检索结果-内蒙古大学图书馆

arXiv 2018年

作者： Rule, Adam Birmingham, Amanda Zuniga, Cristal Altintas, Ilkay Huang, Shih-Cheng Knight, Rob Moshiri, Niema Nguyen, Mai H. Rosenthal, Sara Brin Pérez, Fernando Rose, Peter W. Design Lab UC San Diego San DiegoCA United States Center for Computational Biology and Bioinformatics UC San Diego San DiegoCA United States Department of Pediatrics UC San Diego San DiegoCA United States Data Science Hub San Diego Supercomputer Center UC San Diego San DiegoCA United States Departments of Bioengineering and Computer Science and Engineering Center for Microbiome Innovation UC San Diego San DiegoCA United States Bioinformatics and Systems Biology Graduate Program UC San Diego San DiegoCA United States Department of Statistics Berkeley Institute for Data Science UC Berkeley Lawrence Berkeley National Laboratory BerkeleyCA United States Biomedical Informatics Graduate Program Stanford University StanfordCA United States

Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific progress. Since many experimental studies rely on computational analyses, biologists need guidance on how to set up and document reproducible data analyses or simulations. In this paper, we address several questions about reproducibility. For example, what are the technical and non-technical barriers to reproducible computational studies? What opportunities and challenges do computational notebooks offer to overcome some of these barriers? What tools are available and how can they be used effectively? We have developed a set of rules to serve as a guide to scientists with a specific focus on computational notebook systems, such as Jupyter Notebooks, which have become a tool of choice for many applications. Notebooks combine detailed workflows with narrative text and visualization of results. Combined with software repositories and open source licensing, notebooks are powerful tools for transparent, collaborative, reproducible, and reusable data analyses. Copyright © 2018, The Authors. All rights reserved.

关键词： Digital storage

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The repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

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NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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Correction to: Decision Tree Based Classification of Abdominal Aortic Aneurysms Using Geometry Quantification Measures

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Annals of biomedical engineering 2019年第1期47卷 332页

作者： Shalin A Parikh Raymond Gomez Mirunalini Thirugnanasambandam Sathyajeeth S Chauhan Victor De Oliveira Satish C Muluk Mark K Eskandari Ender A Finol UTSA/UTHSA Joint Graduate Program in Biomedical Engineering University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA. Department of Mechanical Engineering University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA. Department of Management Science and Statistics University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA. Department of Thoracic & Cardiovascular Surgery Allegheny Health Network Allegheny General Hospital 320 E. North Ave. Pittsburgh PA 15212 USA. Division of Vascular Surgery and Department of Radiology Northwestern University Feinberg School of Medicine 420 E. Superior St. Chicago IL 60611 USA. UTSA/UTHSA Joint Graduate Program in Biomedical Engineering University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA. ender.finol@utsa.edu. Department of Mechanical Engineering University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA. ender.finol@utsa.edu.

This erratum is to correct the variable name on the left hand side of Eq. (2). The correct variable name is "Diameter" rather than the stated "Area."

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

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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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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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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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