tbuckley/cabot-search huggingface dataset:
The doctor on the doorstep: Alex Armitage, paediatrician and green campaigner
Authors: Rebecca Coombes
Journal: BMJ (2019)

Alex Armitage, a paediatric emergency doctor, is sitting cross legged in a school hall in east London, surrounded by children from the local Woodcraft Folk group. He is the Green Party candidate for Hackney North and Stoke Newington and is joined by most of the other parties’ candidates.

The children are here for a mock election and want answers on single use plastic, making the UK carbon neutral by 2030, and equal pay. Armitage is on solid ground here because his party has the most radical policies to act on climate change. But, he warns the children, “If we are going to do this, it means the way we live will need to change massively—for example, driving around in cars, buying new clothes all the time, and flying on holiday.” The children are undeterred, and he …
Obesity/overweight and risk of allergic rhinitis: A meta‐analysis of observational studies
Authors: Jianbo Zhou, Fuqiang Luo, Yipeng Han, Hongfei Lou, Xingyao Tang, Luo Zhang
Journal: Allergy (2019)

Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Histone Deacetylase 11 (HDAC11) as a Novel Molecular Target in Mantle Cell Lymphoma
Authors: Alejandro v Villagra, Michelle m Maurin, Fengdong Cheng, Hongwei Wang, Sophie Dessureault, Ed Seto, Jianguo Tao, Ken Wright, Javier Pinilla, Eduardo M. Sotomayor
Journal: Blood (2008)
Next-generation sequencing for BCR-ABL1 kinase domain mutation testing in patients with chronic myeloid leukemia: a position paper
Authors: Simona Soverini, Elisabetta Abruzzese, Monica Bocchia, Massimiliano Bonifacio, Sara Galimberti, Antonella Gozzini, Alessandra Iurlo, Luigiana Luciano, Patrizia Pregno, Gianantonio Rosti, Giuseppe Saglio, Fabio Stagno, Mario Tiribelli, Paolo Vigneri, Giovanni Barosi, Massimo Breccia
Journal: Journal of Hematology & Oncology (2019)

Abstract BCR-ABL1 kinase domain (KD) mutation status is considered to be an important element of clinical decision algorithms for chronic myeloid leukemia (CML) patients who do not achieve an optimal response to tyrosine kinase inhibitors (TKIs). Conventional Sanger sequencing is the method currently recommended to test BCR-ABL1 KD mutations. However, Sanger sequencing has limited sensitivity and cannot always discriminate between polyclonal and compound mutations. The use of next-generation sequencing (NGS) is increasingly widespread in diagnostic laboratories and represents an attractive alternative. Currently available data on the clinical impact of NGS-based mutational testing in CML patients do not allow recommendations with a high grade of evidence to be prepared. This article reports the results of a group discussion among an ad hoc expert panel with the objective of producing recommendations on the appropriateness of clinical decisions about the indication for NGS, the performance characteristics of NGS platforms, and the therapeutic changes that could be applied based on the use of NGS in CML. Overall, these recommendations might be employed to inform clinicians about the practical use of NGS in CML.
Dual systems for all: Higher-order, role-based relational reasoning as a uniquely derived feature of human cognition
Authors: Daniel J Povinelli, Gabrielle C Glorioso, Shannon L Kuznar, Mateja Pavlic
Journal: Behavioral and Brain Sciences (2019)

Abstract Hoerl and McCormack demonstrate that although animals possess a sophisticated temporal updating system, there is no evidence that they also possess a temporal reasoning system. This important case study is directly related to the broader claim that although animals are manifestly capable of first-order (perceptually-based) relational reasoning, they lack the capacity for higher-order, role-based relational reasoning. We argue this distinction applies to all domains of cognition.
Continuing Antipsychotic Medication for Patients With Psychotic Depression in Remission—Reply
Authors: Alastair J. Flint, Samprit Banerjee, Patricia Marino
Journal: JAMA (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 HomeNew OnlineCurrent IssueFor Authors 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) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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 journal
Combination of intratumoural double-stranded RNA (dsRNA) BO-112 with systemic anti-PD-1 in patients with anti-PD-1 refractory cancer
Authors: I. Marquez-Rodas, F. Longo, S. Ponce Aix, M. Jove, B. Rubio, A. Calles Blanco, M.E. Rodriguez-Ruiz, M. Ponz-Sarvise, E. Castañon, P. Gajate, C. Sempere-Ortega, E. Jimenez-Aguilar, P. Lopez-Casas, E. de Miguel, R. Ramos-Medina, A. Calvo, M. Martin, D. Tersago, M. Quintero, I. Melero
Journal: Annals of Oncology (2019)
Notch1 mutation in B Chronic Lymphocytic Lymphocytes Induces Proliferation through Cell Cycle G1/S Phase-Specific Cyclin Overexpression
Authors: Ana M Hurtado López, Tzu Hua Chen-Liang, María Zurdo, Anna Puiggros, Andrea Gómez-Llonín, María-Dolores García-Malo, Francisco José Ortuño, Vicente Vicente Garcia, Blanca Espinet, Andres Jerez
Journal: Blood (2019)
Single-Cell RNA Sequencing Identifies a Pseudo-Immune Differentiation Axis As the Main Source of Functional Heterogeneity in Follicular Lymphoma B-Cells
Authors: Noudjoud Attaf, Inaki Cervera-Marzal, Laurine Gil, Chuang Dong, Jean-Marc Navarro, Lionel Spinelli, Bertrand Nadel, Pierre Milpied
Journal: Blood (2019)
Cell Adhesiveness Serves as a Biophysical Marker for Metastatic Potential
Authors: Pranjali Beri, Anna Popravko, Benjamin Yeoman, Aditya Kumar, Kevin Chen, Enio Hodzic, Alyssa Chiang, Afsheen Banisadr, Jesse K. Placone, Hannah Carter, Stephanie I. Fraley, Parag Katira, Adam J. Engler
Journal: Cancer Research (2019)

Abstract Tumors are heterogeneous and composed of cells with different dissemination abilities. Despite significant effort, there is no universal biological marker that serves as a metric for metastatic potential of solid tumors. Common to disseminating cells from such tumors, however, is the need to modulate their adhesion as they detach from the tumor and migrate through stroma to intravasate. Adhesion strength is heterogeneous even among cancer cells within a given population, and using a parallel plate flow chamber, we separated and sorted these populations into weakly and strongly adherent groups; when cultured under stromal conditions, this adhesion phenotype was stable over multiple days, sorting cycles, and common across all epithelial tumor lines investigated. Weakly adherent cells displayed increased migration in both two-dimensional and three-dimensional migration assays; this was maintained for several days in culture. Subpopulations did not show differences in expression of proteins involved in the focal adhesion complex but did exhibit intrinsic focal adhesion assembly as well as contractile differences that resulted from differential expression of genes involved in microtubules, cytoskeleton linkages, and motor activity. In human breast tumors, expression of genes associated with the weakly adherent population resulted in worse progression-free and disease-free intervals. These data suggest that adhesion strength could potentially serve as a stable marker for migration and metastatic potential within a given tumor population and that the fraction of weakly adherent cells present within a tumor could act as a physical marker for metastatic potential. Significance: Cancer cells exhibit heterogeneity in adhesivity, which can be used to predict metastatic potential.
Mass Spectrometry Imaging Enables Discrimination of Renal Oncocytoma from Renal Cell Cancer Subtypes and Normal Kidney Tissues
Authors: Jialing Zhang, Shirley Q. Li, John Q. Lin, Wendong Yu, Livia S. Eberlin
Journal: Cancer Research (2019)

Precise diagnosis and subtyping of kidney tumors are imperative to optimize and personalize treatment decision for patients. Patients with the most common benign renal tumor, renal oncocytomas, may be overtreated with surgical resection because of limited preoperative diagnostic methods that can accurately identify the benign condition with certainty. In this study, desorption electrospray ionization (DESI)-mass spectrometry (MS) imaging was applied to study the metabolic and lipid profiles of various types of renal tissues, including normal kidney, renal oncocytoma, and renal cell carcinomas (RCC). A total of 73,992 mass spectra from 71 patient samples were obtained and used to build predictive models using the least absolute shrinkage and selection operator (Lasso). Overall accuracies of 99.47% per pixel and 100% per patient for prediction of the three tissue types were achieved. In particular, renal oncocytoma and chromophobe RCC, which present the most significant morphologic overlap and are sometimes indistinguishable using histology alone, were also investigated and the predictive models built yielded 100% accuracy in discriminating these tumor types. Discrimination of three subtypes of RCC was also achieved on the basis of DESI-MS imaging data. Importantly, several small metabolites and lipids species were identified as characteristic of individual tissue types and chemically characterized using tandem MS and high mass accuracy measurements. Collectively, our study shows that the metabolic data acquired by DESI-MS imaging in conjunction with statistical modeling allows discrimination of renal tumors and thus has the potential to be used in the clinical setting to improve treatment of patients with kidney tumor. SIGNIFICANCE: Metabolic data acquired by mass spectrometry imaging in conjunction with statistical modeling allows discrimination of renal tumors and has the potential to be used in the clinic to improve treatment of patients.
Clinicopathologic overlap of psoriasis, eczema, and psoriasiform dermatoses: A retrospective study of T helper type 2 and 17 subsets, interleukin 36, and β-defensin 2 in spongiotic psoriasiform dermatitis, sebopsoriasis, and tumor necrosis factor α inhibitor–associated dermatitis
Authors: Jarish N. Cohen, Sarah Bowman, Zoltan G. Laszik, Jeffrey P. North
Journal: Journal of the American Academy of Dermatology (2019)
T cells instruct myeloid cells to produce inflammasome-independent IL-1β and cause autoimmunity
Authors: Aakanksha Jain, Ricardo A. Irizarry-Caro, Margaret M. McDaniel, Amanpreet Singh Chawla, Kaitlin R. Carroll, Garrett R. Overcast, Naomi H. Philip, Andrew Oberst, Alexander V. Chervonsky, Jonathan D. Katz, Chandrashekhar Pasare
Journal: Nature Immunology (2019)
IMPACT OF A NOVEL MYOCARDIAL PERFUSION IMAGING RISK CLASSIFICATION SCHEME ON REFERRAL FOR CORONARY ANGIOGRAPHY, REVASCULARIZATION, AND MORTALITY
Authors: Anirudh Kumar, Divyang Patel, Serge Harb, Neil Greenberg, Ajay Bhargava, Samir R. Kapadia, Venu Menon, Rory Hachamovitch, Wael A. Jaber, Paul Cremer
Journal: Journal of the American College of Cardiology (2020)
Reduction in mouse allergen exposure is associated with greater lung function growth
Authors: Torie Grant, Wanda Phipatanakul, Matthew Perzanowski, Susan Balcer-Whaley, Roger D. Peng, Jean Curtin-Brosnan, Michelle Newman, Amparito Cunningham, Adnan Divjan, Mary E. Bollinger, Robert A. Wise, Elizabeth C. Matsui
Journal: Journal of Allergy and Clinical Immunology (2019)
Abstract 19681: Receptor Tyrosine Kinase Screening in Ischemic Heart Identifies ROR1 as a Potential Target for the Treatment of Ischemia
Authors: Juho Heliste, Ilkka Paatero, Anne Jokilammi, Deepankar Chakroborty, Christoffer Stark, Timo Savunen, Klaus Elenius
Journal: Circulation (2017)

Introduction: Receptor tyrosine kinases (RTK) are a potential group of targets for the treatment of ischemic heart disease. For example, activation of ErbB2 and ErbB4 improves regeneration of myoca...
Overcoming health care disparities in cancer treatment by instituting a patient navigation program.
Authors: Tarek N. Elrafei, Maria Castaldi, Bassam Shaker, Tina Stanise, Mariaelena Marquez, William Bodner, Louis Juden Reed, Karenza M. Alexis, Marianna Strakhan, Richard J. Gralla
Journal: Journal of Clinical Oncology (2013)

TPS6644 Background: Cancer health disparities affecting low-income and minority patients are well documented. Causes of poor outcomes include treatment delays coupled with social and financial barriers. Navigation interventions have been more commonly applied in cancer screening and in early diagnosis programs than in improving adherence to treatment among those with barriers to care. This report examines the early impact of patient navigation on adherence to prescribed cancer treatment. Methods: We put into place a Patient Navigation Program as a pilot project (supported by an Avon Foundation grant) at our public safety net hospital. Health care coverage: 58% Medicaid, 23% uninsured or undocumented. Navigator duties included care coordination, appointment reminders, patient education materials, translation services, and transportation arrangement. During a 4 month period new medical oncology practice patients felt to be at high risk received navigated care. Data collected prospectively included patient characteristics, cancer type, time from referral to first RT, and compliance with visits; this was compared with usual care historical controls immediately prior to the 4 month period. Results: Patient Navigation Program patient characteristics: N = 52 patients (22 breast cancer, 6 prostate cancer, 5 lung cancer and 19 patients with other cancers). Mean age = 55; 48% Black, 38% Hispanic, 8% Asian, 6% White. Adherence to visits, and time to first RT results are seen in the Table. Conclusions: In the first 4 months of its initiation, this Patient Navigation Program has been associated with observed improvements in adherence to chemotherapy and follow up physician visits, but no impact on time to 1st RT to date. These results document that a Patient Navigation Program can help overcome barriers to good cancer care while identifying RT as an area for further improvement. [Table: see text]
Lung Function Decline in Early HIV Infection: Impact of Antiretroviral Drug Timing and Drug Regimen
Authors: Ken M. Kunisaki, Jason V. Baker, Gary Collins, David M. MacDonald, Elzbieta Bakowska, Kamal Marhoum El Filali, Eriobu Nnakelu, Alberto La Rosa, John E. Connett
Journal: American Journal of Respiratory and Critical Care Medicine (2019)
Abstract C45: NT219, a novel bispecific inhibitor of STAT3 and IRS1/2, combined with chemotherapy or MEK inhibitor in gemcitabine-resistant pancreatic tumors, induced tumor regression
Authors: Hadas Reuveni, Lana Kupershmidt, Neta Moskovits, Evgeny Solomonov, Salomon M Stemmer, Izhak Haviv
Journal: Cancer Research (2019)

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related death worldwide, with poor outcome of current treatments. Major contributors to therapeutic resistance in PDAC include Kras mutations, a dense desmoplastic stroma, and activation of feedback signaling pathways. STAT3 and Insulin Receptor Substrate 1/2 (IRS1/2) regulate tumor survival and metastasis, the crosstalk of the tumor and its microenvironment, and play major role in drug resistance. NT219 is a novel bispecific inhibitor of IRS1/2 and STAT3, leading to IRS1/2 elimination and STAT3 dephosphorylation. The purpose of this study was to assess NT219 activity in PDAC PDX models and define schedule and regimens and combinations to overcome resistance to optimize future clinical protocols. Methods: Patient-derived tumor xenograft (PDX) models of mutated KRAS pancreatic cancer were used to test the efficacy of NT219 in combination with gemcitabine, trametinib, and folfirinox. RNAseq was used to analyze the pharmacodynamic effect of NT219. Pharmacokinetic profile of NT219 was tested. Results: Chemoresistent tumors of 4 PDAC PDX models were exposed to NT219 with gemcitabine demonstrated reversal of pre-existing resistance. One of these models demonstrated complete response in 5 out of 10 mice upon addition of NT219 to gemcitabine. Similar results were observed when NT219 was combined with trametinib (a MEK inhibitor) and with folfirinox (chemotherapy). There was a correlative dose-escalation response of both plasma and tumor levels and the therapeutic effect. NT219 delivered prior to gemcitabine showed a much better response than the inverse schedule/drug administration. RNAseq analysis of the tumors revealed that the combined treatment with NT219 and gemcitabine lowered the levels of IRS1 to 20% of the control group. Similar reductions were observed for STAT3-regulated genes, as well as for Ki67 (a proliferation marker), cyclin D (prognostic marker), and TGFβ (driver of epithelial to mesenchymal transition). Conclusion: NT219 overcomes gemcitabine acquired resistance in PDAC. The combination of NT219 with modern chemotherapy in pancreatic cancer may enhance efficacy and delay acquired resistance in this fatal disease. Citation Format: Hadas Reuveni, Lana Kupershmidt, Neta Moskovits, Evgeny Solomonov, Salomon M Stemmer, Izhak Haviv. NT219, a novel bispecific inhibitor of STAT3 and IRS1/2, combined with chemotherapy or MEK inhibitor in gemcitabine-resistant pancreatic tumors, induced tumor regression [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr C45.
Reply to Zhai et al.
Authors: Juliana Yang, Mouen A. Khashab
Journal: Endoscopy (2019)

See also:Safety and efficacy of the use of lumen-apposing metal stents in the management of postoperative fluid collections: a large, international, multicenter studyEndoscopy 2019; 51(08): 715-721DOI: 10.1055/a-0924-5591See also:Postoperative fluid collections: a new indication for interventional endoscopic ultrasound?Endoscopy 2020; 52(01): 78-78DOI: 10.1055/a-1021-8703
Implementing a junior high school-based programme to reduce sports injuries through neuromuscular training (iSPRINT): a cluster randomised controlled trial (RCT)
Authors: Carolyn A Emery, Carla van den Berg, Sarah Ann Richmond, Luz Palacios-Derflingher, Carly D McKay, Patricia K Doyle-Baker, Megan McKinlay, Clodagh M Toomey, Alberto Nettel-Aguirre, Evert Verhagen, Kathy Belton, Alison Macpherson, Brent E Hagel
Journal: British Journal of Sports Medicine (2019)

Objective To evaluate the effectiveness of a junior high school-based sports injury prevention programme to reduce injuries through neuromuscular training (NMT). Methods This was a cluster randomised controlled trial. Students were recruited from 12 Calgary junior high schools (2014–2017). iSPRINT is a 15 min NMT warm-up including aerobic, agility, strength and balance exercises. Following a workshop, teachers delivered a 12-week iSPRINT NMT (six schools) or a standard-of-practice warm-up (six schools) in physical education classes. The definition of all recorded injuries included injuries that resulted in participants being unable to complete a sport and recreation (S&amp;R) session, lost time from sport and/or seek medical attention. Incidence rate ratios (IRRs) were estimated based on multiple multilevel Poisson regression analyses (adjusting for sex (considering effect modification) and previous injury, offset by S&amp;R participation hours, and school-level and class-level random effects were examined) for intent-to-treat analyses. Results 1067 students (aged 11–16) were recruited across 12 schools (6 intervention schools (22 classes), 6 control schools (27 classes); 53.7% female, 46.3% male). The iSPRINT programme was protective of all recorded S&amp;R injuries for girls (IRR=0.543, 95% CI 0.295 to 0.998), but not for boys (IRR=0.866, 95% CI 0.425 to 1.766). The iSPRINT programme was also protective of each of lower extremity injuries (IRR=0.357, 95% CI 0.159 to 0.799) and medical attention injuries (IRR=0.289, 95% CI 0.135 to 0.619) for girls, but not for boys (IRR=1.055, 95% CI 0.404 to 2.753 and IRR=0.639, 95% CI 0.266 to 1.532, respectively). Conclusion The iSPRINT NMT warm-up was effective in preventing each of all recorded injuries, lower extremity injuries and medically treated S&amp;R injuries in female junior high school students. Trial registration number NCT03312504
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline
Authors: Shujun Ou, Weija Su, Yi Liao, Kapeel Chougule, Jireh R. A. Agda, Adam J. Hellinga, Carlos Santiago Blanco Lugo, Tyler A. Elliott, Doreen Ware, Thomas Peterson, Ning Jiang, Candice N. Hirsch, Matthew B. Hufford
Journal: Genome biology (2019)

Abstract Background Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. Results We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F 1 . Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements. EDTA also deconvolutes nested TE insertions frequently found in highly repetitive genomic regions. Using other model species with curated TE libraries (maize and Drosophila), EDTA is shown to be robust across both plant and animal species. Conclusions The benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. EDTA is open-source and freely available: https://github.com/oushujun/EDTA .