tbuckley/cabot-search huggingface dataset:
Workplace support and affirming behaviors: Moving toward a transgender, gender diverse, and non-binary friendly workplace
Authors: Ann Hergatt Huffman, Maura J. Mills, Satoris S. Howes, M. David Albritton
Journal: International Journal of Transgender Health (2020)

Background: The experiences of transgender, gender diverse, and non-binary (TGDNB) workers remain poorly understood and under-examined in the extant literature, with workplace support perceptions and affirming behaviors of these workers particularly misunderstood.Aims: We address this gap in the literature by presenting and empirically testing a theoretical model that suggests affirming behaviors are differentially related to various sources of TGDNB worker support. We further suggest these sources of support are differentially related to TGDNB employee satisfaction and gender identity openness at work.Methods: We collected data from trans-related social media groups, inviting TGDNB-identifying employees to participate in the study. Quantitative and qualitative data from 263 TGDNB employees were collected through survey administrations.Results: Supervisor and coworker support are related to job and life satisfaction, with supervisor support strongly connected to job satisfaction. The use of gender-affirming pronouns/titles and discouraging derogatory comments at work were related to perceived TGDNB support. Positive transgender organizational climate was strongly related to gender identity openness at work.Discussion: Results highlight a need for better workplace inclusivity and TGDNB-friendly environments, as well as more diversity training and company policy improvements that directly impact the workplace experiences of TGDNB people.
The Duty to Support Learning Health Systems: A Broad Rather than a Narrow Interpretation
Authors: Rieke van der Graaf, Wouter van Dijk, Sara J. M. Laurijssen, Ewoud Schuit, Diederick E. Grobbee, Martine C. de Vries
Journal: The American Journal of Bioethics (2020)

This article refers to:Self-Defeating Codes of Medical Ethics and How to Fix Them: Failures in COVID-19 Response and Beyond
The gut bacterium <i>Extibacter muris</i> produces secondary bile acids and influences liver physiology in gnotobiotic mice
Authors: Theresa Streidl, Isabel Karkossa, Rafael R. Segura Muñoz, Claudia Eberl, Alex Zaufel, Johannes Plagge, Robert Schmaltz, Kristin Schubert, Marijana Basic, Kai Markus Schneider, Mamdouh Afify, Christian Trautwein, René Tolba, Bärbel Stecher, Heidi L. Doden, Jason M. Ridlon, Josef Ecker, Tarek Moustafa, Martin von Bergen, Amanda E. Ramer-Tait, Thomas Clavel
Journal: Gut Microbes (2020)

Extibacter muris is a newly described mouse gut bacterium which metabolizes cholic acid (CA) to deoxycholic acid (DCA) via 7α-dehydroxylation. Although bile acids influence metabolic and inflammatory responses, few in vivo models exist for studying their metabolism and impact on the host. Mice were colonized from birth with the simplified community Oligo-MM12 with or without E. muris. As the metabolism of bile acids is known to affect lipid homeostasis, mice were fed either a low- or high-fat diet for eight weeks before sampling and analyses targeting the gut and liver. Multiple Oligo-MM12 strains were capable of deconjugating primary bile acids in vitro. E. muris produced DCA from CA either as pure compound or in mouse bile. This production was inducible by CA in vitro. Ursodeoxycholic, chenodeoxycholic, and β-muricholic acid were not metabolized under the conditions tested. All gnotobiotic mice were stably colonized with E. muris, which showed higher relative abundances after HF diet feeding. The presence of E. muris had minor, diet-dependent effects on Oligo-MM12 communities. The secondary bile acids DCA and surprisingly LCA and their taurine conjugates were detected exclusively in E. muris-colonized mice. E. muris colonization did not influence body weight, white adipose tissue mass, liver histopathology, hepatic aspartate aminotransferase, or blood levels of cholesterol, insulin, and paralytic peptide (PP). However, proteomics revealed shifts in hepatic pathways involved in amino acid, glucose, lipid, energy, and drug metabolism in E. muris-colonized mice. Liver fatty acid composition was substantially altered by dietary fat but not by E. muris.In summary, E. muris stably colonized the gut of mice harboring a simplified community and produced secondary bile acids, which affected proteomes in the liver. This new gnotobiotic mouse model can now be used to study the pathophysiological role of secondary bile acids in vivo.
Society for Immunotherapy of Cancer (SITC) clinical practice guideline on immunotherapy for the treatment of lymphoma
Authors: Sattva S Neelapu, Sherry Adkins, Stephen M Ansell, Joshua Brody, Mitchell S Cairo, Jonathan W Friedberg, Justin P Kline, Ronald Levy, David L Porter, Koen van Besien, Michael Werner, Michael R Bishop
Journal: Journal for ImmunoTherapy of Cancer (2020)

The recent development and clinical implementation of novel immunotherapies for the treatment of Hodgkin and non-Hodgkin lymphoma have improved patient outcomes across subgroups. The rapid introduction of immunotherapeutic agents into the clinic, however, has presented significant questions regarding optimal treatment scheduling around existing chemotherapy/radiation options, as well as a need for improved understanding of how to properly manage patients and recognize toxicities. To address these challenges, the Society for Immunotherapy of Cancer (SITC) convened a panel of experts in lymphoma to develop a clinical practice guideline for the education of healthcare professionals on various aspects of immunotherapeutic treatment. The panel discussed subjects including treatment scheduling, immune-related adverse events (irAEs), and the integration of immunotherapy and stem cell transplant to form recommendations to guide healthcare professionals treating patients with lymphoma.
Stereotactic ablative body radiotherapy in patients with oligometastatic cancers: a prospective, registry-based, single-arm, observational, evaluation study
Authors: Anastasia Chalkidou, Thomas Macmillan, Mariusz T Grzeda, Janet Peacock, Jennifer Summers, Saskia Eddy, Bola Coker, Hannah Patrick, Helen Powell, Lee Berry, Gareth Webster, Peter Ostler, Peter D Dickinson, Matthew Q Hatton, Ann Henry, Stephen Keevil, Maria A Hawkins, Nick Slevin, Nicholas van As
Journal: The Lancet Oncology (2020)
Social Determinants of Health and Structural Inequities—Root Causes of Diabetes Disparities
Authors: S. Michelle Ogunwole, Sherita H. Golden
Journal: Diabetes Care (2020)

Diabetes is the seventh leading cause of death in the U.S. and remains a significant cause of disability and decreased quality of life (1,2). In 2018, over 34 million people in the U.S. had diabetes (1). Historically marginalized groups such as racial and ethnic minorities, as well as those with lower socioeconomic status, bear a disproportionate burden of diabetes and its associated complications: blindness, neuropathy, limb amputations, chronic kidney disease, cardiovascular disease, and death (1,3). Additionally, the economic burden of diabetes amounts to approximately $237 billion in direct medical costs and $90 billion in lost productivity (4). Diabetes is a public health crisis that must be addressed by acknowledging and intervening on contextual factors outside of traditional medical care if we are to truly make an impact on improving outcomes, particularly for our most marginalized communities.

While contributors to diabetes outcomes are unequivocally multifactorial, cumulative evidence suggests that certain factors play a larger role than others (5). For example, medical care plays a relatively small part (approximately 10–15%) in shaping individual and population-level health outcomes (5,6). In contrast, social and environmental factors, collectively known as the social determinants of health (SDOH), combined account for 50% to 60% of health outcomes and are a key contributor to health and health care disparities (5,6). The World Health Organization’s definition of SDOH also notes that these social and environmental factors are “shaped by the distribution of money, power and resources at global, national and local levels” and are largely responsible for inequities in health outcomes (7). To achieve health equity, we must address SDOH, and do so at …
Hearing Music while Checking a Pulse
Authors: Leanna Wise
Journal: New England Journal of Medicine (2020)

A 65-year-old man who had previously undergone bilateral hip arthroplasty presented with a dislocated hip after a fall. When a handheld Doppler device used to assess the pulses in his feet was placed on the dorsalis pedis, it picked up music in addition to the pulse, as shown in a video.
Optical diagnosis of colorectal polyp images using a newly developed computer-aided diagnosis system (CADx) compared with intuitive optical diagnosis
Authors: Quirine E. W. van der Zander, Ramon M. Schreuder, Roger Fonollà, Thom Scheeve, Fons van der Sommen, Bjorn Winkens, Patrick Aepli, Bu'Hussain Hayee, Andreas B. Pischel, Milan Stefanovic, Sharmila Subramaniam, Pradeep Bhandari, Peter H. N. de With, Ad A. M. Masclee, Erik J. Schoon
Journal: Endoscopy (2020)

Abstract Background Optical diagnosis of colorectal polyps remains challenging. Image-enhancement techniques such as narrow-band imaging and blue-light imaging (BLI) can improve optical diagnosis. We developed and prospectively validated a computer-aided diagnosis system (CADx) using high-definition white-light (HDWL) and BLI images, and compared the system with the optical diagnosis of expert and novice endoscopists. Methods CADx characterized colorectal polyps by exploiting artificial neural networks. Six experts and 13 novices optically diagnosed 60 colorectal polyps based on intuition. After 4 weeks, the same set of images was permuted and optically diagnosed using the BLI Adenoma Serrated International Classification (BASIC). Results CADx had a diagnostic accuracy of 88.3 % using HDWL images and 86.7 % using BLI images. The overall diagnostic accuracy combining HDWL and BLI (multimodal imaging) was 95.0 %, which was significantly higher than that of experts (81.7 %, P = 0.03) and novices (66.7 %, P &lt; 0.001). Sensitivity was also higher for CADx (95.6 % vs. 61.1 % and 55.4 %), whereas specificity was higher for experts compared with CADx and novices (95.6 % vs. 93.3 % and 93.2 %). For endoscopists, diagnostic accuracy did not increase when using BASIC, either for experts (intuition 79.5 % vs. BASIC 81.7 %, P = 0.14) or for novices (intuition 66.7 % vs. BASIC 66.5 %, P = 0.95). Conclusion CADx had a significantly higher diagnostic accuracy than experts and novices for the optical diagnosis of colorectal polyps. Multimodal imaging, incorporating both HDWL and BLI, improved the diagnostic accuracy of CADx. BASIC did not increase the diagnostic accuracy of endoscopists compared with intuitive optical diagnosis.
A multi-center study on safety and efficacy of immune checkpoint inhibitors in cancer patients with kidney transplant
Authors: Naoka Murakami, Patrick Mulvaney, Melissa Danesh, Ala Abudayyeh, Adi Diab, Noha Abdel-Wahab, Maen Abdelrahim, Pascale Khairallah, Shayan Shirazian, Aleksandra Kukla, Itunu O. Owoyemi, Tarek Alhamad, Samir Husami, Madhav Menon, Andrew Santeusanio, Christopher D. Blosser, Sandra Carias Zuniga, Maria Jose Soler, Francesc Moreso, Zain Mithani, David Ortiz-Melo, Edgar A. Jaimes, Victoria Gutgarts, Erik Lum, Gabriel M. Danovitch, Francesca Cardarelli, Reed E. Drews, Claude Bassil, Jennifer L. Swank, Scott Westphal, Roslyn B. Mannon, Keisuke Shirai, Abhijat Kitchlu, Song Ong, Shana M. Machado, Suraj S. Mothi, Patrick A. Ott, Osama Rahma, F. Stephen Hodi, Meghan E. Sise, Shruti Gupta, David E. Leaf, Craig E. Devoe, Rimda Wanchoo, Vinay V. Nair, Chrysalyne D. Schmults, Glenn J. Hanna, Ben Sprangers, Leonardo V. Riella, Kenar D. Jhaveri
Journal: Kidney International (2020)
Vaccinating Detained Migrants against SARS-CoV-2 — Preventing Another Tragedy
Authors: Carlo Foppiano Palacios, Mark A. Travassos
Journal: New England Journal of Medicine (2020)

Vaccinating Detained Migrants against SARS-CoV-2 Covid-19 has devastated refugees and asylum seekers in U.S. federal detention centers, and the Trump administration has devised a workaround for vac...
Kidney Injury in ICU Adults with Severe COVID-19
Authors: Jing Qian, Li Ni, Mengjing Wang, Weichen Zhang, Kangjie Wang, Li Yuan, Jing Chen
Journal: Journal of the American Society of Nephrology (2020)

Qian, Jing; Ni, Li; Wang, Mengjing; Zhang, Weichen; Wang, Kangjie; Yuan, Li; Chen, Jing Author Information
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes
Authors: Jeremy Schwartzentruber, Sarah Cooper, Jimmy Z. Liu, Inigo Barrio-Hernandez, Erica Bello, Natsuhiko Kumasaka, Adam M. H. Young, Robin J. M. Franklin, Toby Johnson, Karol Estrada, Daniel J. Gaffney, Pedro Beltrao, Andrew Bassett
Journal: Nature Genetics (2021)
Safety, tolerability, efficacy, pharmacokinetics, and pharmacodynamics of the oral TYK2 inhibitor PF-06826647 in participants with plaque psoriasis: a phase 1, randomised, double-blind, placebo-controlled, parallel-group study
Authors: Christopher Tehlirian, Elena Peeva, Elizabeth Kieras, Matthew Scaramozza, Erika S Roberts, Ravi Shankar P Singh, Vivek Pradhan, Anindita Banerjee, Sandra Garcet, Li Xi, Jeremy D Gale, Michael S Vincent, James Krueger
Journal: The Lancet Rheumatology (2020)
A dual-modal PET/near infrared fluorescent nanotag for long-term immune cell tracking
Authors: Stefan Harmsen, Emin Ilker Medine, Maxim Moroz, Fuad Nurili, Jose Lobo, Yiyu Dong, Mezruh Turkekul, Naga Vara Kishore Pillarsetty, Richard Ting, Vladimir Ponomarev, Oguz Akin, Omer Aras
Journal: Biomaterials (2020)
Characterization of the Immune Landscape of EGFR-Mutant NSCLC Identifies CD73/Adenosine Pathway as a Potential Therapeutic Target
Authors: Xiuning Le, Marcelo V. Negrao, Alexandre Reuben, Lorenzo Federico, Lixia Diao, Daniel McGrail, Monique Nilsson, Jacqulyne Robichaux, Irene Guijarro Munoz, Sonia Patel, Yasir Elamin, You-Hong Fan, Won-Chul Lee, Edwin Parra, Luisa Maren Solis Soto, Runzhe Chen, Jun Li, Tatiana Karpinets, Roohussaba Khairullah, Humam Kadara, Carmen Behrens, Boris Sepesi, Ruiping Wang, Mingrui Zhu, Linghua Wang, Ara Vaporciyan, Jack Roth, Stephen Swisher, Cara Haymaker, Jianhua Zhang, Jing Wang, Kwok-Kin Wong, Lauren A. Byers, Chantale Bernatchez, Jianjun Zhang, Ignacio I. Wistuba, Don L. Gibbons, Esra A. Akbay, John V. Heymach
Journal: Journal of Thoracic Oncology (2020)
Better prognosis in females with severe COVID-19 pneumonia: possible role of inflammation as potential mediator
Authors: Cristina Mussini, Alessandro Cozzi-Lepri, Marianna Menozzi, Marianna Meschiari, Erica Franceschini, Carlotta Rogati, Gianluca Cuomo, Andrea Bedini, Vittorio Iadisernia, Sara Volpi, Jovana Milic, Roberto Tonelli, Lucio Brugioni, Antonello Pietrangelo, Massimo Girardis, Andrea Cossarizza, Enrico Clini, Giovanni Guaraldi, Erica Bacca, Andrea Bedini, Vanni Borghi, Giulia Burastero, Federica Carli, Giacomo Ciusa, Luca Corradi, Margherita Di Gaetano, Matteo Faltoni, Giacomo Franceschi, Gabriella Orlando, Francesco Pellegrino, Cinzia Puzzolante, Alessandro Raimondi, Antonella Santoro, Marco Tutone, Dina Yaacoub, Alberto Andreotti, Emanuela Biagioni, Filippo Bondi, Stefano Busani, Giovanni Chierego, Marzia Scotti, Lucia Serio, Caterina Bellinazzi, Rebecca Borella, Sara De Biasi, Anna De Gaetano, Lucia Fidanza, Lara Gibellini, Anna Iannone, Domenico Lo Tartaro, Marco Mattioli, Annamaria Paolini, Rossella Fogliani, Grazia Righini, Mario Lugli
Journal: Clinical Microbiology and Infection (2021)
Exercise During the First Trimester of Pregnancy and the Risks of Abnormal Screening and Gestational Diabetes Mellitus
Authors: Samantha F. Ehrlich, Assiamira Ferrara, Monique M. Hedderson, Juanran Feng, Romain Neugebauer
Journal: Diabetes Care (2020)

To estimate the effects of exercise during the first trimester on the risks of abnormal screening and gestational diabetes mellitus (GDM).
Relevance of body mass index as a predictor of systemic therapy outcomes in metastatic melanoma: analysis of the MelBase French cohort data☆
Authors: Y. Di Filippo, S. Dalle, L. Mortier, O. Dereure, S. Dalac, C. Dutriaux, M.-T. Leccia, D. Legoupil, P. Saiag, F. Brunet-Possenti, J.-P. Arnnault, E. Maubec, F. Granel-Brocard, J. De Quatrebarbes, F. Aubin, T. Lesimple, M. Beylot-Barry, P.-E. Stoebner, A. Dupuy, A. Stephan, J.-J. Grob, W. Lefevre, B. Oriano, C. Allayous, C. Lebbé, H. Montaudié
Journal: Annals of Oncology (2020)
Point-of-Care Ultrasound Findings Among Dialysis Patients with COVID-19
Authors: Sadichhya Lohani, Vishnu S. Potluri, Forrest F. Lindsay-McGinn, Jennifer Morganroth, Claire A. Centeno, Christy Moore, Felipe Teran, Nathaniel C. Reisinger
Journal: Journal of the American Society of Nephrology (2020)

Lohani, Sadichhya; Potluri, Vishnu S.; Lindsay-McGinn, Forrest F.; Morganroth, Jennifer; Centeno, Claire A.; Moore, Christy; Teran, Felipe; Reisinger, Nathaniel C. Author Information
Virtual reality for COPD rehabilitation: a technological perspective
Authors: V. Colombo, A. Aliverti, M. Sacco
Journal: Pulmonology (2020)

Virtual Reality (VR) is a promising technology for implementing personalized, motivating and controlled rehabilitation scenarios. Although its clear potential benefits, VR has been poorly investigated in pulmonary rehabilitation. This review analyses the state of the art, by searching the scientific and grey literature, regarding the use of VR for the rehabilitation of patients with chronic obstructive pulmonary disease, providing a technological perspective. First, the main characteristics of the included systems are presented in terms of visualization devices, way of interaction and type of feedback they provide. Then, results of the selected studies are reported considering feasibility, safety, usability and user experience as outcomes. Finally, the main findings are discussed and future directions for research are outlined.
Transcription factor networks of oligodendrogliomas treated with adjuvant radiotherapy or observation inform prognosis
Authors: Jonathan So, Yasin Mamatjan, Gelareh Zadeh, Kenneth Aldape, Fabio Y Moraes
Journal: Neuro-Oncology (2020)

Recent international sequencing efforts have allowed for the molecular taxonomy of lower-grade gliomas (LGG). We sought to analyze The Cancer Genome Atlas (TCGA, 2015) gene expression datasets on molecularly defined oligodendrogliomas (IDH-mutated and 1p/19q-codeleted) patients treated with adjuvant radiation or those observed to discover prognostic markers and pathways.mRNA expression and clinical information of patients with oligodendroglioma were taken from the TCGA "Brain Lower Grade Glioma" provisional dataset. Transcription factor network reconstruction and analysis were performed using the R packages "RTN" and "RTNsurvival." Elastic net regularization and survival modeling were performed using the "biospear," "plsRCox," "survival" packages.From our cohort of 137 patients, 65 received adjuvant radiation and 72 were observed. In the cohort that received adjuvant radiotherapy, a transcription factor activity signature, that correlated with hypoxia, was associated with shorter disease-free survival (DFS) (median = 45 months vs 108 months, P < .001). This increased risk was not seen in patients who were observed (P = .2). Within the observation cohort, a transcription factor activity signature was generated that was associated with poor DFS (median = 72 months. vs 143 months., P < .01).We identified a transcription factor activity signature associated with poor prognosis in patients with molecular oligodendroglioma treated with adjuvant radiotherapy. These patients would be potential candidates for treatment intensification. A second signature was generated for patients who were more likely to progress on observation. This potentially identifies a cohort who would benefit from upfront adjuvant radiotherapy.
Interactive Classification of Whole-Slide Imaging Data for Cancer Researchers
Authors: Sanghoon Lee, Mohamed Amgad, Pooya Mobadersany, Matt McCormick, Brian P. Pollack, Habiba Elfandy, Hagar Hussein, David A. Gutman, Lee A.D. Cooper
Journal: Cancer Research (2020)

Whole-slide histology images contain information that is valuable for clinical and basic science investigations of cancer but extracting quantitative measurements from these images is challenging for researchers who are not image analysis specialists. In this article, we describe HistomicsML2, a software tool for learn-by-example training of machine learning classifiers for histologic patterns in whole-slide images. This tool improves training efficiency and classifier performance by guiding users to the most informative training examples for labeling and can be used to develop classifiers for prospective application or as a rapid annotation tool that is adaptable to different cancer types. HistomicsML2 runs as a containerized server application that provides web-based user interfaces for classifier training, validation, exporting inference results, and collaborative review, and that can be deployed on GPU servers or cloud platforms. We demonstrate the utility of this tool by using it to classify tumor-infiltrating lymphocytes in breast carcinoma and cutaneous melanoma. SIGNIFICANCE: An interactive machine learning tool for analyzing digital pathology images enables cancer researchers to apply this tool to measure histologic patterns for clinical and basic science studies.