Miracle-dz/UniFAR-FTUs huggingface dataset:
An Empirical Study of Fault Localization Families and Their Combinations

The performance of fault localization techniques is critical to their adoption in practice. This paper reports on an empirical study of a wide range of fault localization techniques on real-world faults. Different from previous studies, this paper (1) considers a wide range of techniques from different families, (2) combines different techniques, and (3) considers the execution time of different techniques. Our results reveal that a combined technique significantly outperforms any individual technique (200 percent increase in faults localized in Top 1), suggesting that combination may be a desirable way to apply fault localization techniques and that future techniques should also be evaluated in the combined setting. Our implementation is publicly available for evaluating and combining fault localization techniques.
Psychometric validation of the electronic chronic pain questions (eCPQ) in a primary care setting

Abstract Objective: Collecting data that helps evaluate different types of pain may improve physicians’ decision-making with regard to treatment selection and on-going monitoring of patients. To date, no chronic pain assessments have been widely implemented in primary care. The aim of this study was to psychometrically validate the electronic Chronic Pain Questions (eCPQ) in a primary care setting. Research design and methods: All men and women ≥18 years arriving at two similar primary care clinics in southeastern Michigan were invited to participate. Clinic staff verbally administered the eCPQ to patients and recorded their answers into the electronic medical record (EMR) prior to physician consultation with results available for physician review. Concurrent validity was assessed using Spearman correlations between eCPQ and patient-completed ancillary measures. Known-group validity was assessed by stratifying patients on self-reported chronic pain as well as by pain diagnosis (i.e. ICD-9 codes). To compare patients with chronic pain versus no chronic pain t-tests and chi-square tests were performed. Reproducibility was assessed between interviewer- and self-administration over time. Results: A total of 534 patients were invited to participate and 455 patients consented to take part in the study (85.2% response rate); 395 patients had analyzable eCPQ data; 70.1% were Caucasian; 68.1% female; mean age was 43.4; 52.7% (n = 208) self-reported chronic pain. Correlations between eCPQ and ancillary measures supported concurrent validity. Excellent discrimination between groups was evidenced based on self-reported chronic pain and ICD-9 diagnosis. Patients with self-reported chronic pain reported significantly (p < .0001) higher pain ratings and greater interference with usual activities, sleep, and mood than those without chronic pain. Test–retest reliability between modes (interviewer- vs. self-administration) was excellent as was reproducibility based on self-administration of the eCPQ at two separate time points. Key limitations: Discriminant validity was determined by comparing participants based on ICD codes. Utilizing ICD codes to identify individuals with chronic pain may not be a reliable approach as it is dependent upon providers accurately and consistently entering chronic pain diagnoses in the EMR. Conclusions: The eCPQ has sound psychometric measurement properties, including concurrent validity, discriminant validity, and reproducibility. The eCPQ appears to be useful to identify patients with chronic pain and to assess and monitor symptoms over time.
Inflammatory papillary hyperplasia: A systematic review

Introduction Inflammatory papillary hyperplasia (IPH) is a benign lesion of the palatal mucosa. It is usually found in denture-wearers but also has been reported in patients without a history of use of a maxillary prosthesis use. Objetives The aim of this study is to review the literature to assess the prevalence of denture stomatitis and inflammatory papillary hyperplasia and the etiological factors associated. Material and Methods A search was carried out in PubMed (January 2005 to October 2015) with the key words “inflammatory papillary hyperplasia”, “denture stomatitis”, “granular stomatitis” and “Newton’s type III” The inclusion criteria were studies including at least a sample of 50 apparently healthy patients, articles published from 2005 to 2015 written in English. The exclusion criteria were reviews and non-human studies. Results Out of the 190 studies obtained initially from the search 16 articles were selected to be included in our systematic review. The prevalence of denture stomatitis was 29.56% and 4.44% for IPH. We found 5 cases of denture stomatitis among non-denture-wearer individuals. All IPH cases were associated with the use of prosthesis. Smoking and continued use of ill-fitting dentures turned out to be the most frequent risk factors for developing IPH. Conclusions IPH is a rare oral lesion and its pathogenesis still remains unclear. Its presentation among non-denture-wearers is extremely unusual. Key words:Inflammatory papillary hyperplasia, denture stomatitis, prevalence, granular stomatitis, Newton’s type III stomatitis.
Functional and molecular characterization of luminal and basolateral Cl-/[Formula: see text]exchangers of rat thick limbs.

Cl-/[Formula: see text]exchange was measured in luminal (LMV) and basolateral (BLMV) membrane vesicles purified from rat medullary thick ascending limb (MTAL). Cl-/[Formula: see text]exchange in BLMV and LMV was inhibited by DIDS, with respective IC50 values of 3.2 ± 0.9 and 15.2 ± 5.2 μM, whereas Cl- conductances were DIDS insensitive. At constant external pH, BLMV36Cl-/[Formula: see text]and36Cl-/Cl-exchanges exhibited a sigmoidal pattern of activation as internal pH (pHi) increased from 6.1 to 8.0, whereas LMV36Cl-/Cl-exchange was unchanged between pHi6.7 and 7.8. The 165-kDa AE2 polypeptide and ∼115-kDa AE1-related polypeptide were present only in BLMV. In contrast, AE1-related polypeptides of ∼90 and 95 kDa were present not only in BLMV but also (in variable abundance) in LMV. We conclude that rat MTAL BLMV and LMV express distinct anion exchange activities and distinct sets of AE polypeptides. AE2 (and perhaps AE1) in BLMV likely contribute to[Formula: see text] absorption. In contrast, LMV exchangers may contribute to NaCl absorption via parallel coupling with the luminal Na+/H+antiporters and/or may provide negative feedback regulation of[Formula: see text] absorption.
Estrogen replacement, vascular distensibility, and blood pressures in postmenopausal women.

The pathogenesis of blood pressure (BP) rise in aging women remains unexplained, and one of the many incriminating factors may include abnormalities in arteriolar resistance vessels. The aim of this study was to determine the effects of unopposed estrogen on arteriolar distensibility, baroreceptor sensitivity (BRS), BP changes, and rate-pressure product (RPP). We tested the hypotheses that estrogen replacement therapy (ERT) enhances arteriolar distensibility and ameliorates BRS, which leads to decreases in BP and RPP. Postmenopausal women participated in a single-blind crossover study; the participants of this study, after baseline measurements, were randomly assigned to receive estrogen (ERT) or a drug-free treatment with a 6-wk washout period between treatments. The single-blind design was instituted because subjects become unblinded due to physiological changes (i.e., fluid shifts, weight gain, and secretory changes) associated with estrogen intake. However, investigators and technicians involved in data collection and analyses remained blind. After each treatment, subjects performed identical autonomic tests, during which electrocardiograms, beat-by-beat BPs, and respiration were recorded. The area under the dicrotic notch of the BP wave was used as an index of arteriolar distensibility. The magnitude of the reflex bradycardia after a precipitous rise in BP was used to determine BRS. Power spectral analysis of heart rate variability was used to assess autonomic activity. BPs were recorded from resistance vessels in the finger using a beat-by-beat photoplethysmographic device. RPP, a noninvasive marker of myocardial oxygen consumption, was calculated. Repeated-measures analyses of variance revealed a significantly enhanced arteriolar distensibility and BRS after ERT ( P < 0.05). A trend of a lower sympathovagal balance at rest was observed after ERT; however, this trend did not reach statistical significance ( P = 0.061) compared with the other treatments. The above autonomic changes produced significantly lower systolic and diastolic BP changes and RPPs ( P < 0.05) at rest and during isometric exercise. We conclude that short-term unopposed ERT favorably enhances arteriolar distensibility, BRS, and hemodynamic parameters in postmenopausal women. These findings have clinical implications in the goals for treating cardiovascular risk factors in aging women.
The impact of mass deworming programmes on schooling and economic development: an appraisal of long-term studies

Abstract Background: Documents from advocacy and fund-raising organizations for child mass deworming programmes in low- and middle-income countries cite unpublished economic studies claiming long-term effects on health, schooling and economic development. Methods: To summarize and appraise these studies, we searched for and included all long-term follow-up studies based on cluster-randomized trials included in a 2015 Cochrane review on deworming. We used Cochrane methods to assess risk of bias, and appraised the credibility of the main findings. Where necessary we contacted study authors for clarifications. Results: We identified three studies (Baird 2016, Ozier 2016 and Croke 2014) evaluating effects more than 9 years after cluster-randomized trials in Kenya and Uganda. Baird and Croke evaluate short additional exposures to deworming programmes in settings where all children were dewormed multiple times. Ozier evaluates potential spin-off effects to infants living in areas with school-based deworming. None of the studies used pre-planned protocols nor blinded the analysis to treatment allocation. Baird 2016 has been presented online in six iterations. The work is at high risk of reporting bias and selective reporting, and there are substantive changes between versions. The main cited effects on secondary school attendance and job sector allocation are from post hoc subgroup analyses, which the study was not powered to assess. The study did not find any evidence of effect on nutritional status, cognitive tests or school grades achieved, but these are not reported in the abstracts. Ozier 2016 has been presented online in four iterations, without substantive differences between versions. Higher cognitive test scores were associated with deworming, but the appropriate analysis was underpowered to reliably detect these effects. The size of the stated effect seems inconsistent with the short and indirect nature of the exposure to deworming, and a causal pathway for this effect is unclear. Croke 2014 uses a data set unrelated to the base trial, to report improvements in English and maths test scores. The analysis is at high risk of attrition bias, due to loss of clusters, and is substantially underpowered to assess these effects. Conclusions: In the context of reliable epidemiological methods, all three studies are at risk of substantial methodological bias. They therefore help in generating hypotheses, but should not be considered to provide reliable evidence of effects.
Integrating hepatitis B, hepatitis C and HIV screening into tuberculosis entry screening for migrants in the Netherlands, 2013 to 2015

We evaluated uptake and diagnostic outcomes of voluntary hepatitis B (HBV) and C virus (HCV) screening offered during routine tuberculosis entry screening to migrants in Gelderland and Amsterdam, the Netherlands, between 2013 and 2015. In Amsterdam, HIV screening was also offered. Overall, 54% (461/859) accepted screening. Prevalence of chronic HBV infection (HBsAg-positive) and HCV exposure (anti-HCV-positive) in Gelderland was 4.48% (9/201; 95% confidence interval (CI): 2.37–8.29) and 0.99% (2/203; 95% CI: 0.27–3.52), respectively, all infections were newly diagnosed. Prevalence of chronic HBV infection, HCV exposure and chronic HCV infection (HCV RNA-positive) in Amsterdam was 0.39% (1/256; 95% CI: 0.07–2.18), 1.17% (3/256; 95% CI: 0.40–3.39) and 0.39% (1/256; 95% CI: 0.07–2.18), respectively, with all chronic HBV/HCV infections previously diagnosed. No HIV infections were found. In univariate analyses, newly diagnosed chronic HBV infection was more likely in participants migrating for reasons other than work or study (4.35% vs 0.83%; odds ratio (OR) = 5.45; 95% CI: 1.12–26.60) and was less likely in participants in Amsterdam than Gelderland (0.00% vs 4.48%; OR = 0.04; 95% CI: 0.00–0.69). Regional differences in HBV prevalence might be explained by differences in the populations entering compulsory tuberculosis screening. Prescreening selection of migrants based on risk factors merits further exploration.
Toward monetary cost effective content placement in cloud centric media network

In recent years, technical challenges are emerging on how to efficiently distribute the rapid growing user-generated contents (UGCs) with long-tailed nature. To address this issue, we have previously proposed cloud centric media network (CCMN) for cost-efficient UGCs delivery. In this paper, we further study the content placement problem in CCMN. Our objective is to minimize the monetary cost incurred by using cloud resources to orchestrate an elastic and global content delivery network (CDN) service. In particular, this objective is achieved via a two-step method. First, for a single content, we map it into a k-center problem, and find a logarithmic relationship between the mean hop distance from users to contents, and the reciprocal of replica number. Second, for multiple contents, we formulate a convex optimization with storage and bandwidth capacity constraints, which can be solved by our proposed algorithm. Finally, we verify the algorithm based on real-world traces collected from a popular video website in China. Our numerical results suggest that, the optimal number of replica for each content follows a power law in respect to its popularity, under feasible storage and bandwidth constraints, in a set of deployed backbone networks.
Indexing Techniques for Queries on Nested Objects

Three index organizations are introduced for use in the evaluation of a query in an object-oriented or nested relational database. Detailed models of the three indexes are developed. Using the models, the storage cost, retrieval cost, and update cost of these indexes are evaluated, and a number of observations are made about the use of these indexes for evaluating queries for object-oriented or nested relational databases. A comparison of the combined retrieval and update costs for the three indexes is also included. It is shown that the degree of reference sharing among objects for the various classes in the path influences both the retrieval and update costs. >
Metabolic effects of aldose reductase inhibition during low-flow ischemia and reperfusion.

Several studies have shown that maintenance of glycolysis limits the metabolic and functional consequences of low-flow ischemia. Because diabetic animals are known to have impaired glycolytic metabolism coupled with increased flux through the aldose reductase (AR) pathway, we hypothesized that inhibition of AR would enhance glycolysis and thereby improve metabolic and functional recovery during low-flow ischemia. Hearts ( n = 12) from nondiabetic control and diabetic rats were isolated and retrograde perfused using 11 mM glucose with or without the AR inhibitor zopolrestat (1 μM). Hearts were subjected to 30 min of low-flow ischemia (10% of baseline flow) and 30 min of reperfusion.31P NMR spectroscopy was used to monitor time-dependent changes in phosphocreatine (PCr), ATP, and intracellular pH. Changes in the cytosolic redox ratio of NADH to NAD+ were obtained by measuring the ratio of tissue lactate to pyruvate. Effluent lactate concentrations and oxygen consumption were determined from the perfusate. AR inhibition improved functional recovery in both control and diabetic hearts, coupled with a lower cytosolic redox state and greater effluent lactate concentrations during ischemia. ATP levels during ischemia were significantly higher in AR-inhibited hearts, as was recovery of PCr. In diabetic hearts, AR inhibition also limited acidosis during ischemia and normalized pH recovery on reperfusion. These data demonstrate that AR inhibition maintains higher levels of high-energy phosphates and improves functional recovery upon reperfusion in hearts subjected to low-flow ischemia, consistent with an increase in glycolysis. Accordingly, this approach of inhibiting AR offers a novel method for protecting ischemic myocardium.
Epigenetically silenced PTPRO functions as a prognostic marker and tumor suppressor in human lung squamous cell carcinoma

Protein tyrosine phosphatase receptor-type O (PTPRO), a member of the PTP family, has been frequently reported as potential tumor suppressor in many types of cancer. However, the exact function of PTPRO in lung squamous cell carcinoma (LSCC) remains unclear. Bisulfite sequencing and methylation specific polymerase chain reaction (PCR) were used to identify the methylation status of PTPRO in LSCC cells, and quantitative methylation specific PCR was used to evaluate the methylation levels of PTPRO in LSCC patients. Stably expressing PTPRO vectors were constructed and transfected into H520 and SK-MES-1 cells, followed by MTT and colony formation assays, and analysis of tumor weight and volume in in vivo mouse xenograft models. The present study demonstrated that the CpG island of PTPRO exon 1 was obviously hypermethylated in LSCC cells and tissues. The mRNA expression of PTPRO could be restored by treatment with a demethylation agent. Increased methylation and decreased mRNA levels of PTPRO were observed in LSCC samples compared with adjacent healthy tissues, and were associated with poor prognosis of patients. The mRNA expression of PTPRO was negatively correlated with its methylation level in tumors. Functionally, ectopic PTPRO expression in LSCC cells significantly inhibited the proliferation rates, and colony formation, in comparison with control and non-transfected cells. In vivo assays confirmed the inhibitory effect of PTPRO on LSCC cell growth. In conclusion, these data provided evidence that epigenetic regulation of PTPRO impairs its tumor suppressor role in LSCC, and restoration of PTPRO may be a potential therapeutic strategy.
mtDNA as a Mediator for Expression of Hypoxia-Inducible Factor 1α and ROS in Hypoxic Neuroblastoma Cells

Mitochondria consume O2 to produce ATP and are critical for adaption of hypoxia, but the role of mitochondria in HIF-1α pathway is as yet unclear. In this study, mitochondrial DNA (mtDNA) enriched (SK-N-AS) and depleted (ρ0) cells of neuroblastoma were cultured in a hypoxic chamber to simulate a hypoxic condition and then the major components involved in mitochondrial related pathways, hypoxia-inducible factor 1α (HIF-1α) and reactive oxygen species (ROS) were measured. The results showed that hypoxia-stimulated exposure elevated expression of HIF-1α, which was additionally influenced by level of generated ROS within the cytosol. Moreover, elevation of HIF-1α also resulted in increases of lactate dehydrogenase A (LDH-A) and pyruvate dehydrogenase kinase 1 (PDK1) in both hypoxic cells. The expression of mitochondrial biogenesis related proteins and metabolic components were noted to increase significantly in hypoxic SK-N-AS cells, indicating that mtDNA was involved in mitochondrial retrograde signaling and metabolic pathways. An analysis of dynamic proteins found elevated levels of HIF-1α causing an increased expression of dynamin-related protein 1 (DRP1) during hypoxia; further, the existence of mtDNA also resulted in higher expression of DRP1 during hypoxia. By using siRNA of HIF-1α or DRP1, expression of DRP1 decreased after suppression of HIF-1α; moreover, the expression of HIF-1α was also affected by the suppression of DRP1. In this study, we demonstrated that mtDNA is a mediator of HIF-1α in eliciting metabolic reprogramming, and mitochondrial biogenesis. Identification of a mutual relationship between HIF-1α and DRP1 may be a critical tool in the future development of clinical applications.
Subcellular kinetics of early trypsinogen activation in acute rodent pancreatitis.

To investigate the debated role of intracellular trypsinogen activation and its relation to lysosomal enzyme redistribution in the pathogenesis of acute pancreatitis, rats were infused with the cholecystokinin analog caerulein at 5 μg ⋅ kg-1 ⋅ h-1for intervals up to 3 h, and the changes were contrasted with those in animals receiving saline or 0.25 μg ⋅ kg-1 ⋅ h-1caerulein. Saline or 0.25 μg ⋅ kg-1 ⋅ h-1caerulein did not induce significant changes. In contrast, 5 μg ⋅ kg-1 ⋅ h-1caerulein caused significant hyperamylasemia and pancreatic edema within 30 min. Pancreatic content of trypsinogen activation peptide (TAP) increased continuously (significant within 15 min). TAP generation was predominantly located in the zymogen fraction during the first hour but expanded to other intracellular compartments thereafter. Cathepsin B activity in the zymogen compartment increased continuously throughout the experiments and correlated significantly with TAP generation in the same compartment. Total trypsinogen content increased to 143% with marked interstitial trypsinogen accumulation after 3 h. Supramaximal caerulein stimulation causes trypsinogen activation by 15 min that originates in the zymogen compartment and is associated with increasing cathepsin B activity in this subcellular compartment. However, a much larger pool of trypsinogen survives and accumulates in the extracellular space and may become critical in the evolution of necrotizing pancreatitis.
Reading Intervention Using Interactive Metronome in Children With Language and Reading Impairment

This exploratory study examined the effects of Interactive Metronome (IM) when integrated with a traditional language and reading intervention on reading achievement. Forty-nine school-age children with language and reading impairments were assigned randomly to either an experimental group who received the IM treatment or to a control group who did not. Both groups received language and reading intervention, and the experimental group received an additional four hours of IM treatment during a four-week period. Although both groups made gains in reading rate/fluency and comprehension, the extent of the gains was much larger in the IM group. IM training may be useful for promoting the reading rate/fluency and comprehension of children with language and reading impairments.