nils-herrmann/clean_scirepeval huggingface dataset:
Identification and Validation of Reference Genes for qPCR Detection of Serum microRNAs in Colorectal Adenocarcinoma Patients

Serum microRNAs (miRNAs) have become a highlighted research hotspot, especially for their great potential as a novel promising non-invasive biomarker in cancer diagnosis. The most frequently used approach for serum miRNAs detection is quantitative real time polymerase chain reaction (qPCR). In order to obtain reliable qPCR data of miRNAs expression, the use of reference genes as endogenous control is undoubtly necessary. However, no systematic evaluation and validation of reference genes for normalizing qPCR analysis of serum miRNAs has been reported in colorectal adenocarcinoma. We firstly profiled pooled serum of colorectal adenocarcinoma, colorectal adenoma and healthy controls and selected a list of 13 miRNAs as candidate reference genes. U6 snRNA (U6) and above-mentioned 13 miRNAs were included in further confirmation by qPCR. As a result, 5 miRNAs (miR-151a-3p, miR-4446-3p, miR-221-3p, miR-93-5p and miR-3184-3p) were not detected in all samples and 2 miRNAs (miR-197-3p and miR-26a-5p) were relatively low with median Cq more than 35, and were excluded from further stability analysis. Then variable stability of other 6 miRNAs (miR-103b, miR-484, miR-16-5p, miR-3615, miR-18a-3p and miR-191-5p) and U6 were evaluated using two algorithms: geNorm and NormFinder which both identified miR-191-5p as the most stably expressed reference gene and selected miR-191-5p and U6 as the most stable pair of reference genes. After validating in an independent large cohorts and selecting miR-92a-3p as target miRNA to evaluate the effect of reference gene, we propose that combination of miR-191-5p and U6 could be used as reference genes for serum microRNAs qPCR data in colorectal adenocarcinoma, colorectal adenoma and healthy controls.
Acute and short-term effects of the nonpeptide endothelin-1 receptor antagonist bosentan in humans

In recent years, evidence from various animal experiments has accumulated that emphasizes the role of endothelin-1 in the pathophysiology of several cardiovascular diseases, including congestive heart failure. The recent advent of potent antagonists of this system now allows the assessment of the involvement of endothelin-1 in the maintenance of vascular tone in animals and humans. We report hemodynamic data from two trails in patients with chronic severe congestive heart failure (i.e., reduced left ventricular ejection fraction of <30%, elevated resting pulmonary capillary wedged pressure >15 mmHg, and/or reduced cardiac index of 2.5 L/min/m2 or less) who were treated with the mixed endothelin-type A and type B-receptor antagonist bosentan. In the first study, the acute effect of bosentan (300 mg, intravenous) on hemodynamics and neurohormones was investigated. Bosentan was well tolerated and significantly improved impaired hemodynamics due to systemic and venous vasodilation. In the second trial, bosentan was given orally (0.5 g bid) for 14 days, in addition to conventional triple treatment for congestive heart failure, including digitalis, angiotensin-converting enzyme inhibitors, and diuretics. Cardiac hemodynamics were monitored during the first 24 hours of treatment, and measurements were repeated during the last day of bosentan therapy. Bosentan was well tolerated in these patients as well, and hemodynamic measures were compatible with an additional effect of bosentan after 2 weeks. However, there was a slight increase in heart rate as well. Our result underline the importance of endogenously generated endothelin-1 in congestive heart failure and suggest a potential benefit of endothelin antagonism in such patients. However, long-term studies are needed to establish whether chronic endothelin antagonism has beneficial clinical effects and is capable of improving survival and/or symptoms in severe heart failure patients who remain symptomatic despite standard triple therapy.
A Model-Forest Based Horizontal Fragmentation Approach for Disjunctive Deductive Databases

Disjunctive deductive databases (DDDBs) can capture indeenite information, i.e., imprecise or partial knowledge, of the real world. In this paper we present a method for horizontally fragmenting a DDDB based on the minimal-model forest approach. A minimal-model forest of a DDDB D is a collection of minimal-model trees of D such that each tree represents a set of facts that is disjoint from the set of facts represented in any other tree of D. Eventually, each tree T in the forest is assigned to a fragment along with the rules that utilize the facts represented in T to infer new facts. This approach minimizes the amount of data in D that needs to be processed for any query of D by taking the advantage of the natural partition of data that may appear in D.
Effects of nicotine abstinence and menstrual phase on task performance.

Both menstrual phase and nicotine have been shown to affect task performance. Though conflicting results have been reported, at least one well-controlled study has demonstrated that women at midluteal phase show superior performance on speech articulation and speeded motor coordination tests, but poorer performance on perceptual-spatial tests, than during menses. Smokers have demonstrated superior performance on numerous tasks following nicotine than following placebo. To explore the separate and combined influence of these factors, we studied 13 regularly-menstruating smokers using a two (smoking vs. 12 hours' abstinence) by two (menstrual vs. midluteal phase) factorial design. During each session, subjects completed a test battery including two speeded motor coordination tasks, a computerized reaction time test, and the Stroop (1935) color/word test. Subjects completed the Stroop color and color-word tasks significantly faster after ad lib smoking than after overnight abstinence. No other significant differences emerged. Our findings replicate, in an all-female sample, previous reports that speed of cognitive processing is reduced by nicotine abstinence (or enhanced by nicotine administration). Our failure to observe menstrual cycle effects raises the possibility that the anti-estrogenic effects of smoking may attenuate phase differences in performance.
Long-term effectiveness of highly active antiretroviral therapy on the survival of children and adolescents with HIV infection: a 10-year follow-up study.

Previous observational studies found highly active antiretroviral therapy (HAART) to be associated with improved survival among human immunodeficiency virus (HIV)-infected children and adolescents. However, these studies had limited follow-up of HIV-infected children undergoing HAART. Given that HIV infection is chronic and that exposure to HAART is likely to be life-long, there is a need to evaluate the long-term effect of HAART on survival in this population.



The study included 1236 children and adolescents who were perinatally infected with HIV, who were on study or enrolled after January 1996 in a United States-based multicenter prospective cohort study (Pediatric AIDS Clinical Trials Group 219/219C), and who were not receiving HAART at baseline; subjects were observed for a maximum of 10 years through June 2006. A weighted Cox regression model was used to estimate the effect of HAART on survival, appropriately adjusted for time-varying confounding by severity.



At the end of the 10-year follow-up period (median duration of follow-up, 6.3 years; interquartile range, 4.3-9.8 years), 70% of participants had initiated HAART. Lower CD4 cell percentages, total lymphocyte counts, and albumin levels were associated with an increased probability of initiating HAART. Eighty-five deaths were observed, and the mortality hazard ratio associated with HAART, compared with non-HAART regimens, was 0.24 after adjusting for measured confounding by severity (95% confidence interval, 0.11-0.51).



The use of HAART was highly effective in reducing mortality during the period 1996-2006 among children and adolescents infected with HIV. With improved long-term survival, continued follow-up is necessary to evaluate the effects of prolonged use of HAART on potential adverse events, immune function, growth, sexual maturation, and quality of life in this population.
A mobile phone-based care model for outpatient cardiac rehabilitation: the care assessment platform (CAP)

Cardiac rehabilitation programs offer effective means to prevent recurrence of a cardiac event, but poor uptake of current programs have been reported globally. Home based models are considered as a feasible alternative to avoid various barriers related to care centre based programs. This paper sets out the study design for a clinical trial seeking to test the hypothesis that these programs can be better and more efficiently supported with novel Information and Communication Technologies (ICT).



We have integrated mobile phones and web services into a comprehensive home- based care model for outpatient cardiac rehabilitation. Mobile phones with a built-in accelerometer sensor are used to measure physical exercise and WellnessDiary software is used to collect information on patients' physiological risk factors and other health information. Video and teleconferencing are used for mentoring sessions aiming at behavioural modifications through goal setting. The mentors use web-portal to facilitate personal goal setting and to assess the progress of each patient in the program. Educational multimedia content are stored or transferred via messaging systems to the patients phone to be viewed on demand. We have designed a randomised controlled trial to compare the health outcomes and cost efficiency of the proposed model with a traditional community based rehabilitation program. The main outcome measure is adherence to physical exercise guidelines.



The study will provide evidence on using mobile phones and web services for mentoring and self management in a home-based care model targeting sustainable behavioural modifications in cardiac rehabilitation patients.
An evaluation of sexual functioning in employed outpatients with major depressive disorder treated with desvenlafaxine 50 mg or placebo.

The symptoms of major depressive disorder (MDD) include sexual dysfunction, but antidepressant pharmacotherapies are also associated with treatment-emergent sexual dysfunction.



These secondary and post hoc analyses evaluated sexual functioning in employed adult outpatients with MDD treated with desvenlafaxine (administered as desvenlafaxine succinate) and placebo.



Patients were randomly assigned (2:1 ratio) to 12 weeks of double-blind treatment with desvenlafaxine 50 mg/day or placebo.



The Arizona Sexual Experiences Scale (ASEX) was administered every 4 weeks. Analysis of covariance was used to compare differences in mean change from baseline ASEX scores between desvenlafaxine and placebo for women and men.



There were 422 evaluable patients with baseline ASEX scores (desvenlafaxine, N = 281; placebo, N = 141). Among women (desvenlafaxine, N = 184; placebo, N = 92), baseline scores were 20.0 (5.2) and 20.5 (5.3) for desvenlafaxine and placebo, respectively; mean changes at week 12 were -1.93 (0.37) and -1.03 (0.54), respectively (mean difference: 0.90 [-0.38, 2.18]; P = 0.169). Among men (desvenlafaxine, N = 97; placebo, N = 49), baseline scores were 16.4 (4.9) and 15.9 (4.8) for desvenlafaxine and placebo, respectively; mean changes at week 12 were -1.13 (0.47) and -1.06 (0.70), respectively (mean difference: 0.07 [-1.59, 1.74]; P = 0.932). Significantly greater orgasmic dysfunction at week 12 was observed in the subgroup of men without baseline sexual dysfunction treated with desvenlafaxine relative to placebo. Conversely, women without baseline sexual dysfunction experienced poorer overall sexual functioning and orgasm satisfaction at week 12 with placebo relative to desvenlafaxine treatment. Subgroup analyses of treatment responders and nonresponders found no difference in the proportion of men or women that developed or had resolution of sexual dysfunction in the desvenlafaxine and placebo groups.



With the exception of orgasmic dysfunction in men without preexisting sexual dysfunction, no significant negative effect on sexual functioning was observed over 12 weeks of treatment with desvenlafaxine.
High-Dose Intravenous Vitamin C Combined with Cytotoxic Chemotherapy in Patients with Advanced Cancer: A Phase I-II Clinical Trial

Biological and some clinical evidence suggest that high-dose intravenous vitamin C (IVC) could increase the effectiveness of cancer chemotherapy. IVC is widely used by integrative and complementary cancer therapists, but rigorous data are lacking as to its safety and which cancers and chemotherapy regimens would be the most promising to investigate in detail.



We carried out a phase I-II safety, tolerability, pharmacokinetic and efficacy trial of IVC combined with chemotherapy in patients whose treating oncologist judged that standard-of-care or off-label chemotherapy offered less than a 33% likelihood of a meaningful response. We documented adverse events and toxicity associated with IVC infusions, determined pre- and post-chemotherapy vitamin C and oxalic acid pharmacokinetic profiles, and monitored objective clinical responses, mood and quality of life. Fourteen patients were enrolled. IVC was safe and generally well tolerated, although some patients experienced transient adverse events during or after IVC infusions. The pre- and post-chemotherapy pharmacokinetic profiles suggested that tissue uptake of vitamin C increases after chemotherapy, with no increase in urinary oxalic acid excretion. Three patients with different types of cancer experienced unexpected transient stable disease, increased energy and functional improvement.



Despite IVC's biological and clinical plausibility, career cancer investigators currently ignore it while integrative cancer therapists use it widely but without reporting the kind of clinical data that is normally gathered in cancer drug development. The present study neither proves nor disproves IVC's value in cancer therapy, but it provides practical information, and indicates a feasible way to evaluate this plausible but unproven therapy in an academic environment that is currently uninterested in it. If carried out in sufficient numbers, simple studies like this one could identify specific clusters of cancer type, chemotherapy regimen and IVC in which exceptional responses occur frequently enough to justify appropriately focused clinical trials.
Hepatic estrogen and progesterone receptors in an estrogen-associated hepatic neoplasm

A patient with a benign hepatic neoplasm developing after treatment with estrogenic hormones is described. After excision, the neoplastic tissue was analyzed for the presence of cycosol estrogen and progeterone binding proteins. The noeplasm was classified as focal nodular hyperplasia of the liver and was demonstrated to contain high-affinity cytosol estrogen and progesterone hormone receptors. The estrogen0binding affinity of the neoplasm was three times greater than that of normal liver. Further investigation of cytosol hormone receptors in estrogen associated hepatic neoplasms will be required to define the role of these binding proteins in the possible etiology of certain liver tumors.
Comparative psychometric analysis of vector and isochrone cardiac activation maps

Isochronal cardiac activation maps can be constructed from local activation times associated with spatial locations, and are frequently used to study cardiac arrhythmias. Cardiac velocity vector mapping has been proposed as an alternative method to study cardiac activation in both clinical and research environments. Velocity vectors inherently contain more information than scalar measures of latency, but it is unknown how vector maps and isochronal maps compare when they are used to identify patterns and features associated with arrhythmias. In order to quantitatively compare these two visualization methods, eight cardiologists were asked to complete forced-choice tasks in which they selected ablation sites based on synthetic vector or isochronal maps. Maps varied in arrhythmia complexity, number of vectors or activation times included, and errors in magnitude or angle for maps of velocity vectors. Quantitative comparison was achieved by using psychometric functions to characterize the learning curve and the total number of measurements needed in order to choose a correct ablation site. For simple arrhythmias, performance with vector maps was superior to isochronal maps. Subjects required fewer measurements, and learned more rapidly by studying vector maps. For more complex arrhythmias, there was no significant difference in performance between vector and isochronal maps. However, arrhythmia features were clearer with vector maps, even though this clarity did not necessarily change the ablation site choice. When errors were added to vector maps, performance was satisfactory for angle errors <55/spl deg/, and speed errors did not affect performance.
Effect of sevoflurane combination with epidural anesthesia on myocardial injury in patients with coronary artery disease undergoing non-cardiac surgery.

To determine the effect of sevoflurane combination with epidural anesthesia on myocardial injury in patients with coronary artery disease (CAD) undergoing non-cardiac surgery



The investigation was performed in TianJin NanKai Hospital, TianJin, China from November 2009 to March 2010. Eighty patients with CAD undergoing elective abdominal surgery were randomized into 4 groups: group S1- combined sevoflurane general and epidural anesthesia; group S2 - standard sevoflurane general anesthesia; group P1 - combined propofol general and epidural anesthesia; and group P2 - standard propofol general anesthesia. Mean arterial pressure, central venous pressure, electrocardiogram, and bispectral index was monitored throughout the surgery. The serum levels of interleukin-6 (IL-6), interleukin-8 (IL-8), tumor necrosis factor-alpha TNF-alpha, cardiac troponin I (cTnI), and glycogen phosphorylase BB (GP-BB) was measured at different time points during surgery.



The ST depression in group P1 and S2 was significantly higher than that in group S1 (p=0.000) and lower than that in group P2 (p=0.00). The serum levels of IL-6, IL-8, TNF-alpha, cTnI, and GP-BB in group P1 and S2 were dramatically greater than that in group S1 (p=0.00), and lower than that in group P2 (p=0.00).



Sevoflurane in combination with continuous epidural anesthesia could protect against myocardial damage in patients with CAD, downregulation of IL-6, IL-8, and TNF-alpha might contribute to this protection.
Trends over time of virological and immunological characteristics in the Swiss HIV Cohort Study.

The long-term outcome of antiretroviral therapy (ART) is not assessed in controlled trials. We aimed to analyse trends in the population effectiveness of ART in the Swiss HIV Cohort Study over the last decade.



We analysed the odds of stably suppressed viral load (ssVL: three consecutive values <50 HIV-1 RNA copies/mL) and of CD4 cell count exceeding 500 cells/μL for each year between 2000 and 2008 in three scenarios: an open cohort; a closed cohort ignoring the influx of new participants after 2000; and a worst-case closed cohort retaining lost or dead patients as virological failures in subsequent years. We used generalized estimating equations with sex, age, risk, non-White ethnicity and era of starting combination ART (cART) as fixed co-factors. Time-updated co-factors included type of ART regimen, number of new drugs and adherence to therapy.



The open cohort included 9802 individuals (median age 38 years; 31% female). From 2000 to 2008, the proportion of participants with ssVL increased from 37 to 64% [adjusted odds ratio (OR) per year 1.16 (95% CI 1.15-1.17)] and the proportion with CD4 count >500 cells/μL increased from 40 to >50% [OR 1.07 (95% CI 1.06-1.07)]. Similar trends were seen in the two closed cohorts. Adjustment did not substantially affect time trends.



There was no relevant dilution effect through new participants entering the open clinical cohort, and the increase in virological/immunological success over time was not an artefact of the study design of open cohorts. This can partly be explained by new treatment options and other improvements in medical care.
The Omega-Project--a comparison of two diagnostic strategies for risk- and cost-oriented management of dyspepsia.

In dyspepsia few data are available from the primary care setting on how selective, risk-factor-oriented endoscopy compares with mandatory endoscopy in the diagnostic outcome and in direct and secondary costs. We studied this in a two-armed multicentre trial (omega-project) with primary care physicians.



Patients were enrolled and treated by primary care physicians and referred to a gastroenterologist for upper gastrointestinal endoscopy (UGE). Patients were enrolled in the study if they had had epigastric complaints for more than 1 month and no obvious signs or history of organic disease. In the first arm of the study endoscopy was mandatory, in the second selective, i.e. according to a predefined risk profile. Patients enrolled were treated with prokinetic drugs for 2 months. A further indication for endoscopy was non-response to treatment (reduction of the initial symptoms score by less than two-thirds) in the study with selective endoscopy and relapse within the 2-month follow-up period in both studies. The direct costs from number of consultations with the primary care physician, UGEs, number of prescriptions per patient and also absenteeism in days per week were carefully registered in both groups.



All 172 patients of the mandatory endoscopy study and 203/656 patients enrolled in the selective endoscopy study had an UGE (125 at admission, 78 in the follow-up period). Patients were treated for 4 weeks (cisapride or domperidone) and thereafter followed for 8 weeks, at the end of the observation period the response rates were 80% and 79%, respectively. The prevalence of gastric cancers was similar in both groups (> 1%) but extrapolation from the data collected with compulsory endoscopy suggests that two-fifths of the anticipated peptic lesions remained undetected by following the selective strategy. The cost analysis revealed a 31% cost reduction with the selective strategy--in the Swiss cost system--through a reduction in the number of endoscopies by 67%.



Selective UGE is cheaper and appears not to compromise the response to prokinetics; however, its diagnostic power is less than with mandatory UGE.