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arXiv 2024年

作者： Drnevich, Jenny Tan, Frederick J. Almeida-Silva, Fabricio Castelo, Robert Culhane, Aedin C. Davis, Sean Doyle, Maria A. Geistlinger, Ludwig Ghazi, Andrew R. Holmes, Susan Lahti, Leo Mahmoud, Alexandru Nishida, Kozo Ramos, Marcel Rue-Albrecht, Kevin Shih, David J.H. Gatto, Laurent Soneson, Charlotte Roy J. Carver Biotechnology Center University of Illinois Urbana-Champaign IL United States Johns Hopkins University Department of Biology BaltimoreMD United States Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium VIB Center for Plant Systems Biology Ghent Belgium Department of Medicine and Life Sciences Universitat Pompeu Fabra Barcelona Spain Limerick Digital Cancer Research Centre School of Medicine University of Limerick Ireland University of Colorado Anschutz School of Medicine DenverCO United States Core for Computational Biomedicine Department of Biomedical Informatics Harvard Medical School BostonMA United States Statistics Department Stanford University StanfordCA United States Department of Computing University of Turku Finland Channing Division of Network Medicine Harvard Medical School BostonMA United States RIKEN Center for Biosystems Dynamics Research 6-7-1 Minatojima Minamimachi Chuoku Hyogo Kobe Japan Department of Epidemiology and Biostatistics City University of New York School of Public Health New YorkNY United States MRC WIMM Centre for Computational Biology MRC Weatherall Institute of Molecular Medicine University of Oxford Oxford United Kingdom School of Biomedical Sciences Li Ka Shing Faculty of Medicine The University of Hong Kong Hong Kong Computational Biology and Bioinformatics Unit de Duve Institute UCLouvain Brussels Belgium Friedrich Miescher Institute for Biomedical Research Basel Switzerland SIB Swiss Institute of Bioinformatics Basel Switzerland

Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and best practices available within the Bioconductor project - an open-source software community focused on omics data analysis. This guide serves as a valuable reference for both learners and educators in the *** Codes 97K80 © 2024, CC BY.

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2022-LBA-746-ESGO Implementation of a comprehensive cancer genome profiling programme into clinical practice: an italian experience in a referral centre for gynecological cancers

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International Journal of Gynecological Cancer 2022年 32卷 A468-A469页

作者： Camilla Nero Silvia Pelligra Simona Duranti Flavia Giacomini Floriana Camarda Elena Giudice Alessia Piermattei Francesca Sillano Angelo Minucci Maria de Bonis Giuseppina Raspaglio Luciano Giacò Emanuela Lucci Cordisco Marta de Donato Tina Pasciuto Diana Giannarelli Francesco Fanfani Gian Franco Zannoni Anna Fagotti Domenica Lorusso Giovanni Scambia Gynecologic Oncology Fondazione Policlinico Universitario Agostino Gemelli IRCCS Roma Italy Scientific Directorate Fondazione Policlinico Universitario Agostino Gemelli IRCCS Roma Italy Gynecologic Oncology and Breast Pathology Unit Fondazione Policlinico Universitario Agostino Gemelli IRCCS Roma Italy Genomics Core facility Fondazione Policlinico Universitario Agostino Gemelli IRCCS Roma Italy Bioinformatics Core facility Fondazione Policlinico Universitario Agostino Gemelli IRCCS Roma Italy Medical Genetics Unit Fondazione Policlinico Universitario Agostino Gemelli IRCCS Roma Italy Data Collection Core facility- GSTeP Fondazione Policlinico Universitario Agostino Gemelli IRCCS Roma Italy Epidemiology and Biostatistics core facility- GSTeP Fondazione Policlinico Universitario Agostino Gemelli IRCCS Roma Italy

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Response to Dekker, Stege, and Versteeg

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Journal of the National Cancer Institute 2021年第10期113卷 1436-1437页

作者： Jeanne S Mandelblatt Xingtao Zhou Brent J Small Jaeil Ahn Wanting Zhai Tim Ahles Martine Extermann Deena Graham Paul B Jacobsen Heather Jim Brenna C McDonald Sunita K Patel James C Root Andrew J Saykin Harvey Jay Cohen Judith E Carroll Department of Oncology Cancer Prevention and Control Program Georgetown-Lombardi Comprehensive Cancer Center Georgetown University Washington DC USA. Department of Biostatistics Bioinformatics and Biomathematics Georgetown-Lombardi Comprehensive Cancer Center Georgetown University Washington DC USA. School of Aging Studies University of South Florida and Health Outcome and Behavior Program and Biostatistics Resource Core H. Lee Moffitt Cancer Center and Research Institute at the University of South Florida Tampa FL USA. Department of Biostatistics Bioinformatics and Biomathematics Georgetown-Lombardi Comprehensive Cancer Center Georgetown University Washington DC USA. Department of Psychiatry and Behavioral Sciences Memorial Sloan-Kettering Cancer Center New York NY USA. Department of Oncology Moffitt Cancer Center University of South Florida Tampa FL USA. John Theurer Cancer Center Hackensack NJ USA. Division of Cancer Control and Population Sciences Healthcare Delivery Research Program National Cancer Institute National Institutes of Health Bethesda MD USA. Department of Health Outcomes and Behavior Moffitt Cancer Center and Research Institute University of South Florida Tampa FL USA. Department of Radiology and Imaging Sciences and the Melvin and Bren Simon Cancer Center Center for Neuroimaging Indiana University School of Medicine Indianapolis IN USA. Departments of Population Sciences and Supportive Care Medicine City of Hope Comprehensive Cancer Center Duarte CA USA. Department of Psychiatry and Behavioral Sciences Memorial Sloan Kettering Cancer Center New York NY USA. Departments of Psychiatry and Anesthesiology Weill Medical College of Cornell University New York NY USA. Department of Radiology and Imaging Sciences and the Melvin and Bren Simon Cancer Center Center for Neuroimaging Indiana University School of Medicine Indianapolis IN USA. Department of Medicine Duke University School of Medicine Durham NC USA. UCLA Department of

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(200) Anatomic Maps of Erogenous Sensation & Pleasure in the Penis: Do Circumcised Men Report These Differently Than Uncircumcised Men?

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The Journal of Sexual Medicine 2023年第SUPPLEMENT_1期20卷

作者： Zaliznyak, M Isaacson, D Duralde, E Gaither, T Bresee, C Stelmar, J Yuan, N Topp, K Garcia, M Saint Louis University School of Medicine Department of Urology Northwestern University Feinberg School of Medicine Department of Medicine Beth Israel Deaconess Medical Center Department of Urology David Geffen School of Medicine Biostatistics & Bioinformatics Core Cedars-Sinai Samuel Oschin Comprehensive Cancer Center Division of Urology Cedars-Sinai Medical Center Huntington Plastic Surgery Institute Department of Physical Therapy and Rehabilitation Science University of California San Francisco

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Early NK Cell Proliferation After Umbilical Cord Blood Transplantation Is Associated With Superior Disease-Free Survival Due To Reduced Leukemia Relapse

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Blood 2013年第21期122卷 4610-4610页

作者： Rachel Joy Bergerson Sarah Cooley Julie Curtsinger Ryan Shanley Claudio Brunstein Bruce R Blazar John E. Wagner Jeffrey S. Miller Michael R. Verneris Division of Blood and Marrow Transplantation Department of Pediatrics University of Minnesota Minneapolis MN USA Division of Hematology Oncology and Transplantation University of Minnesota Minneapolis MN USA Lab Medicine and Pathology University of Minnesota Minneapolis MN USA Biostatistics and Bioinformatics Core University of Minnesota Masonic Cancer Center Minneapolis MN USA Blood and Marrow Transplant Program University of Minnesota Minneapolis MN USA University of Minnesota Medical Center Fairview Minneapolis MN USA

Compared to traditional chemotherapy, allogeneic hematopoietic cell transplantation (allo-HCT) has the potential of triggering graft vs. leukemia (GVL) reactions that make this procedure uniquely curative. Despite this, relapse remains the most common cause of treatment failure. Early after allo-HCT the donor immune system reconstitutes within the host and natural killer (NK) cells are the earliest lymphocyte population to recover. Previous studies by us and other investigators have linked rapid lymphocyte recovery and/or high NK cell numbers early after transplant with less relapse. Mechanistically, the reasons for this are unknown. We hypothesized that NK cell proliferation would be associated with allo-HCT outcomes. In a large data set with short-term follow-up we compared stem cell source to NK cell proliferation at Day 28 after transplantation (using Ki67+ staining). In patients undergoing autologous (n=117), sibling (n=57), single umbilical cord blood (sUCB) (n=62) or double umbilical cord blood (dUCB) (n=50) transplantation there were significant differences in the median NK cell proliferation (2.1%, 3.3%, 3.8%, and 19.2%, respectively, p<0.0001). These results suggest that NK cell proliferation is increased when patients are transplanted with stem cell sources that have an increased number of HLA mismatches (dUCB). We next examined factors extrinsic to the NK cells to determine whether differences in the four patient groups were due to these factors. Regulatory T cells (Tregs) are known to negatively regulate the proliferation and activation of a variety of cell types, including NK cells. We utilized the percentage and absolute number of Tregs (defined as CD4+CD25 high FoxP3+CD127 low ) at Day 28 (available for a subset of the above patient samples) and correlated it with the percentage of proliferating NK cells at Day 28 after allogeneic transplant (n=212). The median percentage of Tregs within the lymphocyte fraction was 1.49%. In patients with higher than

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Long term follow-up of a phase II trial of multimodal therapy given in a "sandwich" method for stage III, IV, and recurrent endometrial cancer

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Gynecologic oncology research and practice 2016年第1期3卷 6页

作者： Michelle Glasgow Rachel Isaksson Vogel Jennifer Burgart Peter Argenta Kathryn Dusenbery Melissa A Geller Department of Obstetrics Gynecology and Women's Health Division of Gynecologic Oncology University of Minnesota Minneapolis MN USA. Department of Obstetrics Gynecology and Women's Health Division of Gynecologic Oncology University of Minnesota Minneapolis MN USA Biostatistics and Bioinformatics Core Masonic Cancer Center University of Minnesota Minneapolis MN USA. Eastern Virginia Medical School Norfolk VA USA. Radiation Oncology University of Minnesota Minneapolis MN USA. University of Minnesota MMC 395 420 Delaware St. SE Minneapolis MN 55445 USA.

BACKGROUND:Our objective was to determine if previously reported overall survival (OS) and progression-free survival (PFS) rates are maintained long term following multimodal therapy for advanced and recurrent endometrial cancer and to assess the lymphedema rates associated with this therapy. METHODS:Women with advanced-stage or recurrent endometrial cancer were recruited between 9/2004 and 6/2009 to our previously published Phase II trial. Patients received intravenous docetaxel (75 mg/m2) and carboplatin (AUC = 6) every 3 weeks for 3 cycles before and after radiation therapy. Patient outcomes were updated in July 2014. Data abstracted included presence of lymphedema, disease progression, and death. OS and PFS estimates at 5 years were calculated using Kaplan-Meier methods. RESULTS:Of the 41 patients enrolled, 10 (24 %) had stage IIIA and 21 (51 %) had stage IIIC disease; 32 (78 %) had endometrioid histology; and 35 (85 %) completed the protocol. With a median follow-up of 5 years, 15 of 41 patients have died. The Kaplan-Meier estimate and 95 % CI for OS at 5 years was 70 % (53-82 %). Excluding the two patients with recurrent disease at enrollment, 15 of 39 patients progressed or died during follow-up. The Kaplan-Meier estimate and 95 % CI for PFS at 5 years was 66 % (48-78 %). Fifteen patients (37 %) had medical record documentation of lymphedema following treatment. CONCLUSIONS:After additional follow-up, OS and PFS estimates remain high and in-field recurrences low following "sandwich" therapy. The "sandwich" method remains efficacious for women with stage III-IV or recurrent endometrial cancer.

关键词： Endometrial cancer Lymphedema Sandwich therapy

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Effect of end-stage kidney disease on the return of spontaneous circulation in Taiwanese adults with out-of-hospital cardiac arrest

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Scientific Reports 2023年第1期13卷 1-11页

作者： Hsieh, Ming-Shun Chattopadhyay, Amrita Lu, Tzu-Pin Liao, Shu-Hui Chang, Chia-Ming Lee, Yi-Chen Lo, Wei-En Wu, Jia-Jun Hsieh, Vivian Chia-Rong Hu, Sung-Yuan How, Chorng-Kuang Department of Emergency Medicine Taipei Veterans General Hospital Taoyuan Branch Taoyuan Taiwan Department of Emergency Medicine Taipei Veterans General Hospital Taipei Taiwan School of Medicine National Yang Ming Chiao Tung University Taipei Taiwan Department of Emergency Medicine Taichung Veterans General Hospital Taichung Taiwan Bioinformatics and Biostatistics Core Center of Genomics and Precision Medicine National Taiwan University Taipei Taiwan Department of Public Health National Taiwan University Taipei Taiwan Department of Pathology and Laboratory Taipei Veterans General Hospital Taoyuan Branch Taoyuan Taiwan Institute of Occupational Medicine and Industrial Hygiene National Taiwan University College of Public Health Taipei Taiwan Department of Critical Care Medicine Taipei Veterans General Hospital Taoyuan Branch Taoyuan Taiwan Department of Health Services Administration China Medical University Taichung Taiwan School of Medicine Chung Shan Medical University Taichung Taiwan Institute of Medicine Chung Shan Medical University Taichung Taiwan Department of Post‐Baccalaureate Medicine College of Medicine National Chung Hsing University Taichung Taiwan

Rescuing patients with out-of-hospital cardiac arrest (OHCA), especially those with end-stage kidney disease (ESKD), is challenging. This study hypothesizes that OHCA patients with ESKD undergoing maintenance hemodialysis have (1) higher rates of return of spontaneous circulation (ROSC) during cardio-pulmonary resuscitation (CPR) and (2) lower rates of hyperkalemia and less severe acidosis than those without ESKD. OHCA patients who received CPR between 2011 and 2020 were dichotomized into ESKD and non-ESKD groups. The association of ESKD with “any” and “sustained” ROSC were examined using logistic regression analysis. Furthermore, the effect of ESKD on hospital outcomes for OHCA patients who survived to admission was evaluated using Kaplan–Meier analysis. ESKD patients without “any” ROSC displayed lower potassium and higher pH levels than non-ESKD patients. ESKD was positively associated with “any” ROSC (adjusted-OR: 4.82, 95% CI 2.70–5.16, P < 0.01) and “sustained” ROSC (adjusted-OR: 9.45, 95% CI 3.83–24.13, P < 0.01). Kaplan–Meier analysis demonstrated ESKD patients had a non-inferior hospital survival than non-ESKD patients. OHCA patients with ESKD had lower serum potassium level and less severe acidosis compared to the general population in Taiwan;therefore, should not be treated under the stereotypical assumption that hyperkalemia and acidosis always occur. © 2023, The Author(s).

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Bone Mineral Density (BMD) Reductions After Tenofovir Disoproxil Fumarate (TDF) Initiation Are Not Associated With Changes in Phosphaturia: A Secondary Analysis of ACTG A5224s

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Open Forum Infectious Diseases 2016年第SUPPL_1期3卷

作者： Gupta, Samir Yeh, Eunice Kitch, Douglas Brown, Todd Venuto, Charles Morse, Gene Ha, Belinda Melbourne, Kathy McComsey, Grace Medicine/Infectious Diseases Indiana University School of Medicine Indianapolis Indiana Center for Biostatistics in AIDS Research Harvard T.H. Chan School of Public Health Boston Massachusetts XXX Boston Massachusetts Johns Hopkins University Baltimore MD University of Rochester Medical Center Rochester New York Translational Pharmacology Research Core New York State Center of Excellence in Bioinformatics and Life Sciences School of Pharmacy and Pharmaceutical Sciences University at Buffalo Buffalo New York ViiV Healthcare Research Triangle Park North Carolina Gilead Sciences Foster City California Case Western Reserve University Cleveland Ohio

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ESTIMATED PERFORMANCE FOR AGE: A NOVEL CRITERION FOR RETURN TO SPORT AFTER ANTERIOR CRUCIATE RECONSTRUCTION AND ITS PERFORMANCE COMPARED TO LIMB SYMMETRY INDICES

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Orthopaedic Journal of Sports Medicine 2021年第7_suppl3期9卷

作者： John Magill Danica Vance Thomas Risoli Cynthia Green Emily Reinke Michael Reiman Kristian Thorburg Jonathan Riboh Doctor of Physical Therapy Division Department of Orthopedic Surgery Duke University Durham NC United States of America. Department of Physical therapy and Occupational Therapy Duke University Health System Durham NC United States of America. Department of Orthopedic Surgery James Urbaniak Sport Science Institute Duke University Medical Center Durham NC United States of America. Duke Biostatistics Epidemiology and Research Design (BERD) Methods Core Duke University Durham NC United States of America. Duke Clinical Research Institute Duke University Durham NC United States of America. Department of Biostatistics and Bioinformatics Duke Universtiy Medical Center Durham NC United States of America. Sports Orthopaedic Research Center - Copenhagen (SORC-C) Department of Orthopaedic Surgery Copenhagen University Hospital Amager-Hvidovre Denmark.

INTRODUCTION: The use of physical performance tests (PPT) for assessing readiness for return to sport (RTS) after ACL reconstruction in children is typically assessed based on a limb symmetry index (LSI). However, recent data show that: 1) healthy pediatric athletes have significant limb asymmetries at baseline and 2) the non-operative limb deconditions after ACLR, so return of LSI is not synonymous with return to pre-injury performance. We previously established a cohort of 100 healthy pediatric athletes and created growth curves for performance on 7 common PPT, allowing for the calculation of a performance percentile (PP) for any given individual based on their age. The current study explores the use of PP in a cohort of pediatric patients 6 months out from ACLR. We hypothesized that return to expected performance for age (EPFA, defined as the 50 th percentile of performance among healthy volunteers of a given age) would be a more stringent criterion than 90% LSI.

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Proceedings of the 16th Annual UT-KBRIN bioinformatics Summit 2016: bioinformatics

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BMC bioinformatics 2017年第9期18卷 1-9页

作者： Eric C. Rouchka Juw Won Park Julia H. Chariker David A. Tieri Shreedharkumar Rajurkar Vikas Singh Nishchal K. Verma Yan Cui Mark Farman Bradford Condon Jolanta Jaromczyk Neil Moore Jerzy Jaromczyk Daniel Harris Patrick Calie Eun Kyong Shin Robert L. Davis Arash Shaban-Nejad Joshua M. Mitchell Hunter N. B. Moseley Robert M. Flight Qing Jun Wang Richard M. Higashi Teresa W-M Fan Andrew N. Lane Liangqun Lu Bernie J Daigle Jr. Xi Chen Andrey Smelter Jerzy W. Jaromczyk Bailey K. Phan Nathaniel J. Serpico Ethan G. Toney Li Chen Caroline E. Melton Jennifer R. Mandel Bernie J. Daigle Jr. Hao Chen Kazi I. Zaman Ramin Homayouni Patrick J. Trainor Andrew P. DeFilippis Samantha M. Carlisle Shesh N. Rai Department of Computer Engineering and Computer Science University of Louisville Duthie Center for Engineering Louisville KY 40292 USA Kentucky Biomedical Research Infrastructure (KBRIN) Bioinformatics Core 522 East Gray Street Louisville KY 40292 USA Department of Psychological and Brain Sciences University of Louisville Louisville KY 40292 USA Department of Anatomical Sciences and Neurobiology University of Louisville Louisville KY 40292 USA Department of Electrical Engineering IIT Kanpur India Department of Microbiology Immunology and Biochemistry University of Tennessee Health Science Center Memphis TN 38103 USA Center for Integrative and Translational Genomics University of Tennessee Health Science Center Memphis TN 38103 USA Department of Plant Pathology University of Kentucky Lexington KY 40546 USA UK Healthcare Genomics University of Kentucky Lexington KY 40536 USA Department of Entomology & Plant Pathology University of Tennessee Knoxville TN 37996 USA Department of Forestry University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40508 USA Department of Biological Sciences Eastern Kentucky University Richmond KY 40475 USA University of Tennessee Health Science Center – Oak-Ridge National Lab (UTHSC-ORNL) Center for Biomedical Informatics Department of Pediatrics Memphis TN 38103 USA Department of Molecular & Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Markey Cancer Center University of Kentucky Lexington KY 40536 USA Center for Environmental and Systems Biochemistry University of Kentucky Lexington KY 40536 USA Institute for Biomedical Informatics University of Kentucky Lexington KY 40536 USA Department of Molecular and Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Department of Statistics University of Kentucky Louisville KY

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