tbuckley/cabot-search huggingface dataset:
Cytotoxic T-cell-related gene expression signature predicts improved survival in muscle-invasive urothelial bladder cancer patients after radical cystectomy and adjuvant chemotherapy
Authors: Markus Eckstein, Pamela Strissel, Reiner Strick, Veronika Weyerer, Ralph Wirtz, Carolin Pfannstiel, Adrian Wullweber, Fabienne Lange, Philipp Erben, Robert Stoehr, Simone Bertz, Carol Imanuel Geppert, Nicole Fuhrich, Helge Taubert, Sven Wach, Johannes Breyer, Wolfgang Otto, Maximilian Burger, Christian Bolenz, Bastian Keck, Bernd Wullich, Arndt Hartmann, Danijel Sikic
Journal: Journal for ImmunoTherapy of Cancer (2020)

Background Assessment of the immune status of muscle-invasive bladder cancer (MIBC) has previously shown to be prognostically relevant after treatment with curative intent. We conducted this study to develop a clinically applicable immune gene expression assay to predict prognosis and adjuvant chemotherapy benefit. Patients and methods Gene expression of CD3Z , CD8A and CXCL9 , immune cell (IC) populations including stromal tumor infiltrating lymphocytes (sTILs), T-cells, natural killer cells (NK-cells), macrophages, Programmed cell death protein 1 positive (PD-1) IC and tumor subtypes (MD Anderson Cancer Center/MDACC-approach) were assessed in 187 MIBC patients (Comprehensive Cancer Center Erlangen-EMN/CCC-EMN-cohort). A gene expression signature was derived by hierarchical-clustering and validated in The Cancer Genome Atlas (TCGA)-cohort. IC populations in the TCGA cohort were assessed via CIBERSORT. Benefit of platinum-containing adjuvant chemotherapy was assessed in a pooled cohort of 125 patients. Outcome measurements were disease specific survival, disease-free survival and overall survival. Results The gene expression signature of CXCL9 , CD3Z and CD8A correlates with quantitative amounts of specific IC populations and sTILs (CCC-EMN: ρ-range: 0.44–0.74; TCGA: ρ-range: 0.56–0.82) and allows stratification of three different inflammation levels (inflamed high, inflamed low, uninflamed). Highly inflamed tumors are preferentially basal subtype and show favorable 5-year survival rates of 67.3% (HR=0.27; CCC-EMN) and 55% (HR=0.41; TCGA). Uninflamed tumors are predominantly luminal subtypes and show low 5-year survival rates of 28% (CCC-EMN) and 36% (TCGA). Inflamed tumors exhibit higher levels of PD-1 and Programmed cell death 1 ligand 1 (PD-L1). Patients undergoing adjuvant platinum-based chemotherapy with ‘inflamed high’ tumors showed a favorable 5-year survival rate of 64% (HR=0.27; merged CCC-EMN and TCGA cohort). Conclusion The gene expression signature of CD3Z , CD8A and CXCL9 can assess the immune status of MIBC and stratify the survival of MIBC patients undergoing surgery and adjuvant platinum-based chemotherapy. Furthermore, the assay can identify patients with immunological hot tumors with particular high expression of PD-L1 potentially suitable for immunotherapy.
Withholding of Data Among Academic Geneticists—Reply
Authors: Eric G. Campbell
Journal: JAMA (2002)

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
Risk of Late Postoperative Recurrence of Crohn’s Disease in Patients in Endoscopic Remission After Ileocecal Resection, Over 10 Years at Multiple Centers
Authors: Lieven Pouillon, Thomas Remen, Caroline Amicone, Edouard Louis, Sielte Maes, Catherine Reenaers, Adeline Germain, Cédric Baumann, Peter Bossuyt, Laurent Peyrin-Biroulet
Journal: Clinical Gastroenterology and Hepatology (2020)
Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs
Authors: Rajagopal Murugan, Stephen W. Scally, Giulia Costa, Ghulam Mustafa, Elaine Thai, Tizian Decker, Alexandre Bosch, Katherine Prieto, Elena A. Levashina, Jean-Philippe Julien, Hedda Wardemann
Journal: Nature Medicine (2020)
Scaling Up the Surveillance of Childhood Cancer: A Global Roadmap
Authors: Marion Piñeros, Les Mery, Isabelle Soerjomataram, Freddie Bray, Eva Steliarova-Foucher
Journal: JNCI Journal of the National Cancer Institute (2020)

The World Health Organization recently launched the Global Initiative for Childhood Cancer aiming to substantially increase survival among children with cancer by 2030. The ultimate goal concerns particularly less developed countries where survival estimates are considerably lower than in high-income countries where children with cancer attain approximately 80% survival. Given the vast gap in high-quality data availability between more and less developed countries, measuring the success of the Global Initiative for Childhood Cancer will also require substantial support to childhood cancer registries to enable them to provide survival data at the population level. Based on our experience acquired at the International Agency for Research on Cancer in global cancer surveillance, we hereby review crucial aspects to consider in the development of childhood cancer registration and present our vision on how the Global Initiative for Cancer Registry Development can accelerate the measurement of the outcome of children with cancer.
Persistence of HIV-1 Env-Specific Plasmablast Lineages in Plasma Cells after Vaccination in Humans
Authors: Madhubanti Basu, Michael S. Piepenbrink, Czestochowa Francois, Fritzlaine Roche, Bo Zheng, David A. Spencer, Ann J. Hessell, Christopher F. Fucile, Alexander F. Rosenberg, Catherine A. Bunce, Jane Liesveld, Michael C. Keefer, James J. Kobie
Journal: Cell Reports Medicine (2020)

Induction of persistent HIV-1 Envelope (Env) specific antibody (Ab) is a primary goal of HIV vaccine strategies; however, it is unclear whether HIV Env immunization in humans induces bone marrow plasma cells, the presumed source of long-lived systemic Ab. To define the features of Env-specific plasma cells after vaccination, samples were obtained from HVTN 105, a phase I trial testing the same gp120 protein immunogen, AIDSVAX B/E, used in RV144, along with a DNA immunogen in various prime and boost strategies. Boosting regimens that included AIDSVAX B/E induced robust peripheral blood plasmablast responses. The Env-specific immunoglobulin repertoire of the plasmablasts is dominated by VH1 gene usage and targeting of the V3 region. Numerous plasmablast-derived immunoglobulin lineages persisted in the bone marrow >8 months after immunization, including in the CD138+ long-lived plasma cell compartment. These findings identify a cellular linkage for the development of sustained Env-specific Abs following vaccination in humans.
Clinical and Microbiologic Aspects of Salmonellosis
Authors: George M. Eisenberg, Anthony J. Palazzolo, Harrison F. Flippin
Journal: New England Journal of Medicine (1955)

IT is our impression that the prevalence and clinical significance of salmonellosis, or human infections caused by salmonellas other than the typhoid bacillus, are frequently not appreciated as fully as they should be. A number of factors contribute to this situation. The first is the complexity of the methodology required to establish an unequivocal bacteriologic diagnosis and the lack of adequate facilities for the task in many laboratories, especially the smaller ones. The second is the multiplicity of clinical manifestations associated with these infections that militate against the formulation of a readily recognizable clinical syndrome. As a result definitive diagnosis . . .
Eliminating HIV From Seminal Fluid
Authors: C M Kunin
Journal: JAMA (1992)

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 Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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 journal
Case 36-1965
Authors: Frank C. Wheelock, Austin L. Vickery
Journal: New England Journal of Medicine (1965)

Presentation of CaseA sixty-year-old man was admitted to the hospital because of swelling of the thigh.He had been well until two months previously, when he fell, striking the left hip. There was no evidence of fracture, and he was confined to bed for a few days. Four days before admission swelling and tenderness of the left thigh developed, accompanied by fever. Two days later he became confused. On the following day the temperature rose to 103°F., and he vomited once.For an unknown period he had had diabetes, which was controlled by oral medication. There was no history . . .
Abstract 16670: Urocortin 2 Gene Transfer Reduces the Adverse Effects of Western Diet on Cardiac Function in Mice
Authors: Young Chul Kim, Dimosthenis Giamouridis, Ngai C Lai, Tracy Guo, Bing Xia, Zhenxing Fu, Mei Hua Gao, H. K Hammond
Journal: Circulation (2018)

Diabetes mellitus increases the risk of heart failure. We previously showed that injection of adeno-associated virus 8 encoding urocortin 2 (AAV8.UCn2) increases glucose disposal in insulin resistance and improves function of the failing heart in mice. In the present study, we tested the hypothesis that UCn2 gene transfer would have beneficial effects in diabetic cardiomyopathy. Eight-week-old C57Bl/6J male mice were fed normal chow (NC) or a Western diet (WD, 35% kcal carbohydrate and 45% fat) for 30w, and then received saline or AAV8.UCn2 (1.9x10 13 genome copy/kg) via intravenous injection. Before and 10w after gene transfer, we measured fasting blood glucose, glucose tolerance, and cardiac function via echocardiography and rates of LV pressure development (+dP/dt) and decline (-dP/dt) using micromanometers. We also measured key signaling proteins in the left ventricle (LV). Western diet increased 12h fasting glucose levels compared to normal chow (81% increase; p&lt;.0002). WD vs normal chow reduced LV peak +dP/dt (p=.042) and LV peak -dP/dt (p=.027), although LV ejection fraction (EF) was unchanged. Thus WD induced diabetes and cardiomyopathy with normal EF. Among mice fed WD, UCn2 gene transfer reduced fasting glucose (WD+Saline: 190±11 mg/dL, n=8; WD+UCn2: 149±6 mg/dL, n=8; p=.006), increased LV peak +dP/dt (p=.005; Fig A ), LV peak -dP/dt (p=.007; Fig B ), and reduced Tau (p=.016; Fig C ). In addition, among WD-fed mice, UCn2 gene transfer increased LV EF (p=.005) and the velocity of circumferential fiber shortening (p=.0005). LV samples from WD+UCn2 mice showed increased phosphorylation of PKA catalytic domain (WD+Saline: .2±.04, n=5; WD+UCn2: .3±.02, n=5; p=.03). In conclusion, UCn2 gene transfer increased LV systolic and diastolic function and reduced blood glucose in mice with diabetic cardiomyopathy.
Broadening the Scope of Health Care Ethics Consultation: A Response to Open Peer Commentaries on Patient and Family Description of Ethical Concerns
Authors: Marion Danis, Gail Povar, Hae Lin Cho, Christine Grady, Anita Tarzian, Jed Mangal
Journal: The American Journal of Bioethics (2020)

(2020). Broadening the Scope of Health Care Ethics Consultation: A Response to Open Peer Commentaries on Patient and Family Description of Ethical Concerns. The American Journal of Bioethics: Vol. 20, No. 6, pp. W6-W8.
William Anthony Warburton
Authors: John Bennett
Journal: BMJ (2020)

William Anthony Warburton (“Tony”) was educated at Rydal School in Colwyn Bay before studying medicine at Liverpool University. His hospitality, generosity, and friendly nature became apparent to my wife and me when I was invited for interview in 1978 for a place in the practice in Norwich, where he was junior partner. He and Benita took us out into the city, introduced us to friends, and put us up in their house for the night. We felt at home before we had even started. Over the years Tony and I became close, and I grew to appreciate him as a kind and supportive partner at work, free with sensible and practical advice that helped me a great deal, especially early on when I was finding my feet.

The practice was a converted terraced house on the corner of Clarke Road, just beyond Magdalen Gates to the north. Having done house jobs in Chester, followed by a couple of locum posts, Tony had started there in 1962, joining partners Ronnie Scott, Jim Beveridge, and Guy Ashbee. In those days, each doctor was responsible for his own patients, 24 hours a day, seven days a week, apart from Thursday afternoons, when the practice closed and one partner was on duty to allow the others a break. Tony had quite a struggle persuading the others that it would be a good idea to have a night time and weekend rota, so that they could have time off. He got his way in the end. It is remarkable …
Severe acute respiratory syndrome coronavirus 2 RNA contamination of inanimate surfaces and virus viability in a health care emergency unit
Authors: M. Colaneri, E. Seminari, S. Novati, E. Asperges, S. Biscarini, A. Piralla, E. Percivalle, I. Cassaniti, F. Baldanti, R. Bruno, M.U. Mondelli, R. Bruno, M.U. Mondelli, E. Brunetti, A. Di Matteo, E. Seminari, L. Maiocchi, V. Zuccaro, L. Pagnucco, S. Ludovisi, R. Lissandrin, A. Parisi, P. Sacchi, S.F.A. Patruno, G. Michelone, R. Gulminetti, D. Zanaboni, S. Novati, R. Maserati, P. Orsolini, M. Vecchia
Journal: Clinical Microbiology and Infection (2020)
71P Role of radiomics in predicting molecular phenotypes of female breast cancer
Authors: A. Jajodia, A. Gupta, A. Mehta, A. Chaturvedi, A. Rao, G. Gupta, D.C. Doval, A. Bp, P. Medisetty, S. Bommera, V.P.B. Koyyala, S. Pasricha, M.E. Mayerhoefer, H. Prosch, M.K. Chllamma, M. la Mantia, A. Russo
Journal: Annals of Oncology (2020)
Combining gene expression profiling and machine learning to diagnose B-cell non-Hodgkin lymphoma
Authors: Victor Bobée, Fanny Drieux, Vinciane Marchand, Vincent Sater, Liana Veresezan, Jean-Michel Picquenot, Pierre-Julien Viailly, Marie-Delphine Lanic, Mathieu Viennot, Elodie Bohers, Lucie Oberic, Christiane Copie-Bergman, Thierry Jo Molina, Philippe Gaulard, Corinne Haioun, Gilles Salles, Hervé Tilly, Fabrice Jardin, Philippe Ruminy
Journal: Blood Cancer Journal (2020)

Abstract Non-Hodgkin B-cell lymphomas (B-NHLs) are a highly heterogeneous group of mature B-cell malignancies. Their classification thus requires skillful evaluation by expert hematopathologists, but the risk of error remains higher in these tumors than in many other areas of pathology. To facilitate diagnosis, we have thus developed a gene expression assay able to discriminate the seven most frequent B-cell NHL categories. This assay relies on the combination of ligation-dependent RT-PCR and next-generation sequencing, and addresses the expression of more than 130 genetic markers. It was designed to retrieve the main gene expression signatures of B-NHL cells and their microenvironment. The classification is handled by a random forest algorithm which we trained and validated on a large cohort of more than 400 annotated cases of different histology. Its clinical relevance was verified through its capacity to prevent important misclassification in low grade lymphomas and to retrieve clinically important characteristics in high grade lymphomas including the cell-of-origin signatures and the MYC and BCL2 expression levels. This accurate pan-B-NHL predictor, which allows a systematic evaluation of numerous diagnostic and prognostic markers, could thus be proposed as a complement to conventional histology to guide the management of patients and facilitate their stratification into clinical trials.
Persistence of immunity in children immunised with 13-valent pneumococcal conjugate vaccine and impact on nasopharyngeal carriage: a cross-sectional study
Authors: Rajendra Prasad Janapatla, Mei-Hua Hsu, Chyi-Liang Chen, Sung-Hsi Wei, Ming-Jia Yu, Lin-Hui Su, Tzou-Yien Lin, Cheng-Hsun Chiu
Journal: Thorax (2020)

In 500 children aged ≤10 years after 13-valent pneumococcal conjugate vaccine (PCV)13 immunisation in different schedules, serotypes 19A-specific and 19F-specific immunoglobulin G (IgG) were predicted to persist above 0.35 µg/mL for ≥10 years in all groups, likely due to PCV13-induced memory with natural boosting from residual diseases and colonisation. Generally, serotype-specific IgG could persist above 0.35 µg/mL longer (≥5 years) in the catch-up group than in the 2+1 and 3+1 immunisation groups. 14.5% of the carriage isolates belonged to PCV13 serotypes; statistical analysis revealed that a high serum IgG level (&gt;10.96 µg/mL) will be required to eliminate the point-prevalence nasopharyngeal carriage of serotype 19A.
Tamoxifen: the Long and Short of It
Authors: S. M. Swain
Journal: JNCI Journal of the National Cancer Institute (1996)

The use of the drug tamoxifen in the treatment of early stage breast cancer—as hormone therapy following surgery—is accepted clinical practice. However, the question of how long to continue the drug has been, and still is, a hotly debated topic. The specific concern is, When do the risks outweigh the benefits? It is clear that thousands of women who take tamoxifen will live longer and remain disease free longer as a result (7). But tamoxifen has also been associated with an increased risk for second primary cancers (2J). In this issue of the Journal, two large randomized studies, one by the Swedish Breast Cancer Cooperative Group (4) and the other by the National Surgical Adjuvant Breast and Bowel Project (NSABP) (5), shed light on this very complex question of duration of treatment. The rationale for long-term administration of tamoxifen derives initially from laboratory evidence that mammary tumor development in a mouse model is best inhibited by continuous treatment at an early point after carcinogen exposure (6). Furthermore, estradiol can reactivate tumor growth in mice after tamoxifen treatment is discontinued, suggesting that the drug's action is cytostatic (7). However, the development of tamoxifendependent tumor growth after several months of treatment has also been demonstrated (8), which indicates that clinical trials are essential to determine the optimal duration of treatment in humans. The hypothesis tested in the two large clinical trials reported here is that increased duration of tamoxifen treatment decreases mortality from breast cancer. Each of these trials asks a different question in regard to treatment duration. The Swedish study looks at 2 versus 5 years of tamoxifen therapy, with the primary end points of event-free survival (which does not include the occurrence of second primary cancers) and overall survival. The NSABP B-14 study first compares 5 years of tamoxifen with placebo, using the primary end points of disease-free survival (which includes the occurrence of second primary cancers) and overall survival, followed by a second randomization to an additional 5 years of tamoxifen or no further treatment. The Swedish study included 3887 patients who were postmenopausal, who had axillary lymph node-negative or -positive disease, and who had estrogen receptor (ER)-negative or -positive tumors. The dose of tamoxifen was either 20 or 40 mg per day. The overall conclusion of the authors is that there is an event-free survival benefit as well as a general survival benefit for women receiving tamoxifen for 5 years versus 2 years. This is apparent for patients with ER-positive tumors (node-negative or -positive disease) and is most pronounced during years 6-8 of follow-up, with a median follow-up of 5Vi years.
Why a dearth of sports and exercise medicine/physiotherapy research using hospital electronic medical records? A success story and template for researchers
Authors: Gustavo C Machado, Mary O'Keeffe, Bethan Richards, Chris Needs, Hannah Storey, Chris G Maher
Journal: British Journal of Sports Medicine (2020)

In hospital systems, large volumes of data are routinely collected in digital form. Advances in electronic medical record systems have created digital health data that are well coded and structured, as well as unstructured data such as clinical notes and medical images. These data have value for researchers aiming to improve the quality of healthcare.

Five barriers limit our ability to use and access electronic medical record data for research:

1.  Data are stored across numerous data tables, in a variety of formats, within fragmented or siloed data systems.

2.  Data quality is inconsistent (and at times poor). There are inaccuracies in recording, such as duplicate entries, missing data and incorrect diagnosis codes.

3.  Efficient tools to quickly identify, link and capture relevant electronic medical record data are scarce.

4.  Bureaucratic layers of governance, complex ethics approval processes and privacy legislation restrictions slow research.

5.  Data collected for administrative or compliance purposes may not contain relevant research outcomes.

These barriers mean that, with respect to sports injuries, for example, there are relatively few studies that describe the patterns or the quality and safety of healthcare using hospital-based electronic medical record data,1 2 although these injuries are commonly seen in outpatient clinics, emergency departments and inpatient wards.

We report opportunities to use electronic medical record data …
Accuracy of Patient Identification of Electrocardiogram-Verified Atrial Arrhythmias
Authors: Jeffrey L. Turner, Ann Lyons, Rashmee U. Shah, Brian Zenger, Rachel Hess, Benjamin A. Steinberg
Journal: JAMA Network Open (2020)

This cross-sectional study describes the sensitivity and specificity of patient self-assessment for atrial arrhythmia compared with 12-lead electrocardiogram and describes the association of patient perception of arrhythmia with symptom burden.