Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Analysis can be Improved with Automatic Test Suite Refactoring

Context: Developers design test suites to automatically verify that software meets its expected behaviors. Many dynamic analysis techniques are performed on the exploitation of execution traces from test cases. However, in practice, there is only one trace that results from the execution of one manually-written test case. Objective: In this paper, we propose a new technique of test suite refactoring, called B-Refactoring. The idea behind B-Refactoring is to split a test case into small test fragments, which cover a simpler part of the control flow to provide better support for dynamic analysis. Method: For a given dynamic analysis technique, our test suite refactoring approach monitors the execution of test cases and identifies small test cases without loss of the test ability. We apply B-Refactoring to assist two existing analysis tasks: automatic repair of if-statements bugs and automatic analysis of exception contracts. Results: Experimental results show that test suite refactoring can effectively simplify the execution traces of the test suite. Three real-world bugs that could previously not be fixed with the original test suite are fixed after applying B-Refactoring; meanwhile, exception contracts are better verified via applying B-Refactoring to original test suites. Conclusions: We conclude that applying B-Refactoring can effectively improve the purity of test cases. Existing dynamic analysis tasks can be enhanced by test suite refactoring.
Calpain-mediated Proteolysis of Paxillin Negatively Regulates Focal Adhesion Dynamics and Cell Migration*

The dynamic turnover of integrin-mediated adhesions is important for cell migration. Paxillin is an adaptor protein that localizes to focal adhesions and has been implicated in cell motility. We previously reported that calpain-mediated proteolysis of talin1 and focal adhesion kinase mediates adhesion disassembly in motile cells. To determine whether calpain-mediated paxillin proteolysis regulates focal adhesion dynamics and cell motility, we mapped the preferred calpain proteolytic site in paxillin. The cleavage site is between the paxillin LD1 and LD2 motifs and generates a C-terminal fragment that is similar in size to the alternative product paxillin delta. The calpain-generated proteolytic fragment, like paxillin delta, functions as a paxillin antagonist and impairs focal adhesion disassembly and migration. We generated mutant paxillin with a point mutation (S95G) that renders it partially resistant to calpain proteolysis. Paxillin-deficient cells that express paxillin S95G display increased turnover of zyxin-containing adhesions using time-lapse microscopy and also show increased migration. Moreover, cancer-associated somatic mutations in paxillin are common in the N-terminal region between the LD1 and LD2 motifs and confer partial calpain resistance. Taken together, these findings suggest a novel role for calpain-mediated proteolysis of paxillin as a negative regulator of focal adhesion dynamics and migration that may function to limit cancer cell invasion.
Concentration‐dependent specimen shrinkage in iodine‐enhanced microCT

Iodine potassium iodide (I2KI) solution can be employed as a contrast agent for the visualisation of soft tissue structures in micro‐computed tomography studies. This technique provides high resolution images of soft tissue non‐destructively but initial studies suggest that the stain can cause substantial specimen shrinkage. The degree of specimen shrinkage, and potential deformation, is an important consideration when using the data for morphological studies. Here we quantify the macroscopic volume changes in mouse skeletal muscle, cardiac muscle and cerebellum as a result of immersion in the common fixatives 10% phosphate‐buffered formal saline, 70% ethanol and 3% glutaraldehyde, compared with I2KI staining solution at concentrations of 2, 6, 10 and 20%. Immersion in the I2KI solution resulted in dramatic changes of tissue volume, which were far larger than the shrinkage from formalin fixation alone. The degree of macroscopic change was most dependent upon the I2KI concentration, with severe shrinkage of 70% seen in solutions of 20% I2KI after 14 days' incubation. When using this technique care needs to be taken to use the lowest concentration that will give adequate contrast to minimise artefacts due to shrinkage.
Functional Inducible Nitric Oxide Synthase Gene Variants Associate With Hypertension

AbstractIncreased inducible nitric oxide synthase (iNOS) activity and expression has been associated with hypertension, but less is known whether the 2 known functional polymorphic sites in the iNOS gene (g.–1026 C/A (rs2779249), g.2087 G/A (rs2297518)) affect susceptibility to hypertension. The objective of this study was to investigate the association between the genetic variants of iNOS and diagnosed hypertension in a Finnish cohort.This study included 320 hypertensive cases and 439 healthy controls. All participants were 50-year-old men and women and the data were collected from the Tampere adult population cardiovascular risk study (TAMRISK). DNA was extracted from buccal swabs and iNOS single nucleotide polymorphisms (SNPs) were analyzed using KASP genotyping PCR. Data analysis was done by logistic regression.At the age of 50 years, the SNP rs2779249 (C/A) associated significantly with hypertension (P = 0.009); specifically, subjects carrying the A-allele had higher risk of hypertension compared to those carrying the CC genotype (OR = 1.47; CI = 1.08–2.01; P = 0.015). In addition, a 15-year follow-up period (35, 40, and 45 years) of the same individuals showed that carriers of the A-allele had more often hypertension in all of the studied age-groups. The highest risk for developing hypertension was obtained among 35-year-old subjects (odds ratio [OR] 3.83; confidence interval [CI] = 1.20–12.27; P = 0.024). Those carrying variant A had also significantly higher readings of both systolic (P = 0.047) and diastolic (P = 0.048) blood pressure during the follow-up. No significant associations between rs2297518 (G/A) variants alone and hypertension were found. However, haplotype analysis of rs2779249 and rs2297518 revealed that individuals having haplotype H3 which combines both A alleles (CA–GA, 19.7% of individuals) was more commonly found in the hypertensive group than in the normotensive group (OR = 2.01; CI = 1.29–3.12; P = 0.002). In conclusion, there was a significant association between iNOS genetic variant (rs2779249) and hypertension in the genetically homogenous Finnish population. Those who carried the rare A-allele of the gene had higher risk for hypertension already at the age of 35 years.
Understanding early dementia: EEG, MRI, SPECT and memory evaluation

Abstract Background: An increase in the EEG upper/low a power ratio has been associated with mild cognitive impairment (MCI) due to Alzheimer’s disease (AD) and to the atrophy of temporoparietal brain areas. Subjects with a higher α3/α2 frequency power ratio showed lower brain perfusion than in the low α3/α2 group. The two groups show significantly different hippocampal volumes and correlation with q frequency activity. Methods: Seventy-four adult subjects with MCI underwent clinical and neuropsychological evaluation, electroencephalogram (EEG) recording, and high resolution 3D magnetic resonance imaging (MRI). Twenty-seven of them underwent EEG recording and perfusion single-photon emission computed tomography (SPECT) evaluation. The α3/α2 power ratio and cortical thickness were computed for each subject. The difference in cortical thickness between the groups was estimated. Results: In the higher upper/low a group, memory impairment was more pronounced in both the MRI group and the SPECT MCI groups. An increase in the production of q oscillations was associated with greater interhemisperic coupling between temporal areas. It also correlated with greater cortical atrophy and lower perfusional rate in the temporoparietal cortex. Conclusion: High EEG upper/low α power ratio was associated with cortical thinning and lower perfusion in temporoparietal areas. Moreover, both atrophy and lower perfusion rate significantly correlated with memory impairment in MCI subjects. Therefore, the increase in the EEG upper/low α frequency power ratio could be useful in identifying individuals at risk for progression to AD dementia in a clinical context.
Predicting Progressive Delamination of Composite Material Specimens via Interface Elements

This article describes the application of interface elements to the prediction of progressive delamination in composite materials. The work has been implemented in two separate commercial finite-element computer packages, ABAQUS [1] and LUSAS [2]. In the former case, this has been achieved via a "user subroutine", while in the latter case the elements are embedded directly within the system, either in the standard "release version" of the code or in a research version, to which the authors have access and in which they have implemented various algorithms directly. Comparisons are made with a range of experimental results for composite material specimens. In addition to the finite-element solutions, closed-form results are also presented that are based on a corrected beam theory.
Cytotoxicity and Characterization of Particles Collected From an Indium–Tin Oxide Production Facility

Occupational exposure to indium compound particles has recently been associated with lung disease among workers in the indium–tin oxide (ITO) industry. Previous studies suggested that excessive alveolar surfactant and reactive oxygen species (ROS) may play a role in the development of pulmonary lesions following exposure to indium compounds. However, toxicity at the cellular level has not been comprehensively evaluated. Thus, the aim of this study was to assess which, if any, compounds encountered during ITO production are toxic to cultured cells and ultimately contribute to the pathogenesis of indium lung disease. The compounds used in this study were collected from eight different processing stages at an ITO production facility. Enhanced dark field imaging showed 5 of the compounds significantly associated with cells within 1 h, suggesting that cellular reactions to the compound particles may be occurring rapidly. To examine the potential cytotoxic effects of these associations, ROS generation, cell viability, and apoptosis were evaluated following exposures in RAW 264.7 mouse monocyte macrophage and BEAS-2B human bronchial epithelial cell lines. Both exhibited reduced viability with exposures, while apoptosis only occurred in RAW 264.7 cells. Our results suggested that excessive ROS production is likely not the predominant mechanism underlying indium-induced lung disease. However, the effects on cell viability reveal that several of the compounds are cytotoxic, and therefore, exposures need to be carefully monitored in the industrial setting.
Prescribing exercise for frail elders.

BACKGROUND Frail elders often have chronic illnesses, such as osteoarthritis, hypertension, diabetes, and peripheral vascular disease, for which exercise is a proven means of achieving nonpharmacologic benefits, even at advanced age. Exercise has been shown to enhance the quality of life for these elders. METHODS A literature search of exercise literature applied to older adults and lifestyle modifications was conducted, summarized, and then reviewed with practicing colleagues. RESULTS AND CONCLUSIONS Exercise continues to be an underused therapeutic intervention for frail elders as a result of barriers created by patients themselves, their caregivers, and their health care providers. Family physicians can overcome these barriers by prescribing appropriate exercises and by tailoring the exercise to the functional needs and preferences of their patients. An exercise prescription for frail elders is based on a pragmatic strategy that makes therapeutic exercise both sustainable and safe. Such a strategy incorporates motivational elements and knowledge of achievable benefits.
Optimal adult growth of Daphnia in a seasonal environment

Summary 1. The cladoeeran Daphnia serves as an example of an iteroparous organism, with overlapping generations, that is eapable of substantial adult growth. The life history of Daphnia was modelIed as the eonsequenee of aseries of decisions about alloeation of energetie resourees to growth and reproduetion. 2. We used numerieal methods to find resouree alloeation patterns that maximized fitness of Daphnia in a temporally variable environment. Temporal variation was modelIed as alternating aetive and dormant seasons; length of the aetive season was uniformly distributed. Fitness was measured by the geometrie mean of resting eggs produeed at the end of the aetive season. We examined effeets of mean and range of the aetive season on the optimallife history; we also examined effeets of inereasing (invertebrate predation), eonstant (non-seleetive) and deereasing (fish) size-speeifie survival rates. For eomparison, we found resouree alloeation patterns that max­ imized fitness in a eonstant environment, where fitness was measured by the intrinsie rate of inerease r. 3. Life histories optimized for seasonal environments generally showed earlier maturity and greater adult growth than those optimized for eonstant environments. Adult growth oeeurred with non-seleetive predation, and even with fish predation, eonditions under whieh it does not oeeur in the optimal life his tori es for eonstant environments. 4. Greatest size at maturity and adult growth oeeurred in life histories optimized to invertebrate predation in seasonal environments. Smalkst size at maturity and least adult growth oeeurred in life histories optimized to fish predation. 5. In the optimallife histories, size at maturity generally inereased with mean length of the aetive season. Adult growth reaehed a maximum for mean seasons of length equal to about one-half to one life span of Daphnia. 6. Inereasing the variation in season length deereased adult growth in the optimal life history , but had little effeet on size at maturity. 7. We expeet that life histories are adapted to the long-term average of season length and its variation. If the animals ean deteet the type of predator, seleetion eould favour phenotypie variation in resouree alloeation.
Mathematical and numerical analysis of the spectral characteristics of dielectric microcavities with active regions

We investigate electromagnetic fields and emission thresholds of two-dimensional dielectric microcavities solving the Lasing Eigenvalue Problem (LEP). We propose a new convenient formulation of LEP as a nonlinear spectral problem for a Fredholm holo-morphic operator-valued function and solve LEP for microcavities of arbitrary shape with active regions. We reduce the original problem to the system of Miiller boundary integral equations, which we solve numerically by the Nystrom method. We study properties of the characteristic set theoretically and prove convergence of the Nystrom method.
Aerobic exercise and resting blood pressure among women: a meta-analysis.

PURPOSE The aim of this study was to use the meta-analytic approach to examine the effects of aerobic exercise on resting systolic and diastolic blood pressure among adult women. METHODS Studies were retrieved from computer searches (MEDLINE, Sport Discus, Current Contents) and bibliographies of retrieved articles were cross-referenced. Inclusion criteria were as follows: (1) randomized trials, (2) aerobic activity as the primary exercise intervention, (3) comparative nonexercise control group included, (4) changes in resting systolic and/or diastolic blood pressure assessed for women ages 18 and older, and (5) studies published in English-language journals between January 1966 and January 1998. The primary outcomes retrieved in this study were changes in resting systolic and diastolic blood pressure calculated as the difference (exercise minus control) of the changes (initial minus final) in these mean values. RESULTS Ten studies representing 732 subjects and 36 primary outcomes (19 systolic, 17 diastolic) met the criteria for inclusion. Overall, an approximate 2% decrease in resting systolic and 1% decrease in resting diastolic blood pressure were observed (systolic,;x +/- SD = -2 +/- 2.6 mm Hg, 95% bootstrap confidence interval -3 to -1 mm Hg; diastolic,;x +/- SD = -1 +/- 1.9 mm Hg, 95% bootstrap confidence interval -2 to -1 mm Hg). CONCLUSION Aerobic exercise results in small reductions in resting systolic and diastolic blood pressure among adult women. However, a need exists for additional, well-designed studies on this topic, especially among hypertensive adult women.
HuR and Ago2 Bind the Internal Ribosome Entry Site of Enterovirus 71 and Promote Virus Translation and Replication

EV71 (enterovirus 71) RNA contains an internal ribosomal entry site (IRES) that directs cap-independent initiation of translation. IRES-dependent translation requires the host’s translation initiation factors and IRES-associated trans-acting factors (ITAFs). We reported recently that mRNA decay factor AUF1 is a negative-acting ITAF that binds IRES stem-loop II. We also reported that the small RNA-processing enzyme Dicer produces at least four small RNAs (vsRNAs) from the EV71 IRES. One of these, vsRNA1, derived from IRES stem-loop II, reduces IRES activity and virus replication. Since its mechanism of action is unknown, we hypothesized that it might control association of ITAFs with the IRES. Here, we identified the mRNA stability factor HuR and the RISC subunit Argonaute 2 (Ago2) as two ITAFs that bind stem-loop II. In contrast to AUF1, HuR and Ago2 promote EV71 IRES activity and virus replication. In vitro RNA-binding assays revealed that vsRNA1 can alter association of Ago2, HuR, and AUF1 with stem-loop II. This presents a possible mechanism by which vsRNA1 could control viral translation and replication.
Oral squamous cell carcinoma: a clinicopathological study of 342 Thai cases.

AIM To conduct a clinicopathological review of oral squamous cell carcinoma (SCC) and to analyze it with respect to gender, age at diagnosis, clinical presentation, lesion location, and histological grading. METHODS AND MATERIALS Information on the clinicopathological characteristics of SCC was obtained from pathology reports of 342 cases. RESULTS The male to female ratio was 1:1 and the incidence increased with age. Among the patients 4.7% were younger than 40 years and males were predominant in this subgroup. The alveolar ridge and gingiva were the most commonly affected sites (50%). The majority of the SCC cases presented as ulcers or masses. Swelling and/or pain were the first signs and/or symptoms in most patients (52.6%). The age at diagnosis in relation to the site of occurrence varied. Conventional SCC was the most common subtype (88%). Well-differentiated SCC was the most common histological grading (78.6%). CONCLUSION In the present study, the incidence of SCC was age-related and showed equal gender distribution. CLINICAL SIGNIFICANCE Routine examination of the oral cavity by dental practitioners and other health care providers aids in the early detection of premalignant and malignant oral disease. Dentists can play a significant role in disseminating information regarding oral cancer.
XORP: an open platform for network research

Network researchers face a significant problem when deploying software in routers, either for experimentation or for pilot deployment. Router platforms are generally not open systems, in either the open-source or the open-API sense. In this paper we discuss the problems this poses, and present an eXtensible Open Router Platform (XORP) that we are developing to address these issues. Key goals are extensibility, performance and robustness. We show that different parts of a router need to prioritize these differently, and examine techniques by which we can satisfy these often conflicting goals. We aim for XORP to be both a research tool and a stable deployment platform, thus easing the transition of new ideas from the lab to the real world.
Mitochondrial glutathione replacement restores surfactant synthesis and secretion in alveolar epithelial cells of ethanol-fed rats.

BACKGROUND Chronic alcohol abuse increases the incidence and severity of acute lung injury in critically ill patients. Previously we determined that ethanol ingestion in rats dramatically decreased alveolar epithelial cellular levels of glutathione and surfactant synthesis and secretion in vitro. Previous studies in alcoholic liver disease suggest that mitochondrial glutathione levels, and not cellular levels per se, are involved in the pathogenesis of ethanol-mediated hepatotoxicity. Therefore, we hypothesized that alveolar epithelial mitochondrial glutathione depletion mediates the observed defects in surfactant synthesis and secretion in ethanol-fed rats. METHODS Male Sprague-Dawley rats were fed the Lieber-DeCarli liquid diet with or without ethanol (36% of total calories) for 6 weeks. In some experiments, ethanol-fed rats were then switched to the control diet for 1 week, with or without glutathione supplementation with either N-acetylcysteine (NAC) or procysteine (PRO). Alveolar epithelial type II cells were then isolated and glutathione levels (cytosolic and mitochondrial) and surfactant production (synthesis and secretion) were determined. RESULTS Ethanol ingestion decreased (p < 0.05) mitochondrial and cytosolic levels of glutathione, and surfactant synthesis and secretion in isolated type II cells when compared to cells from control-fed rats. NAC treatment restored (p < 0.05) cytosolic but not mitochondrial glutathione levels (p > 0.05), and had no effect (p > 0.05) on surfactant synthesis and secretion in type II cells isolated from ethanol-fed rats. In contrast, PRO treatment restored (p < 0.05) cytosolic and mitochondrial glutathione levels, and normalized (p < 0.05) surfactant synthesis and secretion in type II cells isolated from ethanol-fed rats. CONCLUSIONS These results suggest that mitochondrial, and not simply cytosolic, replacement of glutathione is necessary to improve surfactant function in critically ill patients with a history of alcohol abuse.
Soft Sweeps

A population can adapt to a rapid environmental change or habitat expansion in two ways. It may adapt either through new beneficial mutations that subsequently sweep through the population or by using alleles from the standing genetic variation. We use diffusion theory to calculate the probabilities for selective adaptations and find a large increase in the fixation probability for weak substitutions, if alleles originate from the standing genetic variation. We then determine the parameter regions where each scenario—standing variation vs. new mutations—is more likely. Adaptations from the standing genetic variation are favored if either the selective advantage is weak or the selection coefficient and the mutation rate are both high. Finally, we analyze the probability of “soft sweeps,” where multiple copies of the selected allele contribute to a substitution, and discuss the consequences for the footprint of selection on linked neutral variation. We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high.