tbuckley/cabot-search huggingface dataset:
A classification based framework for quantitative description of large-scale microarray data.
Authors: Dipen P Sangurdekar, Friedrich Srienc, Arkady B Khodursky
Journal: Genome biology (2006)

Abstract Genome-wide surveys of transcription depend on gene classifications for the purpose of data interpretation. We propose a new information-theoretical-based method to: assess significance of co-expression within any gene group; quantitatively describe condition-specific gene-class activity; and systematically evaluate conditions in terms of gene-class activity. We applied this technique to describe microarray data tracking Escherichia coli transcriptional responses to more than 30 chemical and physiological perturbations. We correlated the nature and breadth of the responses with the nature of perturbation, identified gene group proxies for the perturbation classes and quantitatively compared closely related physiological conditions.
Development of laboratory-based intermittent running protocols that are matched for various physiological parameters
Authors: J D Bartlett, G L Close, B Drust, J P Morton
Journal: British Journal of Sports Medicine (2010)

Data from cycling based protocols demonstrate that high-intensity interval training (HIT) is a more efficient mode of exercise training compared with traditional moderate-intensity continuous (CONT) approaches. The use of cycling based protocols is methodologically advantageous as total work done can be quantified by measuring subject's power output while pedalling on a cycle ergometer. However, examining the efficacy of HIT vs CONT running is more challenging as measurements of heart rate per se may not always reflect energy production. It may therefore be more accurate to prescribe, quantify and match exercise intensity during HIT and CONT running by matching protocols for average velocity corresponding to a particular %VO 2max . The aim of the current study was to develop and match laboratory-based HIT and CONT running protocols for energy expenditure, average intensity, duration and distance run. Eight recreationally active men performed two running protocols consisting of HIT (6×3 min 90% VO 2max interspersed with 6×3 min active recovery at 50% VO 2max with 7-min warm-up and cool-down at 70% VO 2max ) and CONT (50 min continuous running exercise at 70% VO 2max ). Protocols were matched for average intensity (70% VO 2max ), duration (50 min) and distance run (9843±494 m). There was no difference (p&gt;0.05) in average heart rate (88±3% HRmax vs 87±3% HRmax), average VO 2 (71±6% VO 2max vs 73±4% VO 2max ), total VO 2 (162±16 litres vs 166±27 litres) or energy expenditure (811±83 kcal vs 832±136 kcal) between HIT and CONT protocols, respectively. Although ratings of perceived exertion were higher (p&lt;0.05) during HIT compared to CONT (14±1 vs 13±1), HIT was characterised by higher ratings of perceived enjoyment (p&lt;0.05) (88±6 vs 61±12). To the authors' knowledge, this is the first study to have matched HIT and CONT running for all the aforementioned variables. These data provide a controlled experimental model to study the efficacy of HIT vs CONT running. Furthermore, HIT is perceived as more enjoyable than CONT which may have implications for improving exercise adherence in individuals undertaking exercise training to improve human health and/or performance.
A unified science of cultural evolution should incorporate choice
Authors: Barry Sopher
Journal: Behavioral and Brain Sciences (2006)

Analogies between biological and cultural evolution may be illuminating and suggest methods to pursue in the quest for a unified science of cultural evolution. Significant progress, however, is unlikely to be made by trying to fit cultural evolution neatly into a biological evolution schema. A key element defining and differentiating cultural evolution may be the role of conscious human choices.
Relationships of generalized and regional adiposity to insulin sensitivity in men.
Authors: N Abate, A Garg, R M Peshock, J Stray-Gundersen, S M Grundy
Journal: Journal of Clinical Investigation (1995)

The relative impacts of regional and generalized adiposity on insulin sensitivity have not been fully defined. Therefore, we investigated the relationship of insulin sensitivity (measured using hyperinsulinemic, euglycemic clamp technique with [3-3H]glucose turnover) to total body adiposity (determined by hydrodensitometry) and regional adiposity. The latter was assessed by determining subcutaneous abdominal, intraperitoneal, and retroperitoneal fat masses (using magnetic resonance imaging) and the sum of truncal and peripheral skinfold thicknesses. 39 healthy middle-aged men with a wide range of adiposity were studied. Overall, the intraperitoneal and retroperitoneal fat constituted only 11 and 7% of the total body fat. Glucose disposal rate (Rd) and residual hepatic glucose output (rHGO) values during the 40 mU/m2.min insulin infusion correlated significantly with total body fat (r = -0.61 and 0.50, respectively), subcutaneous abdominal fat (r = -0.62 and 0.50, respectively), sum of truncal skinfold thickness (r = -0.72 and 0.57, respectively), and intraperitoneal fat (r = -0.51 and 0.44, respectively) but not to retroperitoneal fat. After adjusting for total body fat, the Rd and rHGO values showed the highest correlation with the sum of truncal skinfold thickness (partial r = -0.40 and 0.33, respectively). We conclude that subcutaneous truncal fat plays a major role in obesity-related insulin resistance in men, whereas intraperitoneal fat and retroperitoneal fat have a lesser role.
P53 Mutation Analysis of Colorectal Liver Metastases: Relation to Actual Survival, Angiogenic Status, and p53 Overexpression
Authors: Koert P. de Jong, Annette S.H. Gouw, Paul M.J.G. Peeters, Marian Bulthuis, Lorian Menkema, Robert J. Porte, Maarten J.H. Slooff, Harry van Goor, Anke van den Berg
Journal: Clinical Cancer Research (2005)

Abstract Purpose: To correlate TP53 mutations with angiogenic status of the tumor and prognosis after liver surgery in patients with colorectal liver metastases and to correlate immunohistochemical staining of p53 protein with TP53 gene mutations. Experimental Design: Tumors of 44 patients with surgically treated colorectal liver metastases were analyzed for (a) TP53 mutations using denaturing gradient gel electrophoresis followed by sequencing, (b) microvessel density using the hot spot overlap technique, (c) apoptotic rate in tumor cells and endothelial cells of tumor microvessels using double immunostaining for anti–cleaved caspase 3 and anti-CD34, and (d) expression of p53 protein using immunohistochemistry. Results:TP53 mutations were detected in 36% of the metastases and occurred more frequently in liver metastases from left-sided colon tumors than from right-sided colon tumors (P = 0.04). In metastases with TP53 mutations, microvessel density was higher compared with tumors with wild-type p53. Endothelial cell apoptosis was not different in tumor microvessels from TP53-mutated versus nonmutated tumors. The 5-year actual survival was not influenced by TP53 mutational status, microvessel density, or endothelial cell apoptotic rate of the tumors. Based on immunohistochemical p53 overexpression, the positive and negative predictive values of TP53 mutations were 61% and 82%. Conclusions: In patients with surgically treated colorectal liver metastases, TP53 mutations and angiogenic status did not influence prognosis. Immunohistochemistry is not a reliable technique for detecting TP53 mutations.
Control of cardiac sarcolemmal adenylate cyclase and sodium, potassium-activated adenosinetriphosphatase activities.
Authors: M Tada, M A Kirchberger, J M Iorio, A M Katz
Journal: Circulation Research (1975)

A plasma membrane preparation purified from guinea pig ventricles without the use of high concentrations of detergents or structure-disrupting salts was used to compare the mechanisms of controlling sodium, potassium-activated adenosinetriphosphatase (Na, K-ATPase) and adenylate cyclase activities. The basal ATPase activity of 4-6 mu moles P1/hour mg-1 protein, measured in 120 mM NaC1 or KC1, was approximately doubled in 100 mM NaC1 plus 20 mM KC1. This increment, the Na, K-ATPase, was abolished by 10-5M ouabain, the K1 for ouabain being approximately 3 X 10-7M. 1-Epinephrine had no effect on Na, K-ATPase, but NaF was inhibitory. Adenylate cyclase, which had a basal activity of approximately 50% by NaC1 or KC1 alone at concentrations up to 0.2M. There was no additional stimulation of adenylate cyclase activity when na+ K+ included together. Both 1-epinephrine and NaF cause significant stimulation of adenylate cyclase, but neither basal nor activated cyclic AMP PRODUCTION WAS INFLUENCED BY OUABAIN. Half-maximal stimulation was seen at approximately 5 X 10-6M 1-epinephrine. Both the catecholamine and NaF increased the V-max ofcardiac plasma membrane adenylate cyclase without significantly influencing Km. Increasing Ca2+ in the range between 10-7 and 10-3M inhibited basal, 1-epinephrine-stimulated, and NaF-stimulated activities. Basal rates of cyclic AMP production were more sensitive to Ca2+ than was 1-epinephrine stimulation was increased from approximately 60% in 0.5 mM EGTA to approximately 150% in 10-7M Ca2+ and 400% in 10-5M Ca2+. The inhibitory effect of Ca2+ on adenylate cyclase activity may represent a negative feed back mechanism by which elevation of intracellular Ca2+ concentration lowers cellular levels of cyclic AMP and thus reduces Ca2+ influx into the myocardium.
Redox/pH dual stimuli-responsive biodegradable nanohydrogels with varying responses to dithiothreitol and glutathione for controlled drug release
Authors: Yuan-Jia Pan, Yuan-Yuan Chen, Dong-Rui Wang, Chuan Wei, Jia Guo, Da-Ru Lu, Chih-Chang Chu, Chang-Chun Wang
Journal: Biomaterials (2012)
Aberrant p53 protein expression is associated with an increased risk of neoplastic progression in patients with Barrett's oesophagus
Authors: Florine Kastelein, Katharina Biermann, Ewout W Steyerberg, Joanne Verheij, Marit Kalisvaart, Leendert H J Looijenga, Hans A Stoop, Laurens Walter, Ernst J Kuipers, Manon C W Spaander, Marco J Bruno
Journal: Gut (2012)

<h3>Objective</h3> The value of surveillance for patients with Barrett9s oesophagus (BO) is under discussion given the overall low incidence of neoplastic progression and lack of discriminative tests for risk stratification. Histological diagnosis of low-grade dysplasia (LGD) is the only accepted predictor for progression to date, but has a low predictive value. The aim of this study was therefore to evaluate the value of p53 immunohistochemistry for predicting neoplastic progression in patients with BO. <h3>Design</h3> We conducted a case–control study within a prospective cohort of 720 patients with BO. Patients who developed high-grade dysplasia (HGD) or oesophageal adenocarcinoma (OAC) were classified as cases and patients without neoplastic progression were classified as controls. P53 protein expression was determined by immunohistochemistry in more than 12 000 biopsies from 635 patients and was scored independently by two expert pathologists who were blinded to long-term outcome. <h3>Results</h3> During follow-up, 49 (8%) patients developed HGD or OAC. P53 overexpression was associated with an increased risk of neoplastic progression in patients with BO after adjusting for age, gender, Barrett length and oesophagitis (adjusted relative risks (RR<sup>a</sup>) 5.6; 95% CI 3.1 to 10.3), but the risk was even higher with loss of p53 expression (RR<sup>a</sup> 14.0; 95% CI 5.3 to 37.2). The positive predictive value for neoplastic progression increased from 15% with histological diagnosis of LGD to 33% with LGD and concurrent aberrant p53 expression. <h3>Conclusions</h3> Aberrant p53 protein expression is associated with an increased risk of neoplastic progression in patients with BO and appears to be a more powerful predictor of neoplastic progression than histological diagnosis of LGD.
Esophageal Cancer in Uruguay: A Case-Control Study&lt;xref ref-type="fn" rid="FN2"&gt;2&lt;/xref&gt;
Authors: A Vassallo, P Correa, E De Stéfani, M Cendán, D Zavala, V Chen, J Carzoglio, H Deneo-Pellegrini
Journal: JNCI Journal of the National Cancer Institute (1985)

Esophageal cancer has constituted a major public health problem in Uruguay, with age-adjusted death rates of 14.5×105 for males and of 3.8×105 for females. A case-control study was undertaken to ascertain the possible association of the local custom of drinking infusions of llex paraguariensis (“maté”) with cancer of the esophagus, after controlling for well-known risk factors, such as alcohol and tobacco consumption. Two hundred twenty-six patients with esophageal cancer and 469 controls (control:case = 2.1) were interviewed at the time of admission or consultation at the Oncology Institute of Montevideo from 1979 through 1984. Males showed elevated risks of esophageal cancer associated with heavy tobacco [relative risk (RR) = 10.8] and alcohol (RR = 10.3) exposures. Among females, the independent effects of tobacco and alcohol were nonsignificant. Maté consumption had an independent effect in both males and females, with odds ratios of 6.5 and 34.6, respectively, for heavy users. Moreover, a well-defined dose response was evident in both sexes.
Metabolic Disconnection Between the Mediodorsal Nucleus of the Thalamus and Cortical Brodmann’s Areas of the Left Hemisphere in Schizophrenia
Authors: Serge A Mitelman, William Byne, Eileen M Kemether, Erin A Hazlett, Monte S Buchsbaum
Journal: American Journal of Psychiatry (2005)

The authors' goal was to examine interregional correlations of thalamocortical metabolic activity during a verbal learning task in schizophrenia.They used [18F]fluorodeoxyglucose positron emission tomography in 41 unmedicated patients with schizophrenia and 59 normal comparison subjects.A metabolic disconnection was observed in patients with schizophrenia in the left hemisphere between the mediodorsal nucleus and widespread frontotemporal cortical regions, and stronger-than-normal intercorrelations were found between the pulvinar and superior temporal, selected parietal, posterior cingulate, and occipital areas.Deficits in the functional interrelationships between the left frontotemporal cortices and the left mediodorsal nucleus of the thalamus complement inferences from postmortem and magnetic resonance imaging volumetric studies identifying a thalamic diathesis in schizophrenia.
Expression of CD44 in normal and rheumatoid synovium and cultured synovial fibroblasts.
Authors: K J Henderson, J C Edwards, J G Worrall
Journal: Annals of the Rheumatic Diseases (1994)

OBJECTIVE--To determine if expression of CD44, the principal receptor for hyaluronan, was altered in rheumatoid (RA) synovium and cultured rheumatoid synovial fibroblasts. METHODS--Synovium was obtained from normal adult human joints (n = 4) and from joints of patients with RA (n = 5). Specific monoclonal antibodies to CD44 were used in immunofluorescence of whole synovium and cultured synovial fibroblasts and in quantitative Western blotting and ELISA of CD44 in cultured synovial fibroblasts. RESULTS--CD44 was restricted to the lining layer in normal synovium but present, in reduced concentrations, throughout rheumatoid synovium. Cultured rheumatoid cells were 19% larger in area and showed far fewer and less extensive CD44-positive cytoplasmic extensions, together with reduced staining intensity compared with normal. Quantitative Western blotting normalised for cell protein showed a 75% reduction (normal = 1754 (835), rheumatoid = 409 (84) mean (SD) arbitrary units) in the amount of CD44 in rheumatoid cells compared with normal, and enzyme linked immunosorbent assay (ELISA) of cultured cell monolayers normalised for cell number indicated a 29% reduction (normal = 0.707 (0.110), rheumatoid = 0.504 (0.103), mean (SD) optical density at 405 nm). CONCLUSIONS--Rheumatoid synovial cells showed altered morphology and reduced CD44 expression compared with normal cells. CD44, by means of modulated associations with the cytoskeleton, may be involved in cell shape change.
Cholesterol Esters (CE) Derived From Hepatic Sterol O-Acyltransferase 2 (SOAT2) Are Associated With More Atherosclerosis Than CE From Intestinal SOAT2
Authors: Jun Zhang, Janet K. Sawyer, Stephanie M. Marshall, Kathryn L. Kelley, Matthew A. Davis, Martha D. Wilson, J. Mark Brown, Lawrence L. Rudel
Journal: Circulation Research (2014)

Cholesterol esters (CE), especially cholesterol oleate, generated by hepatic and intestinal sterol O-acyltransferase 2 (SOAT2) play a critical role in cholesterol homeostasis. However, it is unknown whether the contribution of intestine-derived CE from SOAT2 would have similar effects in promoting atherosclerosis progression as for liver-derived CE.To test whether, in low-density lipoprotein receptor null (LDLr(-/-)) mice, the conditional knockout of intestinal SOAT2 (SOAT2(SI-/SI-)) or hepatic SOAT2 (SOAT2(L-/L-)) would equally limit atherosclerosis development compared with the global deletion of SOAT2 (SOAT2(-/-)).SOAT2 conditional knockout mice were bred with LDLr(-/-) mice creating LDLr(-/-) mice with each of the specific SOAT2 gene deletions. All mice then were fed an atherogenic diet for 16 weeks. SOAT2(SI-/SI-)LDLr(-/-) and SOAT2(-/-)LDLr(-/-) mice had significantly lower levels of intestinal cholesterol absorption, more fecal sterol excretion, and lower biliary cholesterol levels. Analysis of plasma LDL showed that all mice with SOAT2 gene deletions had LDL CE with reduced percentages of cholesterol palmitate and cholesterol oleate. Each of the LDLr(-/-) mice with SOAT2 gene deletions had lower accumulations of total cholesterol and CE in the liver compared with control mice. Finally, aortic atherosclerosis development was significantly lower in all mice with global or tissue-restricted SOAT2 gene deletions. Nevertheless, SOAT2(-/-)LDLr(-/-) and SOAT2(L-/L-)LDLr(-/-) mice had less aortic CE accumulation and smaller aortic lesions than SOAT2(SI-/SI-)LDLr(-/-) mice.SOAT2-derived CE from both the intestine and liver significantly contribute to the development of atherosclerosis, although the CE from the hepatic enzyme appeared to promote more atherosclerosis development.
Salicylates and Reye's Syndrome: Epidemiologic Data as a Basis of Action
Authors: E. Russell Alexander
Journal: JAMA (1982)

Anecdotal observations that what we now know as Reye's syndrome (RS) was associated with ingestion of salicylates preceded the definition of this syndrome.<sup>1</sup>Reye and coworkers<sup>2</sup>first delineated the syndrome of encephalopathy and fatty degeneration of the viscera following a mild viral illness. We now know that RS follows influenza (particularly type B), chickenpox, and other viral illnesses. It occurs with an annual incidence of one to two children per 100,000 persons younger than 18 years. Of this total, 221 to 551 cases were reported per year for the years 1973 through 1981, with a death-to-case ratio of 22% to 42%. After many descriptive studies of RS, a variety of etiologic hypotheses have been entertained, including insecticides and related chemicals, aflatoxins, and salicylates.<sup>3</sup> Case-control epidemiologic studies were initiated in three separate states to investigate many possible associations with RS. The first was by Starko and colleagues<sup>4</sup>
Slob, a Novel Protein that Interacts with the Slowpoke Calcium-Dependent Potassium Channel
Authors: W.Michael Schopperle, Mats H. Holmqvist, Yi Zhou, Jing Wang, Zheng Wang, Leslie C. Griffith, Inna Keselman, Felicity Kusinitz, Daniel Dagan, Irwin B. Levitan
Journal: Neuron (1998)
Comparative Tuberculin Reactions
Authors: Thomas H. Rea
Journal: JAMA (1974)

<h3>To the Editor.—</h3> The report of comparative tuberculin reactions by Erdtmann, Dixon, and Llewellyn (228:479, 1974) is a welcome study in individuals without proven pulmonary tuberculosis. We have done a similar study in a population without pulmonary tuberculosis, not suspect, and not known contacts of tuberculosis patients. Our interest arose when it became evident that some of our lepromatous leprosy patients could not be tested with tuberculin stabilized by polysorbate 80 (Tween 80), the antigen recently recommended for routine use. Of other studies comparing tuberculins in patients with proven tuberculosis,<sup>1,2</sup>none has dealt with the comparison of reactions elicited by different tuberculins in patients without active tuberculosis or suspicion thereof. Could the reactions elicited by the Parke-Davis &amp; Co., 5-tuberculin unit (tu) PPD pill be established as valid in those patients lost to further observation? Twenty-three patients with lepromatous leprosy and 49 with diverse illnesses were tested. Tuberculin, purified
Refinement and Psychometric Evaluation of the Impact of Cancer Scale
Authors: Catherine M Crespi, Patricia A Ganz, Laura Petersen, Adrienne Castillo, Bette Caan
Journal: JNCI Journal of the National Cancer Institute (2008)

Instruments are needed to measure the influence of cancer on quality of life in the expanding population of long-term cancer survivors. We conducted refinement and psychometric evaluation of the Impact of Cancer (IOC) scale by use of data from a large sample of long-term breast cancer survivors and developed an instrument, the Impact of Cancer version 2 (IOCv2), to measure quality of life outcomes.