nils-herrmann/clean_scirepeval huggingface dataset:
A bottom-up, knowledge-aware approach to integrating and querying web data services

As a wealth of data services is becoming available on the Web, building and querying Web applications that effectively integrate their content is increasingly important. However, schema integration and ontology matching with the aim of registering data services often requires a knowledge-intensive, tedious, and error-prone manual process.
 We tackle this issue by presenting a bottom-up, semi-automatic service registration process that refers to an external knowledge base and uses simple text processing techniques in order to minimize and possibly avoid the contribution of domain experts in the annotation of data services. The first by-product of this process is a representation of the domain of data services as an entity-relationship diagram, whose entities are named after concepts of the external knowledge base matching service terminology rather than being manually created to accommodate an application-specific ontology. Second, a three-layer annotation of service semantics (service interfaces, access patterns, service marts) describing how services “play” with such domain elements is also automatically constructed at registration time. When evaluated against heterogeneous existing data services and with a synthetic service dataset constructed using Google Fusion Tables, the approach yields good results in terms of data representation accuracy.
 We subsequently demonstrate that natural language processing methods can be used to decompose and match simple queries to the data services represented in three layers according to the preceding methodology with satisfactory results. We show how semantic annotations are used at query time to convert the user's request into an executable logical query. Globally, our findings show that the proposed registration method is effective in creating a uniform semantic representation of data services, suitable for building Web applications and answering search queries.
What is the best sequential treatment strategy in the treatment of depression? Adding pharmacotherapy to psychotherapy or vice versa?

Insufficient response to monotreatment for depression is a common phenomenon in clinical practice. Even so, evidence indicating how to proceed in such cases is sparse.



This study looks at the second phase of a sequential treatment algorithm, in which 103 outpatients with moderately severe depression were initially randomized to either short-term supportive psychodynamic therapy (PDT) or antidepressants. Patients who reported less than 30% symptom improvement after 8 weeks were offered combined treatment. Outcome measures were the Hamilton Depression Rating Scale (HAM-D), the Clinical Global Impression of Severity and Improvement, the SCL-90 depression subscale and the EuroQOL questionnaire.



Despite being nonresponsive, about 40% of patients preferred to continue with monotherapy. At treatment termination, patients initially randomized to PDT had improved more than those initially receiving antidepressants, as indicated by the HAM-D and the EuroQOL, independently of whether the addition was accepted or not.



Starting with psychotherapy may be preferable in mildly and moderately depressed outpatients. For patients who receive either PDT or antidepressants, combined therapy after early nonresponse seems to be helpful. Nevertheless, this sequential strategy is not always preferred by patients.
Rationale and design of a prospective trial to assess the sensitivity and positive predictive value of implantable intrathoracic impedance monitoring in the prediction of heart failure hospitalizations: the SENSE-HF study.

Intrathoracic impedance monitoring is a new diagnostic tool for patients with heart failure that may aid early identification of decompensation and pulmonary congestion.



The Sensitivity of the InSync Sentry feature for the Prediction of Heart Failure (ie, SENSE-HF) trial is a prospective multicenter international study designed to evaluate the sensitivity and positive predictive value (PPV) of the intrathoracic impedance diagnostic tool, OptiVol, present in Medtronic implantable devices. A total of 500 patients will be enrolled in the trial, with follow-up for up to 24 months. The study has 3 phases. Phase I is double-blind, and evaluates retrospectively the sensitivity and PPV of the intrathoracic impedance data for the prediction of hospitalization with the signs and/or symptoms of pulmonary congestion. At 6 months, the patient enters Phase II, which evaluates the clinical utility of the nominal "alarm" threshold value for identification of episodes of decompensation. The patient enters the final phase (Phase III) after an episode of decompensation correctly identified by the Fluid Trend data ("true" positive alarm), with data collection on how physicians use the Fluid Trend data to influence management. An end point committee adjudicates health care utilizations events (hospitalizations and doctor visits) for their association with signs and/or symptoms of pulmonary congestion.



The study completed recruitment during 2008.
Spontaneous forniceal rupture: Can it be treated conservatively?

Spontaneous forniceal rupture is one of the possible complications of urolithiasis. The mechanism of forniceal rupture is not well explained in the literature. Most of the cases presented with sudden onset of acute renal colic and diagnosed by noncontrast CT (NCCT). Until now there is no solid consensus about the ideal management of such a condition.



To study indications and validity of conservative management of spontaneous caliceal rupture.



This is an observational prospective study.



All cases diagnosed as spontaneous forniceal rupture in our departments from 2011 to 2015 were enrolled. All cases were diagnosed with NCCT or CT-Urography.. Non complicated patients were primarily managed conservatively. Intervention (DJ stent insertion, nephrostomy tube insertion, or urgent ureteroscopy) was reserved to complicated cases or solitary kidney. Drainage of urinoma was done in cases with sizable urinoma (more than 100 ml3).



A total of 40 patients: Twenty eight (70%) patients had normal serum creatinine level at presentation, while 12 (30%) patients had elevated serum creatinine. Twenty three (57.5%) patients were successfully managed conservatively, their mean size of stone was 6.2 ± 2 mm and the hospital stay was 3.1 ± 1.9 days. Eighteen patients (42.5%) underwent interventions. Their stone size was 4.5 ± 2.1 mm and the hospital stay for the interventional group was 4.2 ± 1.8 days.


 USED
Mann-Whitney test was used for testing difference between means because the data groups are not parametric. Otherwise, simple descriptive statestics were used.



Spontaneous forniceal rupture is more likely to occur with smaller distal ureteric stones. Conservative management is a valid option in non-complicated cases. Intervention should be reserved to complicated cases or cases with sizable urinoma.
Hyperinsulinemia and cognitive decline in a middle-aged cohort.

Determining modifiable risks factors for cognitive decline and dementia are a public health priority as we seek to prevent dementia. Type 2 diabetes and related disorders such as hyperinsulinemia increase with aging and are increasing in the U.S. population. Our objective was to determine whether hyperinsulinemia is associated with cognitive decline among middle-aged adults without type 2 diabetes, dementia, or stroke in the Atherosclerosis Risk in Communities (ARIC) cohort.



Middle-aged adults (aged 45-64 years at baseline) in the ARIC cohort had fasting insulin and glucose assessed between 1987 and 1989. Subjects with dementia, type 2 diabetes, or stroke at baseline were excluded from analysis. Three tests of cognitive function available at baseline and 6 years later were delayed word recall (DWR), digit symbol subtest (DSS), and first letter word fluency (WF). Cross-sectional comparisons and linear regression models were computed for cognitive tests at baseline and change in cognitive test scores to determine whether cognitive function was associated with two measures of insulin resistance, fasting insulin and homeostasis model assessment (HOMA). Linear regression models controlled for age, sex, race, marital status, education level, smoking status, alcohol use, depression, hypertension, and hyperlipidemia.



In unadjusted and adjusted analyses, hyperinsulinemia based on fasting insulin and HOMA at baseline was associated with significantly lower baseline DWR, DSS, and WF scores and a greater decline over 6 years in DWR and WF.



Insulin resistance is a potentially modifiable midlife risk factor for cognitive decline and dementia.
Model selection criterion for causal parameters in structural mean models based on a quasi-likelihood.

Structural mean models (SMMs) have been proposed for estimating causal parameters in the presence of non-ignorable non-compliance in clinical trials. To obtain a valid causal estimate, we must impose several assumptions. One of these is the correct specification of the structural model. Building on Pan's work (2001, Biometrics 57, 120-125) on developing a model selection criterion for generalized estimating equations, we propose a new approach for model selection of SMMs based on a quasi-likelihood. We provide a formal model selection criterion that is an extension of Akaike's information criterion. Using subset selection of baseline covariates, our method allows us to understand whether the treatment effect varies across the available baseline covariate levels, and/or to quantify the treatment effect on a specific covariates level to target specific individuals to maximize treatment benefit. We present simulation results in which our method performs reasonably well compared to other testing methods in terms of both the probability of selecting the correct model and the predictive performances of the individual treatment effects. We use a large randomized clinical trial of pravastatin as a motivation.
Nitric oxide synthase inhibition reduces glucose uptake during exercise in individuals with type 2 diabetes more than in control subjects.

Nitric oxide (NO) synthase inhibition reduces leg glucose uptake during cycling without reducing leg blood flow (LBF) in young, healthy individuals. This study sought to determine the role of NO in glucose uptake during exercise in individuals with type 2 diabetes. Nine men with type 2 diabetes and nine control subjects matched for age, sex, peak pulmonary oxygen uptake (VO(2) peak), and weight completed two 25-min bouts of cycling exercise at 60 +/- 2% VO(2) peak, separated by 90 min. N(G)-monomethyl-L-arginine (L-NMMA) (total dose 6 mg/kg) or placebo was administered into the femoral artery for the final 15 min of exercise in a counterbalanced, blinded, crossover design. LBF was measured by thermodilution in the femoral vein, and leg glucose uptake was calculated as the product of LBF and femoral arteriovenous glucose difference. During exercise with placebo, glucose uptake was not different between control subjects and individuals with diabetes; however, LBF was lower and arterial plasma glucose and insulin levels were higher in individuals with diabetes. L-NMMA had no effect on LBF or arterial plasma glucose and insulin concentrations during exercise in both groups. L-NMMA significantly reduced leg glucose uptake in both groups, with a significantly greater reduction (P = 0.04) in the diabetic group (75 +/- 13%, 5 min after L-NMMA) compared with the control group (34 +/- 14%, 5 min after L-NMMA). These data suggest a greater reliance on NO for glucose uptake during exercise in individuals with type 2 diabetes compared with control subjects.
Number of cervical biopsies and sensitivity of colposcopy.

To examine the influence that type of medical training and number of biopsies have on sensitivity of colposcopically guided biopsies.



Among 408 women with an adequate enrollment colposcopy and a diagnosis of cervical intraepithelial neoplasia (CIN) 3 or cancer (CIN 3+) over 2 years in the Atypical Squamous Cells of Undetermined Significance/Low-Grade Squamous Intraepithelial Lesions (ASCUS-LSIL) Triage Study, we evaluated factors influencing the sensitivity of the enrollment colposcopic procedure. We used contingency table analysis to examine confounding variables and chi(2) tests to ascertain statistical significance.



Overall, 69.9% of women with a cumulative diagnosis of CIN 3+ had a "true-positive" enrollment colposcopically guided biopsy result of CIN 2 or worse (CIN 2+), the threshold that would trigger excisional therapy. The sensitivity of the procedure did not vary significantly by type of colposcopist. However, the sensitivity was significantly greater when the colposcopists took two or more biopsies instead of one (P<.01), a pattern observed across all types of colposcopists. Independent of the severity of the colposcopic impression, the frequency with which colposcopists took two or more biopsies instead of one varied (in descending order) from nurse practitioners to general gynecologists to gynecologic oncology fellows to gynecologic oncologists (P<.01).



Colposcopy with guided biopsy or biopsies detects approximately two thirds of CIN 3+. Although the sensitivity of the procedure does not differ significantly by type of medical training, it is greater when two or more biopsies are taken.
Effect of hydroxymethylglutaryl-CoA reductase inhibitors on low-density lipoprotein cholesterol, interleukin-6, and high-sensitivity C-reactive protein in end-stage renal disease.

This study was conducted to determine the effect of statins on the serum levels of interleukin-6 (IL-6), low-density lipoprotein cholesterol (LDLC), and high-sensitivity C-reactive protein (HSCPR).  This randomized clinical trial was carried out on 95 hemodialysis patients divided into three groups of atorvastatin, 10 mg; simvastatin, 20 mg; and lovastatin, 40 mg, daily, administered for 2 months. Levels of serum HSCRP, IL-6, and LDLC were all measured before and after the study period.  At baseline, 59% of the hemodialysis patients presented with elevated HSCRP, 46.3% them had increased IL-6, and 26.3% had an increased LDLC level. The three drugs were capable to lower the level of HSCRP, among which atorvastatin had the highest effect size (41.8% reduction, P = .001). Lovastatin stood in the next (37.6% reduction, P = .02), while HSCRP reduction was not significant in the simvastatin group (25% reduction, P = .14). Neither of the drugs significantly reduced IL-6 levels. Effects of atorvastatin and simvastatin on the LDLC levels were significant, while lovastatin had a marginal effect.  Use of statins resulted in CRP reduction in patients on hemodialysis. Atorvastatin was much more effective than lovastatin, while CRP reduction was not significant by simvastatin. However, simvastatin had the greatest impact on LDLC. None of these drugs could reduce IL-6 levels within 2 months.
Circulating and urinary transforming growth factor beta1, Amadori albumin, and complications of type 1 diabetes: the EURODIAB prospective complications study.

Transforming growth factor (TGF)-beta1 is overexpressed in diabetes as a consequence of hyperglycemia and the creation of early glycated end products and may be responsible for the characteristic structural renal changes associated with diabetes. We sought to examine the role of both urinary and circulating TGF-beta1 and its promoter Amadori albumin in the vascular complications of type 1 diabetes.



The present article reports on a nested case-control study from the EURODIAB Prospective Complications Study of Europeans with type 1 diabetes. Case subjects (n = 356) were all individuals with one or more complications of diabetes; control subjects (n = 185) were all individuals with no evidence of complications.



Urinary TGF-beta1 and Amadori albumin were elevated in patients with micro- or macroalbuminuria. Standardized regression effects (SREs) for macroalbuminuria versus normoalbuminuria were 2.45 (95% CI 1.88-3.18, P = 0.0001 for urinary TGF-beta1) and 1.67 (1.34-2.07, P = 0.001 for Amadori albumin). The SRE for urinary TGF-beta1 remained statistically significant when adjusted for HbA(1c), Amadori albumin, and blood pressure. Circulating TGF-beta1 was elevated in individuals with proliferative retinopathy compared with individuals without retinopathy (SRE 1.29 [1.07-1.550], P = 0.007). This result was attenuated to 1.16 (0.95-1.43, P = 0.2) in the multivariate model, largely because of HbA(1c).



Elevated levels of urinary TGF-beta1 in macroalbuminuria were associated with elevations in Amadori albumin and HbA(1c) and also in blood pressure. In contrast, only circulating TGF-beta1 was related to proliferative retinopathy, and HbA(1c) largely accounted for this. These findings may indicate novel pathways for understanding mechanisms and therapeutic interventions.
Effect of Propofol and Desflurane on Immune Cell Populations in Breast Cancer Patients: A Randomized Trial

Several factors can affect the perioperative immune function. We evaluated the effect of propofol and desflurane anesthesia on the surgery-induced immune perturbation in patients undergoing breast cancer surgery. The patients were randomly assigned to receive propofol (n = 20) or desflurane (n = 20) anesthesia. The total and differential white blood cell counts were determined with lymphocyte subpopulations before and 1 hr after anesthesia induction and at 24 hr postoperatively. Plasma concentrations of interleukin (IL)-2 and IL-4 were also measured. Both propofol and desflurane anesthesia preserved the IL-2/IL-4 and CD4(+)/CD8(+) T cell ratio. Leukocytes were lower in the propofol group than in the desflurane group at 1 hr after induction (median [quartiles], 4.98 [3.87-6.31] vs. 5.84 [5.18-7.94] 10(3)/µL) and 24 hr postoperatively (6.92 [5.54-6.86] vs. 7.62 [6.22-9.21] 10(3)/µL). NK cells significantly decreased 1 hr after induction in the propofol group (0.41 [0.34-0.53] to 0.25 [0.21-0.33] 10(3)/µL), but not in the desflurane group (0.33 [0.29-0.48] to 0.38 [0.30-0.56] 10(3)/µL). Our findings indicate that both propofol and desflurane anesthesia for breast cancer surgery induce a favorable immune response in terms of preservation of IL-2/IL-4 and CD4(+)/CD8(+) T cell ratio in the perioperative period. With respect to leukocytes and NK cells, desflurane anesthesia is associated with less adverse immune responses than propofol anesthesia during surgery for breast cancer.
Comparison of Immediate With Delayed Stenting Using the Minimalist Immediate Mechanical Intervention Approach in Acute ST-Segment-Elevation Myocardial Infarction: The MIMI Study.

Delayed stent implantation after restoration of normal epicardial flow by a minimalist immediate mechanical intervention aims to decrease the rate of distal embolization and impaired myocardial reperfusion after percutaneous coronary intervention. We sought to confirm whether a delayed stenting (DS) approach (24-48 hours) improves myocardial reperfusion, versus immediate stenting, in patients with acute ST-segment-elevation myocardial infarction undergoing primary percutaneous coronary intervention.



In the prospective, randomized, open-label minimalist immediate mechanical intervention (MIMI) trial, patients (n=140) with ST-segment-elevation myocardial infarction ≤12 hours were randomized to immediate stenting (n=73) or DS (n=67) after Thrombolysis In Myocardial Infarction 3 flow restoration by thrombus aspiration. Patients in the DS group underwent a second coronary arteriography for stent implantation a median of 36 hours (interquartile range 29-46) after randomization. The primary end point was microvascular obstruction (% left ventricular mass) on cardiac magnetic resonance imaging performed 5 days (interquartile range 4-6) after the first procedure. There was a nonsignificant trend toward lower microvascular obstruction in the immediate stenting group compared with DS group (1.88% versus 3.96%; P=0.051), which became significant after adjustment for the area at risk (P=0.049). Median infarct weight, left ventricular ejection fraction, and infarct size did not differ between groups. No difference in 6-month outcomes was apparent for the rate of major cardiovascular and cerebral events.



The present findings do not support a strategy of DS versus immediate stenting in patients with ST-segment-elevation infarction undergoing primary percutaneous coronary intervention and even suggested a deleterious effect of DS on microvascular obstruction size.
Interaction between early life stress and alcohol dependence on neural stress reactivity.

Stress response biologic systems are altered in alcohol-dependent individuals. Early life stress (ELS) is associated with a heightened risk of alcohol dependence, presumably because of stress-induced neuroplastic changes. This study was designed to assess the contribution of ELS to a stress-induced neural response in alcohol-dependent participants. Fifteen alcohol-dependent men abstinent for 3-5 weeks and 15 age- and race-matched healthy controls were studied. Anticipatory anxiety was induced by a conditioned stimulus paired with an uncertain physically painful unconditioned stressor. Neural response was assessed with functional magnetic resonance imaging. ELS was assessed with the Childhood Adversity Interview. There was a significant interaction between ELS and group on blood-oxygen-level-dependent (BOLD) amplitude during anticipatory anxiety in the right amygdala and bilateral orbitofrontal cortex, posterior putamen and insula. Higher ELS scores were associated with decreased BOLD amplitude during anticipatory anxiety in alcohol-dependent, but not control, participants. These findings suggest that ELS interacts with alcohol dependence to induce a muted cortico-striatal response to high threat stimuli. Allostatic changes due to both ELS and excessive alcohol use may jointly induce persistent changes in the neural response to acute stressors.
Effects of a Plant-Based High-Carbohydrate/High-Fiber Diet Versus High–Monounsaturated Fat/Low-Carbohydrate Diet on Postprandial Lipids in Type 2 Diabetic Patients

To search for a better dietary approach to treat postprandial lipid abnormalities and improve glucose control in type 2 diabetic patients.



According to a randomized crossover design, 18 type 2 diabetic patients (aged 59 +/- 5 years; BMI 27 +/- 3 kg/m(2)) (means +/- SD) in satisfactory blood glucose control on diet or diet plus metformin followed a diet relatively rich in carbohydrates (52% total energy), rich in fiber (28 g/1,000 kcal), and with a low glycemic index (58%) (high-carbohydrate/high-fiber diet) or a diet relatively low in carbohydrate (45%) and rich in monounsaturated fat (23%) (low-carbohydrate/high-monounsaturated fat diet) for 4 weeks. Thereafter, they shifted to the other diet for 4 more weeks. At the end of each period, plasma glucose, insulin, lipids, and lipoprotein fractions (separated by discontinuous density gradient ultracentrifugation) were determined on blood samples taken at fasting and over 6 h after a test meal having a similar composition as the corresponding diet.



In addition to a significant decrease in postprandial plasma glucose, insulin responses, and glycemic variability, the high-carbohydrate/high-fiber diet also significantly improved the primary end point, since it reduced the postprandial incremental areas under the curve (IAUCs) of triglyceride-rich lipoproteins, in particular, chylomicrons (cholesterol IAUC: 0.05 +/- 0.01 vs. 0.08 +/- 0.02 mmol/l per 6 h; triglycerides IAUC: 0.71 +/- 0.35 vs. 1.03 +/- 0.58 mmol/l per 6 h, P < 0.05).



A diet rich in carbohydrate and fiber, essentially based on legumes, vegetables, fruits, and whole cereals, may be particularly useful for treating diabetic patients because of its multiple effects on different cardiovascular risk factors, including postprandial lipids abnormalities.