tbuckley/cabot-search huggingface dataset:
Abstract 3186: Comparative analysis of different total RNA sequencing approaches
Authors: Christine J. Sumner, Daniela Munafo, Larry McReynolds, Brad Langhorst, Ping Liu, Lynne Apone, Fiona Stewart, Eileen Dimalanta, Theodore Davis
Journal: Cancer Research (2012)

Abstract Initial transcriptomic studies largely relied on hybridization-based microarray technologies and offered a limited ability to fully catalogue and quantify the diverse RNA molecules that are expressed from genomes over wide ranges of levels. Massively parallel cDNA sequencing, or Total RNA-Seq, has allowed many advances in the characterization and quantification of transcriptomes; an offer a new appreciation for the complexity of the Transcriptome, encompassing a multitude of previously unknown coding and non-coding RNA species, particularly small RNAs, including micro RNAs. This work investigates the performance of different strategies for Total RNA-Seq using multiple next generation sequencing platforms. Standard RNA-sequencing approaches generally require double-stranded cDNA Synthesis, which erases RNA strand information. Synthesis of a randomly primed double-stranded cDNA followed by addition of adaptors for next-generation sequencing leads to the loss of information about which strand was present in the original mRNA template. The polarity of the transcript is important for correct annotation of novel genes, identification of antisense transcripts with potential regulatory roles, and for correct determination of gene expression levels in the presence of antisense transcripts. Here, we examine the performance of strand-specific RNA libraries made by direct ligation of adaptor on to the RNA. We analyze the effect of different RNA fragmentation methods (divalent cations plus heat versus enzymatic fragmentation) and we provide a comparative data analysis (library complexity, continuity of gene coverage, strand specificity and 3′and 5′-end bias analysis). Identification and analysis of small RNA by deep sequencing requires preparation of a di-tagged cDNA library, which leads to adaptor-dimer formation that strongly contaminates the library. We have developed a novel method to generate di-tagged small RNA libraries free of adapter-dimer contamination without introducing any additional enzymatic steps or gel purifications. This method has optimized the 3′adaptor-ligation reaction to recover and to increase representation of the 2′-O-modified RNAs present in a biological sample. To reduce cost and increase sample throughput we have developed a barcode strategy to tag samples during library construction. The multiplexed libraries can then be pooled together before size selection, reducing the number of steps in the workflow. This technique reduces bias by ligation, increases representation of modified small RNAs and simplifies workflow during library construction for small RNA analysis and discovery. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3186. doi:1538-7445.AM2012-3186
P3-07-34: Occult Metastasis in Sentinel Node: Should This Affect the Clinical Decision Making? A Systematic Review and Meta-Analysis.
Authors: A Valachis, A Nearchou, NP Polyzos, P Lind, J Berqvist
Journal: Cancer Research (2011)

Abstract Background: The role of occult metastases (micrometastasis or isolated tumor cells [ITC]) in sentinel lymph nodes (SLN) remains a field of debate and speculation. The purpose of this systematic review and meta-analysis was to investigate the prognostic relevance of occult metastases in SLN. Methods: We searched PubMed, without year or language restriction through June 2011, for studies on patients with invasive breast cancer with micrometastasis or ITC in the SLN and presented Hazard Ratios (HR) on Overall Survival (OS) / Disease-Free Survival (DFS) or enough data for HR-calculation. We used fixed- or random-effects meta-analyses, as appropriate, to calculate pooled estimates of HR. Results: Fifteen studies were considered eligible. Of those, 3 studies were excluded due to the lack of data for HR-calculation. Both the presence of ITC (5 studies; 1264 patients with ITC) and micrometastasis (10 studies; 1093 patients with micrometastasis) were associated with worse DFS (pooled HR 1.29, 95% Confidence Interval [CI]: 1.09−1.52, P-value = 0.002 for ITC, pooled HR 1.45, 95% CI: 1.28−1.64, P-value &amp;lt; 0.001 for micrometastasis). No significant differences were observed regarding OS neither for the presence of ITC (5 studies; 877 patients with ITC; pooled HR 1.20, 95% CI 0.98−1.46) nor for micrometastasis (8 studies; 1094 patients with micrometastasis; pooled HR 1.36, 95% CI: 0.98−1.88). Conclusion: Based on the current evidence, it seems that the presence of occult metastasis in SLN is of prognostic significance in regard to DFS. However, the clinical significance of this difference is questioned since it cannot be translated into differences in OS. In anticipation of randomized trials aimed to evaluating the optimal management of each category of tumor burden within SLN, current evidence suggest a limited clinical significance of occult metastases in SLN. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-07-34.
Erratum to “En route to new blockbuster anti-histamines: surveying the offspring of the expanding histamine receptor family” [Trends Pharmacol. Sci. 32 (4) (2011) 250–257]
Authors: Rob Leurs, Henry F. Vischer, Maikel Wijtmans, Iwan J.P. de Esch
Journal: Trends in Pharmacological Sciences (2011)
Technological challenges in diagnosis and management of HIV infection in resource limited settings
Authors: Purnima Madhivanan, Karl Krupp
Journal: BMJ (2007)

With the HIV epidemic in its third decade appropriate use of technology in resource limited settings has taken on added importance as priorities shift from detection and prevention to care and support for people living with HIV. At the same time there is a continuing need for evaluation of and improvement in the critical diagnostic tools such as rapid tests for HIV which have become indispensable in settings with a high prevalence of infection. In this weeks BMJ two studies look at such evaluations. MacLennan and colleagues assess the diagnostic accuracy and clinical utility of a simplified flow cytometry method for measuring CD4 counts that promises a more affordable alternative for routine clinical use in resource limited settings. Gray and colleagues highlight problems encountered with the use of rapid tests for HIV screening in rural Rakai Uganda. (excerpt)
Abuse of the mushroom Panaeolus foenisecii.
Authors: P Cooles
Journal: BMJ (1980)

CommentReports on the presence of psilocybin and psilocin in Panaeolus foenesecii are confused, since both have been detected in some samples of this mushroom but not in all.It is usually considered a "latent psilocybin" mushroom, because psilocybin and psilocin may not necessarily be present in a particular specimen.
Psychiatric illness in inpatients with neurological disorders: patients' views on discussion of emotional problems with neurologists.
Authors: K W Bridges, D P Goldberg
Journal: BMJ (1984)

The prevalence of psychiatric morbidity in inpatients with neurological disorders and the extent to which it is detected by neurologists were measured by using a two stage model of psychiatric assessment and from information recorded in the patients' medical notes. The prevalence of psychiatric morbidity was estimated as 39%, of which 72% was unrecognised by the neurologists. Only a minority of patients with an uncertain physical diagnosis had a psychiatric illness, showing the error in assuming that a patient's physical symptoms arise from a psychological disturbance if an organic aetiology cannot be determined. When the patients were interviewed on their discharge from hospital they were divided on whether they had wished to discuss their mood with neurologists while they were in hospital. The reasons that they gave suggested that interactions between patients and doctors and the lack of ward facilities for private consultations with doctors are important determinants of hidden psychiatric morbidity in medical inpatients.
Abstract P6-05-01: Basal and induced receptor profiles cluster cell lines into subtypes and predict drug response in a panel of breast cancer lines
Authors: BM Schoeberl, EA Pace, M Niepel, M Hafner, DH Chai, PK Sorger
Journal: Cancer Research (2013)

Abstract Molecular subtype is a critical determinant of therapeutic approaches in breast cancer. The subtype is based on the expression of three receptors: The Her2/ErbB2 receptor tyrosine kinase (RTK), whose over-expression defines the HER2amp subtype, and the estrogen or progesterone nuclear hormone receptors, whose over-expression defines the HR+ subtype. Triple negative breast cancers (TNBCs) express low levels of all three receptors. HER2amp status serves as a biomarker for therapy with anti-Her2/ErbB2 antibodies such as trastuzumab or pertuzumab and HR+ status is a biomarker for therapy with hormone receptor antagonists such as tamoxifen. TNBCs are usually treated with cytotoxic chemotherapy. However, breast cancer subtypes are heterogeneous, clinical and mRNA subtypes are not identical, and even the best available biomarker, HER2amp status, correctly predicts response to trastuzumab in only a subset of patients. Projects such as the Cancer Cell Line Encyclopedia aim to identify drug response determinants by relating dose-response profiles for multiple compounds to genomic features across cancer cell collections. Recent studies have suggested that measures of target activity such as phosphorylation are more correlated with drug response than mutation status or gene expression, and steady-state protein data is becoming available for tumors and cell lines. However, few studies have tried to relate the biochemistry of signal transduction to drug response on a large scale, mainly because the measurements are demanding and the utility of the approach is unproven. In this work, we ask whether measurement of the basal and perturbed states of immediate-to-early signaling proteins in serum-starved cells, a robust measurement that can be collected with relatively little biological variability, is predictive of tumor subtype as well as of drug response. We measured the abundance and basal phosphorylation state of nuclear and cell surface receptors and of downstream signaling kinases in the standardized NCI-ICBP43 cell line collection. Because perturbation reveals features of signal transduction that are not apparent by steady state profiling, and because biological ligands present in the microenvironment can alter drug sensitivity, we also collected response profiles by exposing cells to a diverse set of growth factors and cytokines and measuring the activities of downstream signaling kinases before and after ligand addition. We present how the resulting set of ∼3×105 receptor and cell response measurements segregated with clinical subtype and how these proteomic measurements predict the sensitivity of cells to a range of targeted anti-cancer drugs. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-05-01.
Relationship of solar keratosis and history of skin cancer to objective measures of actinic skin damage
Authors: C. D. J. HOLMAN, B. K. ARMSTRONG, P. R. EVANS, G. J. LUMSDEN, K. J. DALLIMORE, C. J. MEEHAN, J. BEAGLEY, I. M. GIBSON
Journal: British Journal of Dermatology (1984)

Two methods for the assessment of severity of actinic skin damage were evaluated in a population-based survey of 1216 subjects. After controlling for the effects of age, skin texture changes graded by cutaneous microtopography were found to be associated strongly with the presence of solar keratoses and a past history of non-melanotic skin cancer. Changes in skin condition graded by paraocular photography had a weaker relationship with the presence of keratoses and showed no association with non-melanotic skin cancer. These results, together with a higher level of agreement between observers in grading cutaneous microtopographs, support the use of cutaneous microtopography as an index of actinic skin damage in epidemiological research.
Multiplexing studies of effects of rapid atrial pacing on the area of slow conduction during atrial flutter in canine pericarditis model.
Authors: A Shimizu, A Nozaki, Y Rudy, A L Waldo
Journal: Circulation (1991)

BACKGROUND We report that rapid atrial pacing interrupts atrial flutter when the orthodromic wave front from the pacing impulse is blocked in an area of slow conduction in the reentry circuit. To characterize the area of slow conduction during atrial flutter and rapid pacing, we studied 11 episodes of induced atrial flutter, mean cycle length 157 +/- 20 msec, in eight dogs with sterile pericarditis. METHODS AND RESULTS Atrial electrograms were recorded simultaneously from 95 pairs of right atrial electrodes during the interruption of atrial flutter by rapid atrial pacing, mean cycle length 139 +/- 21 msec. Areas of slow conduction during atrial flutter were demonstrated at one to three sites in the reentry circuit. After rapid pacing captured the reentry circuit, one area of slow conduction either disappeared (10 episodes) or the degree of slow conduction in an area of slow conduction decreased (one episode). Both changes were in association with activation of the region by a wave front from the pacing impulse that arrived from a direction different than that during the induced atrial flutter. Interruption of atrial flutter during rapid pacing occurred when the orthodromic wave front from the pacing impulse blocked in an area of slow conduction that had either newly evolved during rapid pacing (seven episodes) or that was previously present (four episodes). CONCLUSIONS Areas of slow conduction present during atrial flutter and rapid pacing of atrial flutter are functional and depend on both the atrial rate and the direction of the circulating wave fronts. Interruption of atrial flutter by rapid pacing results from block of the orthodromic wave front of the pacing impulse in an area of slow conduction in the reentry circuit.
Efficacy and Safety of House Dust Mites Allergen Extracts Tablets in Adults With Allergic Rhinitis Patients
Authors: K.C. Bergmann, M. Worm, W.J. Fokkens, A.I. Tabar, M. Melac, O. de Beaumont, H. Nguyen, P. Demoly
Journal: Journal of Allergy and Clinical Immunology (2010)
INFECTION WITH FLY LARVÆ, ANTHOMYIA CANALICULARIS.
Authors: H. C. BLANKMEYER
Journal: JAMA (1907)

An interesting case of infection with this larvæ was brought to my observation in May, 1906, by Dr. George E. Lyon, Toledo, Ill. With the assistance of Mr. N. C. Gilbert of the University of Wisconsin, a practical zoologist, the identification was made and a search through literature revealed but seventeen cases heretofore reported, as follows: Five in America, five in Germany, and the remainder scattered throughout France, England, Sweden and the Argentine Republic, a rather wide range of territory. <i>Anthomyia canalicularis</i>is the larva of the very small black house fly so often seen on windows. The flies, which are often found parasitic in man, lay eggs on decaying vegetables, the larvæ varying in size from ⅛ to ¼ inches in length. The body proper is long and narrow, has developed lateral branchii or gills, and is divided into segments, ten or fourteen, according to age. They are beset
The Little Black Book of Primary Care: Pearls and References
Authors: Jo Ann Rosenfeld
Journal: JAMA (1997)

This squat, oversized "pocket-book" is written as a "starter notebook" for students or residents in primary care, to be placed in a white coat pocket and "add[ed] to and modifi[ed]" by "noting new data... in the blank spaces or margins." Anyone who bought this book, however, would not only be totally confused, overinformed, and unable to extract information necessary to treat primary care patients, but would also get acute and chronic muscle strain from its pure weight. As well, there are no blank spaces or margins to write notes in. Individuals buy pocket or spiral books for rapid access to important information that might be difficult to find or take time to extract from larger texts. For detailed information or an in-depth discussion about pathophysiological controversies, students and physicians seek large textbooks, libraries, and journal articles, not "pocket-brains." Students might keep a notebook with jottings about the drugs for a
Dutch health reforms have failed, say ministers
Authors: T Sheldon
Journal: BMJ (1994)

The reforms of Dutch health care have failed, according to an investigation by an all party committee of government ministers. The committee made a scathing attack on the government, political parties, and health organisations, claiming that all those who had been involved in the reforms had their own “agendas, strategies and aims.” It said that at times political opportunism had triumphed over decision making, while pressure groups had enjoyed too much influence.

The report, which focuses on the failure of the plans for reform produced by the former Labour party health minister Hans …
The Relation of Bacteriuria to Blood Pressure as Revealed by an Epidemiologic Study Among Nuns and Working Women.
Authors: Calvin M. Kunin
Journal: Annals of Internal Medicine (1968)

s1 May 1968The Relation of Bacteriuria to Blood Pressure as Revealed by an Epidemiologic Study Among Nuns and Working Women.Calvin M. Kunin, M.D., F.A.C.P., Regina C. McCormack, M.D.Calvin M. Kunin, M.D., F.A.C.P.Search for more papers by this author, Regina C. McCormack, M.D.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-68-5-1181_3 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptFrequency of bacteriuria and distribution of blood pressure, by age, were determined in 2,882 white and 422 negro nuns and 2,302 white and 396 negro control women working in similar occupations. Bacteriuria was 12.8, 2.8, and 1.4 times more frequent among white control women than among white nuns at ages 15 to 34, 35 to 54, and 55 or more years, respectively. It was 14.2 and 5.3 times higher for negro control women than for nuns aged 15 to 34 and 35 to 54 years. These differences were highly significant statistically. The prevalence of bacteriuria among nuns aged 15 to... This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: Charlottesville, Virginia PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 1 May 1968Volume 68, Issue 5Page: 1181-1182KeywordsBlood pressureEpidemiology Issue Published: 1 May 1968 PDF downloadLoading ...
Medicolegal Investigation of Death: Guidelines for the Application of Pathology to Crime Investigation
Authors: David M. Spain
Journal: JAMA (1973)

Medicolegal investigation of death, in the past decade, has assumed an increasingly important role extending far beyond the immediate investigation of suspected homicide, suicide, or accidental death. The epidemic of malpractice suits; the emergence of iatrogenic disease as a major phenomenon; the increasingly watchful eye of minority groups as related to alleged police brutality and violation of civil rights; and the increasing complexity of industrial toxicology and fatalities related to such exposure require greater aptitude and more skillful and scientific application of the principles of forensic pathology. This monograph, although listed modestly as a guideline for the application of pathology to crime investigation, also begins to serve the needs of those involved in these broader aspects of the problem. This is a well-ordered, concise, and clearly written text. The illustrations and tables are adequate and to the point. Particularly welcome are the chapters devoted to identification of human remains, with
Ichthyosis prematurity syndrome: Clinical evaluation of 17 families with a rare disorder of lipid metabolism
Authors: Denis Khnykin, Jørgen Rønnevig, Margareta Johnsson, Jan C. Sitek, Harm-Gerd K. Blaas, Ingrid Hausser, Finn-Eirik Johansen, Frode L. Jahnsen
Journal: Journal of the American Academy of Dermatology (2011)
An indirect approach for the study of the elastic modulus of the brachial artery in patients with essential hypertension
Authors: M E SAFAR, G M LONDON, R G ASMAR, C J HUGUES, S A LAURENT
Journal: Cardiovascular Research (1986)

Journal Article An indirect approach for the study of the elastic modulus of the brachial artery in patients with essential hypertension Get access M E SAFAR, M E SAFAR From the Diagnostic Centre and the Hypertension Research Centre, Broussais Hospital. Paris Search for other works by this author on: Oxford Academic PubMed Google Scholar G M LONDON, G M LONDON From the Diagnostic Centre and the Hypertension Research Centre, Broussais Hospital. Paris Search for other works by this author on: Oxford Academic PubMed Google Scholar R G ASMAR, R G ASMAR From the Diagnostic Centre and the Hypertension Research Centre, Broussais Hospital. Paris Search for other works by this author on: Oxford Academic PubMed Google Scholar C J HUGUES, C J HUGUES From the Diagnostic Centre and the Hypertension Research Centre, Broussais Hospital. Paris Search for other works by this author on: Oxford Academic PubMed Google Scholar S A LAURENT S A LAURENT From the Diagnostic Centre and the Hypertension Research Centre, Broussais Hospital. Paris Search for other works by this author on: Oxford Academic PubMed Google Scholar Cardiovascular Research, Volume 20, Issue 8, August 1986, Pages 563–567, https://doi.org/10.1093/cvr/20.8.563 Published: 01 August 1986
Progression of Plasminogen Activator Inhibitor-1 and Fibrinogen Levels in Relation to Incident Type 2 Diabetes
Authors: Andreas Festa, Ken Williams, Russell P. Tracy, Lynne E. Wagenknecht, Steven M. Haffner
Journal: Circulation (2006)

Several studies have shown that fibrinolytic and coagulation abnormalities as well as low-grade inflammation predict cardiovascular disease and type 2 diabetes. We studied in the Insulin Resistance Atherosclerosis Study the relation of incident diabetes to dynamic changes of plasminogen activator inhibitor-1 (PAI-1) and fibrinogen.After a follow-up of 5.2 years, diabetes developed in 140 (16.6%) of 843 individuals (57% women; mean age [range], 54.7 [40, 69] years) (converters versus nonconverters). Baseline and follow-up levels of PAI-1 and fibrinogen (demographically and smoking adjusted) were higher in converters versus nonconverters (mean [SE]): at baseline, 23.7 ng/mL (1.5) versus 14.5 (0.4) and 286.2 mg/dL (4.8) versus 273.6 (2.1); at follow-up, 45.3 ng/mL (3.2) versus 25.9 (0.8) and 292.0 mg/dL (5.6) versus 275.2 (2.5); all P<0.05. In a demographically and smoking-adjusted logistic regression model, the change in PAI-1 was related to incident diabetes (OR for a 1-SD change [CI], 1.75 [1.37, 2.22]; P<0.001) after adjusting for baseline PAI-1 levels. After further adjusting for insulin sensitivity (SI) or waist, change in PAI-1 remained significantly related to incident diabetes (OR, 1.66 [1.28, 2.15], and 1.64 [1.28, 2.10]; P<0.001). In contrast, change in fibrinogen was not significantly related to incident diabetes.Progression of PAI-1 levels over time, in addition to high baseline PAI-1 levels, is associated with incident diabetes. PAI-1 levels (but not fibrinogen) further increase with the rising glucose levels and the development of diabetes. These findings extend the current knowledge on the relation of fibrinolysis and coagulation abnormalities to the development of type 2 diabetes.