tbuckley/cabot-search huggingface dataset:
Abstract 3788: Sensitive detection of oncoviruses integrated into a comprehensive tumor immuno-genomics platform
Authors: Gabor Bartha, Robin Li, Shujun Luo, John West, Richard Chen
Journal: Cancer Research (2019)

Abstract Introduction HPV, HBV, HCV and EBV viruses are causally linked to over 11% of cancers worldwide while KSHV, HTLV and MCV are linked to an additional 1%. As use of immunotherapy expands to a broader variety of cancers, it is important to understand how these oncoviruses may be impacting the overall immune response in patients as part of the tumor and tumor microenvironment. However, typical cancer diagnostic and genomic biomarker assays do not include oncovirus detection. Methods To enable detection of these oncoviruses, we have developed ImmunoID NeXT, a novel augmented exome and transcriptome based platform that comprehensively characterizes tumor and tumor microenvironment from a single sample. As part of the platform assay design we developed targeting for the following oncoviruses: HPV, HBV, HCV, EBV, KSHV and HTLV. Furthermore we developed analytics for detecting these viruses from both the DNA and RNA data. To test the ability of the platform to detect these oncoviruses, we identified a set of 11 EBV cell lines from Coriell in which EBV was used as a transformant. We obtained another 23 cell lines from ATCC containing HPV16, HPV18, HPV45, HPV68, HBV, EBV, KSHV, HTLV1 and HTLV2 in which the oncoviruses were known to be in the tumors from which the cell lines were created. We have also started running a series a FFPE tumor samples of unknown status. We extracted DNA and RNA from all these samples, made libraries and sequenced them on a NovaSeq to 30G. High quality read counts were computed for all targeted oncoviruses. Results We detected EBV in all the Coriell cell lines in both DNA and RNA indicating strong sensitivity of the platform. Wide dynamic range suggests quantification may be possible as well. In the DNA there was no signal from any other oncovirus indicating high specificity. In the ATCC samples we detected 23 out of 23 oncoviruses expected in both the DNA and RNA. We detected all the different types of oncoviruses that we targeted except for HCV because it wasn’t in any sample. In all but one case the signals were strong. False positive detections appear to be rare. Much less than 1% of the overall exome/transcriptome reads map to oncoviruses in all cases. Conclusions Oncovirus detection integrated into an augmented exome and transcriptome assay is sensitive and specific. Oncoviral characterization of the tumor as part of a comprehensive tumor immunogenomics platform can serve and an important additional biomarker for understanding immunotherapy response. Citation Format: Gabor Bartha, Robin Li, Shujun Luo, John West, Richard Chen. Sensitive detection of oncoviruses integrated into a comprehensive tumor immuno-genomics platform [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 3788.
For Whose Benefit Do We Write?
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
Effect of immunosuppressive and antiviral agents on hepatitis B virus replication in vitro
Authors: J MCMILLAN
Journal: Hepatology (1995)

Hepatitis B virus (HBV) DNA-transfected hepatoma cells were incubated with the immunosuppressive agents prednisolone, azathioprine, and cyclosporin A (CsA) and the antiviral agents ganciclovir and foscarnet to investigate the effects of these compounds on HBV replication. Prednisolone and azathioprine increased intracellular viral DNA and RNA levels approximately twofold and fourfold, respectively. Treatment with CsA did not alter the levels of viral RNA or DNA. A combination of all three immunosuppressive agents increased the level of intracellular viral DNA eightfold, indicating an additive effect. Incubation of the cells in the presence of foscarnet decreased levels of both single-stranded and relaxed circular viral DNA, and in the presence of ganciclovir decreased the levels of relaxed circular viral DNA, predictable effects from their known mechanism of action. The stimulatory effect on viral replication induced by the combination of immunosuppressive agents was substantially inhibited by ganciclovir-foscarnet treatment. These observations could have implications for the management of recurrent HBV infection after liver transplantation.
Cost effectiveness of nurse delivered endoscopy: findings from randomised multi-institution nurse endoscopy trial (MINuET)
Authors: G. Richardson, K. Bloor, J. Williams, I. Russell, D. Durai, W. Y. Cheung, A. Farrin, S. Coulton
Journal: BMJ (2009)

<b>Objective</b> To compare the cost effectiveness of nurses and doctors in performing upper gastrointestinal endoscopy and flexible sigmoidoscopy. <b>Design</b> As part of a pragmatic randomised trial, the economic analysis calculated incremental cost effectiveness ratios, and generated cost effectiveness acceptability curves to address uncertainty. <b>Setting</b> 23 hospitals in the United Kingdom. <b>Participants</b> 67 doctors and 30 nurses, with a total of 1888 patients, from July 2002 to June 2003. <b>Intervention</b> Diagnostic upper gastrointestinal endoscopy and flexible sigmoidoscopy carried out by doctors or nurses. <b>Main outcome measure</b> Estimated health gains in QALYs measured with EQ-5D. Probability of cost effectiveness over a range of decision makers' willingness to pay for an additional quality adjusted life year (QALY). <b>Results</b> Although differences did not reach traditional levels of significance, patients in the doctor group gained 0.015 QALYs more than those in the nurse group, at an increased cost of about £56 (€59, $78) per patient. This yields an incremental cost effectiveness ratio of £3660 (€3876, $5097) per QALY. Though there is uncertainty around these results, doctors are probably more cost effective than nurses for plausible values of a QALY. <b>Conclusions</b> Though upper gastrointestinal endoscopies and flexible sigmoidoscopies carried out by doctors cost slightly more than those by nurses and improved health outcomes only slightly, our analysis favours endoscopies by doctors. For plausible values of decision makers' willingness to pay for an extra QALY, endoscopy delivered by nurses is unlikely to be cost effective compared with endoscopy delivered by doctors. <b>Trial registration</b> International standard RCT 82765705
Patient-initiated laboratory testing: applauding the inevitable
Authors: H. B. Soloway
Journal: JAMA (1990)

THE TREND of direct patient access to health care started insidiously a long time ago. First there were bathroom scales and home thermometers. To these have been added home blood pressure measuring devices and glucose monitoring strips and instruments and a variety of test kits that can be purchased in drugstores and supermarkets. Consumers may currently use such kits to determine if they are pregnant, have occult blood in their stool, have high levels of blood or urine glucose, or have recently ovulated. The popularity of these devices and kits underscores today's consumers' sophistication, willingness to play active roles in their own health care, and desire for convenient alternatives to the traditional mechanisms by which they obtain health data. According to one major market-research firm, sales of home health kits doubled between 1981 and 1986. In 1989, the estimated sales volume was $750 million, and projected 1995 sales exceed $1
Christian Scientists claim healing efficacy equal if not superior to that of medicine
Authors: A. Skolnick
Journal: JAMA (1990)

IN THE WAKE of convictions of parents for what has been called the religiously motivated medical neglect of their children, the Christian Science Church is trying to persuade state legislatures that its particular form of healing by prayer is as least as effective as medicine. Child protection advocates suggest that this new "more secular strategy" is in response to the recent failure of some religious exemption statutes to protect church members from prosecution when their children die from medical neglect. While the church claims religious exemptions from provisions of child abuse and neglect laws are a First Amendment right, courts consistently have ruled that religious freedom does not allow parents to withhold life-saving medical care from children (<i>The Law's Response When Religious Beliefs Against Medical Care Impact on Children</i>. Sioux City, Iowa: CHILD, Inc; 1990). In the meantime, legislation recently adopted in Colorado, Texas, and Louisiana, and under consideration elsewhere,
Correction of Author’s Name
Journal: JAMA Neurology (2018)

Majida Charif, PhD; Alessia Nasca, MSc; Kyle Thompson, PhD; Sylvie Gerber, PhD; Christine Makowski, MD; Neda Mazaheri, MSc; Céline Bris, PhD; David Goudenège, PhD; Andrea Legati, PhD; Reza Maroofian, MPhil; Gholamreza Shariati, MD, PhD; Eleonora Lamantea, MSc; Sila Hopton, BSc; Anna Ardissone, MD; Isabella Moroni, MD; Melania Giannotta, MD; Corinna Siegel, MD; Tim M. Strom, MD; Holger Prokisch, PhD; Catherine Vignal-Clermont, MD; Sabine Derrien, MD; Xavier Zanlonghi, MD; Josseline Kaplan, MD, PhD; Christian P. Hamel, MD, PhD; Stephanie Leruez, MD; Vincent Procaccio, MD, PhD; Dominique Bonneau, MD, PhD; Pascal Reynier, MD, PhD; Frances E. White, MRes; Steven A. Hardy, PhD; Inês A. Barbosa, PhD; Michael A. Simpson, PhD; Roshni Vara, MD; Yaumara Perdomo Trujillo, MD; Hamind Galehdari, PhD; Charu Deshpande, MD; Tobias B. Haack, MD, PhD; Jean-Michel Rozet, PhD; Robert W. Taylor, PhD, FRCPath; Daniele Ghezzi, PhD; Patrizia Amati-Bonneau, MD; Guy Lenaers, PhD
Laser Used With X-ray Speeds Tumor Regression
Journal: JAMA (1966)

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
Superior Mesenteric Vein-Inferior Vena Cava Shunt in Treatment of Portal Hypertension
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 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
Correction
Authors: J Crabtree, Colonel Gregg, B Hickey, R Sykes, J Laurent, A Salter, A Pugh, Surgeon Lieutenants, H Black, A Hazell, J Rivers, R Cole, W Lamb, E Hayward, I Sturton, B Ramsay, R Lewis, R Pyle, B Taylor, A Charles, T Williams
Journal: BMJ (1965)
Dr. Glasgow a Graduate.
Journal: JAMA (1924)

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
Abstract P041: Cumulative Exposure to Air Pollution, Socioeconomic Status and Post-Myocardial Infarction Outcomes in Central Israel. A Cohort Study
Authors: Noa Molshatzki, David Broday, Silvia Koton, Yuval ., Vicki Myers, Yaacov Drory, David Steinberg, Yariv Gerber
Journal: Circulation (2012)

Objective: In a community-based cohort of myocardial infarction (MI) survivors, we examined whether cumulative residential exposure to air pollutants constitutes a risk factor for adverse outcomes. Methods: Patients aged ≤65 years (n=1,428), admitted with first MI in 1992-1993 to the 8 hospitals serving the population of central Israel, were followed up through 2005. Extensive data were collected on socio-demographic, clinical, and environmental factors. Daily measures of nitrogen dioxide (NO 2 ), nitric oxide (NO) and fine particles (PM 2.5 ) recorded at air quality monitoring stations were summarized and cumulative exposure was estimated for each patient based on geo-coded residential location at study entry. Cox models were used to assess the hazard ratios (HRs) for all-cause death, cardiac death, recurrent MI, heart failure and stroke associated with a 10 μ g/m 3 increase in pollutant exposure. Results: Patients residing in more polluted areas had better socioeconomic status at both the individual and neighborhood levels. Exposure to pollutants was inversely associated with outcomes. However, these associations were either removed or reversed upon multivariable adjustment for socioeconomic and clinical variables (HRs [95% CIs] of PM 2.5 are reported in the Table). Conclusions: In this unique setting and in contrast to other reports, better socioeconomic status was associated with higher exposure to pollution. In multivariable models accounting for socioeconomic and clinical variables, we observed a weak positive association between PM 2.5 exposure and post-MI outcomes, consistent with findings in the general population. Considering exposure misclassification, the true association is likely stronger. Unadjusted Multivariable-Adjusted All-Cause Death 0.93 (0.53-1.62) 1.51 (0.85-2.67) Cardiac Death 0.74 (0.38-1.44) 1.37 (0.70-2.68) Recurrent MI 1.06 (0.62-1.81) 1.67 (0.96-2.92) Heart Failure 0.60 (0.32-1.12) 1.39 (0.73-2.62) Stroke 0.64 (0.29-1.40) 1.04 (0.46-2.33)
Errata: Vol. 65, No. 20
Journal: MMWR Morbidity and Mortality Weekly Report (2016)

In the MMWR report, "Fatal Abusive Head Trauma Among Children Aged <5 Years - United States, 1999-2014," multiple errors occurred in the figure on page 507 (corrected text is noted by underline). The top box should have read, "The underlying cause code in the death record must indicate assault as the intent of injury." The bottom left box should have read, "Abusive head trauma diagnosis codes (S02.0-S02.1, S02.7-S02.9, S04.0, S06.0-S06.9, S07.1, S07.8-S07.9, S09.7-S09.8, T90.2, T90.5, T90.8-T90.9)." The bottom right box should have read, "Must exclude all abusive head trauma injury codes," and "Must exclude all of these traumatic brain injury diagnosis codes."
TCT-568 Multi-Center, Randomized Evaluation of the Elixir DESyne® Novolimus Eluting Coronary Stent System with Biodegradable Polymer Compared to a Zotarolimus-Eluting Coronary Stent System: 4-Year Results from the EXCELLA BD Study®
Authors: Stefan Verheye, Alexandre Abizaid, Roberto Botelho, Ricardo A. Costa, Luiz F. Tanajura, Katsuhisa Waseda, Lynn Morrison, Sara Toyloy, Peter J. Fitzgerald, Joachim Schofer
Journal: Journal of the American College of Cardiology (2015)
Insurance Coverage and Care of Patients with Non–ST-Segment Elevation Acute Coronary Syndromes
Authors: James E. Calvin, Matthew T. Roe, Eric D. Peterson
Journal: Annals of Internal Medicine (2007)

Letters7 August 2007Insurance Coverage and Care of Patients with Non–ST-Segment Elevation Acute Coronary SyndromesJames E. Calvin, MD, Matthew T. Roe, MD, MHS, and Eric D. Peterson, MD, MPHJames E. Calvin, MDFrom Rush University Medical Center, Chicago, IL 60612, and Duke Clinical Research Institute, Durham, NC 27705.Search for more papers by this author, Matthew T. Roe, MD, MHSFrom Rush University Medical Center, Chicago, IL 60612, and Duke Clinical Research Institute, Durham, NC 27705.Search for more papers by this author, and Eric D. Peterson, MD, MPHFrom Rush University Medical Center, Chicago, IL 60612, and Duke Clinical Research Institute, Durham, NC 27705.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-147-3-200708070-00015 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail IN RESPONSE:Dr. Ross points out that our recent study defined insurance status on the basis of the patient's primary insurance provider. Data on the provision of secondary insurance coverage were not collected before 2003. As a result, we cannot distinguish Medicaid patients who were also enrolled in managed care programs or who had dual Medicaid and Medicare coverage. After November 2003, we collected data on multiple insurers but grouped patients in a hierarchy based on 1) managed care, 2) Medicare, and 3) Medicaid. Thus, Dr. Ross is correct in stating that this strategy may have excluded Medicaid patients who ... Author, Article, and Disclosure InformationAuthors: James E. Calvin, MD; Matthew T. Roe, MD, MHS; Eric D. Peterson, MD, MPHAffiliations: From Rush University Medical Center, Chicago, IL 60612, and Duke Clinical Research Institute, Durham, NC 27705.Disclosures: None disclosed. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetailsSee AlsoInsurance Coverage and Care of Patients with Non–ST-Segment Elevation Acute Coronary Syndromes James E. Calvin , Matthew T. Roe , Anita Y. Chen , Rajendra H. Mehta , Gerard X. Brogan Jr. , Elizabeth R. DeLong , Dan J. Fintel , W. Brian Gibler , E. Magnus Ohman , Sidney C. Smith Jr. , and Eric D. Peterson Insurance Coverage and Care of Patients with Non–ST-Segment Elevation Acute Coronary Syndromes Joseph S. Ross Metrics 7 August 2007Volume 147, Issue 3Page: 212KeywordsAcute coronary syndromeConflicts of interestHealth care providersMedicarePatientsSocioeconomic status ePublished: 7 August 2007 Issue Published: 7 August 2007 Copyright & PermissionsCopyright © 2007 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
Re: Timothy J. Wilt, Tien N. Vo, Lisa Langsetmo, et al. Radical Prostatectomy or Observation for Clinically Localized Prostate Cancer: Extended Follow-up of the Prostate Cancer Intervention Versus Observation Trial (PIVOT). Eur Urol. In press. https://doi.org/10.1016/j.eururo.2020.02.009
Authors: Roderick C.N. van den Bergh, Massimo Valerio, Derya Tilki, Giorgio Gandaglia
Journal: European Urology (2020)
Hepatitis C in adults and adolescents with hemophilia: A randomized, controlled trial of interferon alfa-2b and ribavirin
Authors: M Fried
Journal: Hepatology (2002)

Adolescents and adults with inherited disorders of coagulation have one of the highest prevalence rates of hepatitis C among known risk groups. Few data are available on the use of combination therapy with interferon and ribavirin in this population. Patients 13 years of age and older who were positive for hepatitis C virus (HCV) RNA by polymerase chain reaction and negative for human immunodeficiency virus were randomized to receive interferon alfa-2b (3 million units 3 times a week) plus ribavirin (1,000 mg/day) or interferon alfa-2b alone for 48 weeks with 24 weeks of posttreatment follow-up. Patients started on interferon alone who remained positive for HCV RNA at week 12 crossed over to treatment with interferon plus ribavirin. A total of 113 patients were treated. Thirty-seven patients were younger than 18 years. At the end of treatment, 18 of 56 (32%) treated with interferon plus ribavirin and 6 of 57 (11%) treated with interferon alone were negative for HCV RNA (P = .005). Sustained virologic response in the combination arm was 29% (16 of 56) compared with 7% (4 of 57) for those started on interferon alone (P = .027). Among adolescents younger than 18 years who were treated with combination therapy, 10 of 17 (59%) had sustained response compared with 6 of 39 (15%) of adult patients on the same regimen (P = .001). In conclusion, in this U.S. multicenter, randomized trial of therapy for HCV in patients with inherited bleeding disorders, sustained virologic response rate was significantly improved for patients treated with interferon and ribavirin compared with those started on interferon alone. Adolescents treated with combination therapy had a significantly higher sustained response than adults did on the same regimen. (HEPATOLOGY 2002;36:967-972.)