tbuckley/cabot-search huggingface dataset:
Cloud-scale RNA-sequencing differential expression analysis with Myrna
Authors: Ben Langmead, Kasper D Hansen, Jeffrey T Leek
Journal: Genome biology (2010)

As sequencing throughput approaches dozens of gigabases per day, there is a growing need for efficient software for analysis of transcriptome sequencing (RNA-Seq) data. Myrna is a cloud-computing pipeline for calculating differential gene expression in large RNA-Seq datasets. We apply Myrna to the analysis of publicly available data sets and assess the goodness of fit of standard statistical models. Myrna is available from http://bowtie-bio.sf.net/myrna.
Pest and allergen exposure and abatement in inner-city asthma: A Work Group Report of the American Academy of Allergy, Asthma &amp; Immunology Indoor Allergy/Air Pollution Committee
Authors: William J. Sheehan, Pitud A. Rangsithienchai, Robert A. Wood, Don Rivard, Sasawan Chinratanapisit, Matthew S. Perzanowski, Ginger L. Chew, James M. Seltzer, Elizabeth C. Matsui, Wanda Phipatanakul
Journal: Journal of Allergy and Clinical Immunology (2010)
Osteopetrosis: A Clinical and Metabolic Study.
Authors: Thomas J. Lord
Journal: Annals of Internal Medicine (1965)

s1 May 1965Osteopetrosis: A Clinical and Metabolic Study.Thomas J. Lord, M.D., C. Conrad Johnston Jr., M.D., Norman J. Lavy, M.D., A. Donald Merritt, M.D., F.A.C.P., William P. Deiss Jr., M.D., F.A.C.P.Thomas J. Lord, M.D.Search for more papers by this author, C. Conrad Johnston Jr., M.D.Search for more papers by this author, Norman J. Lavy, M.D.Search for more papers by this author, A. Donald Merritt, M.D., F.A.C.P.Search for more papers by this author, William P. Deiss Jr., M.D., F.A.C.P.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-62-5-1078_1 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptThirty-six patients in two families were studied roentgenographically for evidence of osteopetrosis. Eleven patients (five males, and six females) were found to have changes typical of the disease. In ten patients with osteopetrosis, acid phosphatase levels were elevated as compared with normal values found in the remainder of both families. Fractures were the most common clinical manifestation of the disease, with four males having a total of 44 fractures, and two females with a total of 6. Optic atrophy occurred in one male. Osteomyelitis occurred in one male in our series, and there was good evidence of this also being... This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: Indianapolis, Indiana PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 1 May 1965Volume 62, Issue 5Page: 1078-1078KeywordsAcid phosphataseAtrophyOsteomyelitis Issue Published: 1 May 1965 PDF DownloadLoading ...
Expression of extracellular RNA in synovial tissue and RNase activity in synovial fluid of rheumatoid arthritis patients
Authors: B Zimmermann, S Fischer, H Stürz, S Rehart, A Lehr, U Müller-Ladner, K T Preissner, E Neumann
Journal: Annals of the Rheumatic Diseases (2012)

Background RNA is required for protein biosynthesis. However, extracellular RNA (exRNA) is also present within tissues and actively secreted by cells. Examples for the exRNA-activity are a pro-coagulative effect and an enhanced permeability of the blood-brain-barrier by exRNA. Furthermore, specific exRNAs are accumulated in the serum in cancer and these exRNA have actually been identified as tumour-markers. A pro-inflammatory effect of extracellular DNA due to tissue damage has been described in rheumatoid arthritis (RA). Therefore, the authors analysed the presence and the expression pattern of exRNA in the joint as well as the activity of RNase in the synovial fluid of RA patients. Methods Synovium from RA and OA patients (n=3 each) were stained with 4′,6-diamidin-2-phenylindole (DAPI) to locate DNA and SYTO RNASelect Green Fluorescent Stain to locate RNA in the tissue. A serial tissue section was stained with H&E to identify the lining layer and sublining. The expression pattern of RNA was analyed by comparing the RNA and DNA staining with the HE-staining on serial sections. In addition, the RNase activity of the synovium of different patient groups (RA: n=4; OA: n=3 and psoriatic arthritis (PsA): n=5) was measured using the Quant-iT RNA Assay Kit. Results RNA and DNA signals were detectable in all areas of the synovium. Merging the RNA and DNA signals showed a co-localisation of the signals within the nucleus of the cell. Interestingly, an intensive cytoplasmatic and exRNA signal could be observed in the lining layer of RA and OA patients with stronger signal intensity in the RA lining. Due to the increased thickness of the lining layer in RA patients, an increased amount of exRNA in RA patients when compared to OA was detectable. This signal was not co-localised with the DNA. A reduced RNase activity was measured in the synovial fluid of patients with RA (20.1±3.61) and PsA (21.3±2.5) in comparison to OA patients (35.8±4.5), reaching statistical significance when comparing PsA to OA patients (p=0,033). In addition, RNase activity was inversely correlated to CRP serum level (r=−0.43). Conclusion In OA and especially RA patients, exRNA is present in the synovial lining layer. RNase activity in the synovial fluid seems to be reduced in patients with chronic inflammation (RA and PSA) in contrast to OA. The increased amounts of exRNA could demonstrate a new pro-inflammatory mechanism active in chronic inflamed tissue that could be important for the perpetuation and chronification of inflammation.
Cerebrospinal Fluid Leak From Epidural Spinal Anesthesia Detected by Radionuclide Cisternogram
Authors: CHAN H. PARK, JAMES ZHANG, SUNG M. KIM, CHARLES INTENZO, JONG D. LEE
Journal: Clinical Nuclear Medicine (1993)

Following epidural spinal anesthesia for cesarean section, a patient developed severe postural headache on the third day after the C-section. A clinically suspected cerebrospinal fluid leak from inadvertent spinal anesthesia was undiagnosed for 19 months despite multiple diagnostic attempts at the local hospital. Finally, a radionuclide cisternogram of the lumbosacral region, performed after the injection of ln-111 DTPA demonstrated the cerebrospinal fluid leak.
Thrombolysis for Acute Transmural Myocardial Infarction
Authors: DENNIS M. MANNING
Journal: Annals of Internal Medicine (1987)

Letters and Corrections1 July 1987Thrombolysis for Acute Transmural Myocardial InfarctionDENNIS M. MANNING, M.D.DENNIS M. MANNING, M.D.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-107-1-120_2 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptTo the editor: In that the recommendations of Drs. Smith and Kennedy (1) on the use of thrombolysis for acute myocardial infarction included the limited use of intravenous streptokinase, and considering that this thoughtful review in Annals is likely to influence physician behavior considerably, I would appreciate their comment on a study that very likely was published after their manuscript was prepared.Schroder and colleagues (2) have reported results of a prospective placebo-controlled, double-blind trial of intravenous streptokinase in the treatment of acute myocardial infarction. Published in the January issue ofJournal of the American College of Cardiology, this study...References1. SMITHKENNEDY BJ. Thrombolysis in the treatment of acute transmural myocardial infarction. Ann Intern Med. 1987;106:414-20. LinkGoogle Scholar2. SCHRODERNEUHAUSLEIZOROVICZ RKA. A prospective placebo-controlled double-blind multicenter trial of intravenous streptokinase in acute myocardial infarction (ISAM): long-term mortality and morbidity. J Am Coll Cardiol. 1987;9:197-203. CrossrefMedlineGoogle Scholar3. SATLERLEVINEKENT LSK. Aortic dissection masquerading as acute myocardial infarction: implication for thrombolytic therapy without cardiac catheterization. Am J Cardiol. 1984;54:1134-5. CrossrefMedlineGoogle Scholar1. WHITEBROWNTAKAYAMABRANDTNORRIS HMMPR. Improved left ventricular function and early survival with intravenous streptokinase: a double blind trial [Abstract]. Circulation. 1986;74(suppl 2): II-5. Google Scholar2. . Intravenous streptokinase given within 0-4 hours of onset of myocardial infarction reduced mortality in ISIS-2 [Letter]. Lancet. 1987; 1:502. MedlineGoogle Scholar3. . Effectiveness of intravenous thrombolytic treatment in acute myocardial infarction. Lancet. 1986;1:397-402. MedlineGoogle Scholar4. . Announcement of protocol change in thrombolysis in myocardial infarction trial [Letter]. Am Coll Cardiol. 1987;9:467. CrossrefMedlineGoogle Scholar This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: Mercy Hospital of Pittsburgh Pittsburgh, PA 15219 PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 1 July 1987Volume 107, Issue 1Page: 120-121KeywordsAcute myocardial infarctionBehaviorMyocardial infarction Issue Published: 1 July 1987 PDF DownloadLoading ...
Reply to Francesco Montorsi and Giorgio Gandaglia's Letter to the Editor re: Georgios Gakis, Stephen A. Boorjian, Alberto Briganti, et al. The Role of Radical Prostatectomy and Lymph Node Dissection in Lymph Node–Positive Prostate Cancer: A Systematic Review of the Literature. Eur Urol 2014;66:191–9
Authors: Georgios Gakis, Christian G. Stief
Journal: European Urology (2014)
Abstract 2992: Transcriptional silencing of amplicons by histone deacetylase inhibition
Authors: Tae Hoon Kim, Yoon Jung Kim, Katharine R. Cecchini, Susan Radke, Amanika Kumar, Kimberly Geyda, Murli Narayan, David Tuck, Lyndsay Harris
Journal: Cancer Research (2010)

Abstract Inhibition of cancer cell growth by histone deacetylase (HDAC) inhibitors has been observed in a number of malignancies. Multiple mechanisms have been proposed to explain the cancer-specific cytotoxic effect of HDAC inhibition, including transcriptional activation of pro-apoptotic and differentiation programs that become epigenetically silenced during tumorigenesis. Here, we report a direct transcriptional repression mechanism of histone deacetylase inhibition that selectively targets genomic amplicons, providing genetic and epigenetic alterations as a basis for the cancer selective cytotoxicity of these drugs. Our study implicates distinct epigenetic structures at the oncogenic amplicons that might be targeted for cancer drug development. 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 2992.
Ian George Logan Craig
Authors: A. Craig
Journal: BMJ (2013)

Ian George Logan Craig was born in Beckenham in 1919, the third of four children. His father, originally from Berwickshire, took his family back to Scotland at the end of the 1920s but died in 1932. The family then moved to Aberdeen, where Ian attended the grammar school. He gained a Carnegie scholarship to study medicine at Aberdeen University, but his studies were interrupted when he developed osteomyelitis. He was fortunate to survive without long term disability but bore the scars of the sequestra to the end of his life.

Ian worked …
Radiation-Induced Coronary Artery Disease
Authors: Gerald P. Tracy
Journal: JAMA (1974)

A 35-year-old woman developed symptoms of severe angina pectoris 19 months after radiotherapy to the mediastinum. The patient was shown to have extensive coronary artery disease by coronary angiography. Extensive exposure of the heart to radiation may pose an additional risk factor for the development of coronary vessel disease. (<i>JAMA</i>228:1660-1662, 1974)
Integrated pest management in the U.S.: progress and promise.
Authors: C B Huffaker, B A Croft
Journal: Environmental Health Perspectives (1976)

In the U.S., where heavy use of insecticides has been commonplace for years, the development of proper integrated insect pest control cannot get underway unless there is a changed use pattern for such chemicals. A changed use pattern, however, cannot be accomplished without much study to establish the requirements for integrated control for each major crop situation. In this paper recent developments in a number of crop areas in the U.S. in which the necessary study has been begun are reviewed. Important phases in the development of integrated control programs include: the single tactics phase, the multitactic phase, phase, the biological monitoring phase, the modeling phase, the management and optimization phase, and the implementation phase. Several crops are discussed in relation to how far along we are in the development of practical programs of insect pest control. These are cotton, apples, alfalfa, soybeans, citrus, corn, cereal grains, tobacco and pine forests. Several of these programs have already made substantial headway, e.g., those for cotton, alfalfa, apples, tobacco, and soybeans, although the accomplishments have not been even or parellel with respect to the phases of development where progress has been good. The review of developments in these crops suggests that programs of control for individual crops and perhaps for complexes of associated crops will be developed according to specific needs of the crop, the geographic area and the pests, the technologies available and the socioeconomic and political factors of relevance. The tendency will be toward greater use of science in pest control decision-making, with extensive use of biological monitoring to establish realistic levels of threatened damage to the crop, and greater concern given to possible profit reductions and environmental disturbances of applying an insecticide, as well as the possible gain from doing so.
Mutation of an mutL Homologue in a Navajo Family With Hereditary Nonpolyposis Colorectal Cancer
Authors: H. T. Lynch, T. Drouhard, S. Lanspa, T. Smyrk, P. Lynch, J. Lynch, B. Vogelstein, M. Nystro-Lathi, P. Sistonen, P. Peltomaki, A. de la Chapelle
Journal: JNCI Journal of the National Cancer Institute (1994)

Journal Article Mutation of an mutL Homologue in a Navajo Family With Hereditary Nonpolyposis Colorectal Cancer Get access Henry T. Lynch, Henry T. Lynch Department of Preventive Medicine, Creighton University School of MedicineOmaha, Neb. Correspondence to : Henry T. Lynch, M.D., Department of Preventive Medicine, Creighton University School of Medicine, 2500 Califormia Plaza, Omaha, NE 68178. Search for other works by this author on: Oxford Academic PubMed Google Scholar Thomas Drouhard, Thomas Drouhard Tuba City Indian Medical CenterTuba City, Ariz. Search for other works by this author on: Oxford Academic PubMed Google Scholar Stephen Lanspa, Stephen Lanspa Department of Gastroenterology, Creighton University School of MedicineOmaha, Neb. Search for other works by this author on: Oxford Academic PubMed Google Scholar Thomas Smyrk, Thomas Smyrk Department of Pathology, Clarkson HospitalOmaha Search for other works by this author on: Oxford Academic PubMed Google Scholar Patrick Lynch, Patrick Lynch Division of Gastrointestinal Oncology, The University of Texas M. D. Anderson Cancer CenterHouston Search for other works by this author on: Oxford Academic PubMed Google Scholar Jane Lynch, Jane Lynch Department of Preventive Medicine, Creighton University School of MedicineOmaha, Neb. Search for other works by this author on: Oxford Academic PubMed Google Scholar Bert Vogelstein, Bert Vogelstein The Johns Hopkins Oncology CenterBaltimore, Md. Search for other works by this author on: Oxford Academic PubMed Google Scholar Minna Nyströ-Lathi, Minna Nyströ-Lathi Departmentof Medical Genetics, University of HelsinkiFinland Search for other works by this author on: Oxford Academic PubMed Google Scholar P. Sistonen, P. Sistonen Department of Medical Genetics, University of Helsinki; and Finnish Red Cross Blood Transfusion ServiceHelsinki Search for other works by this author on: Oxford Academic PubMed Google Scholar Päivi Peltomäki, Päivi Peltomäki Departmentof Medical Genetics, University of HelsinkiFinland Search for other works by this author on: Oxford Academic PubMed Google Scholar ... Show more Albert de la Chapelle Albert de la Chapelle Departmentof Medical Genetics, University of HelsinkiFinland Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 86, Issue 18, 21 September 1994, Pages 1417–1419, https://doi.org/10.1093/jnci/86.18.1417 Published: 21 September 1994 Article history Received: 28 April 1994 Revision received: 15 June 1994 Accepted: 24 June 1994 Published: 21 September 1994
Abstract 908A: RAD51C germline mutations in breast and ovarian cancer cases from high-risk families
Authors: Jessica N. Clague, Greg Wilhoite, Aaron Adamson, Jeffrey N. Weitzel, Susan L. Neuhausen
Journal: Cancer Research (2011)

Abstract Purpose: BRCA1 and BRCA2 account for approximately 80% of cases of hereditary breast and ovarian cancer. Additional genes involved in DNA repair have been identified as predisposing to breast cancer. One such gene RAD51C, essential for homologous recombination repair, has been reported to be a rare breast cancer susceptibility gene. Several pathogenic RAD51C mutations have been identified in BRCA1- and BRCA2-negative breast and ovarian cancer families but not in families with breast cancer alone. Methods: We performed complete sequencing of RAD51C in germline DNA of 286 female breast and ovarian cancer cases with a family history of breast and ovarian cancer. They had been previously tested for mutations in BRCA1 and BRCA2 and were negative. We screened 133 breast cancer cases, 119 ovarian cancer cases, and 34 with both breast and ovarian cancer. The in-silico SIFT and Polyphen programs were used to predict possible pathogenicity of non-synonomous variants. Two-hybrid screening is currently being performed to assess functionality of four of the non-synonomous variants. Results: Fifteen DNA sequence variants were identified among the 286 cases; including four intronic, one 5’ UTR, one promoter, three synonymous, six non-synonymous variants. None were truncating. Of these variants, six have been previously identified and have rs numbers, whereas the remaining nine are novel. Nine of the variants were private (seen in one individual) and the other six were detected in more than one individual. Of the six non-synonomous variants, SIFT and Polyphen predicted that two were likely pathogenic, with predictions based on degree of conservation of the affected residue. An additional two non-synonomous variants are in important domains of the protein and may also be pathogenic. We are currently investigating potential functional importance of these four variants through yeast-two-hybrid assays. Conclusions: Our results provide further evidence that Rad51C is a breast and ovarian cancer susceptibility locus. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 908A. doi:10.1158/1538-7445.AM2011-908A
PMO-065 Repair of fractured central venous catheters for parenteral nutrition: techniques and risk of infection
Authors: M Small, G A D Major, S M Gabe
Journal: Gut (2012)

<h3>Introduction</h3> Tunnelled central venous catheters (CVCs) are the best method of vascular access for long-term parenteral nutrition. Failure of intravenous access can necessitate emergeny admission. Removing and replacing CVCs is painful, risks infection and venous thrombosis, and uses costly healthcare resources. Simple techniques to repair fractures in the external part of CVCs can prolong CVC life but repairs have been associated with increased rates of catheter-related bloodstream infection (CRBSI). <h3>Methods</h3> Between January 2010 and December 2011 all repairs of CVC fractures were recorded. Fractures were defined as “external” when only the outer sheath of the CVC was ruptured, and “full” when both inner and outer sheaths of the CVC were ruptured, with evidence of leakage. External fractures were repaired with waterproof, non-absorbent tape. Full fractures were repaired with the manufacturer9s repair kit, including a metal spike inserted into the lumen across the new join. We recorded rates of successful repair and any instance of CRBSI within 30 days of the repair. <h3>Results</h3> <h3>Conclusion</h3> CVC fracture repair is effective and safe. Repair of external fracture is easily done with waterproof, non-absorbable tape. Formal repair can prevent emergency admission and act a bridge to planned CVC replacement. It may also have a role in further prolonging the useful life of tunnelled CVCs. In our patient cohort repair is not associated with subsequent infection. <h3>Competing interests</h3> None declared. <h3>Reference</h3> 1. <b>Lundgren IS</b>, Zhou C, Malone FR, <i>et al.</i> Central venous catheter repair is associated with an increased risk of bacteremia and central line associated bloodstream infection in pediatric patients. <i>Pediatr Infect Dis J</i>, 2011.
Geographic Variation in Health Care Spending in the United States
Authors: Joseph P. Newhouse, Alan M. Garber
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
PERMEABILITY OF THE HUMAN PLACENTA TO ANTIBODIES
Authors: Alexander S. Wiener, I. Jerome Silverman
Journal: The Journal of Experimental Medicine (1940)

The ratio of the titers of various antibodies, namely, hemagglutinins and syphilitic reagin, in the maternal blood to that of the corresponding antibody in the cord blood was found to be relatively constant, falling somewhere between 8 and 16. This figure may be considered the "index of permeability" of human placenta to antibodies, or the coefficient of distribution of antibodies between maternal and cord blood. The possible application of these findings to the study of the placental permeability to sensitizing antibodies (or reagins) is discussed.