tbuckley/cabot-search huggingface dataset:
Covid-19: doctors’ leaders warn that staff could quit and may die over lack of protective equipment
Authors: Melanie Newman
Journal: BMJ (2020)

The BMA has called the shortage of personal protection equipment (PPE) across the NHS “totally unacceptable” and warned the government that without proper kits some doctors treating patients with covid-19 may die.

Chaand Nagpaul, the BMA’s Chair of Council, has called for the government to be transparent about the level of supplies it has.

The Royal College of GPs has also raised concerns about the protective kits being provided to primary care staff and has called for guidance on how and when they should be using PPE during patient consultations.

Reports from BMA members suggest that, in general, supplies of PPE were not getting through to frontline NHS staff, or if they were it was in small amounts, was rationed, or was not offering enough protection

In response to a call for doctors’ experiences of getting PPE, one told the BMA, “Coughed on by covid patients all day today. No visors available. Tomorrow I’m borrowing my nine year old’s safety specs she got in a science party bag. I wish this was actually a joke.”

Nagpaul said, “A construction worker wouldn’t be allowed to work without a hard hat and proper boots. Even a bee keeper wouldn’t inspect a hive without proper protective clothing. And yet …
CAROTID ARTERY ENDARTERECTOMY VERSUS CAROTID ARTERY STENTING FOR RESTENOSIS AFTER CAROTID ARTERY ENDARTERECTOMY: A SYSTEMATIC REVIEW AND META-ANALYSIS
Authors: Anil Kumar Jonnalagadda, Pavlos Texakalidis, Stefanos Giannopoulos, Damianos G. Kokkinidis, Ehrin J. Armstrong, Theofilos Machinis, Jabbour M. Pascal
Journal: Journal of the American College of Cardiology (2018)
TCT-757 Long-Term Results Following Transcatheter Aortic Valve Implantation
Authors: Pablo Codner, Abid Assali, Hana Vaknin-Assa, Yaron Shapira, Gabriel Greenberg, Katia Orvin, Leor Perl, Marina Kupershmidt, Tamir Bental, Alexander Sagie, Ran Kornowski
Journal: Journal of the American College of Cardiology (2014)
Clinical and biological implications of target occupancy in CLL treated with the BTK inhibitor acalabrutinib
Authors: Clare Sun, Pia Nierman, Ellen K. Kendall, Jean Cheung, Michael Gulrajani, Sarah E. M. Herman, Christopher Pleyer, Inhye E. Ahn, Maryalice Stetler-Stevenson, Constance M. Yuan, Irina Maric, Erika M. Gaglione, Hailey M. Harris, Stefania Pittaluga, Min Hui Wang, Priti Patel, Mohammed Z. H. Farooqui, Raquel Izumi, Ahmed Hamdy, Todd Covey, Adrian Wiestner
Journal: Blood (2020)
Clinical and molecular characterization of virus-positive and virus-negative Merkel cell carcinoma
Authors: Gabriel J. Starrett, Manisha Thakuria, Tianqi Chen, Christina Marcelus, Jingwei Cheng, Jason Nomburg, Aaron R. Thorner, Michael K. Slevin, Winslow Powers, Robert T. Burns, Caitlin Perry, Adriano Piris, Frank C. Kuo, Guilherme Rabinowits, Anita Giobbie-Hurder, Laura E. MacConaill, James A. DeCaprio
Journal: Genome Medicine (2020)

Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine carcinoma of the skin caused by either the integration of Merkel cell polyomavirus (MCPyV) and expression of viral T antigens or by ultraviolet-induced damage to the tumor genome from excessive sunlight exposure. An increasing number of deep sequencing studies of MCC have identified significant differences between the number and types of point mutations, copy number alterations, and structural variants between virus-positive and virus-negative tumors. However, it has been challenging to reliably distinguish between virus positive and UV damaged MCC.
Kidney International and the COVID-19 infection
Authors: Brad H. Rovin, Pierre Ronco, P. Toby Coates, Olivier Devuyst, Tilman B. Drueke, Jürgen Floege, Agnes B. Fogo, T. Alp Ikizler, Masaomi Nangaku, Jai Radhakrishnan, Germaine Wong, Christina Wyatt
Journal: Kidney International (2020)

The Editorial Team of Kidney International would like to reassure our readership that we will continue to bring you high-quality information throughout the COVID-19 pandemic to help all of us deal with the crisis and provide high-quality care to our patients. We have a mechanism in place to rapidly review and arrive at publication decisions for papers on the COVID-19–related implications for the kidney and release these papers in an open access format within one week after acceptance. We believe the best way nephrologists can contribute to the fight against this disease is by arming ourselves with the best and most up-to-date data possible. The Editors of Kidney International would also like to thank all of our reviewers for their outstanding work in guiding the publication of high-impact papers. We understand that for most of us now many of our academic activities have been curtailed as we focus our efforts on combating the virus. We apologize to our authors for any delays encountered in the review process for non–COVID-19–related articles. Normal turnaround time for Kidney International averages 14 days for all original manuscripts, and we will make every effort to maintain a short review process during this time of stress. During the first quarter of 2020 the number of submitted manuscripts to Kidney International has increased by 15%, and we are grateful to the authors for choosing to publish with us despite the pandemic. We are very much aware of the huge professional and personal difficulties authors are facing, including the shutdown of laboratories and the virtual standstill of most clinical trials, and we will take these difficulties into account during the review process. Despite all of these challenges, the Editorial Team remains dedicated to the mission of Kidney International, and we are proud to serve the kidney community and contribute, together with the International Society of Nephrology, to global kidney health. We are happy to hear from our readership and will appreciate any suggestions of how we can help you manage during this crisis. List of Associate Editors P. Toby Coates, Olivier Devuyst, Tilman B. Drueke, Jürgen Floege, Agnes B. Fogo, T. Alp Ikizler, Masaomi Nangaku, Jai Radhakrishnan, Germaine Wong, and Christina Wyatt.
TCT-658 Neurologic Outcomes with Embolic Protection Devices in Patients Undergoing Transcatheter Aortic Valve Replacement: A Systematic Review and Meta-Analysis of Randomized Controlled Trials
Authors: Gennaro Giustino, Roxana Mehran, Roland Veltkamp, Michela Faggioni, George Danias, Usman Baber, George Dangas
Journal: Journal of the American College of Cardiology (2016)
Presenting machine learning model information to clinical end users with model facts labels
Authors: Mark P. Sendak, Michael Gao, Nathan Brajer, Suresh Balu
Journal: npj Digital Medicine (2020)

There is tremendous enthusiasm surrounding the potential for machine learning to improve medical prognosis and diagnosis. However, there are risks to translating a machine learning model into clinical care and clinical end users are often unaware of the potential harm to patients. This perspective presents the "Model Facts" label, a systematic effort to ensure that front-line clinicians actually know how, when, how not, and when not to incorporate model output into clinical decisions. The "Model Facts" label was designed for clinicians who make decisions supported by a machine learning model and its purpose is to collate relevant, actionable information in 1-page. Practitioners and regulators must work together to standardize presentation of machine learning model information to clinical end users in order to prevent harm to patients. Efforts to integrate a model into clinical practice should be accompanied by an effort to clearly communicate information about a machine learning model with a "Model Facts" label.
Faecal microbiota transplantation from metabolically compromised human donors accelerates osteoarthritis in mice
Authors: ZeYu Huang, Jing Chen, BoLei Li, Benhua Zeng, Ching-Heng Chou, Xin Zheng, JingWei Xie, Hao Li, Yu Hao, Guo Chen, FuXing Pei, Bin Shen, Virginia B Kraus, Hong Wei, Xuedong Zhou, Lei Cheng
Journal: Annals of the Rheumatic Diseases (2020)

Objectives Emerging evidence suggests that the microbiome plays an important role in the pathogenesis of osteoarthritis (OA). We aimed to test the two-hit model of OA pathogenesis and potentiation in which one ‘hit’ is provided by an adverse gut microbiome that activates innate immunity; the other ‘hit’ is underlying joint damage. Methods Medical history, faecal and blood samples were collected from human healthy controls (OA-METS-, n=4), knee OA without metabolic syndrome (OA+METS-, n=7) and knee OA with metabolic syndrome (OA+METS+, n=9). Each group of human faecal samples, whose microbial composition was identified by 16S rRNA sequencing, was pooled and transplanted into germ-free mice 2 weeks prior to meniscal/ligamentous injury (MLI) (n≥6 per group). Eight weeks after MLI, mice were evaluated for histological OA severity and synovitis, systemic inflammation and gut permeability. Results Histological OA severity following MLI was minimal in germ-free mice. Compared with the other groups, transplantation with the OA+METS+ microbiome was associated with higher mean systemic concentrations of inflammatory biomarkers (interleukin-1β, interleukin-6 and macrophage inflammatory protein-1α), higher gut permeability and worse OA severity. A greater abundance of Fusobacterium and Faecalibaterium and lesser abundance of Ruminococcaceae in transplanted mice were consistently correlated with OA severity and systemic biomarkers concentrations. Conclusion The study clearly establishes a direct gut microbiome-OA connection that sets the stage for a new means of exploring OA pathogenesis and potentially new OA therapeutics. Alterations of Fusobacterium , Faecalibaterium and Ruminococcaceae suggest a role of these particular microbes in exacerbating OA.
TCT-39 Three-Year Outcomes with the Fully Repositionable and Retrievable Lotus™ Transcatheter Aortic Replacement Valve in 120 High-Risk Surgical Patients with Severe Aortic Stenosis: Results from the REPRISE II CE-Mark Study
Authors: Ian Meredith, Vicki Houle, Darren Walters, Nicolas Dumonteil, Stephen Worthley, Didier Tchetche, Ganesh Manoharan, Daniel Blackman, Gilles Rioufol, David Hildick-Smith, Robert Whitbourn, Thierry Lefevre, Ruediger Lange, Ralf Mueller, Simon Redwood, Dominic J. Allocco, Keith D. Dawkins
Journal: Journal of the American College of Cardiology (2016)
CALCIFIED PLAQUES IN PATIENTS WITH ACUTE CORONARY SYNDROMES
Authors: Tomoyo Sugiyama, Erika Yamamoto, Francesco Fracassi, Hang Lee, Taishi Yonetsu, Tsunekazu Kakuta, Tsunenari Soeda, Yoshihiko Saito, Bryan Yan, Osamu Kurihara, Masamichi Takano, Giampaolo Niccoli, Filippo Crea, Takumi Higuma, Shigeki Kimura, Yoshiyasu Minami, Junya Ako, Tom Adriaenssens, Niklas Boeder, Holger Nef, James Fujimoto, Valentin Fuster, Aloke Finn, Erling Falk, Ik-Kyung Jang
Journal: Journal of the American College of Cardiology (2019)
SAFETY AND EFFICACY OF A PHARMACO-INVASIVE STRATEGY IN ST-ELEVATION MYOCARDIAL INFARCTION: A PATIENT POPULATION STUDY COMPARING A PHARMACO-INVASIVE STRATEGY TO A PRIMARY PERCUTANEOUS CORONARY INTERVENTION STRATEGY WITHIN A REGIONAL SYSTEM
Authors: Mohammed Rashid, Nita Guron, Jordan Bernick, Aun-Yeong Chong, Alexander Dick, Michael Froeschl, Chris Glover, Benjamin Hibbert, Marino Labinaz, Jean-Francois Marquis, Christina Christina, Derek So, Michel Le May
Journal: Journal of the American College of Cardiology (2016)
Suggestions for infection prevention and control in digestive endoscopy during current 2019-nCoV pneumonia outbreak in Wuhan, Hubei province, China
Authors: Yafei Zhang, Xiaodan Zhang, Lan Liu, Hongling Wang, Qiu Zhao
Journal: Endoscopy (2020)

See also: Application of an anti-aerosol box for esophagogastroduodenoscopy during the COVID-19 pandemic: double up the protectionEndoscopy 2020; 52(08): 704-705DOI: 10.1055/a-1168-6841
Nonalcoholic Steatohepatitis
Authors: Adam C. Sheka, Oyedele Adeyi, Julie Thompson, Bilal Hameed, Peter A. Crawford, Sayeed Ikramuddin
Journal: JAMA (2020)

<h3>Importance</h3> Nonalcoholic steatohepatitis (NASH) is the inflammatory subtype of nonalcoholic fatty liver disease (NAFLD) and is associated with disease progression, development of cirrhosis, and need for liver transplant. Despite its importance, NASH is underrecognized in clinical practice. <h3>Observations</h3> NASH affects an estimated 3% to 6% of the US population and the prevalence is increasing. NASH is strongly associated with obesity, dyslipidemia, type 2 diabetes, and metabolic syndrome. Although a number of noninvasive tests and scoring systems exist to characterize NAFLD and NASH, liver biopsy is the only accepted method for diagnosis of NASH. Currently, no NASH-specific therapies are approved by the US Food and Drug Administration. Lifestyle modification is the mainstay of treatment, including dietary changes and exercise, with the primary goal being weight loss. Substantial improvement in histologic outcomes, including fibrosis, is directly correlated with increasing weight loss. In some cases, bariatric surgery may be indicated to achieve and maintain the necessary degree of weight loss required for therapeutic effect. An estimated 20% of patients with NASH will develop cirrhosis, and NASH is predicted to become the leading indication for liver transplants in the US. The mortality rate among patients with NASH is substantially higher than the general population or patients without this inflammatory subtype of NAFLD, with annual all-cause mortality rate of 25.56 per 1000 person-years and a liver-specific mortality rate of 11.77 per 1000 person-years. <h3>Conclusions and Relevance</h3> Nonalcoholic steatohepatitis affects 3% to 6% of the US population, is more prevalent in patients with metabolic disease and obesity, progresses to cirrhosis in approximately 20% of cases, and is associated with increased rates of liver-specific and overall mortality. Early identification and targeted treatment of patients with nonalcoholic steatohepatitis are needed to improve patient outcomes, including directing patients toward intensive lifestyle modification to promote weight loss and referral for bariatric surgery as indicated for management of obesity and metabolic disease.
Estimating the infection and case fatality ratio for coronavirus disease (COVID-19) using age-adjusted data from the outbreak on the Diamond Princess cruise ship, February 2020
Authors: Timothy W Russell, Joel Hellewell, Christopher I Jarvis, Kevin van Zandvoort, Sam Abbott, Ruwan Ratnayake, Stefan Flasche, Rosalind M Eggo, W John Edmunds, Adam J Kucharski
Journal: Eurosurveillance (2020)

Adjusting for delay from confirmation to death, we estimated case and infection fatality ratios (CFR, IFR) for coronavirus disease (COVID-19) on the Diamond Princess ship as 2.6% (95% confidence interval (CI): 0.89–6.7) and 1.3% (95% CI: 0.38–3.6), respectively. Comparing deaths on board with expected deaths based on naive CFR estimates from China, we estimated CFR and IFR in China to be 1.2% (95% CI: 0.3–2.7) and 0.6% (95% CI: 0.2–1.3), respectively.
INFLUENCE OF OPERATOR EXPERIENCE AND PCI VOLUME ON TRANSFEMORAL ACCESS TECHNIQUES: A COLLABORATION OF INTERNATIONAL CARDIOVASCULAR SOCIETIES
Authors: Daniel Nelson, Abdulla Damluji, Nish Patel, Marco Valgimigli, Stephan Windecker, Robert Byrne, Tejas Patel, Emmanouil Brilakis, Subhash Banerjee, Jorge Mayol, Warren Cantor, Carlos Alfonso, Sunil V. Rao, Mauro Moscucci, Mauricio Cohen
Journal: Journal of the American College of Cardiology (2018)
VALOR2: characterization of large-scale structural variants using linked-reads
Authors: Fatih Karaoğlanoğlu, Camir Ricketts, Ezgi Ebren, Marzieh Eslami Rasekh, Iman Hajirasouliha, Can Alkan
Journal: Genome biology (2020)

Abstract Most existing methods for structural variant detection focus on discovery and genotyping of deletions, insertions, and mobile elements. Detection of balanced structural variants with no gain or loss of genomic segments, for example, inversions and translocations, is a particularly challenging task. Furthermore, there are very few algorithms to predict the insertion locus of large interspersed segmental duplications and characterize translocations. Here, we propose novel algorithms to characterize large interspersed segmental duplications, inversions, deletions, and translocations using linked-read sequencing data. We redesign our earlier algorithm, VALOR, and implement our new algorithms in a new software package, called VALOR2.
Tracking cancer progression: from circulating tumor cells to metastasis
Authors: Francesc Castro-Giner, Nicola Aceto
Journal: Genome Medicine (2020)

The analysis of circulating tumor cells (CTCs) is an outstanding tool to provide insights into the biology of metastatic cancers, to monitor disease progression and with potential for use in liquid biopsy-based personalized cancer treatment. These goals are ambitious, yet recent studies are already allowing a sharper understanding of the strengths, challenges, and opportunities provided by liquid biopsy approaches. For instance, through single-cell-resolution genomics and transcriptomics, it is becoming increasingly clear that CTCs are heterogeneous at multiple levels and that only a fraction of them is capable of initiating metastasis. It also appears that CTCs adopt multiple ways to enhance their metastatic potential, including homotypic clustering and heterotypic interactions with immune and stromal cells. On the clinical side, both CTC enumeration and molecular analysis may provide new means to monitor cancer progression and to take individualized treatment decisions, but their use for early cancer detection appears to be challenging compared to that of other tumor derivatives such as circulating tumor DNA. In this review, we summarize current data on CTC biology and CTC-based clinical applications that are likely to impact our understanding of the metastatic process and to influence the clinical management of patients with metastatic cancer, including new prospects that may favor the implementation of precision medicine.
TCT-453 Correlates and Impact of Coronary Artery Calcifications in Women Undergoing Percutaneous Coronary Intervention with Drug-Eluting Stents: From the Women in Innovation and Drug-Eluting Stents (WIN-DES) Collaboration
Authors: Gennaro Giustino, Usman Baber, Samantha Sartori, Gregg Stone, Martin Leon, Stephan Windecker, Patrick Serruys, Adnan Kastrati, William Wijns, Philippe Gabriel Steg, Melissa Aquino, George Danias, Marco Valgimigli, Marie-Claude Morice, Edoardo Camenzind, Giora Weisz, Pieter Smits, David Kandzari, Clemens von Birgelen, George Dangas, Soeren Galatius, Raban Jeger, Takeshi Kimura, Hyo-Soo Kim, Alaide Chieffo, Roxana Mehran
Journal: Journal of the American College of Cardiology (2016)
Endobiliary radiofrequency ablation combined with bilateral metal stent placement for malignant hilar biliary obstruction
Authors: Tadahisa Inoue, Mayu Ibusuki, Rena Kitano, Yuji Kobayashi, Tomohiko Ohashi, Yukiomi Nakade, Yoshio Sumida, Kiyoaki Ito, Masashi Yoneda
Journal: Endoscopy (2020)

The effectiveness of endobiliary radiofrequency ablation (RFA) is still uncertain, especially in patients with malignant hilar biliary obstruction (MHBO). We examined the efficacy of endobiliary RFA followed by bilateral self-expandable metal stent (SEMS) placement for unresectable MHBO.41 patients met the eligibility criteria for study inclusion. We evaluated the technical success, functional success, and recurrent biliary obstruction (RBO) associated with RFA with bilateral SEMS placement.The technical and functional success rates were both 95.1 % (39/41). The RBO rate was 38.5 % (15/39), and the median time to RBO was 230 days. Stricture length was positively correlated with time to RBO in the multivariate analysis (P = 0.03). The median time to RBO was significantly longer in patients with strictures > 15 mm in length than in those with strictures ≤ 15 mm (314 vs. 156 days; P = 0.02).The present study showed that endobiliary RFA with bilateral SEMS placement achieved good results, but selection of patients with an appropriate stricture length may be needed to obtain a sufficient ablative effect.
TMEM16A ameliorates vascular remodeling by suppressing autophagy via inhibiting Bcl-2-p62 complex formation
Authors: Xiao-Fei Lv, Ya-Juan Zhang, Xiu Liu, Hua-Qing Zheng, Can-Zhao Liu, Xue-Lin Zeng, Xiang-Yu Li, Xiao-Chun Lin, Cai-Xia Lin, Ming-Ming Ma, Fei-Ran Zhang, Jin-Yan Shang, Jia-Guo Zhou, Si-Jia Liang, Yong-Yuan Guan
Journal: Theranostics (2020)

Rationale: Transmembrane member 16A (TMEM16A) is a component of calcium-activated chloride channels that regulate vascular smooth muscle cell (SMC) proliferation and remodeling.Autophagy, a highly conserved cellular catabolic process in eukaryotes, exerts important physiological functions in vascular SMCs.In the current study, we investigated the relationship between TMEM16A and autophagy during vascular remodeling.Methods: We generated a transgenic mouse that overexpresses TMEM16A specifically in vascular SMCs to verify the role of TMEM16A in vascular remodeling.Techniques employed included immunofluorescence, electron microscopy, co-immunoprecipitation, and Western blotting.Results: Autophagy was activated in aortas from angiotensin II (AngII)-induced hypertensive mice with decreased TMEM16A expression.The numbers of light chain 3B (LC3B)-positive puncta in aortas correlated with the medial cross-sectional aorta areas and TMEM16A expression during hypertension.SMC-specific TMEM16A overexpression markedly inhibited AngII-induced autophagy in mouse aortas.Moreover, in mouse aortic SMCs (MASMCs), AngII-induced autophagosome formation and autophagic flux were blocked by TMEM16A upregulation and were promoted by TMEM16A knockdown.The effect of TMEM16A on autophagy was independent of the mTOR pathway, but was associated with reduced kinase activity of the vacuolar protein sorting 34 (VPS34) enzyme.Overexpression of VPS34 attenuated the effect of TMEM16A overexpression on MASMC proliferation, while the effect of TMEM16A downregulation was abrogated by a VPS34 inhibitor.Further, co-immunoprecipitation assays revealed that TMEM16A interacts with p62.TMEM16A overexpression inhibited AngII-induced p62-Bcl-2 binding and enhanced Bcl-2-Beclin-1 interactions, leading to suppression of Beclin-1/VPS34 complex formation.However, TMEM16A downregulation showed the opposite effects.Conclusion: TMEM16A regulates the four-way interaction between p62, Bcl-2, Beclin-1, and VPS34, and coordinately prevents vascular autophagy and remodeling
TCT-676 Outcomes Following Percutaneous Coronary Intervention in Saphenous Vein Grafts With and Without Embolic Protection Device
Authors: Ahmad Shoaib, Tim Kinnaird, Nick Curzen, Peter Ludman, Chee Khoo, Muhammad Rashid, James Nolan, Azfar Zaman, Mamas Mamas
Journal: Journal of the American College of Cardiology (2019)
TCTAP A-124 Clinical Outcomes of Pedal Artery Angioplasty for Patients with Ischemic Wounds; Results from the Multicenter Rendezvous Registry
Authors: Tatsuya Nakama, Kazushi Urasawa, Hiroshi Ando, Daisuke Kamoi, Yoshinori Tsubakimoto, Yoshisato Shibata
Journal: Journal of the American College of Cardiology (2017)
CLINICAL AND PHYSIOLOGIC OUTCOMES OF FRACTIONAL FLOW RESERVE-GUIDED PERCUTANEOUS CORONARY INTERVENTION IN PATIENTS WITH SERIAL STENOSES WITHIN ONE CORONARY ARTERY
Authors: Hack-Lyoung Kim, Ji-Hyun Kim, Han-Mo Yang, Kyung-Woo Park, Hyun-Jae Kang, Bon-Kwon Koo, Sang-Hyun Kim, In-Ho Chae, Dong-Ju Choi, Hyo-Soo Kim, Byung-Hee Oh, Young-Bae Park
Journal: Journal of the American College of Cardiology (2012)