tbuckley/cabot-search huggingface dataset:
THU0539 Less Emphasis on Self Critique among Basic Science Compared to Clinical Science Manuscripts in Rheumatology Literature
Authors: H. Yazici, F. Gogus, F. Esen, Y. Yazici
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> An honest self critique is or should be an important part of scientific output. Even though explicitly underlined in scientific authorship guidelines like CONSORT (1) and STROBE (2) we had the impression that many journal articles in rheumatology did not give this due importance. Furthermore we also had the impression that self critique was less frequent in basic than in clinical science articles. <h3>Objectives</h3> To formally quantify self critique in clinical and basic science articles separately in 3 widely read rheumatology journals. <h3>Methods</h3> The 2012 January, May and September issues of Ann Rheum Dis, Arthritis Rheum and Rheumatology were selected. All original, full articles with discussion sections were analyzed by 2 independent observers (FG, HY) to survey whether they were of mainly basic or clinical science content. Their discussion sections were electronically scanned to assess whether the word "limit" or its derivatives (i.e limits, limitations, etc.) (limit.der) were ever used and whether, when used, these words implied self critique. In addition each observer sought for the presence of any discussion sentences by which the authors had resorted to self critique regardless whether they had included the word "limit" or a "limit.der" A third observer (YY) had the final say in instances where the initial two observers disagreed whether an article had mainly clinical or basic science content. <h3>Results</h3> 231 articles were surveyed. 137 (59%) were of clinical and 94 (41%) of basic science content. The Table shows the number of articles that contained the word "limit" and/or a limit.der" in the discussion sections of these articles as well as the presence of any form of self critique which included the presence of the word "limit" or a "limit. der". The statistically significant differences between the two kinds of articles persisted when each journal was assessed separately (data not given). In 4/231(1.7%) instances the word "limit" or a "limit.der" was used in a different context. <h3>Conclusions</h3> Around one half of the original articles in our leading rheumatology journals lacked self critique. This was significantly more pronounced in basic science manuscripts. We propose that such self critique should be highlighted perhaps even more in the scientific authorship guidelines especially in those related to basic science, including animal work. Also a higher priority should be given to its presence in peer review. <h3>References</h3> Altman DG, Schulz KF, Moher D, et al, CONSORT Group. Ann Intern Med 2001;134:663–94. von Elm E, Altman DG, Egger M, et al, STROBE Initiative. Lancet 2007;370:1453–7. <h3>Disclosure of Interest</h3> H. Yazici: None Declared, F. Gogus: None Declared, F. Esen: None Declared, Y. Yazici Grant/research support from: BMS, Genentech, Centocor, Celgene, Consultant for: Abbott, BMS, Celgene, Genentech, Horizon, Janssen, Pfizer, UCB
Natural orifice transluminal endoscopic surgery
Authors: X. Dray
Journal: Endoscopy (2010)

This year, Digestive Disease Week (DDW; 1 – 5 May, New Orleans, Louisiana, USA) marked a decade of research and development into natural orifice transluminal endoscopic surgery (NOTES). Kalloo and Kantsevoy reported on the first NOTES procedure (transgastric peritoneoscopy) in a survival porcine model at DDW in 2000 [1], and 2 years later the same team presented an experimental series of tubal ligation in the pig model. At DDW 2002, Rao and Reddy also reported on the first human case (transgastric NOTES appendectomy) in a video session [2] [3].
Efficiencies of the NJp, Maximum Likelihood, and Bayesian Methods of Phylogenetic Construction for Compositional and Noncompositional Genes
Authors: Ruriko Yoshida, Masatoshi Nei
Journal: Molecular Biology and Evolution (2016)

At the present time it is often stated that the maximum likelihood or the Bayesian method of phylogenetic construction is more accurate than the neighbor joining (NJ) method. Our computer simulations, however, have shown that the converse is true if we use p distance in the NJ procedure and the criterion of obtaining the true tree ( Pc expressed as a percentage) or the combined quantity ( c ) of a value of Pc and a value of Robinson–Foulds' average topological error index ( d T ). This c is given by Pc (1 − d T / d T max) = Pc ( m − 3 − d T /2)/( m − 3), where m is the number of taxa used and d T max is the maximum possible value of d T , which is given by 2( m − 3). This neighbor joining method with p distance (NJp method) will be shown generally to give the best data-fit model. This c takes a value between 0 and 1, and a tree-making method giving a high value of c is considered to be good. Our computer simulations have shown that the NJp method generally gives a better performance than the other methods and therefore this method should be used in general whether the gene is compositional or it contains the mosaic DNA regions or not.
Abstract 1519: Peroxisome proliferator-activated receptor ≤ promotes colonic inflammation and inflammation-associated tumorigenesis
Authors: Dingzhi Wang, Lixia Guo, Wei Ning, Hong Wu, Rupesh Chaturved, Keith Wilson, Raymond N. DuBois
Journal: Cancer Research (2012)

Abstract Although epidemiologic and experimental evidence strongly indicates chronic inflammation as a risk factor for cancer, it remains unclear how chronic inflammation contributes carcinogenesis. Peroxisome proliferator-activated receptor ≤ (PPARδ) is one member of PPAR family that belongs to the nuclear hormone receptor superfamily and is also ligand-dependent transcription factor. Although PPARδ has been shown to be involved in chronic inflammation and the progression of hereditary and sporadic CRC, its role in inflammation-induced carcinogenesis is not defined. The aim of our present study was to determine whether PPARδ contributes to the pathogenesis of colonic inflammation and inflammation-associated carcinogenesis. Here we present genetic evidence demonstrating that deletion of PPARδ diminishes colonic inflammation accompanied with reducing infiltration of immune cells and the expression of pro-inflammatory chemokines and cytokines in a mouse model of colitis. These PPARδ-dependent chemokines are responsible for recruitment of leukocytes from the circulation to local inflammatory sites and the tumor microenvironment. Our results further reveal that activation of PPARδ induces COX-2 expression in colonic epithelial cells. Importantly, COX-2-derived PGE2 stimulates macrophages to produce pro-inflammatory chemokines and cytokines. More intriguingly, loss of PPARδ attenuated colonic chronic inflammation and colitis-associated adenoma growth via PGE2 signaling in two mouse models of colitis-associated tumorigenesis. Collectively, our results demonstrate that PPARδ promotes colonic chronic inflammation and colitis-associated tumor growth via a PGE2 signaling which mediates the crosstalk between tumor epithelial cells and macrophages. Our data further supports the notion that the existence of crosstalk between PPARδ and COX-2 signaling in CRC progression. These findings indicate that PPARδ plays a pivotal role in connecting colonic inflammation to cancer progression and may represent a potential therapeutic target for prevention or treatment of colorectal cancer. 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 1519. doi:1538-7445.AM2012-1519
P1054 NEED FOR EDUCATIONAL PROGRAMS AND SUPPORT DURING ANTIVIRAL TREATMENT FOR CHRONIC HEPATITIS B IN IMMIGRANTS. EVIDENCE FROM THE CATALAN GIV-2002/2012-CHB THERAPEUTIC COHORT
Authors: D. Acero Fernandez, M.J. Ferri Iglesias, C. López Nuñez, M. Barenys Lacha, R. Louvriex Freire, J. Peñafiel Muñoz, S. Fábregas Tió, C. Lopez Oliu, L. Vidal Plana, M. Hombrados Verde
Journal: Journal of Hepatology (2014)
Long-Term Follow-up of Unilateral Pallidotomy in Advanced Parkinson's Disease
Authors: Jennifer Fine, Jan Duff, Robert Chen, William Hutchison, Andres M. Lozano, Anthony E. Lang
Journal: New England Journal of Medicine (2000)

Although the short-term benefits of posteroventral pallidotomy for patients with advanced Parkinson's disease have been well documented, little is known about the long-term outcome of the procedure.
Congenital Adrenal Hyperplasia Due to 21-Hydroxylase Deficiency
Authors: Jeffrey S. Flier, Lisa H. Underhill, Gordon B. Cutler, Louisa Laue
Journal: New England Journal of Medicine (1990)

CONGENITAL adrenal hyperplasia due to 21-hydroxylase deficiency is a relatively common genetic disorder. On the basis of worldwide screening programs, the incidence has been calculated to be approximately 1 per 14,000 births.1 Despite impressive advances in treatment and in our understanding of the molecular events that cause congenital adrenal hyperplasia,2 3 4 5 patients with this disorder continue to have problems that reflect the inadequacy of current treatment.6 7 8 9 10 11 12 13 14 15 The response to treatment varies, and the excellent response in some patients should not obscure the need to improve treatment outcomes overall. This review addresses five questions concerning the pathophysiology and treatment of congenital adrenal . . .
Accuracy of breast MRI in predicting tumor extent.
Authors: K Yao, D Rachel, D Bova, M Hulvat, K Rychlik
Journal: Cancer Research (2009)

Abstract Abstract #4022 Introduction: The use of breast MRI to delineate tumor extent prior to surgical resection is becoming more commonplace. How well breast MRI predicts tumor size and extent compared to standard breast imaging is still under investigation.&amp;#x2028; Objective: To determine which imaging modality; mammogram (MGM), ultrasound (U/S), or MRI most accurately predicted tumor size and number of tumor foci.&amp;#x2028; Methods: This was a retrospective review of a prospectively collected database of all breast MRIs performed prior to surgical resection for invasive and noninvasive breast cancer. MGM, U/S, and MRI reports were reviewed and correlated with pathologic tumor size and number of foci.&amp;#x2028; Results: A total of 89 patients with breast cancer underwent bilateral breast MRI prior to surgical resection. Sixty (67%) of the tumors were ductal carcinomas, 21 (24%) were lobular carcinomas, 7 (7%) ductal carcinoma in situ and 2 (2%) were mixed ductal and lobular. The mean tumor size was 1.5cm (0.1-6.0cm) and 32 (38%) were node positive. Fifty three (60%) of the patients underwent lumpectomy and 36 (40%) underwent mastectomy. Of the three imaging modalities, MGM, U/S, and MRI; MRI predicted tumor size significantly more accurately then MGM or U/S (correlation coefficient 0.59 vs 0.78 vs 0.81 respectively). MRI also predicted the number of foci significantly more accurately then MGM or U/S (correlation coefficient 0.48 vs. 0.44 vs. 0.26 respectively). MRI overestimated tumor size by at least 1cm in 12 (14%) patients and the number of tumor foci in 11(16%) patients.&amp;#x2028; &amp;#x2028; Thirteen (15%) of the patients benefitted from MRI while 14 (16%) did not.&amp;#x2028; Conclusions: MRI predicted tumor size and number of foci more accurately then MGM or U/S. Despite these findings, MRI overestimated tumor size and number of tumor foci in a greater percentage of patients then MGM or U/S. More studies are needed to determine the true value of MRI for preoperative surgical planning. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 4022.
The Risk of Embolic Stroke -- Another Piece of the Puzzle
Authors: J. Philip Kistler
Journal: New England Journal of Medicine (1994)

The three disease processes responsible for most ischemic strokes are large-vessel atherothrombotic disease (accounting for about 14 percent of ischemic strokes), small-vessel atherothrombotic or lipohyalinotic disease (i.e., lacunar stroke, accounting for about 27 percent), and embolic disease (accounting for about 59 percent).1,2 Among patients with large-vessel atherothrombotic disease leading to ischemic strokes and transient cerebral ischemic attacks, two thirds have stenosis of more than 70 percent at the bifurcation of the common carotid artery.3,4 In these circumstances, properly selected symptomatic patients, and possibly also asymptomatic patients, benefit from expertly performed carotid endarterectomy. Among the other one third of . . .
SP0015 Implementing Ultrasound into Rheumatology Clinical Practice - A Sucessful Model in Austria
Authors: G.M. Supp
Journal: Annals of the Rheumatic Diseases (2014)

<h3></h3> The regular availability of diagnostic musculoskeletal ultrasonography in daily clinical routine is becoming increasingly important in rheumatology outpatient departments. Facing an increasing number of patients and a multitude of tasks, rheumatologists often face heavy case loads, resulting in limited time allotted to patient examination. Working as part of a multidisciplinary team, health professionals can take over several tasks from physicians, ranging from biometrical tests to counselling. In line with this, health professionals such as radiographic technicians and sonographers trained in musculoskeletal ultrasound can help and support daily rheumatology practice in outpatient clinics and can facilitate the undertaking of scientific studies. <h3>Disclosure of Interest</h3> None declared <h3>DOI</h3> 10.1136/annrheumdis-2014-eular.6159
Stat Bite Cancer Mortality by Age
Authors: B. Miller
Journal: JNCI Journal of the National Cancer Institute (1994)

Journal Article Stat Bite Cancer Mortality by Age Get access Barry Miller Barry Miller Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 86, Issue 4, 16 February 1994, Page 257, https://doi.org/10.1093/jnci/86.4.257 Published: 16 February 1994
Endoscopic removal of migrating silastic band after vertical banding gastroplasty
Authors: S. Chen Yi Mei, W. Tam, G. Nind, R. Singh
Journal: Endoscopy (2010)

A 33-year-old woman was investigated for persistent dysphagia, severe gastroesophageal reflux disease, and refractory vomiting. She had undergone vertical banding gastroplasty (VBG) 5 years earlier to manage her obesity and had successfully lost 90 kg in weight. This was performed following failed laparoscopic adjustable gastric banding (LAGB), in which significant reflux symptoms required deflation of the band. Physical examination was normal. Upper gastrointestinal endoscopy revealed a gastric pouch at 35 – 46 cm from the incisors, which contained residual food particles. Within the gastric lumen, migration of a silastic band from the VBG was noted ([Fig. 1]).
455 GS-9620 INDUCES A PRESYSTEMIC INNATE IMMUNE RESPONSE IN THE ABSENCE OF SERUM INTERFERON OR ADVERSE EFFECTS IN BOTH NON-CLINICAL SPECIES AND HUMANS
Authors: D. Tumas, A. Fosdick, X. Zheng, R. Lanford, J. Hesselgesser, C. Frey, W. Grushenka, R. Halcomb, U. Lopatin
Journal: Journal of Hepatology (2012)
Insulin Secretion in Obesity
Authors: Robert A. Kreisberg, Buris R. Boshell, John DiPlacido, Roy F. Roddam
Journal: New England Journal of Medicine (1967)

ALTHOUGH hyperinsulinemia has been well established in obese subjects1 , 2 only some demonstrate abnormalities of glucose tolerance. It has been suggested that the ability of the obese subject to maintain normal glucose tolerance is a function of B-cell reserve, implying that insulin secretory rates and plasma insulin levels would be higher in obese subjects with normal glucose tolerance than in those with abnormal glucose tolerance. However, if obese subjects with abnormal glucose tolerance were demonstrated to have higher insulin levels than those with normal glucose tolerance, insulin resistance would be a more suitable explanation.This investigation was undertaken to study the . . .
Abstract 1589: Low shear stress induces the novel tumor endothelial marker CLEC14A that mediates cell migration and vascular development
Authors: Manuela Mura, Xiadong Zhuang, Henrik Vorschmitt, Rajeeb K. Swain, Sarah Durant, John M. Herbert, Helen Sheldon, Maud Andre, Sharon Sanderson, Gary Reynolds, Katie Glen, Nguyet-Thin Luu, Helen McGettrick, Phillip Antczak, Francesco Falciani, Gerard Nash, Zsuzsanna Nagy, Roy Bicknell
Journal: Cancer Research (2010)

Abstract Experimental evidence using animal models has proven the efficacy of targeting a tumor endothelial marker (TEM) in eradicating large solid tumours. It follows that a well characterised tumor endothelial marker would offer much promise as an anti-cancer target. Despite many efforts by numerous groups, a well defined tumor endothelial marker in man has remained elusive. CLEC14A is a novel endothelial specific C-type lectin that is a member of the endosialin/TEM1 and thrombomodulin family of lectins. Protein sequence alignment of CLEC14A shows conservation from fish to man and endothelial specificity of expression is seen in the embryonic zebrafish. Detailed analysis of CLEC14A expression using human tissue arrays showed that CLEC14A is absent in human adult tissue but highly expressed in endothelium across a wide range of tumour tissues. CLEC14A is a superior tumor endothelial marker to Robo4 in terms of specificity and level of expression on the cell surface. CLEC14A is only expressed by endothelium in the absence of shear stress and this could explain its tumor specific expression due to poor blood flow in ill-formed tumor vessels. Functional studies have shown that CLEC14A is present on filopodia and mediates endothelial cell migration and tube formation. Anti-sera to CLEC14A similarly inhibited these processes suggesting that anti-CLEC14A monoclonal antibodies would have anti-angiogenic activity. The expression profile of CLEC14A, its cell surface localisation and inhibition of pro-angiogenic activities by anti-sera make CLEC14A a uniquely interesting target. 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 1589.
1087 PEGINTERFERON-ALFA MONO-THERAPY SHOWS FAVOURABLE OUTCOME WHEN INITIATED EARLY AFTER DIAGNOSIS OF ACUTE HCV IN HIV-INFECTED PATIENTS
Authors: C. Boesecke, S. van Assen, H.-J. Stellbrink, A. Baumgarten, P. Ingiliz, C. Schwarze-Zander, J.-C. Wasmuth, A.I.M. Hoepelman, J.K. Rockstroh, J.E. Arends
Journal: Journal of Hepatology (2012)
P429 URSODEOXYCHOLIC ACID VIA REGULATION OF BILE ACIDS AND MAMMALIAN TARGET OF RAPAMYCIN TO IMPROVE LIPID METABOLISM DISORDERS WITH NON-ALCOHOLIC AND ALCOHOL-INDUCED FATTY LIVER DISEASE
Authors: H.M. Liu, T.Y. Lee, J.F. Liao, H.C. Lin
Journal: Journal of Hepatology (2014)
S138 Treating idiopathic pulmonary fibrosis with the addition of co-trimoxazole
Authors: L. Shulgina, A. Cahn, E. Chilvers, H. Parfrey, A. Clark, E. Wilson, O. Twentyman, T. Davison, J. Curtin, A. Wilson
Journal: Thorax (2011)

<h3>Background</h3> Idiopathic pulmonary fibrosis is a fatal condition with limited treatment options; however in a previous small study co-trimoxazole has been shown to be beneficial. <h3>Methods</h3> In a double-blind, multi-centre study, 181 patients with usual interstitial pneumonia (n=166) or fibrotic non-specific interstitial pneumonia (n=15) were randomised to receive co-trimoxazole 960 mg twice daily or placebo for 12 months in addition to their usual care. Measurements were made of forced vital capacity (FVC), total lung capacity, total lung diffusing capacity of carbon monoxide, Medical Research Council dyspnoea score, St George9s Respiratory Questionnaire and quality adjusted life years (QALYs). All cause mortality, costs and adverse events were recorded. <h3>Results</h3> Co-trimoxazole had no effect on FVC or other measures of lung function. However in the per-protocol analysis, co-trimoxazole resulted in a significant reduction in mortality (HR of 0.2 (0.06, 0.78)), significant improvements in the symptom domain of St George9s Respiratory Questionnaire (mean difference −5.30 (−11.99, 1.40) units) and QALYs gained (mean difference 0.12 (0.01, 0.22) QALYs), and a reduction in the percentage of patients requiring an increase in oxygen therapy (OR 0.05 (0.00, 0.61)) compared to placebo. Furthermore, the use of co-trimoxazole reduced respiratory tract infections. The incremental cost per QALY gained was £21 391 (52.74% probability of being below £30 000; intention to treat analysis, UK societal perspective). <h3>Conclusion</h3> The addition of co-trimoxazole therapy to standard treatment for Idiopathic pulmonary fibrosis had no effect on lung function or disease progression but resulted in a fivefold reduction in mortality and was cost-effective at UK thresholds.
Abstract 3920: EphA2 transcription is regulated by activation of Ras / MEK2 / cytoplasmic ERK pathway in pancreatic cancer
Authors: Pavel A. Levin, Thiruvengadam Arumugam, David J. McConkey, Shrikanth Reddy, Craig D. Logsdon
Journal: Cancer Research (2010)

Abstract Background: We have previously shown that the EphA2 receptor is overexpressed in pancreatic cancer. Silencing of EphA2 receptor in combination with gemcitabine decreases tumor growth and metastases in a mouse model of gemcitabine resistant pancreatic cancer. However, regulation of EphA2 expression in pancreatic cancer is unknown. The objective of this study was to determine a possible relationship between Ras/MAPK pathway and EphA2. Methods: Pancreatic cancer cell lines, MPanc96 and MiaPaca-2, were used in this study. Ras was silenced with 2 different siRNA constructs; EphA2 protein and RNA expression levels were measured. ERK involvement in EphA2 regulation was analyzed by treating cells with 2 inhibitors for MEK (U0126 and PD 98059) and siRNA specific for either MEK1 or MEK2. Effect of MEK inhibition on EphA2 mRNA stability was examined by blocking mRNA synthesis with actinomycin D and measuring mRNA degradation by Q-PCR. In order to investigate the role of subcellular localization of ERK in regulation of EphA2 expression, we overexpressed cytoplasmic anchor protein PEA-15, which binds to ERK and sequesters it to the cytoplasm. Results: Silencing of mutant K-Ras decreased EphA2 mRNA and protein levels. EphA2 mRNA and protein levels decreased in a time- and dose-dependent manner after treatment with MEK chemical inhibitors. Inhibition of MEK activity did not affect EphA2 mRNA stability. Silencing of MEK2 but not MEK1 decreased EphA2 mRNA levels. Overexpression of PEA-15 depleted nuclear ERK, indicated by the absence of phosphorylated Fra-1. Depletion of the nuclear ERK did not affect EphA2 transcription, suggesting that EphA2 is regulated through the cytoplasmic ERK. Conclusions: These data suggest that EphA2 levels are regulated by the RAS / MEK2 / cytoplasmic ERK pathway via regulation of EphA2 mRNA transcription. 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 3920.