tbuckley/cabot-search huggingface dataset:
Generation and evaluation of artificial mental health records for Natural Language Processing
Authors: Julia Ive, Natalia Viani, Joyce Kam, Lucia Yin, Somain Verma, Stephen Puntis, Rudolf N. Cardinal, Angus Roberts, Robert Stewart, Sumithra Velupillai
Journal: npj Digital Medicine (2020)

A serious obstacle to the development of Natural Language Processing (NLP) methods in the clinical domain is the accessibility of textual data. The mental health domain is particularly challenging, partly because clinical documentation relies heavily on free text that is difficult to de-identify completely. This problem could be tackled by using artificial medical data. In this work, we present an approach to generate artificial clinical documents. We apply this approach to discharge summaries from a large mental healthcare provider and discharge summaries from an intensive care unit. We perform an extensive intrinsic evaluation where we (1) apply several measures of text preservation; (2) measure how much the model memorises training data; and (3) estimate clinical validity of the generated text based on a human evaluation task. Furthermore, we perform an extrinsic evaluation by studying the impact of using artificial text in a downstream NLP text classification task. We found that using this artificial data as training data can lead to classification results that are comparable to the original results. Additionally, using only a small amount of information from the original data to condition the generation of the artificial data is successful, which holds promise for reducing the risk of these artificial data retaining rare information from the original data. This is an important finding for our long-term goal of being able to generate artificial clinical data that can be released to the wider research community and accelerate advances in developing computational methods that use healthcare data.
Emergency Use Authorization of Remdesivir
Authors: Michael G. Ison, Cameron Wolfe, Helen W. Boucher
Journal: JAMA (2020)

This Viewpoint reviews the FDA's May 2020 Emergency Use Authorization of the antiviral drug remdesivir for treatment of COVID-19 and discusses the need for a transparent distribution plan of a drug not otherwise available in the US and for which demand will likely exceed supply.
DIFFERENCES IN THE DISTRIBUTION OF HISTOLOGY OF COLORECTAL ADENOMAS BETWEEN INDIVIDUALS UNDER AND OVER THE AGE OF 50
Authors: D Penz, B Majcher, E Waldmann, A Hinterberger, LM Rockenbauer, A Szymanska, A Asaturi, M Trauner, M Ferlitsch
Journal: Endoscopy (2020)

Aims While the incidence of Colorectal cancer(CRC) is decreasing among individuals over 50 years it is increasing within younger adults. A study by Reinier et al showed that CRC among young adults is now diagnosed at a later stage compared to 1990, indicating that the increasing incidences are not an effect of a shift in age at diagnosis. However, it is still unknown if there are differences among precursor adenomas between adults < 50 years compared to those above.
THINK ABOUT KLIPPEL-TRENAUNAY SYNDROME IN RECURRENT RECTAL BLEEDING PRESENTATION – CASE REPORT
Authors: I Lolic, V Milivojević, VM Zarić, N Jocić, D Popovic, T Glišić, I Ranković, O Matejic, D Tomić
Journal: Endoscopy (2020)

Aims The aim of this paper was to draw attention to the possible rare causes of recurrent rectal bleeding.
ROLE OF EUS IN CASES OF DILATED CBD WITH BORDERLINE LFT DERANGEMENT WITH INCONCLUSIVE OTHER IMAGING
Authors: P Desai, M Kabrawala, C Patel, P Kalra, R Prajapati, N Patel
Journal: Endoscopy (2020)

Aims To see the diagnostic yield of EUS prior to ERCP for patients with dilated CBD and other inconclusive imaging studies with normal or borderline derangement of LFT.
EFFECT OF PROPHYLACTIC CLIPPING FOLLOWING COLORECTAL RESECTION: A META-ANALYSIS OF RANDOMIZED CONTROLLED TRIALS
Authors: M Spadaccini, E Albéniz, H Pohl, R Maselli, VT Chandrasekar, L Correale, A Anderloni, S Carrara, A Fugazza, E Vespa, P Sharma, DK Rex, C Hassan, A Repici
Journal: Endoscopy (2020)

Aims The efficacy of prophylactic clipping for post-polypectomy bleeding(PPB) prevention is still controversial, and data from previous meta-analyses are inconclusive. We performed a systematic review and meta-analysis of randomized controlled trials(RCTs) to assess the efficacy of prophylactic clipping for preventing PPB following high- and low-risk resections.
PET ligands [ <sup>18</sup> F]LSN3316612 and [ <sup>11</sup> C]LSN3316612 quantify <i>O</i> -linked-β- <i>N</i> -acetyl-glucosamine hydrolase in the brain
Authors: Shuiyu Lu, Mohammad B. Haskali, Kevin M. Ruley, Nicolas J.-F. Dreyfus, Susan L. DuBois, Soumen Paul, Jeih-San Liow, Cheryl L. Morse, Aneta Kowalski, Robert L. Gladding, Jeremy Gilmore, Adrian J. Mogg, S. Michelle Morin, Peter J. Lindsay-Scott, J. Craig Ruble, Nancy A. Kant, Sergey Shcherbinin, Vanessa N. Barth, Michael P. Johnson, Maria Cuadrado, Enrique Jambrina, Andrew J. Mannes, Hugh N. Nuthall, Sami S. Zoghbi, Cynthia D. Jesudason, Robert B. Innis, Victor W. Pike
Journal: Science Translational Medicine (2020)

We aimed to develop effective radioligands for quantifying brain O-linked-β-N-acetyl-glucosamine (O-GlcNAc) hydrolase (OGA) using positron emission tomography in living subjects as tools for evaluating drug target engagement. Posttranslational modifications of tau, a biomarker of Alzheimer's disease, by O-GlcNAc through the enzyme pair OGA and O-GlcNAc transferase (OGT) are inversely related to the amounts of its insoluble hyperphosphorylated form. Increase in tau O-GlcNAcylation by OGA inhibition is believed to reduce tau aggregation. LSN3316612, a highly selective and potent OGA ligand [half-maximal inhibitory concentration (IC50) = 1.9 nM], emerged as a lead ligand after in silico analysis and in vitro evaluations. [3H]LSN3316612 imaged and quantified OGA in postmortem brains of rat, monkey, and human. The presence of fluorine and carbonyl functionality in LSN3316612 enabled labeling with positron-emitting fluorine-18 or carbon-11. Both [18F]LSN3316612 and [11C]LSN3316612 bound reversibly to OGA in vivo, and such binding was blocked by pharmacological doses of thiamet G, an OGA inhibitor of different chemotype, in monkeys. [18F]LSN3316612 entered healthy human brain avidly (~4 SUV) without radiodefluorination or adverse effect from other radiometabolites, as evidenced by stable brain total volume of distribution (VT) values by 110 min of scanning. Overall, [18F]LSN3316612 is preferred over [11C]LSN3316612 for future human studies, whereas either may be an effective positron emission tomography radioligand for quantifying brain OGA in rodent and monkey.
Endoscopic submucosal dissection with double-clip traction for recurrent adenoma
Authors: Jérémie Albouys, Sophie Geyl, Anne Guyot, Aurélie Charissoux, Romain Legros, Mathieu Pioche, Jérémie Jacques
Journal: Endoscopy (2020)

The adenoma recurrence rate is 10 % – 30 % [1] [2] after piecemeal resection of the colorectum, making this a particularly challenging type of lesion for endoscopic resection. Underwater endoscopic mucosal resection (EMR), full-thickness resection [3], and “cold avulsion snare type coagulation” have been demonstrated as potentially effective endoscopic procedures in Western countries. In Japan, endoscopic submucosal dissection (ESD) is the first-line treatment for recurrent adenoma but is difficult to perform owing to the high degree of fibrosis. In Europe, colorectal ESD is unpopular for treating such lesions because of the difficulties associated with recurrence. We report a case of rapid ESD of a 15-mm recurrent adenoma of the colon.
MORAY THROUGH-THE-NEEDLE MICRO-FORCEPS COULD UNMASK THE REAL NATURE OF A PANCREATIC CYST
Authors: E Dabizzi, S Landi, M Bassi, S Ghersi, V Cennamo
Journal: Endoscopy (2020)

Prompt identification of cyst with stigmata of malignant transformation, could be the key for pancreatic cancer prevention. As well, detection of benign features could stop worthless follow-up and reassure patients.
THE ASSESSMENT OF HIGH-RESOLUTION OESOPHAGEAL MANOMETRY WITH NONOBSTRUCTIVE DYSPHAGIA
Authors: S Ghani, S Asmae, S Ilham, S Mouna, K Nawal
Journal: Endoscopy (2020)

Aims The aim of this study is to assess the prevalence and to identify the type of esophageal motor disorders in patients with nonobstructive dysphagia according to Chicago classification.
Repeated introduction and spread of the MRSA clone t304/ST6 in northern Europe
Authors: M.D. Bartels, P. Worning, L.P. Andersen, M. Bes, H. Enger, C.G. Ås, T.A. Hansen, B.J. Holzknecht, K.W. Larssen, F. Laurent, B. Mäkitalo, B. Pichon, O. Svartström, H. Westh
Journal: Clinical Microbiology and Infection (2020)
MR-Spectroscopy at 3.0-and 7.0-Tesla in NAFLD as in-vivo tool for monitoring changes in fat and energy metabolism with potential identification of NASH and advanced fibrosis
Authors: S Traussnigg, C Kienbacher, E Halilbasic, M Gajdosik, L Valkovic, M Chmelik, J Stift, H Hofer, P E Steindl-Munda, L Kazemi-Shirazi, M Peck-Radosavljevic, P Ferenci, A Ba-Ssalamah, F Wrba, M Krebs, S Trattnig, M Krssak, M Trauner
Journal: Hepatology (2013)
G Protein–Coupled Receptor Deorphanizations
Authors: Olivier Civelli, Rainer K. Reinscheid, Yan Zhang, Zhiwei Wang, Robert Fredriksson, Helgi B. Schiöth
Journal: The Annual Review of Pharmacology and Toxicology (2011)

G protein-coupled receptors (GPCRs) are major regulators of intercellular interactions. They initiate these actions by being activated by a wide variety of natural ligands. Historically, ligands were discovered first, but the advent of molecular biology reversed this trend. Most GPCRs are identified on the basis of their DNA sequences and thus are initially unmatched to known natural ligands. They are termed orphan GPCRs. Discovering their ligands-i.e., "deorphanizing" the GPCRs-gave birth to the field of reverse pharmacology. This review discusses the present status of GPCR deorphanization, presents a few examples of successes and surprises, and highlights difficulties encountered in these efforts.
IMPACT OF DEEP TARGETED NEXT GENERATION SEQUENCING ON THE WORK-UP OF PATIENTS WITH PANCREAS CYSTS OR DILATED DUCT - A PROSPECTIVE STUDY WITH EUS-GUIDED FNA
Authors: D Schmitz, AL Volckmar, D Kazdal, AM Nahm, N Weller, M Doll, P Kienle, R Magdeburg, P Schirmacher, J Rudi, A Stenzinger
Journal: Endoscopy (2020)

Aims Pancreas cysts or dilated pancreatic ducts were often detected by cross sectional imaging methods, but only mucinous neoplasia may develop pancreas cancer. Precise distinction between mucinous and non-mucinous cysts is crucial for clinical decision. We performed a prospective study (NCT03820531) on patients with pancreas cyst(s) and/or dilated main duct including Next Generation Sequencing (NGS) in the diagnostic work up of EUS-guided FNA.
LARGE SUPERFICIAL NEOPLASMS IN INFLAMMATORY BOWEL DISEASES: ENDOSCOPIC SUBMUCOSAL DISSECTION STRATEGY
Authors: F Iacopini, R Pica, E Calabrese, F Montagnese, T Gotoda, G Costamagna, Y Saito
Journal: Endoscopy (2020)

Aims Patients with long-standing active inflammatory bowel diseases (IBD) have an increased risk of colorectal dysplasia. Guidelines recommend endoscopic resection for superficial neoplasms when en bloc is feasible but endoscopic submucosal dissection (ESD) has been reported in small series with no long-term outcomes. Aim was to evaluate ESD clinical outcomes for large IBD superficial neoplasms.
A FUNCTIONAL GENOMICS APPROACH TO THE IDENTIFICATION OF BR :MARKERS OF SURVIVAL IN SEVERE SEPSIS DUE TO COMMUNITY ACQUIRED PNEUMONIA
Authors: J Radhakrishinan, E M Svoren, P Ellis, C Langford, P Huttor, E Davenport, A Thorpe, C Gerrard, J C Knight, C J Hinds, Investiga Gasg.
Journal: Intensive Care Medicine (2011)
UNDERWATER EMR FOR ADENOMATOUS LESION WITH DEEP EXTENSION INTO THE APPENDICEAL ORIFICE (AO)
Authors: H Uchima, J Antonio Colan Hernandez, D Luna, EN Caballero, I Marin, M Calafat, M Puertas, I Iborra, A Aguilar, E Domenech, VM De Vega
Journal: Endoscopy (2020)

When the involvement is deep, surgery is usually the first recommendation, however in some cases of deep involvement an endoscopic treatment can be performed.
PHASE I TRIAL OF A HIGHLY IMMUNOGENIC T-CELL VACCINE FOR HEPATITIS C VIRUS BASED ON NOVEL ADENOVIRAL VECTORS FROM RARE SEROTYPES
Authors: E Barnes, F Antonella, S Aston, K Smith, A C Brown, S Capone, M Ambrosio, Harrison Gal., V Ammendola, M Bartiromo, C Traboni, L Siani, A Sparacino, M Naddeo, S Colloca, R Cortese, A Nicosia, P Klenerman
Journal: Hepatology (2009)
Interdisciplinary oncology education: A survey of trainees and program directors in the United States.
Authors: Adil S. Akthar, Sabha Ganai, Olwen Mary Hahn, Ronald John Maggiore, Ezra E.W. Cohen, Mitchell Posner, Steven J. Chmura, Andrew R. Howard, Daniel William Golden
Journal: Journal of Clinical Oncology (2014)

e17617 Background: High quality cancer treatment requires optimal coordination of multidisciplinary care. Therefore, oncologists must have a strong understanding of collaborating specialties. This study examines the current state of interdisciplinary (ID) oncology education, focusing on which teaching methods trainees and program directors (PDs) consider most effective. Methods: Companion web-based surveys were sent to trainees and PDs in the United States for adult and pediatric hematology/oncology (med onc), oncologic surgical fellowships including specialties (surg onc), radiation oncology (rad onc), and hospice/palliative medicine (HPM). Question responses were Yes/No, five-point Likert scales (1=not at all, 2=somewhat, 3=moderately, 4=quite, 5=extremely), or free response. Results: Responses included (trainees/PDs): 254/55 med onc, 160/42 surg onc, 102/24 rad onc, and 41/20 HPM. Trainees consistently reported lower rates of ID education compared with PDs: med onc 57 vs. 77%, surg onc 30 vs. 44%, rad onc 70 vs. 89%, geriatric oncology 19 vs. 30%, and HPM 55 vs. 74%. The usefulness of lectures, rotations, and tumor board attendance to the ID educational experience was rated statistically different by both trainees and PDs. The Table is representative data for the usefulness of ID lectures as perceived by trainees. Conclusions: While oncology residents and fellows weigh the usefulness of ID education differently, they desire ID education. Trainees report less formal ID training compared with PDs. These data demonstrate differences in the utility of lectures, rotations, and tumor boards for ID oncology education based on oncologic specialty. These data suggest that training programs should promote current ID training opportunities, potentially expand their roles, and explain the rationale for their importance. Perceived usefulness of lectures Median [Interquartile range] Med onc lectures Surg onc lectures Rad onc lectures Ger onc lectures HPM lectures Med onc trainees - 3[2-4] 4[3-4] 3[2-4] 4[3-5] Surg onc trainees 4[3-5] - 4[3-4] 2[1-3] 2[1.5-3] Rad onc trainees 4[3-4] 4[3-4] - 3[2-4] 3[2-4] HPM trainees 4[3-5] 3[2-4] 4[3-4] - - Kruskall-Wallis p 0.35 <0.01 0.86 <0.01 <0.01
Accumulation of Maillard reaction products in skin collagen in diabetes and aging.
Authors: D G Dyer, J A Dunn, S R Thorpe, K E Bailie, T J Lyons, D R McCance, J W Baynes
Journal: Journal of Clinical Investigation (1993)

To investigate the contribution of glycation and oxidation reactions to the modification of insoluble collagen in aging and diabetes, Maillard reaction products were measured in skin collagen from 39 type 1 diabetic patients and 52 nondiabetic control subjects. Compounds studied included fructoselysine (FL), the initial glycation product, and the glycoxidation products, N epsilon-(carboxymethyl) lysine (CML) and pentosidine, formed during later Maillard reactions. Collagen-linked fluorescence was also studied. In nondiabetic subjects, glycation of collagen (FL content) increased only 33% between 20 and 85 yr of age. In contrast, CML, pentosidine and fluorescence increased five-fold, correlating strongly with age. In diabetic patients, collagen FL was increased threefold compared with nondiabetic subjects, correlating strongly with glycated hemoglobin but not with age. Collagen CML, pentosidine and fluorescence were increased up to twofold in diabetic compared with control patients: this could be explained by the increase in glycation alone, without invoking increased oxidative stress. There were strong correlations among CML, pentosidine and fluorescence in both groups, providing evidence for age-dependent chemical modification of collagen via the Maillard reaction, and acceleration of this process in diabetes. These results support the description of diabetes as a disease characterized by accelerated chemical aging of long-lived tissue proteins.
ENDOSCOPIC FOLLOW-UP OF HIGH-RISK ADENOCARCINOMA ARISING FROM BARRETT’S ESOPHAGUS (BE), RESULTS OF 120 PATIENTS FROM THE DUTCH BARRETT EXPERT CENTER COHORT
Authors: EA Nieuwenhuis, SN van Munster, BLAM Weusten, A Alkhalaf, BE Schenk, E Schoon, W Curvers, AD Koch, SEM van de Ven, EPD Verheij, A Kumcu, WB Nagengast, M Houben, JJGHM Bergman, RE Pouw
Journal: Endoscopy (2020)

Aims After radical endoscopic resection(ER) of esophageal adenocarcinoma(EAC) in BE with high-risk(HR) features, optimal management is unclear. This concerns three groups: HR-T1a-EAC (poorly(G3)/undifferentiated(G4) cancer a/o lymphovascular invasion(LV+)); low-risk(LR) T1b-EAC (submucosal invasion< 500um, no G3/G4, no LV); HR-T1b EAC (invasion>500um, G3/G4, a/o LV+). Endoscopic follow-up(FU) to detect lymph node metastases(N+) at a curable stage is considered in selected cases, however, optimal FU strategy is unclear. Aim was to evaluate outcomes of endoscopic FU in all patients treated by radical ER for HR-T1a or T1b-EAC.
Physician trainees raise concerns about modified recruitment process
Authors: Abi Rimmer
Journal: BMJ (2020)

Changes to the physician specialty training recruitment process have caused distress and led to many high achieving candidates going without posts, juniors say.

The covid-19 pandemic has meant that face-to-face interviews for physician training posts were cancelled and that trainees’ self-assessment scores were used instead to assess their suitability to enter a training programme.

However, although there were 10 domains for self-assessment, the physician specialty recruitment office decided that only five would be used to assess trainees applying for physician specialties: quality improvement, teaching experience, MRCP(UK) results, training in teaching, and presentations.

An analysis of …
Gut feeling from Wuhan: advice for gastrointestinal endoscopy performed during the COVID-19 outbreak
Authors: Zhen Ding, Pradermchai Kongkam, Thanawat Luangsukrerk, Jun Liu, Yaping Cheng, Thawee Ratanachu-ek, Rungsun Rerknimitr
Journal: Endoscopy (2020)

See also: SARS-CoV-2 in the bile of a patient with COVID-19-associated gallbladder diseaseEndoscopy 2020; 52(12): 1148-1148DOI: 10.1055/a-1290-7446
Modified endoscopic vacuum therapy in the management of a duodenal transmural defect
Authors: Diogo Turiani Hourneaux de Moura, Epifânio Silvino do Monte Junior, Kelly E. Hathorn, Flaubert Sena de Medeiros, Christopher C. Thompson, Eduardo Guimarães Hourneaux de Moura
Journal: Endoscopy (2020)

Gastrointestinal (GI) transmural defects are associated with high rates of morbidity and mortality [1] [2]. Endoscopic vacuum therapy (EVT) has become a safe and effective tool for intraluminal treatment of these conditions, as it promotes changes in perfusion, microdeformation and macrodeformation of the tissue, and decreases bacterial contamination and local edema to facilitate healing. However, the high cost of the sponge system may limit widespread use of this technique [3]. In this video, we describe a cost-effective modified EVT for the treatment of transmural GI defects ([Fig. 1 a]).
EFFICACY AND SAFETY OF A NEW ENDOSCOPIC BILIARY ACCESS TECHNIQUE
Authors: A Panarese, E Shahini, A Pisani
Journal: Endoscopy (2020)

Aims Biliary cannulation is a challenging and time expensive technique during endoscopic retrograde cholangiopancreatography (ERCP), as it may fail in about 20% of cases. Several alternatives to conventional method of sphincterotome and guidewire have been proposed to date, although occur not negligible adverse events in such cases. Our primary endpoint was to assess the effectiveness and safety of deep common bile duct (CBD) cannulation after a new pre-cut with “short-incision” of papilla (fistulotomy-like). The secondary endpoint was to estimate the complication’s rate and the procedural time.
Atezolizumab plus Bevacizumab — A Landmark in Liver Cancer
Authors: Robin K. Kelley
Journal: New England Journal of Medicine (2020)

More than a decade ago, sorafenib became the first systemic therapy that conferred a meaningful survival benefit in the treatment of advanced hepatocellular carcinoma.1 Since then, no treatment had surpassed the effect of sorafenib in the first line until the regimen of atezolizumab and bevacizumab now reported by Finn and colleagues in this issue of the Journal.2 Treatment with the combination of atezolizumab, a programmed death ligand 1 (PD-L1) inhibitor, and bevacizumab, a monoclonal antibody targeting the vascular endothelial growth factor, resulted in significantly longer overall and progression-free survival as well as strikingly better patient-reported outcomes than sorafenib. These data . . .
Treatment of Lung Cancer
Authors: A H MCCALLUM
Journal: BMJ (1965)

MEDICAL JOURNAT renal failure.The hypertension which is an integral part of diabetic nephropathy causes hyalinization of the media of the arterioles, especially the afferent glomerular ones.Micro- angiopathy affecting the nutrient vessels to the nerve fibres produces irreversible neuropathy.Similar lesions have been demonstrated in the skin,5 and are a possible explanation for the high incidence of superficial infection.Diabetics are very prone to atheroma of the large arteries.This develops early and is more advanced in extent than in non-diabetic subjects of the same age.6The cause of this premature atheroma is unknown.Though even well-
Valganciclovir as Add-on to Standard Therapy in Glioblastoma Patients
Authors: Giuseppe Stragliotto, Mattia Russel Pantalone, Afsar Rahbar, Jiri Bartek, Cecilia Söderberg-Naucler
Journal: Clinical Cancer Research (2020)

Abstract Purpose: Several groups have reported a prevalence of human cytomegalovirus (CMV) in glioblastoma close to 100%. Previously, we reported that treatment with the antiviral drug valganciclovir as an add-on to standard therapy significantly prolonged survival in 50 patients with glioblastoma. Here, we present an updated retrospective analysis that includes an additional 52 patients. Experimental Design: From December 2006 to November 2019, 102 patients with newly diagnosed glioblastoma received valganciclovir as an add-on to standard therapy. No additional toxicity was observed. Contemporary controls were 231 patients with glioblastoma who received similar baseline therapy. Results: Patients with newly diagnosed glioblastoma receiving valganciclovir had longer median overall survival (OS 24.1 vs. 13.3 months, P &amp;lt; 0.0001) and a 2-year survival rate (49.8% vs. 17.3%) than controls. Median time-to-tumor progression was also longer than in controls; 9.9 (0.7–67.5 months) versus 7.3 (1.2–49 months), P = 0.0003. Valganciclovir improved survival in patients with radical or partial resection and an unmethylated or methylated MGMT promoter gene. Conclusions: Valganciclovir prolonged median OS of patients with newly diagnosed glioblastoma (with methylated or unmethylated MGMT promoter gene) and was safe to use.