tbuckley/cabot-search huggingface dataset:
High Resolution Comparative Genomic Hybridization (CGH) Indicates That Genomic Profiles Are Very Heterogeneous for HER2 and TOP2A in FISH-Amplified Human Breast Cancer Specimens.
Authors: H. McArthur, E. Brogi, S. Patil, M. Wigler, L. Norton, J. Hicks, C. Hudis
Journal: Cancer Research (2009)

Abstract Background: Clinical studies relating TOP2A and HER2 status by FISH and response to specific drug therapies, including anthracyclines, have yielded inconsistent results. The discordance across studies appears to reflect, in part, the well-documented limitations of FISH testing, including the use of large FISH probes to evaluate the relatively small genes of interest. However, it is also likely that the dichotomization of gene status into “amplified” or “non-amplified” categories inadequately describes complex changes across the gene areas of interest. Identification and delineation of specific amplification-deletion patterns in this region may be of significant clinical interest and could provide deeper insight into mechanisms of drug resistance. Consequently, we selected a subset of HER2 and TOP2A amplified specimens (by FISH) from an ongoing study of CGH, and examined individual amplification-deletion patterns by CGH.Methods: 471 consecutive, archived, formalin-fixed paraffin-embedded, &amp;gt;1cm, HER2 2+ and 3+ by immunohistochemistry primary breast cancer specimens diagnosed between January 2000 and 2006 were selected. HER2 status was evaluated by FISH at MSKCC and CGH at Cold Spring Harbor Laboratory (CSHL) for all 471 specimens in a double-blinded experiment and clinical correlates evaluated. TOP2A status was also evaluated by FISH at MSKCC and CGH at CSHL in the subset of 64 HER2 2+ by IHC, HER2 FISH-positive specimens. Individual genome profiles by CGH were examined for 20 HER2 and TOP2A FISH co-amplified specimens.Results: 45 specimens had results available for analysis, 20 of which were amplified for both HER2 and TOP2A by FISH. By CGH: 6/20 (30%) were not amplified for HER2 or TOP2A; 4/20 (20%) had homogeneous amplification of HER2 and TOP2A; 8/20 (40%) had HER2 &amp;gt; TOP2A amplification; and 2/20 (10%) had TOP2A &amp;gt; HER2 amplification. Individual genome profiles around HER and TOP2A were examined by CGH. Marked heterogeneity was observed across specimens.Conclusions: CGH at the genome level suggests that current dichotomization strategies for classifying HER2 and TOP2A status appear to incompletely describe and represent the heterogeneity of genomic lability in these regions. The dichotomization of gene amplification results by FISH may contribute to the discordance demonstrated in reported some clinical studies. Studies exploring clinical correlates are underway. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3165.
A case of cold-dependent exercise-induced anaphylaxis
Authors: M. Ii, K. Sayama, M. Tohyama, K. Hashimoto
Journal: British Journal of Dermatology (2002)

Summary Exercise‐induced anaphylaxis (EIA) is a form of physical urticaria that is induced by exercise. A 16‐year‐old Japanese boy had a 4‐year history of recurrent wealing and dyspnoea after physical exercise such as jogging, playing handball or riding a bicycle in winter. The episodes were not associated with ingestion of foods including wheat or soya bean. A provocation test, with 15 min of exercise and 2 min of cold stimulation immediately before or immediately after the exercise, elicited a weal that was localized to the test area. A challenge test with ingestion of boiled soya beans and exercise did not elicit a weal. Therefore, in this case, cold exposure, but not food ingestion, was essential for inducing EIA. Cold‐dependent EIA is different from cold urticaria, food‐dependent EIA, cholinergic urticaria and cold‐induced cholinergic urticaria, and may be a distinct entity.
US report calls for tighter controls on complementary medicine
Authors: C. Marwick
Journal: BMJ (2002)

Complementary medical treatments such as acupuncture, massage, and herbal and nutritional treatments must be evaluated with the same standards of quality, rigour, and ethics as conventional treatments, states the US Commission on Complementary and Alternative Medicine.

“First class scientific research is crucial to helping people—and those who care for them—make the wisest healthcare decisions,” said Dr James Gordon, the commission's chairman.

The commission, established two years ago by President Bill Clinton, was charged with making legislative and administrative recommendations to help develop public policies that would maximise the benefits, if any, …
COMPARISON OF RENAL FUNCTION AFTER SURGICAL VERSUS ENDOVASCULAR ANEURYSM REPAIR IN PATIENTS WITH ABDOMINAL AORTIC ANEURYSM AND CHRONIC RENAL FAILURE
Authors: Jung–Woo Son, Young–Guk Ko, Dong–Ho Shin, Jung–Sun Kim, Byeong–Keuk Kim, Myeong–Ki Hong, Yang Soo Jang, Donghoon Choi
Journal: Journal of the American College of Cardiology (2013)
PELLAGRA-LIKE SKIN LESIONS APPEARING IN THE COURSE OF A KETOGENIC DIET
Authors: Riley H. Guthrie
Journal: JAMA (1930)

The case here reported illustrates a relatively new complication—a dietary deficiency syndrome—due to poorly supervised ketogenic diet. B. R., a woman, aged 20, single, the only child of living and healthy parents, was reared in comfortable circumstances. Her early development was uneventful except for whooping cough at 1½ years, and measles at 8 years. There was nothing relevant in the family history. Nocturnal convulsions were first observed at 14. Various methods of treatment were tried in her case. At 16 she was given glandular therapy in the form of whole gland pituitary substance and thyroid extract because her basal metabolic rate was —24 per cent and she was slightly overweight. At that time she presented some vaguely described neurologic signs; i. e., some cranial nerve involvement and positive Babinski reflex on the left. About this time her tonsils were removed. The convulsions gradually became more frequent, both nocturnal and diurnal.
Medical Professional Liability and the Delivery of Obstetrical Care
Authors: Victoria P. Rostow, Marian Osterweis, Roger J. Bulger
Journal: New England Journal of Medicine (1989)

ON October 11, 1989, the Institute of Medicine of the National Academy of Sciences released a report on a two-year study of the effects of medical professional liability on the delivery of obstetrical care.1 The report, which is summarized below, and its companion volume of supporting material set forth the deliberations of an interdisciplinary committee of 14 experts. To carry out its objectives, the committee commissioned more than 20 papers from distinguished specialists in various fields, commissioned three surveys to gather new data, and reviewed more than 50 state and national surveys. As part of its data collection, the committee . . .
Virus Hepatitis with Features of Prolonged Bile Retention
Authors: S. Shaldon, S. Sherlock
Journal: BMJ (1957)

LUPUS ERYTHEMATOSUS MEDITJOURNALPrevious work has shown that a gamma-globulin fraction is responsible for the L.E. cell phenomenon of Hargraves, a part of which involves alteration of the nuclear material of white cells.This suggests that the L.E. cell factor is of an antibody nature, and the present demonstration in tissue-cell nuclei of a fixed globulin derived from L.E. positive serum adds sup- port to this hypothesis.The present work also confirms a recent finding of _____________________________, Mellors et al.Pso.6.-Ntin-specsfic fluoreacence of (1957), w h o d e - cytoplasmic granules in certain leucocytes scribed specific (? eosinophils).Unfixed blood film pre-localization of treated wvth normal serum, then stained fluorescein -conju- with conjugate.Nuclei remam nonfluorescent.( x 480.) gated antiglobulinserum in the nuclei of the white cells in an L.E. cell preparation.It thus seems very likely that the " L.E. factor " active against leucocytes is also the factor reacting with the tissue-cell nuclei reported here.Further work may show whether the existence in lupus erythematosus of an immunological mechanism involving tissue-cell nuclei can account for the presence of altered nuclear material in this disease.We wish to acknowledge the help of Dr. E.
The Child with Frequent Colds
Authors: M. L. Poston
Journal: BMJ (1946)

3-Methylindole (3MI) is a naturally occurring pulmonary toxin that requires metabolic activation. Previous studies have shown that 3MI-induced pneumotoxicity resulted from cytochrome P-450-catalyzed dehydrogenation of 3MI to an electrophilic methylene imine (3-methyleneindolenine), which covalently bound to cellular macromolecules. Multiple cytochrome P-450s are capable of metabolizing 3MI to several different metabolites, including oxygenated products. In the present study, the role of human CYP2F1 in the metabolism of 3MI was examined to determine whether it catalyzes dehydrogenation rather than hydroxylation or ring oxidation. Metabolism was examined using microsomal fractions from human lymphoblastoid cells that expressed the recombinant human CYP2F1 P-450 enzyme. Expression of CYP2F1 in the lymphoblastoid cells proved to be an appropriate expression system for this enzyme. Products were analyzed using HPLC and the mercapturate, 3-[(<i>N</i>-acetylcystein-<i>S</i>-yl)methyl]indole, of the reactive intermediate was identified and quantified. Product analysis showed that human CYP2F1 efficiently catalyzed the dehydrogenation of 3MI to the methylene imine without detectable formation of indole-3-carbinol or 3-methyloxindole. High substrate concentrations of 3MI strongly inhibited production of the dehydrogenated product, a result that may indicate the existence of mechanism-based inhibition of CYP2F1 by 3MI. Recombinant CYP2F1 demonstrated remarkable selectivity for the bioactivation of 3MI to the putative dehydrogenated reactive electrophile. Bioactivation of naphthalene to its pneumotoxic epoxide by CYP2F1 was also demonstrated.
Middle-Lobe Atelectasis Due to Endobronchial Sarcoidosis, with Hypercalcemia and Renal Impairment
Authors: Gerald J. Goldenberg, Richard H. Greenspan
Journal: New England Journal of Medicine (1960)

OVER a decade ago, Graham, Burford and Mayer1 introduced the term "middle-lobe syndrome" to describe a state of chronic atelectasis and pneumonitis in the middle lobe due to bronchial compression by enlarged hilar lymph nodes. In 1937 Brock, Cann and Dickinson2 stressed the occurrence of atelectasis from bronchial compression by tuberculous hilar lymphadenopathy in children. In 1946 Brock3 explained the vulnerability of the middle-lobe bronchus to this process on the basis of its length, pliability, acute angle of origin and surrounding cuff of lymph nodes draining not only the right middle lobe but also the right lower lobe. Brock4 emphasized . . .
Hemagglutinating Virus of Japan (HVJ) Envelope Vector as a Versatile Gene Delivery System
Authors: Yasufumi Kaneda, Toshihiro Nakajima, Tomoyuki Nishikawa, Seiji Yamamoto, Hiroyuki Ikegami, Naho Suzuki, Hitomi Nakamura, Ryuichi Morishita, Hitoshi Kotani
Journal: Molecular Therapy (2002)

We have developed a simple method for converting the lipid envelope of an inactivated virus to a gene transfer vector. Hemagglutinating virus of Japan (HVJ; Sendai virus) envelope vector was constructed by incorporating plasmid DNA into inactivated HVJ particles. This HVJ envelope vector introduced plasmid DNA efficiently and rapidly into various cell lines, including cancer cells and several types of primary cell culture. Efficiency of gene transfer was greatly enhanced by protamine sulfate and centrifugation. Fluorescein isothiocyanate-labeled oligodeoxynucleotides (FITC-ODN) were also delivered to cells at > 95% efficiency. When HVJ envelope vector was injected into organs directly, reporter gene expression was observed in organs including liver, brain, skin, uterus, tumor masses, lung, and eye. When HVJ envelope vector containing luciferase gene was injected into mouse tail vein, luciferase gene expression was detected primarily in spleen. FITC-ODN were also delivered to spleen cells by intravenous injection of HVJ envelope. These results suggest that HVJ envelope vector will be useful for both ex vivo and in vivo gene therapy experiments. We have developed a simple method for converting the lipid envelope of an inactivated virus to a gene transfer vector. Hemagglutinating virus of Japan (HVJ; Sendai virus) envelope vector was constructed by incorporating plasmid DNA into inactivated HVJ particles. This HVJ envelope vector introduced plasmid DNA efficiently and rapidly into various cell lines, including cancer cells and several types of primary cell culture. Efficiency of gene transfer was greatly enhanced by protamine sulfate and centrifugation. Fluorescein isothiocyanate-labeled oligodeoxynucleotides (FITC-ODN) were also delivered to cells at > 95% efficiency. When HVJ envelope vector was injected into organs directly, reporter gene expression was observed in organs including liver, brain, skin, uterus, tumor masses, lung, and eye. When HVJ envelope vector containing luciferase gene was injected into mouse tail vein, luciferase gene expression was detected primarily in spleen. FITC-ODN were also delivered to spleen cells by intravenous injection of HVJ envelope. These results suggest that HVJ envelope vector will be useful for both ex vivo and in vivo gene therapy experiments.
Treatment, and Retreatment, of Cushing's Disease
Authors: Robert D. Utiger
Journal: New England Journal of Medicine (1997)

The proximate cause of the clinical manifestations of Cushing's syndrome — obesity, facial plethora, hirsutism, hypertension, muscle weakness, lethargy, and depression — is excess cortisol secretion. Few of these clinical manifestations are specific to the syndrome, but the presence of several of them should lead clinicians to suspect it (and when many are present, the changes may be dramatic). The next steps are to confirm the presence of cortisol excess and then to determine its cause.The predominant causes of Cushing's syndrome are excess corticotropin secretion, whether from a pituitary tumor (Cushing's disease) or a nonendocrine tumor, and adrenal tumors, . . .
Manual for Authors and Editors: Editorial Style and Manuscript Preparation
Authors: Edward Huth
Journal: JAMA (1982)

Manuscript editors working on as many journals as are published by the American Medical Association must come to hundreds of decisions every day on proper use of abbreviations and symbols, correct punctuation, clear structure of tables, and other aspects of publication style. The AMA wants uniformity in style among its journals, and this uniformity can come only from adherence to the same rules. This<i>Manual</i>provides those rules, in 110 of its 184 pages, and shows how they are applied, with examples drawn mostly from medical and other scientific texts. Aspects of style covered include abbreviations and symbols, accents and diacritic marks, capitalization, Greek letters, mathematical and statistical expressions, nomenclature, numbers, plural terms, punctuation, units of measure, word choice, special uses of typefaces, and formats for main structural units of papers (title, authorship statement, footnotes and annotations, tables, legends, and references). The opening 31 pages touch—lightly and, for the most
Mitosis Trumps T Stage and Proposed International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society Classification for Prognostic Value in Resected Stage 1 Lung Adenocarcinoma
Authors: Edwina Elizabeth Duhig, Andrew Dettrick, David Burleigh Godbolt, John Pauli, Anthony van Zwieten, Aaron Richard Hansen, Ian Anthony Yang, Kwun Meng Fong, Belinda Edith Clarke, Rayleen Veronica Bowman
Journal: Journal of Thoracic Oncology (2014)
Government gives NHS 250m for UK winter health pressures
Authors: J. Warden
Journal: BMJ (1998)

An immediate injection of £250m ($400m) to help the NHS meet winter pressures has been announced by Britain's chancellor of the exchequer, Gordon Brown. This is less than last year's allocation of £300m for the same purpose, which was considered instrumental in avoiding a winter crisis, although the weather was mild and waiting lists for elective surgery rose sharply during this period.

The new funding amounts to £209m for England, £22m …
IMPACT OF ANEMIA IN MEN AND WOMEN WITH ST-SEGMENT ELEVATION MYOCARDIAL INFARCTION: THE HORIZONS-AMI TRIAL
Authors: Kenichi Tsujita, Eugenia Nikolsky, Alexandra J. Lansky, Louise Gambone, Lynn Vandertie, Adriano Caixeta, George Dangas, Bruce R. Brodie, Dariusz Dudek, Martin Mö;ckel, Andrzej Ochala, Roxana Mehran, Gregg W. Stone
Journal: Journal of the American College of Cardiology (2010)
Routine programmed electrical stimulation in survivors of acute myocardial infarction for prediction of spontaneous ventricular tachyarrhythmias during follow-up: Results, optimal stimulation protocol and cost-effective screening
Authors: John P. Bourke, David A.B. Richards, David L. Ross, Elizabeth M. Wallace, Mark A. McGuire, John B. Uther
Journal: Journal of the American College of Cardiology (1991)
Pre-B cells and other possible precursor lymphoid cell lines derived from patients with X-linked agammaglobulinemia
Authors: SM Fu, JN Hurley, JM McCune, HG Kunkel, RA Good
Journal: The Journal of Experimental Medicine (1980)

A group of unique Epstein-Barr virus-containing cell lines was derived from the bone marrow of three patients with X-linked agammaglobulinemia. Efforts to obtain cell lines from the peripheral blood of these patients were uniformly unsuccessful. Immunofluorescence analyses as well as biosynthetic studies with [(35)S]methionine indicated unusual patterns of Ig synthesis in many of these bone marrow derived lines. Seven of the lines were of particular interest in that two produced no Ig of any type; two others showed no Ig by fluorescence but small amounts by [(35)S]methionine labeling; one expressed only cytoplasmic μ chains without any evidence of light chain synthesis, and two produced primarily μ chains with only slight amounts of light chains. One of the lines without membrane or cytoplasmic Ig studied in detail grew like a typical lymphoid line and was carried in intermittent culture over a period of 2 yr without Ig expression. One line grew quite differently and resembled the round cell type described previously, which has been obtained from a variety of sources. The cell line with cytoplasmic μ chains and no light-chain expression had the characteristic properties of pre-B cells. Three normal type Ig-producing cell lines also were obtained from the patients. The accumulated evidence obtained in the present study indicates that these unusual cell lines represent normal precursor cells of the B-cell lineage; these grew out in these cases because of the virtual absence of mature B cells that ordinarily overgrow the culture system. However, the possibility that in certain instances they reflect abnormal Ig synthesis characteristic of the disease has not been ruled out.
Constitutive expression of interleukin 14 (IL-14) in transgenic mice leads to enhanced responses to vaccinations and autoimmunity
Authors: C. Xu, C. Zhang, L. Shen, D.E. Skyes, H. Zeng, S. Tang, P.D. Soloway, S. Brooks, S. Sharma, R.J. Ford, Y. Lin-Lee, J. Horn, L. Martin, L. Ludwig, P. Liang, J.L. Ambrus
Journal: Journal of Allergy and Clinical Immunology (2005)
Variceal Bleeding and Portal Hypertension: New Lights on Old Horizon
Authors: D. K. Bhasin, I. Siyad
Journal: Endoscopy (2004)

New clinical, endoscopic, and imaging modalities for diagnosing varices and predicting bleeding are being investigated. Transnasal endoscopy and ultrathin battery-powered esophagoscopes are being used to improve patient comfort and compliance. Patients who respond to portal pressure-reducing drugs not only have a reduced risk of bleeding, but also a reduced risk of developing other complications, with improved survival. Nitrates have been shown to have no definite role in primary prophylaxis against variceal bleeding. The hemodynamic response to treatment has an independent prognostic value for the risk of variceal bleeding. Newer drugs have been investigated for reducing the hepatic venous pressure gradient, but with little success. Survival after bleeding has increased due to improved patient care and technological advances. Combined radiographic and endoscopic management of gastric varices is evolving and appears to be promising. Nonvariceal bleeding from portal hypertensive gastropathy is increasingly being recognized as a potential cause of bleeding in patients with portal hypertension, and pharmacotherapy with octreotide appears to be promising for the treatment of this condition. Variceal band ligation in children has been found to be as safe and effective as in adults.
Exploring the Uses of RNAi — Gene Knockdown and the Nobel Prize
Authors: René Bernards
Journal: New England Journal of Medicine (2006)

The Nobel Prize in Physiology or Medicine was awarded this year to Andrew Fire (Stanford University School of Medicine) and Craig Mello (University of Massachusetts Medical School) for their discovery of a new form of gene silencing. Nearly 9 years ago, Fire and Mello and their colleagues reported that exposing cells of the nematode Caenorhabditis elegans to double-stranded RNA resulted in specific and efficient gene silencing.1 They also observed that double-stranded RNA is far more potent than sense or antisense RNA in silencing the gene that shares its sequence, and they dubbed the silencing process "RNA interference" (RNAi). Because RNAi . . .
Thunderstorms and iPods — Two Reports of the Same Case
Authors: Eric J. Heffernan, Peter L. Munk, Luck J. Louis
Journal: New England Journal of Medicine (2007)

To the Editor: After we submitted our letter about thunderstorms and iPods to the Journal (July 12 issue),1 other authors from our hospital published a separate report about the same case,2 unbeknownst to us when we submitted our letter. Their report was published in May, 3 months after we completed the literature search for our letter. We regret this duplication. We were unaware of the other author group.
Renal and hormonal responses to repeated treatment with enalapril in non-azotemic cirrhosis with ascites
Authors: Akihiro Ohnishi, Shigeto Murakami, Makoto Harada, Kazuhiro Osaka, Kohji Wada, Masazumi Odagiri, Takumi Tsuchiya, Teruji Tanaka
Journal: Journal of Hepatology (1994)
Quantitating the Occult
Authors: Walter L. Peterson, John S. Fordtran
Journal: New England Journal of Medicine (1985)

Physicians are faced all too frequently with middle-aged patients who present with vague abdominal problems or rectal bleeding and who on evaluation are found to have colon cancer. A discouraging proportion of these relatively young people already have local spread of the disease or metastases to the liver.Spurred on by such cases, many physicians encourage asymptomatic patients who are over 40 to undergo annual testing for occult blood in stool as part of a screening program, in the hope that colon cancers may be detected at an early, curable stage or that adenomatous polyps may be found and removed . . .
Frequent occurrence of BCL6 rearrangements in nodular lymphocyte predominance Hodgkin lymphoma but not in classical Hodgkin lymphoma
Authors: Iwona Wlodarska, Peet Nooyen, Brigitte Maes, José I. Martı́n-Subero, Reiner Siebert, Patrick Pauwels, Chris De Wolf-Peeters, Anne Hagemeijer
Journal: Blood (2002)