tbuckley/cabot-search huggingface dataset:
Annals Graphic Medicine - Six Months
Authors: Sabrina M. Saeed
Journal: Annals of Internal Medicine (2020)

Web Exclusives7 July 2020Annals Graphic Medicine - Six MonthsFREESabrina M. Saeed, BASabrina M. Saeed, BABrown University, Providence, Rhode Island (S.M.S.)Author, Article, and Disclosure Informationhttps://doi.org/10.7326/G19-0069 SectionsAboutVisual AbstractPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Download figure Download PowerPoint Download figure Download PowerPoint Download figure Download PowerPoint Download figure Download PowerPoint Download figure Download PowerPoint Download figure Download PowerPoint Comments0 CommentsSign In to Submit A Comment Author, Article, and Disclosure InformationAffiliations: Brown University, Providence, Rhode Island (S.M.S.)Acknowledgment: "Six Months" is part of the first Medical Comics Project at Brown University. Funded by the Warren Alpert Medical School and the Arnold P. Gold Foundation in 2019, the Medical Comics Project engaged premedical students in reflective exercises and the development of original graphic narratives.Disclosures: The author has disclosed no conflicts of interest. The form can be viewed at www.acponline.org/authors/icmje/ConflictOfInterestForms.do?msNum=G19-0069.Author/Illustrator Information: A recent graduate of Brown University, Sabrina Saeed is currently conducting research in surgical oncology at H. Lee Moffitt Cancer Center and Research Institute in Tampa, Florida. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 7 July 2020Volume 173, Issue 1Page: W3-W9KeywordsConflicts of interestDisclosureExerciseGraduate medical educationHealth care ePublished: 7 July 2020 Issue Published: 7 July 2020 Copyright & PermissionsCopyright © 2020 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
Multi-site fMRI analysis using privacy-preserving federated learning and domain adaptation: ABIDE results
Authors: Xiaoxiao Li, Yufeng Gu, Nicha Dvornek, Lawrence H. Staib, Pamela Ventola, James S. Duncan
Journal: Medical Image Analysis (2020)

Deep learning models have shown their advantage in many different tasks, including neuroimage analysis. However, to effectively train a high-quality deep learning model, the aggregation of a significant amount of patient information is required. The time and cost for acquisition and annotation in assembling, for example, large fMRI datasets make it difficult to acquire large numbers at a single site. However, due to the need to protect the privacy of patient data, it is hard to assemble a central database from multiple institutions. Federated learning allows for population-level models to be trained without centralizing entities' data by transmitting the global model to local entities, training the model locally, and then averaging the gradients or weights in the global model. However, some studies suggest that private information can be recovered from the model gradients or weights. In this work, we address the problem of multi-site fMRI classification with a privacy-preserving strategy. To solve the problem, we propose a federated learning approach, where a decentralized iterative optimization algorithm is implemented and shared local model weights are altered by a randomization mechanism. Considering the systemic differences of fMRI distributions from different sites, we further propose two domain adaptation methods in this federated learning formulation. We investigate various practical aspects of federated model optimization and compare federated learning with alternative training strategies. Overall, our results demonstrate that it is promising to utilize multi-site data without data sharing to boost neuroimage analysis performance and find reliable disease-related biomarkers. Our proposed pipeline can be generalized to other privacy-sensitive medical data analysis problems. Our code is publicly available at: https://github.com/xxlya/Fed_ABIDE/.
Pharmacotranscriptomics of peptide drugs with neuroprotective properties
Authors: Lyudmila V. Dergunova, Ivan B. Filippenkov, Svetlana A. Limborska, Nikolai F. Myasoedov
Journal: Medicinal Research Reviews (2020)

Abstract Here we present a review of studies on the effects of peptides with neuroprotective properties on gene transcription in nerve cells. The few published works in this area clearly demonstrate massive changes in cell transcriptomes induced by peptides under normal conditions and under conditions of experimental brain ischemia. These changes significantly affect signaling and metabolic pathways, affecting various body systems and confirming the multiple target actions of peptides. The importance of noncoding RNAs in the regulation of these processes is shown, and we discuss the prospects of research for determining the main mechanisms of peptide regulation, which is necessary for the further development of drugs with targeted neuroprotective effects.
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases
Authors: Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor
Journal: Genomics Proteomics & Bioinformatics (2020)

Biological databases represent an extraordinary collective volume of work. Diligently built up over decades and comprising many millions of contributions from the biomedical research community, biological databases provide worldwide access to a massive number of records (also known as entries) [1]. Starting from individual laboratories, genomes are sequenced, assembled, annotated, and ultimately submitted to primary nucleotide databases such as GenBank [2], European Nucleotide Archive (ENA) [3], and DNA Data Bank of Japan (DDBJ) [4] (collectively known as the International Nucleotide Sequence Database Collaboration, INSDC). Protein records, which are the translations of these nucleotide records, are deposited into central protein databases such as the UniProt KnowledgeBase (UniProtKB) [5] and the Protein Data Bank (PDB) [6]. Sequence records are further accumulated into different databases for more specialized purposes: RFam [7] and PFam [8] for RNA and protein families, respectively; DictyBase [9] and PomBase [10] for model organisms; as well as ArrayExpress [11] and Gene Expression Omnibus (GEO) [12] for gene expression profiles. These databases are selected as examples; the list is not intended to be exhaustive. However, they are representative of biological databases that have been named in the “golden set” of the 24th Nucleic Acids Research database issue (in 2016). The introduction of that issue highlights the databases that “consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database” [13]. In addition, the associated information about sequences is also propagated into non-sequence databases, such as PubMed (https://www.ncbi.nlm.nih.gov/pubmed/) for scientific literature or Gene Ontology (GO) [14] for function annotations. These databases in turn benefit individual studies, many of which use these publicly available records as the basis for their own research.
P-123 Outcomes and predictive factors of regorafenib benefit in patients with metastatic colorectal cancer in a real-life setting
Authors: N. Martínez Lago, B. Carnero Lopez, J. De la Cámara Gomez, F. Vázquez-Rivera, A. Fernández Montes, N. de Dios, A. Carral Maseda, M. Pellón Augusto, S. Candamio Folgar, M. Reboredo-Lopez, M. Salgado Fernandez, E. Gallardo Martin, M. Covela-Rúa, B. Graña Suarez, M. Carmona Campos, E. Brozos Vázquez, C. Reboredo Rendo, G. Quintero Aldana, C. Grande Ventura, Y. Vidal Ínsua, J. Méndez Méndez
Journal: Annals of Oncology (2020)
Factors Associated with Cloth Face Covering Use Among Adults During the COVID-19 Pandemic — United States, April and May 2020
Authors: Kiva A. Fisher, John P. Barile, Rebecca J. Guerin, Kayla L. Vanden Esschert, Alexiss Jeffers, Lin H. Tian, Amanda Garcia-Williams, Brian Gurbaxani, William W. Thompson, Christine E. Prue
Journal: MMWR Morbidity and Mortality Weekly Report (2020)

the White House Coronavirus Task Force and CDC announced a new behavioral recommendation to help slow the spread of coronavirus disease 2019 by encouraging the use of a cloth face covering when out in public (1).Widespread use of cloth face coverings has not been studied among the U.S. population, and therefore, little is known about encouraging the public to adopt this behavior.Immediately following the recommendation, an Internet survey sampled 503 adults during April 7-9 to assess their use of cloth face coverings and the behavioral and sociodemographic factors that might influence adherence to this recommendation.The same survey was administered 1 month later, during May 11-13, to another sample of 502 adults to assess changes in the prevalence estimates of use of cloth face coverings from April to May.Within days of the release of the first national recommendation for use of cloth face coverings, a majority of persons who reported leaving their home in the previous week reported using a cloth face covering (61.9%).Prevalence of use increased to 76.4% 1 month later, primarily associated with increases in use among non-Hispanic white persons (54.3% to 75.1%), persons aged ≥65 years (36.6% to 79.2%), and persons residing in the Midwest (43.7% to 73.8%).High rates were observed in April and by May, increased further among non-Hispanic black persons (74.4% to 82.3%), Hispanic or Latino persons (77.3% to 76.2%), non-Hispanic persons of other race (70.8% to 77.3%), persons aged 18-29 years (70.1% to 74.9%) and 30-39 years (73.9% to 84.4%), and persons residing in the Northeast (76.9% to 87.0%).The use of a cloth face covering was associated with theory-derived constructs that indicate a favorable attitude toward them, intention to use them, ability to use them, social support for using them, and beliefs that they offered protection for self, others, and the community.Research is needed to understand possible barriers to using cloth face coverings and ways to promote their consistent and correct use among those who have yet to adopt this behavior.Survey questions were administered by Porter Novelli Public Services (PN) and ENGINE Insights through PN View 360,* * Porter Novelli and ENGINE Insights collaborate on the PN View 360 surveys (http://styles.porternovelli.com/pn-view
Targeting castration-resistant prostate cancer with a novel RORγ antagonist elaiophylin
Authors: Jianwei Zheng, Junfeng Wang, Qian Wang, Hongye Zou, Hong Wang, Zhenhua Zhang, Jianghe Chen, Qianqian Wang, Panxia Wang, Yueshan Zhao, Jing Lu, Xiaolei Zhang, Songtao Xiang, Haibin Wang, Jinping Lei, Hong-Wu Chen, Peiqing Liu, Yonghong Liu, Fanghai Han, Junjian Wang
Journal: Acta Pharmaceutica Sinica B (2020)

Prostate cancer (PCa) patients who progress to metastatic castration-resistant PCa (mCRPC) mostly have poor outcomes due to the lack of effective therapies. Our recent study established the orphan nuclear receptor RORγ as a novel therapeutic target for CRPC. Here, we reveal that elaiophylin (Elai), an antibiotic from Actinomycete streptomyces, is a novel RORγ antagonist and showed potent antitumor activity against CRPC in vitro and in vivo. We demonstrated that Elai selectively binded to RORγ protein and potently blocked RORγ transcriptional regulation activities. Structure–activity relationship studies showed that Elai occupied the binding pocket with several key interactions. Furthermore, Elai markedly reduced the recruitment of RORγ to its genomic DNA response element (RORE), suppressed the expression of RORγ target genes AR and AR variants, and significantly inhibited PCa cell growth. Importantly, Elai strongly suppressed tumor growth in both cell line based and patient-derived PCa xenograft models. Taken together, these results suggest that Elai is novel therapeutic RORγ inhibitor that can be used as a drug candidate for the treatment of human CRPC.
P-65 Locally advanced/metastatic gastric cancer: Real-world data on first-line treatment with oxaliplatin and cisplatin-based doublets
Authors: H. Luna Pais, A. Mansinho, F. Branco, C. Alvim, S. Lobo-Martins, G. Fernandes, L. Fernandes, A. Matos, R. Paiva, S. Dâmaso, R. Brás, I. Pinho, A. Donato, P. Semedo, J. Albuquerque, L. Ribeiro
Journal: Annals of Oncology (2020)
Transcriptional Changes in Kidney Allografts with Histology of Antibody-Mediated Rejection without Anti-HLA Donor-Specific Antibodies
Authors: Jasper Callemeyn, Evelyne Lerut, Henriette de Loor, Ingrid Arijs, Olivier Thaunat, Alice Koenig, Vannary Meas-Yedid, Jean-Christophe Olivo-Marin, Philip Halloran, Jessica Chang, Lieven Thorrez, Dirk Kuypers, Ben Sprangers, Leentje Van Lommel, Frans Schuit, Marie Essig, Wilfried Gwinner, Dany Anglicheau, Pierre Marquet, Maarten Naesens
Journal: Journal of the American Society of Nephrology (2020)

Circulating donor-specific anti-HLA antibodies (HLA-DSAs) are often absent in serum of kidney allograft recipients whose biopsy specimens demonstrate histology of antibody-mediated rejection (ABMR). It is unclear whether cases involving ABMR histology without detectable HLA-DSAs represent a distinct clinical and molecular phenotype.In this multicenter cohort study, we integrated allograft microarray analysis with extensive clinical and histologic phenotyping from 224 kidney transplant recipients between 2011 and 2017. We used the term ABMR histology for biopsy specimens that fulfill the first two Banff 2017 criteria for ABMR, irrespective of HLA-DSA status.Of 224 biopsy specimens, 56 had ABMR histology; 26 of these (46.4%) lacked detectable serum HLA-DSAs. Biopsy specimens with ABMR histology showed overexpression of transcripts mostly related to IFNγ-induced pathways and activation of natural killer cells and endothelial cells. HLA-DSA-positive and HLA-DSA-negative biopsy specimens with ABMR histology displayed similar upregulation of pathways and enrichment of infiltrating leukocytes. Transcriptional heterogeneity observed in biopsy specimens with ABMR histology was not associated with HLA-DSA status but was caused by concomitant T cell-mediated rejection. Compared with cases lacking ABMR histology, those with ABMR histology and HLA-DSA had higher allograft failure risk (hazard ratio [HR], 7.24; 95% confidence interval [95% CI], 3.04 to 17.20) than cases without HLA-DSA (HR, 2.33; 95% CI, 0.85 to 6.33), despite the absence of transcriptional differences.ABMR histology corresponds to a robust intragraft transcriptional signature, irrespective of HLA-DSA status. Outcome after ABMR histology is not solely determined by the histomolecular presentation but is predicted by the underlying etiologic factor. It is important to consider this heterogeneity in further research and in treatment decisions for patients with ABMR histology.
Frequency and Results of Cryoglobulin Retesting in 4,963 Patients: Comment on the Article by Kolopp‐Sarda et al
Authors: Patrizia Natali, Daria Debbia, Tommaso Trenti, Giuliana Galassi, Johanna Chester, Gilda Sandri, Maria T. Mascia
Journal: Arthritis & Rheumatology (2020)
Anxiety and Depression Leads to Anti–Tumor Necrosis Factor Discontinuation in Inflammatory Bowel Disease
Authors: Casandra Dolovich, Charles N. Bernstein, Harminder Singh, Zoann Nugent, Aruni Tennakoon, Leigh Ann Shafer, Ruth Ann Marrie, Jitender Sareen, Laura E. Targownik
Journal: Clinical Gastroenterology and Hepatology (2020)
<i>Prdm9</i>Intersubspecific Interactions in Hybrid Male Sterility of House Mouse
Authors: Amisa Mukaj, Jaroslav Piálek, Vladana Fotopulosova, Andrew Parker Morgan, Linda Odenthal-Hesse, Emil D Parvanov, Jiri Forejt
Journal: Molecular Biology and Evolution (2020)

Abstract The classical definition posits hybrid sterility as a phenomenon when two parental taxa each of which is fertile produce a hybrid that is sterile. The first hybrid sterility gene in vertebrates, Prdm9, coding for a histone methyltransferase, was identified in crosses between two laboratory mouse strains derived from Mus mus musculus and M. m. domesticus subspecies. The unique function of PRDM9 protein in the initiation of meiotic recombination led to the discovery of the basic molecular mechanism of hybrid sterility in laboratory crosses. However, the role of this protein as a component of reproductive barrier outside the laboratory model remained unclear. Here, we show that the Prdm9 allelic incompatibilities represent the primary cause of reduced fertility in intersubspecific hybrids between M. m. musculus and M. m. domesticus including 16 musculus and domesticus wild-derived strains. Disruption of fertility phenotypes correlated with the rate of failure of synapsis between homologous chromosomes in meiosis I and with early meiotic arrest. All phenotypes were restored to normal when the domesticus Prdm9dom2 allele was substituted with the Prdm9dom2H humanized variant. To conclude, our data show for the first time the male infertility of wild-derived musculus and domesticus subspecies F1 hybrids controlled by Prdm9 as the major hybrid sterility gene. The impairment of fertility surrogates, testes weight and sperm count, correlated with increasing difficulties of meiotic synapsis of homologous chromosomes and with meiotic arrest, which we suppose reflect the increasing asymmetry of PRDM9-dependent DNA double-strand breaks.
Commonwealth Neuroendocrine Tumour Research Collaboration and the North American Neuroendocrine Tumor Society Guidelines for the Diagnosis and Management of Patients With Lung Neuroendocrine Tumors: An International Collaborative Endorsement and Update of the 2015 European Neuroendocrine Tumor Society Expert Consensus Guidelines
Authors: Simron Singh, Emily K. Bergsland, Cynthia M. Card, Thomas A. Hope, Pamela L. Kunz, David T. Laidley, Ben Lawrence, Simone Leyden, David C. Metz, Michael Michael, Lucy E. Modahl, Sten Myrehaug, Sukhmani K. Padda, Rodney F. Pommier, Robert A. Ramirez, Michael Soulen, Jonathan Strosberg, Arthur Sung, Alia Thawer, Benjamin Wei, Bin Xu, Eva Segelov
Journal: Journal of Thoracic Oncology (2020)
dalbavancinとバンコマイシン含有レジメンによるMRSA中心ライン関連血流感染症の治療後のdalbavancin非感受性,バンコマイシン中間耐性黄色ブドウ球菌(VISA)の出現【Powered by NICT】
Authors: B J Werth, R Jain, A Hahn, L Cummings, T Weaver, A Waalkes, D Sengupta, S J Salipante, R M Rakita, S M Butler-Wu
Journal: Clinical Microbiology and Infection (2018)
Characteristics of Persons Who Died with COVID-19 — United States, February 12–May 18, 2020
Authors: Jonathan M. Wortham, James T. Lee, Sandy Althomsons, Julia Latash, Alexander Davidson, Kevin Guerra, Kenya Murray, Emily McGibbon, Carolina Pichardo, Brian Toro, Lan Li, Marc Paladini, Meredith L. Eddy, Kathleen H. Reilly, Lisa McHugh, Deepam Thomas, Stella Tsai, Mojisola Ojo, Samantha Rolland, Maya Bhat, Katherine Hutchinson, Jennifer Sabel, Seth Eckel, Jim Collins, Catherine Donovan, Anna Cope, Breanna Kawasaki, Sarah McLafferty, Nisha Alden, Rachel Herlihy, Bree Barbeau, Angela C. Dunn, Charles Clark, Pamela Pontones, Meagan L. McLafferty, Dean E. Sidelinger, Anna Krueger, Leslie Kollmann, Linnea Larson, Stacy Holzbauer, Ruth Lynfield, Ryan Westergaard, Richard Crawford, Lin Zhao, Jonathan M. Bressler, Jennifer S. Read, John Dunn, Adele Lewis, Gillian Richardson, Julie Hand, Theresa Sokol, Susan H. Adkins, Brooke Leitgeb, Talia Pindyck, Taniece Eure, Karen Wong, Deblina Datta, Grace D. Appiah, Jessica Brown, Rita Traxler, Emilia H. Koumans, Sarah Reagan-Steiner
Journal: MMWR Morbidity and Mortality Weekly Report (2020)

approximately 1.3 million cases of coronavirus disease 2019 (COVID-19) and 83,000 COVID-19-associated deaths were reported in the United States (1).Understanding the demographic and clinical characteristics of decedents could inform medical and public health interventions focused on preventing COVID-19-associated mortality.This report describes decedents with laboratory-confirmed infection with SARS-CoV-2, the virus that causes COVID-19, using data from 1) the standardized CDC case-report form (case-based surveillance) (https://www.cdc.gov/coronavirus/2019-ncov/php/reporting-pui.html) and 2) supplementary data (supplemental surveillance), such as underlying medical conditions and location of death, obtained through collaboration between CDC and 16 public health jurisdictions (15 states and New York City).
Tumor-associated myeloid cells provide critical support for T-ALL
Authors: Aram Lyu, Todd A. Triplett, Seo Hee Nam, Zicheng Hu, Dhivya Arasappan, Wesley H. Godfrey, Rachel Y. Ames, Adviti Sarang, Hilary J. Selden, Chang-Han Lee, George Georgiou, Terzah M. Horton, Lauren I. R. Ehrlich
Journal: Blood (2020)
Abstract 12482: Serum Alkaline Phosphatase is a Predictor of Mortality, Myocardial Infarction, or Stent Thrombosis after Implantation of Coronary Drug-Eluting Stent
Authors: Jun-Bean Park, Do-yoon Kang, Han-Mo Yang, Hyun-Jai Cho, Kyung Woo Park, Hae-Young Lee, Hyun-Jae Kang, Bon-Kwon Koo, Byung-Hee Oh, Young-Bae Park, Hyo-Soo Kim
Journal: Circulation (2012)

Background The association between ALP and mortality was reported in several subgroups of patients. But, the role of ALP in overall CAD patients after PCI remains unknown. The aim of this study was...
Cyclin-dependent–like kinase 5 is required for pain signaling in human sensory neurons and mouse models
Authors: Paolo La Montanara, Arnau Hervera, Lucas L. Baltussen, Thomas H. Hutson, Ilaria Palmisano, Francesco De Virgiliis, Guiping Kong, Jessica Chadwick, Yunan Gao, Katalin Bartus, Qasim A. Majid, Nikos Gorgoraptis, Kingsley Wong, Jenny Downs, Tommaso Pizzorusso, Sila K. Ultanir, Helen Leonard, Hongwei Yu, David S. Millar, Nagy Istvan, Nicholas D. Mazarakis, Simone Di Giovanni
Journal: Science Translational Medicine (2020)

CDKL5 controls nociception in human neurons and murine models of CDKL5 deficiency disorder via CaMKII-dependent mechanisms.
P-267 Signet-ring cell carcinoma of the colon: 10-case experience of the Medical Oncology Department at Hassan II University Hospital
Authors: S. Berrad, L. Nouikh, H. Erraichi, L. Amaadour, K. Oualla, Z. Benbrahim, A. Samia, M. Nawfel
Journal: Annals of Oncology (2020)
Abstract 14127: Association Between Blood Product Transfusion and In-Hospital Clinical Outcomes in Patients Undergoing Type A Aortic Dissection Repair in the United States
Authors: Eirini Apostolidou, Frank W Sellke, Herbert D Aronow, Dhaval Kolte, Kevin F Kennedy, Neel R Sodha, James G Fingleton, Afshin Ehsan
Journal: Circulation (2019)

Introduction: Blood product transfusion is associated with adverse outcomes following cardiac surgical procedures. Little is known about the impact of transfusion in patients undergoing type A aort...
P-365 Association between baseline serum levels of miRNA-143 and hepatocyte growth factor in patients with RAS wild type metastatic colorectal cancer treated with first-line anti-EGFR therapy
Authors: Z. Mihaylova, M. Radanova, D. Ivanova, G. Mihaylova, V. Petrova, D. Petkova, I. Donev
Journal: Annals of Oncology (2020)
Abstract 13160: Ten-Year Legacy Effects of Previous STRRIDE Exercise Training Intervention on Measures of Cardiorespiratory Fitness
Authors: Leanna M Ross, Casey C Kuka, Lucy W Piner, Johanna L Johnson, Cris A Slentz, William E Kraus
Journal: Circulation (2018)

Introduction: The Studies Targeting Risk Reduction Interventions through Defined Exercise (STRRIDE) Reunion assessed changes in cardiometabolic health 10 years after study participation. We investi...
The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity
Authors: Elisabeth Salzer, Samaneh Zoghi, Máté G. Kiss, Frieda Kage, Christina Rashkova, Stephanie Stahnke, Matthias Haimel, René Platzer, Michael Caldera, Rico Chandra Ardy, Birgit Hoeger, Jana Block, David Medgyesi, Celine Sin, Sepideh Shahkarami, Renate Kain, Vahid Ziaee, Peter Hammerl, Christoph Bock, Jörg Menche, Loïc Dupré, Johannes B. Huppa, Michael Sixt, Alexis Lomakin, Klemens Rottner, Christoph J. Binder, Theresia E. B. Stradal, Nima Rezaei, Kaan Boztug
Journal: Science Immunology (2020)

HEM1 deficiency causes heritable autoimmunity and immunodeficiency.