tbuckley/cabot-search huggingface dataset:
Abstract 5332: Comparison of variant calling from whole exome and transcriptome sequencing using CLC Cancer Research Workbench
Authors: Anne Arens, Anne-Mette K. Hein, Uwe Appelt, Anika Joecker, Søren Mønsted, Bjarne Knudsen, Naomi Thomson, Richard Lussier, Cecilie Boysen, Roald Forsberg
Journal: Cancer Research (2014)

Abstract The now commonplace application of whole exome and genome sequencing in cancer research and diagnostics has allowed for rapid identification of SNPs and InDels in protein coding regions, but neither method is able to reveal situations of incomplete penetrance. That is, while possible cancer causing allele variants can be detected with these methods, this does not mean these alleles are actually expressed. Reasons for this are various and include epigenetic effects and changes, transcription regulation mechanisms, mRNA degradation and epistasis. By contrast, transcriptome sequencing (RNA-seq) can be used to identify the alleles being expressed. This method has the additional benefits of providing insight into the transcript expression levels, expressed allele isoforms and offers the possibility of identifying instances of fusion transcripts. Such knowledge about variants expressed in tumor cells is crucial for the identification of effective drug targets. Here, we illustrate the benefits of combining whole exome sequencing with RNA-seq by analyzing whole exome and RNA-seq datasets from uveal melanoma samples with our newly developed CLC Cancer Research Workbench. This software suite enables the complete analysis of both approaches, including variant calling, followed by the comparison of the called variants. The analysis will be carried out using user-friendly, automated workflows distributed with the CLC Cancer Research Workbench. In this work, we discuss and compare variants identified in the exome and RNA-seq datasets using our algorithms, and focus particularly on variants identified in the exome data that appear not to be expressed in the tumor samples. Citation Format: Anne Arens, Anne-Mette K. Hein, Uwe Appelt, Anika Joecker, Søren Mønsted, Bjarne Knudsen, Naomi Thomson, Richard Lussier, Cecilie Boysen, Roald Forsberg. Comparison of variant calling from whole exome and transcriptome sequencing using CLC Cancer Research Workbench. [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 5332. doi:10.1158/1538-7445.AM2014-5332
Recovery from porphyria cutanea tarda with no specific therapy other than avoidance of hepatic toxins
Authors: G. C. TOPI, A. AMANTEA, D. GRISO
Journal: British Journal of Dermatology (1984)

Journal Article Recovery from porphyria cutanea tarda with no specific therapy other than avoidance of hepatic toxins Get access G. C. TOPI, G. C. TOPI Department of Experimental Dermatology, Istituto S. Maria e S. Gallicano, Via S. Gallicano 25, Rome, Italy Prof. G. C. Topi, Istituto S. Maria e S. Gallicano, Via S. Gallicano 25, Rome, Italy. Search for other works by this author on: Oxford Academic Google Scholar A. AMANTEA, A. AMANTEA Department of Experimental Dermatology, Istituto S. Maria e S. Gallicano, Via S. Gallicano 25, Rome, Italy Search for other works by this author on: Oxford Academic Google Scholar D. GRISO D. GRISO Department of Experimental Dermatology, Istituto S. Maria e S. Gallicano, Via S. Gallicano 25, Rome, Italy Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 111, Issue 1, 1 July 1984, Pages 75–82, https://doi.org/10.1111/j.1365-2133.1984.tb04019.x Published: 01 July 1984 Article history Accepted: 18 January 1984 Published: 01 July 1984
Endothelial von Willebrand factor regulates angiogenesis
Authors: Richard D. Starke, Francesco Ferraro, Koralia E. Paschalaki, Nicola H. Dryden, Thomas A. J. McKinnon, Rachel E. Sutton, Elspeth M. Payne, Dorian O. Haskard, Alun D. Hughes, Daniel F. Cutler, Mike A. Laffan, Anna M. Randi
Journal: Blood (2010)
Intensive care management of head-injured patients in Europe: a survey from the European Brain Injury Consortium
Authors: Nino Stocchetti, Kay I. Penny, Mark Dearden, Reinder Braakman, François Cohadon, Fausto Iannotti, Françoise Lapierre, Abbi Karimi, Andrew Maas, Gordon D. Murray, Juha Ohman, Lennard Persson, Franco Servadei, Graham M. Teasdale, Tomasz Trojanowski, Andy Unterberg on behalf of the European
Journal: Intensive Care Medicine (2001)
A Pilot Study on EGFR-Targeted Molecular Imaging of PET/CT With 11C-PD153035 in Human Gliomas
Authors: Jikui Sun, Li Cai, Kai Zhang, AnLing Zhang, PeiYu Pu, WeiDong Yang, Shuo Gao
Journal: Clinical Nuclear Medicine (2013)

11C-PD153035, a potent and specific ATP-competitive tyrosine kinase inhibitor (TKI) of the EGF receptor, has been developed for PET imaging of epidermal growth factor receptor (EGFR) in lung cancer. The objective of the present study was to investigate the relationship of the accumulation of 11C-PD153035 and the EGFR expression level in human gliomas and to explore whether 11C-PD153035 can be used in the molecular imaging of glioma with EGFR overexpression. Eleven patients with histopathologically proven gliomas underwent 11C-PD153035 PET/CT examination before surgery. Combining MRI with the 11C-PD153035 PET/CT image, 2 specimens from different 11C-PD153035 uptake regions of each tumor and adjacent normal brain tissue were selected as the biopsy targets through the stereotactic technique. The radioactivity concentrations were analyzed as the mathematical maximum standardized uptake value (SUVmax) in region of interest (ROI). The EGFR expression in the biopsied tissues was analyzed by immunohistochemical staining (IHC) and western blotting. The SUVmax/WM (11C-PD153035 uptake in the white matter of the contralateral normal hemisphere) ratio was used to indicate the EGFR expression level in the ROI in PET/CT, and it was correlated with the EGFR expression detected by IHC and western blot analysis. The results demonstrated that 6 of the 8 patients with glioblastoma (GBM) were obviously visualized by 11C-PD153035 PET/CT, whereas 2 patients with GBM, 1 with anaplastic astrocytoma, and 2 with oligodendroglioma did not show significant 11C-PD153035 uptake. There were positive correlations between the SUVmax/WM and the results of IHC (r = 0.955, P < 0.01) and western blotting(r = 0.889, P < 0.010). Our preliminary findings suggest that 11C-PD153035 PET/CT is a promising method for the EGFR-targeted molecular imaging of human GBM, which may be translated into the clinic to select the appropriate population of patients for EGFR-targeted therapy and to assess the early targeted therapeutic response of malignant gliomas.
Poor outcome in progressive sclerosing cholangitis after septic shock
Authors: H. Kulaksiz, D. Heuberger, S. Engler, A. Stiehl
Journal: Endoscopy (2008)

See also: Commentaire de travail de H. Kulaksiz et al., pp. 214Endoscopy 2008; 40(03): 356-357DOI: 10.1055/s-0032-1306818
Fuel homeostasis and carnitine metabolism in rats with secondary biliary cirrhosis
Authors: Stephan Krahenbuhl, Eric P. Brass
Journal: Hepatology (1991)

Energy metabolism is abnormal in patients and experimental animals with liver cirrhosis. To help better understand the abnormalities, fuel homeostasis and carnitine metabolism were studied in fed and 24-hr-starved rats with secondary biliary cirrhosis induced by bile duct ligation for 4 wk. Plasma ketone body concentrations were decreased by 67% in starved, bile duct-ligated rats compared with control rats. In contrast, plasma nonesterified fatty acid concentrations were not different between bile duct-ligated and control rats in the fed or the fasted state. Plasma triglyceride concentrations showed the expected decrease with starvation in control rats, but were increased with starvation in bile duct-ligated rats. Urinary excretion of dicarboxylic acids was increased in both fed and fasted bile duct ligated-rats compared with the respective control groups. Compared with control rats, hepatic total carnitine content (per gram of liver) was increased by 24% in fed and by 36% in fasted, bile duct-ligated rats. Fed, bile duct-ligated rats had an increased short-chain acylcarnitine-to-carnitine ratio in liver, plasma and urine compared with control rats. Analysis of the hepatic coenzyme A pool showed decreased coenzyme A content in fed and fasted bile duct-ligated rats compared with control rats. Hepatic long-chain acylcarnitine and long-chain acyl-coenzyme A content increased with starvation both in control and bile duct-ligated rats. The rise in plasma nonesterified fatty acid concentration and hepatic long-chain acylcarnitine and long-chain acylcoenzyme A contents with starvation in bile duct-ligated rats are consistent with unaltered hepatic availability of fatty acids.(ABSTRACT TRUNCATED AT 250 WORDS)
PWE-140 Comparison Of 4 Serum Markers Panels of Fibrosis in Chc: Variants of the Hyaluronic Acid (HA) Assay Significantly Affect Their Diagnostic Performance: Abstract PWE-140 Table
Authors: S Tanwar, P M Trembling, B Hogan, E L Ellis, J Parkes, P Grant, E Nastouli, D Schuppan, W M Rosenberg
Journal: Gut (2013)

Introduction The detection of advancing fibrosis in patients with CHC and prior treatment failure is important for ascertaining prognosis. HA has been used alone and as a constituent component of fibrosis marker panels. The aim of this study was to compare the performance of 4 marker panels in the detection of moderate-to-severe fibrosis (Metavir F2–4) and to assess the influence on diagnostic performance of using 2 different validated assays for HA. Methods 80 patients with CHC, all non-responders or relapsers to IFN-based treatment, were included in this study. Sera obtained within 6 months of liver biopsy were used to measure 4 biomarker panels incorporating HA (ELF, Fibrospect-II, Hepascore, Fibrometer-2G) using 2 validated assays for HA (ELISA-Siemens, radiometric-Pharmacia). Diagnostic performance for the detection of moderate-to-severe fibrosis was assessed by AUROC and by evaluating biomarker performance at published thresholds. Results The prevalence of moderate-to-severe fibrosis was 63% (F0–8%, F1–29%, F2–24%, F3–30%, F4–9%). The AUROC of the Siemens HA assay was higher than the Pharmacia assay (0.80 Vs. 0.69, P = 0.005). Incorporating the Siemens assay for HA, the performance of the panels were not statistically significantly different but Fibrometer 2G generated the highest AUROC. Using the Siemens assay, ELF and Fibrometer 2G had the highest PPV and NPV respectively (88% and 100% using published thresholds). The use of the Pharmacia assay for HA to calculate the biomarkers did not reduce the discriminatory ability of the 4 panels (p = NS). However whereas the other panels were largely unaffected, the use of the Pharmacia assay resulted in a dramatic reduction in the performance of published thresholds of the ELF test with the a priori and a posteriori probability of fibrosis being equal. View this table: Abstract PWE-140 Table Conclusion In this study the performance of the 4 biomarker panels to detect moderate-to-severe fibrosis was comparable. The diagnostic performance of biomarker panels may be significantly effected by the selection of the individual component assays as demonstrated by comparison of the results obtained with different HA assays. Disclosure of Interest None Declared.
Making Optimum Use of the Microbiology Laboratory
Authors: Raymond C. Bartlett
Journal: JAMA (1982)

IN PART I of this series, attention was drawn to the pitfalls physicians may encounter in the submission of specimens that are commonly contaminated with indigenous and colonizing bacteria. These pitfalls apply especially to specimens from the respiratory tract, superficial wounds, draining lesions, and the female genital tract. It is difficut to obtain material from the site of presumptive infection without contaminating it with the bacteria that are present on skin or mucous membranes. Not only are urine and sputum specimens often collected by the patient, but the specimens often are not seen by either nurses or physicians to assess evidence of gross contamination. However, criteria can be applied to the examination of these specimens in the laboratory to establish the probability that any bacteria that may be isolated will more likely reflect contamination than infection.<sup>1</sup>In such cases, microbiologists should request collection of another specimen, emphasizing special effort
Cardiovascular Manifestations of the Hurler Syndrome
Authors: L. JEROME KROVETZ, ANDREW E. LORINCZ, GEROLD L. SCHIEBLER
Journal: Circulation (1965)

Hemodynamic observations in 15 cases of the Hunter-Hurler syndrome are reported. Required premedication was two to three times that usually needed. No major complications or deaths occurred. As a group, these individuals tend to have slight elevations of pulmonary artery pressures and more definite elevations of systemic arterial pressures. They generally have normal cardiac outputs and, thus, elevations of total systemic, total pulmonary, and pulmonary arteriolar resistances. In only one case was there clinical and angiocardiographic evidence of valvular involvement, that case having aortic insufficiency. In another case there was only angiocardiographic evidence of mitral insufficiency. Only one child was in congestive heart failure at the time of the study. There was no evidence of coronary artery disease. The ascending limb right ventricular pressure curve was frequently notched and the pressure rise time of the left ventricle (dp/dt) was low. No case had a congenital malformation of the heart. Those individuals who have normal vascular bed resistances appear to live longer than those who have elevated resistances early in life. The prognosis is also better for the male Hurler of the sex-linked variety than for those cases due to autosomal recessive inheritance.
Triggers of ventricular tachyarrhythmias and therapeutic effects of nicorandil in canine models of LQT2 and LQT3 syndromes
Authors: Masaomi Chinushi, Hidehiro Kasai, Minoru Tagawa, Takashi Washizuka, Yukio Hosaka, Yuko Chinushi, Yoshifusa Aizawa
Journal: Journal of the American College of Cardiology (2002)
Expression of ephrin-B1 in hepatocellular carcinoma: possible involvement in neovascularization
Authors: Yoshiyuki Sawai, Shinji Tamura, Koji Fukui, Nobuyuki Ito, Kazuho Imanaka, Ayuko Saeki, Shigeru Sakuda, Shinichi Kiso, Yuji Matsuzawa
Journal: Journal of Hepatology (2003)
Reversible cell-cycle entry in adult kidney podocytes through regulated control of telomerase and Wnt signaling
Authors: Marina Shkreli, Kavita Y Sarin, Matthew F Pech, Natalia Papeta, Woody Chang, Stephanie A Brockman, Peggie Cheung, Eunice Lee, Frank Kuhnert, Jean L Olson, Calvin J Kuo, Ali G Gharavi, Vivette D D'Agati, Steven E Artandi
Journal: Nature Medicine (2011)
The Indispensable Role of Professional Judgment in Genomic Medicine
Authors: Amy L. McGuire, Laurence B. McCullough, James P. Evans
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
Hyperimmunoglobulinaemia D syndrome in India: report of two siblings with a novel mutation
Authors: A Lawrence, F Hol, A Aggarwal, J P H Drenth
Journal: Annals of the Rheumatic Diseases (2006)

Hyperimmunoglobulinaemia D syndrome (HIDS) is an autosomal recessive auto-inflammatory syndrome caused by mutation in the mevalonate kinase (MVK) gene.1 It presents with febrile episodes starting in infancy with increased serum immunoglobulin (Ig)D levels.2 It is mostly described in people of Dutch or North European descent.3 Isolated cases have been reported from Turkey,4 Japan5 and Qatar.6 No case of HIDS has been reported from South Asia.

A 15-year-old boy from Kerala, India, presented with history of febrile episodes lasting 3–7 days since the age of 3 months. The episodes of fever were variably associated with polyarthritis, abdominal pain, headache, vomiting, diarrhoea, pleuritic chest pain and erythematous papular rash. The episodes occurred at an interval of 1–6 months. He underwent a laparotomy at the age of 8 years, when …
Survival after yttrium-90 resin microsphere radioembolization of hepatocellular carcinoma across Barcelona clinic liver cancer stages: A European evaluation
Authors: Bruno Sangro, Livio Carpanese, Roberto Cianni, Rita Golfieri, Daniele Gasparini, Samer Ezziddin, Philipp M. Paprottka, Francesco Fiore, Mark Van Buskirk, Jose Ignacio Bilbao, Giuseppe Maria Ettorre, Rita Salvatori, Emanuela Giampalma, Onelio Geatti, Kai Wilhelm, Ralf Thorsten Hoffmann, Francesco Izzo, Mercedes Iñarrairaegui, Carlo Ludovico Maini, Carlo Urigo, Alberta Cappelli, Alessandro Vit, Hojjat Ahmadzadehfar, Tobias Franz Jakobs, Secondo Lastoria
Journal: Hepatology (2011)

A multicenter analysis was conducted to evaluate the main prognostic factors driving survival after radioembolization using yttrium-90-labeled resin microspheres in patients with hepatocellular carcinoma at eight European centers. In total, 325 patients received a median activity of 1.6 GBq between September 2003 and December 2009, predominantly as whole-liver (45.2%) or right-lobe (38.5%) infusions. Typically, patients were Child-Pugh class A (82.5%), had underlying cirrhosis (78.5%), and had good Eastern Cooperative Oncology Group (ECOG) performance status (ECOG 0-1; 87.7%), but many had multinodular disease (75.9%) invading both lobes (53.1%) and/or portal vein occlusion (13.5% branch; 9.8% main). Over half had advanced Barcelona Clinic Liver Cancer (BCLC) staging (BCLC C, 56.3%) and one-quarter had intermediate staging (BCLC B, 26.8%). The median overall survival was 12.8 months (95% confidence interval, 10.9-15.7), which varied significantly by disease stage (BCLC A, 24.4 months [95% CI, 18.6-38.1 months]; BCLC B, 16.9 months [95% CI, 12.8-22.8 months]; BCLC C, 10.0 months [95% CI, 7.7-10.9 months]). Consistent with this finding , survival varied significantly by ECOG status, hepatic function (Child-Pugh class, ascites, and baseline total bilirubin), tumor burden (number of nodules, alpha-fetoprotein), and presence of extrahepatic disease. When considered within the framework of BCLC staging, variables reflecting tumor burden and liver function provided additional prognostic information. The most significant independent prognostic factors for survival upon multivariate analysis were ECOG status, tumor burden (nodules >5), international normalized ratio >1.2, and extrahepatic disease. Common adverse events were: fatigue, nausea/vomiting, and abdominal pain. Grade 3 or higher increases in bilirubin were reported in 5.8% of patients. All-cause mortality was 0.6% and 6.8% at 30 and 90 days, respectively.This analysis provides robust evidence of the survival achieved with radioembolization, including those with advanced disease and few treatment options.
Endotracheal Tube Compression
Authors: Stephen M. Ayres
Journal: JAMA (1969)

<h3>To the Editor:—</h3> The recently published report on endotracheal tube compression by Dr. Dietz and colleagues (<b>206</b>:2512, 1968) rightly emphasized the potential difficulties encountered in their use. Endotracheal intubation should be the primary form of airway management in most patients, and tubes can generally be left in place for at least five to seven days. Tracheal irritation may be minimized by the use of adequate sedation since much of the tracheal trauma is due to repeated twisting of the head while in position. While compression of the tube from an overinflated cuff, kinking of the tube due to head twisting, biting of an endotracheal tube on the mouth, or edema of the nasopharynx constricting a nasotracheal tube are all potential hazards, continued adequate ventilation can be assured if a volume-cycled respirator is used. While not stated in the case report, I would suspect that ventilation was assisted by a pressure-cycled
Secular Changes in U.S. Prediabetes Prevalence Defined by Hemoglobin A1c and Fasting Plasma Glucose
Authors: Kai McKeever Bullard, Sharon H. Saydah, Giuseppina Imperatore, Catherine C. Cowie, Edward W. Gregg, Linda S. Geiss, Yiling J. Cheng, Deborah B. Rolka, Desmond E. Williams, Carl J. Caspersen
Journal: Diabetes Care (2013)

OBJECTIVE Using a nationally representative sample of the civilian noninstitutionalized U.S. population, we estimated prediabetes prevalence and its changes during 1999–2010. RESEARCH DESIGN AND METHODS Data were from 19,182 nonpregnant individuals aged ≥12 years who participated in the 1999–2010 National Health and Nutrition Examination Surveys. We defined prediabetes as hemoglobin A1c (A1C) 5.7 to &amp;lt;6.5% (39 to &amp;lt;48 mmol/mol, A1C5.7) or fasting plasma glucose (FPG) 100 to &amp;lt;126 mg/dL (impaired fasting glucose [IFG]). We estimated the prevalence of prediabetes, A1C5.7, and IFG for 1999–2002, 2003–2006, and 2007–2010. We calculated estimates age-standardized to the 2000 U.S. census population and used logistic regression to compute estimates adjusted for age, sex, race/ethnicity, poverty-to-income ratio, and BMI. Participants with self-reported diabetes, A1C ≥6.5% (≥48 mmol/mol), or FPG ≥126 mg/dL were included. RESULTS Among those aged ≥12 years, age-adjusted prediabetes prevalence increased from 27.4% (95% CI 25.1–29.7) in 1999–2002 to 34.1% (32.5–35.8) in 2007–2010. Among adults aged ≥18 years, the prevalence increased from 29.2% (26.8–31.8) to 36.2% (34.5–38.0). As single measures among individuals aged ≥12 years, A1C5.7 prevalence increased from 9.5% (8.4–10.8) to 17.8% (16.6–19.0), a relative increase of 87%, whereas IFG remained stable. These prevalence changes were similar among the total population, across subgroups, and after controlling for covariates. CONCLUSIONS During 1999–2010, U.S. prediabetes prevalence increased because of increases in A1C5.7. Continuous monitoring of prediabetes is needed to identify, quantify, and characterize the population of high-risk individuals targeted for ongoing diabetes primary prevention efforts.
Infectious Diseases Report Calls for Global Control
Authors: Charles Marwick
Journal: JAMA (1995)

WHILE<i>The Hot Zone</i>, a book recounting an outbreak of Ebola virus infection among monkeys in a laboratory near Washington, DC, has hit the best seller lists and the public recently followed with anxiety the course of an outbreak of Ebola virus among humans in Zaire, a government group has just turned out a report that declares that the United States is severely limited in its ability to detect and respond to just such disease outbreaks, whether here or in foreign countries. The report,<i>Emerging and Re-emerging Infectious Diseases</i>, highlights the need for setting up some system of disease surveillance and control so that outbreaks like the one in Zaire are recognized early enough to institute control measures. "At the present time, a formal system of disease surveillance does not exist on a global scale," the report states. The report was prepared by an interagency government working group convened by