Miracle-dz/UniFAR-FTUs huggingface dataset:
Query quality prediction and reformulation for source code search: The Refoqus tool

Developers search source code frequently during their daily tasks, to find pieces of code to reuse, to find where to implement changes, etc. Code search based on text retrieval (TR) techniques has been widely used in the software engineering community during the past decade. The accuracy of the TR-based search results depends largely on the quality of the query used. We introduce Refoqus, an Eclipse plugin which is able to automatically detect the quality of a text retrieval query and to propose reformulations for it, when needed, in order to improve the results of TR-based code search. A video of Refoqus is found online at http://www.youtube. com/watch? v=UQlWGiauyk4.
The Field of Streams: Sagittarius and Its Siblings

We use Sloan Digital Sky Survey (SDSS) Data Release 5 (DR5) u, g, r, i, z photometry to study Milky Way halo substructure in the area around the north Galactic cap. A simple color cut (g - r < 0.4) reveals the tidal stream of the Sagittarius dwarf spheroidal galaxy, as well as a number of other stellar structures in the field. Two branches (A and B) of the Sagittarius stream are clearly visible in an RGB composite image created from three magnitude slices, and there is also evidence for a still more distant wrap behind the A branch. A comparison of these data with numerical models suggests that the shape of the Galactic dark halo is close to spherical.
Research Paper: Detection of Pediatric Respiratory and Diarrheal Outbreaks from Sales of Over-the-counter Electrolyte Products

OBJECTIVE To determine whether sales of electrolyte products contain a signal of outbreaks of respiratory and diarrheal disease in children and, if so, how much earlier a signal relative to hospital diagnoses. DESIGN Retrospective analysis was conducted of sales of electrolyte products and hospital diagnoses for six urban regions in three states for the period 1998 through 2001. MEASUREMENTS Presence of signal was ascertained by measuring correlation between electrolyte sales and hospital diagnoses and the temporal relationship that maximized correlation. Earliness was the difference between the date that the exponentially weighted moving average (EWMA) method first detected an outbreak from sales and the date it first detected the outbreak from diagnoses. The coefficient of determination (r2) measured how much variance in earliness resulted from differences in sales' and diagnoses' signal strengths. RESULTS The correlation between electrolyte sales and hospital diagnoses was 0.90 (95% CI, 0.87-0.93) at a time offset of 1.7 weeks (95% CI, 0.50-2.9), meaning that sales preceded diagnoses by 1.7 weeks. EWMA with a nine-sigma threshold detected the 18 outbreaks on average 2.4 weeks (95% CI, 0.1-4.8 weeks) earlier from sales than from diagnoses. Twelve outbreaks were first detected from sales, four were first detected from diagnoses, and two were detected simultaneously. Only 26% of variance in earliness was explained by the relative strength of the sales and diagnoses signals (r2 = 0.26). CONCLUSION Sales of electrolyte products contain a signal of outbreaks of respiratory and diarrheal diseases in children and usually are an earlier signal than hospital diagnoses.
Susceptibility to in vitro tolerance induction of adult B cells from mice with an X-linked B-cell defect

Previous studies from this laboratory have indicated that the susceptibility to in vitro tolerance induction is restricted to B cells early in their development (12,14). In this study, a modification of the in vitro splenic focus technique was used to determine whether 2,4- dinitrophenyl (DNP)-specific splenic B cells from adult (CBA/N X DBA/2)F1 males are susceptible to in vitro tolerance induction. The results demonstrate that greater than 50% of the DNP-specific B cells in the adult F1 male are tolerizable and therefore immature by this criterion. Moreover, the findings define at least two subpopulation in adult CBA/N mice, one of which is tolerizable. These findings are consistent with the hypothesis that the lymphoid population in the adult CBA/N mouse is characteristic of a neonatal B-cell population.
Seasonal Patterns of Birth in Patients with Glioblastoma

Seasonal distribution of birth rates was only recently described in patients with high‐grade gliomas. We analyzed 501 cases from the database of a Regional Cancer Center in Bavaria to assess annual periodicity in the birth dates of glioma patients. Prior to analysis, the number of births per month was normalized [number of births×100,000/total number of births in Germany] to obtain birth rates per month. The approximation of the time series data by a one‐year cosine model found that the glioblastoma birth rate exhibits a statistically significant annual variation, with the peak rate in January. Vitamin intake, infections, and other as‐yet‐unknown factors and exposures during pre‐ and perinatal early life may contribute to the seasonality of birth rate in patients with brain tumors.
Opening the black box of technology adoption: The motive-technology-belief framework

A qualitative empirical study explores the psychological process by which transportation consumers adopt alternatives to single occupancy vehicles. The study's findings give rise to the Motive-Technology-Belief (MTB) framework, a theory that conceives of technology adoption in terms of three mental structures: motives are inner mental reasons; technologies are tools that pertain to motives; and beliefs are associations between motives and/or technologies. Their behavioral interactions are governed by three conscious processes: selecting is the process of choosing a tool in response to an immediate need; evaluating is the process of forming beliefs about tools; and maintaining is the process of determining the functional status of tools. They are augmented by five unconscious auxiliary processes: perceiving, focusing, framing, consolidating, and acting. The primary contribution of the paper is a framework for a causal adoption process theory that is solidly grounded in empirical observations and prior literature, and is well-suited to guide the construction of simulated consumer agents. The theory establishes a foundation for agent-based market simulation that gives new product development and service innovation managers improved ability to forecast emerging market conditions.
Treadmill Exercise Training Prevents Myocardial Mechanical Dysfunction Induced by Androgenic-Anabolic Steroid Treatment in Rats

Elevated concentrations of testosterone and its synthetic analogs may induce changes in cardiovascular function. However, the effects of the combination of anabolic/androgenic steroid (AAS) treatment and exercise training on systolic and diastolic cardiac function are poorly understood. In the present study, we aimed to investigate the effects of low-dose steroid treatment (stanozolol) on cardiac contractile parameters when this steroid treatment was combined with exercise training in rats and the effects of chronic steroid treatment on the Frank-Starling (length-tension curves) relationship. Male Wistar rats were randomly assigned to one of four groups: U (untrained), US (untrained and treated with stanozolol 5 mg/kg/week), T (trained, 16 m/min/1 h) and TS (trained and treated with stanozolol 5 mg/kg/week). Continuous exercise training was conducted 5 days/week for 8 consecutive weeks. The speed of the treadmill was gradually increased to a final setting of 16 m/min/1 h. Experiments were divided into two independent series: 1) central hemodynamic analysis for mean arterial blood pressure (MAP) and cardiac output (CO) measurements and 2) isolated papillary muscle preparation in Krebs solution. Stanozolol treatment significantly increased the MAP and the heart size in untrained and trained rats (U 113±2; T 106±2; US 138±8 and TS 130±7 mmHg). Furthermore, stanozolol significantly decreased developed tension and dT/dt (maximal and minimal) in U rats. However, the developed tension was completely restored by training. The Frank/Starling relationship was impaired in rats treated with stanozolol; however, again, training completely restored diastolic function. Taken together, the present data suggest that AAS treatment is able to decrease cardiac performance (systolic and diastolic functions). The combination of stanozolol and physical training improved cardiac performance, including diastolic and systolic functions, independent of changes in central hemodynamic parameters. Therefore, changes in ventricular myocyte calcium transients may play a cardioprotective role.
Escapees on the X chromosome.

In many organisms, differentiation of the sex chromosome complement resulted in the coordinated regulation of genes on whole chromosomes to equalize gene expression between the sexes. In mammals, X inactivation evolved to restore equal expression of X-linked genes in males and females (1). Although X inactivation consists in the general repression of most genes on the X, some genes escape inactivation (reviewed in ref. 2). Recent advances in the Human Genome Project now allow the inactivation status of many X-linked genes to be systematically studied. In this issue of PNAS, Carrel et al. (3) report such a systematic analysis. Their data are so extensive that they are summarized in the paper but are fully accessible only as a file on the World Wide Web (www.pnas.org/supplementary.shtml).
Protective effects of probiotic Lactobacillus plantarum BJ0021 on liver and kidney oxidative stress and apoptosis induced by endosulfan in pregnant rats

Abstract Endosulfan (EDS) is one of the most widely organochlorine insecticide used in many parts of the world, although it is currently banned or severely restricted in use in some countries. EDS causes a variety of negative effects in non-target species including humans. Therefore, the aim of the present study was to investigate the possible protective effects of Lactobacillus plantarum BJ0021 on toxicity, oxidative stress, and apoptosis induced by EDS intoxication on liver and kidneys of pregnant rats. This pesticide induced a significant increase in total cholesterol, alanine-amino transferase (ALAT), aspartate-amino transferase (ASAT), alkaline phosphatase (ALP), gamma-glutamyl transpeptidase (GGT), urea and creatinine in serum, while urinary urea and creatinine were lower than those of the control group. In the liver and kidney, lipid peroxidation increased significantly, the antioxidant levels, such as superoxide dismutase (SOD) and catalase (CAT) were markedly depressed and TdT-mediated dUTP-biotin Nick End Labeling (TUNEL) revealed more apoptotic cells. In contrast, co-administration of L. plantarum BJ0021 to EDS-treated animals ameliorated most of these biochemical parameters, but the activity of antioxidant enzymes (SOD, CAT) did not modify and the number of apoptotic nuclei remained significantly raised in kidney compared to control. In conclusion, the administration of L. plantarum BJ0021 decreased apoptosis and might play a protective role in reducing toxicity of EDS in pregnant rats.
ORBS and the limits of static slicing

Observation-based slicing is a recently-introduced, language-independent slicing technique based on the dependencies observable from program behaviour. Due to the well-known limits of dynamic analysis, we may only compute an under-approximation of the true observation-based slice. However, because the observation-based slice captures all possible dependence that can be observed, even such approximations can yield insight into the limitations of static slicing. For example, a static slice, S, that is strictly smaller than the corresponding observation based slice is potentially unsafe. We present the results of three sets of experiments on 12 different programs, including benchmarks and larger programs, which investigate the relationship between static and observation-based slicing. We show that, in extreme cases, observation-based slices can find the true minimal static slice, where static techniques cannot. For more typical cases, our results illustrate the potential for observation-based slicing to highlight limitations in static slicers. Finally, we report on the sensitivity of observation-based slicing to test quality.
A Prospective Treatment Option for Lysosomal Storage Diseases: CRISPR/Cas9 Gene Editing Technology for Mutation Correction in Induced Pluripotent Stem Cells

Ease of design, relatively low cost and a multitude of gene-altering capabilities have all led to the adoption of the sophisticated and yet simple gene editing system: clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9). The CRISPR/Cas9 system holds promise for the correction of deleterious mutations by taking advantage of the homology directed repair pathway and by supplying a correction template to the affected patient’s cells. Currently, this technique is being applied in vitro in human-induced pluripotent stem cells (iPSCs) to correct a variety of severe genetic diseases, but has not as of yet been used in iPSCs derived from patients affected with a lysosomal storage disease (LSD). If adopted into clinical practice, corrected iPSCs derived from cells that originate from the patient themselves could be used for therapeutic amelioration of LSD symptoms without the risks associated with allogeneic stem cell transplantation. CRISPR/Cas9 editing in a patient’s cells would overcome the costly, lifelong process associated with currently available treatment methods, including enzyme replacement and substrate reduction therapies. In this review, the overall utility of the CRISPR/Cas9 gene editing technique for treatment of genetic diseases, the potential for the treatment of LSDs and methods currently employed to increase the efficiency of this re-engineered biological system will be discussed.
Mechanism of endothelin-1-induced contraction in rabbit basilar artery.

BACKGROUND AND PURPOSE Endothelin-1 (ET-1) is suggested to be a major cause of cerebral vasospasm after subarachnoid hemorrhage. However, the mechanism of ET-1-induced contraction in cerebral arteries remains unclear. This study was undertaken to demonstrate the possible role of protein tyrosine kinase (PTK), mitogen-activated protein kinase (MAPK), and protein kinase C (PKC) in ET-1-induced contraction. METHODS PD-98059, damnacanthal, wortmannin, AG-490, genistein, calphostin C, and staurosporine were used to inhibit, or relax, the ET-1-induced contraction of basilar artery, studied with an isometric tension system. Immunoprecipitation of MAPK in ET-1-stimultated rings of basilar artery without or with the above inhibitors was studied with Western blot. RESULTS (1) ET-1 produced concentration-dependent contraction and MAPK immunoprecipitation in rabbit basilar artery by activation of ET(A) but not ET(B) receptors. (2) MAPK inhibitors PD-98059 and U-0126 produced dose-dependent inhibition of ET-1-induced contraction. (3) The Src tyrosine kinase inhibitor damnacanthal, the phosphatidylinositol-3 kinase inhibitor wortmannin, and the Janus tyrosine kinase(2) inhibitor AG-490 abolished ET-1-induced contraction. (4) The PKC inhibitor staurosporine but not calphostin C abolished ET-1-induced contraction, and the PTK inhibitor genistein partially reduced ET-1-induced contraction. (5) In arteries precontracted by ET-1, PD-98059, U-0126, wortmannin, AG-490, genistein, and staurosporine produced concentration-dependent relaxation. (6) ET-1 induced a biphasic and time-dependent MAPK immunoprecipitation. (7) PD-98059, U-0126, genistein, AG-490, and damnacanthal, but not staurosporine or wortmannin, abolished the effect of ET-1 on MAPK immunoreactivity. CONCLUSIONS This study demonstrated that MAPK may be involved in ET-1-induced contraction in rabbit basilar artery. MAPK is downstream of PTK, Src, and Janus tyrosine kinase pathways but may not be downstream of phosphatidylinositol-3 kinase pathways. The possible involvement of PKC in ET-1-induced contraction requires further investigation. Inhibition of these pathways may offer alternative treatment for ET-1-induced contraction and cerebral vasospasm.
AN ANALYSIS OF READING ERRORS OF DYSLEXIC READERS IN HINDI AND ENGLISH

The present study examined the nature of reading errors made by dyslexic readers in Hindi and English. A detailed analysis of error type showed 60% and 57% of phonological errors; 15% and 35% of orthographic errors; 25% and 7% of mixed errors; and 0.38% and 0.94% of unrelated errors in Hindi and English, respectively. Further, in both Hindi and English, the majority (65% & 69%, respectively) were the scaffolding errors, followed by the errors preserving the initial phoneme (22% & 23%, respectively), errors preserving the final phoneme (9% & 6%, respectively) and errors with orthographic overlap (4% & 2%, respectively). In Hindi, a far greater percentage of nonword (89%) than word (11%) errors was found, whereas in English, 54% of nonword and 46% of word errors was found. A significant correlation was found between reading accuracy in Hindi and in English. The findings are discussed in terms of linguistic interdependence hypothesis and orthographic transparency.
Study on properties of elastic core-spun yarns containing a mix of spandex and PET/PTT bi-component filament as core

This paper presents a development of elastic core-spun yarn containing a mix of spandex and polyethylene terephthalate/polytrimethylene terephthalate (PET/PTT) bi-component filament as core to obtain better yarn properties, especially for elastic property. Eight types of core-spun yarns, consisting of different core components with various values of linear density and covered with cotton fibers, were produced using a modified ring-spinning machine with a core spinning attachment. The influences of core components, linear density, and draw ratio of spandex on yarn structure and properties were investigated. The experimental results demonstrate that core-spun yarns containing a mix of spandex and PET/PTT bi-component filament have much lower yarn stress decay as well as lower hairiness and CVm value of evenness compared to the yarns using only spandex. For the yarns containing a mix of spandex and PET/PTT bi-component filament, the yarns containing 70 denier spandex have higher elongation and stress decay compared to the yarns containing 40 denier spandex. The test results show that the elongation of yarns containing a mix of spandex and PET/PTT bi-component filament increases with the increase of the draw ratio of spandex. The stress decay of yarns containing a mix of 70 denier spandex and PET/PTT filament shows a similar trend to the elongation. Moreover, the yarn samples containing a mix of spandex and PET/PTT filament as core exhibit good yarn evenness, with very few thick places and neps, as well as low yarn hairiness.
Interpretation of serologic tests for typhoid fever.

Although the incidence of typhoid fever in this country has been decreasing,1sporadic outbreaks continue to occur.2,3Increasing numbers of military personnel and private citizens are being exposed to typhoid during foreign travel to areas where the disease is endemic; consequently, the diagnosis of typhoid fever remains an important problem. The definitive diagnostic procedure is isolation ofSalmonella typhosafrom blood, stool, or occasionally, urine, but serologic tests are still widely used. This communication will briefly discuss the following aspects of serologic tests for typhoid fever: the antigens used, cross-reactivity with other salmonellae, traditional interpretive criteria of test results, serologic response in the vaccinated patient, the effect of antibiotic treatment on antibody response, and the Vi test for identifying typhoid carriers. Diagnostic tests for typhoid bacillus, such as Widal's reaction, are tube dilution tests which measure agglutinating antibodies against O and H antigens. The Vi antigen is used
Prediction error estimation: a comparison of resampling methods

MOTIVATION In genomic studies, thousands of features are collected on relatively few samples. One of the goals of these studies is to build classifiers to predict the outcome of future observations. There are three inherent steps to this process: feature selection, model selection and prediction assessment. With a focus on prediction assessment, we compare several methods for estimating the 'true' prediction error of a prediction model in the presence of feature selection. RESULTS For small studies where features are selected from thousands of candidates, the resubstitution and simple split-sample estimates are seriously biased. In these small samples, leave-one-out cross-validation (LOOCV), 10-fold cross-validation (CV) and the . 632+ bootstrap have the smallest bias for diagonal discriminant analysis, nearest neighbor and classification trees. LOOCV and 10-fold CV have the smallest bias for linear discriminant analysis. Additionally, LOOCV, 5- and 10-fold CV, and the . 632+ bootstrap have the lowest mean square error. The . 632+ bootstrap is quite biased in small sample sizes with strong signal-to-noise ratios. Differences in performance among resampling methods are reduced as the number of specimens available increase. SUPPLEMENTARY INFORMATION A complete compilation of results and R code for simulations and analyses are available in Molinaro et al. (2005) (http://linus.nci.nih.gov/brb/TechReport.htm).
Genetic markers substantiate long-term storage and utilization of sperm by female painted turtles

Most studies of genetic parentage in natural populations have been limited to a single breeding season or reproductive episode and, thus, provide only a snapshot of individuals’ mating behaviours. Female turtles can store viable sperm in their reproductive tracts for as long as several years, but the extent to which this capacity is utilized in nature has remained unknown. Here, we employ microsatellite markers to assess genetic paternity in successive clutches of individually marked, free-ranging female painted turtles (Chrysemys picta) over a four year period. The genetic data from 113 clutches from this natural population demonstrate that most females (80.5%) remated each year and that each female generally used a single male’s sperm to fertilize all clutches laid within a year. However, sperm usage among females varied considerably, and some females apparently used sperm that had been stored for up to three years to fertilize some or all eggs laid in consecutive nesting seasons. Thus, remating by females is not necessary for continued offspring production from a given sire. Furthermore, 13.2% of all clutches examined showed evidence of multiple paternity, and the genetic paternity patterns across years suggest a ‘last in, first out’ operation of the females’ sperm storage tubules.