tbuckley/cabot-search huggingface dataset:
Abstract 1678: Accurate detection of expressed variation in RNA-seq
Authors: Lisle E. Mose, David Marron, Joel S. Parker
Journal: Cancer Research (2019)

Abstract Somatic variant detection has long been an area of great interest and critical importance in cancer research and treatment. DNA-Seq based somatic variant calling pipelines have been maturing over the last several years and although there is still room for improvement, several methods have been developed capable of accurately detecting somatic variants from matched tumor/normal DNA. RNA-Seq has become a widely used tool for measuring gene and isoform abundance, identifying alternative splicing, and detection of gene fusions. Detection of expressed variation is receiving growing interest, however computational methods to detect this variation have received far less attention than that of DNA-Seq. We have developed an optimized RNA-Seq pipeline based upon the ABRA2 realigner capable of accurately detecting expressed somatic variation in RNA-Seq. We applied this pipeline to the TCGA Breast Cancer dataset. To assess the impact of identification of expressed variation as an indicator of variant significance, we compared the expression state of the top 20 cohort wide significantly mutated genes (SMG) as identified by The Cancer Genome Atlas Network (2012) with all other genes. At the median for SMGs, 23 somatic variants are expressed with over 90% of variants detected in DNA being expressed. For non-SMGs, the median number of expressed variants is 1 and the median fraction of expressed variants is 50%. Among non-SMGs, a total of six genes exceed the median total number of expressed variants and fraction of expressed variants for SMGs (AHNAK, CHD4, ERBB2, FASN, FOXA1 and MYH9). All of these variants have been previously implicated in breast cancer, however none of these variants were among the cohort wide SMGs identified in the original study and only FOXA1 was identified as being a subtype specific SMG (ER+,ER+/HER2-). Notably, variants in the massive TTN gene are found to be coding 73% of the time, but expressed in only 8% of cases. This is substantially less than the 90% found in SMGs and a likely indicator that TTN mutations are passenger variants. The median and third quartile RNA variant allele frequency (VAF) for SMGs is .41 and .69 versus .32 and .46 for DNA. By comparison, the median and third quartile VAF for non-SMGS was 0 and .27 in RNA and .20 and .30 for DNA. The increased VAF for RNA SMGs is a likely indicator of selection and can potentially further be used to identify variants of significance. We believe these results demonstrate the utility of variant expression as a potentail tool to aid in assessment of variant significance. Citation Format: Lisle E. Mose, David Marron, Joel S. Parker. Accurate detection of expressed variation in RNA-seq [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 1678.
From xerosis to nummular dermatitis. The dehydration dermatosis
Authors: T. G. Rollins
Journal: JAMA (1968)

A universal problem, especially in temperate climates in the winter season, is dehydration of the skin. Untreated, it progresses from simple dryness to patches of pruritic, eczematous nummular dermatitis. Decreased humidity in an artificially heated environment, excessive bathing, decreased perspiration, and a decrease in natural skin oil contribute to the development of this dermatosis. There are individual variations in susceptibility to the condition, but it can develop in almost anyone. Although most common on the lower extremities, neither the trunk nor upper extremities is exempt. The condition is predominantly seen in adults, especially in older men. The symptoms vary with the severity of the condition. These may range from mild "prickling" discomfort to severe intractable pruritus. Early in the disease, examination reveals diffuse, fine dry scaling, with accentuation of the skin markings (Fig 1). If left untreated, the condition gradually evolves into erythematous nummular patches (Fig 2). The surfaces of
Treatment of traumatic hyphema
Authors: D. C. Love
Journal: JAMA (1985)

<h3>To the Editor.—</h3> I refer to Dr Kershner's<sup>1</sup>letter challenging the routine use of oral steroids for traumatic hyphema as advocated by Dr Yasuna.<sup>2</sup>Although the authors admit that the treatment of traumatic hyphema is controversial, I was surprised that neither author mentioned the use of antifibrinolytic therapy with aminocaproic acid for this condition. I feel it is important that the general medical community be informed about this therapy that is being recommended by experts in the field for routine use in the management of traumatic hyphema.<sup>3</sup> Two prospective, double-blind, randomized clinical trials in humans<sup>4,5</sup>plus one in rabbits<sup>6</sup>have been consistent in showing a 28% to 32% rebleeding rate in controls with only a 3% to 5% incidence of repeated hemorrhage in aminocaproic acid-treated eyes. The proposed mechanism involves competitive inhibition of the body's fibrinolytic system, thus preventing early fibrin dissolution before recently injured
Ulcers and gastritis
Authors: S. Pang, W. Leung, D. Graham
Journal: Endoscopy (2007)

Upper gastrointestinal bleeding (UGIB) remains a major problem worldwide. Over time the management issues have changed and a paradigm shift occurred when it became clearly established that eradication of Helicobacter pylori would "cure" peptic ulcers, including the elimination of new ulcers, recurrent ulcers, and ulcer complications. The subsequent recognition that H. pylori infections increased the risk of complications from nonsteroidal anti-inflammatory drugs (NSAIDs) led to the recommendation to test NSAID and aspirin users for H. pylori, and to eradicate the infection whenever it is found. Unfortunately, eradication of H. pylori is no longer straightforward, as clinicians are facing the increasing challenge of resistant strains. Moreover, eradication of H. pylori alone will not solve the problem of NSAID ulcer complications because NSAIDs themselves increase the risk of UGIB. Unresolved issues include identification of the circumstances in which particular traditional NSAIDs or cyclo-oxygenase-2 (COX-2)-selective inhibitors are preferred, and the actual role for gastroprotective co-therapy.
Nintendo Surgery
Authors: Richard M. Satava
Journal: JAMA (1992)

<h3>To the Editor.</h3> —Laparoscopic cholecystectomy has burst onto the world stage, but perhaps it has long been in the subconscious, especially of our younger video-generation surgeons. This new surgery should not be regarded as a novelty, but rather as the first blush of a profound change in the viewing of the art and craft of medicine. It is the announcement of the coming of age of the "Nintendo surgeon." The combination of endoscopy and laparoscopy and the technologies of video, miniaturization, and computers permitted the birth of laparoscopic surgery and is leading to revolutionary innovations, such as telepresence surgery.<sup>1</sup>We should not fence off this new development and create another specialty, but rather acknowledge its roots and commonality with general surgery. Let laparoscopic cholecystectomy be the harbinger that ushers in a widening of perspective and a multidisciplinary approach to all fields of medicine. The opinions or assertions contained herein
Foreign Medical Schools
Authors: Henry R. Mason
Journal: JAMA (1971)

Financial data regarding the operation of basic science departments in 13 foreign medical schools were collected in person in a recent visit to these schools attended by more than 2,000 American students. Special effort has been made to tabulate these data on a comparable basis with the usual organization of basic science departments in US medical schools. However, no attempt has been made to compare the organization of these departments with those in US schools.
Definitive chemoradiotherapy may be standard treatment options in clinical stage I esophageal cancer
Authors: T. Ura, K. Muro, Y. Shimada, K. Shirao, H. Igaki, Y. Tachimori, H. Kato, Y. Ito, A. Imai, Y. Kagami
Journal: Journal of Clinical Oncology (2004)

4017 Background: We have reported that definitive chemoradiotherapy (CRT) achieved high CR rate and good short-term survival with mild toxicity for clinical stage I (T1N0M0) esophageal squamous cell carcinoma (ESCC) in a phase II study (Kato et al; Proc ASCO 2003). In order to reexamine this treatment, we performed following retrospective analysis in our institution. Methods: Treatment consisted of continuous infusion of 5FU at a dose of 700mg/m2/day on days 1 to 4, combined with cisplatin at a dose of 70mg/rn2 on day 1, and concurrent radiation therapy at a dose of 30 Gy in 15 fractions over 3 weeks. This schedule was repeated twice every 4 weeks, for a total radiation dose of 60 Gy with one week split. Results: From June 1997 to May 2002, 73 patients were analyzed. There were 12 females and 61 males whose median age was 63 years. There were 68 CRs for CR rate of 93% (95% confidence interval; 87–99%). Five patients with residual tumor successfully underwent EMR or esophagectomy. Grade 4 neutropenia occurred in 1%. Grade 3 esophagitis, nausea, and stomatitis occurred in 7%, 6%, and 1%, respectively. Regarding late radiation morbidity, grade 2 pneumonitis, pleural effusion, and pericardial effusion occurred in 18%, 3%, and 3%, respectively. Late radiation morbidity was relatively frequent, but no toxicities interfering with function were seen. Ten patients with recurrent mucosal lesions were successfully treated by EMR. Four patients with recurrent disease successfully underwent surgery. Local recurrence after CR was relatively frequent, but salvage treatment can be safely carried out. Until June 2003, of 11 patients died, 7 died of the recurrence and 4 died of other diseases. With a median follow-up duration of 3 years, the 1, 3, 5-year survival rates were 96%, 80%, and 77%, respectively. This survival data is comparable with that obtained by ordinary surgery in Japan. Conclusions: Definitive CRT may be standard treatment options in clinical stage I ESCC. This regimen could be considred as a test arm of phase III study to compare with surgery in patients with stage I ESCC. No significant financial relationships to disclose.
l -Arginine decreases blood pressure and left ventricular hypertrophy in rats with experimental aortic coarctation
Authors: Y.-P. Sun, B.-Q. Zhu, A.E.M. Browne, L.-R. Gao, T.M. Chou, K. Chatterjee, K. Sudhir, W.W. Parmley
Journal: Journal of the American College of Cardiology (1998)
Cluster Headaches
Authors: M. A. Hopkinson
Journal: JAMA (1962)

<h3>To the Editor:—</h3> I should be grateful if any of your readers (or their wives) who suffer from cluster headaches (synonyms: migrainous neuralgia, histamine cephalalgia, and periodic migraine) as I do would communicate with me. My intention is to send a detailed questionnaire to such correspondents in the English-speaking world, not only inquiring into their histories, but also trying to ascertain their opinions as to etiology and treatment. If, from the several hundred thousand physicians in the Commonwealth and the U.S.A., a few hundred answers were received, some statistical sense might be made of this neglected medical conundrum. I assure any physician who writes me, concerning himself or his wife, that when all the replies to the questionnaire are correlated, he will receive a summary of results. If the number of answers warrants it, an article on this ubiquitous problem may be published.
MYD88 L265P Mutation in Waldenstrom's Macroglogulinemia
Authors: Stephanie Poulain, Christophe Roumier, Audrey Decambron, Aline Renneville, Charles Herbaux, Elisabeth Bertrand, Sabine Tricot, Agnes Daudignon, Sylvie Galiegue-Zouitina, Olivier Theisen, Nathalie Grardel, Valérie Soenen, Olivier Nibourel, Catherine Roche-Lestienne, Bruno Quesnel, Patrick Duthilleul, Claude Preudhomme, Xavier Leleu
Journal: Blood (2012)
MEDICAL MEN AND LIFE INSURANCE.
Journal: JAMA (1997)

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
Workshop report Photopatch testing - methods and indications
Journal: British Journal of Dermatology (1997)

Journal Article Workshop report Photopatch testing ‐ methods and indications Get access BRITISH PHOTODERMATOLOGY GROUP BRITISH PHOTODERMATOLOGY GROUP Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 136, Issue 3, 1 March 1997, Pages 371–376, https://doi.org/10.1046/j.1365-2133.1997.5671521.x Published: 01 March 1997 Article history Accepted: 30 September 1996 Published: 01 March 1997
Review: Limited evidence suggests that statins are safe in patients with liver disease
Authors: Eric R. Bates
Journal: Annals of Internal Medicine (2008)

ACP Journal Club19 August 2008Review: Limited evidence suggests that statins are safe in patients with liver diseaseEric R. Bates, MDEric R. Bates, MDUniversity of Michigan, Ann Arbor, Michigan, USA (E.R.B.)Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-149-4-200808190-02012 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Source CitationOnofrei MD, Butler KL, Fuke DC, Miller HB. Safety of statin therapy in patients with preexisting liver disease. Pharmacotherapy. 2008;28:522-9. https://pubmed.ncbi.nlm.nih.gov/18363535Clinical Impact RatingsGIM/FP/GP: Cardiology: Endocrinology: Gastroenterology: Reference1 McKenney JM, Davidson MH, Jacobson TA, Guyton JR, National Lipid Association Statin Safety Assessment Task Force. Final conclusions and recommendations of the National Lipid Association Statin Safety Assessment Task Force. Am J Cardiol. 2006;97:89C-94C. [PMID: 16581336] Google Scholar Author, Article, and Disclosure InformationAffiliations: University of Michigan, Ann Arbor, Michigan, USA (E.R.B.)This article was published at Annals.org on 5 August 2008. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 19 August 2008Volume 149, Issue 4Page: JC2-12KeywordsAminotransferasesLiver diseasesLiver function testsSafetySafety studiesStatinsTransferases ePublished: 19 August 2008 Issue Published: 19 August 2008 CopyrightCopyright © 2008 by American College of Physicians. All Rights Reserved.PDF DownloadLoading ...
Journal of Nervous and Mental Disease, Baltimore
Journal: JAMA (1969)

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
THE TREATMENT OF EPILEPSY BY EXCISION OF THE CERVICAL SYMPATHETIC.
Journal: JAMA (1899)

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
Error in Figure Legends
Journal: JAMA (2016)

Alison J. Rodger, MD; Valentina Cambiano, PhD; Tina Bruun, RN; Pietro Vernazza, MD; Simon Collins; Jan van Lunzen, PhD; Giulio Maria Corbelli; Vicente Estrada, MD; Anna Maria Geretti, MD; Apostolos Beloukas, PhD; David Asboe, FRCP; Pompeyo Viciana, MD; Félix Gutiérrez, MD; Bonaventura Clotet, PhD; Christian Pradier, MD; Jan Gerstoft, MD; Rainer Weber, MD; Katarina Westling, MD; Gilles Wandeler, MD; Jan M. Prins, PhD; Armin Rieger, MD; Marcel Stoeckle, MD; Tim Kümmerle, PhD; Teresa Bini, MD; Adriana Ammassari, MD; Richard Gilson, MD; Ivanka Krznaric, PhD; Matti Ristola, PhD; Robert Zangerle, MD; Pia Handberg, RN; Antonio Antela, PhD; Sris Allan, FRCP; Andrew N. Phillips, PhD; Jens Lundgren, MD; for the PARTNER Study Group
An outbreak of diarrhea and hemolytic uremic syndrome from Escherichia coli O157:H7 in fresh-pressed apple cider
Authors: R. E. Besser
Journal: JAMA (1993)

<h3>Objective.</h3> —<i>Esherichia coli</i>O157:H7 causes hemorrhagic colitis and the hemolytic uremic syndrome. In the fall of 1991, an outbreak of<i>E coli</i>O157:H7 infections in southeastern Massachusetts provided an opportunity to identify transmission by a seemingly unlikely vehicle. <h3>Design.</h3> —Case-control study to determine the vehicle of infection. New England cider producers were surveyed to assess production practices and determined the survival time of<i>E coli</i>O157:H7 organisms in apple cider. <h3>Results.</h3> —Illness was significantly associated with drinking one brand of apple cider. Thirteen (72%) of 18 patients but only 16 (33%) of 49 controls reported drinking apple cider in the week before illness began (odds ratio [OR], 8.3; 95% confidence interval [CI], 1.8 to 39.7). Among those who drank cider, 12 (92%) of 13 patients compared with two (13%) of 16 controls drank cider from cider mill A (lower 95% CI, 2.9;<i>P</i>&lt;.01). This mill pressed cider in a manner similar to that used by other small cider producers: apples were not washed, cider was not pasteurized, and no preservatives were added. In the laboratory,<i>E coli</i>O1 57:H7 organisms survived for 20 days in unpreserved refrigerated apple cider. Addition of sodium benzoate 0.1% reduced survival to less than 7 days. <h3>Conclusions.</h3> —Fresh-pressed, unpreserved apple cider can transmit<i>E coli</i>O157:H7 organisms, which cause severe infections. Risk of transmission can be reduced by washing and brushing apples before pressing, and preserving cider with sodium benzoate. Consumers can reduce their risk by only drinking cider made from apples that have been washed and brushed. (<i>JAMA</i>. 1993;269:2217-2220)
Chemotherapeutic Activity of Clofazimine and Its Analogues against <i>Mycobacterium tuberculosis</i>: <i>In Vitro</i>, Intracellular, and <i>In Vivo</i> Studies
Authors: Chinnaswamy Jagannath, M. Venkata Reddy, Subramanian Kailasam, J. F. O'Sullivan, Pattisapu R. J. Gangadharam
Journal: American Journal of Respiratory and Critical Care Medicine (1995)

Clofazimine (CFM), a riminophenazine drug, is primarily used in therapy for leprosy and Mycobacterium avium infections. With an objective of identifying drugs active against Mycobacterium tuberculosis, including those with multi-drug resistance, we investigated CFM and nine of its chemical analogues. Among these, B746 and B4101 had better activity than CFM against six drug-susceptible and nine single/multiple drug-resistant M. tuberculosis strains. B746 also showed slightly better activity than CFM against intracellular M. tuberculosis in J774A.1 macrophages and was comparable to CFM in its in vivo activity against experimental tuberculosis in C57BL/6 mice. Interestingly, it caused less pigmentation in internal organs.
Reply
Authors: M. Monti, M. Barbareschi
Journal: British Journal of Dermatology (1997)

Journal Article Reply Get access M. Monti, M. Monti Institute of Dermatologlcal Science, University of Milan, Via Pace, 9‐20122, Milan, Italy Search for other works by this author on: Oxford Academic Google Scholar M. Barbareschi M. Barbareschi Institute of Dermatologlcal Science, University of Milan, Via Pace, 9‐20122, Milan, Italy Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 136, Issue 4, 1 April 1997, Page 635, https://doi.org/10.1111/j.1365-2133.1997.tb02166.x Published: 01 April 1997
One Shot
Authors: Bridget M. Kuehn
Journal: JAMA (2009)

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