tbuckley/cabot-search huggingface dataset:
Abstract 1632: Deep learning functional associations using histopathology images
Authors: Javad Noorbakhsh, Saman Farahmand, Mohammad Soltanieh Ha, Sandeep Namburi, Kourosh Zarringhalam, Jeff Chuang
Journal: Cancer Research (2019)

Abstract Histopathological images have critical value for understanding cancer subtype, local structure, and malignancy. Manual interpretation of such images can be time-consuming and error-prone, while also failing to make use of the power of image aggregation for coordinated data mining. Large-scale patient cohorts such as TCGA provide high-resolution H&amp;E images that complement other -omics data, with the important advantage that images provide spatial information about heterogeneity and stromal cell interactions. We implemented a convolutional neural network (CNN) to classify H&amp;E slides according to tissue type, cancer subtype, and genomic mutations. We modified the CNN architecture of Inception v3 according to our problem and trained it with tiled whole slide images from 31 solid cancers in TCGA, and evaluated our algorithm on holdout data. We first classified tumor/normal status from the images and determined AUC values for each cancer type. We then applied our method for tissue classification in a multilabel classification scenario. Furthermore, in few cancers (e.g. gastric cancer) we determined cancer subtypes using supervised learning. Finally we evaluated our model for classifying mutational status of cancer-related genes. To improve classification accuracy, we modified Inception architecture for multi-task classification by replacing the final fully-connected layer by a shared layer which provides the input to individual task layers corresponding to each gene mutation. Furthermore, we adopted image segmentation approaches (e.g.. auto-thresholding) to improve sample background removal, and used several approaches (e.g. resampling, cross entropy weighting) to rebalance the data. In some cases we achieved high classification results (e.g. AUC=0.7 for TP53 in lung adenocarcinoma). Our study suggests that histological images can be used to classify tumors according to their mutational status, and can provide biomarkers for molecular subtyping. Citation Format: Javad Noorbakhsh, Saman Farahmand, Mohammad Soltanieh Ha, Sandeep Namburi, Kourosh Zarringhalam, Jeff Chuang. Deep learning functional associations using histopathology images [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 1632.
Cholesterol Guidelines
Authors: W.E. Feeman
Journal: Annals of Internal Medicine (1989)

Letters and Corrections15 December 1989Cholesterol GuidelinesW.E. Feeman Jr., MDW.E. Feeman Jr., MDSearch for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-111-12-1047 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptTo the Editor: American physicians may be surprised, but much of the rest of the medical world is not enamored of the cholesterol guidelines set forth by the National Cholesterol Education Program (NCEP). In general, the British medical profession believes that Americans are going overboard in their approach to preventing atherosclerotic disease. The British response to American enthusiasm is medical nihilism; British physicians test and treat only persons at extremely high risk.The Toronto Working Group on Cholesterol Policy plan, discussed in a recent editorial by Dr. Garber (1), seems to be a reasonable compromise. However, this plan is simply...Reference1. Garber A. Where to draw the line against cholesterol. Ann Intern Med. 1989;111:625-7. LinkGoogle Scholar This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: 640 South Wintergarden Road Bowling Green, OH 43402 PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 15 December 1989Volume 111, Issue 12Page: 1047-1048KeywordsCholesterolMedical education Issue Published: 15 December 1989 PDF DownloadLoading ...
NEW YORK LETTER FROM OUR REGULAR CORRESPONDENT.
Authors: None P. B. P.
Journal: JAMA (1885)

New York, Jan. 3, 1885. The annual collections in aid of the various hospitals were made, as usual, on the last Saturday and Sunday of the year; but it will not be possible, for some time yet, to announce the amount contributed. This work is under the charge of the Hospital Saturday and Sunday Association, an organization created for this special purpose, and each year its managers endeavor to render the machinery of its operations more and more perfect, so that the collections may be made as systematically and the contributions secured may be as large as possible. During the autumn and early part of the winter an active canvass has been carried on among the various trades through the agency of auxiliary organizations; and the number of these auxiliaries, through the labors of the central organization, has continued to increase until it now includes nearly all the leading lines
Anesthesiology, Philadelphia
Journal: JAMA (1967)

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
Blood Groups Differ on Donor Deferral
Authors: M. Mitka
Journal: JAMA (2001)

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
First results of a phase III multicenter randomized controlled trial of intensity modulated (IMRT) versus conventional radiotherapy (RT) in head and neck cancer (PARSPORT: ISRCTN48243537; CRUK/03/005)
Authors: C. Nutting, R. A'Hern, M. S. Rogers, M. A. Sydenham, F. Adab, K. Harrington, S. Jefferies, C. Scrase, B. K. Yap, E. Hall
Journal: Journal of Clinical Oncology (2009)

LBA6006 Background: Xerostomia is the most common late toxicity of RT to the head and neck. IMRT dose distributions reduce the dose delivered to parotid gland. PARSPORT investigated the role of IMRT in reducing xerostomia in patients with head and neck cancer. Methods: The PARSPORT trial compared two radiotherapy delivery methods in the treatment of patients with pharyngeal tumors (T1–4, N0–3, M0). Patients received 65Gy in 30 fractions over 6 weeks delivered using either CT planned parallel opposed lateral fields or parotid-sparing IMRT. Stratification was by site of tumor and center. The primary endpoint was incidence of LENT-SOMA ≥G2 xerostomia one year after treatment. Secondary endpoints included acute toxicities (CTCAE v3) and other late RTOG and LENT-SOMA radiation toxicities. Proportions of patients with ≥G2 toxicity were compared using exact tests. For secondary endpoints a significance level of 1% was used. Results: 94 patients (47 RT; 47 IMRT) were randomized between 2003 and 2007 from six UK centers. 80 patients had oropharyngeal tumors and 14 hypopharyngeal. Radiotherapy was given as primary treatment in 71 patients and post-operatively in 23. 22 patients had AJCC stage I/II disease. Median follow-up was 31.9 months (IQR: 26.6 –38.8). Twelve month LENT-SOMA ≥G2 xerostomia scores were observed in 74% (25/34) of RT and 40% (15/38) of IMRT patients (p=0.005). Corresponding values at 18 months were 71% (15/21) and 29% (9/31) (p=0.004). On the RTOG scale, 12 month ≥G2 xerostomia was reported in 64% (21/33) RT vs 41% (15/37) IMRT patients (p=0.06). The 18 month incidence was 81% 17/21 RT vs 20% (6/30) IMRT (p<0.001). Acute radiotherapy related ≥G2 fatigue was more prevalent in the IMRT group (76% vs 41% p=0.001). No differences in acute mucositis or pain scores were seen. At 12 months, no statistically significant differences were seen in other late toxicities. No differences were observed between overall survival and locoregional control rates. Conclusions: Sparing the salivary glands through use of IMRT significantly reduces the incidence of xerostomia in patients with pharyngeal tumors. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Elekta, Varian Medical Systems
Gastrojejunocolic fistula secondary to benign ulcer
Authors: L. J. Blumen
Journal: JAMA (1970)

<h3>To the Editor.—</h3> Only 37 cases of gastrocolic fistula arising from benign gastric ulcer have been described since the original recognition of this fistula as a clinical syndrome in 1755. In a review of the literature from 1920 to the present, Sterns and Bird<sup>1</sup>found only 13 cases. The inclusion of the jejunum as part of the fistulization process, namely the gastrojejunocolic fistula, adds another serious complication to the patient's already disturbed metabolic state. Gastrojejunocolic fistula has been seen occasionally in extensive cases of malignancy, in ulcerative colitis, and after previous gastric surgery. To our knowledge, no report has been made to date of a gastrojejunocolic fistula complicating an unoperated benign gastric ulcer. The following is such a case. <h3>Report of a Case.—</h3> A 52-year-old woman presented with the chief complaint of dizziness and faintness. She had had no gastrointestinal symptoms with the exception of heartburn until two months before
Reply to Fabiana Gregucci and Alba Fiorentino's Letter to the Editor re: Liselotte M.S. Boevé, Maarten C.C.M. Hulshof, André N. Vis, et al. Effect on Survival of Androgen Deprivation Therapy Alone Compared to Androgen Deprivation Therapy Combined with Concurrent Radiation Therapy to the Prostate in Patients with Primary Bone Metastatic Prostate Cancer in a Prospective Randomized Clinical Trial: Data from the HORRAD Trial. Eur Urol 2019;75:410–8
Authors: André N. Vis, Liselotte M.S. Boevé
Journal: European Urology (2019)
<i>Announcement</i>: Click It or Ticket Campaign — May 23–June 5, 2016
Journal: MMWR Morbidity and Mortality Weekly Report (2016)

Click It or Ticket is a national campaign coordinated annually by the National Highway Traffic Safety Administration to increase the proper use of seat belts. In 2014, more than 21,000 passenger vehicle occupants died in motor vehicle crashes in the United States; 49% were unrestrained at the time of the crash (1). An additional 2.4 million occupants (restrained and unrestrained) were treated in emergency departments for nonfatal crash-related injuries (2).
DIPHTHERIA PREVENTION WORK IN THE PUBLIC SCHOOLS OF NEW YORK CITY
Journal: JAMA (1921)

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
Metoposcopy and kindred arts
Authors: L. S. King
Journal: JAMA (1973)

August 5, 1968, marked a significant event in the history of science, for on that date was published in<i>JAMA</i>(<b>205</b>:470) the first controlled study in metoposcopy. The reader may immediately ask, what is that? Indeed, the people of the world can be divided into two classes—those who know the meaning of "metoposcopy" and those who do not. The first group comprises a handful of antiquarians. Everyone else falls into the second group. The term might thus seem to have little general appeal, but I nevertheless suggest sound reason for discussing it: metoposcopy forms a part of the vast intellectual realm that interpenetrates the history of thought and the history of science. This is the realm of the occult that bridges the gap between magic and science. "Metoposcopy" means literally the observation of the forehead, and the term refers to the information about the past and the future that
Vaginal bleeding in early pregnancy.
Authors: J C Bignall, D C Burns
Journal: BMJ (1980)

stood Mendelian inheritance well.They found it virtually impossible to accept the concept of the healthy carrier.The usual response was to agree politely that the child was perfectly healthy and did not need any treatment, but that children should be tested as young as possible-"so that it can be treated in time."Since completing this study we have been aware of the comparative simplicity of coun- selling families who come for testing, or have already been tested, if there is prior knowledge of their condition.They might, for example, have relatives with a haemoglobinopathy or trait, might have been tested themselves in pregnancy, or might have been referred by a doctor of their own ethnic background.We conclude that mass screening for haemo- globinopathy is unjustified, at least in this country.We advocate instead further health education about haemoglobinopathies together with financial support for hospitals recognised as able to offer both adequate testing and coun- selling.
Alcoholic Ketoacidosis
Authors: David W. Jenkins
Journal: JAMA (1971)

Three alcoholic women (ages 27 to 44) were studied during episodes of severe ketoacidosis and dehydration. In two, these incidents were recurrent. Just before admission, an increase in alcohol consumption was followed by anorexia, vomiting, dehydration, and hyperpnea. On admission, blood glucose level was normal or moderately elevated, glycosuria was absent or trivial, and alcohol had disappeared from blood, but ketoacidosis was sometimes severe. Although blood transfusion was sometimes necessary to combat hypotension, patients usually improved when given only glucose and saline solution without insulin. Slightly impaired glucose tolerance was present soon after admission. Direct damage to hepatic mitochondria by alcohol, persisting long after alcohol is gone, appears to be the best explanation of the underlying defect, although some additional factor peculiar to the patient appears to be necessary to explain the rarity of the syndrome.
Effect of Ethinyl Estradiol on Chronic Active Hepatitis
Authors: Joseph M. Guattery
Journal: Annals of Internal Medicine (1996)

Letters15 October 1996Effect of Ethinyl Estradiol on Chronic Active HepatitisJoseph M. Guattery, MD, William W. Faloon, MD, and Daniel L. Biery, DOJoseph M. Guattery, MDUniversity of Rochester School of Medicine and Dentistry, Rochester, NY 14642Search for more papers by this author, William W. Faloon, MDUniversity of Rochester School of Medicine and Dentistry, Rochester, NY 14642Search for more papers by this author, and Daniel L. Biery, DOUniversity of Rochester School of Medicine and Dentistry, Rochester, NY 14642Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-125-8-199610150-00028 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail TO THE EDITOR:A decrease in serum liver enzyme levels in patients with primary biliary cirrhosis during treatment with ethinyl estradiol [1] led to a study of this drug in six women with chronic inflammatory liver disease. Patient ages ranged from 28 to 72 years (mean, 60 years). All aspartate aminotransferase and other serum enzyme levels were greater than twice the normal level for more than 6 months. Examination of liver biopsy specimens showed inflammation, piecemeal necrosis, or fibrosis. One patient was positive for the antibody to hepatitis C virus, 1 had autoimmune chronic active hepatitis, 1 was positive for ...References1. Guattery JM, Faloon WW. Effect of estradiol upon serum enzymes in primary biliary cirrhosis. Hepatology. 1987; 7:737-42. Google Scholar2. McFarlane IG. Autoimmunity and hepatotrophic viruses. Semin Liv Dis. 1991; 11:223-33. Google Scholar3. Lunel F. Hepatitis C virus and autoimmunity: fortuitous association or reality? [Editorial] Gastroenterology. 1994; 107:1550-5. Google Scholar Author, Article, and Disclosure InformationAffiliations: University of Rochester School of Medicine and Dentistry, Rochester, NY 14642 PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 15 October 1996Volume 125, Issue 8Page: 700KeywordsAutoimmune hepatitisDrugsEnzymesEstradiolHepatitis C virusHepatitis E virusInflammationLiverLiver fibrosisSerum glutamic oxaloacetic transaminase Issue Published: 15 October 1996 CopyrightCopyright © 1996 by American College of Physicians. All Rights Reserved.PDF DownloadLoading ...
Grants
Journal: JAMA (1999)

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
Errata for Volume VIII, Number 1
Journal: Circulation Research (1960)

Footnotes for Table 4 should read as follows: * = three normal volunteer subjects ages 26-36 (ref. 5) and 5 "essentially" normal subjects ages 26-69 (ref. 6). † = nineteen normal and convalescent subjects without cardiopulmonary disease, ages 17-28 (unpublished).
THE SURGERY OF THE TRIGEMINAL TRACT
Journal: JAMA (1921)

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
HOSPITAL REPORTS
Journal: BMJ (1901)

noon.The urine was not scanty.I prescribed opium I gr.every four hours, and stopped the urotropine.On May 23rd all trace of blood had disappeared from the urine, which was again highly ammoniacal, and I again put him on urotropine fgrs.thrice daily.The same evening, after having taken in al I5 grs. of urotropine, he felt a return of the burning feel- ing in the urethra, and again he passed a little blood in the last quantity of the urine.On visiting him on the morning of May 24th IHfound he had of his own accord stopped the urotropine.In this case I believe the bladder to have been 'the source -of the haemorrhage, and it is the first instance I have had of .anyinjurious effects following the use of this valuable drug.
Erratum for the Research Article: “The ERBB network facilitates KRAS-driven lung tumorigenesis” by B. Kruspig, T. Monteverde, S. Neidler, A. Hock, E. Kerr, C. Nixon, W. Clark, A. Hedley, S. Laing, S. B. Coffelt, J. Le Quesne, C. Dick, K. Vousden, C. P. Martins, D. J. Murphy
Journal: Science Translational Medicine (2018)