tbuckley/cabot-search huggingface dataset:
Abstract 2353: A comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer
Authors: Levi Waldron, Markus Riester, Michael Birrer, Giovanni Parmigiani
Journal: Cancer Research (2014)

Abstract Numerous gene signatures of patient prognosis for late-stage, high-grade serous ovarian cancer (HSOC) have been proposed, but diverse data and methods make these difficult to compare or prioritize for clinical application. However, the corresponding volume of publicly available expression data creates an opportunity to validate previous findings and to develop more robust signatures. To establish the current state of HSOC prognostic gene signatures, we undertook a systematic review and meta-analysis of the publicly available microarray data and published prognostic gene signatures. This effort generated a curated database of 1,319 clinically annotated HSOC microarray assays from 10 studies (Ganzfried et al., DATABASE 2013) and implementations of 14 published prognostic signatures for evaluation in independently available data. For each published prognostic signature we evaluated 1) its reproducibility, 2) its prognostic accuracy for overall survival in independent datasets, and 3) the prognostic value of the genes used in each signature relative to random gene sets. Twelve published models performed better than 97.5% of randomized risk scores, and six out-performed 97.5% of random signatures of the same size trained on the same data. The four top-ranked models achieved overall validation C-Indices of 0.56 to 0.60, and shared anti-correlation with expression of immune response pathways. Most models demonstrated lower accuracy in new datasets than in validation sets presented in their publication. This analysis provides definitive support for several prognostic models, but confirms that these require improvement to be of clinical value. This work addresses outstanding controversies in the ovarian cancer literature, including whether the prognostic signature proposed by The Cancer Genome Atlas Consortium (Nature 2011) improved on existing signatures, the impact of batch effects on a frequently re-used, high-profile dataset (Dressman et al., J Clin Oncol 2007), and the prognostic value of a recently proposed DNA damage repair signature (Kang et al., J Natl Cancer Inst 2012). Finally, this work provides a reproducible framework for meta-analytic evaluation of gene signatures. Citation Format: Levi Waldron, Markus Riester, Michael Birrer, Giovanni Parmigiani. A comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2353. doi:10.1158/1538-7445.AM2014-2353
Elimination From the Body of Tobacco Products by Smokers and Passive Smokers
Authors: Daniel W. Sepkovic
Journal: JAMA (1986)

<h3>To the Editor.—</h3> Epidemiologic studies have indicated an association of environmental smoke exposure with tobacco-related disease.<sup>1-4</sup>The composition of tobacco sidestream smoke differs significantly from that of mainstream smoke.<i>N</i>-nitrosamines, benzo[<i>a</i>]pyrene, carbon monoxide, nicotine, and heavy metals are more abundant in sidestream than in mainstream smoke.<sup>5</sup> Exposure to such harmful chemical compounds in heavily polluted environments may constitute a health risk to passively exposed individuals. By measuring cotinine in plasma and in urine, we have estimated the rate of elimination of this end product of nicotine metabolism in both smokers and passively exposed nonsmokers. Ten smokers reported to the clinic each day at 9:30 AM for blood sampling. At noon on day 5, the subjects quit smoking. Blood samples were taken daily from day 5 through day 12. All urine voided was collected daily throughout the study period. Four nonsmokers, aged 25 to 35 years,
Genes Outside the Nucleus Have Large Effects on Cell Metabolism
Authors: Tracy Hampton
Journal: JAMA (2013)

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
Yet Another Reason to Quit
Authors: Joan Stephenson
Journal: JAMA (1998)

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
Blackwater Fever in West Africa
Authors: E. W. Skipper, G. L. Haine
Journal: BMJ (1945)

For a period of 20 months we were stationed at a general hos- pital in one of the West African colonies.This hospital was situated in well-drained uplands, its precincts being practically free of the anopheline mosquito, but within two miles the hills descended-into large areas of swampy ground where subtertian malaria was rife.Most of the cases of malaria and all the cases of blackwater fever treated in this hospital came from these areas.During the 20-month period 2,355 cases of sub- tertian malaria in British and Allied personnel were admitted, the majority being from the British Army.In the same interval 7 cases of blackwater fever were admitted.There were no deaths from either disease.These cases of blackwater fever are presented because it is felt that this disease is of special importance while British and Allied troops are living and fighting in countries in which it occurs, and because it is not very rare for individuals to develop it after return to the United Kingdom from the Tropics.Such a case, rapidly fatal, was seen by one of us.An account of the clinical features and treatment of subtertian malaria in British troops in West Africa has already been given by Hughes and Bomford (1944).Blackwater fever is a disease characterized by a sudden intravascular haemolysis, with the liberation of oxyhaemoglobin in the plasma.From this, methaemoglobin and methaemalbumin (" pseudo-methaemoglobin ") are formed.Oxyhaemoglobin and methaemoglobin are excreted in the urine together with acid haematin, these blood pigments imparting the typical porter or stout colour to the urine.Methaemoglobin, with its much larger molecule, is never excreted.The two most important characteristics of the dis.ease-namely, the haemolysis and the anuria-will be separately discussed.Relationship to Malaria Blackwater fever is now universally regarded as a complication of malaria, especially of the subtertian form.Stephens (1937) was able to collect only 7 cases in which it was asso- ciated with benign tertian or quartan fever.A fatal case fol- lowing P. ovdle infection is quoted by Fairley (1939).It is
Poisoning: Toxicology, Symptoms and Treatments
Authors: Edward Tabor
Journal: JAMA (1987)

This is the newest revision of a well-known textbook and reference on poisoning. Its readable style and its wide-ranging contents must be weighed against the apparent shortcomings of this revision. The book gives the impression of not having been completely brought up-to-date. It contains references to the 17th and 18th editions of the<i>United States Pharmacopeia</i>, whereas the current edition is the 21st. It mentions a government agency by a name that was eliminated in a reorganization four years ago. It discusses an antidote for overuse of iodine therapy for corneal herpes simplex, a therapy that has not been recommended in more than 15 years. It includes diagnostic tests, such as thymol turbidity and cephalin flocculation, that have not been used for almost 20 years. It refers to the discovery of the transfer of antibiotic resistance between bacteria as having occurred "more recently," although this is a discovery that was
PROLONGED USE OF CHLOROFORM IN A CASE OF INFANTILE CONVULSIONS
Authors: W.C. Williamson
Journal: BMJ (1856)

and not by reflex action from the direct impression of the spirt on the nerves of the stomach.Another question presents itself, Whether the brandy would have had so powerful an effect if the diarrhea had not been present?which fact also explains the rapid di- gestion and absorption of the arrow-root.Again; Had the brandy any influence in augmenting the action of the aperient powder (of which the child's elder aister took the larger portion, without any unusual effect), so as to produce a state of dysentery requiring special
The Residual Tumor Autophagy Marker LC3B Serves as a Prognostic Marker in Local Advanced Breast Cancer after Neoadjuvant Chemotherapy
Authors: Sheng Chen, Yi-Zhou Jiang, Liang Huang, Ruo-Ji Zhou, Ke-Da Yu, Yin Liu, Zhi-Ming Shao
Journal: Clinical Cancer Research (2013)

Abstract Purpose: This study sought to investigate the prognostic value of the autophagy marker microtubule–associated protein chain 3B (LC3B) in patients with residual tumors after neoadjuvant chemotherapy (NCT) for locally advanced breast cancer (LABC). Patients and Methods: The expression of LC3B in residual breast cancer cells was assessed by immunohistochemistry in surgical specimens from 229 patients diagnosed with histologically proven invasive breast cancer. All patients underwent NCT followed by mastectomy and were considered nonpathologic complete responders (non-pCR) after a pathologic evaluation. The prognostic value of various clinicopathologic factors was evaluated. Results: The LC3B density was similar between the peripheral and central area of the tumors (P = 0.328) but was significantly lower in the extratumoral area (P &amp;lt; 0.001 and P &amp;lt; 0.001, respectively). Furthermore, LC3B density, which correlated with Beclin-1 expression, Ki-67 index, and breast cancer subtype, served as an independent prognostic factor for both relapse-free survival (RFS; P = 0.012) and overall survival (OS; P = 0.008); the prognostic value of LC3B was most significant in triple-negative patients. Using a combination of LC3B expression and the status of residual involved lymph nodes, the patients were classified into four groups with different risks of relapse and death (P &amp;lt; 0.001 for RFS and P = 0.003 for OS). Conclusion: LC3B can be used as a prognostic marker in patients with non-pCR after NCT for breast cancer, which highlights the importance of autophagy in the biologic behavior of chemoresistant cancer cells. Furthermore, evaluating and targeting autophagy in the neoadjuvant setting may help prevent disease relapse in patients with non-pCR. Clin Cancer Res; 19(24); 6853–62. ©2013 AACR.
Anaphylaxis and Immunologic Insulin Resistance in a Diabetic Woman with Ketoacidosis
Authors: Jonathan M Ross, Mandakolathur R Murali, Teresita C DeLara, Robert G Cheron
Journal: Diabetes Care (1984)

A diabetic woman presented with diabetic ketoacidosis after demonstrating immediate-type hypersensitivity to heterologous insulin. She had had interrupted insulin therapy in the past. Insulin requirements during the course of treatment for the acidosis suggested marked resistance, with 50,000 U of insulin needed in the first 36 h. Anaphylaxis requiring intubation and emergency treatment developed after intravenous purified pork insulin was administered. Elevated titers of insulin-specific IgG (441.6 U/L serum) demonstrated immunologic insulin resistance. Positive intradermal skin tests for beef and pork insulins and detection of insulin-specific IgE by RAST assay revealed concurrent immediate-type allergy. A review of the literature revealed the unique occurrence in this patient of simultaneous ketoacidosis, insulin allergy, anaphylaxis, and immunologic resistance. Interrupted insulin therapy in susceptible individuals remains a potential danger, even with the availability of purified insulin preparations.
Abstract 4401: Antibody-mediated targeting of the uPA proteolytic activity neutralizes uPA functions <i>in vivo</i>
Authors: Ida K. Lund, Annika Jögi, Birgitte Rønø, Morten G. Rasch, Leif R. Lund, Kasper Almholt, Henrik Gårdsvoll, Niels Behrendt, John Rømer, Gunilla Høyer-Hansen
Journal: Cancer Research (2010)

Abstract Urokinase-type plasminogen activator (uPA) plays a central role in tissue remodeling processes, during both normal physiological conditions and cancer progression. Most of our understanding of the role of uPA in vivo is derived from studies using gene-targeted uPA-deficient mice. To enable in vivo studies on the acute and specific interference with uPA functionality in adult mice, we have now developed murine monoclonal antibodies (mAbs) directed against murine uPA by immunization of uPA-deficient mice with the recombinant protein. Guided by ELISA, Western blotting, SPR and enzyme kinetic analyses, we have selected two highly potent and inhibitory anti-uPA mAbs (mU1 and mU3). Both mAbs recognize epitopes located on the B-chain of uPA that encompasses the catalytic site. In activity assays in vitro, mU1 blocked uPA-catalyzed plasminogen activation as well as plasmin-mediated pro-uPA activation, whereas mU3 only was directed against the first of these reactions. We provide evidence that acute disruption of uPA activity in the adult mouse was effective with mU1, but not mU3, because only mU1 rescued mice treated with a uPA-activable anthrax pro-toxin. Moreover, systemic administration of mU1 (i) delayed wound healing in tissue-type plasminogen activator (tPA)-deficient mice, and (ii) impaired uPA-mediated hepatic fibrinolysis in tPA-deficient mice, resulting in a phenotype mimicking that of uPA;tPA double-deficient mice. Importantly, these results demonstrate the specific antagonist-directed targeting of mouse uPA at the enzyme activity level in normal physiological processes in vivo. Preliminary results indicate that wild-type mice, which have been transplanted with murine Lewis lung carcinoma cells, display significant reduction in primary tumour growth, when treated with mU1 as compared to placebo-treated (i.e. PBS-treated) littermates. We thus suggest that mU1 is an excellent mAb candidate for therapeutic intervention studies in mouse cancer models. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4401.
Freud: The Man and the Cause
Authors: Harry Trosman
Journal: JAMA (1981)

Readers interested in the life of Freud owe a debt of gratitude to Ronald W. Clark, the author of<i>Freud: The Man and the Cause</i>. He has presented a fair account that is not burdened by ideological bias. While appreciative of Freud's achievement, he has remained free of idealizing tendencies and has indicated where the data for understanding are incomplete. Although the book is written for popular consumption, those who are scholars of Freud's life will be enriched by the contents as well. New material, published in neither Jones' biography nor in Schur's account, appears in print for the first time. Letters written by Freud to an adolescent friend, Eduard Silberstein, which are now in the Library of Congress, Washington, DC, and in Colchester, England, as well as the correspondence between Freud and a nephew, Samuel Freud of Manchester, England, add further dimensions to Freud's personality. There is an unknown
NECESSITY OF VOCAL PHYSIOLOGY AND SYSTEMATIC VOICE TRAINING IN OUR PUBLIC SCHOOLS AND COLLEGES FOR THE PREVENTION OF DISEASES OF THE LARYNX.Address on Laryngology. Read at the Forty-third Annual Session of the State Medical Society of Pennsvlvania, held at Williamsport, Pa., May 16 to 19, 1893.
Authors: J. WALTER PARK
Journal: JAMA (1893)

The State Medical Society of Pennsylvania in 1883 passed a resolution that there should be annual alternating addresses on the subjects of ophthalmology, otology and laryngology, but for various reasons laryngology was omitted in 1889, hence the first and last address on this subject was delivered by my esteemed friend, Dr. Charles E. Sajous of Philadelphia, in this city seven years ago. In looking over his very able address, I notice he pointed out to you the importance and relationship of laryngology to the general practitioner, as well as some of the advancements in laryngology up to that time. I will endeavor to-day to give you a continuation of the advancements on this subject, but in a somewhat different line of thought, viz: the necessity of systematic physical voice training in our public schools and colleges for the prevention of some of our most prevalent diseases of the larynx. This
Microangiopathic Hemolytic Anemia in Defibrination Syndromes.
Authors: Robert J. Jacobson
Journal: Annals of Internal Medicine (1970)

Meeting Abstracts1 May 1970Microangiopathic Hemolytic Anemia in Defibrination Syndromes.Robert J. Jacobson, M.B., B.Ch., Dudley P. Jackson, M.D., F.A.C.P.Robert J. Jacobson, M.B., B.Ch.Search for more papers by this author, Dudley P. Jackson, M.D., F.A.C.P.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-72-5-794_3 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptFragmentation of red blood cells has been reported in association with disseminated intravascular coagulation. The proportion of red blood cells showing morphologic alterations associated with fragmentation was graded from 0 to III in smears of peripheral blood from 40 patients with defibrination. All patients had hypofibrinogenemia (mean, 70 mg/100 ml), and most had thrombocytopenia, but none had hypertension. Smears from 23 (58%) patients revealed no evidence of microangiopathic hemolytic anemia. The diagnoses in these patients were: 10 with abruptio placenta; 6 with carcinoma; 4 with intrauterine fetal death; and 1 each with septicemia, purpura fulminans, and Rocky Mountain spotted fever.... This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: Baltimore, Md. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics Cited ByThe Syndrome of Intravascular Coagulation 1 May 1970Volume 72, Issue 5Page: 794-794KeywordsBlood cellsDisseminated intravascular coagulationFetal deathHemolytic anemiaHypertensionPlacentaRed blood cellsRocky Mountain spotted feverSepsis Issue Published: 1 May 1970 PDF DownloadLoading ...
Croatian academic is found guilty of plagiarism
Authors: Geoff Watts
Journal: BMJ (2007)

A Croatian government committee that is investigating a senior academic and obstetrician has ruled unanimously that allegations of plagiarism in his published work are well founded.

In an opinion issued on 15 May the Committee for Ethics in Science and Higher Education declared that Asim Kurjak of Zagreb University Medical School was guilty of “violations of the [committee's] ethics code . . . and of common norms in biomedical publishing.”

The allegations were originally made in the BMJ by Iain Chalmers of the James Lind Library in Oxford ( BMJ 2006;333:594-7 doi: 10.1136/bmj.38968.611296.F7).

The saga began in the late 1980s when Dr Chalmers was preparing a systematic review of epidural anaesthesia. He noticed that much of the text and data in …
The effect of topical benzamil and amiloride on nasal potential difference in cystic fibrosis
Authors: H.c. Rodgers, A.J. Knox
Journal: European Respiratory Journal (1999)

The electrochemical defect in the bronchial epithelium in cystic fibrosis (CF) consists of defective chloride secretion and excessive sodium reabsorption. The sodium channel blocker, amiloride, has been shown to reversibly correct the sodium reabsorption in CF subjects, but long term studies of amiloride have been disappointing due to its short duration of action. Benzamil, a benzyl substituted amiloride analogue, has a longer duration of action than amiloride in cultured human nasal epithelium. The results of the first randomized, placebo controlled, double blind, crossover study are reported here comparing the effects of benzamil and amiloride on nasal potential difference (nasal PD) in CF. Ten adults with CF attended on three occasions. At each visit baseline nasal PD was recorded, the drug (amiloride 1 x 10(-3) M, benzamil 1.7 x 10(-3) M, or 0.9% sodium chloride) was administered topically via a nasal spray, and nasal PD was measured at 15, 30 min, 1, 2, 4 and 8 h. Results were expressed as maximum change in nasal PD from baseline (PDmax), time for PDmax to return to 50% of baseline (t0.5), and the area under the curve (AUC). PDmax values for benzamil (20.6+/-0.9 mV) and amiloride (20.3+/-1.6 mV), were similar. The duration of effect was much longer for benzamil as measured as either AUC or t0.5 AUC values were 11.8+/-1.6 mV for benzamil, 2.8+/-0.4 mV for amiloride and 0.6+/-0.4 mV for placebo. The AUC value for benzamil was significantly greater than amiloride (95% confidence interval (CI) for the difference 5.3-12.7 mV, p&lt;0.0001). t0.5 values were 4.3+/-0.7 h for benzamil and 0.6+/-0.1 h for amiloride (95% CI for the difference 2.0-5.3 h, p&lt;0.001). It is concluded that benzamil has a similar maximal effect to amiloride but a more prolonged duration of action on nasal potential difference in cystic fibrosis. Benzamil may be a useful sodium channel blocker for the long-term treatment of the biochemical defect in the lungs of patients with cystic fibrosis.