Miracle-dz/UniFAR-FTUs huggingface dataset:
MeCC: memory comparison-based clone detector

In this paper, we propose a new semantic clone detection technique by comparing programs' abstract memory states, which are computed by a semantic-based static analyzer. Our experimental study using three large-scale open source projects shows that our technique can detect semantic clones that existing syntactic- or semantic-based clone detectors miss. Our technique can help developers identify inconsistent clone changes, find refactoring candidates, and understand software evolution related to semantic clones.
A new bound on the neutrino mass from the sdss baryon acoustic peak

We have studied bounds on the neutrino mass using new data from the Sloan Digital Sky Survey measurement of the baryon acoustic peak. We find that even in models with a running spectral index where the number of neutrinos and the dark energy equation of state are allowed to vary, the bound on the sum of neutrino masses is robustly below 0.5 eV. Using the SDSS Lyman-α constraint on the amplitude of the matter power spectrum at small scales pushes the bound to ∑ mν ≤ 0.30 eV (95% C.L.). A new bound on the neutrino mass from the SDSS baryon acoustic peak 2
Novel Approaches to the Parametric Cubic-Spline Interpolation

The cubic-spline interpolation (CSI) scheme can be utilized to obtain a better quality reconstructed image. It is based on the least-squares method with cubic convolution interpolation (CCI) function. Within the parametric CSI scheme, it is difficult to determine the optimal parameter for various target images. In this paper, a novel method involving the concept of opportunity costs is proposed to identify the most suitable parameter for the CCI function needed in the CSI scheme. It is shown that such an optimal four-point CCI function in conjunction with the least-squares method can achieve a better performance with the same arithmetic operations in comparison with the existing CSI algorithm. In addition, experimental results show that the optimal six-point CSI scheme together with cross-zonal filter is superior in performance to the optimal four-point CSI scheme without increasing the computational complexity.
HIV-1 Envelope Glycoprotein Resistance to Monoclonal Antibody 2G12 Is Subject-Specific and Context-Dependent in Macaques and Humans

HIV-1 Envelope (Env) protein is the sole target of neutralizing antibodies (NAbs) that arise during infection to neutralize autologous variants. Under this immune pressure, HIV escape variants are continuously selected and over the course of infection Env becomes more neutralization resistant. Many common alterations are known to affect sensitivity to NAbs, including residues encoding potential N-linked glycosylation sites (PNGS). Knowledge of Env motifs associated with neutralization resistance is valuable for the design of an effective Env-based vaccine so we characterized Envs isolated longitudinally from a SHIVSF162P4 infected macaque for sensitivity to neutralizing monoclonal antibodies (MAbs) B12, 2G12, 4E10 and 2F5. The early Env, isolated from plasma at day 56 after infection, was the most sensitive and the late Env, from day 670, was the most resistant to MAbs. We identified four PNGS in these Envs that accumulated over time at positions 130, 139, 160 and 397. We determined that removal of these PNGS significantly increased neutralization sensitivity to 2G12, and conversely, we identified mutations by in silico analyses that contributed resistance to 2G12 neutralization. In order to expand our understanding of these PNGS, we analyzed Envs from clade B HIV-infected human subjects and identified additional glycan and amino acid changes that could affect neutralization by 2G12 in a context-dependent manner. Taken together, these in vitro and in silico analyses of clade B Envs revealed that 2G12 resistance is achieved by previously unrecognized PNGS substitutions in a context-dependent manner and by subject-specific pathways.
Admission heart rate predicts mortality following primary percutaneous coronary intervention for ST-elevation myocardial infarction: an observational study.

BACKGROUND The prognostic value of admission heart rate (HR) on long-term mortality in ST-elevation myocardial infarction (STEMI) remains uncertain in the modern era of primary percutaneous coronary intervention (PPCI). This study aimed to assess the predictive value of admission HR on long-term mortality following PPCI and the influence of beta-blockers on postdischarge survival. METHODS Retrospective analysis of prospectively collected data on 2310 PPCI-treated STEMI patients at a regional tertiary center between March 2008 and June 2010. RESULTS Patients were classified according to admission HR into either low (≤70 beat per minute [bpm], n = 1015) or high HR group (>70 bpm, n = 1295). At a median follow-up of 559 days, all-cause mortality was 7.0% in the low HR group compared to 12.7% in the high-HR group. In the Cox proportional hazard model, adjusted for several confounders, the hazard ratio (95% confidence interval) for all-cause mortality in the high HR group was 1.59 (1.15-2.20; P = 0.005). Every 10-bpm increase in admission HR was associated with 17% increase in all-cause mortality. Beta-blockers on discharge was associated with a reduction in postdischarge mortality only in the high HR group (adjusted hazard ratio, 0.49 [0.31-0.77; P = 0.002]), but not in the low HR group (adjusted hazard ratio, 0.74 [0.37-1.49; P = 0.33]). CONCLUSIONS Elevated admission heart rate in PPCI-treated STEMI patients is associated with long-term all-cause mortality. Beta blocker therapy improved postdischarge survival in patients with elevated admission heart rate.
Mechanisms That Produce Nitric Oxide–Mediated Relaxation of Cerebral Arteries During Atherosclerosis

Background and Purpose— The first goal of the present study was to examine the hypothesis that relaxation of cerebral arteries to nitric oxide in primates is dependent on activation of soluble guanylate cyclase (sGC). The second goal was to determine whether the role of sGC in mediating responses to nitric oxide is altered in atherosclerosis. Methods— Basilar arteries from normal and atherosclerotic monkeys were studied in vitro. After precontraction with prostaglandin F2&agr; (0.1 to 1 &mgr;mol/L), concentration-response curves to authentic nitric oxide (1 nmol/L to 1 &mgr;mol/L), sodium nitroprusside (10 nmol/L to 10 &mgr;mol/L; a nitric oxide donor), and papaverine (10 nmol/L to 10 &mgr;mol/L; a non–nitric oxide, non–sGC-dependent stimulus) were generated in the presence and absence of 1H-[1,2,4]-oxadiazolo[4,3-a]quinoxalin-1-one (ODQ; 1 and 10 &mgr;mol/L; an inhibitor of sGC). The effect of ODQ on basal tone of basilar arteries from normal and atherosclerotic monkeys was also examined. Results— Nitric oxide, sodium nitroprusside, and papaverine produced relaxation that was similar (P >0.05) in normal and atherosclerotic monkeys. ODQ produced marked inhibition (P <0.05) of vasorelaxation in response to nitric oxide and nitroprusside but not papaverine. For example, relaxation of the basilar artery in response to nitric oxide (0.1 &mgr;mol/L) was inhibited by approximately 85% and 73% by ODQ (1 &mgr;mol/L) in normal and atherosclerotic monkeys, respectively. ODQ produced contraction of the basilar arteries, and the increase in tension to ODQ was greater in normal (2.7±0.3 g; mean±SE) than in atherosclerotic monkeys (1.4±0.4 g;P <0.05). In contrast, contraction to prostaglandin F2&agr; was similar in the basilar artery from normal and atherosclerotic monkeys. Conclusions— These findings suggest that (1) relaxation of cerebral arteries in primates in response to nitric oxide is normally dependent, in large part, on activation of sGC and (2) the influence of sGC (via reduced production and/or activity of basal nitric oxide) on cerebral vascular tone is reduced in atherosclerosis.
Effects of transplacental exposure to diethylstilbestrol on carcinogenic susceptibility during postnatal life in hamster progeny.

Prenatal exposure to a single dose of diethylstilbestrol (DES) produced a significant increase in carcinogenic response of hamster progeny that were subsequently subjected to the carcinogenic stimulus of 7,12-dimethylbenz(a)anthracene (DMBA) during postnatal life. The compounds were administered according to the following schedules. The pregnant animals (second group) received a single dose of DES, 10 mg/kg, on Day 14 of gestation. Postnatally, at 6 weeks of age, the progeny were given DMBA, 25 mg/kg p.o. , twice weekly for 8 weeks. The first group received DMBA at 6 weeks of age, 30 mg/kg p.o. , twice weekly for 18 weeks. The progeny exposed to DES prenatally and DMBA postnatally (DES-DMBA-exposed progeny) developed a greater multiplicity of tumors per tumor-bearing animal (p less than 0.001) and higher rates of neoplasms of the reproductive tract, e.g., ovarian and uterine tumors, mammary gland and forestomach tumors, and dermal melanomas. The prenatally DES-exposed progeny also had significantly higher incidences of malignant tumors, e.g., carcinomas of the mammary gland (p less than 0.001) and carcinomas of the forestomach (p less than 0.001), than did the hamsters given DMBA alone during postnatal life. Endocrine imbalance produced by exposure in utero may heighten the sensitivity of the progeny to development of neoplasms after a challenge with carcinogenic stimuli in adult life. The significance of these experimental data to the human situation is discussed.
Multi-objective PID-controller tuning for a magnetic levitation system using NSGA-II

This paper investigates the issue of PID-controller parameter tuning for a magnetic levitation system using the non-dominated sorting genetic algorithm (NSGA-II). The magnetic levitation system is inherently unstable and the PID-controller parameters are hard to find using conventional methods. Based on four different performance measures, derived from the step response of the levitation system, the algorithm is used to find a set of non-dominated parameters for a PID-controller that can stabilize the system and minimize the performance measures.
Insulin-like peptide genes in honey bee fat body respond differently to manipulation of social behavioral physiology

SUMMARY Nutrient sensitive insulin-like peptides (ILPs) have profound effects on invertebrate metabolism, nutrient storage, fertility and aging. Many insects transcribe ILPs in specialized neurosecretory cells at changing levels correlated with life history. However, the major site of insect metabolism and nutrient storage is not the brain, but rather the fat body, where functions of ILP expression are rarely studied and poorly understood. Fat body is analogous to mammalian liver and adipose tissue, with nutrient stores that often correlate with behavior. We used the honey bee (Apis mellifera), an insect with complex behavior, to test whether ILP genes in fat body respond to experimentally induced changes of behavioral physiology. Honey bee fat body influences endocrine state and behavior by secreting the yolk protein precursor vitellogenin (Vg), which suppresses lipophilic juvenile hormone and social foraging behavior. In a two-factorial experiment, we used RNA interference (RNAi)-mediated vg gene knockdown and amino acid nutrient enrichment of hemolymph (blood) to perturb this regulatory module. We document factor-specific changes in fat body ilp1 and ilp2 mRNA, the bee's ILP-encoding genes, and confirm that our protocol affects social behavior. We show that ilp1 and ilp2 are regulated independently and differently and diverge in their specific expression-localization between fat body oenocyte and trophocyte cells. Insect ilp functions may be better understood by broadening research to account for expression in fat body and not only brain.
Intubation-mediated Intratracheal (IMIT) Instillation: A Noninvasive, Lung-specific Delivery System

Respiratory disease studies typically involve the use of murine models as surrogate systems. However, there are significant physiologic differences between the murine and human respiratory systems, especially in their upper respiratory tracts (URT). In some models, these differences in the murine nasal cavity can have a significant impact on disease progression and presentation in the lower respiratory tract (LRT) when using intranasal instillation techniques, potentially limiting the usefulness of the mouse model to study these diseases. For these reasons, it would be advantageous to develop a technique to instill bacteria directly into the mouse lungs in order to study LRT disease in the absence of involvement of the URT. We have termed this lung specific delivery technique intubation-mediated intratracheal (IMIT) instillation. This noninvasive technique minimizes the potential for instillation into the bloodstream, which can occur during more invasive traditional surgical intratracheal infection approaches, and limits the possibility of incidental digestive tract delivery. IMIT is a two-step process in which mice are first intubated, with an intermediate step to ensure correct catheter placement into the trachea, followed by insertion of a blunt needle into the catheter to mediate direct delivery of bacteria into the lung. This approach facilitates a >98% efficacy of delivery into the lungs with excellent distribution of reagent throughout the lung. Thus, IMIT represents a novel approach to study LRT disease and therapeutic delivery directly into the lung, improving upon the ability to use mice as surrogates to study human respiratory disease. Furthermore, the accuracy and reproducibility of this delivery system also makes it amenable to Good Laboratory Practice Standards (GLPS), as well as delivery of a wide range of reagents which require high efficiency delivery to the lung.
ACA-mandated elimination of cost sharing for preventive screening has had limited early impact.

OBJECTIVES The Affordable Care Act eliminated patient cost sharing for evidence-based preventive care, yet the impact of this policy on colonoscopy and mammography rates is unclear. We examined the elimination of cost sharing among small business beneficiaries of Humana, a large national insurer. STUDY DESIGN This was a retrospective interrupted time series analysis of whether the change in cost-sharing policy was associated with a change in screening utilization, using grandfathered plans as a comparison group. METHODS We compared beneficiaries in small business nongrandfathered plans that were required to eliminate cost sharing (intervention) with those in grandfathered plans that did not have to change cost sharing (control). There were 63,246 men and women aged 50 to 64 years eligible for colorectal cancer screening, and 30,802 women aged 50 to 64 years eligible for breast cancer screening. The primary outcome variables were rates of colonoscopy and mammography per person-month, with secondary analysis of colonoscopy rates coded as preventive only. RESULTS There was no significant change in the level or slope of colonoscopy and mammography utilization for intervention plans relative to the control plans. There was also no significant relevant change among those colonoscopies coded as preventive. CONCLUSIONS The results suggest that the implementation of the policy is not having its intended effects, as cost sharing rates for colonoscopy and mammography did not change substantially, and utilization of colonoscopy and mammography changed little, following this new policy approach.
Long-term follow-up after tight control of blood pressure in type 2 diabetes.

BACKGROUND Post-trial monitoring of patients in the United Kingdom Prospective Diabetes Study (UKPDS) examined whether risk reductions for microvascular and macrovascular disease, achieved with the use of improved blood-pressure control during the trial, would be sustained. METHODS Among 5102 UKPDS patients with newly diagnosed type 2 diabetes mellitus, we randomly assigned, over a 4-year period beginning in 1987, 1148 patients with hypertension to tight or less-tight blood-pressure control regimens. The 884 patients who underwent post-trial monitoring were asked to attend annual UKPDS clinics for the first 5 years, but no attempt was made to maintain their previously assigned therapies. Annual questionnaires completed by patients and general practitioners were used to follow patients who were unable to attend the clinic in years 1 through 5, and questionnaires were used for all patients in years 6 to 10. Seven prespecified aggregate clinical end points were examined on an intention-to-treat basis, according to the previous randomization categories. RESULTS Differences in blood pressure between the two groups during the trial disappeared within 2 years after termination of the trial. Significant relative risk reductions found during the trial for any diabetes-related end point, diabetes-related death, microvascular disease, and stroke in the group receiving tight, as compared with less tight, blood-pressure control were not sustained during the post-trial follow-up. No risk reductions were seen during or after the trial for myocardial infarction or death from any cause, but a risk reduction for peripheral vascular disease associated with tight blood-pressure control became significant (P=0.02). CONCLUSIONS The benefits of previously improved blood-pressure control were not sustained when between-group differences in blood pressure were lost. Early improvement in blood-pressure control in patients with both type 2 diabetes and hypertension was associated with a reduced risk of complications, but it appears that good blood-pressure control must be continued if the benefits are to be maintained. (UKPDS 81; Current Controlled Trials number, ISRCTN75451837.)
Abi3bp Regulates Cardiac Progenitor Cell Proliferation and Differentiation

Rationale: Cardiac progenitor cells (CPCs) are thought to differentiate into the major cell types of the heart: cardiomyocytes, smooth muscle cells, and endothelial cells. We have recently identified ABI family, member 3 (NESH) binding protein (Abi3bp) as a protein important for mesenchymal stem cell biology. Because CPCs share several characteristics with mesenchymal stem cells, we hypothesized that Abi3bp would similarly affect CPC differentiation and proliferation. Objective: To determine whether Abi3bp regulates CPC proliferation and differentiation. Methods and Results: In vivo, genetic ablation of the Abi3bp gene inhibited CPC differentiation, whereas CPC number and proliferative capacity were increased. This correlated with adverse recovery after myocardial infarction. In vitro, CPCs, either isolated from Abi3bp knockout mice or expressing an Abi3bp shRNA construct, displayed a higher proliferative capacity and, under differentiating conditions, reduced expression of both early and late cardiomyocyte markers. Abi3bp controlled CPC differentiation via integrin-&bgr;1, protein kinase C-&zgr;, and v-akt murine thymoma viral oncogene homolog. Conclusions: We have identified Abi3bp as a protein important for CPC differentiation and proliferation.
Hydrologic Model Parameter Optimisation

Deterministic rainfall-runoff models require parameter calibration with the aim of matching the modeled streamflow record to an observed record as closely as possible. Much attention has been focused on automated methods of model calibration using meta-heuristics, such as genetic algorithms. In this study, two meta-heuristic algorithms were compared: the shuffled complex evolution (SCE) algorithm and a real coded genetic algorithm (GA). The GA was modified with a fitness scaler based on a Boltzmann distribution, which was used to adjust the level of elitism of the selection operator. This was found to improve the performance of the GA. The algorithms were compared using a range of configurations on two test problems the two parameter Rosenbrock function and the six parameter Hartman function. A relatively small number of objective function evaluations were allowed so as to test the ability of the functions to converge under adverse conditions (that is, limited computational runtime). These functions were found to be best solved with different strategies. The Hartman function was found to respond better to a more elitist strategy, and the Rosenbrock function was solved with a more egalitarian strategy with higher population diversity. On both functions, the best configuration of the SCE algorithm was found to perform favorably compared to the best configurations of the GA. The best performing configurations of these algorithms were applied to the calibration of a rainfall runoff model of a catchment in Tasmania. The model was a two-tap Australian Water Balance Model (AWBM) consisting of eight parameters, with 10 years of data and a six month warm up period. 20 trials were performed on each algorithm, and in each trial the data were randomly split into train and test sets of nine and one year’s data respectively. The more egalitarian strategies (which maintain higher population diversity, as taken from the algorithm configurations found to best suit the Rosenbrock function) were found to be favorable for both the SCE and the GA. When comparing results on the test data, this difference was marginal. The difference in performance was more apparent on the results of the SCE algorithm. A recommendation of this paper is to develop a catalogue of the performance of several algorithms under different configurations on a range of test objective functions. This could be used to assist in the configuration of meta-heuristics on a range of applied problems, such as the calibration of additional rainfall runoff models.
Positive feedback in the transition from sexual reproduction to parthenogenesis

Understanding how new phenotypes evolve is challenging because intermediate stages in transitions from ancestral to derived phenotypes often remain elusive. Here we describe and evaluate a new mechanism facilitating the transition from sexual reproduction to parthenogenesis. In many sexually reproducing species, a small proportion of unfertilized eggs can hatch spontaneously (‘tychoparthenogenesis’) and develop into females. Using an analytical model, we show that if females are mate-limited, tychoparthenogenesis can result in the loss of males through a positive feedback mechanism whereby tychoparthenogenesis generates female-biased sex ratios and increasing mate limitation. As a result, the strength of selection for tychoparthenogenesis increases in concert with the proportion of tychoparthenogenetic offspring in the sexual population. We then tested the hypothesis that mate limitation selects for tychoparthenogenesis and generates female-biased sex ratios, using data from natural populations of sexually reproducing Timema stick insects. Across 41 populations, both the tychoparthenogenesis rates and the proportions of females increased exponentially as the density of individuals decreased, consistent with the idea that low densities of individuals result in mate limitation and selection for reproductive insurance through tychoparthenogenesis. Our model and data from Timema populations provide evidence for a simple mechanism through which parthenogenesis can evolve rapidly in a sexual population.
Properties of Natural Fibers Separated from Chromolaena odorata and Mikania micrantha

ABSTRACT This paper reports the possibility of separating natural fibers from two invasive alien plants Chromolaena odorata and Mikania micrantha. These two are considered as high-risk species on the basis their invasiveness and being a menace to the natural biodiversity of Kerala, India. Water retting and alkali extraction methods were used for the separation of stem fibers. Fibers obtained showed similar properties to currently used common fibers. Based on morphometric measurements and derived values, such as slenderness ratio, flexibility ratio, and Runkel ratio, these fibers are expected to be suitable for industrial purposes.