can be generated by a variety of different molecular mechanisms such as protein scaffolding, lipid or protein asymmetry, cytoskeletal forces, etc. These mechanisms have the net effect of generating stresses on the bilayer that are translated into distinct final shapes of the membrane. We propose reversing this input-output relationship by using the shape of a curved membrane to infer physical quantities like the magnitude of the applied forces acting on the bilayer. To do this, we calculate the normal and tangential tractions along the membrane using the known material properties of the membrane along with its shape. These tractions are a quantitative measure of the response of the membrane to external forces or sources of spontaneous curvature. We demonstrate the utility of this approach first by showing that the magnitude of applied force can be inferred from the shape of the membrane alone in both simulations and experiments of membrane tubulation. Next, we show that membrane budding by local differences in spontaneous curvature is driven purely by the generation of traction in the radial direction and the emergence of an effective line tension at the boundary of these regions. Finally, we show that performing this calculation on images of phase-separated giant vesicles yields a line tension similar to experimentally determined values. Copyright © 2017, The Authors. All rights reserved.

关键词： Lipid bilayers

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Genetic drivers of heterogeneity in type 2 diabetes pathophysiology

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Nature 2024年第8003期627卷 347-357页

作者： Ken Suzuki Konstantinos Hatzikotoulas Lorraine Southam Henry J Taylor Xianyong Yin Kim M Lorenz Ravi Mandla Alicia Huerta-Chagoya Giorgio E M Melloni Stavroula Kanoni Nigel W Rayner Ozvan Bocher Ana Luiza Arruda Kyuto Sonehara Shinichi Namba Simon S K Lee Michael H Preuss Lauren E Petty Philip Schroeder Brett Vanderwerff Mart Kals Fiona Bragg Kuang Lin Xiuqing Guo Weihua Zhang Jie Yao Young Jin Kim Mariaelisa Graff Fumihiko Takeuchi Jana Nano Amel Lamri Masahiro Nakatochi Sanghoon Moon Robert A Scott James P Cook Jung-Jin Lee Ian Pan Daniel Taliun Esteban J Parra Jin-Fang Chai Lawrence F Bielak Yasuharu Tabara Yang Hai Gudmar Thorleifsson Niels Grarup Tamar Sofer Matthias Wuttke Chloé Sarnowski Christian Gieger Darryl Nousome Stella Trompet Soo-Heon Kwak Jirong Long Meng Sun Lin Tong Wei-Min Chen Suraj S Nongmaithem Raymond Noordam Victor J Y Lim Claudia H T Tam Yoonjung Yoonie Joo Chien-Hsiun Chen Laura M Raffield Bram Peter Prins Aude Nicolas Lisa R Yanek Guanjie Chen Jennifer A Brody Edmond Kabagambe Ping An Anny H Xiang Hyeok Sun Choi Brian E Cade Jingyi Tan K Alaine Broadaway Alice Williamson Zoha Kamali Jinrui Cui Manonanthini Thangam Linda S Adair Adebowale Adeyemo Carlos A Aguilar-Salinas Tarunveer S Ahluwalia Sonia S Anand Alain Bertoni Jette Bork-Jensen Ivan Brandslund Thomas A Buchanan Charles F Burant Adam S Butterworth Mickaël Canouil Juliana C N Chan Li-Ching Chang Miao-Li Chee Ji Chen Shyh-Huei Chen Yuan-Tsong Chen Zhengming Chen Lee-Ming Chuang Mary Cushman John Danesh Swapan K Das H Janaka de Silva George Dedoussis Latchezar Dimitrov Ayo P Doumatey Shufa Du Qing Duan Kai-Uwe Eckardt Leslie S Emery Daniel S Evans Michele K Evans Krista Fischer James S Floyd Ian Ford Oscar H Franco Timothy M Frayling Barry I Freedman Pauline Genter Hertzel C Gerstein Vilmantas Giedraitis Clicerio González-Villalpando Maria Elena González-Villalpando Penny Gordon-Larsen Myron Gross Lindsay A Guare Sophie Hackinger Liisa Hakaste Sohee Han Andrew T Hattersley Christian Herder Momoko Horikoshi Annie-Green Howard Willa Centre for Genetics and Genomics Versus Arthritis Centre for Musculoskeletal Research Division of Musculoskeletal and Dermatological Sciences University of Manchester Manchester UK. Department of Diabetes and Metabolic Diseases Graduate School of Medicine University of Tokyo Tokyo Japan. Department of Statistical Genetics Osaka University Graduate School of Medicine Suita Japan. Institute of Translational Genomics Helmholtz Zentrum München German Research Center for Environmental Health Neuherberg Germany. konstantinos.hatzikotoulas@helmholtz-munich.de. Institute of Translational Genomics Helmholtz Zentrum München German Research Center for Environmental Health Neuherberg Germany. Center for Precision Health Research National Human Genome Research Institute National Institutes of Health Bethesda MD USA. British Heart Foundation Cardiovascular Epidemiology Unit Department of Public Health and Primary Care University of Cambridge Cambridge UK. Heart and Lung Research Institute University of Cambridge Cambridge UK. Department of Epidemiology School of Public Health Nanjing Medical University Nanjing China. Department of Biostatistics and Center for Statistical Genetics University of Michigan Ann Arbor MI USA. Corporal Michael J. Crescenz VA Medical Center Philadelphia PA USA. Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania Perelman School of Medicine Philadelphia PA USA. Department of Genetics University of Pennsylvania Perelman School of Medicine Philadelphia PA USA. Programs in Metabolism and Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA. Diabetes Unit and Center for Genomic Medicine Massachusetts General Hospital Boston MA USA. TIMI Study Group Division of Cardiovascular Medicine Brigham and Women's Hospital Harvard Medical School Boston MA USA. William Harvey Research Institute Barts and the London School of Medicine and Dentistry Queen Mary University of London L

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes and molecular mechanisms that are often specific to cell type. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P < 5 × 10) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.

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Author Correction: Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes

Nature cancer

引用

Nature cancer 2023年 2023 May 19页

作者： Do Young Hyeon Dowoon Nam Youngmin Han Duk Ki Kim Gibeom Kim Daeun Kim Jingi Bae Seunghoon Back Dong-Gi Mun Inamul Hasan Madar Hangyeore Lee Su-Jin Kim Hokeun Kim Sangyeop Hyun Chang Rok Kim Seon Ah Choi Yong Ryoul Kim Juhee Jeong Suwan Jeon Yeon Woong Choo Kyung Bun Lee Wooil Kwon Seunghyuk Choi Taewan Goo Taesung Park Young-Ah Suh Hongbeom Kim Ja-Lok Ku Min-Sik Kim Eunok Paek Daechan Park Keehoon Jung Sung Hee Baek Jin-Young Jang Daehee Hwang Sang-Won Lee School of Biological Sciences Seoul National University Seoul Republic of Korea. Department of Chemistry and Center for Proteogenome Research Korea University Seoul Republic of Korea. Department of Surgery and Cancer Research Institute Seoul National University College of Medicine Seoul Republic of Korea. Department of Anatomy and Cell Biology and Department of Biomedical Sciences Seoul National University College of Medicine Seoul Republic of Korea. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology (KAIST) Seoul Republic of Korea. Creative Research Initiatives Center for Epigenetic Code and Diseases Seoul National University Seoul Republic of Korea. Department of Biological Sciences College of Natural Sciences and Department of Molecular Science and Technology Ajou University Suwon Republic of Korea. Department of Pathology Seoul National University College of Medicine Seoul Korea. Department of Computer Science Hanyang University Seoul Republic of Korea. Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. Department of Statistics Seoul National University Seoul Republic of Korea. Korean Cell Line Bank Laboratory of Cell Biology Cancer Research Institute Seoul National University College of Medicine Seoul Korea. Department of New Biology Daegu Gyeongbuk Institute of Science and Technology Daegu Republic of Korea. Department of Biological Sciences College of Natural Sciences and Department of Molecular Science and Technology Ajou University Suwon Republic of Korea. dpark@ajou.ac.kr. Department of Anatomy and Cell Biology and Department of Biomedical Sciences Seoul National University College of Medicine Seoul Republic of Korea. keehoon.jung@snu.ac.kr. Institute of Allergy and Clinical Immunology Seoul National University Medical Research Center Seoul Republic of Korea. keehoon.jung@snu.ac.kr. School of Biological Sciences Seoul National University Seoul Republic of

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Cover Image

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Developmental Neurobiology 2018年第7期78卷

作者： Irene Cheng Lucy Jin Lucy C. Rose Christopher D. Deppmann Department of Biology University of Virginia Charlottesville Virginia 22903 Neuroscience Graduate Program University of Virginia Charlottesville Virginia 22903 Department of Cell Biology University of Virginia Charlottesville Virginia 22903 Department of Biomedical Engineering University of Virginia Charlottesville Virginia 22903

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