tbuckley/cabot-search huggingface dataset:
Xenograft-based, platform-independent gene signatures to predict response to alkylating chemotherapy, radiation, and combination therapy for glioblastoma
Authors: Shuang G Zhao, Menggang Yu, Daniel E Spratt, S Laura Chang, Felix Y Feng, Michelle M Kim, Corey W Speers, Brett L Carlson, Ann C Mladek, Theodore S Lawrence, Jann N Sarkaria, Daniel R Wahl
Journal: Neuro-Oncology (2019)

Predictive molecular biomarkers to select optimal treatment for patients with glioblastoma and other cancers are lacking. New strategies are needed when large randomized trials with correlative molecular data are not feasible.Gene signatures (GS) were developed from 31 orthotopic glioblastoma patient-derived xenografts (PDXs), treated with standard therapies, to predict benefit from radiotherapy (RT-GS), temozolomide (Chemo-GS), or the combination (ChemoRT-GS). Independent validation was performed in a heterogeneously treated clinical cohort of 502 glioblastoma patients with overall survival as the primary endpoint. Multivariate Cox analysis was used to adjust for confounding variables and evaluate interactions between signatures and treatment.PDX models recapitulated the clinical heterogeneity of glioblastoma patients. RT-GS, Chemo-GS, and ChemoRT-GS were correlated with benefit from treatment in the PDX models. In independent clinical validation, higher RT-GS scores were associated with increased survival only in patients receiving RT (P = 0.0031, hazard ratio [HR] = 0.78 [0.66-0.92]), higher Chemo-GS scores were associated with increased survival only in patients receiving chemotherapy (P < 0.0001, HR = 0.66 [0.55-0.8]), and higher ChemoRT-GS scores were associated with increased survival only in patients receiving ChemoRT (P = 0.0001, HR = 0.54 [0.4-0.74]). RT-GS and ChemoRT-GS had significant interactions with treatment on multivariate analysis (P = 0.0009 and 0.02, respectively), indicating that they are bona fide predictive biomarkers.Using a novel PDX-driven methodology, we developed and validated 3 platform-independent molecular signatures that predict benefit from standard of care therapies for glioblastoma. These signatures may be useful to personalize glioblastoma treatment in the clinic and this approach may be a generalizable method to identify predictive biomarkers without resource-intensive randomized trials.
A monopoly on knowledge is bad for patients
Authors: Roger Weeks
Journal: BMJ (2019)

Patients and their doctors should be grateful to deBronkart for highlighting the lack of access to new information about illnesses.1 Clearly the advice of Abigail Adams to her president and husband, John Adams, has been ignored not just in the US but worldwide. The unlimited power of academics with a monopoly on knowledge is unchanged. The delivery of such knowledge to patients (and their doctors) at …
Les polypes minuscules et les petits polypes sont-ils dangereux?
Authors: A Ben Mohamed, M Medhioub, A Khsiba, M Mahmoudi, L Hamzaoui, MM Azouz
Journal: Endoscopy (2019)

De petits polypes coliques (6 – 9 mm) et minuscules (1 – 5 mm) sont fréquemment retrouvés à la coloscopie. L'histologie demeure à ce jour le gold-standard pour l'évaluation des polypes malgré d'importantes différences histo-pathologiques inter-observateur dans la distinction entre les adénomes et les polypes hyperplasiques. En raison de la prévalence relativement élevée et de l'insignifiance clinique des petits polypes hyperplasiques du côté gauche, le coût associé à leur exérèse et leur étude anatomopathologique reste injustifié.
PROBE-BASED CONFOCAL LASER ENDOMICROSCOPY IS A MANDATORY TOOL IN EVALUATION OF NEOANGIOGENESIS IN LOCALLY ADVANCED GASTRIC CANCER AND IN RECTAL CANCER PATIENTS
Authors: S Maiero, R Magris, G Guarnieri, M Fornasarig, E Pivetta, M Mongiat, V De Re, E Canton, V Canzonieri, A De Paoli, A Buonadonna, D Serraino, C Belluco, P Spessotto, R Cannizzaro
Journal: Endoscopy (2019)

Probe-based Confocal Laser Endomicroscopy (pCLE) is an advanced endoscopic technique which provides high resolution images of the mucosa and of the microvasculature. The aim of study was to evaluate if pCLE can provide accurate information about tumor vascular pattern before and after neoadjuvant radio-chemoterapy (RT/CT) achieving a more accurate diagnosis and patient-tailored targeted treatment in locally advanced Gastric Cancer (GC) and in Rectal Cancer (RC) patients.
Youth-Nominated Support Team Intervention for Suicidal Adolescents and Mortality Outcomes
Authors: Katie Zhou, Irene Melisa Karina
Journal: JAMA Psychiatry (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 Psychiatry 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 Psychiatry journal
Association Between Incident Exposure to Benzodiazepines in Early Pregnancy and Risk of Spontaneous Abortion
Authors: Odile Sheehy, Jin-Ping Zhao, Anick Bérard
Journal: JAMA Psychiatry (2019)

Benzodiazepine use in early pregnancy is associated with spontaneous abortion (SA). However, to date, the association between specific benzodiazepine agent exposure and the risk of SA has not been examined.To quantify the risk of SA associated with gestational benzodiazepine incident use by drug class, duration of action, and specific benzodiazepine agent.This nested case-control study within the Quebec Pregnancy Cohort, Montreal, Quebec, Canada, includes all pregnancies covered by the Quebec Prescription Drug Insurance Plan from January 1, 1998, through December 31, 2015. Each case was randomly matched with up to 5 controls. Statistical analysis was performed from January 1, 1998, through December 31, 2015.Benzodiazepine exposure was defined as 1 or more filled prescriptions between the first day of the last menstrual period and the index date (the calendar date of the SA diagnosis). Benzodiazepine exposure was categorized by overall use, long- or short-acting benzodiazepine, and specific benzodiazepine agents.Spontaneous abortion defined as a pregnancy loss between the beginning of the sixth week of gestation and the 19th completed week of gestation. Conditional logistic regression models were used to calculate odds ratios (OR) and 95% CIs.Of the 442 066 pregnancies included in the Quebec Pregnancy Cohort, 27 149 (6.1%) ended with SA, with a mean (SD) maternal age of 24.2 (6.5) years. Among pregnancies ending with SA, 375 (1.4%) were among women exposed to benzodiazepines in early pregnancy compared with 788 (0.6%) of the 134 305 matched control pregnancies (crude OR, 2.39; 95% CI, 2.10-2.73). Adjusting for potential confounders, including maternal mood and anxiety disorders before pregnancy, and compared with nonuse, benzodiazepine exposure in early pregnancy was associated with an increased risk of SA (adjusted OR, 1.85; 95% CI, 1.61-2.12). The risk was similar among pregnancies exposed to short-acting (284 exposed cases; adjusted OR, 1.81; 95% CI, 1.55-2.12) and long-acting (98 exposed cases; adjusted OR, 1.73; 95% CI, 1.31-2.28) benzodiazepines during early pregnancy. All benzodiazepine agents were independently associated with an increased risk of SA (range of adjusted ORs, 1.13-3.43).An increased risk of SA was observed among early pregnancies with incident exposure to short- and long-acting benzodiazepines and all specific benzodiazepine agents during early pregnancy. Insomnia, anxiety, and mood disorders are prevalent during pregnancy; clinicians should carefully evaluate the risk-benefit ratio of prescribing benzodiazepines in early pregnancy since alternative nonpharmacologic treatments exist.
ENDOSCOPIC ULTRASOUND-GUIDED BIOPSY OF SUBEPITHELIAL GASTROINTESTINAL LESIONS – JUST WET-IT
Authors: I Pita, J Fernandes, P Pimentel-Nunes, P Monteiro, M Dinis-Ribeiro, P Bastos
Journal: Endoscopy (2019)

Endoscopic ultrasound-guided fine-needle aspiration biopsy (EUSFNAB) is the main method for acquisition of tissue from gastrointestinal subepithelial lesions (SELs). Despite the development of new needles, diagnostic yield remains low. The reason may be an ineffective transmission of negative pressure with the dry technique, as these lesions often have high cellular cohesion. A new method of aspiration has been described, where the needle is filled with saline (wet suction technique, WST), with promising results in pancreatic lesions. This method hasn't been tested in SELs.
Assessing the Association Between Dipeptidyl Peptidase 4 Inhibitor Use and Inflammatory Bowel Disease Through Drug Adverse Event Reporting
Authors: Tiansheng Wang, Wenchao Lu, Dandan Li, Huilin Tang, Jeff Y. Yang, John B. Buse, Til Stürmer
Journal: Diabetes Care (2019)

Inflammatory bowel disease (IBD), including Crohn disease (CD) and ulcerative colitis (UC), is an autoimmune digestive system disease (1). A recent cohort study using the U.K. Clinical Practice Research Datalink (CPRD) involving 7,231 dipeptidyl peptidase 4 inhibitor (DPP4i) users with 49 IBD cases indicated that new use of DPP4is over a median duration of 1.6 years was associated with IBD risk in patients with type 2 diabetes compared with other noninsulin antihyperglycemic drugs (hazard ratio 1.75, 95% CI 1.22, 2.49) (2). Current evidence regarding the effect of DPP4is on IBD risk is very limited. We thus performed a disproportionality analysis using the U.S. Food and Drug Administration Adverse Event Reporting System (FAERS) database, which contains all adverse events spontaneously reported to the Food and Drug Administration since 2004 (3).

We downloaded the FAERS data files from 2004 1st quarter to 2017 3rd quarter, used generic and trade names to identify DPP4is (sitagliptin, saxagliptin, linagliptin, alogliptin, and vildagliptin) and comparator drugs, and identified outcomes using Medical Dictionary for Regulatory Activities terms. The primary outcome was IBD (both CD and UC), and secondary outcomes were CD and UC, separately. The safety signal of DPP4is and IBD was assessed by reporting odds ratio (ROR) using two-by-two contingency tables (4). A signal was defined as an ROR of ≥2. The data were analyzed by SAS 9.4 …
THE ROLE OF ENTEROSCOPY IN THE PREOPERATIVE DIAGNOSIS OF BLEEDING GASTROINTESTINAL STROMAL TUMORS OF THE SMALL INTESTINE
Authors: DE Seleznev, EV Ivanova, OI Yudin, EV Tikhomirova, MA Shumikhina, ED Fedorov
Journal: Endoscopy (2019)

Bleeding gastrointestinal stromal tumors (GISTs) of the small bowel (SB) previously were diagnosed late or required open surgery. Video capsule endoscopy (VCE) and balloon-assisted enteroscopy (BAE) change surgical approach for these patients.
Abstract B84: Physiologic pancreatic cancer imaging using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI)
Authors: Laura E. Fischer, Matthias Schabel, Bryan Foster, Charles R. Thomas, William Rooney, Brett C. Sheppard, Erin W. Gilbert
Journal: Cancer Research (2016)

Abstract Background: Accurately identifying and monitoring pancreatic ductal adenocarcinoma (PDA) remains a significant challenge. Whereas conventional imaging (CT and MRI) report only anatomic information, dynamic contrast-enhanced MRI (DCE-MRI) has the ability to show physiologic differences in tissue perfusion based on the kinetics of IV-contrast. We coupled DCE-MRI with data-modeling methods to obtain reproducible, high-resolution physiologic images in a series of patients with and without PDA in order to more accurately identify PDA. Methods: Patients with borderline-resectable PDA (BR-PDA) or at high-risk for PDA (HR), but without cancer were imaged with DCE-MRI. T1-weighted images were collected during IV contrast injections [Figure 1]. Both tumor and the pancreatic body or non-tumor pancreas were identified and using dual-compartment pharmacokinetic modelling, DCE-MRI parameters were quantified and compared between groups. Results: Between 6/2014 and 2/2015, 12 DCE-MRIs were completed: 9 HR and 3 BR-PDA. Significant differences in the DCE-MRI parameters blood flow (F), first-pass extraction (E), mean capillary transit-time (tc), transfer constant (Ktrans), volume of extravascular-extracellular space (Ve) and blood volume (Vb) were found in normal HR pancreases vs. the tumors in BR-PDA patients [Table 1A]. When comparing non-tumoral pancreases in both cohorts, only F, Ktrans, and Vb differed [Table 1B]. Conclusions: DCE-MRI of the pancreas is feasible and provides imaging biomarkers of vascular structure and function in both tumoral and non-tumoral pancreases which may allow for earlier and more accurate identification of PDA in these high risk populations. Citation Format: Laura E. Fischer, Matthias Schabel, Bryan Foster, Charles R. Thomas, Jr., William Rooney, Brett C. Sheppard, Erin W. Gilbert.{Authors}. Physiologic pancreatic cancer imaging using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr B84.
THE SAFETY OF COLD SNARE POLYPECTOMY (CSP) ON ANTITHROMBOTIC THERAPY
Authors: Y Kimoto, K Ohata, Y Minato, T Nakao, N Konishi, R Ishii, K Kanda, R Negishi, S Ogawa, M Takita, R Takeda, E Sakai, T Muramoto, T Shiga, H Tanaka, N Matsuhashi
Journal: Endoscopy (2019)

Cold snare polypectomy (CSP) is a safer and more efficacious polypectomy technique without electrocautery, therefore it is widely used for the removal of small polyps (< 10 mm). Recent studies have revealed that delayed bleeding and perforation are few observed in CSP. However the safety of CSP in patients who are on antithrombotic therapy have not been fully evaluated. The aim of this study was to determine the safety of CSP in patients who are currently on antithrombotic therapy.
IS THERE AN ASSOCIATION BETWEEN THE MAJOR PAPILLA MORPHOLOGY AND THE SIZE OF THE TERMINAL COMMON BILE DUCT? – A PROSPECTIVE COHORT STUDY
Authors: J Fernandes, M Moreira, T Araújo, I Costa, J Fonseca, H Ribeiro, S Giestas, F Lucas, D Libânio, D Martinez-Ares, G Alexandrino, D Horta, L Lourenço, J Reis, J Ramada, M Certo, J Canena, L Lopes
Journal: Endoscopy (2019)

In endoscopic retrograde cholangiopancreatography (ERCP), the risk of adverse events during precut is increased when the terminal bile duct (tBD) is not dilated. Some studies suggest that the major papilla morphology, particularly its width is determined by the prominence of the supra- and intra-duodenal portion of the tBD. The study aim was to assess if the terminal bile duct diameter can be determined by inspecting the major papilla morphology/width during duodenoscopy.
National action plans to tackle NCDs: role of stakeholder network analysis
Authors: Ruth F Hunter, Kremlin Wickramasinghe, Toker Ergüder, Abdulkadir Bolat, Hakan Oğuz Arı, Hasan Hüseyin Yıldırım, Pavel Ursu, Gareth Robinson, Joao Breda, Bente Mikkelsen, Paul Connolly, Mike Clarke, Frank Kee
Journal: BMJ (2019)

Academia 1 Fig 1 | Example of a public health stakeholder network. 6The nodes represent organisations and the lines represent ties between organisations.The larger nodes represent the organisations with the most collaborators on 21 August
Eosinophil-guided corticosteroid therapy in patients admitted to hospital with COPD exacerbation (CORTICO-COP): a multicentre, randomised, controlled, open-label, non-inferiority trial
Authors: Pradeesh Sivapalan, Therese S Lapperre, Julie Janner, Rasmus R Laub, Mia Moberg, Charlotte S Bech, Josefin Eklöf, Freja S Holm, Karin Armbruster, Praleene Sivapalan, Christiane Mosbech, Aras K M Ali, Niels Seersholm, Jon T Wilcke, Eva Brøndum, Tine P Sonne, Finn Rønholt, Helle F Andreassen, Charlotte S Ulrik, Jørgen Vestbo, Jens-Ulrik S Jensen
Journal: The Lancet Respiratory Medicine (2019)
An Acquired High-Risk Chromosome Instability Phenotype in Multiple Myeloma: Jumping 1q Syndrome
Authors: Jeffery R. Sawyer, Erming Tian, Brian A Walker, Christopher P. Wardell, Joshua Epstein, Janet L Lukacs, Gael M. Sammartino, Clyde Bailey, Carolina D. Schinke, Sharmilan Thanendrarajan, Maurizio Zangari, Faith E. Davies, Frits van Rhee, Gareth Morgan
Journal: Blood (2018)
An Unbalanced Monocyte Macrophage Polarization in the Bone Marrow Microenvironment of Patients with Poor Graft Function after Allogeneic Hematopoietic Stem Cell Transplantation
Authors: Hong-Yan Zhao, Song Yang, Ting-Ting Han, Qi Wen, Min-Min Shi, Yu Wang, Lan-Ping Xu, Xiaohui Zhang, Xiao-Jun Huang, Yuan Kong
Journal: Blood (2017)
Baseline Level of Hepatitis B Core Antibody Predicts Spontaneous Hepatitis B e Antigen (HBeAg) Seroconversion in HBeAg‐Positive Children With a Normal Alanine Aminotransferase Level
Authors: Ho‐Sheng Chen, Jia‐Feng Wu, Tung‐Hung Su, Huey‐Ling Chen, Hong‐Yuan Hsu, Ning‐Shao Xia, Pei‐Jer Chen, Mei‐Hwei Chang
Journal: Hepatology (2019)

It is not clear whether baseline hepatitis B core antibody (anti‐HBc) level in hepatitis B e antigen (HBeAg)‐positive children with a normal alanine aminotransferase (ALT) level is predictive of spontaneous HBeAg seroconversion. We investigated the correlation between anti‐HBc level and the natural course of chronic hepatitis B (CHB) virus (HBV) infection in children, particularly the ability of baseline anti‐HBc level to predict spontaneous HBeAg seroconversion during long‐term follow‐up. HBeAg‐positive children with untreated CHB and a normal ALT level were followed longitudinally. Anti‐HBc level was determined by double‐sandwich immunoassay. Effects of anti‐HBc levels and other parameters on spontaneous HBeAg seroconversion and the natural course of CHB were assessed. A total of 182 children (106 males) with a median age at enrollment of 10.6 years (interquartile range [IQR], 10.3‐15.3) were followed for a median of 19.8 years (IQR, 11.9‐21.9). Spontaneous HBeAg seroconversion occurred in 85 children (46.7%) during the follow‐up. A baseline anti‐HBc titer of &gt;500 IU/mL (hazard ratio [HR] = 2.81), HBV genotype B and B + C (HR = 3.46), and a baseline hepatitis B surface antigen titer of ≤4.8 log 10 IU/mL (HR = 3.09) were predictive of spontaneous HBeAg seroconversion, based on multivariable survival analysis ( P &lt; 0.001). In cases remaining HBeAg positive, their anti‐HBc levels increased gradually during follow‐up because of ongoing inflammation. Conclusion: Baseline anti‐HBc level is predictive of spontaneous HBeAg seroconversion in HBeAg‐positive children with a normal ALT level. Anti‐HBc level reflects anti‐HBV immune response in the HBeAg‐positive normal ALT phase of CHB.
Removal of a migrated biliary stent perforating the colonic wall: a case description of endoscopic repair
Authors: Konstantinos Hnaris, Robert Bechara
Journal: Endoscopy (2019)

Endoscopically placed biliary stents are commonly used for the treatment of pancreaticobiliary disorders. Plastic biliary stent migration is a complication that occurs in 6 % – 7.5 % of cases [1]. Perforation of the gastrointestinal tract secondary to stent migration is a rare event, occurring in less than 1 % of cases. Reported cases of this complication have required surgery for stent removal and repair. This is a case report of a migrated biliary stent causing a perforation that was managed endoscopically.
Fibrinogen‐Based Hydrogel Modulus and Ligand Density Effects on Cell Morphogenesis in Two‐Dimensional and Three‐Dimensional Cell Cultures
Authors: Andrei Yosef, Olga Kossover, Iris Mironi‐Harpaz, Arianna Mauretti, Sonia Melino, Joseph Mizrahi, Dror Seliktar
Journal: Advanced Healthcare Materials (2019)

Abstract There is a need to further explore the convergence of mechanobiology and dimensionality with systematic investigations of cellular response to matrix mechanics in 2D and 3D cultures. Here, a semisynthetic hydrogel capable of supporting both 2D and 3D cell culture is applied to investigate cell response to matrix modulus and ligand density. The culture materials are fabricated from adducts of polyethylene glycol (PEG) or PluronicF127 and fibrinogen fragments, formed into hydrogels by free‐radical polymerization, and characterized by shear rheology. Control over the modulus of the materials is accomplished by changing the concentration of synthetic PEG‐diacrylate crosslinker (0.5% w/v), and by altering the molecular length of the PEG (10 and 20 kDa). Control over ligand density is accomplished by changing fibrinogen concentrations from 3 to 12 mg mL −1 . In 2D culture, cell motility parameters, including cell speed and persistence time are significantly increased with increasing modulus. In both 2D and 3D culture, cells express vinculin and there is evidence of focal adhesion formation in the high stiffness materials. The modulus‐ and ligand‐dependent morphogenesis response from the cells in 2D culture is contradictory to the same measured response in 3D culture. In 2D culture, anchorage‐dependent cells become more elongated and significantly increase their size with increasing ligand density and matrix modulus. In 3D culture, the same anchorage‐dependent cells become less spindled and significantly reduce their size in response to increasing ligand density and matrix modulus. These differences arise from dimensionality constraints, most notably the encapsulation of cells in a non‐porous hydrogel matrix. These insights underscore the importance of mechanical properties in regulating cell morphogenesis in a 3D culture milieu. The versatility of the hydrogel culture environment further highlights the significance of a modular approach when developing materials that aim to optimize the cell culture environment.
GERMAN ESD REGISTRY – FIRST RESULTS
Authors: C Fleischmann, A Probst, A Ebigbo, S Faiss, B Schuhmacher, HP Allgaier, D Hartmann, FL Dumoulin, C Rust, J Pohl, H Mörk, J Albert, R ReinehrI, F Kolligs, J Mayerle, K Caca, M Götz, U Denzer, J Hampe, I Schiefke, H Messmann
Journal: Endoscopy (2019)

In Europe, endoscopic submucosal dissection (ESD) is not yet the standard treatment for premalignant or early malignant lesions in the gastrointestinal (GI)-tract. High quality data is limited to single center studies. In this study, we present the first results of the German ESD registry which was set up to evaluate and assess the technical success, curative resection rate, economic aspects as well as long term outcomes of ESD procedures performed in Germany.