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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College 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 Ne

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Analysis of hierarchical organization in gene expression networks reveals underlying principles of collective tumor cell dissemination and metastatic aggressiveness of inflammatory breast cancer

arXiv

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arXiv 2017年

作者： Tripathi, Shubham Jolly, Mohit Kumar Woodward, Wendy A. Levine, Herbert Deem, Michael W. PhD Program in Systems Synthetic and Physical Biology Rice University HoustonTX77005 United States Center for Theoretical Biological Physics Rice University HoustonTX77005 United States Department of Radiation Oncology University of Texas MD Anderson Cancer Center HoustonTX77030 United States MD Anderson Morgan Welch Inflammatory Breast Cancer Research Program and Clinic University of Texas MD Anderson Cancer Center HoustonTX77030 United States Department of Bioengineering Rice University HoustonTX77005 United States Department of Physics and Astronomy Rice University HoustonTX77005 United States

Background: Clusters of circulating tumor cells (CTCs), despite being rare, may account for more than 95% of metastases. Cells in these clusters do not undergo a complete epithelial-to-mesenchymal transition (EMT) but retain some epithelial traits as compared to individually disseminating tumor cells. Determinants of single cell dissemination versus collective dissemination remain elusive. Inflammatory breast cancer (IBC), a highly aggressive breast cancer subtype that chiefly metastasizes via CTC clusters, is a promising model for studying mechanisms of collective tumor cell dissemination. Previous studies on breast cancer and adult acute myeloid leukemia, motivated by a theory that suggests physical systems with hierarchical organization tend to be more adaptable, have found that the expression of metastasis associated genes is more hierarchically organized in cases of successful metastases. Methods: We used the cophenetic correlation coefficient (CCC) to quantify the hierarchical organization in the expression networks of two distinct gene sets, collective dissemination associated genes and IBC associated genes, in cancer cell lines and in tumor samples from breast cancer patients. Hypothesizing that a higher CCC for collective dissemination associated genes and for IBC associated genes would be associated with a more evident epithelial phenotype and with worse outcomes in breast cancer patients, we evaluated the correlation of CCC with different phenotypic groups. Results: The CCC of both gene networks, the collective dissemination associated gene network and the IBC associated gene network, was higher in (a) epithelial cell lines as compared to mesenchymal cell lines and (b) tumor samples from IBC patients, as compared to samples from non-IBC breast cancer patients. A higher CCC of both networks was also correlated with a higher rate of metastatic relapse in breast cancer patients. Neither the levels of CDH1 gene expression, nor gene set enrichment analysis cou

关键词： Pathology

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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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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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Author Correction: Aplp1 interacts with Lag3 to facilitate transmission of pathologic α-synuclein

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Nature communications 2024年第1期15卷 6413页

作者： Xiaobo Mao Hao Gu Donghoon Kim Yasuyoshi Kimura Ning Wang Enquan Xu Ramhari Kumbhar Xiaotian Ming Haibo Wang Chan Chen Shengnan Zhang Chunyu Jia Yuqing Liu Hetao Bian Senthilkumar S Karuppagounder Fatih Akkentli Qi Chen Longgang Jia Heehong Hwang Su Hyun Lee Xiyu Ke Michael Chang Amanda Li Jun Yang Cyrus Rastegar Manjari Sriparna Preston Ge Saurav Brahmachari Sangjune Kim Shu Zhang Yasushi Shimoda Martina Saar Haiqing Liu Sin Ho Kweon Mingyao Ying Creg J Workman Dario A A Vignali Ulrike C Muller Cong Liu Han Seok Ko Valina L Dawson Ted M Dawson Neuroregeneration and Stem Cell Programs Institute for Cell Engineering Johns Hopkins University School of Medicine Baltimore MD 21205 USA. xmao4@jhmi.edu. Department of Neurology Johns Hopkins University School of Medicine Baltimore MD 21205 USA. xmao4@jhmi.edu. Adrienne Helis Malvin Medical Research Foundation New Orleans LA 70130-2685 USA. xmao4@jhmi.edu. Neuroregeneration and Stem Cell Programs Institute for Cell Engineering Johns Hopkins University School of Medicine Baltimore MD 21205 USA. Department of Neurology Johns Hopkins University School of Medicine Baltimore MD 21205 USA. Department of Neurology Nanjing Brain Hospital Nanjing Jiangsu 210029 PR China. Medical College Yangzhou University Yangzhou Jiangsu 225001 PR China. Department of Pharmacology College of Medicine Dong-A University 32 Daesin Gongwwon-ro Seo-gu Busan 49201 Republic of Korea. Adrienne Helis Malvin Medical Research Foundation New Orleans LA 70130-2685 USA. Department of Anesthesiology West China Hospital Sichuan University. The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences West China Hospital Sichuan University Chengdu Sichuan 610041 PR China. Interdisciplinary Research Center on Biology and Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences 26 Qiuyue Road Shanghai 201210 China. University of the Chinese Academy of Sciences 19 A Yuquan Road Shijingshan District Beijing 100049 China. Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA. Department of Materials Science and Engineering Whiting School of Engineering Johns Hopkins University Baltimore MD 21218 USA. Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA. Picower Institute for Learning and Memory Cambridge MA 02139 USA. Harvard-MIT MD/PhD Program Harvard Medical School Boston MA 02115 USA. Department of Biological Science and Biotechnology Chungbuk Nati

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Triaxial MMG investigation during FES-induced cycle movements

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Journal of Physics: Conference Series 2016年第1期705卷

作者： M C Gelain G N Nogueira-Neto P Nohama P M Gewehr Master's student of Electrical Engineering and Industrial Informatics at UTFPR (Rehabilitation engineering laboratory phone: +55 (41) 3310-4489) Brazil PhD in Biomedical Engineering researcher and professor of Computer Engineering at Pontifícia Universidade Católica do Paraná (PUCPR) Brazil PhD in Biomedical Engineering researcher and full professor at the PPGTS stricto sensu program at Pontifícia Universidade Católica do Paraná (PUCPR) Brazil PhD in Medical Physics Bioengineering and professor of Biomedical engineering at UTFPR Brazil

Spinal cord injury is damage to the spinal cord that results in loss of functions, causes muscle, joint and bone deficits, moreover it increases the muscle tone level. FEScycling is an alternative rehabilitation process to conserve the musculoskeletal system affected by the injury in the functional state. The aim of this study is to get the legs bilaterally synchronized by FES and compare MMG signal responses. The preliminary protocol consists of five consecutive contractions. The first and the last contractions were discarded and the three intermediate contractions were analyzed. A ratio between MMG values of muscle responses during propulsion and return of pedalling phases was calculated for each cycle and each leg. The applied FES profile consisted of pulse and burst on time of 250 us and 5 ms and frequencies of 1000 Hz and 20 Hz, respectively. Results showed that greater MMG RMS values tend to occur during the propulsion phase than in the return phase. MMG Z axis of RLL and MMG X axis of LLL were the axes that presented the greatest ratios. The MMG RMS signal showed that greater values tend to occur during the propulsion phase than in the return phase of the same thigh.

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Direct detection of adenovirus in environmental waste waters by portable optical fiber sensor platform

Direct detection of adenovirus in environmental waste waters...

引用

12th IEEE SENSORS 2013 Conference

作者： Yildirim, Nimet Li, Dan Long, Feng Gu, April Z. Bioengineering PhD Program Northeastern University Boston United States Department of Civil and Environmental Engineering Northeastern University Boston United States State Key Joint Laboratory of Environment Simulation and Pollution Control Environmental Science and Engineering Tsinghua University Beijing China Department of Environment Science and Engineering Tsinghua University Beijing China 360 Huntington Ave. Boston MA 02115 United States

ISBN: (纸本)9781467346405

Reusable and portable evanescent wave biosensor for rapid, sensitive and highly selective direct detection of adenoviruses was developed. Here, specific antibody for the hexon protein of the virus was used as a recognition element. Linear detection range was determined from 100PFU/ml to 2000PFU/ml. This direct detection system can be regenerated successfully with over 5 times without significant deterioration of the sensor performance. The developed biosensor system has high specificity towards adenovirus, and it was applied to environmental waste water samples for the detection of adenovirus with 95 to 117% recovery and 1.1 to 8.1% cv values (n=2). © 2013 IEEE.

关键词： Optical fibers

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26th Annual Computational Neuroscience Meeting (CNS*2017) of the Organization for Computational Neuroscience Antwerp, Belgium, July 15-20, 2017

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 59-59页

作者： [Anonymous] Indiana University Purdue University Indianapolis Indianapolis IN 46032 USA Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis IN 46032 USA Department of Mathematics East Carolina University Greenville NC 27858 USA Jülich Supercomputing Centre Forschungszentrum Jülich 52425 Jülich Germany Future Systems Swiss National Supercomputing Centre 8092 Zurich Switzerland User Engagement and Support Swiss National Supercomputing Centre 6900 Lugano Switzerland Institut de Neurosciences des Systèmes Aix Marseille Univ 13005 Marseille France Simulation Lab Neuroscience Forschungszentrum Jülich Jülich Germany Department of Experimental Psychology Ghent University 9000 Ghent Belgium Donders Center for Cognitive Neuroimaging Radboud University 6525HR Nijmegen The Netherlands Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO 80309 USA Department of Neurosurgery Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Neurology Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Otolaryngology Johns Hopkins School of Medicine Baltimore MD 21287 USA INSERM U968 Paris France Sorbonne Universités UPMC University Paris 06 UMR_S 968 Institut de la Vision Paris France CNRS UMR_7210 Paris France Department of Computer Architecture and Technology University of Granada (CITIC) Granada Spain Sorbonne Universités UPMC Univ Paris 06 INSERM CNRS Institut de la Vision Paris France Department of Adaptive Machine Systems Osaka University Osaka Japan Department of Computer Science University of Cergy-Pontoise Cergy-Pontoise France Department of Physics and Astronomy College of Charleston Charleston SC 29424 USA School of Physics Faculty of Science University of Sydney Sydney NSW 2006 Australia Center of Excellence for Integrative Brain Function Australian Research Council Sydney Australia Max Planck Institute for Human Cognitive and Brain Sciences Saxony Lei

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Erratum to “Detergent-Enzymatic Decellularization of Swine Blood Vessels: Insight on Mechanical Properties for Vascular Tissue Engineering”

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BioMed Research International 2014年第1期2014卷 412838-412838页

作者： Alessandro F. Pellegata M. Adelaide Asnaghi Ilaria Stefani Anna Maestroni Silvia Maestroni Tommaso Dominioni Sandro Zonta Gianpaolo Zerbini Sara Mantero Department of Chemistry Materials and Chemical Engineering “Giulio Natta” Politecnico di Milano Piazza Leonardo da Vinci 32 20133 Milano Italypolimi.it PhD Program in Bioengineering Politecnico di Milano Piazza Leonardo da Vinci 32 20133 Milano Italypolimi.it Complication of Diabetes Unit Division of Metabolic and Cardiovascular Sciences San Raffaele Scientific Institute Milan Italyunisr.it General Surgery I Fondazione IRCCS Pol. San Matteo Pavia ***

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Direct Detection of Adenovirus in Environmental Waste Waters by Portable Optical Fiber Sensor Platform

Direct Detection of Adenovirus in Environmental Waste Waters...

引用

IEEE Sensors

作者： Nimet Yildirim Dan Li Feng Long April Z. Gu Bioengineering PhD Program Northeastern University Boston US State Key Joint Laboratory of Environment Simulation and Pollution Control Environmental Science and Engineering Tsinghua University Beijing China Department of Environment Science and Engineering Tsinghua University Beijing China Department of Civil and Environmental Engineering Northeastern University Boston US

ISBN: (纸本)9781467346412

关键词： ADENOVIRUS DETECTION DIRECT

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