nils-herrmann/clean_scirepeval huggingface dataset:
Optimizing strategies for telescoping languages: procedure strength reduction and procedure vectorization

At Rice University, we have undertaken a project to construct a framework for generating high-level problem solving languages that can achieve high performance on a variety of platforms.The underlying strategy, called telescoping languages, builds problem-solving systems from domain-specific libraries and scripting langauges. To accomplish this it extensively preanalyzes and transforms the library to produce a scripting language precompiler that optimizes library calls within the scripts as if they were primitives in the underlying language.
A major technical issue is how to preoptimize a library for use in applications that are yet to be seen. To address this issue, we have conducted a study of applications written in Matlab by the signal processing group at Rice University. This has identified a collection of old and new optimizations that show promise for this particular domain. Two promising new optimizations are procedure vectorization and procedure strength reduction.The latter of these is particularly useful in this problem domain and we expect it to be just as applicable in other contexts as well.
We report on the results of an exploration of the effectiveness of procedure strength reduction on three real Digital Signal Processing (DSP) applications. By transforming these programs according to the strategies described in this paper, we were able to achieve speedups ranging from 10 to 40 percent over the entire application — speedups for individual functions were even more dramatic.
A multicenter, randomized, double-blind clinical trial of combination therapy with Anbainuo, a novel recombinant human TNFRII:Fc fusion protein, plus methotrexate versus methotrexate alone or Anbainuo alone in Chinese patients with moderate to severe rheumatoid arthritis

This study aims to evaluate the clinical and radiological efficacy as well as safety profiles of Anbainuo, a recombinant human Fc fusion protein, combined with methotrexate (MTX) versus MTX alone or Anbainuo alone in the treatment of Chinese patients with moderate to severe rheumatoid arthritis (RA). In this 24-week, multicenter, double-blind, active comparator-controlled study, 396 RA patients were randomized into combination therapy group (Anbainuo plus MTX), Anbainuo group, or MTX group. Clinical response was assessed using the American College of Rheumatology (ACR)-N, ACR20, ACR50, ACR70, and van der Heijde modification of Sharp score, among which ACR-N and ACR20 were defined as primary major endpoints. After 24 weeks of treatment, the ACR-N in the combination therapy group (12.79 ± 9.24 %) was significantly higher than that in Anbainuo group (9.56 ± 11.16 %) and in MTX group (5.08 ± 11.1 %) (p = 0.00 and p = 0.00, respectively). Patients in Anbainuo group had significantly higher ACR-N than those in MTX group (p = 0.02). More patients in the combination therapy group (53.6 %) achieved ACR50 improvement response than those in the MTX group (30.8 %). ACR70 of combination therapy group (27.7 %) was significantly higher than that of Anbainuo group (15.8 %) and MTX group (7.70 %), with no significant difference between Anbainuo group and MTX group. DAS28-ESR in the combination therapy group was significantly reduced compared to either monotherapy groups. Moreover, DAS28-ESR was significantly lower in Anbainou group than in MTX group. The combination therapy group also showed significantly less radiographic progression than the MTX group (p = 0.03). The total adverse events (AE) in the combination group (40.9 %) was significantly higher than those in the MTX group (28.8 %) (p < 0.05). Anbainuo combined with MTX therapy can effectively control the disease activity and radiographic progression of RA, while the incidence of AE also increased compared to either Anbainuo or MTX.
Brain volume changes after withdrawal of atypical antipsychotics in patients with first-episode schizophrenia.

The influence of antipsychotic medication on brain morphology in schizophrenia may confound interpretation of brain changes over time. We aimed to assess the effect of discontinuation of atypical antipsychotic medication on change in brain volume in patients. Sixteen remitted, stable patients with first-episode schizophrenia, schizoaffective or schizophreniform disorder and 20 healthy controls were included. Two magnetic resonance imaging brain scans were obtained from all subjects with a 1-year interval. The patients either discontinued (n = 8) their atypical antipsychotic medication (olanzapine, risperidone, or quetiapine) or did not (n = 8) discontinue during the follow-up period. Intracranial volume and volumes of total brain, cerebral gray and white matter, cerebellum, third and lateral ventricle, nucleus caudatus, nucleus accumbens, and putamen were obtained. Multiple linear regression analyses were used to assess main effects for group (patient-control) and discontinuation (yes-no) for brain volume (change) while correcting for age, sex, and intracranial volume. Decrease in cerebral gray matter and caudate nucleus volume over time was significantly more pronounced in patients relative to controls. Our data suggest decreases in the nucleus accumbens and putamen volumes during the interval in patients who discontinued antipsychotic medication, whereas increases were found in patients who continued their antipsychotics. We confirmed earlier findings of excessive gray matter volume decrements in patients with schizophrenia compared with normal controls. We found evidence suggestive of decreasing volumes of the putamen and nucleus accumbens over time after discontinuation of medication. This might suggest that discontinuation reverses effects of atypical medication.
The risk of viral rebound in the year after delivery in women remaining on antiretroviral therapy

The objective of this study is to assess the risk of viral rebound in postpartum women on suppressive combination antiretroviral therapy (cART).



Using data from the UK Collaborative HIV Cohort (UK CHIC) study and the UK and Ireland National Study of HIV in Pregnancy and Childhood (NSHPC), women with HIV-RNA 50 copies/ml or less at delivery in 2006-2011, who started life-long cART during pregnancy (n = 321) or conceived on cART (n = 618), were matched by age, duration on cART and time period, with at least one control (non-postpartum). The cumulative probability of viral rebound (HIV-RNA >200 copies/ml) was assessed by Kaplan-Meier analysis; adjusted hazard ratios (aHRs) for the 0-3 and 3-12 months postdelivery (cases)/pseudo-delivery (controls) were calculated in Cox proportional hazards models.



In postpartum women who conceived on cART, 5.9% [95% confidence interval (95% CI) 4.0-7.7] experienced viral rebound by 3 months, and 2.2% (1.4-3.0%) of their controls. The risk of viral rebound was higher in postpartum women than in controls during the first 3 months [aHR 2.63 (1.58-4.39)] but not during the 3-12 months postdelivery/pseudo-delivery. In postpartum women who started cART during pregnancy, 27% (22-32%) experienced viral rebound by 3 months, and 3.0% (1.6-4.4%) of their controls. The risk of viral rebound was higher in postpartum women than in controls during both postdelivery/pseudo-delivery periods [<3 months: aHR 6.63 (3.58-12.29); 3-12 months: aHR 4.05 (2.03-8.09)].



In women on suppressive cART, the risk of viral rebound is increased following delivery, especially in the first 3 months, which may be related to reduced adherence, indicating the need for additional adherence support for postpartum women.
One-year outcome of patients with atrial fibrillation undergoing coronary artery stenting: an analysis of the AFCAS registry.

Most evidence regarding the efficacy and safety of the antithrombotic regimens for patients with atrial fibrillation (AF) undergoing percutaneous coronary intervention with stent (PCI-S) derives from small, single-center, retrospective datasets. To obtain further data on this issue, we carried out the prospective, multicenter, observational Management of patients with Atrial Fibrillation undergoing Coronary Artery Stenting (AFCAS) registry (Clinicaltrials.gov identifier NCT00596570).



We hypothesize that the antithrombotic treatment of AF patients undergoing PCI-S is variable and the clinical outcome may vary according to the different regimens.



Consecutive AF patients undergoing PCI-S at 17 European institutions were included and followed for 1 year. Outcome measures included: (1) major adverse cardiac/cerebrovascular events (MACCE), including all-cause death, myocardial infarction, repeat revascularization, stent thrombosis, or stroke/transient ischemic attack, and (2) bleeding, and were compared according to the antithrombotic regimen adopted. A propensity-score analysis was carried out to adjust for baseline and procedural differences.



Out of the 975 patients enrolled, 914 were included in the final analysis. The mean CHADS2 score was 2.2 ± 1.2, and 71% of patients had a CHADS2 score ≥2. Triple therapy (TT) of vitamin K antagonist (VKA), aspirin, and clopidogrel was prescribed to 74% of patients, dual antiplatelet therapy to 18%, and VKA plus clopidogrel to 8%. At 1-year follow-up, no significant differences were found in the occurrence of MACCE and bleeding among the 3 antithrombotic regimens, even when adjusted for propensity score.



In this large, real-world population of AF patients undergoing PCI-S, TT was the antithrombotic regimen most frequently prescribed. Although several limitations need to be acknowledged, in our study the 1-year efficacy and safety of TT, dual antiplatelet therapy, and VKA plus clopidogrel was comparable.
Liver transplantation in the Nordic countries – An intention to treat and post-transplant analysis from The Nordic Liver Transplant Registry 1982–2013

The Nordic Liver Transplant Registry (NLTR) accounts for all liver transplants performed in the Nordic countries since the start of the transplant program in 1982. Due to short waiting times, donor liver allocation has been made without considerations of the model of end-stage liver disease (MELD) score. We aimed to summarize key outcome measures and developments for the activity up to December 2013.



The registry is integrated with the operational waiting-list and liver allocation system of Scandiatransplant (www.scandiatransplant.org) and accounted at the end of 2013 for 6019 patients out of whom 5198 were transplanted. Data for recipient and donor characteristics and relevant end-points retransplantation and death are manually curated on an annual basis to allow for statistical analysis and the annual report.



Primary sclerosing cholangitis, acute hepatic failure, alcoholic liver disease, primary biliary cirrhosis and hepatocellular carcinoma are the five most frequent diagnoses (accounting for 15.3%, 10.8%, 10.6%, 9.3% and 9.0% of all transplants, respectively). Median waiting time for non-urgent liver transplantation during the last 10-year period was 39 days. Outcome has improved over time, and for patients transplanted during 2004-2013, overall one-, five- and 10-year survival rates were 91%, 80% and 71%, respectively. In an intention-to-treat analysis, corresponding numbers during the same time period were 87%, 75% and 66%, respectively.



The liver transplant program in the Nordic countries provides comparable outcomes to programs with a MELD-based donor liver allocation system. Unique features comprise the diagnostic spectrum, waiting times and the availability of an integrated waiting list and transplant registry (NLTR).
Randomised trial of ambulatory oxygen in oxygen-dependent COPD.

We would like to thank T.L. Petty for his interesting comments regarding our trial of ambulatory oxygen (AO) in chronic obstructive pulmonary disease (COPD) . The question raised by T.L. Petty was the following: when is the best time to initiate AO in oxygen-dependent COPD? He suggested AO should be provided as early as possible after the introduction of long-term oxygen therapy (LTOT) to avoid rapid adjustment to the limitations imposed by the stationary oxygen delivery system.
Effects of a new calcium sensitizer, levosimendan, on haemodynamics, coronary blood flow and myocardial substrate utilization early after coronary artery bypass grafting.

The aim of the study was to evaluate the effects on systemic and coronary haemodynamics and myocardial substrate utilization of a new calcium sensitizer, levosimendan, after coronary artery bypass grafting.



Twenty-three low-risk patients were included in this randomized and double-blind study. They received placebo (n = 8), 8 (n = 8) or 24 (n = 7) micrograms.kg-1 of levosimendan after coronary artery bypass operation. Systemic and coronary sinus haemodynamics with thermodilution and myocardial substrate utilization were measured. The heart rate increased 11 beats.min-1 after the higher dose (P < 0.05). Cardiac output increased by 0.7 and 1.61.min-1 (P < 0.05 for both) after 8 and 24 micrograms.kg-1 of levosimendan, respectively. Systemic and pulmonary vascular resistance decreased significantly after both doses. Coronary sinus blood flow increased by 28 and 42 ml/(P = 0.054 for the combined effect) after the lower and higher dose, respectively. Myocardial oxygen consumption or substrate extractions did not change statistically significantly.



Despite improved cardiac performance, levosimendan did not increase myocardial oxygen consumption or change myocardial substrate utilization. Thus levosimendan has the potential to treat low cardiac output states after cardiopulmonary bypass surgery.
Effect of redesigned Indian mixed meals on blood glucose and insulin levels in normal versus type 2 diabetic subjects--a comparative study.

This study reports the glycemic as well as insulinemic response of seven types of Indian vegetarian mixed meals (MMs). Each of the seven MMs was given at weekly intervals to both normal and type 2 diabetic subjects on the same day to reduce variations in food preparations. In this Indian study, each MM consisted of five to six food items with a low glycemic index (GI) ranging from 28.98 to 46.12%, glycemic load ranging from 15.58 to 23.8 g and energy value (calculated) from each test meal ranging from 403 to 502 kcal. All the seven meals were found to have postprandial glycemic control in normal subjects which ranged from 86 to 102.4 mg%, and a good postprandial glycemic control in type 2 diabetic subjects which ranged from 132.8 to 148.4 mg%, and hence appropriate for routine consumption by diabetic subjects. The glycemic and insulinemic pattern of all these MMs was similar in normal and diabetic subjects. Sustained intake of such low GI MMs by diabetic can result in good glycemic control.
Long-Term Outcome of Critically Ill Adult Patients with Acute Epiglottitis

Acute epiglottitis is a potentially life threatening disease, with a growing incidence in the adult population. Its long-term outcome after Intensive Care Unit (ICU) hospitalization has rarely been studied.



Thirty-four adult patients admitted for acute epiglottitis were included in this retrospective multicentric study. The mean age was 44 ± 12 years (sex ratio: 5.8). Sixteen patients (47%) had a history of smoking while 8 (24%) had no previous medical history. The average time of disease progression before ICU was 2.6 ± 3.6 days. The main reasons for hospitalization were continuous monitoring (17 cases, 50%) and acute respiratory distress (10 cases, 29%). Microbiological documentation could be made in 9 cases (26%), with Streptococcus spp. present in 7 cases (21%). Organ failure at ICU admission occurred in 8 cases (24%). Thirteen patients (38%) required respiratory assistance during ICU stay; 9 (26%) required surgery. Two patients (6%) died following hypoxemic cardiac arrest. Five patients (15%) had sequelae at 1 year. Patients requiring respiratory assistance had a longer duration of symptoms and more frequent anti inflammatory use before ICU admission and sequelae at 1 year (p < 0.05 versus non-ventilated patients). After logistic regression analysis, only exposure to anti-inflammatory drugs before admission was independently associated with airway intervention (OR, 4.96; 95% CI, 1.06-23.16).



The profile of the cases consisted of young smoking men with little comorbidity. Streptococcus spp. infection represented the main etiology. Outcome was favorable if early respiratory tract protection could be performed in good conditions. Morbidity and sequelae were greater in patients requiring airway intervention.
[Children and adolescent's drawing for the diagnosis of migraine].

Migraine is frequent in children. Children's drawings of their symptoms can help to identify it.



To evaluate the accuracy of children's drawings to identify migraine in those who suffer from headache.  We evaluated 48 patients aged 5 to 19 years, assisted for headache. In all cases they were asked to draw what happened to them before and during the episode, and then the drawing was analyzed by a pediatric neurologist ("artistic diagnosis"). Afterwards, all were evaluated by another pediatric neurologist ("clinical diagnosis"). Sensitivity (Se), specificity (Sp), negative (NPV) and positive (PPV) predictive values of the "artistic diagnosis" to predict "clinical diagnosis" were calculated. Possible interaction of age, Intellectual Standard Score (ISS), maternal education and previous contact with a neurologist was evaluated by logistic regression.



After controlling by those factors, the "artistic diagnosis" was found to be an independent predictor of the "clinical diagnosis" of migraine (p < 0.01, OR: 23), achieving Se: 69,6%, Sp: 88%, PPV: 84,2% and NPV: 75,9. The performance was still better when only subjects with ISS >/= 70 were considered.



Children tend to communicate their symptoms more effectively through drawings than verbally. The "artistic diagnosis" was accurate to predict the "clinical diagnosis" of migraine.
Age-Associated Changes in Monocyte and Innate Immune Activation Markers Occur More Rapidly in HIV Infected Women

Aging is associated with immune dysfunction and the related development of conditions with an inflammatory pathogenesis. Some of these immune changes are also observed in HIV infection, but the interaction between immune changes with aging and HIV infection are unknown. Whilst sex differences in innate immunity are recognized, little research into innate immune aging has been performed on women.



This cross-sectional study of HIV positive and negative women used whole blood flow cytometric analysis to characterize monocyte and CD8(+) T cell subsets. Plasma markers of innate immune activation were measured using standard ELISA-based assays.



HIV positive women exhibited elevated plasma levels of the innate immune activation markers CXCL10 (p<0.001), soluble CD163 (sCD163, p = 0.001), sCD14 (p = 0.022), neopterin (p = 0.029) and an increased proportion of CD16(+) monocytes (p = 0.009) compared to uninfected controls. Levels of the innate immune aging biomarkers sCD163 and the proportion of CD16(+) monocytes were equivalent to those observed in HIV negative women aged 14.5 and 10.6 years older, respectively. CXCL10 increased with age at an accelerated rate in HIV positive women (p = 0.002) suggesting a synergistic effect between HIV and aging on innate immune activation. Multivariable modeling indicated that age-related increases in innate immune biomarkers CXCL10 and sCD163 are independent of senescent changes in CD8(+) T lymphocytes.



Quantifying the impact of HIV on immune aging reveals that HIV infection in women confers the equivalent of a 10-14 year increase in the levels of innate immune aging markers. These changes may contribute to the increased risk of inflammatory age-related diseases in HIV positive women.
Color velocity imaging quantification in the detection of intracranial collateral flow.

The development of intracranial collateral circulation is associated with a lower risk of stroke. A noninvasive technique that can reliably detect the presence of intracranial collaterals would be a valuable factor in the assessment of risk in patients with occlusive cerebrovascular disease.



Color velocity imaging quantification was used to measure the blood flow volume of the common carotid and vertebral arteries in 40 patients with carotid occlusive disease. The blood flow volumes in these arteries were correlated with angiographic evidence of collaterals to establish the best cutoffs for detecting intracranial collateral circulation.



A blood flow volume of either > or =370 mL/min in the common carotid artery or > or =120 mL/min in the vertebral artery was indicative of the presence of intracranial collaterals. The sensitivity and specificity for the common carotid artery were 92.3% [95% confidence interval (CI), 62.1 to 99.6] and 92.1% (95% CI, 77.5 to 97.9), respectively. The sensitivity and specificity for the vertebral artery were 75.0% (95% CI, 35.6 to 95.5) and 87.5% (95% CI, 66.5 to 96.7), respectively.



Color velocity imaging quantification offers a noninvasive, accurate method for detecting the presence of intracranial collateral circulation and quantifying its magnitude. This technique would be a useful adjunct in screening or continuous monitoring of patients with severe carotid occlusive disease.
Use of Home Peritoneal Dialysis by Cuba's Nephrology Institute, 2007-2012.

Peritoneal dialysis is a maintenance therapy option for patients with end-stage renal disease. Continuous ambulatory peritoneal dialysis in Cuba was introduced in December 2007, and automated peritoneal dialysis one year later. This paper presents the outcomes attained with this blood purification technique, enabling an assessment to decide on scaling up its use in Cuba.



Describe the clinical course of patients in the first five years of the Home Peritoneal Dialysis Program at Havana's Nephrology Institute.



An observational, descriptive study with a retrospective cohort was conducted. The universe comprised the 40 Nephrology Institute patients who underwent treatment with home peritoneal dialysis from December 20, 2007 to December 20, 2012. Relative and absolute frequencies were calculated for the study variables and the Kaplan-Meier method was used for survival curves for patients and for the peritoneum as dialysis membrane.  Of the 40 patients in the program, 23 were men and 17 were women, primarily aged 40 to 59 years. The most frequent causes of chronic kidney failure were hypertension (42.5%), glomerulopathies (22.5%), and diabetes mellitus (22.5%). A total of 103 complications occurred, both infectious (68, 66%) and non-infectious (35, 34%). The most common infectious complication was peritonitis (45, 66.2%); the most frequent non-infectious complication was catheter displacement (13, 37.1%). Seven patients left the peritoneal dialysis program. Of these, three died, two lost function of the peritoneum as a dialysis membrane, one received a kidney transplant and one recovered kidney function. Survival was 100% at one year, 97% at 2 years, 93.2% at 3 and 4 years, and 92% at 5 years. However, the peritoneal membrane was functional in 100% of patients during the first 2 years, decreasing to 96% at 3 and 4 years and to 88.6% at 5 years.



In our setting, peritoneal dialysis attained outcomes similar to those obtained internationally, which supports its usefulness as a renal replacement therapy method in Cuban patients with end-stage renal disease.