tbuckley/cabot-search huggingface dataset:
Longitudinal Outcomes of COVID-19–Associated Collapsing Glomerulopathy and Other Podocytopathies
Authors: Satoru Kudose, Dominick Santoriello, Andrew S. Bomback, Miroslav Sekulic, Ibrahim Batal, M. Barry Stokes, Iman A. Ghavami, Jung S. Kim, Maddalena Marasa, Katherine Xu, Yonatan Peleg, Jonathan Barasch, Pietro Canetta, Hila Milo Rasouly, Ali G. Gharavi, Glen S. Markowitz, Vivette D. D’Agati
Journal: Journal of the American Society of Nephrology (2021)

The long-term outcome of COVID-19-associated collapsing glomerulopathy is unknown.We retrospectively identified 76 native kidney biopsies from patients with history of COVID-19 between March 2020 and April 2021. Presenting and outcome data were obtained for all 23 patients with collapsing glomerulopathy and for seven patients with noncollapsing podocytopathies. We performed APOL1 genotyping by Sanger sequencing, immunostaining for spike and nucleocapsid proteins, and in situ hybridization for SARS-CoV-2.The 23 patients with COVID-19-associated collapsing glomerulopathy were median age 57 years (range, 35-72), included 16 men, and were predominantly (91%) Black. Severity of COVID-19 was mild or moderate in most (77%) patients. All but one patient presented with AKI, 17 had nephrotic-range proteinuria, and six had nephrotic syndrome. Fourteen (61%) patients required dialysis at presentation. Among 17 patients genotyped, 16 (94%) were high-risk APOL1. Among 22 (96%) patients with median follow-up at 155 days (range, 30-412), 11 (50%) received treatment for COVID-19, and eight (36%) received glucocorticoid therapy for podocytopathy. At follow-up, 19 (86%) patients were alive, and 15 (68%) were dialysis free, including seven of 14 who initially required dialysis. The dialysis-free patients included 64% (seven of 11) of those treated for COVID-19 and 75% (six of eight) of those treated with glucocorticoids for podocytopathy. Overall, 36% achieved partial remission of proteinuria, 32% had no remission, and 32% reached combined end points of ESKD or death. Viral infection of the kidney was not detected.Half of 14 patients with COVID-19-associated collapsing glomerulopathy requiring dialysis achieved dialysis independence, but the long-term prognosis of residual proteinuric CKD remains guarded, indicating a need for more effective therapy.
Abstract 9948: Serum Total Bilirubin Levels Predict Amputation Events in Type 2 Diabetic Mellitus
Authors: Kim H Chan, Roland Stocker, David Sullivan, Kushwin Rajamani, Martin Ng, Rachel O'Connell, Anthony Keech
Journal: Circulation (2011)

Objectives: Bilirubin is well known for its antioxidant and anti-inflammatory properties, and may protect against vascular disease. It has previously been demonstrated that higher serum bilirubin levels were associated with reduced peripheral arterial disease (PAD) prevalence. However, the relationship between bilirubin and lower limb amputation, a consequence of PAD, is currently unknown. We hypothesized that bilirubin protects against amputation events in type 2 diabetic patients with PAD. Methods: The relationship between baseline serum total bilirubin level and amputation events was analyzed in 9795 type 2 diabetic patients from the FIELD (Fenofibrate Intervention and Event Lowering in Diabetes) study in a pre-specified subsidiary analysis. Lower limb amputation was adjudicated blinded to treatment allocation. Relevant clinical and biochemical data were available for analyses. Bilirubin was analyzed continuously using Cox regression techniques. Results: Serum bilirubin level was significantly inversely associated with lower limb amputation rate. When bilirubin was analyzed continuously, patients with lower bilirubin levels had an increased risk of amputation compared with patients with higher bilirubin levels (HR 1.38 per 5 µmol/L decrease in bilirubin, 95% CI 1.07-1.79, p=0.013). The same association persisted after adjustment for baseline variables including age, sex, height, smoking status, alcohol intake, GGT, ALT, HbA1c, and history of hypertension, hypercholesterolemia, previous PAD, prior revascularization, amputation, ulcer, neuropathy, renal dysfunction and diabetic retinopathy (p=0.032), as well as treatment allocation (placebo vs. fenofibrate). Conclusion: Our results identify a highly significant inverse relationship between serum bilirubin level and lower limb amputation rate. Our data is consistent with the hypothesis that bilirubin plays a protective role against amputation in the setting of type 2 diabetes.
FP07.05 DREAM3R: Durvalumab With Chemotherapy as First Line Treatment in Advanced Pleural Mesothelioma - A Phase 3 Randomised Trial
Authors: P. Forde, M. Stockler, P.S. Kok, C. Brown, Z. Sun, K. O'Byrne, S. Yip, V. Anagnostou, A. Cook, W.J. Lesterhuis, B. Hughes, H. Kindler, A. Tsao, M. Zauderer, A. Bricker, M. Oostendorp, D. Marinucci, K. Fitzpatrick, K. Ford, N. Pavlakis, J. Brahmer, S. Ramalingam, A. Nowak
Journal: Journal of Thoracic Oncology (2021)
FP15.01 Randomized Single-Blind Comparative Study of Midazolam Plus Pethidine Combination and Midazolam During Bronchoscopy
Authors: C. Mimura, M. Katsurada, M. Tachihara, N. Katsurada, N. Takata, H. Sato, J. Yoshioka, K. Furukawa, M. Yumura, T. Otoshi, Y. Yasuda, T. Kiriu, D. Hazama, T. Nagano, M. Yamamoto, Y. Nishimura, K. Kobayashi
Journal: Journal of Thoracic Oncology (2021)
Abstract 12114: Quantification of the Impact of Long-Term Storage at -80°C on the Human Plasma Metabolome - Results of an Epidemiologic Cohort
Authors: Ulrike E Rennefahrt, Sebastian Neuber, Beate Kamlage, Nicole Christiansen, Bianca Bethan, Philipp Schatz, Lars Lind
Journal: Circulation (2018)

Introduction: High-quality biological samples are one pre-requirement for the outcome of research studies and valid data sets are crucial for successful biomarker development. Considering the varia...
Reply
Authors: Martin Lagging, Karolina Rembeck, Jesper Waldenström, Staffan Nilsson, Kristina Nyström, Anna Martner, Magnus Lindh, Gunnar Norkrans, Johan Westin, Court Pedersen, Martti Färkkilä, Nina Langeland, Mads Rauning Buhl, Kristine Mørch, Peer B. Christensen, Kristoffer Hellstrand
Journal: Hepatology (2014)

We thank Dai et al. for their interest in our study reporting that homo- or heterozygosity at Ars1127354 or Crs7270101, that is, variants of the ITPA gene encoding reduced ITPase activity, were associated with increased likelihood of achieving sustained virological response (SVR) accompanied by reduced relapse rate among treatment-adherent hepatitis C virus (HCV) genotype 2/3-infected patients1 receiving pegylated interferon (Peg-IFN)-α2a and ribavirin 800 mg daily for 12 or 24 weeks in the NORDynamIC study.2 In their letter, they request further information on possible associations between rapid virological response (RVR; i.e., undetectable HCV RNA week 4), ITPase activity, and SVR. RVR was indeed significantly associated with increased likelihood of achieving SVR (P < 0.001 in both treatment arms; chi-squared test), but ITPase activity was not significantly associated with the likelihood of achieving RVR (43%, 65%, 61%, and 63% for ITPase activity ≤10%, 30%, 60%, and 100%, respectively; Fig. 1). When the two were combined in a logistic regression analysis, both were significantly associated with SVR for 12 and 24 weeks of treatment. In this regard, we wish to mention that we previously reported that achieving HCV RNA <1,000 IU/mL day 7, that is, immediately preceding the second dose of Peg-IFN, is superior to RVR for predicting likelihood of SVR after shortened treatment.3-5 When ITPase activity, HCV RNA <1,000 IU/mL day 7 and RVR were combined in a logistic regression analysis, the former two were significant associated with SVR after 12 weeks of treatment (P = 0.027 for ITPase activity and P = 0.002 for HCV RNA <1,000 IU/mL day 7), whereas RVR was not (P = 0.068). In conclusion, the higher likelihood of SVR among patients with reduced ITPase activity is not explained by more efficient early elimination of virus. Martin Lagging, M.D., Ph.D.1 Karolina Rembeck, M.D.1 Jesper Waldenström, M.D.1 Staffan Nilsson, Ph.D.2 Kristina Nyström, Ph.D.1 Anna Martner, Ph.D.1 Magnus Lindh, M.D., Ph.D.1 Gunnar Norkrans, M.D., Ph.D.1 Johan Westin, M.D., Ph.D.1 Court Pedersen, M.D., Ph.D.3 Martti Färkkilä, M.D., Ph.D.4 Nina Langeland, M.D., Ph.D.5 Mads Rauning Buhl, M.D., Ph.D.6 Kristine Mørch, M.D.5 Peer B. Christensen, M.D., Ph.D.3 Kristoffer Hellstrand, M.D., Ph.D.1 1Department of Infectious Diseases/Virology Institute of Biomedicine Sahlgrenska Academy University of Gothenburg Gothenburg, Sweden 2Department of Mathematical Sciences Chalmers University of Technology Gothenburg, Sweden 3Department of Infectious Diseases University of Southern Denmark Odense, Denmark 4Department of Gastroenterology Helsinki University Helsinki, Finland 5Department of Medicine Haukeland University Hospital and Institute of Medicine University of Bergen Bergen, Norway 6Department of Infectious Diseases Aarhus University Aarhus, Denmark
MA10.01 Prospective Evaluation of the International Lung Screening Trial (ILST) Protocol for Management of First Screening LDCT
Authors: R. Myers, J. Mayo, S. Atkar-Khattra, R. Yuan, J. Yee, J. English, A. Mcguire, K. Grant, L. Dewar, M. Tammemagi, S. Lam
Journal: Journal of Thoracic Oncology (2021)
Life expectancy and risk of death in 6791 communities in England from 2002 to 2019: high-resolution spatiotemporal analysis of civil registration data
Authors: Theo Rashid, James E Bennett, Christopher J Paciorek, Yvonne Doyle, Jonathan Pearson-Stuttard, Seth Flaxman, Daniela Fecht, Mireille B Toledano, Guangquan Li, Hima I Daby, Eric Johnson, Bethan Davies, Majid Ezzati
Journal: The Lancet Public Health (2021)

BackgroundHigh-resolution data for how mortality and longevity have changed in England, UK are scarce. We aimed to estimate trends from 2002 to 2019 in life expectancy and probabilities of death at different ages for all 6791 middle-layer super output areas (MSOAs) in England.MethodsWe performed a high-resolution spatiotemporal analysis of civil registration data from the UK Small Area Health Statistics Unit research database using de-identified data for all deaths in England from 2002 to 2019, with information on age, sex, and MSOA of residence, and population counts by age, sex, and MSOA. We used a Bayesian hierarchical model to obtain estimates of age-specific death rates by sharing information across age groups, MSOAs, and years. We used life table methods to calculate life expectancy at birth and probabilities of death in different ages by sex and MSOA.FindingsIn 2002–06 and 2006–10, all but a few (0–1%) MSOAs had a life expectancy increase for female and male sexes. In 2010–14, female life expectancy decreased in 351 (5·2%) of 6791 MSOAs. By 2014–19, the number of MSOAs with declining life expectancy was 1270 (18·7%) for women and 784 (11·5%) for men. The life expectancy increase from 2002 to 2019 was smaller in MSOAs where life expectancy had been lower in 2002 (mostly northern urban MSOAs), and larger in MSOAs where life expectancy had been higher in 2002 (mostly MSOAs in and around London). As a result of these trends, the gap between the first and 99th percentiles of MSOA life expectancy for women increased from 10·7 years (95% credible interval 10·4–10·9) in 2002 to reach 14·2 years (13·9–14·5) in 2019, and for men increased from 11·5 years (11·3–11·7) in 2002 to 13·6 years (13·4–13·9) in 2019.InterpretationIn the decade before the COVID-19 pandemic, life expectancy declined in increasing numbers of communities in England. To ensure that this trend does not continue or worsen, there is a need for pro-equity economic and social policies, and greater investment in public health and health care throughout the entire country.FundingWellcome Trust, Imperial College London, Medical Research Council, Health Data Research UK, and National Institutes of Health Research.
P66.05 Correlation Between Expression of Immune Cell-Related Molecular Markers and Prognosis in Small Cell Lung Cancer (SCLC)
Authors: Y. Guo, L. Liu, J. Zhang, X. Wang, F. Teng, S. Wang, T. Li, T. Xie, P. Xing, J. Li, L. Yang
Journal: Journal of Thoracic Oncology (2021)
Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance
Authors: Soheil Yousefi, Ruizhi Deng, Kristina Lanko, Eva Medico Salsench, Anita Nikoncuk, Herma C. van der Linde, Elena Perenthaler, Tjakko J. van Ham, Eskeatnaf Mulugeta, Tahsin Stefan Barakat
Journal: Genome Medicine (2021)

Non-coding regulatory elements (NCREs), such as enhancers, play a crucial role in gene regulation, and genetic aberrations in NCREs can lead to human disease, including brain disorders. The human brain is a complex organ that is susceptible to numerous disorders; many of these are caused by genetic changes, but a multitude remain currently unexplained. Understanding NCREs acting during brain development has the potential to shed light on previously unrecognized genetic causes of human brain disease. Despite immense community-wide efforts to understand the role of the non-coding genome and NCREs, annotating functional NCREs remains challenging.
Allergen-specific T cells and clinical features of food allergy: Lessons from CoFAR immunotherapy cohorts
Authors: M. Cecilia Berin, Charuta Agashe, A. Wesley Burks, David Chiang, Wendy F. Davidson, Peter Dawson, Alexander Grishin, Alice K. Henning, Stacie M. Jones, Edwin H. Kim, Donald Y.M. Leung, Madhan Masilamani, Amy M. Scurlock, Scott H. Sicherer, Robert A. Wood, Hugh A. Sampson
Journal: Journal of Allergy and Clinical Immunology (2021)
Improving the noninvasive classification of glioma genetic subtype with deep learning and diffusion-weighted imaging
Authors: Julia Cluceru, Yannet Interian, Joanna J Phillips, Annette M Molinaro, Tracy L Luks, Paula Alcaide-Leon, Marram P Olson, Devika Nair, Marisa LaFontaine, Anny Shai, Pranathi Chunduru, Valentina Pedoia, Javier E Villanueva-Meyer, Susan M Chang, Janine M Lupo
Journal: Neuro-Oncology (2021)

Abstract Background Diagnostic classification of diffuse gliomas now requires an assessment of molecular features, often including IDH-mutation and 1p19q-codeletion status. Because genetic testing requires an invasive process, an alternative noninvasive approach is attractive, particularly if resection is not recommended. The goal of this study was to evaluate the effects of training strategy and incorporation of biologically relevant images on predicting genetic subtypes with deep learning. Methods Our dataset consisted of 384 patients with newly diagnosed gliomas who underwent preoperative MRI with standard anatomical and diffusion-weighted imaging, and 147 patients from an external cohort with anatomical imaging. Using tissue samples acquired during surgery, each glioma was classified into IDH-wildtype (IDHwt), IDH-mutant/1p19q-noncodeleted (IDHmut-intact), and IDH-mutant/1p19q-codeleted (IDHmut-codel) subgroups. After optimizing training parameters, top performing convolutional neural network (CNN) classifiers were trained, validated, and tested using combinations of anatomical and diffusion MRI with either a 3-class or tiered structure. Generalization to an external cohort was assessed using anatomical imaging models. Results The best model used a 3-class CNN containing diffusion-weighted imaging as an input, achieving 85.7% (95% CI: [77.1, 100]) overall test accuracy and correctly classifying 95.2%, 88.9%, 60.0% of the IDHwt, IDHmut-intact, and IDHmut-codel tumors. In general, 3-class models outperformed tiered approaches by 13.5%-17.5%, and models that included diffusion-weighted imaging were 5%-8.8% more accurate than those that used only anatomical imaging. Conclusion Training a classifier to predict both IDH-mutation and 1p19q-codeletion status outperformed a tiered structure that first predicted IDH-mutation, then 1p19q-codeletion. Including apparent diffusion coefficient (ADC), a surrogate marker of cellularity, more accurately captured differences between subgroups.
Impaired antioxidant KEAP1-NRF2 system in amyotrophic lateral sclerosis: NRF2 activation as a potential therapeutic strategy
Authors: Silvia Bono, Marco Feligioni, Massimo Corbo
Journal: Molecular Neurodegeneration (2021)

Abstract Background Oxidative stress (OS) is an imbalance between oxidant and antioxidant species and, together with other numerous pathological mechanisms, leads to the degeneration and death of motor neurons (MNs) in amyotrophic lateral sclerosis (ALS). Main body Two of the main players in the molecular and cellular response to OS are NRF2, the transcription nuclear factor erythroid 2-related factor 2, and its principal negative regulator, KEAP1, Kelch-like ECH (erythroid cell-derived protein with CNC homology)-associated protein 1. Here we first provide an overview of the structural organization, regulation, and critical role of the KEAP1-NRF2 system in counteracting OS, with a focus on its alteration in ALS. We then examine several compounds capable of promoting NRF2 activity thereby inducing cytoprotective effects, and which are currently in different stages of clinical development for many pathologies, including neurodegenerative diseases. Conclusions Although challenges associated with some of these compounds remain, important advances have been made in the development of safer and more effective drugs that could actually represent a breakthrough for fatal degenerative diseases such as ALS.
Abstract 11671: Family Encouragement for a Healthy Diet Predicts Diet Quality in Hispanic Adults at Risk for Cardiovascular Disease
Authors: Salman Alreshidi, Kaitlin Voigts, Terry A Lennie, Gia Mudd-martin
Journal: Circulation (2019)

Introduction: Family support for healthy diet may impact diet quality especially among Hispanics for whom familismo, or prioritization of family over the individual, is known to influence behavior....
P59.20 Natural History of KRAS Mutant Non-Small-Cell Lung Cancer in the Immunotherapy Era: A Single-Centre Retrospective Study
Authors: P. Bironzo, F. Jacobs, M. Cani, M.L. Reale, F. Tabbò, E. Olmetto, E. Capelletto, V. Napoli, F. Passiglia, A. Listì, L. Righi, M. Di Maio, S. Novello, G. Scagliotti
Journal: Journal of Thoracic Oncology (2021)
Comment on Rosenstock et al. Impact of a Weekly Glucagon-Like Peptide 1 Receptor Agonist, Albiglutide, on Glycemic Control and on Reducing Prandial Insulin Use in Type 2 Diabetes Inadequately Controlled on Multiple Insulin Therapy: A Randomized Trial. Diabetes Care 2020;43:2509–2518
Authors: Chinmay S. Marathe, Karen L. Jones, Christopher K. Rayner, Tongzhi Wu, Michael Horowitz
Journal: Diabetes Care (2021)

We read with interest the study by Rosenstock et al. (1), which demonstrates that in patients with type 2 diabetes managed on a basal-bolus insulin regimen, switching three prandial insulin injections for a long-acting glucagon-like peptide 1 receptor agonist (GLP-1RA), albiglutide, while maintaining the basal insulin, represents an effective strategy for optimizing glycemic control with reduced risks of hypoglycemia and weight gain along with increased convenience. In the cohort studied, baseline glycated hemoglobin levels were 7.8 ± 0.6% (albiglutide group) and 7.7 ± 0.6% (placebo group), indicating that in many participants, postprandial glycemic excursions were the dominant contributor of hyperglycemia. Achieving good glycemic control in those patients would, …
P53.08 Concomitant Fibrates and Immunotherapy in Non-Small Cell Lung Cancer Patients in the Veterans Health Administration
Authors: W. Stokes, M. Behera, R. Jiang, D. Gutman, Z. Huang, F. Giuste, A. Burns, N. Sebastian, S. Ramalingam, V. Sukhatme, M. Lowe, S. Ramalingam, V. Sukhatme, D. Moghanaki
Journal: Journal of Thoracic Oncology (2021)
Tritium Assay by Liquid Scintillation Spectrometry
Authors: Jack Leibman, Frank A. Gotch, Isidore S. Edelman
Journal: Circulation Research (1960)

Data have been presented which indicate that the liquid scintillation spectrometer provides a convenient and accurate method for the assay of tritium in body fluids. By means of arterial disappearance curves and comparative measurements of concentrations in plasma, transudates, and cerebrospinal fluid from 1 to 6 hours after simultaneous injection, the distribution rates of tritiated water were compared to those of deuterium oxide. No significant difference was found in the behavior of these tracers under the conditions of this study. It is concluded, therefore, that THO and D2O are equally reliable for studies on the kinetics of water distribution and for the measurement of total body water.
A systematic review of smartphone-based human activity recognition methods for health research
Authors: Marcin Straczkiewicz, Peter James, Jukka-Pekka Onnela
Journal: npj Digital Medicine (2021)

Abstract Smartphones are now nearly ubiquitous; their numerous built-in sensors enable continuous measurement of activities of daily living, making them especially well-suited for health research. Researchers have proposed various human activity recognition (HAR) systems aimed at translating measurements from smartphones into various types of physical activity. In this review, we summarized the existing approaches to smartphone-based HAR. For this purpose, we systematically searched Scopus, PubMed, and Web of Science for peer-reviewed articles published up to December 2020 on the use of smartphones for HAR. We extracted information on smartphone body location, sensors, and physical activity types studied and the data transformation techniques and classification schemes used for activity recognition. Consequently, we identified 108 articles and described the various approaches used for data acquisition, data preprocessing, feature extraction, and activity classification, identifying the most common practices, and their alternatives. We conclude that smartphones are well-suited for HAR research in the health sciences. For population-level impact, future studies should focus on improving the quality of collected data, address missing data, incorporate more diverse participants and activities, relax requirements about phone placement, provide more complete documentation on study participants, and share the source code of the implemented methods and algorithms.
Development of extracellular vesicle-based medicinal products: A position paper of the group “Extracellular Vesicle translatiOn to clinicaL perspectiVEs – EVOLVE France”
Authors: Amanda K.A. Silva, Marie Morille, Max Piffoux, Surendar Arumugam, Phlippe Mauduit, Jérôme Larghero, Arnaud Bianchi, Kelly Aubertin, Olivier Blanc-Brude, Danièle Noël, Emilie Velot, Célia Ravel, Céline Elie-Caille, Anna Sebbagh, Chantal Boulanger, Claire Wilhelm, Gabriel Rahmi, Isabelle Raymond-Letron, Kondareddy Cherukula, Tristan Montier, Christophe Martinaud, Jean-Marie Bach, Olivier Favre-Bulle, Jolanda Spadavecchia, Christian Jorgensen, Philippe Menasché, Clotilde Aussel, Joël Chopineau, Mathilde Mosser, Matti Ullah, Nicolas Sailliet, Nathalie Luciani, Noëlle Mathieu, Pierre-Emmanuel Rautou, Sophie Brouard, Wilfrid Boireau, Sébastien Jauliac, Marianne Dedier, Jean-Hugues Trouvin, Florence Gazeau, Marina Trouillas, Juliette Peltzer, Antoine Monsel, Sébastien Banzet
Journal: Advanced Drug Delivery Reviews (2021)