tbuckley/cabot-search huggingface dataset:
ENDOSCOPIC VACUUM THERAPY FOR AN ESOPHAGEAL PERFORATION AFTER FOREIGN BODY INGESTION: RESOLUTION AFTER A SINGLE SESSION
Authors: R Morais, F Vilas-Boas, M Silva, P Pereira, G Macedo
Journal: Endoscopy (2019)

A 70-year old man was admitted to the Emergency Department due to persistent chest pain after foreign body ingestion (chicken bone) five days before. He referred fever but denied dyspnea or other symptoms. Chest computed tomography revealed in the thoracic esophagus, in the same plane of the left cardiac atrium, a linear and dense formation with 30 mm, with esophageal perforation and presence of an adjacent collection (23 × 31 × 61 mm). After multidisciplinary discussion it was decided to try to remove the foreign body and close the esophageal defect endoscopically. Upper endoscopy was performed and revealed presence of a foreign body penetrated in the esophageal wall. The adjacent mucosa was congestive and purulent drainage was noticed. Foreign body was removed with forceps and a luminal defect with 5 mm was observed, compatible with esophageal perforation. Considering the associated presence of an adjacent collection it was decided to perform endoscopic vacuum therapy (EVT) to try to close the defect and treat the collection simultaneously. The sponge was placed in the lumen with an overtube. The patient was admitted on total parenteral nutrition, antibiotics and antifungal. Five days after, upper endoscopy was repeated with removal of the sponge. On inspection, it was observed granulation tissue on the previous location of the defect, with apparent resolution of the perforation. Chest CT was repeated, with no contrast extravasation and significant improvement of the collection dimensions (27 × 17 mm). The patient completed antibiotic course, initiated oral diet and was discharged. He remains well in the follow-up.
Using Genomics to Differentiate Multiple Primaries From Metastatic Lung Cancer
Authors: Stephen J. Murphy, Faye R. Harris, Farhad Kosari, Simone Barreto Siqueira Parrilha Terra, Aqsa Nasir, Sarah H. Johnson, Vishnu Serla, James B. Smadbeck, Geoffrey C. Halling, Giannoula Karagouga, William R. Sukov, Konstantinos Leventakos, Ping Yang, Tobias Peikert, Aaron S. Mansfield, Dennis A. Wigle, Eunhee S. Yi, Benjamin R. Kipp, George Vasmatzis, Marie-Christine Aubry
Journal: Journal of Thoracic Oncology (2019)

IntroductionGenomic technologies present a promising mechanism of resolving the clinical dilemma of distinguishing independent primary tumors from intrapulmonary metastases in NSCLC. We evaluated the utility of discordant mapping somatic junctions from chromosomal rearrangements in diagnosing metastatic disease compared to the current standard histologic review.Material and MethodsMate-pair sequencing was performed on DNA extracted from 76 distinct tumors from 37 cases of multiple lung cancers. Discordant mapping junctions and chromosomal copy levels were assessed for each tumor. Blood-derived DNA was available on 22 of these cases for germline assessments. A lung cancer next-generation sequencing panel was additionally performed on tumor pairs from 17 patients.ResultsWhereas mate-pair sequencing was able to classify lineage in all tumor pairs, histologic review appeared to misclassify lineage in 9 of 33 (27%) same-histology tumor pair comparisons. Based on disagreement between the reviewing pathologists, histopathologic lineage was classified as indeterminate in seven cases. In two cases where pathologists agreed on a metastatic call, no shared junctions were found suggesting independent primaries. Although germline junctions passing algorithmic filters were common, on average less than three were present and all had predictable structures of small focal rearrangements or transposons. Evaluation of shared chromosomal copy changes and driver mutations through a lung cancer next-generation sequencing panel, while informative, were nondefinitive in calling lineage in all cases.ConclusionsThe highly unique nature and prevalence of chromosomal rearrangement in lung cancers provide a useful and definitive technique for calling lineage in multifocal lung cancer.
Complex inter-relationship of body mass index, gender and serum creatinine on survival: exploring the obesity paradox in melanoma patients treated with checkpoint inhibition
Authors: Girish S. Naik, Sushrut S. Waikar, Alistair E. W. Johnson, Elizabeth I. Buchbinder, Rizwan Haq, F. Stephen Hodi, Jonathan D. Schoenfeld, Patrick A. Ott
Journal: Journal for ImmunoTherapy of Cancer (2019)

<h3>Background</h3> A male gender driven obesity paradox (improved survival for overweight/obese patients compared to normal weight) was recently shown in melanoma in the context of checkpoint inhibition (anti-PD-1/anti-CTLA4 monotherapy) in a pooled meta-analysis. We characterized the relationship of Body Mass Index (BMI) with survival and explored gender-based interactions with surrogates of body composition/malnutrition in the context of PD-1 blockade as monotherapy or in combination with ipilimumab in a real-world setting. <h3>Methods</h3> Advanced melanoma patients who received at least one dose of pembrolizumab, nivolumab, or nivolumab plus ipilimumab (combination) from June 2014 to September 2016 were included in this retrospective cohort study (<i>N</i> = 139). Overall Survival (OS) and Progression Free Survival (PFS) were the main outcomes. Analysis was performed using Random Survival Forests (RSF)/ multivariable Cox Proportional-Hazards models. <h3>Results</h3> Overweight/Class-I (25- &lt; 35 kg/m<sup>2</sup>) obese patients had a significantly lower risk of mortality (adjusted-HR:0.26; 95%CI:0.1–0.71; <i>p</i>-value = <i>0.008</i>) and progressive disease (adjusted-HR:0.43; 95%CI:0.19–0.95; <i>p</i>-value:<i>0.038</i>) compared to normal-weight (18.5- &lt; 25 kg/m<sup>2</sup>). Class II/III obesity (compared to normal-weight) had an adjusted HR of 0.42 (95%CI: 0.1–1.77; <i>p</i>-value: 0.238) for OS and 1 (95%CI:0.34–2.94; <i>p</i>-value:0.991) for PFS. Exploration of interactions for OS showed that the association was predominantly driven by males (adjusted-HR<sub>males</sub>:0.11; 95%CI:0.03–0.4; adjusted-HR<sub>females</sub>: 0.56; 95%CI:0.16–1.89<sub>;</sub><i>p</i>-value<sub>interaction</sub>:<i>0.044</i>); the association was not seen in patients with serum creatinine&lt; 0.9 mg/dL (adjusted-HR:0.43; 95%CI:0.15–1.24; <i>p</i>-value<sub>interaction</sub>:<i>0.020</i>), who were predominantly females. These observations were made in both the anti-PD-1 monotherapy (<i>n</i> = 79) and combination therapy (anti-PD-1/CTLA-4, <i>n</i> = 60) cohorts. <h3>Conclusions</h3> The findings support the existence of an "obesity paradox" restricted to overweight/Class-I obesity in the real-world setting; the association was driven predominantly by males who largely had higher serum creatinine levels, a surrogate for skeletal muscle mass in the setting of metastatic disease. These observations suggest that sarcopenia (low skeletal muscle mass) or direct measures of body mass composition may be more suitable predictors of survival in melanoma patients treated with PD-1 blockade (monotherapy/combination).
Abstract 14229: Transient Anterograde Amnesia in the Setting of Takotsubo Cardiomyopathy
Authors: Ahmad Jabbar, Alegra Grieb, Ryan Nelson, Aaron Sweeney
Journal: Circulation (2017)

Introduction: Takotsubo cardiomyopathy (TC) and transient anterograde amnesia (TGA) are both believed to be stress-induced responses. We present a case of TC and 12 hours of TGA in the setting of no identifiable stressors. Case Presentation: A 61 year-old white man presented with a sudden onset of typical chest pain that lasted 20 minutes and was relieved on its own. Initial EKG showed nonspecific ST-T wave changes but was not diagnostic of an acute myocardial infarction. About 3 hours after presenting to the hospital the patient could no longer remember why he was there and could not recall any recent events leading up to his presentation, his long term memory was completely intact. An evaluation for possible stroke was initiated. CT scans of the head and MRI/A of the brain were non-diagnostic. His laboratory work up was notable for an initial troponin I of 0.9 and a peak of 4.2 six hours later. He underwent a diagnostic coronary angiogram that showed no obstructive coronary artery disease. A transthorac...
Postpublication Metrics of Randomized Clinical Trials With and Without Null Findings
Authors: Stuart B. Murray, James A. Heathers, Rebecca M. Schauer, Scott Griffiths, Deborah Mitchison, Jonathan M. Mond, Jason M. Nagata
Journal: JAMA (2019)

This study examined the association between RCT findings supporting or rejecting the trials’ experimental hypotheses and postpublication metrics reflecting scientific and public interest; namely, citations, Altimetric scores, and views.
Trends in Incidence and Stage at Diagnosis of Colorectal Cancer in Adults Aged 40 Through 49 Years, 1975-2015
Authors: Reinier G. S. Meester, Ajitha Mannalithara, Iris Lansdorp-Vogelaar, Uri Ladabaum
Journal: JAMA (2019)

This cancer epidemiology study uses SEER program data to describe trends in stage of incident colorectal cancer in adults aged 40-49 years between 1975 and 2015 to understand if apparent increases in incidence are due to earlier detection or true increases in risk.
NOD-like receptor family, pyrin domain containing 3 (NLRP3) contributes to inflammation, pyroptosis, and mucin production in human airway epithelium on rhinovirus infection
Authors: Tao Liu, Yu Tao Zhou, Li Qiu Wang, Li Yue Li, Qing Bao, Shuo Tian, Mei Xin Chen, He Xin Chen, Jun Cui, Chun Wei Li
Journal: Journal of Allergy and Clinical Immunology (2019)
COLD SNARE PIECEMEAL ENDOSCOPIC MUCOSAL RESECTION (CSP-EMR) OF LARGE SESSILE COLONIC POLYPS ≥20 MM IS FEASIBLE, SAFE AND EFFECTIVE
Authors: D Mangira, K Cameron, JH Koo, A Moss
Journal: Endoscopy (2019)

EMR is the standard therapy for resection of large (≥20 mm) non-malignant sessile colonic polyps. Serious adverse events are mostly due to electrocautery. This could be avoided by cold-snare-EMR. We hypothesized that aggressive wide field cold snare piecemeal EMR (CSP-EMR) could be as effective as conventional EMR, but with fewer adverse events. The study evaluated safety and efficacy of CSP-EMR for ≥20 mm sessile colonic polyps.
Abstract P355: Sleep Duration is Associated With the Metabolic Syndrome Independent of Depression Symptoms The Polish Norwegian Study
Authors: Georgeta Vaidean, Marta Manczuk
Journal: Circulation (2017)

Introduction: Short- and long sleep durations have emerged as potential cardiovascular risk factors. Yet, the relation with metabolic syndrome (MetSyn) remains uncertain due to potential residual confounding by depression and comorbidities. Purpose: To test whether compared to adequate-sleepers, short and/or long- sleepers have higher prevalence of MetSyn, independent of current depression or past psychiatric illnesses. Methods: Cross-sectional data of 12754 participants, age 45 to 64 years, in an ongoing cohort study, with structured questionnaires and fasting blood samples. We categorized self-reported sleep duration as short (le 5 h), adequate (6-8 h) or long (ge9 h). Metabolic syndrome was defined based on AHA/NHLBI’s criteria. Depression symptoms were ascertained with a culturally-adapted, 7-item Patient Health Questionnaire. We estimated multivariable-adjusted prevalence ratios using Poisson regression models with robust standard error estimates. Results: Compared to adequate sleepers, both short- and long -sleepers were less likely to be men, to drink alcohol, and be current smokers but more likely to have history of cardiovascular diseases and hypertension. Among short-, adequate and long-sleepers the prevalence of self-reported past psychiatric diseases was 2.28%, 1.59% and 8.50% respectively (p =0.0001) and the prevalence of current antidepressant use was 5.09%, 2.52% and 10.26% respectively (p=&lt;0.0001). Similarly, the prevalence of 5 or more depressive symptoms was 39.36%, 22.09% and 26.98% respectively (p =0.0001). The prevalence of MetSyn among short-, adequate and long-sleepers was 45.38%, 38.12% and 49.56% respectively (p =0.0001). Compared to adequate sleepers, the prevalence of MetSyn remained higher among short-sleepers (PR 1.10, 95% CI 1.01-1.19) and among long-sleepers (PR 1.15, 95%CI 1.02-1.30), after adjusting for age, sex, smoking, alcohol, coffee intake, physical activity, education, non-cardiovascular chronic diseases, past psychiatric diseases, current depression symptoms and current antidepressant drugs use. Difficulties with sleep initiation were not associated with MetSyn. In a subgroup analysis restricted to those with BMI 25-29.9 kg/m 2 , compared to adequate sleepers, the prevalence of MetSyn remained higher among short-sleepers (PR 1.16, 95% CI 1.02-1.32) and among long-sleepers (PR 1.29, 95%CI 1.04-1.60) after multivariable adjustment. Conclusion: Both short and long sleep duration are associated with the presence of MetSyn, independent of past psychiatric conditions or current depression symptoms or treatment.
International consensus statement on the diagnosis and management of autosomal dominant polycystic kidney disease in children and young people
Authors: Charlotte Gimpel, Carsten Bergmann, Detlef Bockenhauer, Luc Breysem, Melissa A. Cadnapaphornchai, Metin Cetiner, Jan Dudley, Francesco Emma, Martin Konrad, Tess Harris, Peter C. Harris, Jens König, Max C. Liebau, Matko Marlais, Djalila Mekahli, Alison M. Metcalfe, Jun Oh, Ronald D. Perrone, Manish D. Sinha, Andrea Titieni, Roser Torra, Stefanie Weber, Paul J. D. Winyard, Franz Schaefer
Journal: Nature Reviews Nephrology (2019)

These recommendations were systematically developed on behalf of the Network for Early Onset Cystic Kidney Disease (NEOCYST) by an international group of experts in autosomal dominant polycystic kidney disease (ADPKD) from paediatric and adult nephrology, human genetics, paediatric radiology and ethics specialties together with patient representatives. They have been endorsed by the International Pediatric Nephrology Association (IPNA) and the European Society of Paediatric Nephrology (ESPN). For asymptomatic minors at risk of ADPKD, ongoing surveillance (repeated screening for treatable disease manifestations without diagnostic testing) or immediate diagnostic screening are equally valid clinical approaches. Ultrasonography is the current radiological method of choice for screening. Sonographic detection of one or more cysts in an at-risk child is highly suggestive of ADPKD, but a negative scan cannot rule out ADPKD in childhood. Genetic testing is recommended for infants with very-early-onset symptomatic disease and for children with a negative family history and progressive disease. Children with a positive family history and either confirmed or unknown disease status should be monitored for hypertension (preferably by ambulatory blood pressure monitoring) and albuminuria. Currently, vasopressin antagonists should not be offered routinely but off-label use can be considered in selected children. No consensus was reached on the use of statins, but mTOR inhibitors and somatostatin analogues are not recommended. Children with ADPKD should be strongly encouraged to achieve the low dietary salt intake that is recommended for all children. This Consensus Statement developed on behalf of the Network for Early Onset Cystic Kidney Disease provides guidance on counselling, diagnosing and monitoring children with autosomal dominant polycystic kidney disease based on current evidence and a multi-stakeholder discussion of ethical issues.
Lyme neuroborreliosis epidemiology in Sweden 2010 to 2014: clinical microbiology laboratories are a better data source than the hospital discharge diagnosis register
Authors: Viktor Dahl, Karin T Wisell, Christian G Giske, Anders Tegnell, Anders Wallensten
Journal: Eurosurveillance (2019)

Background In a study from 2013 that prioritised communicable diseases for surveillance in Sweden, we identified Lyme borreliosis as one of the diseases with highest priority. In 2014, when the present study was designed, there were also plans to make neuroborreliosis notifiable within the European Union. Aim We compared possibilities of surveillance of neuroborreliosis in Sweden through two different sources: the hospital discharge register and reporting from the clinical microbiology laboratories. Methods We examined the validity of ICD-10 codes in the hospital discharge register by extracting personal identification numbers for all cases of neuroborreliosis, defined by a positive cerebrospinal fluid–serum anti- Borrelia antibody index, who were diagnosed at the largest clinical microbiology laboratory in Sweden during 2014. We conducted a retrospective observational study with a questionnaire sent to all clinical microbiology laboratories in Sweden requesting information on yearly number of cases, age group and sex for the period 2010 to 2014. Results Among 150 neuroborreliosis cases, 67 (45%) had received the ICD-10 code A69.2 (Lyme borreliosis) in combination with G01.9 (meningitis in bacterial diseases classified elsewhere), the combination that the Swedish National Board of Health and Welfare recommends for neuroborreliosis. All 22 clinical laboratories replied to our questionnaire. Based on laboratory reporting, the annual incidence of neuroborreliosis in Sweden was 6.3 cases per 100,000 in 2014. Conclusion The hospital discharge register was unsuitable for surveillance of neuroborreliosis, whereas laboratory-based reporting was a feasible alternative. In 2018, the European Commission included Lyme neuroborreliosis on the list of diseases under epidemiological surveillance.
FDG-Avid Hürthle Cell Thyroid Adenoma
Authors: Run Yu, Martin S. Auerbach
Journal: Clinical Nuclear Medicine (2019)

Incidental thyroid uptake is found in approximately 2.5% of patients who undergo FDG PET for nonthyroid malignancy; approximately a third of the FDG PET thyroid incidentalomas are malignant, including primary thyroid malignancies and metastasis. We describe a 50-year-old woman, a potential heart transplant candidate with history of breast cancer, who was found by FDG PET/CT to harbor a large thyroid mass with intense FDG uptake. Biopsy and molecular study demonstrated that the thyroid mass was a Hürthle cell adenoma. This case highlights that Hürthle cell neoplasm should be included in the differential diagnosis of a thyroid nodule with very high FDG avidity.
The RNA binding protein HuR influences skeletal muscle metabolic flexibility in rodents and humans
Authors: Randall L. Mynatt, Robert C. Noland, Carrie M. Elks, Bolormaa Vandanmagsar, David S. Bayless, Allison C. Stone, Sujoy Ghosh, Eric Ravussin, Jaycob D. Warfel
Journal: Metabolism (2019)
Correction: Efficacy and Safety of the Biosimilar ABP 215 Compared with Bevacizumab in Patients with Advanced Nonsquamous Non–small Cell Lung Cancer (MAPLE): A Randomized, Double-blind, Phase III Study
Authors: Nicholas Thatcher, Jerome H. Goldschmidt, Michael Thomas, Michael Schenker, Zhiying Pan, Luis Paz-Ares Rodriguez, Valery Breder, Gyula Ostoros, Vladimir Hanes
Journal: Clinical Cancer Research (2019)

In the original version of this article (1), Fig. 1 was incomplete and the "Methods" sections of both the abstract and the article stated that patients received drugs thrice weekly instead of every three weeks. These errors have been corrected in the latest online HTML and PDF versions of the article. The authors regret these errors.
Deep Learning Deepens the Analysis of Alternative Splicing
Authors: Xudong Zou, Xin Gao, Wei Chen
Journal: Genomics Proteomics & Bioinformatics (2019)

The ever-increasing high-volume and high-dimensional genomics data on the one hand challenge traditional data analysis approaches, and on the other hand provide ample opportunities for developing novel analytic strategies.In recent years, deep learning has been driving the next wave of artificial intelligence and machine learning.Now, Yi Xing's lab reported DARTS [1], a novel computational framework that leverages the power of both deep learning and Bayes hierarchical framework for differential alternative splicing (AS) analysis.Trained on the huge volume of publicly-available RNA-seq datasets, DARTS could largely increase the accuracy of AS analysis, in particular for those with low sequencing depth, by taking both genomic features and expression levels of RNA-binding proteins (RBPs) into consideration.
Reply letter to: Letter to the editor on the article “Virtual reality simulator versus box-trainer to teach minimally invasive procedures: A meta-analysis"
Authors: H.G. Guedes, Z.M.C.C. Ferreira, L.R.S. Leão, E.F.S. Montero, J.P. Otoch, E.L.A. Artifon
Journal: International Journal of Surgery (2019)
Spindle cell carcinoma of the breast: Rare cancer with potentially targetable biomarkers
Authors: Z. Gatalica, S. Vranic, P. Stafford, J. Palazzo, F. Skenderi, J. Swensen, J. Xiu, D. Spetzler
Journal: Annals of Oncology (2019)

Background: Spindle cell carcinoma is a rare, metaplastic breast cancer (<1% of all breast carcinomas), with reportedly triple-negative (TNBC: ER-/PR-/Her2-) phenotype, associated with a marked resistance to conventional chemotherapy and overall poor outcome. Methods: Twenty pure spindle cell carcinomas of the breast (15 primary and 5 recurrent/metastatic) were comprehensively explored for biomarkers of immuno-oncology (I-O) and targeted therapies using immunohistochemistry and DNA (592 genes panel) and RNA (52 genes panel) sequencing. A cohort of 603 TNBC cases analyzed with NGS was used as a control for the total mutational burden (TMB). Results: Majority (18/20) of spindle cell carcinomas were triple negative. Estrogen (2 cases) and androgen receptor (one case) expression above the therapeutic thresholds were rarely detected. Pathogenic mutations were detected in 80% including PIK3CA (30%), TP53 (25%), HRAS (20%), NF1 (20%), and PTEN (10%) as the most frequent. One case with matched pre- and post-chemotherapy samples analysis exhibited a consistent mutational profile (PIK3CA and HRAS mutations) in both samples. No gene fusions were identified in matched samples. No NTRK expression was detected in 4 tested cases. In comparison to the large (>600 patients) cohort of TNBC (11 mutations/Mb as 80th percentile cutoff value), the TMB in spindle cell carcinomas was low (below 80th percentile) in all cases (3-9 mutations/Mb). All tumors were microsatellite stable. Tumor cells (TC) PD-L1 expression was present in 6/18 cases. Conclusions: Spindle cell carcinoma of the breast exhibits mutational profile similar to the published data in other types of metaplastic breast carcinomas. All spindle cell carcinomas have a low TMB and were microsatellite stable. PD-L1 expression was detected in one third of cases and may guide therapy trials with immune checkpoint inhibitors. Rare cases with ER and AR expression were detected and were candidates for respective hormonal therapies. Legal entity responsible for the study: Zoran Gatalica. Funding: Has not received any funding. Disclosure: Z. Gatalica, P. Stafford, J. Swensen, J. Xiu, D. Spetzler: Employee: Caris Life Sciences. All other authors have declared no conflicts of interest.
A RISK SCORING MODEL FOR THE PREDICTION OF DELAYED BLEEDING AFTER COLORECTAL ENDOSCOPIC SUBMUCOSAL DISSECTION
Authors: JS Byeon, EM Song, M Seo, JW Cho, YJ Lee, BI Lee, JS Kim, SW Jeon, HJ Jang, DH Yang, BD Ye
Journal: Endoscopy (2019)

Delayed bleeding is an important adverse event after colorectal endoscopic submucosal dissection (ESD). We aimed to investigate the incidence and risk factors of delayed bleeding after colorectal ESD, and to develop a risk scoring model for predicting delayed bleeding.