tbuckley/cabot-search huggingface dataset:
Comparison of fine-needle aspiration and fine-needle biopsy devices for endoscopic ultrasound-guided sampling of solid lesions: a systemic review and meta-analysis
Authors: Priscilla A. van Riet, Nicole S. Erler, Marco J. Bruno, Djuna L. Cahen
Journal: Endoscopy (2020)

Endoscopic ultrasound (EUS)-guided tissue acquisition is extensively used, but the optimal sampling device is still a matter of debate. We performed meta-analyses on studies comparing fine-needle aspiration (FNA) with fine-needle biopsy (FNB) needles, and studies comparing different FNB needles.Online databases were searched for randomized controlled trials (RCTs) of at least 50 cases with a suspected solid pancreatic or nonpancreatic lesion that compared FNA with FNB needles. Outcome measures included diagnostic accuracy, adequacy, number of passes, presence of tissue cores, and adverse events. We also performed meta-regression analysis on the effect of FNB design on diagnostic accuracy. Quality was assessed using the QUADAS-2 tool.18 RCTs comparing FNA with FNB needles were included. FNB provided a higher pooled diagnostic accuracy (87 % vs. 80 %; P = 0.02) and tissue core rate (80 % vs. 62 %; P = 0.002), and allowed diagnosis with fewer passes (P = 0.03), in both pancreatic and nonpancreatic lesions. A total of 93 studies were included comparing different FNB devices. Pooled diagnostic accuracy was higher for forward-facing bevel needles than for the reverse bevel needle. In this analysis, study quality was low and heterogeneity was high (I2 = 80 %).FNB outperformed FNA when sampling pancreatic and nonpancreatic lesions. Forward-facing bevel FNB needles seemed to outperform the reverse bevel FNB needle, but the low quality of evidence prevents us from making strong recommendations on the optimal FNB design.
Dianne Mary Burton
Authors: Sarah Hubbold
Journal: BMJ (2020)

After house jobs in Bristol, Suffolk, and Leeds, Dianne Mary Burton was a consultant in child and adolescent psychiatry in York in 1975-76. Subsequently she worked as a part time specialist in child psychiatry for Tameside AHA from 1976 to 1979. She then worked as a full time consultant in the Macclesfield district of Cheshire, from …
Phenotype and kinetics of SARS-CoV-2–specific T cells in COVID-19 patients with acute respiratory distress syndrome
Authors: Daniela Weiskopf, Katharina S. Schmitz, Matthijs P. Raadsen, Alba Grifoni, Nisreen M. A. Okba, Henrik Endeman, Johannes P. C. van den Akker, Richard Molenkamp, Marion P. G. Koopmans, Eric C. M. van Gorp, Bart L. Haagmans, Rik L. de Swart, Alessandro Sette, Rory D. de Vries
Journal: Science Immunology (2020)

SARS-CoV-2 has been identified as the causative agent of a global outbreak of respiratory tract disease (COVID-19). In some patients the infection results in moderate to severe acute respiratory distress syndrome (ARDS), requiring invasive mechanical ventilation. High serum levels of IL-6, IL-10 and an immune hyperresponsiveness referred to as a 'cytokine storm' have been associated with poor clinical outcome. Despite the large numbers of COVID-19 cases and deaths, information on the phenotype and kinetics of SARS-CoV-2-specific T cells is limited. Here, we studied 10 COVID-19 patients who required admission to an intensive care unit and detected SARS-CoV-2-specific CD4+ and CD8+ T cells in 10 out of 10 and 8 out of 10 patients, respectively. We also detected low levels of SARS-CoV-2-reactive T cells in 2 out of 10 healthy controls not previously exposed to SARS-CoV-2, which is indicative of cross-reactivity due to past infection with 'common cold' coronaviruses. The strongest T-cell responses were directed to the spike (S) surface glycoprotein, and SARS-CoV-2-specific T cells predominantly produced effector and Th1 cytokines, although Th2 and Th17 cytokines were also detected. Furthermore, we studied T-cell kinetics and showed that SARS-CoV-2-specific T cells are present relatively early and increase over time. Collectively, these data shed light on the potential variations in T-cell responses as a function of disease severity, an issue that is key to understanding the potential role of immunopathology in the disease, and also inform vaccine design and evaluation.
Letter to the Editor: Comment on Alpha‐Fetoprotein Decrease From &gt;1,000 to &lt;500 ng/mL in Patients With Hepatocellular Carcinoma Leads to Improved Posttransplant Outcomes
Authors: Sami Akbulut, Tevfik Tolga Sahin, Sezai Yilmaz
Journal: Hepatology (2020)
Ten-Year Follow-Up Survival of the Medicine, Angioplasty, or Surgery Study (MASS II)
Authors: Whady Hueb, Neuza Lopes, Bernard J. Gersh, Paulo R. Soares, Expedito E. Ribeiro, Alexandre C. Pereira, Desiderio Favarato, Antonio Sérgio C. Rocha, Alexandre C. Hueb, Jose A.F. Ramires
Journal: Circulation (2010)

Background— This study compared the 10-year follow-up of percutaneous coronary intervention (PCI), coronary artery surgery (CABG), and medical treatment (MT) in patients with multivessel coronary artery disease, stable angina, and preserved ventricular function. Methods and Results— The primary end points were overall mortality, Q-wave myocardial infarction, or refractory angina that required revascularization. All data were analyzed according to the intention-to-treat principle. At a single institution, 611 patients were randomly assigned to CABG (n=203), PCI (n=205), or MT (n=203). The 10-year survival rates were 74.9% with CABG, 75.1% with PCI, and 69% with MT ( P =0.089). The 10-year rates of myocardial infarction were 10.3% with CABG, 13.3% with PCI, and 20.7% with MT ( P &lt;0.010). The 10-year rates of additional revascularizations were 7.4% with CABG, 41.9% with PCI, and 39.4% with MT ( P &lt;0.001). Relative to the composite end point, Cox regression analysis showed a higher incidence of primary events in MT than in CABG (hazard ratio 2.35, 95% confidence interval 1.78 to 3.11) and in PCI than in CABG (hazard ratio 1.85, 95% confidence interval 1.39 to 2.47). Furthermore, 10-year rates of freedom from angina were 64% with CABG, 59% with PCI, and 43% with MT ( P &lt;0.001). Conclusions— Compared with CABG, MT was associated with a significantly higher incidence of subsequent myocardial infarction, a higher rate of additional revascularization, a higher incidence of cardiac death, and consequently a 2.29-fold increased risk of combined events. PCI was associated with an increased need for further revascularization, a higher incidence of myocardial infarction, and a 1.46-fold increased risk of combined events compared with CABG. Additionally, CABG was better than MT at eliminating anginal symptoms. Clinical Trial Registration Information— URL: http://www.controlled-trials.com. Registration number: ISRCTN66068876.
Dysregulation of microRNA expression in the skin during cutaneous adverse drug reactions
Authors: Eric Pedruzzi, François Chasset, Isabelle Duroux‐Richard, David Bocarra, Florence Apparailly, Julien Nourikyan, Mathilde Lumy, Simon de Bernard, Olivia Bonduelle, Laurent Buffat, Behazine Combadière, Angèle Soria
Journal: Allergy (2020)

Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Cell-Type-Specific Outcome Representation in the Primary Motor Cortex
Authors: Shahar Levy, Maria Lavzin, Hadas Benisty, Amir Ghanayim, Uri Dubin, Shay Achvat, Zohar Brosh, Fadi Aeed, Brett D. Mensh, Yitzhak Schiller, Ron Meir, Omri Barak, Ronen Talmon, Adam W. Hantman, Jackie Schiller
Journal: Neuron (2020)
Multisystem Inflammatory Syndrome in Children in New York State
Authors: Elizabeth M. Dufort, Emilia H. Koumans, Eric J. Chow, Elizabeth M. Rosenthal, Alison Muse, Jemma Rowlands, Meredith A. Barranco, Angela M. Maxted, Eli S. Rosenberg, Delia Easton, Tomoko Udo, Jessica Kumar, Wendy Pulver, Lou Smith, Brad Hutton, Debra Blog, Howard Zucker
Journal: New England Journal of Medicine (2020)

A multisystem inflammatory syndrome in children (MIS-C) is associated with coronavirus disease 2019. The New York State Department of Health (NYSDOH) established active, statewide surveillance to describe hospitalized patients with the syndrome.
Yottixel – An Image Search Engine for Large Archives of Histopathology Whole Slide Images
Authors: Shivam Kalra, H.R. Tizhoosh, Charles Choi, Sultaan Shah, Phedias Diamandis, Clinton J.V. Campbell, Liron Pantanowitz
Journal: Medical Image Analysis (2020)

With the emergence of digital pathology, searching for similar images in large archives has gained considerable attention. Image retrieval can provide pathologists with unprecedented access to the evidence embodied in already diagnosed and treated cases from the past. This paper proposes a search engine specialized for digital pathology, called Yottixel, a portmanteau for "one yotta pixel," alluding to the big-data nature of histopathology images. The most impressive characteristic of Yottixel is its ability to represent whole slide images (WSIs) in a compact manner. Yottixel can perform millions of searches in real-time with a high search accuracy and low storage profile. Yottixel uses an intelligent indexing algorithm capable of representing WSIs with a mosaic of patches which are then converted into barcodes, called "Bunch of Barcodes" (BoB), the most prominent performance enabler of Yottixel. The performance of the prototype platform is qualitatively tested using 300 WSIs from the University of Pittsburgh Medical Center (UPMC) and 2,020 WSIs from The Cancer Genome Atlas Program (TCGA) provided by the National Cancer Institute. Both datasets amount to more than 4,000,000 patches of 1000 × 1000 pixels. We report three sets of experiments that show that Yottixel can accurately retrieve organs and malignancies, and its semantic ordering shows good agreement with the subjective evaluation of human observers.
cfNOMe — A single assay for comprehensive epigenetic analyses of cell-free DNA
Authors: Florian Erger, Deborah Nörling, Domenica Borchert, Esther Leenen, Sandra Habbig, Michael S. Wiesener, Malte P. Bartram, Andrea Wenzel, Christian Becker, Mohammad R. Toliat, Peter Nürnberg, Bodo B. Beck, Janine Altmüller
Journal: Genome Medicine (2020)

Abstract Cell-free DNA (cfDNA) analysis has become essential in cancer diagnostics and prenatal testing. We present cfNOMe , a two-in-one method of measuring cfDNA cytosine methylation and nucleosome occupancy in a single assay using non-disruptive enzymatic cytosine conversion and a custom bioinformatic pipeline. We show that enzymatic cytosine conversion better preserves cfDNA fragmentation information than does bisulfite conversion. Whereas previously separate experiments were required to study either epigenetic marking, cfNOMe delivers reliable results for both, enabling more comprehensive and inexpensive epigenetic cfDNA profiling. cfNOMe has the potential to advance biomarker discovery and diagnostic usage in diseases with systemic perturbations of cfDNA composition.
Serum metabolites reflecting gut microbiome alpha diversity predict type 2 diabetes
Authors: Cristina Menni, Jialing Zhu, Caroline I Le Roy, Olatz Mompeo, Kristin Young, Casey M. Rebholz, Elizabeth Selvin, Kari E. North, Robert P Mohney, Jordana T Bell, Eric Boerwinkle, Tim D Spector, Massimo Mangino, Bing Yu, Ana M Valdes
Journal: Gut Microbes (2020)

Type 2 diabetes (T2D) is associated with reduced gut microbiome diversity, although the cause is unclear. Metabolites generated by gut microbes also appear to be causative factors in T2D. We therefore searched for serum metabolites predictive of gut microbiome diversity in 1018 females from TwinsUK with concurrent metabolomic profiling and microbiome composition. We generated a Microbial Metabolites Diversity (MMD) score of six circulating metabolites that explained over 18% of the variance in microbiome alpha diversity. Moreover, the MMD score was associated with a significantly lower odds of prevalent (OR[95%CI] = 0.22[0.07;0.70], P = .01) and incident T2D (HR[95%CI] = 0.31[0.11,0.90], P = .03). We replicated our results in 1522 individuals from the ARIC study (prevalent T2D: OR[95%CI] = 0.79[0.64,0.96], P = .02, incident T2D: HR[95%CI] = 0.87[0.79,0.95], P = .003). The MMD score mediated 28%[15%,94%] of the total effect of gut microbiome on T2D after adjusting for confounders. Metabolites predicting higher microbiome diversity included 3-phenylpropionate(hydrocinnamate), indolepropionate, cinnamoylglycine and 5-alpha-pregnan-3beta,20 alpha-diol monosulfate(2) of which indolepropionate and phenylpropionate have already been linked to lower incidence of T2D. Metabolites correlating with lower microbial diversity included glutarate and imidazole propionate, of which the latter has been implicated in insulin resistance. Our results suggest that the effect of gut microbiome diversity on T2D is largely mediated by microbial metabolites, which might be modifiable by diet.
Effects of combined renin–angiotensin–aldosterone system inhibitor and beta‐blocker treatment on outcomes in heart failure with reduced ejection fraction: insights from <scp>BIOSTAT‐CHF</scp> and <scp>ASIAN‐HF</scp> registries
Authors: Wouter Ouwerkerk, Tiew‐Hwa K. Teng, Jasper Tromp, Wan Ting Tay, John G. Cleland, Dirk J. van Veldhuisen, Kenneth Dickstein, Leong L. Ng, Chim C. Lang, Stefan D. Anker, Faiez Zannad, Chung‐Lieh Hung, Jitendra P.S. Sawhney, Ajay Naik, Wataru Shimizu, Nobuhisa Hagiwara, Gurpreet Singh Wander, Inder Anand, A. Mark Richards, Adriaan A. Voors, Carolyn S.P. Lam
Journal: European Journal of Heart Failure (2020)
Colchicine for the Treatment of Myocardial Injury in Patients With Coronavirus Disease 2019 (COVID-19)—An Old Drug With New Life?
Authors: Amir B. Rabbani, Rushi V. Parikh, Asim M. Rafique
Journal: JAMA Network Open (2020)

Spyridon G. Deftereos, MD, PhD; Georgios Giannopoulos, MD, PhD; Dimitrios A. Vrachatis, MD, MSc, PhD; Gerasimos D. Siasos, MD, MSc, PhD; Sotiria G. Giotaki, MD; Panagiotis Gargalianos, MD, PhD; Simeon Metallidis, MD, PhD; George Sianos, MD, PhD; Stefanos Baltagiannis, MD, MSc; Periklis Panagopoulos, MD, PhD; Konstantinos Dolianitis, MD, MSc; Efthalia Randou, MD; Konstantinos Syrigos, MD, PhD; Anastasia Kotanidou, MD, PhD; Nikolaos G. Koulouris, MD, PhD; Haralampos Milionis, MD, PhD; Nikolaos Sipsas, MD, PhD; Charalampos Gogos, MD, PhD; George Tsoukalas, MD, PhD; Christoforos D. Olympios, MD, PhD; Eleftheria Tsagalou, MD, PhD; Ilias Migdalis, MD, PhD; Styliani Gerakari, MD; Christos Angelidis, MD; Dimitrios Alexopoulos, MD, PhD; Pericles Davlouros, MD, PhD; George Hahalis, MD, PhD; Ioannis Kanonidis, MD, PhD; Demosthenes Katritsis, MD, PhD; Theofilos Kolettis, MD, PhD; Antonios S. Manolis, MD, PhD; Lampros Michalis, MD, PhD; Katerina K. Naka, MD, PhD; Vlasios N. Pyrgakis, MD, PhD; Konstantinos P. Toutouzas, MD, PhD; Filippos Triposkiadis, MD, PhD; Konstantinos Tsioufis, MD, PhD; Emmanouil Vavouranakis, MD, PhD; Luis Martinèz-Dolz, MD, PhD; Bernhard Reimers, MD; Giulio G. Stefanini, MD, MSc, PhD; Michael Cleman, MD, PhD; John Goudevenos, MD, PhD; Sotirios Tsiodras, MD, PhD; Dimitrios Tousoulis, MD, PhD; Efstathios Iliodromitis, MD, PhD; Roxana Mehran, MD, PhD; George Dangas, MD, PhD; Christodoulos Stefanadis, MD, PhD; on behalf of the GRECCO-19 investigators
Cancer Cell Invasion of Mammary Organoids with Basal‐In Phenotype
Authors: Eric Parigoris, Soojung Lee, David Mertz, Madeleine Turner, Amy Y. Liu, Jason Sentosa, Sabra Djomehri, Hao Chen Chang, Kathryn Luker, Gary Luker, Celina G. Kleer, Shuichi Takayama
Journal: Advanced Healthcare Materials (2020)

This paper describes mammary organoids with a basal-in phenotype where the basement membrane is located on the interior surface of the organoid. A key materials consideration to induce this basal-in phenotype is the use of a minimal gel scaffold that the epithelial cells self-assemble around and encapsulate. When MDA-MB-231 breast cancer cells are co-cultured with epithelial cells from day 0 under these conditions, cells self-organize into patterns with distinct cancer cell populations both inside and at the periphery of the epithelial organoid. In another type of experiment, the robust formation of the basement membrane on the epithelial organoid interior enables convenient studies of MDA-MB-231 invasion in a tumor progression-relevant direction relative to epithelial cell-basement membrane positioning. That is, the study of cancer invasion through the epithelium first, followed by the basement membrane to the basal side, is realized in an experimentally convenient manner where the cancer cells are simply seeded on the outside of preformed organoids, and their invasion into the organoid is monitored. Interestingly, invasion is more prominent when tumor cells are added to day 7 organoids with less developed basement membranes compared to day 16 organoids with more defined ones.
Suspension of marketing authorization for ingenol mebutate
Authors: M.F. Mohd Mustapa, D. Berker, J.M. McGregor, L.S. Exton, B.R. Hughes, N.J. Levell
Journal: British Journal of Dermatology (2020)

Linked Article:de Berker et al. Br J Dermatol 2017; 176:20–43.
Implications of ST Changes During Normal Echocardiography—Reply
Authors: Melissa A. Daubert, Eric J. Velazquez, Tracy Y. Wang
Journal: JAMA Internal Medicine (2020)

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The ongoing torture and medical neglect of Julian Assange
Authors: William Hogan, Stephen Frost, Lissa Johnson, Thomas G Schulze, E Anthony S Nelson, William Frost
Journal: The Lancet (2020)

On Feb 17, 2020, Doctors for Assange demanded an end to the torture and medical neglect of Julian Assange.1 Yet no responsible authority has acted. Nils Melzer, the UN Special Rapporteur on Torture and other Cruel, Inhuman or Degrading Treatment or Punishment, and two medical experts visited Mr Assange in prison in May, 2019, concluding that his treatment constituted psychological torture, a form of torture aimed at destroying the personality of an individual.2 The situation has deteriorated since then, with continued abuses of Mr Assange's fundamental rights and the medical risks posed by COVID-19.
SuccSite: Incorporating Amino Acid Composition and Informative <i>k</i>-Spaced Amino Acid Pairs to Identify Protein Succinylation Sites
Authors: Hui-Ju Kao, Van-Nui Nguyen, Kai-Yao Huang, Wen-Chi Chang, Tzong-Yi Lee
Journal: Genomics Proteomics & Bioinformatics (2020)

Protein succinylation is a biochemical reaction in which a succinyl group (-CO-CH2-CH2-CO-) is attached to the lysine residue of a protein molecule. Lysine succinylation plays important regulatory roles in living cells. However, studies in this field are limited by the difficulty in experimentally identifying the substrate site specificity of lysine succinylation. To facilitate this process, several tools have been proposed for the computational identification of succinylated lysine sites. In this study, we developed an approach to investigate the substrate specificity of lysine succinylated sites based on amino acid composition. Using experimentally verified lysine succinylated sites collected from public resources, the significant differences in position-specific amino acid composition between succinylated and non-succinylated sites were represented using the Two Sample Logo program. These findings enabled the adoption of an effective machine learning method, support vector machine, to train a predictive model with not only the amino acid composition, but also the composition of k-spaced amino acid pairs. After the selection of the best model using a ten-fold cross-validation approach, the selected model significantly outperformed existing tools based on an independent dataset manually extracted from published research articles. Finally, the selected model was used to develop a web-based tool, SuccSite, to aid the study of protein succinylation. Two proteins were used as case studies on the website to demonstrate the effective prediction of succinylation sites. We will regularly update SuccSite by integrating more experimental datasets. SuccSite is freely accessible at http://csb.cse.yzu.edu.tw/SuccSite/.
Endoscopic band ligation and over-the-scope clip placement for refractory bleeding of Dieulafoy ulcer in the jejunum
Authors: Takafumi Yano, Takayuki Nagai, Koki Yamanaka, Masato Hanzawa, Kosuke Kodama, Takashi Abe, Kazunari Murakami
Journal: Endoscopy (2020)

A 68-year-old man, who underwent surgery for gastric cancer (distal gastrectomy and Billroth I reconstruction) in the past and was taking dabigatran 15 mg orally because of brain infarction, came to our hospital with a chief complaint of lightheadedness. He had marked anemia (hemoglobin 5.6 g/dL). Endoscopy detected bleeding from a Dieulafoy ulcer in the upper jejunum. A clip was applied to stop the bleeding ([Fig. 1 a, b]).
Loss of hepatic Mboat7 leads to liver fibrosis
Authors: Veera Raghavan Thangapandi, Oskar Knittelfelder, Mario Brosch, Eleonora Patsenker, Olga Vvedenskaya, Stephan Buch, Sebastian Hinz, Alexander Hendricks, Marina Nati, Alexander Herrmann, Devavrat Ravindra Rekhade, Thomas Berg, Madlen Matz-Soja, Klaus Huse, Edda Klipp, Josch K Pauling, Judith AH Wodke, Jacobo Miranda Ackerman, Malte von Bonin, Elmar Aigner, Christian Datz, Witigo von Schönfels, Sophie Nehring, Sebastian Zeissig, Christoph Röcken, Andreas Dahl, Triantafyllos Chavakis, Felix Stickel, Andrej Shevchenko, Clemens Schafmayer, Jochen Hampe, Pallavi Subramanian
Journal: Gut (2020)

The rs641738C>T variant located near the membrane-bound O-acyltransferase domain containing 7 (MBOAT7) locus is associated with fibrosis in liver diseases, including non-alcoholic fatty liver disease (NAFLD), alcohol-related liver disease, hepatitis B and C. We aim to understand the mechanism by which the rs641738C>T variant contributes to pathogenesis of NAFLD.
Reach agreement on GP safeguarding fees or risk legal action, judge tells local agencies
Authors: Clare Dyer
Journal: BMJ (2020)

Local authorities, the police, and clinical commissioning groups (CCGs) could face a mass of civil claims by GPs if they fail to reach agreement locally on whether fees are to be paid for doctors’ safeguarding work, a High Court judge has declared.1

Mr Justice Swift dismissed a judicial review test case brought by the BMA that argued that the local safeguarding arrangements plan in Northamptonshire was unlawful, a breach of the Children Act, or irrational in failing to consider how work undertaken by GPs would be funded.

He said it was “unfortunate” that the BMA had taken such an indirect route to try to secure a ruling that GPs should be paid for producing …