tbuckley/cabot-search huggingface dataset:
Comprehensive Genomic Profiling Identifies Novel Genetic Predictors of Response to Anti–PD-(L)1 Therapies in Non–Small Cell Lung Cancer
Authors: Wenfeng Fang, Yuxiang Ma, Jiani C. Yin, Shaodong Hong, Huaqiang Zhou, Ao Wang, Fufeng Wang, Hua Bao, Xue Wu, Yunpeng Yang, Yan Huang, Hongyun Zhao, Yang W. Shao, Li Zhang
Journal: Clinical Cancer Research (2019)

Abstract Purpose: Immune checkpoint inhibitors (ICI) have revolutionized cancer management. However, molecular determinants of response to ICIs remain incompletely understood. Experimental Design: We performed genomic profiling of 78 patients with non–small cell lung cancer (NSCLC) who underwent anti–PD-(L)1 therapies by both whole-exome and targeted next-generation sequencing (a 422-cancer-gene panel) to explore the predictive biomarkers of ICI response. Tumor mutation burden (TMB), and specific somatic mutations and copy-number alterations (CNA) were evaluated for their associations with immunotherapy response. Results: We confirmed that high TMB was associated with improved clinical outcomes, and TMB quantified by gene panel strongly correlated with WES results (Spearman's ρ = 0.81). Compared with wild-type, patients with FAT1 mutations had higher durable clinical benefit (DCB, 71.4% vs. 22.7%, P = 0.01) and objective response rates (ORR, 57.1% vs. 15.2%, P = 0.02). On the other hand, patients with activating mutations in EGFR/ERBB2 had reduced median progression-free survival (mPFS) compared with others [51.0 vs. 70.5 days, P = 0.0037, HR, 2.47; 95% confidence interval (CI), 1.32–4.62]. In addition, copy-number loss in specific chromosome 3p segments containing the tumor-suppressor ITGA9 and several chemokine receptor pathway genes, were highly predictive of poor clinical outcome (survival rates at 6 months, 0% vs. 31%, P = 0.012, HR, 2.08; 95% CI, 1.09–4.00). Our findings were further validated in two independently published datasets comprising multiple cancer types. Conclusions: We identified novel genomic biomarkers that were predictive of response to anti–PD-(L)1 therapies. Our findings suggest that comprehensive profiling of TMB and the aforementioned molecular markers could result in greater predictive power of response to ICI therapies in NSCLC.
White, red, and mixed lesions of oral mucosa: A clinicopathologic approach to diagnosis
Authors: Saman Warnakulasuriya
Journal: Periodontology 2000 (2019)

Abstract A wide range of conditions could present as persistent white or red, or mixed white and red patches on the oral mucosa. Discussed here are some common conditions encountered in clinical practice that appear as white or red patches, together with some rare, but clinically significant, conditions. Based on pathognomonic features, major diagnostic criteria are outlined to help with the differential diagnosis, while some require further investigation (eg, biopsy and/or microbiologic or hematologic investigation) to confirm the provisional clinical diagnosis. Two conditions that require special consideration are leukoplakia and erythroplakia, as they have the potential to transform to cancer.
ENDOSCOPIC REMOVAL OF A COLONIC FOREIGN BODY USING A LOOP CUTTER DEVICE
Authors: F Pires, R Araújo, A Carvalho, J Pinho, R Cardoso, J Constantino, D Martins, P Sousa, E Cancela, A Castanheira, P Ministro, A Silva
Journal: Endoscopy (2019)

Foreign body ingestion is a common event in childhood but can also happen in adulthood, usually occurring accidentally during a meal. The authors report the case of a 61 year-old female, with no relevant personal history, who was sent to the emergency department due to a foreign body lodged in the sigmoid colon that was identified on an outpatient colonoscopy performed due to lower abdominal pain and episodic fever in the last 3 months. The physical examination and laboratory tests were unremarkable. An abdominal computed tomography confirmed a foreign body with 46 × 5 mm on the rectosigmoid junction, associated with colic wall thickening and densification of the surrounding fat, with no evidence of fluid collections nor intraperitoneal free air. Endoscopic removal was attempted but the foreign body had its ends lodged into the colonic wall (diverticula area), with inflammatory signs and a small quantity of purulent drainage and it was decided to hospitalize the patient and start intravenous antibiotics. Endoscopy was repeated under general anesthesia two days later. A loop cutter device was used to cut the foreign body, with extraction of the two ends with grasping forceps. The sites of previous contact with the colic wall were closed with endoclips. The patient was discharged five days later without any complaints. The authors highlight the therapeutic innovation presented in this case, where an alternative use of a device enabled a safe and minimally invasive resolution and emphasize the excellent iconography collected on video.
UNDERWATER ENDOSCOPIC MUCOSAL RESECTION – A PROSPECTIVE COHORT STUDY
Authors: J Fernandes, T Araújo, R Ramos, C Vicente, J Tristan, F Lucas, J Canena, L Lopes, C Casteleiro
Journal: Endoscopy (2019)

Underwater endoscopic mucosal resection (uEMR) is a recent endoscopic technique in which water (exclusively) is instilled in the colon lumen, causing its distension. There is a submucosal floating effect and the muscularis propria stays away because of its greater density, which precludes the need for injection. With this study we intend to evaluate the efficacy and safety of uEMR in the resection of colonic lesions.
Dilatation endoscopique des sténoses peptiques: évaluation clinique et facteurs prédictifs d'échec
Authors: E Bel Hadj Mabrouk, S Ayadi, M Ayari, Y Zaimi, K El Jeri, Y Said, L Mouelhi, R Debbeche
Journal: Endoscopy (2019)

Les sténoses peptiques représentent l'étiologie la plus fréquente des bénignes oesophagiennes. Dans la littérature, elle présente environ 60 à 80% d'entre elles. Ces sténoses sont dues à une exposition chronique à l'acidité gastrique. Le diagnostic positif ainsi que la prise en charge thérapeutique se basent principalement sur l'endoscopie digestive haute. Nous proposons dans ce travail de rapporter le profil clinique et évolutif de nos patients ainsi que d'évaluer le traitement endoscopique.
HIGH PERFORMANCE OF A NEW FRANSEEN NEEDLE FOR ENDOSCOPIC ULTRASOUND-GUIDED FINE-NEEDLE BIOPSY IN SOLID LESIONS: A RETROSPECTIVE MULTICENTER STUDY
Authors: G de Nucci, G Del Vecchio Blanco, A Amato, E Forti, G Santo Mezzi, G Mogavero, E Domenico Mandelli, G Manes
Journal: Endoscopy (2019)

Endoscopic ultrasound-guided fine needle aspiration (FNA) is the standard choice to sample gastrointestinal/pancreatic lesions. EUS-FNA is accurate when rapid on-site evaluation (ROSE) is performed, but ROSE is not always available. EUS-guided fine needle biopsy (EUS-FNB) can give a a better chance to reach a diagnosis providing more tissue. It is not simple to use 19-gauge needles especially in transduodenal settings for risk of complications.A new needle for EUS-FNB, the AcquireTM needle is available from 2016. Data for pancreatic and non pancreatic solid lesions are available but these are based only on small sample size studies. The aim of our study is to perform a retrospective evaluation of all sampling procedures performed using the 22/25 gauge AcquireTM needle in patients with solid lesions.
The Role of Microcirculatory Dysfunction in the Pathophysiology and Treatment of Venous Leg Ulcers—Reply
Authors: Julia Slark, John Parsons, Andrew Jull
Journal: JAMA Dermatology (2019)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Dermatology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Dermatology journal
THE ROLE OF THE JUXTAPAPILLARY DIVERTICULA IN ENDOSCOPIC RETROGRADE CHOLANGIOPANCREATOGRAPHY – BASED ON THE HUNGARIAN ERCP REGISTRY
Authors: T Bakucz, Á Orbán-Szilágyi, D Pécsi, S Gódi, F Pakodi, I Altorjay, G Kovács, Á Patai, L Czakó, Z Szepes, P Hegyi, Á Vincze, T Gyökeres
Journal: Endoscopy (2019)

Contradictory data show that juxtapapillary diverticula could be frequently associated with bile duct stones, cannulation failure and higher rates of complications. In this study we compared success and complications of the ERCP's in patients with and without juxtapapillary diverticula based on our national ERCP registry.
Transcriptional versus metabolic control of cell fitness during cell competition
Authors: Katerina Lawlor, Salvador Pérez-Montero, Ana Lima, Tristan A. Rodríguez
Journal: Seminars in Cancer Biology (2019)

The maintenance of tissue homeostasis and health relies on the efficient removal of damaged or otherwise suboptimal cells. One way this is achieved is through cell competition, a fitness quality control mechanism that eliminates cells that are less fit than their neighbours. Through this process, cell competition has been shown to play diverse roles in development and in the adult, including in homeostasis and tumour suppression. However, over the last few years it has also become apparent that certain oncogenic mutations can provide cells with a competitive advantage that promotes their expansion via the elimination of surrounding wild-type cells. Thus, understanding how this process is initiated and regulated will provide important insights with relevance to a number of different research areas. A key question in cell competition is what determines the competitive fitness of a cell. Here, we will review what is known about this question by focussing on two non-mutually exclusive possibilities; first, that the activity of a subset of transcription factors determines competitive fitness, and second, that the outcome of cell competition is determined by the relative cellular metabolic status.
GUIDE-WIRE AND CONTRAST INJECTION CANNULATION (MIXED TECHNIQUE) IS SUPERIOR TO EXCLUSIVE GUIDE-WIRE BILIARY CANNULATION FOR PREVENTION OF POST-ERCP PANCREATITIS (PEP): A DOUBLE-BLIND, CONTROLLED, RANDOMIZED TRIAL
Authors: J Pereira Lima, ID Arciniegas, I Contin, G Pereira Lima, CE Oliveira dos Santos, F Onofrio
Journal: Endoscopy (2019)

PEP is the most common complication of ERCP. In the last few years, some studies have demonstrated that the use of guide-wire cannulation (GW-C) instead of contrast injection reduces the rate of PEP. Thus, the GW-C technique has become gold standard and contrast injection an almost proscribed technique, although the majority of studies favouring the GW-C technique has shown exaggerated rates of PEP in the contrast cannulation group or do not allow cross-over between both techniques. In this study, we intend to compare GW-C with the mixed technique (GW and/or contrast injection at endoscopist's discretion).
ENDOSCOPIC PERORAL DRAINAGE (EPOD) OF PERITONEAL POST BARIATRIC SURGERY COLLECTION AND ABSCESSES
Authors: A Baptista, A Salinas, W García, M Guzman, M Davila
Journal: Endoscopy (2019)

Pancreatic collections endodrainage is a rationale for Endoscopic Peroral Drainage (EPOD) in cases of peritoneal abscess after Bariatric surgery leaks. Reoperation has a high morbidity and CTdrainage has limitations.
Abstract 9958: Fitness in Young Adulthood is Independently Associated With Improved Survival and Cardiovascular Risk: The CARDIA study
Authors: Ravi Shah, Venkatesh Murthy, Laura Colangelo, Jared Reis, Bharath Venkatesh-Ambale, Ravi Sharma, Siddique Abbasi, David Goff, J. Jeffrey Carr, Jamal Rana, James Terry, Claude Bouchard, Mark Sarzynski, Aaron Eisman, Tomas Neilan, Saumya Das, Michael Jerosch-Herold, Gregory Lewis, Joao Lima
Journal: Circulation (2015)

Introduction: Though cardiorespiratory fitness (CRF) is a well-established prognostic marker in older adults, the relationship between changes in CRF during early adulthood and long-term cardiovascular structure, function, and events remain unknown. Hypothesis: CRF and its change over time in young adults is associated with long-term outcome and cardiovascular disease (CVD). Methods: 4,872 American adults age 18-30 years underwent treadmill exercise testing at a baseline study visit in 1985-1986, and 2,472 individuals who underwent repeat treadmill testing 7 years later in CARDIA. Participants were followed for a median of 26.9 years, with assessment of obesity, echocardiographic left ventricular (LV) mass and strain, coronary artery calcification (CAC), and vital status and incident CVD. Incident CVD (cardiovascular death, heart failure, myocardial infarction, peripheral artery disease and stroke) and all-cause mortality were uniformly adjudicated. Results: From 4,872 individuals, 273 (5.6%) died and 193 (4%) experienced CVD events at a median 26.9 year follow-up. After full adjustment, each additional minute of baseline exercise test duration was associated with a 13% lower hazard of death (hazard ratio HR 0.87, 95% CI 0.81-0.92, P&lt;0.0001) and a 9% lower hazard of CVD (HR 0.91, 95% CI 0.84-0.98, P=0.008). Higher baseline fitness was associated with decreased risk of LV hypertrophy (P=0.009) and higher global longitudinal strain (P&lt;0.0001) at Year 25. Fitness was not associated with CAC. A 1-minute reduction in fitness by Year 7 was associated with a 20% increased hazard of death and CVD, along with a greater probability of LV hypertrophy and more impaired strain. There was no association between change in fitness and CAC. Conclusions: Higher fitness at baseline and improvement in fitness early in adulthood are favorably associated with CVD and mortality risk. Fitness and changes in fitness are associated with myocardial hypertrophy and dysfunction, but not CAC. Regular efforts to ascertain and improve CRF in young adulthood may play a critical role in promoting cardiovascular health and interrupting early CVD pathogenesis.
Male breast cancer, a heterogeneous entity: Experience from a cancer center
Authors: J.C. Carvalho, M. Peixoto, T. Cunha Pereira, A.R. Garcia, M. Mariano, S. Broco, I. Pazos, T. Carvalho, J. Ribeiro, G. Sousa
Journal: Annals of Oncology (2019)

Background: Male Breast Cancer (MBC) represents 1% of all breast cancers, as well as less than 1% of malignant neoplasm in male. Methods: Describe male population with breast cancer (BC) in our institute from 2007 to 2017. Methods: Unicentric, retrospective and descriptive study with inclusion of all male individuals with diagnosis of invasive breast carcinoma. Data was obtained through clinical process review and analyzed with SPSS®. Results: There were included 66 cases of invasive male breast carcinoma with a median age at diagnosis of 66,5 years old, [24-88] and an initial ECOG PS of 0 in 73% (n = 48). Locally advanced disease was diagnosis on 47% (n = 30) of patients, meanwhile 44% of cases were early BC at the diagnosis. Stage IV disease occurred on 9% (n = 6), and 6 % (n = 4) of patients had bilateral BC. The most frequent molecular subtype was Luminal B-Like (67% n = 44), and cerB-2 overexpression occurred in 10,6% (n = 7). The most frequent symptom was breast lump (89% n = 59). At the time of diagnosis, clinical suspected axillary lymph nodes were detected on 68% of the cases and gynecomastia was present in 28%. The percentage of cases observed after 6 months of symptoms onset was 30%. Positive family history of neoplasms occurred on 71% of cases, including 26% with BC family history. Pre-existing neoplasia was observed in 20% of patients, namely prostate adenocarcinoma as the most frequent diagnosis. Near 53% of the cases were followed on familiar cancer risk appointment, with 4,5%, (n = 3) of cases positive for BRCA2 pathologic mutations. Neoadjuvant chemotherapy was performed in 33% (n = 22). Surgery was performed on 94% (n = 62) of the patients. The pathologic response rate was 90%. In adjuvant setting, 70% (n = 46) of patients received hormonotherapy and 47% (n = 31) radiotherapy. The median time to recurrence was 33 months, [11-147]. Near 23% (n = 15) of patients progressed and the most frequent secondary location was bone (60%). The median OS was 8 years, 95% CI[6,5 -9,5]. Conclusions: MBC is diagnosed later, presenting a more advanced stage, and the majority of patients had expression of hormonal receptors. Despite the late diagnosis, good disease control was achieved. This study in addition to being in accordance with literature reflects the importance of follow-up in family risk consultation. Legal entity responsible for the study: Joana Cunha Carvalho. Funding: Has not received any funding. Disclosure: All authors have declared no conflicts of interest.
Biopsies étagées sur une coloscopie normale chez les patients ayant une diarrhée chronique. Quel apport?
Authors: Z Bouhnoun, A Arramdani, H Abid, N Lahmidani, M Elyoussfi, N Aqodad, DA Benajah, A Ibrahimi, M Elabkari
Journal: Endoscopy (2019)

Les diarrhées chroniques représentent un motif de consultation fréquent dont le diagnostic étiologique s'impose. L'endoscopie joue un rôle très important dans la prise en charge des diarrhées chroniques dont l'indication reste très discutable due à la crainte de multiplier des examens dangereux et inutiles chez les patients présentant des troubles fonctionnels intestinaux. Le but de notre travail est de revoir l'indication et l'intérêt des biopsies systématique chez les patients souffrants de diarrhées chroniques et chez qui la coloscopie était normale.
Tumor perfusion during bevacizumab and irinotecan in recurrent glioblastoma: A multimodal approach.
Authors: Marica Eoli, Anna Luisa Di Stefano, Domenico Aquino, Alessandro Scotti, Elena Anghileri, Lucia Cuppini, Elena Prodi, Gaetano Finocchiaro, Maria Grazia Bruzzone
Journal: Journal of Clinical Oncology (2013)

2074 Background: Angiogenesis is a requirement for progression of glioblastoma (GBM) and vascular endothelial growth factor (VEGF) is a mediator of neo-angiogenesis in this tumor. Bevacizumab (Bev), an antibody directed to VEGF, was recently used to treat GBM. However in vivo modifications induced by treatment are still not clearly understood. Aim of this study is to analyze tumor changes induced by Irinotecan (Ir) and Bev, using two different methodologies: relative CBV variation (rCBV) and Difference Perfusion Maps (DPMs). Methods: 42 recurrent GBM patients underwent Bev (10 mg/kg) and Ir (125 or 340 mg/m 2 ) treatment every 2 weeks and were followed up with a radiological protocol, including Dynamic Susceptibility Contrast MRI every 8 weeks. Radiological responses were assessed based on RANO criteria (Wen et al, 2012). Two methods were used to assess perfusion changes. In method A, relative CBV variation after 8 weeks of treatment was calculated through semi-automatic ROI placement in the same anatomic region as in baseline. In method B, relative CBV variations with respect to baseline values were calculated into the evolving tumour region by means of a voxel-by-voxel difference. DPMs were created showing where rCBV significantly increased, decreased or remained unchanged. Results: After a median follow-up of 33.5 months median overall survival (OS) was 35.0 weeks and median progression free survival (PFS) was 20.0 weeks. Method A showed a significant decrease of rCBV for patients with stable disease or partial response after 8 weeks of treatment (p = 0.01) while progressing patients maintained elevated levels of rCBV (p = 0.38). Method B, based on DPMs, showed that patients presenting rCBV increase higher than 25° percentile (corresponding to rCBV increase higher than 18% of tumor volume) had a significantly longer PFS (p = 0.045) and OS (p = 0.016). Conclusions: Using DPM we observed that early increase in global perfusion is related to better survival. This may suggest that Bev, when effective, reduces blood-brain barrier permeability with a higher contrast retention in vessels. If confirmed by further studies this measure could be useful in identifying responders to Bev.
Erratum to: Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development
Authors: Linda Szabo, Robert Morey, Nathan J. Palpant, Peter L. Wang, Nastaran Afari, Chuan Jiang, Mana M. Parast, Charles E. Murry, Louise C. Laurent, Julia Salzman
Journal: Genome biology (2016)

In this version of this article that was originally published [1] the authors had analysed two HeLa samples, SRR1637089 and SRR1637090, in Fig. 3 of the original publication. The authors had respectively analysed the samples as RNaseR+ and Ribominus, due to their incorrect annotations in a public database, but they were both Ribominus samples. The authors have now analysed appropriate positive and negative controls using their method, KNIFE, and find_circ. The results are presented in an amended version of Fig. 3c, please see updated version below. Furthermore, the authors have now provided a list of accession codes for the ENCODE data they analysed, please see the Table 1 below. Please note this was not part of the original article. Source (cell line name or tissue type), Type of sample (tissue, polyA+ cell line, or polyA- cell line), and Accession code for all ENCODE data analyzed.]