tbuckley/cabot-search huggingface dataset:
Abstract 754: A comprehensive immunogenomics profiling platform enables the exploration of the intricate relationship between TMB, MSI, Neoantigen and HLA status among multiple cancers
Authors: Jie Wang, Ao Li, Jiawei Wang, Zhaoze Cheng
Journal: Cancer Research (2019)

Abstract With the rapid advancement of immune therapy on cancer treatment, there is an increasing demand for accurate and comprehensive profile of tumor immunogenomics landscape in order to broaden our knowledge on predicting patient response as well as to facilitate drug development process. We established a cloud based analytical platform to comprehensively characterize genomic features that are potentially related to patients’ responses to immunotherapy. We implemented a neoantigen prediction pipeline based on whole exome sequencing (WES) and transcriptome sequencing data that integrates accurate HLA typing based on WES, somatic variant detection/phasing, RNA expression, class I MHC binding prediction as well as peptide epitope ranking. Among that, the HLA typing pipeline was validated using 73 Chinese and Japanese subjects covering &amp;gt;60 known class I HLA alleles with an accuracy above 95%. In addition, we also developed and validated methods to compute microsatellite instability (MSI) and tumor mutation burden (TMB) based on either a 600 gene panel or WES. Thirdly, this platform also enables the detection of HLA somatic variants and loss of heterozygosity events based on WES data. Next, we applied this analysis platform to process 127 samples across four cancer types (colon, rectal, endometrial and gastric) from TCGA as well as two Chinese cohorts of 100 non-small cell lung cancers and 30 esophageal squamous cell carcinomas sequenced at WuXi NextCODE. Within the TCGA cohort, the data reveals that patients with MSI High status produces significantly more neoantigens than patients with MS Stable status (7.06±4.60 vs 0.71±0.64, p = 7.65e-16, neo-peptides per Mb). Number of neopeptides predicted from each frameshift event is significantly higher than that from each missense mutation (1.30±1.56 vs 0.58±0.54, p = 2.86e-11, neo-peptides per Mb). We also observed strong correlation between TMB and neoantigen burden across multiple cancer types. In conclusion, we have developed a immunogenomics solution that captures tumors’ TMB, MSI, neoantigen as well as deleterious events associated with their HLAs. This platform will allow more comprehensive molecular features assessed to potentially improve the prediction of patients’ response to immune therapy. Citation Format: Jie Wang, Ao Li, Jiawei Wang, Zhaoze Cheng. A comprehensive immunogenomics profiling platform enables the exploration of the intricate relationship between TMB, MSI, Neoantigen and HLA status among multiple cancers [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 754.
Typographical Errors in Figure
Authors: Alexander Flint
Journal: JAMA Neurology (2015)

ing a statin as an outpatient.We find a similar strong relationship between inpatient statin use and outcomes when we perform this type of analysis.Among patients not taking a statin as an outpatient prior to hospitalization, the odds ratio for inpatient statin use in multivariable logistic regression predicting being alive at day 30 is 2.81 (95% CI, 2.12-3.73;P < .001)and the odds ratio for inpatient statin use predicting discharge to home or inpatient rehabilitation facility is 2.02 (95% CI, 1.6-2.54;P < .001).It should also be noted that in the original article, we also showed the converse of this analysis: among outpatient statin users, statin cessation in the inpatient setting is strongly associated with worsened outcomes (Figures 1 and3).
Is Simple Acute Erysipelas a Local or a Constitutional Disease?
Authors: J. Higginbottom
Journal: BMJ (1864)

<h3>Abstract</h3> Shrews in the genus <i>Episoriculus</i> are among the least known mammals in China. It occurs mainly in the Himalayas and the Hengduan Mountains. We report the sequencing and analyses of one mitochondrial gene (Cyt <i>b</i>) and three nuclear genes (Apob, Brca1, and Rag2) for 77 specimens, and analyses of morphological measurements for 56 specimens. Phylogenetic and morphological studies answer three longstanding questions. First, <i>Episoriculus sacratus</i> and <i>E. umbrinus</i> are valid species, and not subspecies of <i>E. caudatus</i>. Second, <i>Pseudosoriculus fumidus</i> is a valid taxon that does not belong to the genus <i>Episoriculus</i>. Third, the genus <i>Episoriculus</i> has eight valid species: <i>E. baileyi, E. caudatus, E. leucops, E. macrurus, E. sacratus, E. soluensis, Episoriculus</i> sp., and <i>E. umbrinus</i>. Ultimately, we erected subgenus <i>Longacauda</i> subgen. nov. for morphologically distinct <i>E. macrurus</i>, which leaves the nominate subgenus <i>Episoriculus</i> with the remaining seven congeners.
Small-Bowel Endoscopy
Authors: J D Waye
Journal: Endoscopy (2003)

This review of the literature on endoscopy of the small bowel focuses on published reports, and does not include abstracts. The literature was reviewed for the period September 2001 to September 2002. MEDLINE was searched under the topics of “small-bowel endoscopy”, “small bowel”, “enteroscopy”, “obscure bleeding”, and “wireless endoscopy”, and a hand search was also carried out of the major gastroenterology journals, along with a review of the tables of contents of all journals that could be identified as being related to gastroenterology or gastrointestinal endoscopy. Sonde small-bowel enteroscopy is no longer an option, and has been rightfully retired as an investigation tool for the small bowel. There is still a place for further evaluation of push enteroscopy, as evidenced by the 11 papers published since the last review of small-bowel endoscopy in 2002. In the field of intraoperative enteroscopy, only one series and a handful of case reports have appeared. By contrast, wireless capsule endoscopy of the small bowel has captured the imagination of gastroenterologists throughout the world. Up to 2003, there have not been many published papers concerning this new diagnostic modality, since patients with obscure gastrointestinal bleeding or suspected small-bowel disease are relatively scarce. Large numbers of abstracts concerning capsule endoscopy have been submitted for presentation at major gastroenterology and gastrointestinal endoscopy meetings over the past 2 years, and the enthusiasm for this new technique of small-bowel imaging has increased with reports of its successful application.
ADDRESS OF WELCOME, TO THE AMERICAN MEDICAL ASSOCIATION, AT THE MEETING IN BALTIMORE, MAY 7, 1895.
Journal: JAMA (1895)

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
Motion, not immobility, advocated for healing synovial joints
Authors: M. Korcok
Journal: JAMA (1981)

Orthopedic surgeons who "make a fetish out of applying plaster casts" should instead look to the use of motion to heal injured or diseased synovial joints. They should also realize, says Robert B. Salter, MD, professor and head of orthopaedic surgery at the University of Toronto Faculty of Medicine, that it is possible to regenerate articular cartilage with relative comfort and little inconvenience to the patient if one is willing to set aside plaster of Paris. Speaking to the 50th annual meeting of the Royal College of Physicians and Surgeons of Canada in Toronto, Salter said that the traditional concept that tissue, including cartilage, must be rested in order to heal "really is not valid" and the concept itself "must be put to rest." Salter was reporting not only on his long-term experimental investigations on the healing of fullthickness defects in articular cartilage in animals, but also on his subsequent
No Intimations as Yet
Journal: JAMA (2018)

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
Lymphatic System: The Body's Amazon
Journal: JAMA (1966)

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THE PERIL TO THE COMMUNITY OF ALCOHOLIC MANIA.
Journal: JAMA (2005)

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ITEMS.
Journal: JAMA (1892)

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
Hyperkalemia In Chronic Renal Failure
Authors: William D. Deep
Journal: JAMA (1968)

<h3>To the Editor:—</h3> The rarity of the spontaneous development of severe hyperkalemia in nonoliguric chronic renal failure is poorly appreciated. Among the many reports of hyperkalemia in renal insufficiency we have not found a well-documented case of life-threatening hyperkalemia in a patient with stable chronic uremia without oliguria, sodium depletion, excessive potassium load, adrenal insufficiency, or other precipitating cause. We are now treating a patient with chronic glomerulonephritis in which there is a tendency for dangerous hyperkalemia to develop. <h3>Report of a Case:—</h3> In 1959, signs of acute glomerulonephritis after a streptococcal sore throat developed in a 30-year-old white man. Progressive renal deterioration ensued. For the past two years the blood urea nitrogen (BUN) level has stabilized in the 120-140 mg/100 cc range. His medications have been methyldopa, hydralazine, and digoxin. He has been emaciated and hyperpigmented and has suffered constant fatigue. His hemoglobin level has slowly fallen to 6.6
Abstract P332: Self-perceived Psychological Factors and Their Impact on Ideal Cardiovascular Health by Gender: the Baptist Health South Florida (BHSF) Employee Study
Authors: Lena Mathews, Oluseyi Ogunmoroti, Roger S Blumenthal, Ovie Utuama, Maribeth Rouseff, Sankalp Das, Emir Veledar, Theodore Feldman, Arthur Agatston, Khurram Nasir, Erin D Michos
Journal: Circulation (2017)

Introduction: Psychological factors including stress are associated with adverse cardiovascular (CV) disease outcomes. Gender differences exist in both the perception of stress and the magnitude of the stress response. We hypothesize that self-perceived psychological stressors would have a greater impact on women compared to men as measured by the American Heart Association Life’s Simple Seven (LS7) health metrics. Methods: This was a cross-sectional study conducted among employees of BHSF. The LS7 metrics (smoking, physical activity, diet, body mass index, blood pressure, cholesterol and glucose) were each scored as ideal (2), intermediate (1), or poor (0), with composite scores ranging from 0 to 14. Total scores were categorized as optimal (11-14), average (9-10) and inadequate (0-8). We used multinomial logistic regression to compare psychological factors obtained by questionnaire (self-perceived stress, life satisfaction, hopelessness, sadness, depression, anxiety) with the LS7 score (inadequate score served as reference). The model was stratified by gender and adjusted for age, ethnicity, and education level. Results: Of the 9,056 participants, 74% were female, 17% white, 57% Hispanic, 16% black, with a mean age of 43±12 years. Self-perceived adverse psychological factors were associated with being less likely to achieve adequate and optimal LS7 scores (Table). For example both women and men, respectively, with self-perceived stress were less likely to have optimal LS7 metrics [OR 0.47 (95% CI 0.40-0.56) vs. 0.50 (0.36-0.69)]. There were some interactions by gender (P &lt;0.05), but the results were qualitatively similar in both men and women. Conclusions: In an ethnically diverse population, participants with negative self-perceived psychological factors are more likely to have inadequate CV health as measured by LS7. Contrary to our hypothesis, in general, men and women were similarly affected by adverse psychological factors. Addressing psychological stressors may be one mechanism to improve CV health.
Outcome of Third Salvage Autologous Stem Cell Transplantation in Multiple Myeloma
Authors: Laurent Garderet, Simona Iacobelli, Anja van Biezen, Linda Koster, Peter Dreger, Jan-Erik Johansson, Xavier Leleu, Michael Potter, Marta Krejci, Christian Peschel, Jakub Radocha, Arnold Ganser, Bernd Metzner, Nicoli Paoli, Kerstin Schäfer-Eckart, David Pohlreich, Pascal Lenain, Mariella Grasso, Denis Caillot, Hermann Einsele, Henrik Sengeloev, Nathalie Meuleman, Fabio Ciceri, Stefan Schönland, Nicolaus Kröger
Journal: Blood (2016)
Diphtheria in Russia a reminder of risk
Authors: P. B. Fontanarosa
Journal: JAMA (1995)

THE ONGOING and expanding diphtheria epidemic occurring in the New Independent States (NIS) of the former Soviet Union is a vivid reminder that infectious diseases considered to be under control in developed countries carry the potential for resurgence and for causing significant morbidity and mortality. Moreover, this epidemic not only underscores the critical importance of routine periodic vaccinations for achieving and maintaining protective antibody levels, but also makes imminent the need for physicians in developed countries to be able to readily diagnose and treat a rarely seen disease. See also p 1250. Diphtheria is uncommon in the United States and in most developed countries that have successful immunization programs. According to Iain Hardy, MD, a medical epidemiologist in the National Immunization Program at the Centers For Disease Control and Prevention (CDC), "only 40 cases of diphtheria were reported in the United States from 1980 to 1992, with 70% occurring in
Disability as a Public Health Outcome in the Aging Population
Authors: J. M. Guralnik
Journal: Annual Review of Public Health (1996)

Improvements in life expectancy in the twentieth century have resulted from major declines in mortality at younger ages, but it is less well recognized that mortality declines at older ages have also played a substantial role in prolonging expectation of life. A person reaching age 65 in 1900 could expect to live an additional 11.9 years. Life expectancy at age 65 rose to 14.4 years by 1960 and then increased by about three years in the next three decades, reaching 17.5 years in 1992 (56, 70). As a greater proportion of the population survives to very old ages, the public health impact of the burden of disease and disability and related utilization of medical care and need for supportive and long-term care has become an important concern. In particular, the ability of the older person to function independently in the community is a critically important public health issue. A growing body of research in the last decade has addressed the measurement of disability, factors related to its onset, consequences of disability, and the potential for preventive interventions. This article summarizes the state of the art in these areas and discusses their public health relevance.
Subject Index, v.1-17: A-Isaacs
Journal: Journal of Clinical Investigation (1940)

of meeting of either The American Society for Clinical Investi- gation or the Central Society for Clinical Research.If observations have been made on animals the fact is mentioned in the title; all other titles refer to studies on man.Hyper-and hypofunction of various organs are listed under the organs.The exchange of various chemical substances is listed under the substances; the energy exchange under Metabolism.The vitamins are designated by the letters of the alphabet under Vitamin; thus Vitamin C appears and not ascorbic acid.Endocrines are listed under hormones, the various glands of internal secretion, and various syndromes.
NATHAN SMITH DAVIS, M.D.
Journal: JAMA (1904)

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
Assault weapons as a public health hazard
Authors: T. A. Noel
Journal: JAMA (1992)

<h3>In Reply.</h3> —The weapons that Dr Kleber had in mind during my interview with him<sup>1</sup>include guns such as the Tec-9 and the Tec-22, manufactured by Intratec (Miami, Fla). Other companies manufacture similar weapons. The Tec-9 carries a clip of 32 rounds, the Tec-22 carries a clip of 30. They are described as semiautomatic pistols. Thus, Dr Kohanski is correct in bringing me to task for describing such weapons as "machine guns." A semiautomatic weapon requires a pull of the trigger for each round to be fired; a machine gun will continue firing until the ammunition runs out, as long as the trigger is held back. However, the point may well be only a technical distinction. The March 10, 1992, issue of the<i>New York Times</i>quoted LeRoy Martin, Superintendent of Police in Chicago, Ill, commenting on these weapons: "They are designed to spray whole groups of people, and