tbuckley/cabot-search huggingface dataset:
Abstract 3417: Genomic analyses of clear cell papillary kidney cancers reveal large metabolic alterations and activation of the hypoxia pathway
Authors: David Lindgren, Jonas Sjolund, Helen Nilsson, Borje Ljungberg, Martin Johansson, Hakan Axelson
Journal: Cancer Research (2019)

Abstract Tumors arising from the nephron of the kidney are collectively called renal cell carcinomas (RCCs). Recent high-throughput genomics endeavors, such as the TCGA initiative, have provided a roadmap for a deepened molecular understanding of these tumor types. With the aim to characterize RCCs that do not conform to the most common subtypes of RCC we scrutinized RNA-Seq transcriptomes of kidney tumor samples supplied by the TCGA project. Dimensionality reduction analyses revealed one defined a transcriptional subset of RCCs, which upon re-review of tissue histology could be classified as clear cell papillary RCC (ccpRCC). In line with previous analyses, samples were defined by overexpression of KRT7, CA9, CCND1 and GATA3 and harbored few genomic alterations as well as a limited number of gene mutations; only mTOR was found recurrently mutated. We observed upregulation of the Hypoxia inducible factor (HIF) pathway, possibly caused by VHLinactivation by gene promoter methylation in the majority of ccpRCCs. This may explain the morphological resemblance of ccpRCCs to VHL driven conventional clear cell RCCs. Further, the methylomes of ccpRCCs were distinct from other tumors and transcription factors specific for epithelial cells of the distal nephron were overexpressed, thus suggesting distinct tumor ontogeny of ccpRCCs compared to other renal tumors. Citation Format: David Lindgren, Jonas Sjolund, Helen Nilsson, Borje Ljungberg, Martin Johansson, Hakan Axelson. Genomic analyses of clear cell papillary kidney cancers reveal large metabolic alterations and activation of the hypoxia pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3417.
Incorrect Mean Historical Deaths in Table Estimating Deaths Following Hurricane Maria
Authors: Christopher Wallis, Allan Detsky, Eddy Fan
Journal: JAMA (2019)

In Reply As Ms Sharma and colleagues highlight, RCTs have gained a dominant role in medical research due to their ability to generate an unbiased estimate treatment effect in the study sample.However, as discussed in our Viewpoint 1 and elsewhere, 2 there are significant barriers to the conduct of RCTs for devices and procedures.To rely on intrinsic motivation among physicians to conduct these trials as Sharma and colleagues suggest seems unrealistic, albeit optimistic, given the self-interest of those who develop and promote new health technologies.We believe that in the absence of a regulatory environment that mandates RCTs for procedures, these trials will continue to be relatively uncommon.Important evidence in support of this prediction lies in the 21st Century Cures Act that has enabled the US Food and Drug Administration to promulgate the use of so-called real-world data (eg, observational data from insurance databases, disease registries) in the approval of new indications for pharmaceutical agents. 3,4 We thank Mr Dewar and Dr Shamy for drawing attention to their valuable framework for considering both the relevance and feasibility of RCTs in medical procedures.
Thrombolytic Therapy in Haemolyticuraemic Syndrome
Authors: H Jopling
Journal: BMJ (1975)

tensifying efforts to raise further money.The scientific section of the report includes details of closer links between the cell biologists and clinicians studying breast cancer and of trials in progress of chemotherapy as an adjunct to surgical removal of breast tumours.The Medical Oncology Unit at St. Bartholomew's Hospital is continuing its work on leukaemias and Hodgkin's disease, while longer-term research continues at the Tumour Immunology Unit and tihe Mill Hill laboratories.Research expenditure during the year ended September 1974 amounted to £51 million, 95% of the total received from the public and from invest- ment income. Classification of LeprosyA set of transparencies showing clinical and hiistological features of leprosy has been prepared by Drs.W.
Letter by Wang et al Regarding Article, “Age at Diagnosis of Type 2 Diabetes Mellitus and Associations With Cardiovascular and Mortality Risks”
Authors: Daxin Wang, Tian Chen, Xinquan Yang
Journal: Circulation (2019)

such 2 parameters of different medical treatments and then to associate with the survival or cardiovascular outcomes in men and women, we thus might get the some information of CVD risk-reduction management in an age-stratified population and find personalized therapeutic strategies that could benefit the patients in the long term.
Epidemiologic Studies of Ionizing Radiation and Cancer: Past Successes and Future Challenges
Authors: Jonathan M. Samet
Journal: Environmental Health Perspectives (1997)

The health effects of radiation have been a focus for research since early in the 20th century.As the century ends, extensive experimental and epidemiologic evidence has been accumulated that addresses the adverse consequences of radiation exposure; epidemiologic studies of radiation-exposed groups from the general population and specific occupational groups provide quantitative estimates of the cancer risks associated with exposure.This report provides a perspective on the extensive epidemiologic evidence on the health effects of ionizing radiation and on likely needs for further epidemiologic research on radiation and health.Epidemiologic studies have proved informative on the quantitative risks of radiation-caused cancer but we now face the challenges of more precisely characterizing risks at lower levels of exposure and also of assessing modifiers of the risks, including dose rate, genetic susceptibility, and other environmental exposures.This report considers investigative approaches, such as pooled analysis of multiple data sets, that can be used to address these complex questions and the limitations of these approaches for addressing societal concerns about the risks of radiation exposure.
Balancing incentives. How should physicians be reimbursed?
Authors: L P Casalino
Journal: JAMA (1992)

The May 15, 1991,<i>JAMA</i>theme issue presented 14 different proposals for reforming the US medical care system. Though these proposals varied widely, they encompassed only three proposed methods for paying physicians: fee-for-service, salary, and capitation. When examined from a perspective that considers the incentives affecting practicing physicians, each of these methods has serious flaws. I outline these flaws and suggest an alternative method for reimbursing primary care physicians: that of combining capitation and fee-for-service. Specialists would be paid fee-for-service, but the cost of specialty care would be limited by giving each primary care physician a budget for such care. Consistent failure by a physician to stay within the budget would result in ongoing review, but not in direct financial sanctions. This system of reimbursing physicians is intended to balance incentives so that physicians can concentrate on making medical decisions with a minimum of distraction by third parties and by personal financial considerations. (<i>JAMA</i>. 1992;267:403-405)
PLK-1 is upregulated in barrett's adenocarcinoma and is a surrogate marker of aneuploidy
Authors: J. M. Dunn, S. A. McDonald, D. Oukrif, R. J. Haidry, M. A. Butt, E. Lovat, L. B. Lovat, G. H. Williams, M. R. Novelli
Journal: Gut (2011)

<h3>Introduction</h3> DNA ploidy abnormalities, measured by flow or image cytometry, are markers of genomic instability that inform on future cancer risk in patients with Barrett9s oesophagus (BO). Barriers to routine clinical use include cost, availability and interlaboratory reproducibility. DNA replication licensing factors (RLFs) ensure precise duplication of the genome and contribute to genomic stability, and may therefore act as surrogate markers of DNA ploidy abnormalities. RLFs have great potential for routine clinical use as they are measured by immunohistochemistry (IHC). <h3>Aims</h3> To establish a surrogate IHC marker for DNA ploidy that can be utilised as a high throughput screening tool for the assessment of cancer risk in BO. <h3>Methods</h3> Oesophagectomy specimens from 10 patients with Barrett9s adenocarcinoma were evaluated. A total of 54 areas were marked representing the metaplasia-dysplasia-carcinoma sequence. These were removed by laser capture microdissection (LCM) and processed for image cytometry DNA ploidy analysis (ICDA). Serial 4 μm sections were cut and stained for 5 RLFs by standard immunohistochemistry protocols, and the labelling index of percentage positive cells (LI) was calculated for each marked area. These scores were then correlated with histology and DNA ploidy abnormalities. <h3>Results</h3> There was a significant difference in the LI of geminin, cdc7 kinase and Polo like kinase 1 (PLK-1) between non-dysplastic BO and HGD/Cancer. There was no significant difference between these two groups for KI67 or mcm2. PLK-1 had the highest degree of correlation with DNA ploidy status with a Pearson coefficient r<sup>2</sup> = 0.776 (p&lt;0.01). When using a cut off score of 30%, the sensitivity and specificity of PLK-1 for the detection of aneuploidy was 86% and 100% respectively. <h3>Conclusion</h3> This is the first time geminin, cdc7 kinase and PLK-1 have been shown to be upregulated in Barrett9s dysplasia and adenocarcinoma. PLK-1, a key regulator of mitosis, correlated most closely with aneuploidy measured on LCM tissue and holds great potential as a biomarker in BO.
L'intelligence artificielle peut aider à prédire le besoin d'une chirurgie complémentaire après résection d'un canceer colorectal T1.
Journal: Endoscopy (2018)

Ce papier par Ichimasa et al. est le premier à décrire l’apport de l’intelligence artificielle pour prédire la nécessité de chirurgie complémentaire dans les cancers superficiels (T1) colo-rectaux. La pertinence clinique est majeure puisque le risque d’envahissement ganglionnaire et de métastases à distance concerne environ 10 % de ces patients en cas de résection endoscopique incomplète ou de présence de facteurs pronostiques péjoratifs sur le spécimen de résection. A l’heure actuelle, les guidelines recommandent donc un traitement chirurgical complémentaire dans cette situation, mais seules 8 à 16 % des chirurgies sont réellement nécessaires, les autres pièces opératoires étant indemnes de lésions carcinomateuses. De plus, la chirurgie colorectale complémentaire comporte un risque non nul de morbi-mortalité. Dans ce contexte, il est nécessaire de développer des aides à la décision cliniques de chirurgie complémentaire ou d’abstention, et l’avènement de l’intelligence artificielle et des “big datas” représente une opportunité majeure.
Incorrect Author Name
Authors: D Hester, Leah Eisenberg, Laura Guidry-Grimes, D Micah Hester, Erin Demartino, Cavan Doyle, Paul Mueller
Journal: JAMA (2019)

violating a patient's values and interests expressed through an authorized proxy, restrictions on a woman's right to choose before viability, and tensions between following the law and meeting well-established obligations to patients. 3 Clinicians in Arkansas have confronted and may continue to confront situations that require them to be aware of the state's law in these regards.We want their decisions to be informed of the potential legal restrictions on what may be their otherwise wellconsidered and ethically justifiable determinations to follow a pregnant woman's advance directive or to honor a surrogate's decision to stop life-sustaining measures to meet with the patient's own values and interests.
Cotton Dust and the Lung
Authors: GERALD J. BECK
Journal: Annals of Internal Medicine (1984)

Letters and Corrections1 January 1984Cotton Dust and the LungGERALD J. BECK, PH.D., E. NEIL SCHACHTER, M.D., LUCINDA R. MAUNDER, M.A., RICHARD S.F. SCHILLING, M.D., D.SC.GERALD J. BECK, PH.D.Search for more papers by this author, E. NEIL SCHACHTER, M.D.Search for more papers by this author, LUCINDA R. MAUNDER, M.A.Search for more papers by this author, RICHARD S.F. SCHILLING, M.D., D.SC.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-100-1-162_2 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptTo the editor: Pratt and Lynn, in their response (1) to our study of chronic lung disease in cotton textile workers (2, 3), have used the wrong tables (6. 10 to 6.13) from our report (3) to support their hypothesis that "nonsmoking cotton worker's impairment might regress after retirement."The data Pratt and Lynn cite from our study are for all cotton workers, those active as well as those no longer working in the mill, rather than only retired workers as their letter states. Because we have shown, and they recognize, that workers who have left the mill on the...References1. PRATTLYNN PW. Lung disease in cotton workers [Letter]. Ann Intern Med. 1983;99:278. LinkGoogle Scholar2. BECKSCHACHTERMAUNDERSCHILLING GELR. A prospective study of chronic lung disease in cotton textile workers. Ann Intern Med. 1982;97:645-51. LinkGoogle Scholar3. BECKMAUNDERSCHACHTERSCHILLING GLER. Follow-up of Active and Retired Cotton Textile Workers. Report to the U.S. Department of Labor. Springfield, Virginia: National Technical Information Service, 1982. Publication no. PB 82-240516. Google Scholar This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: Yale University School of Medicine New Haven, CT 06510 Medical Research Council London England PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics Cited ByCotton Dust, Smoking, and the LungPHILIP C. PRATT, M.D., WILLIAM S. LYNN, M.D. 1 January 1984Volume 100, Issue 1Page: 162-162KeywordsDustLungs Issue Published: 1 January 1984 PDF DownloadLoading ...
Upper trunk brachial plexopathy in football players
Authors: W. C. Robertson
Journal: JAMA (1979)

Ten football players seen from 1973 through 1977 at the University of Wisconsin Hospitals were found to have clinical and electrodiagnostic evidence of injury to the upper trunk of the brachial plexus. Each had upper limb paresis following one or more blows to the head or shoulders. The development of persistent weakness often was preceded by burning paresthesias in the upper limb. Our experience suggests that the syndrome of burning paresthesias and subsequent arm weakness frequently is secondary to stretching of the brachial plexus. (<i>JAMA</i>241:1480-1482, 1979)
THE POPULAR "ARSENICALS"
Journal: JAMA (1920)

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
Lymphocyte-Depletion Hodgkin's Disease
Journal: New England Journal of Medicine (1973)

histological picture was characterized by a massive, almost syncytial growth of reticulum cells with many Reed-Stemnberg cells, severe lymphocyte depletion, and albsence of eosinophils, plasma cells, or fiibrinoid necrosis.This picture was completely differ- ent from the entity described as Hodgkin's sarcoma.Deelmant and I concluded that this disease could be described, both on clinical and on pathological grounds, as a separate entity.I had the opportunity to discuss these cases personally in 1955 with both Dr.F. Parker and Dr. R. J. Lukes, who were at that time rather sceptical about my pro- posal to mark off this disease from classic Hodgkin's disease as a separate subgroup.However, it should be borne in mind that in 1955 discussions about the immunological nature of Hodgkin's disease were still un- heard of.A good account of identical cases had already been given in 1953 by Miss
GONOCOCCAL RHINITIS
Authors: E. W. Assinder
Journal: BMJ (1931)

I MEDnICAL 3JOUR NAL 37 " The all-important factor in the production of chilblains is the shibboleth . . . of cold bedrooms which has come to us from our Victorian forebears," I venture to think that he goes, not only beyond the facts, but that he is also a little unjust.At the present day so many of the country's ills are heaped upon Victorian shoulders that a few chilblains more or less will not, perhaps, make m.luch difference.Still, it is just as well to be fair, and, seeing that chilblains have been so called for a very long time, and that nearly a century before the Victorian era Johnson derived the word chilblain from " chill, cold, and blain," and defined it as "sores made by frost," it
Obituaries
Journal: JAMA (1987)

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
Benign Tumors of the Stomach
Authors: Seymour Fiske Ochsner
Journal: JAMA (1965)

The symptoms, pathological types, and roentgenologic manifestations were evaluated in 80 patients with benign gastric tumors. Abdominal pain was present in 41, indigestion in 38, and bleeding in 22. Gastric tumors are of many histological types; in this series 38 were epithelial adenomas and 26 submucosal leiomyomas. In 48 patients, positive radiographic findings were demonstrated. A sharply defined filling defect was noted in 45, a smooth or slightly irregular surface in 44, a round or oval shape in 43, and a submucosal location of tumor in 26. Special radiographic signs, such as ulceration, central necrosis, pedunculation, alteration in shape, prolapse into the duodenum, or presence of calcification, phleboliths, or filiform duct in the tumor permit a more precise radiological diagnosis.
Medical Literature
Authors: Saty Satya-Murti
Journal: JAMA (2006)

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
Cathepsin S inhibitor prevents autoantigen presentation and autoimmunity
Authors: Kaoru Saegusa, Naozumi Ishimaru, Kumiko Yanagi, Rieko Arakaki, Kouichi Ogawa, Ichiro Saito, Nobuhiko Katunuma, Yoshio Hayashi
Journal: Journal of Clinical Investigation (2002)

The cysteine endoprotease cathepsin S mediates degradation of the MHC class II invariant chain Ii in human and mouse antigen-presenting cells. Studies described here examine the functional significance of cathepsin S inhibition on autoantigen presentation and organ-specific autoimmune diseases in a murine model for Sjögren syndrome. Specific inhibitor of cathepsin S (Clik60) in vitro markedly impaired presentation of an organ-specific autoantigen, 120-kDa α-fodrin, by interfering with MHC class II–peptide binding. Autoantigen-specific T cell responses were significantly and dose-dependently inhibited by incubation with Clik60, but not with inhibitor s of cathepsin B or L. Clik60 treatment of mouse salivary gland cells selectively inhibited autopeptide-bound class II molecules. Moreover, the treatment with Clik60 in vivo profoundly blocked lymphocytic infiltration into the salivary and lacrimal glands, abrogated a rise in serum autoantibody production, and led to recovery from autoimmune manifestations. Thus, inhibition of cathepsin S in vivo alters autoantigen presentation and development of organ-specific autoimmunity. These data identify selective inhibition of cysteine protease cathepsin S as a potential therapeutic strategy for autoimmune disease processes.
Questions and Answers
Journal: JAMA (1963)

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