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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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Restoration of LAT activity improves CAR T cell sensitivity and persistence in response to antigen-low acute lymphoblastic leukemia

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Cancer Cell 2025年第3期43卷 482-502.e9页

作者： Pham-Danis, Catherine Novak, Amanda J. Danis, Etienne McClellan, Samantha M. Leach, Lillie Yarnell, Michael C. Ebmeier, Christopher C. Tasian, Sarah K. Kohler, M. Eric Department of Pediatrics University of Colorado Anschutz Medical Campus Aurora 80045 CO United States Department of Biomedical Informatics University of Colorado Anschutz Medical Campus Aurora 80045 CO United States Biostatistics & Bioinformatics Shared Resource University of Colorado Cancer Center Aurora 80045 CO United States Division of Oncology and Center for Childhood Cancer Research Children's Hospital of Philadelphia Philadelphia 19104 PA United States Proteomics and Mass Spectrometry Core Department of Biochemistry University of Colorado Boulder 80309 CO United States Department of Pediatrics & Abramson Cancer Center University of Pennsylvania Perelman School of Medicine Philadelphia 19104 PA United States Division of Blood and Marrow Transplantation & Cellular Therapy Center for Cancer and Blood Disorders Children's Hospital Colorado Aurora 80045 CO United States

Chimeric antigen receptor (CAR) T cells induce responses in patients with relapsed/refractory leukemia;however, long-term efficacy is frequently limited by relapse. The inability to target antigen-low cells is an intrinsic vulnerability of second-generation CAR T cells and underlies most relapses following CD22BBz CAR T cell therapy. Here, we interrogate CD22BBz CAR signaling in response to low antigen and find inefficient phosphorylation of the linker for activation of T cells (LAT) limiting downstream signaling. To overcome this, we designed the adjunctive LAT-activating CAR T cell (ALA-CART) platform, pairing a second-generation CAR with a LAT-CAR incorporating the intracellular domain of LAT. ALA-CART cells demonstrate reduced differentiation during manufacturing and increased LAT phosphorylation, MAPK signaling, and AP-1 activity. ALA-CART cells show improved cytotoxicity, proliferation, persistence, and efficacy against antigen-low leukemias that were refractory to clinically active CD22BBz CAR T cells. Restoration of LAT signaling through the ALA-CART platform represents a promising strategy for overcoming multiple mechanisms of CAR T cell failure. © 2025 The Authors

关键词： ALL CAR T cells immunotherapy LAT T cell signaling

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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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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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High Baseline Plasma Anthranilic Acid Predicts Remission Upon Acute-Series Ketamine Infusion for Treatment-Resistant Depression

Biological Psychiatry Global Open Science

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Biological Psychiatry Global Open Science 2025年第4期5卷

作者： Stephen A. Murata Zachary B. Madaj Colt D. Capan Ryan D. Sheldon Rif S. El-Mallakh Sagar V. Parikh William V. Bobo Fernando S. Goes Owen M. Wolkowitz Jennifer L. Vande Voort Louis J. Nykamp Balwinder Singh Gustavo C. Medeiros Erik B. Nelson Michael E. Thase Gregory F. Oxenkrug Mark A. Frye John F. Greden Eric D. Achtyes Lena C. Brundin Michigan State University College of Human Medicine Grand Rapids Michigan Pine Rest Christian Mental Health Services Grand Rapids Michigan Bioinformatics and Biostatistics Core Van Andel Institute Grand Rapids Michigan Mass Spectrometry Core Van Andel Institute Grand Rapids Michigan Department for Neurodegenerative Sciences Van Andel Research Institute Grand Rapids Michigan University of Louisville Louisville Kentucky University of Michigan Ann Arbor Michigan Mayo Clinic Jacksonville Florida Johns Hopkins University Baltimore Maryland University of California San Francisco San Francisco California Mayo Clinic Rochester Minnesota University of Maryland School of Medicine Baltimore Maryland University of Cincinnati Cincinnati Ohio University of Pennsylvania Philadelphia Pennsylvania Tufts University School of Medicine Boston Massachusetts Western Michigan University Homer Stryker M.D. School of Medicine Kalamazoo Michigan

Background Treatment-resistant depression (TRD) remains a challenge, but intravenous racemic ketamine offers rapid antidepressant effects. Reliable biomarkers are needed. In this study, we examined kynurenine pathway metabolites and inflammatory cytokines as predictors of ketamine response. Methods The Bio-K study was a multicenter, open-label trial of 74 patients with TRD who received 3 ketamine infusions over 11 days. Remission (Montgomery–Åsberg Depression Rating Scale [MADRS] score ≤9) was assessed 24 hours post infusion 3, with a subset of study participants continuing weekly infusions. Plasma biomarkers (9 kynurenines, 14 cytokines) were measured at baseline and post infusion. Mixed-effects models and logistic regression analyses were used, adjusting for sex, age, body mass index, benzodiazepine use, and baseline MADRS scores. Second-generation p values were used to determine significance. Results Of the 74 participants, 52% ( n = 38) achieved remission. Higher baseline anthranilic acid (AA) levels predicted remission (β = −0.93, p = .02). Composite ratios, including AA:intercellular adhesion molecule-1 (ICAM-1) (β = −1.15, p = .002) and AA:tryptophan (TRP) (β = −0.98, p = .007), significantly improved predictive accuracy (area under the receiver operating characteristic curve = 0.75 vs. 0.64, p = .03). The findings were independent of demographic and clinical covariates. Conclusions Elevated AA levels and AA-based biomarker ratios predicted ketamine remission in patients with TRD, supporting biomarker-driven personalized treatment. These findings highlight immunometabolic mechanisms in ketamine response.

关键词： Anthranilic acid Bio-K Ketamine Kynurenine pathway Predictive biomarker Treatment-resistant depression

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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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1128P Preliminary results of first-in-human study of 225-Actinium MTI-201 (225Ac-MTI-201) in metastatic uveal melanoma

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Annals of Oncology 2024年 35卷 S742-S742页

作者： N.I. Khushalani G. El-Haddad K. Gage M. Budzevich M. Schell E.G. Moros C. Tichacek W. Gibbons R. Rogers M. Nickels L. Tetteh Z. Eroglu L. Karapetyan A.S. Brohl J. Markowitz A. Tarhini K. Hayes L. Hazlehurst M. McLaughlin D. Morse Cutaneous Oncology H. Lee Moffitt Cancer Center Tampa FL USA Diagnostic Imaging and Interventional Radiology H. Lee Moffitt Cancer Center Tampa FL USA Core Facility H. Lee Moffitt Cancer Center Tampa FL USA Biostatistics and Bioinformatics H. Lee Moffitt Cancer Center Tampa FL USA Radiation Oncology H. Lee Moffitt Cancer Center Tampa FL USA Mallinckrodt Institute of Radiology Washington University School of Medicine St. Louis MO USA Modulation Therapeutics Morgantown WV USA Metabolism and Physiology H. Lee Moffitt Cancer Center Tampa FL USA

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Correction: Improvements in lung function following vitamin C supplementation to pregnant smokers are associated with buccal DNA methylation at 5 years of age

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Clinical epigenetics 2024年第1期16卷 59页

作者： Lyndsey E Shorey-Kendrick Cindy T McEvoy Kristin Milner Julia Harris Julie Brownsberger Robert S Tepper Byung Park Lina Gao Annette Vu Cynthia D Morris Eliot R Spindel Division of Neuroscience Oregon National Primate Research Center Oregon Health and Science University Beaverton OR 97006 USA. shorey@ohsu.edu. Department of Pediatrics Pape Pediatric Research Institute Oregon Health and Science University Portland OR USA. Department of Pediatrics Oregon Health and Science University Portland OR USA. Department of Pediatrics Herman B Wells Center for Pediatric Research Indiana University School of Medicine Indianapolis IN USA. Biostatistics Shared Resources Knight Cancer Institute Bioinformatics and Biostatistics Core Oregon National Primate Research Center Oregon Health and Science University Portland State University School of Public Health Portland OR USA. Oregon Clinical and Translational Research Institute Oregon Health and Science Department of Medical Informatics and Clinical Epidemiology Oregon Health and Science University Portland OR USA. Division of Neuroscience Oregon National Primate Research Center Oregon Health and Science University Beaverton OR 97006 USA.

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WorkflowHub: a registry for computational workflows

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Scientific data 2025年第1期12卷 837页

作者： Ove Johan Ragnar Gustafsson Sean R Wilkinson Finn Bacall Stian Soiland-Reyes Simone Leo Luca Pireddu Stuart Owen Nick Juty José M Fernández Tom Brown Hervé Ménager Björn Grüning Salvador Capella-Gutierrez Frederik Coppens Carole Goble Australian BioCommons University of Melbourne Melbourne Victoria Australia. Oak Ridge Leadership Computing Facility Oak Ridge National Laboratory Oak Ridge Tennessee USA. Department of Computer Science The University of Manchester Manchester UK. Informatics Institute University of Amsterdam Amsterdam The Netherlands. Center for Advanced Studies Research and Development in Sardinia (CRS4) Pula Cagliari Italy. Barcelona Supercomputing Center (BSC) Barcelona Spain. Spanish National Bioinformatics Institute (INB) Barcelona Spain. Leibniz Institute for Zoo- and Wildlife Research Berlin Germany. Institut Pasteur Université Paris Cité Bioinformatics of Biostatistics Hub Paris 75015 France. CNRS UMS 3601 Institut Français de Bioinformatique Evry France. Albert-Ludwigs-Universität Freiburg Freiburg Germany. VIB Data Core VIB Technologies Ghent Belgium. Department of Computer Science The University of Manchester Manchester UK. carole.goble@manchester.ac.uk.

The rising popularity of computational workflows is driven by the need for repetitive and scalable data processing, sharing of processing know-how, and transparent methods. As both combined records of analysis and descriptions of processing steps, workflows should be reproducible, reusable, adaptable, and available. Workflow sharing presents opportunities to reduce unnecessary reinvention, promote reuse, increase access to best practice analyses for non-experts, and increase productivity. In reality, workflows are scattered and difficult to find, in part due to the diversity of available workflow engines and ecosystems, and because workflow sharing is not yet part of research practice. WorkflowHub provides a unified registry for all computational workflows that links to community repositories, and supports both the workflow lifecycle and making workflows findable, accessible, interoperable, and reusable (FAIR). By interoperating with diverse platforms, services, and external registries, WorkflowHub adds value by supporting workflow sharing, explicitly assigning credit, enhancing FAIRness, and promoting workflows as scholarly artefacts. The registry has a global reach, with hundreds of research organisations involved, and more than 800 workflows registered.

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#1056 Multi-omic characterization of naïve treatment samples of epithelial ovarian cancer addressed to neoadjuvant chemotherapy: an hypothesis-generating study on biomarkers of response to platinum-based chemotherapy

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International Journal of Gynecological Cancer 2024年 34卷 A577-A578页

作者： Rita Trozzi Luca Mastrantoni Camilla Nero Simona Duranti Valentina Iacobelli Angelo Minucci Tina Pasciuto Luciano Giacò Gian Franco Zannoni Diana Giannarelli Domenica Lorusso Maria De Bonis Claudia Marchetti Anna Fagotti Giovanni Scambia Department of Women Children and Public Health Sciences Fondazione Policlinico Universitario Agostino Gemelli IRCCS Rome Italy UOC Oncologia medica Fondazione Policlinico Universitario Agostino Gemelli IRCCS Rome Italy Università Cattolica del Sacro Cuore Rome Italy Facoltà di Medicina e Chirurgia Università Cattolica del Sacro Cuore Rome Italy Scientific Directorate Fondazione Policlinico Universitario Agostino Gemelli IRCCS Rome Italy Departmental Unit of Molecular and Genomic Diagnostics Fondazione Policlinico Universitario Agostino Gemelli IRCCS Rome Italy Data Collection Research Core Facility Gemelli Science and Technology Park (GSTeP) Fondazione Policlinico Universitario Agostino Gemelli IRCCS Rome Italy Bioinformatics Research Core Facility Gemelli Science and Technology Park (GSTeP) Fondazione Policlinico Universitario Agostino Gemelli IRCCS Rome Italy Biostatistics Unit Gemelli Science and Technology Park (GSTeP) Fondazione Policlinico Universitario Agostino Gemelli IRCCS Rome Rome Italy

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