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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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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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Author Correction: Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

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Nature biotechnology 2020年第11期38卷 1356页

作者： Hyun Min Kang Meena Subramaniam Sasha Targ Michelle Nguyen Lenka Maliskova Elizabeth McCarthy Eunice Wan Simon Wong Lauren Byrnes Cristina M Lanata Rachel E Gate Sara Mostafavi Alexander Marson Noah Zaitlen Lindsey A Criswell Chun Jimmie Ye Department of Biostatistics and Center for Statistical Genetics University of Michigan School of Public Health Ann Arbor Michigan USA. hmkang@umich.edu. Biological and Medical Informatics Graduate Program University of California San Francisco San Francisco California USA. Institute for Human Genetics (IHG) University of California San Francisco San Francisco California USA. Institute for Computational Health Sciences University of California San Francisco San Francisco California USA. Department of Epidemiology and Biostatistics University of California San Francisco San Francisco California USA. Department of Bioengineering and Therapeutic Sciences University of California San Francisco San Francisco California USA. Medical Scientist Training Program (MSTP) University of California San Francisco San Francisco California USA. Department of Microbiology and Immunology University of California San Francisco San Francisco California USA. Diabetes Center University of California San Francisco San Francisco California USA. Innovative Genomics Institute University of California Berkeley Berkeley California USA. Department of Neurology University of California San Francisco San Francisco California USA. Developmental and Stem Cell Biology Graduate Program University of California San Francisco San Francisco California USA. Department of Medicine University of California San Francisco San Francisco California USA. Rosalind Russell/Ephraim P Engleman Rheumatology Research Center University of California San Francisco San Francisco California USA. Department of Statistics University of British Columbia Vancouver British Columbia Canada. UCSF Helen Diller Family Comprehensive Cancer Center University of California San Francisco San Francisco California USA. Chan Zuckerberg Biohub San Francisco California USA. Lung Biology Center University of California San Francisco San Francisco California USA. Department of Orofacial Sciences Universi

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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Absence seizure susceptibility correlates with pre-ictal β oscillations

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Journal of Physiology Paris 2016年第4期110卷 372-381页

作者： Sorokin, Jordan M. Paz, Jeanne T. Huguenard, John R. Stanford Neurosciences Graduate Training Program United States Department of Neurology and Neurological Sciences Stanford University School of Medicine Stanford 94305 CA United States Department of Bioengineering Stanford University School of Medicine Stanford 94305 CA United States Gladstone Institutes San Francisco 94158 CA United States

Absence seizures are generalized, cortico-thalamo-cortical (CTC) high power electroencephalographic (EEG) or electrocorticographic (ECoG) events that initiate and terminate suddenly. ECoG recordings of absence seizures in animal models of genetic absence epilepsy show a sudden spike-wave-discharge (SWD) onset that rapidly emerges from normal ECoG activity. However, given that absence seizures occur most often during periods of drowsiness or quiet wakefulness, we wondered whether SWD onset correlates with pre-ictal changes in network activity. To address this, we analyzed ECoG recordings of both spontaneous and induced SWDs in rats with genetic absence epilepsy. We discovered that the duration and intensity of spontaneous SWDs positively correlate with pre-ictal 20–40 Hz (β) spectral power and negatively correlate with 4–7 Hz (Ø) power. In addition, the output of thalamocortical neurons decreases within the same pre-ictal window of time. In separate experiments we found that the propensity for SWD induction was correlated with pre-ictal β power. These results argue that CTC networks undergo a pre-seizure state transition, possibly due to a functional reorganization of cortical microcircuits, which leads to the generation of absence seizures. © 2017 Elsevier Ltd

关键词： Brain-state Epilepsy Networks Oscillations Thalamocortical

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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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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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Dark Excitons: Dark-Exciton-Mediated Fano Resonance from a Single Gold Nanostructure on Monolayer WS2at Room Temperature (Small 31/2019)

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Small 2019年第31期15卷

作者： Mingsong Wang Zilong Wu Alex Krasnok Tianyi Zhang Mingzu Liu He Liu Leonardo Scarabelli Jie Fang Luis M. Liz-Marzán Mauricio Terrones Andrea Alù Yuebing Zheng Department of Mechanical Engineering Texas Materials Institute The University of Texas at Austin Austin TX 78712 USA Photonics Initiative Advanced Science Research Center Physics Program Graduate Center Department of Electrical Engineering City College of the City University of New York New York NY 10031 USA Department of Materials Science and Engineering Department of Physics Department of Chemistry Center for 2-Dimensional and Layered Materials The Pennsylvania State University University Park PA 16802 USA Department of Chemistry and Biochemistry California NanoSystems Institute University of California Los Angeles Los Angeles CA 90095 USA Bionanoplasmonics Laboratory CIC biomaGUNE Paseo de Miramón 182 20014 Donostia-San Sebastián Spain Ikerbasque Basque Foundation for Science 48013 Bilbao Spain Biomedical Research Networking Center in Bioengineering Biomaterials and Nanomedicine CIBER-BBN 20014 Donostia-San Sebastián Spain

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Evaluation of Three Machine Learning Algorithms as Classifiers of Premature Ventricular Contractions on ECG beats.

Evaluation of Three Machine Learning Algorithms as Classifie...

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Global Medical Engineering Physics Exchanges/Pan American Health Care Exchanges Conference

作者： M. M. Casas R. L. Avitia M. A. Reyna A. Cárdenas Bioengineering Graduate Program Autonomous University of Baja California. Mexicali BC Mex Department of Bioengineering and Environmental Health Autonomous University of Baja California Mexicali BC Mex Mathematics and Computer Science Department University of Missouri-St Louis MO USA

ISBN: (纸本)9781509024872

According to the World Health Organization, cardiovascular diseases (CVD) are the main cause of death worldwide. An estimated 17.5 million people died from CVD in 2012, representing 31% of all global deaths. The electrocardiogram (ECG) is a central tool for the pre-diagnosis of heart diseases. Many advances on ECG arrhythmia classification have been developed in the last century;however, there is still research to identify malignant waveforms on ECG beats. The premature ventricular complexes (PVC) are known to be associated with malignant ventricular arrhythmias and in sudden cardiac death (SCD) cases. Detecting this kind of arrhythmia has been crucial in clinical applications. In this work, we extracted 80 different features from 108,653 ECG classified beats of the MIT-BIH database in order to classify the Normal, PVC and other kind of ECG beats. We evaluated three classifier algorithms based on Machine Learning with different parameters and we got a total of 14 models. We used the F1 score and we compared predictive values as a measured of classifier evaluations. Results show that we could have a F1 scores near to the unit, showing the models are higher than 93% of performance.

关键词： Electrocardiogram (ECG) Premature Ventricular Contraction (PVC) Arrhythmia classifier Logistic Regression (LG) Neural Network (NN) Support Vector Machines (SVM)

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Microneedle cuff electrodes for extrafascicular peripheral nerve interfacing

Microneedle cuff electrodes for extrafascicular peripheral n...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Yogi A. Patel Andrew Willsie Isaac P. Clements Ricardo Aguilar Swaminathan Rajaraman Robert J. Butera Bioengineering Graduate Program Georgia Institute of Technology Atlanta GA USA Axion BioSystems Atlanta GA USA Department of Biomedical Engineering Georgia Institute of Technology Atlanta GA USA

Objective. The work presented here describes a new tool for peripheral nerve interfacing, called the microneedle cuff (μN-cuff) electrode. Approach. μN arrays are designed and integrated into cuff electrodes for penetrating superficial tissues while remaining non-invasive to delicate axonal tracts. Main results. In acute testing, the presence of 75 μm height μNs decreased the electrode-tissue interface impedance by 0.34 kΩ, resulting in a 0.9 mA reduction in functional stimulation thresholds and increased the signal-to-noise ratio by 9.1 dB compared to standard (needle-less) nerve cuff electrodes. Preliminary acute characterization suggests that μN-cuff electrodes provide the stability and ease of use of standard cuff electrodes while enhancing electrical interfacing characteristics. Significance. The ability to stimulate, block, and record peripheral nerve activity with greater specificity, resolution, and fidelity can enable more precise spatiotemporal control and measurement of neural circuits.

关键词： Electrodes Standards Impedance Signal to noise ratio Force Impedance measurement Rats

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A novel method to assess angle sensor performance for wearable exoskeletal joint kinematics

A novel method to assess angle sensor performance for wearab...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Nicholas B. Bolus Géza F. Kogler Omer T. Inan Bioengineering Graduate Research Program at the Georgia Institute of Technology Atlanta GA School of Applied Physiology at the Georgia Institute of Technology Atlanta GA School of Electrical and Computer Engineering at the Georgia Institute of Technology Atlanta GA

Full range of motion (ROM) at a joint is necessary for efficient and adaptive movement; as such, it is an essential clinical evaluation measure for assessing an individual's motor function, which can be affected by any number of musculoskeletal injuries and neuropathies. Measurement of joint ROM in the clinic has classically been accomplished statically through the use of a manual goniometer. More recent efforts in the fields of prosthetics and orthotics have demonstrated the potential utility of wearable systems (e.g., exoskeletons, orthoses) designed to control joint motion(s) and instrumented with sensors capable of capturing joint angle data dynamically. This paper presents a novel methodology to assess the performance of a variety of angle sensors in the context of wearable joint angle measurement, particularly for use in articulated ankle-foot orthoses (AFOs). Dynamic and static errors are considered, and a cost-benefit analysis of a variety of off-the-shelf and custom-built sensors is reported to provide comparative data for selecting a sensor to measure joint motion in wearable exoskeletal systems. All of the sensors considered reported angular errors below 5° across all tests, though the optical encoder consistently demonstrated the highest accuracy (

关键词： Optical sensors Potentiometers Adaptive optics Robot sensing systems Legged locomotion Magnetic hysteresis

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