tbuckley/cabot-search huggingface dataset:
Insights from immuno-oncology: the Society for Immunotherapy of Cancer Statement on access to IL-6-targeting therapies for COVID-19
Authors: Paolo Antonio Ascierto, Bernard A Fox, Walter J Urba, Ana Carrizosa Anderson, Michael B Atkins, Ernest C Borden, Julie R Brahmer, Lisa H Butterfield, Alessandra Cesano, Daniel S Chen, Tanja D de Gruijl, Robert O Dillman, Charles G Drake, Leisha A Emens, Thomas F Gajewski, James L Gulley, F Stephen Hodi Jr, Patrick Hwu, David Kaufman, Howard L Kaufman, Michael T Lotze, Douglas G McNeel, Kim A Margolin, Francesco M Marincola, Michael J Mastrangelo, Marcela V Maus, David R Parkinson, Pedro J Romero, Paul M Sondel, Stefani Spranger, Mario Sznol, George J Weiner, Jon M Wigginton, Jeffrey S Weber
Journal: Journal for ImmunoTherapy of Cancer (2020)

The hypoxia and profound inflammatory response associated with the pneumonitis observed with the SARS-CoV-2 virus responsible for the recent COVID-19 pandemic has overwhelmed intensive care facilities in the epicenters of infection including Wuhan, China, Northern Italy and in the USA, the Seattle
Population-based case-finding to identify subjects with undiagnosed asthma or COPD
Authors: Matthew Preteroti, G. Alex Whitmore, Katherine L. Vandemheen, J. Mark FitzGerald, Catherine Lemière, Louis-Philippe Boulet, Erika Penz, Stephen K. Field, Samir Gupta, R. Andrew McIvor, Irvin Mayers, Paul Hernandez, Diane Lougheed, Martha Ainslie, Christopher Licskai, Tanweer Azher, Ian Fraser, Masoud Mahdavian, Shawn D. Aaron
Journal: European Respiratory Journal (2020)

Background ∼5–10% of adults may have undiagnosed airflow obstruction. The objective of this study was to develop a population-based case-finding strategy to assess the prevalence of undiagnosed airflow obstruction (asthma or COPD) amongst adults with respiratory symptoms in Canada. Methods Adults without a previous history of asthma, COPD or lung disease were recruited using random digit-dialling and asked if they had symptoms of dyspnoea, cough, sputum or wheeze within the past 6 months. Those who answered affirmatively completed the Asthma Screening Questionnaire (ASQ), COPD-Diagnostic Questionnaire (COPD-DQ) and COPD Assessment Test (CAT). Those with an ASQ score of ≥6 or a COPD-DQ score of ≥20 underwent pre- and post-bronchodilator spirometry to diagnose asthma or COPD. Results 12 117 individuals were contacted at home and assessed for study eligibility. Of the 1260 eligible individuals, 910 (72%) enrolled and underwent spirometry. Ultimately, 184 subjects (20% of those enrolled) had obstructive lung disease (73 asthma and 111 COPD). Individuals found to have undiagnosed asthma or COPD had more severe respiratory symptoms and impaired quality of life compared with those without airflow obstruction. The ASQ, COPD-DQ, and CAT had ROC areas for predicting undiagnosed asthma or COPD of 0.49, 0.64 and 0.56, respectively. Four descriptive variables (age, BMI, sex and pack-years smoked) produced better receiver operating characteristic (ROC) values than the questionnaires (ROC area=0.68). Conclusion 20% of randomly selected individuals who report respiratory symptoms in Canada have undiagnosed airflow obstruction due to asthma or COPD. Questionnaires could exclude subjects at low risk but lack the ability to accurately find subjects with undiagnosed disease.
ZAP-70 Versus CD38 Expression as the Prognostic Factors in B-Cell Chronic Lymphocytic Leukemia.
Authors: Iwona Hus, Agnieszka Bojarska-Junak, Monika Podhorecka, Ewa Wasik-Szczepanek, Malgorzata Sieklucka, Katarzyna Skorzynska, Jacek Rolinski, Anna Dmoszynska
Journal: Blood (2004)
The changing face of cancer in the elderly—Only a demographic change?
Authors: Y. Rottenberg, T. Peretz
Journal: Journal of Clinical Oncology (2006)

18597 Background: In industrial countries, the cancer burden of the elderly is high and is increased. One reason is longer life expectancy. Increasing age standardized rates of cancer in this age group compared to younger groups may also explain this phenomenon. Methods: Two age groups were examined, above and below 65 years. Each age group was further divided into men and women. The age standardized rates for all cancers combined among the Jewish population in Israel were identified through the Israel Cancer Registry during the years 1973–2002. In addition, lung and colorectal cancers according to sexes, prostate cancer in men and breast cancer in women were examined. Results: Between the first 5 years of the study (1973–1977) and the last 5 years (1998–2002) the age standardized rates for all cancers combined were raised by about one third in the two age groups. In males, the overall change was higher in the older group (42% in men aged 65 years and older compared to 31% in men younger than 65). However, the rise in the younger group was more prominent in females (42% in women younger than 65 years compared to 33 % in women aged 65 and older). The most outstanding increase was in prostate cancer in men, but mainly in the younger group (176% in the older group and 368% in the younger group) followed by breast cancer in women, more prominent in the older group (64% in the older group and 50% in the younger group). In both sexes, more noticeable increases were noted in the older groups in colorectal cancer and in lung cancer. Between the years 1993–1997 and 1998–2002 shifts towards stabilization and even a decrease was noted in some of the cancers that were examined. In men aged 65 years and older rates for all cancers combined were decreased by 2.5%, among the specific tumors and a decrease was noted in lung cancer (6.7%) and prostate cancer (5.8%). The rates for all cancers combined among the older women were slightly decreasing (2.0%). No decrease was noted in the specific tumors in this group. Among the younger groups in both sexes, no decrease (defined &gt;0.5%) was noted. Conclusions: These data argue against the hypothesis that the overall change in the cancer burden in the aged could be also explained by differences changes in the risk of developing cancer between these two age groups. No significant financial relationships to disclose.
Description of two anaphylaxis phenotypes in children: The utility of a clustering analysis approach
Authors: Guillaume Pouessel, Jean Christophe Dubus, Stéphanie Lejeune, Hélène Béhal, Guilhem Noël, Etienne Beaudouin, Antoine Deschildre, Jérémy Corriger
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.
Positron Emission Tomography Imaging of Poly–(Adenosine Diphosphate–Ribose) Polymerase 1 Expression in Breast Cancer
Authors: Elizabeth S. McDonald, Robert K. Doot, Austin R. Pantel, Michael D. Farwell, Robert H. Mach, Kara N. Maxwell, David A. Mankoff
Journal: JAMA Oncology (2020)

This nonrandomized clinical trial tested [18F]FluorThanatrace as a method for measuring regional poly–(adenosine diphosphate–ribose) polymerase 1 expression in breast cancer and as a potential functional biomarker for breast cancer poly–(adenosine diphosphate–ribose) polymerase inhibitor response.
Causes of long wait time in health consultation services and strategies to reduce them: an observational study in rural Haiti
Authors: Jude Altema, RN Kenide Bien-Aime, RN Marie Carine Roger, Wendell Blaise
Journal: The Lancet Global Health (2020)

BackgroundWHO data show that wait times for clinic patients globally vary between 30 min and 2 h, but at Saint Boniface Hospital in Fond-des-Blancs, Haiti, wait times range between 3 h and 8 h. Wait times are important to health-care delivery since patients lose days of work and urgent cases can be delayed. In this study we aimed to analyse wait times during general and specialised medical consultations in order to identify the causes of prolonged waiting times in outpatient clinic as well as potential avenues to reduce future wait times.MethodsWe administered a semi-structured questionnaire to patients in the outpatient clinic recording arrival time, time spent waiting at various check points (eg pharmacy, laboratory), and overall satisfaction with their visit. Patients were welcomed by a research worker at the hospital entrance and then observed until their release from the hospital, noting points of congestion and time spent at each service. The team then implemented three Plan-Do-Study-Act (PDSA) style process improvement interventions that aimed to decrease average wait time for patients and streamline patient flow through hospital outpatient services. We repeated the questionnaire 3 months after implementation of process improvements, capturing changes in baseline measures and outcomes.FindingsBetween January and March, 2014, a total sample of 300 patients completed the questionnaire; 100 patients at baseline and 200 at follow-up. Mean total wait time was 4 h (SD 4). The main contributors to wait time were waiting for laboratory results, lack of knowledge of hospital flow, and lack of staff engagement to resolve barriers. Three PDSA cycles were done on each of these three contributors. After the PDSA cycles, the mean wait time was reduced by 1 h to 3 h (SD 2).InterpretationImproving the clinic process with the use of PDSA cycles resulted in reduced wait times at Saint Boniface hospital. While numerous challenges remain, this study highlighted the importance of implementation of a structured triage system for outpatient clinic visits. As we progressed toward this goal, we later observed a considerable increase in the number of visits per year, which we attribute to improved patient satisfaction.FundingNone
ESGE and ESGENA Position Statement on gastrointestinal endoscopy and the COVID-19 pandemic
Authors: Ian M. Gralnek, Cesare Hassan, Ulrike Beilenhoff, Giulio Antonelli, Alanna Ebigbo, Maria Pellisè, Marianna Arvanitakis, Pradeep Bhandari, Raf Bisschops, Jeanin E. Van Hooft, Michal F. Kaminski, Konstantinos Triantafyllou, George Webster, Heiko Pohl, Irene Dunkley, Björn Fehrke, Mario Gazic, Tatjana Gjergek, Siiri Maasen, Wendy Waagenes, Marjon de Pater, Thierry Ponchon, Peter D. Siersema, Helmut Messmann, Mario Dinis-Ribeiro
Journal: Endoscopy (2020)

Abstract We are currently living in the throes of the COVID-19 pandemic that imposes a significant stress on health care providers and facilities. Europe is severely affected with an exponential increase in incident infections and deaths. The clinical manifestations of COVID-19 can be subtle, encompassing a broad spectrum from asymptomatic mild disease to severe respiratory illness. Health care professionals in endoscopy units are at increased risk of infection from COVID-19. Infection prevention and control has been shown to be dramatically effective in assuring the safety of both health care professionals and patients. The European Society of Gastrointestinal Endoscopy (www.esge.com) and the European Society of Gastroenterology and Endoscopy Nurses and Associates (www.esgena.org) are joining forces to provide guidance during this pandemic to help assure the highest level of endoscopy care and protection against COVID-19 for both patients and endoscopy unit personnel. This guidance is based upon the best available evidence regarding assessment of risk during the current status of the pandemic and a consensus on which procedures to perform and the priorities on resumption. We appreciate the gaps in knowledge and evidence, especially on the proper strategy(ies) for the resumption of normal endoscopy practice during the upcoming phases and end of the pandemic and therefore a list of potential research questions is presented. New evidence may result in an updated statement.
Immunoglobulin Gene Repertoire in Ocular Adnexa Lymphomas (OAL): Hints on the Nature of the Antigenic Stimulation
Authors: Antonis Dagklis, Maurilio Ponzoni, Andres JM Ferreri, Maria Giulia Cangi, Lorenza Pecciarini, Riccardo Dolcetti, Kostas Stamatopoulos, Claudio Doglioni, Paolo Ghia
Journal: Blood (2008)
Faecal calprotectin indicates intestinal inflammation in COVID-19
Authors: Maria Effenberger, Felix Grabherr, Lisa Mayr, Julian Schwaerzler, Manfred Nairz, Markus Seifert, Richard Hilbe, Stefanie Seiwald, Sabine Scholl-Buergi, Gernot Fritsche, Rosa Bellmann-Weiler, Günter Weiss, Thomas Müller, Timon Erik Adolph, Herbert Tilg
Journal: Gut (2020)

<h3>Objectives</h3> To examine the interactions between SARS-CoV-2 positive players and other players during rugby league matches and determine within-match SARS-CoV-2 transmission risk. <h3>Methods</h3> Four Super League matches in which SARS-CoV-2 positive players were subsequently found to have participated were analysed. Players were identified as increased-risk contacts, and player interactions and proximities were analysed by video footage and global positioning system (GPS) data. The primary outcome was new positive cases of SARS-CoV-2 within 14 days of the match in increased-risk contacts and other players participating in the matches. <h3>Results</h3> Out of 136 total players, there were 8 SARS-CoV-2 positive players, 28 players identified as increased-risk contacts and 100 other players in the matches. Increased-risk contacts and other players were involved in 11.4±9.0 (maximum 32) and 4.0±5.2 (maximum 23) tackles, respectively. From GPS data, increased-risk contacts and other players were within 2 m of SARS-CoV-2 positive players on 10.4±18.0 (maximum 88) and 12.5±20.7 (maximum 121) occasions, totalling 65.7±137.7 (maximum 689) and 89.5±169.4 (maximum 1003) s, respectively. Within 14 days of the match, one increased-risk contact and five players returned positive SARS-CoV-2 reverse transcriptase PCR (RT-PCR) tests, and 27 increased-risk contacts and 95 other participants returned negative SARS-CoV-2 RT-PCR tests. Positive cases were most likely traced to social interactions, car sharing and wider community transmission and not linked to in-match transmission. <h3>Conclusion</h3> Despite tackle involvements and close proximity interactions with SARS-CoV-2 positive players, in-match SARS-CoV-2 transmission was not confirmed. While larger datasets are needed, these findings suggest rugby presents a lower risk of viral transmission than previously predicted.
Reply to Cemachovic
Authors: Akira Kurita, Shujiro Yazumi
Journal: Endoscopy (2020)

We appreciate Dr. Cemachovic’s thoughtful comments regarding our manuscript. Endoscopic retrograde cholangiopancreatography (ERCP) is traditionally performed with patients in the prone position [1] [2] [3]. The prone position is considered optimal for visualization and cannulation of the papilla and for obtaining high quality radiographic images. In fact, most institutions in Japan do perform ERCP in the prone position using total intravenous anesthesia.
Abstract B34: The ALPK1/TIFA/NF-kB axis links a bacterial carcinogen to replication stress and DNA damage
Authors: Michael Bauer, Zuzana Nascakova, Anca Mihai, Anne Müller
Journal: Cancer Research (2020)

Abstract Exposure of gastric epithelial cells to the bacterial carcinogen Helicobacter pylori causes DNA double-strand breaks. Here, we show that H. pylori-induced DNA damage occurs co-transcriptionally in S-phase cells that activate NF-kB signaling upon innate immune recognition of LPS biosynthetic intermediates, such as ADP-heptose, by the ALPK1/TIFA pathway. DNA damage is accompanied by replication fork stalling as determined by DNA fiber assay and can be observed also in gastric organoids derived from bariatric surgery patients. We link H. pylori-induced DNA damage to the formation of RNA/DNA hybrids (R-loops), as overexpression of the R-loop-processing enzyme RNAse H1 prevents DNA damage and replication stress. R-loops form in infected cells as a consequence of ADP-heptose/ALPK1/TIFA/NF-kB signaling. Factors associated with R-loop processing and prevention are recurrently mutated in gastric cancer. In summary, our results link bacterial infection and NF-kB-driven innate immune responses to DNA damage, replication stress, and carcinogenesis. Citation Format: Michael Bauer, Zuzana Nascakova, Anca Mihai, Anne Müller. The ALPK1/TIFA/NF-kB axis links a bacterial carcinogen to replication stress and DNA damage [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B34.
scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Authors: Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan
Journal: Genome biology (2020)

Abstract Single-cell chromatin accessibility sequencing has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. However, there is a lack of open-source software for comprehensive processing, analysis, and visualization of such data generated using all existing experimental protocols. Here, we present scATAC-pro for quality assessment, analysis, and visualization of single-cell chromatin accessibility sequencing data. scATAC-pro computes a range of quality control metrics for several key steps of experimental protocols, with a flexible choice of methods. It generates summary reports for both quality assessment and downstream analysis. scATAC-pro is available at https://github.com/tanlabcode/scATAC-pro .
Asthma rescue treatments, time to reboot
Authors: Jeremy Charriot, Mina Gaga, Carey Suehs, Arnaud Bourdin
Journal: European Respiratory Journal (2020)

Short-acting β2-agonists (SABAs) are inseparable from asthma. The word "Ventolin" has not only entered common language, but it profoundly symbolises relief from breathing distress, quite similar to how "nitroglycerin" supposedly rescues the heart. After the Second World War, synthetic corticosteroids revolutionised asthma management and gained nobility once an inhaled formulation was available [1]. Intriguingly, despite the fact that chronic airway inflammation is inherent to the definition of asthma, as needed SABA was kept in guidelines as the preferred option for the mildest patients, and this until the very recent latest update from the Global Initiative for Asthma (GINA) [2]. Erroneous conclusions were driven from pharmaco-epidemiological studies when it was reported that more than half of asthma patients fell into this "first-step". In hindsight, the latter classification seems overly facile and in denial of any notion of chronicity, not to mention the possibility of addressing a more difficult inflammation management strategy requiring treatment adherence or patient education. Simultaneously, the medical community was faced with a diagnostic paradox given that spirometry improvement (forced expiratory volume in 1 s) during a SABA challenge should indicate the appropriateness of an ICS. The resulting "pro-irresponsible-SABA" environment may help explain why SABA continues to beat all records as the top anti-asthma drug consumed worldwide. Towards true SABA stewardship <http://bit.ly/2wVHu5W>
A Multianalyte Panel Consisting of Extracellular Vesicle miRNAs and mRNAs, cfDNA, and CA19-9 Shows Utility for Diagnosis and Staging of Pancreatic Ductal Adenocarcinoma
Authors: Zijian Yang, Michael J. LaRiviere, Jina Ko, Jacob E. Till, Theresa Christensen, Stephanie S. Yee, Taylor A. Black, Kyle Tien, Andrew Lin, Hanfei Shen, Neha Bhagwat, Daniel Herman, Andrew Adallah, Mark H. O'Hara, Charles M. Vollmer, Bryson W. Katona, Ben Z. Stanger, David Issadore, Erica L. Carpenter
Journal: Clinical Cancer Research (2020)

Abstract Purpose: To determine whether a multianalyte liquid biopsy can improve the detection and staging of pancreatic ductal adenocarcinoma (PDAC). Experimental Design: We analyzed plasma from 204 subjects (71 healthy, 44 non-PDAC pancreatic disease, and 89 PDAC) for the following biomarkers: tumor-associated extracellular vesicle miRNA and mRNA isolated on a nanomagnetic platform that we developed and measured by next-generation sequencing or qPCR, circulating cell-free DNA (ccfDNA) concentration measured by qPCR, ccfDNA KRAS G12D/V/R mutations detected by droplet digital PCR, and CA19-9 measured by electrochemiluminescence immunoassay. We applied machine learning to training sets and subsequently evaluated model performance in independent, user-blinded test sets. Results: To identify patients with PDAC versus those without, we generated a classification model using a training set of 47 subjects (20 PDAC and 27 noncancer). When applied to a blinded test set (N = 136), the model achieved an AUC of 0.95 and accuracy of 92%, superior to the best individual biomarker, CA19-9 (89%). We next used a cohort of 20 patients with PDAC to train our model for disease staging and applied it to a blinded test set of 25 patients clinically staged by imaging as metastasis-free, including 9 subsequently determined to have had occult metastasis. Our workflow achieved significantly higher accuracy for disease staging (84%) than imaging alone (accuracy = 64%; P &amp;lt; 0.05). Conclusions: Algorithmically combining blood-based biomarkers may improve PDAC diagnostic accuracy and preoperative identification of nonmetastatic patients best suited for surgery, although larger validation studies are necessary.
Increasing the threshold for patient global assessment in defining remission may have a different impact in patients with early and established rheumatoid arthritis
Authors: Serena Bugatti, Ludovico De Stefano, Ennio Giulio Favalli, Roberto Caporali, Carlomaurizio Montecucco
Journal: Annals of the Rheumatic Diseases (2020)

A significant proportion of patients with rheumatoid arthritis (RA) misses the target of disease remission solely because of the patient global assessment of disease activity (PGA) exceeding the cut-off of 1.1–5 As PGA may also reflect non-inflammatory symptoms, its inclusion as a driver of intensification of immunosuppressive therapy is currently been questioned.6 Complete omission of the patients’ perspective, however, impairs functional outcomes and the ability to discriminate effective treatments from placebo.7 As such, different thresholds for the PGA are being tested, with a recent proposal from randomised clinical trials suggesting a suitable cut-off of 2.8

Here, we evaluated the performance of modifying the Boolean definition of remission9 by increasing the cut-off of the PGA to 28 in real life. Data were retrieved from 826 consecutive patients from two University Hospitals with an observation period of 12 months. Five hundred and thirty-five were patients with early RA (median (IQR) symptoms’ duration 16 [9–28] weeks) started on …