tbuckley/cabot-search huggingface dataset:
The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos
Authors: Feifei Li, Danyang Wang, Ruigao Song, Chunwei Cao, Zhihua Zhang, Yu Wang, Xiaoli Li, Jiaojiao Huang, Qiang Liu, Naipeng Hou, Bingxiang Xu, Xiao Li, Xiaomeng Gao, Yan Jia, Jianguo Zhao, Yanfang Wang
Journal: Genome biology (2020)

Abstract Background Pigs are important animals for agricultural and biomedical research, and improvement is needed for use of the assisted reproductive technologies. Determining underlying mechanisms of epigenetic reprogramming in the early stage of preimplantation embryos derived from in vitro fertilization (IVF), parthenogenesis, and androgenesis will not only contribute to assisted reproductive technologies of pigs but also will shed light into early human development. However, the reprogramming of three-dimensional architecture of chromatin in this process in pigs is poorly understood. Results We generate three-dimensional chromatin profiles for pig somatic cells, IVF, parthenogenesis, and androgenesis preimplantation embryos. We find that the chromosomes in the pig preimplantation embryos are enriched for superdomains, which are more rare in mice. However, p(s) curves, compartments, and topologically associated domains (TADs) are largely conserved in somatic cells and are gradually established during preimplantation embryogenesis in both mammals. In the uniparental pig embryos, the establishment of chromatin architecture is highly asynchronized at all levels from IVF embryos, and a remarkably strong decompartmentalization is observed during zygotic genome activation (ZGA). Finally, chromosomes originating from oocytes always establish TADs faster than chromosomes originating from sperm, both before and during ZGA. Conclusions Our data highlight a potential unique 3D chromatin pattern of enriched superdomains in pig preimplantation embryos, an unusual decompartmentalization process during ZGA in the uniparental embryos, and an asynchronized TAD reprogramming between maternal and paternal genomes, implying a severe dysregulation of ZGA in the uniparental embryos in pigs.
Drop dermoscopy for teledermatology
Authors: Feroze Kaliyadan, Puravoor Jayasree, Karalikkattil T. Ashique
Journal: Journal of the American Academy of Dermatology (2020)

There has been an explosion in the practice of teledermatology recently because of the COVID-19 pandemic. This includes patient-initiated consultations. One of the main limitations of patient-initiated consultations is the difficulty of incorporating dermoscopy. A drop of clear alcohol-based sanitizer is applied over the lesion to be examined, and the patient (or a helper) takes a photograph of the lesion through the fluid. The fluid reduces the reflection from the surface and helps visualization of the subsurface structures (Figs 1 and 2). Any smartphone or point-and-shoot camera is good enough for the imaging, making it easy to transfer the image to the dermatologist. The quality and resolution are better when dedicated cameras with macro mode capabilities are used.Fig 2A, Small cherry angioma: clinical image. B, Image taken after applying alcohol solution.View Large Image Figure ViewerDownload Hi-res image Download (PPT) Blum and Giacomel1Blum A. Giacomel J. "Tape dermatoscopy": constructing a low-cost dermatoscope using a mobile phone, immersion fluid and transparent adhesive tape.Dermatol Pract Concept. 2015; 5: 87-93Crossref PubMed Google Scholar have previously described a concept called tape dermoscopy, in which smartphones are used to take dermoscopic images of skin lesions after the immersion fluid is applied, followed by covering of the area with a transparent adhesive tape. The method we describe is simpler and faster, and it avoids the practical difficulties of having to apply adhesive tape over a liquid surface. The main limitations in our method are the minimal magnification (although the inherent zoom of the capture device can be used) and the reflection of the flash interfering with the image quality. The reflection can be reduced by trying out different angles while taking the image. Although the quality of the dermoscopy is obviously not comparable to that of standard dermoscopes, this can be an easy-to-use, simple screening and triage tool in the context of patient-initiated teledermatology.
Olaparib and durvalumab in patients with germline BRCA-mutated metastatic breast cancer (MEDIOLA): an open-label, multicentre, phase 1/2, basket study
Authors: Susan M Domchek, Sophie Postel-Vinay, Seock-Ah Im, Yeon Hee Park, Jean-Pierre Delord, Antoine Italiano, Jerome Alexandre, Benoit You, Sara Bastian, Matthew G Krebs, Ding Wang, Saiama N Waqar, Mark Lanasa, Joon Rhee, Haiyan Gao, Vidalba Rocher-Ros, Emma V Jones, Sakshi Gulati, Anna Coenen-Stass, Iwanka Kozarewa, Zhongwu Lai, Helen K Angell, Laura Opincar, Pia Herbolsheimer, Bella Kaufman
Journal: The Lancet Oncology (2020)
A care team-based classification and population management schema for connected diabetes care
Authors: Brian J. Levine, Kelly L. Close, Robert A. Gabbay
Journal: npj Digital Medicine (2020)

It has been proposed that telehealth may help to combat the epidemic of diabetes and other chronic diseases in the US. As a result of rapid technological advancement over the past decade, there has been an explosion in virtual diabetes management program offerings rooted in smartphone technology, connected devices for blood glucose monitoring, and remote coaching or support. Such offerings take many forms with unique features. We provide a care team-based classification system for connected diabetes care programs and highlight their strengths and limitations. We also include a framework for how the different classes of connected diabetes care may be deployed in a health system to promote improved population health.
Impact of the COVID-19 lockdown on the management and control of patients with GCA
Authors: Roman Praliaud, Helene Greigert, Maxime Samson, Marianne Zeller, Mathieu Boulin, Philip Bielefeld, André Ramon, Yves Cottin, Bernard Bonnotte
Journal: Annals of the Rheumatic Diseases (2020)

We read with interest the letter by Monti et al 1 reporting that patients with chronic arthritis treated with disease-modifying antirheumatic drugs do not seem to be at increased risk for severe complications from COVID-19. However, the indirect complications linked to the COVID-19 epidemic and the resulting lockdown must also be considered. This unprecedented situation has caused significant physical and psychological stress in many individuals. Previous studies have suggested that inflammatory rheumatic diseases are related to physiological stress2 3; we therefore assessed the impact of the COVID-19 lockdown on treatment adherence and disease stability in patients with giant cell arteritis (GCA). In this chronic inflammatory vasculitis, the duration and adherence to treatment (mainly glucocorticoids) are major factors in disease control and relapse prevention.4 5

A cross-sectional phone survey was conducted during the lockdown in 79 patients with GCA (n=79) living at home and who have been followed up at the Dijon University Hospital since January 2018. Three trained interviewers used a standardised questionnaire …
Efficacy and Safety of Sintilimab Plus Pemetrexed and Platinum as First-Line Treatment for Locally Advanced or Metastatic Nonsquamous NSCLC: a Randomized, Double-Blind, Phase 3 Study (Oncology pRogram by InnovENT anti-PD-1-11)
Authors: Yunpeng Yang, Zhehai Wang, Jian Fang, Qitao Yu, Baohui Han, Shundong Cang, Gongyan Chen, Xiaodong Mei, Zhixiong Yang, Rui Ma, Minghong Bi, Xiubao Ren, Jianying Zhou, Baolan Li, Yong Song, Jifeng Feng, Juan Li, Zhiyong He, Rui Zhou, Weimin Li, You Lu, Yingyi Wang, Lijun Wang, Nong Yang, Yan Zhang, Zhuang Yu, Yanqiu Zhao, Conghua Xie, Ying Cheng, Hui Zhou, Shuyan Wang, Donglei Zhu, Wen Zhang, Li Zhang
Journal: Journal of Thoracic Oncology (2020)

IntroductionSintilimab, an anti–programmed death 1 antibody, plus pemetrexed and platinum had revealed promising efficacy for nonsquamous NSCLC in a phase 1b study. We conducted a randomized, double-blind, phase 3 study to compare the efficacy and safety of sintilimab with placebo, both in combination with such chemotherapy (ClinicalTrials.gov: NCT03607539).MethodsA total of 397 patients with previously untreated, locally advanced or metastatic nonsquamous NSCLC without sensitizing EGFR or anaplastic lymphoma kinase genomic aberration were randomized (2:1 ratio) to receive either sintilimab 200 mg or placebo plus pemetrexed and platinum once every 3 weeks for four cycles, followed by sintilimab or placebo plus pemetrexed therapy. Crossover or treatment beyond disease progression was allowed. The primary end point was progression-free survival (PFS) as judged by an independent radiographic review committee.ResultsAs of November 15, 2019, the median follow-up was 8.9 months. The median PFS was significantly longer in the sintilimab-combination group than that in the placebo-combination group (8.9 versus 5.0 mo; hazard ratio, 0.482, 95% confidence interval [CI]: 0.362–0.643; p < 0.00001). The confirmed objective response rate was 51.9% (95% CI: 45.7%–58.0%) in the sintilimab-combination group and 29.8% (95% CI: 22.1%–38.4%) in placebo-combination group. The incidence of grade 3 or higher adverse events was 61.7% in sintilimab-combination group and 58.8% in placebo-combination group.ConclusionsIn Chinese patients with previously untreated, locally advanced or metastatic nonsquamous NSCLC, the addition of sintilimab to chemotherapy with pemetrexed and platinum resulted in considerably longer PFS than with chemotherapy alone with manageable safety profiles.
Colin Alban Bryant McLaren
Authors: Anthony Rubin, Leslie Shutt
Journal: BMJ (2020)

Colin Alban Bryant McLaren was a Mancunian who ventured south to study medicine at Birmingham University. He started his anaesthetic training in Wolverhampton, but this was interrupted in 1953 by the obligatory period of national service, which he did as a singlehanded anaesthetist in Egypt. A substantive post in the Services followed, and in 1956 he began an outstanding career with the Royal Air Force. In 1961 he passed the FFARCS examination, and in 1964 he was appointed consultant anaesthetist at the Royal Air Force Hospital at Wroughton in Wiltshire, where he was head of the department for more than 20 years. He coordinated anaesthetic escorts on aeromedical evacuation flights, including personally acting …
Contiguous and stochastic CHH methylation patterns of plant DRM2 and CMT2 revealed by single-read methylome analysis
Authors: Keith D. Harris, Assaf Zemach
Journal: Genome biology (2020)

Cytosine methylome data is commonly generated through next-generation sequencing, with analyses averaging methylation states of individual reads. We propose an alternative method of analysing single-read methylome data. Using this method, we identify patterns relating to the mechanism of two plant non-CG-methylating enzymes, CMT2 and DRM2. CMT2-methylated regions show higher stochasticity, while DRM2-methylated regions have higher variation among cells. Based on these patterns, we develop a classifier that predicts enzyme activity in different species and tissues. To facilitate further single-read analyses, we develop a genome browser, SRBrowse, optimised for visualising and analysing sequencing data at single-read resolution.
Emergency Visits for Thunderstorm-Related Respiratory Illnesses Among Older Adults
Authors: Eric Zou, Christopher Worsham, Nolan H. Miller, David Molitor, Julian Reif, Anupam B. Jena
Journal: JAMA Internal Medicine (2020)

This cross-sectional study examines the association between thunderstorm-related atmospheric changes and emergency department visits for acute respiratory illnesses among Medicare beneficiaries.
Accuracy of Ultrasound for Evaluation of Colorectal Segments in Patients With Inflammatory Bowel Diseases: A Systematic Review and Meta-analysis
Authors: Shintaro Sagami, Taku Kobayashi, Yusuke Miyatani, Shinji Okabayashi, Hajime Yamazaki, Toshihiko Takada, Kenji Kinoshita, Mariangela Allocca, Reiko Kunisaki, Pradeep Kakkadasam Ramaswamy, Manabu Shiraki, Toshifumi Hibi, Yuki Kataoka
Journal: Clinical Gastroenterology and Hepatology (2020)
Prevalence and Prognostic Significance of Malnutrition in Patients With Acute Coronary Syndrome
Authors: Sergio Raposeiras Roubín, Emad Abu Assi, María Cespón Fernandez, Cristina Barreiro Pardal, Andrea Lizancos Castro, Jose Antonio Parada, David Dobarro Pérez, Sonia Blanco Prieto, Xavier Rossello, Borja Ibanez, Andrés Íñiguez Romo
Journal: Journal of the American College of Cardiology (2020)
AB0019 Effect of extracellular sodium concentration in byglican and decorin synthesis by human chondrocytes
Authors: IA Ferraz-Amaro, E Trujillo, MF Arteaga, I Cozar, J Avila, S Bustabad, T Gonzalez, P Martin-Vasallo
Journal: Annals of the Rheumatic Diseases (2001)

<h3>Background</h3> An altered chondrocytes phenotipic expression of biglycan and decorin is an early event in osteoarthritis (OA). Changes in extracellular matrix sodium concentration ([Na+]) occurs in OA. Previous results suggested that chondrocytes are sensitive to changes in their extracellular [Na+] environment and respond with variations in the matrix synthesis. <h3>Objectives</h3> Here we have studied the influence of extracellular [Na+] on the metabolism of small proteoglycans, biglycan and decorin, in a human chondrocyte-like cell line, C20/A4. <h3>Methods</h3> Extracellular deposition of biglycan and decorin was analysed in C20A4 cells cultured: 1) inmunohistochemically using specific antibodies against biglycan and decorin and secondary IFTC conjugated antibodies; and 2) in SDS-PAGE electrophoresis and blotting using the corresponding antibodies. <h3>Results</h3> Fluorescence inmunohistochemically shows specific extracellular expression of biglycan and decorin in chondrocytes cultured in estandard [Na+] (154 nm) and western blotting intensities of these small proteoglycans varied with [Na+]. <h3>Conclusion</h3> This study demostrates that biglycan and decorin are expressed in the human chondrocyte cell line C20A4. We are now searching if [Na+] variations is able to produce cualitative or cuantitative alterations in the matrix synthesis as it have been found in osteoarthritis. -Supported by FIS grant 99/0695-
Effectiveness of Medical Therapy for Functional Mitral Regurgitation in Heart Failure With Reduced Ejection Fraction
Authors: Anna Sannino, Sivakumar Sudhakaran, Gregory Milligan, Anima Chowdhury, Ayman Haq, Molly Szerlip, Milton Packer, Paul A. Grayburn
Journal: Journal of the American College of Cardiology (2020)
Abstract 13842: Comparing a Novel Machine Learning Method to the Martin-Hopkins Equation for Low-Density Lipoprotein Cholesterol Estimation for Levels Below 70 Mg/dl
Authors: Yasin Hussain, Gupreet Singh, Zhuoran Xu, Evan Sholle, Kelly Michalak, Kristina Dolan, Gabriel Maliakal, Mohit Pandey, Benjamin Lee, Alexander v Rosendael, Lohendran Baskaran, James K Min, Leslee Shaw, Subhi Alaref
Journal: Circulation (2019)

Introduction: Low-density lipoprotein cholesterol (LDL-C) lowering is a target in both primary and secondary prevention for atherosclerotic cardiovascular disease. Current methods of estimation hav...
Abstract 13392: Sex and Race Differences in Heart Failure Risk in Late Life: The Atherosclerosis Risk in Communities (ARIC) Study
Authors: Alvin Chandra, Hicham Skali, Brian Claggett, Joseph Rossi, Patricia Chang, Stuart D Russell, Kunihiro Matsushita, Dalane W Kitzman, Suma H Konety, Thomas Mosley, Scott D Solomon, Amil M Shah
Journal: Circulation (2019)

Introduction: Heart failure (HF) risk differs by race and sex, with black Americans demonstrating higher HF incidence in early adulthood and mid-life. Limited data is available regarding race- and ...
SARS-CoV-2 causes a specific dysfunction of the kidney proximal tubule
Authors: Alexis Werion, Leila Belkhir, Marie Perrot, Gregory Schmit, Selda Aydin, Zhiyong Chen, Andrea Penaloza, Julien De Greef, Halil Yildiz, Lucie Pothen, Jean Cyr Yombi, Joseph Dewulf, Anais Scohy, Ludovic Gérard, Xavier Wittebole, Pierre-François Laterre, Sara E. Miller, Olivier Devuyst, Michel Jadoul, Johann Morelle, Frank Aboubakar, Souad Acid, Nadia Amini, Sarah Bailly, Christophe Beauloye, Diego Castanares-Zapatero, Emmanuel Coche, Christine Collienne, Pascale Cornette, Isabelle De Brauwer, Mélanie Dechamps, Florence Dupriez, Antoine Froidure, Quentin Garnir, Bernhard Gerber, Benoît Ghaye, Isabelle Gilard, Sophie Gohy, Charles Grégoire, Philippe Hantson, Luc-Marie Jacquet, Benoit Kabamba, Shakeel Kautbally, Nicolas Lanthier, Fatima Larbaoui, Giuseppe Liistro, Frédéric Maes, Virginie Montiel, Benny Mwenge, Sophie Pierard, Charles Pilette, Anne Catherine Pouleur, Amaury Sogorb, Peter Starkel, Hector Rodriguez-Villalobos, Maximilien Thoma, Olivier Van Caeneghem, David Vancraeynest
Journal: Kidney International (2020)
Circulating Tumor DNA Is a Reliable Measure of Tumor Burden at Diagnosis of Diffuse Large B Cell Lymphoma: An International Reproducibility Study
Authors: David M. Kurtz, Michael Jin, Joanne Soo, Florian Scherer, Alexander Craig, Jacob J Chabon, Joseph G Schroers-Martin, Chih Long Liu, Henning Stehr, Christine Schmitz, Ulrich Duehrsen, Andreas Hüttmann, Anne Ségolène Cottereau, Michel Meignan, Olivier Casasnovas, Jason R. Westin, Gianluca Gaidano, Davide Rossi, Mark Roschewski, Wyndham H. Wilson, Maximilian Diehn, Ash A. Alizadeh
Journal: Blood (2017)
Susceptibility to COVID‐19 in Patients Treated With Antimalarials: A Population‐Based Study in Emilia‐Romagna, Northern Italy
Authors: Carlo Salvarani, Pamela Mancuso, Federica Gradellini, Nilla Viani, Paolo Pandolfi, Massimo Reta, Giuliano Carrozzi, Gilda Sandri, Gianluigi Bajocchi, Elena Galli, Francesco Muratore, Luigi Boiardi, Nicolò Pipitone, Giulia Cassone, Stefania Croci, Anna Maria Marata, Massimo Costantini, Paolo Giorgi Rossi
Journal: Arthritis & Rheumatology (2020)

To evaluate the susceptibility to coronavirus disease 2019 (COVID-19) in patients with autoimmune conditions treated with antimalarials in a population-based study. All residents treated with chloroquine (CQ)/hydroxychloroquine (HCQ) from July through December 2019 and living in 3 provinces of Regione Emilia-Romagna were identified by drug prescription registries and matched with the registry containing all residents living in the same areas who have had swabs and tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated. A total of 4,408 patients were identified. The prevalence of patients receiving antimalarials was 0.85 per 1,000 men and 3.3 per 1,000 women. The cumulative incidence of testing during the study period was 2.7% in the general population and 3.8% among those receiving CQ or HCQ, while the cumulative incidence of testing positive was 0.55% in the general population and 0.70% among those receiving CQ/HCQ. Multivariate models showed that those receiving CQ/HCQ had a slightly higher probability of being tested compared to the general population (OR 1.09 [95% CI 0.94-1.28]), the same probability of being diagnosed as having COVID-19 (OR 0.94 [95% CI 0.66-1.34]), and a slightly lower probability of being positive once tested (OR 0.83 [95% CI 0.56-1.23]). None of the differences were significant. Our findings do not support the use of antimalarials as a prophylactic treatment of COVID-19.
Latent Class Growth Analysis of Gout Flare Trajectories: A Three‐Year Prospective Cohort Study in Primary Care
Authors: Lorraine Watson, John Belcher, Elaine Nicholls, Sara Muller, Christian Mallen, Edward Roddy
Journal: Arthritis & Rheumatology (2020)

Objective To investigate the existence of distinct classes of gout flare trajectories and compare their gout‐specific, comorbid, and sociodemographic characteristics. Methods In a prospective cohort study, adults with gout who were registered with 20 general practices self‐reported the number of gout flares experienced at baseline and after 6, 12, 24, and 36 months via postal questionnaires. Latent class growth analysis (LCGA) was used to identify distinct gout flare trajectory classes. Statistical criteria and clinical interpretability were used to decide the optimal number of classes. Baseline comorbidities, medications, and sociodemographic and gout‐specific characteristics of members of each class were described. Results A total of 1,164 participants (mean ± SD age 65.6 ± 12.5 years; 972 [84%] male) were included. Six latent gout flare trajectory classes were identified: “frequent and persistent” (n = 95), “gradually worsening” (n = 276), “frequent then improving” (n = 14), “moderately frequent” (n = 287), “moderately frequent then improving” (n = 143), and “infrequent” (n = 349). The “frequent and persistent” trajectory had the most class members classified as obese and, along with the “gradually worsening” class, the highest proportion who were socioeconomically deprived. The “frequent and persistent,” “gradually worsening,” and ”frequent then improving” classes had the highest proportions of class members with an estimated glomerular filtration rate &lt;60 ml/minute/1.73 m 2 . The “infrequent” gout flare class was associated with more frequent allopurinol use and lower urate levels. Conclusion Six distinct gout flare trajectories were identified. Infrequent flares were associated with allopurinol use and lower serum urate levels, supporting the use of urate‐lowering therapy to reduce flare frequency. The characteristics of flare trajectory classes could help to target interventions and improve patient care.
Unique Cholangiocyte‐Targeted IgM Autoantibodies Correlate With Poor Outcome in Biliary Atresia
Authors: Yuhuan Luo, Dania Brigham, Joseph Bednarek, Richard Torres, Dong Wang, Sara Ahmad, Cara L. Mack
Journal: Hepatology (2020)

Background and Aims The etiology of biliary atresia (BA) is not known and is likely multifactorial, including a genetic predisposition, a viral or environmental trigger, an aberrant autoimmune response targeting cholangiocytes, and unique susceptibilities of the neonatal bile ducts to injury. Damaged cholangiocytes may express neo self‐antigens and elicit autoreactive T‐cell‐mediated inflammation and B‐cell production of autoantibodies. The aim of this study was to discover autoantibodies in BA that correlated with outcomes. Approach and Results An autoantigen microarray encompassing approximately 9,500 autoantigens was used to screen for serum immunoglobulin M (IgM) and immunoglobulin G (IgG) autoantibodies in patients with BA or other liver disease controls. Validation of candidate autoantibodies by enzyme‐linked immunosorbent assay on a second cohort of subjects (6‐12 months following Kasai portoenterostomy) and correlations of autoantibodies with outcomes were performed (serum bilirubin levels and need for liver transplant in first 2 years of life). Mean anti‐chitinase 3‐like 1 (CHI3L1), anti‐delta‐like ligand (DLL‐4), and antisurfactant protein D (SFTPD) IgM autoantibodies in BA were significantly higher compared with controls, and IgM autoantibody levels positively correlated with worse outcomes. Immunofluorescence revealed cholangiocyte‐predominant expression of CHI3L1, DLL‐4, and SFTPD. The humoral autoantibody response was associated with C3d complement activation and T‐cell autoimmunity, based on detection of cholangiocyte‐predominant C3d co‐staining and peripheral blood autoreactive T cells specific to CHI3L1, DLL‐4 and SFTPD, respectively. Conclusions BA is associated with cholangiocyte‐predominant IgM autoantibodies in the first year after Kasai portoenterostomy. Anti‐CHI3L1, anti‐DLL‐4, and anti‐SFTPD IgM autoantibody correlations with worse outcomes and the detection of C3d on cholangioctyes and antigen‐specific autoreactive T cells suggest that autoimmunity plays a role in the ongoing bile duct injury and progression of disease.