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

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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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Long-Term Survival in Myelofibrosis after Allogeneic Hematopoietic Cell Transplantation Using Fludarabine/Melphalan Conditioning Regimen

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BLOOD 2017年第Sup1期130卷 199-199页

作者： Ali, Haris Aldoss, Ibrahim Yang, Dongyun Afkhami, Michelle Al Malki, Monzr M. Cao, Thai Forman, Stephen J. Marcucci, Guido Mei, Matthew Nakamura, Mokhtari Ryotaro O'Donnell, Margaret Pillai, Raju Pullarkat, Vinod Salhotra, Amandeep Stein, Anthony S. Snyder, David S. Department of Hematology/HCT City of Hope Medical Center Duarte CA Department of Hematology/HCT City of Hope Duarte CA Department of Information Sciences-BRI City of Hope National Medical Center Duarte CA Department of Pathology City of Hope National Medical Center Duarte CA Department of Hematology/HCT City of Hope National Medical Center Duarte CA Division of Hematopoietic Stem Cell and Leukemia Research Gehr Family Center for Leukemia Research Beckman Research Institute at City of Hope Duarte CA Department of Clinical Translational Program Development City of Hope National Medical Center Duarte CA Department of Hematologic Malignancies Translational Science Gehr Family Center for Leukemia Research Beckman Research Institute. City of Hope National Medical Center Duarte CA Gehr Family Center for Leukemia Research City of Hope Duarte CA

Allogeneic hematopoietic cell transplantation (AlloHCT) is the only curative approach for myelofibrosis (MF). However the significant risk of morbidity and mortality associated with this treatment necessitate careful patient selection and intense peri-transplant management. Here we report on the clinical outcome of a large cohort of MF patients who underwent alloHCT with fludarabine/melphalan (FluMel) condition regimen at City of Hope (COH).A total of 110 consecutive patients with MF (primary MF: n=58, secondary MF: n=52) without prior acute leukemic transformation, underwent allo-HCT between 2004 and 2017 at COH. Median age at the time of transplant was 58.5 years (range: 38-72 years) with median interval from diagnosis of primary or secondary MF to HCT of 15.2 months (range: 1.6-332.5 months). A majority of patients (n=107) received peripheral blood stem cells and 3 were transplanted with bone marrow as stem cell source. AlloHCT donors were matched related (MRD: n=49), matched unrelated (MUD: n=32), mismatched unrelated (MMUD: n=27), mismatched relative (n=1), or haploidentical family (n=1). Dynamic international prognostic scoring system (DIPSS) score at the time of alloHCT was Intermediate-2 or high risk in 83 patients (76%). All patients received FluMel conditioning. Graft-versus-host disease (GVHD) prophylaxis was predominantly sirolimus/tacrolimus-based regimen, n=100 (91%). Of the 110 patients, 16 had splenectomy prior to alloHCT. Cytogenetics information was available for 104 out of 110 patients; among which, 60 patients had abnormal cytogenetics including but not limited to deletion 20q, trisomy 8 and trisomy *** but 2 patients were engrafted. After median follow-up of 56.8 months (range: 1.3-158.5 months) in surviving patients, 2- and 5-years overall survival (OS) were 74% (95% CI: 65-82%) and 65% (95% CI:54-73%), respectively (figure 1a.); 100 days, 2- and 5-years non-relapse mortality (NRM) were 12% (95%CI: 0.06-0.18), 18% (95% CI: 11-26%) and 24% (95

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A synthetic biological secondary metabolite,Lycogen^TM,produced and extracted from Rhodobacter sphaeroides WL-APD911 in an optimizatioal scale-up strategy

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Food Science and Human Wellness 2017年第4期6卷 195-201页

作者： Cheng-Chin Wang Shi-Ying Huang Shu-Hung Huang Zhi-Hong Wen Jyun-Ying Huang Wen-Sheng Liu Hui-Min David Wang Research and Development Department Chia-Yi SteelTainan 717TaiwanChina College of Oceanology and Food Science Quanzhou Normal UniversityQuanzhou 362000China Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae Quanzhou 362000China Division of Plastic Surgery Department of SurgeryKaohsiung Medical University HospitalKaohsiung Medical UniversityKaohsiung 807TaiwanChina Graduate Institute of Medicine College of MedicineKaohsiung Medical UniversityKaohsiung 807TaiwanChina Center for Stem Cell Research Kaohsiung Medical UniversityKaohsiung 807TaiwanChina Department of Surgery Faculty of MedicineCollege of MedicineKaohsiung Medical UniversityKaohsiung 807TaiwanChina Orthopaedic Research Center Kaohsiung Medical UniversityKaohsiung 807TaiwanChina Doctoral Degree Program in Marine Biotechnology National Sun Yat-sen University and Academia SinicaKaohsiung 804TaiwanChina Marine Biomedical Laboratory and Center for Translational Biopharmaceuticals Department of Marine Biotechnology and ResourcesNational Sun Yat-sen UniversityKaohsiung 804TaiwanChina Graduate Institute of Biomedical Engineering National Chung Hsing UniversityTaichung 402TaiwanChina Department and Graduate Institute of Aquaculture National Kaohsiung Marine UniversityKaohsiung 811TaiwanChina Asia-Pacific Biotech Developing Inc.Kaohsiung 803TaiwanChina Department of Medical Research China Medical University HospitalChina Medical UniversityTaichung 404TaiwanChina

The optimization of fermentation medium is important for synthetic biological secondary metabolite *** effect of rotation speed,inoculum amount,and medium supplements on the cell growth and Lycogen^TM secretion of photobacterium Rhodobacter sphaeroides WL-APD911 was *** results reveal that a higher rotational speed exhibit a higher cell density,and the increasing in the amount of inoculum amount show a slight augment on the growth of *** *** the case of nitrogen sources adding,Lycogen^TM production was achieved with a 0.5 mM l-lysine ***,the attention of Tween 80 presented a tremendous increase in the secondary *** surface methodology(RSM)exhibited the optimization of medium supplements for Lycogen^TM invention is accomplished at molasses concentration of 10 g/L,yeast extract concentration of 40 g/L,0.3%Tween 80 and NaCl concentration of 5 g/L,***,the batch fermentation is carried out in both 5 L and 20 L fermentors to study the scale-up process factors to be *** a 20 L fermentor,Lycogen^TM yields under the optimal culture condition are over 2 times than in the shake *** present results provide the Lycogen^TM optimal culture mediums,scale-up procedures and efficient extractions from *** WL-APD911.

关键词： Rhodobacter sphaeroides WL-APD911 Lycogen^TM Response surface methodology(RSM) Ferementation

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Cover Image, Volume 6, Issue 4

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WIREs developmental Biology 2017年第4期6卷

作者： Hirotaka Tao Yasuhiko Kawakami Chi-chung Hui Sevan Hopyan Program in Developmental and Stem Cell Biology Research Institute The Hospital for Sick Children Toronto Canada Department of Genetics Cell Biology and Development Stem Cell Institute University of Minnesota Minneapolis MN USA Department of Molecular Genetics University of Toronto Toronto Canada Division of Orthopaedic Surgery Hospital for Sick Children and University of Toronto Toronto Canada

The cover image, by Hirotaka Tao et al., is based on the Advanced Review The two domain hypothesis of limb prepattern and its relevance to congenital limb anomalies , DOI: 10.1002/wdev.270 .

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Using robotics as the technological foundation for the TPACK framework in K-12 classrooms 122

Using robotics as the technological foundation for the TPACK...

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2015 122nd ASEE Annual Conference and Exposition

作者： Brill, Anthony Steven Listman, Jennifer B. Kapila, Vikram NYU Polytechnic School of Engineering Program Development and Evaluation Center for K12 STEM Education United States

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From Dissemination to Propagation: A New Paradigm for Education Developers

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Change 2017年第4期49卷 35-42页

作者： Froyd, Jeffrey E. Henderson, Charles Cole, Renée S. Friedrichsen, Debra Khatri, Raina Stanford, Courtney Jeffrey E. Froyd is a Research Professor at Texas A&M University. His research interests include sustained adoption of improvements in learning and teaching systematic reviews in engineering education evaluation of faculty campus climates and assessment of complex learning outcomes. Charles Henderson is a Professor at Western Michigan University with a joint appointment between the Department of Physics and the Mallinson Institute for Science Education. His research focuses on promoting productive changes in higher education at the individual department institution and national levels. Renée S. Cole is an Associate Professor of Chemistry at the University of Iowa. She teaches introductory and advanced courses in chemistry and runs a research program focused on the design and assessment of instructional materials and teaching strategies and faculty professional development. Debra Friedrichsen founded and operates a small consulting company. She received her Ph.D. from Oregon State University in Chemical Engineering with a dissertation focused on engineering education. Debra also has a MBA a MS and a patent for sensor development. Raina Khatri is a doctoral student in the Mallinson Institute for Science Education at Western Michigan University. Her research focus is understanding how education developers in STEM can promote sustained adoption of their innovations. Courtney Stanford is a postdoctoral researcher in the Department of Chemistry at Virginia Commonwealth University. Her current research focuses on the identification development and assessment of process skills (also known as professional skills) in active learning undergraduate STEM classrooms.

Scholarly studies and national reports document failure of current efforts to achieve broad, sustained adoption of research-based instructional practices, despite compelling bodies of evidence supporting efficacy of many of these practices. The authors of this paper argue that many change agents who are working to promote systemic adoption of these teaching practices use approaches that are characterized by what the authors call the "dissemination paradigm." A dissemination paradigm characterizes patterns of these current, failing efforts. Change agents, working within the dissemination paradigm, try to convince adopters that their innovations can help their students. Efforts within the dissemination paradigm have not led, and are unlikely to lead, to systemic adoption. The authors offer the "propagation paradigm" as an alternative with the potential to produce improved results. Change agents, working within the propagation paradigm, engage with adopters early and often to understand their instructional systems and interactively develop a strong product adaptable to specific contexts.

关键词： Models Change Agents Teaching Methods Information Dissemination Educational Innovation Instructional Systems stem Education Comparative Analysis

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Identification of cis Elements for Spatio-temporal Control of DNA Replication

SSRN

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SSRN 2018年

作者： Sima, Jiao Chakraborty, Abhijit Dileep, Vishnu Michalski, Marco Rivera-Mulia, Juan Carlos Trevilla-Garcia, Claudia Klein, Kyle N. Bartlett, Daniel Washburn, Brian K. Paulsen, Michelle T. Vera, Daniel Nora, Elphège P. Kraft, Katerina Mundlos, Stefan Bruneau, Benoit G. Ljungman, Mats Fraser, Peter Ay, Ferhat Gilbert, David M. Department of Biological Science Florida State University 319 Stadium Drive TallahasseeFL32306 United States La Jolla Institute for Allergy and Immunology 9420 Athena Circle San diegoCA92037 United States Nuclear Dynamics Program The Babraham Institute Babraham Research Campus CambridgeCB22 3AT United Kingdom Departments of Radiation Oncology and Environmental Health Sciences Center for RNA Biomedicine University of Michigan Medical School Ann ArborMI48109-2800 United States Center for Genomics and Personalized Medicine Florida State University TallahasseeFL32306-4295 United States Gladstone Institute of Cardiovascular Disease Roddenberry Center for Stem Cell Biology and Medicine at Gladstone San FranciscoCA94158 United States Department of Pediatrics Cardiovascular Research Institute University of California at San Francisco San FranciscoCA94158 United States Max Planck Institute for Molecular Genetics RG Development & Disease Berlin14195 Germany Institute for Medical and Human Genetics Charité Universitäts Medizin Berlin Berlin13353 Germany UC San Diego School of Medicine San diegoCA92093 United States

The temporal order of DNA replication (replication timing, RT) is highly coupled with genome architecture, but cis-elements regulating spatio-temporal control of replicatio have remained elusive. We performed an extensive series of CRISPR mediated deletions and inversions and high-resolution capture Hi-C of a pluripotency associated domain (DppA2/4) in mouse embryonic stem cells. Whereas CTCF mediated loops and chromatin domain boundaries were dispensable, deletion of three intra-domain prominent CTCF-independent 3D contact sites caused a domain-wide delay in RT, shift in sub-nuclear chromatin compartment and loss of transcriptional activity, These "early replication control elements" (ERCEs) display prominent chromatin features resembling enhancers/promoters and individual and pair-wise deletions of the ERCEs confirmed their partial redundancy and interdependency in controlling domain-wide RT and transcription. Our results demonstrate that discrete cis-regulatory elements mediate domain-wide RT, chromatin compartmentalization, and transcription, representing a major advance in dissecting the relationship between genome structure and function. © 2018, The Authors. All rights reserved.

关键词： stem cells

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Author Correction: A recellularized human colon model identifies cancer driver genes

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Nature biotechnology 2019年第7期37卷 820页

作者： Huanhuan Joyce Chen Zhubo Wei Jian Sun Asmita Bhattacharya David J Savage Rita Serda Yuri Mackeyev Steven A Curley Pengcheng Bu Lihua Wang Shuibing Chen Leona Cohen-Gould Emina Huang Xiling Shen Steven M Lipkin Neal G Copeland Nancy A Jenkins Michael L Shuler Department of Biomedical Engineering Cornell University Ithaca New York USA. Cancer Research Program Houston Methodist Research Institute Houston Texas USA. Department of Medicine Weill Cornell Medical College New York New York USA. Department of Genetic Medicine Weill Cornell Medical College New York New York USA. Genetics Genomics and Development Cornell University Ithaca New York USA. University of Texas Medical School at Houston Houston Texas USA. Department of Chemistry Rice University Houston Texas USA. Department of Surgery Baylor College of Medicine Houston Texas USA. Department of Biological and Environmental Engineering Cornell University Ithaca New York USA. Chemical Biology in Surgery Weill Cornell Medical College New York New York USA. Department of Biochemistry Weill Cornell Medical College New York New York USA. Department of Stem Cell Biology and Regenerative Medicine Cleveland Clinic Cleveland Ohio USA. Department of Colorectal Surgery Cleveland Clinic Cleveland Ohio USA. Cancer Research Program Houston Methodist Research Institute Houston Texas USA. njenkins2@***. Department of Biomedical Engineering Cornell University Ithaca New York USA. mls50@cornell.edu.

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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Native diversity buffers against severity of non-native tree invasions ( vol 621,pg 773 , 2023 )

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NATURE 2023年第7982期622卷 E2-E2页

作者： Delavaux, Camille S. Crowther, Thomas W. Zohner, Constantin M. Robmann, Niamh M. Lauber, Thomas van den Hoogen, Johan Kuebbing, Sara Liang, Jingjing de-Miguel, Sergio Nabuurs, Gert-Jan Reich, Peter B. Abegg, Meinrad Yao, Yves C. Adou Alberti, Giorgio Zambrano, Angelica M. Almeyda Alvarado, Braulio Vilchez Alvarez-Davila, Esteban Alvarez-Loayza, Patricia Alves, Luciana F. Ammer, Christian Anton-Fernandez, Clara Araujo-Murakami, Alejandro Arroyo, Luzmila Avitabile, Valerio Aymard, Gerardo A. Baker, Timothy R. Balazy, Radomir Banki, Olaf Barroso, Jorcely G. Bastian, Meredith L. Bastin, Jean-Francois Birigazzi, Luca Birnbaum, Philippe Bitariho, Robert Boeckx, Pascal Bongers, Frans Bouriaud, Olivier Brancalion, Pedro H. S. Brandl, Susanne Brienen, Roel Broadbent, Eben N. Bruelheide, Helge Bussotti, Filippo Gatti, Roberto Cazzolla Cesar, Ricardo G. Cesljar, Goran Chazdon, Robin Chen, Han Y. H. Chisholm, Chelsea Cho, Hyunkook Cienciala, Emil Clark, Connie Clark, David Colletta, Gabriel D. Coomes, David A. Valverde, Fernando Cornejo Corral-Rivas, Jose J. Crim, Philip M. Cumming, Jonathan R. Dayanandan, Selvadurai de Gasper, Andre L. Decuyper, Mathieu Derroire, Geraldine DeVries, Ben Djordjevic, Ilija Dolezal, Jiri Dourdain, Aurelie Obiang, Nestor Laurier Engone Enquist, Brian J. Eyre, Teresa J. Fandohan, Adande Belarmain Fayle, Tom M. Feldpausch, Ted R. Ferreira, Leandro V. Fischer, Markus Fletcher, Christine Frizzera, Lorenzo Gamarra, Javier G. P. Gianelle, Damiano Glick, Henry B. Harris, David J. Hector, Andrew Hemp, Andreas Hengeveld, Geerten Herault, Bruno Herbohn, John L. Herold, Martin Hillers, Annika Coronado, Euridice N. Honorio Hui, Cang Ibanez, Thomas T. Amaral, Ieda Imai, Nobuo Jagodzinski, Andrzej M. Jaroszewicz, Bogdan Johannsen, Vivian Kvist Joly, Carlos A. Jucker, Tommaso Jung, Ilbin Karminov, Viktor Kartawinata, Kuswata Kearsley, Elizabeth Kenfack, David Kennard, Deborah K. Kepfer-Rojas, Sebastian Keppel, Gunnar Khan, Mohammed Latif Killeen, Timothy J. Kim, Hyun Seok Kitayama, Kanehiro Kohl, Michael Korju Institute of Integrative Biology ETH Zurich (Swiss Federal Institute of Technology) Zurich Switzerland Department of Genetics Evolution and Environment University College London London UK The Forest School at The Yale School of the Environment Yale University New Haven CT USA Department of Forestry and Natural Resources Purdue University West Lafayette IN USA Department of Agriculture Forestry and Bioresources Seoul National University Seoul South Korea Department of Crop and Forest Sciences University of Lleida Lleida Spain Joint Research Unit CTFC–AGROTECNIO–CERCA Solsona Spain Wageningen University and Research Wageningen The Netherlands World Agroforestry (ICRAF) Nairobi Kenya Department of Forest Resources University of Minnesota St Paul MN USA Hawkesbury Institute for the Environment Western Sydney University Penrith New South Wales Australia Institute for Global Change Biology and School for Environment and Sustainability University of Michigan Ann Arbor MI USA Swiss Federal Institute for Forest Snow and Landscape Research WSL Birmensdorf Switzerland UFR Biosciences University Félix Houphouët-Boigny Abidjan Côte d’Ivoire Department of Agricultural Food Environmental and Animal Sciences University of Udine Udine Italy Faculty of Science and Technology Free University of Bolzano Bolzano Italy Spatial Ecology and Conservation Laboratory Department of Tourism Recreation and Sport Management University of Florida Gainesville FL USA Forestry School Tecnológico de Costa Rica TEC Cartago Costa Rica Fundacion ConVida Universidad Nacional Abierta y a Distancia UNAD Medellin Colombia Field Museum of Natural Histiory Chicago IL USA Center for Tropical Research Institute of the Environment and Sustainability UCLA Los Angeles CA USA Silviculture and Forest Ecology of the Temperate Zones University of Göttingen Göttingen Germany Division of Forest and Forest Resources Norwegian Institute of Bioeconomy Research (NIBIO) Ås Norway Museo de Hi

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