Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of coincidental correctness and mitigation of its impact on fault localization

Researchers have argued that for failure to be observed the following three conditions must be met: <i>C</i><sub><i>R</i></sub> = the defect was reached; <i>C</i><sub><i>I</i></sub> = the program has transitioned into an infectious state; and <i>C</i><sub><i>P</i></sub> = the infection has propagated to the output. <i>Coincidental Correctness</i> (CC) arises when the program produces the correct output while condition C<sub>R</sub> is met but not C<sub>P</sub>. We recognize two forms of coincidental correctness, weak and strong. In <i>weak CC</i>, C<sub>R</sub> is met, whereas C<sub>I</sub> might or might not be met, whereas in <i>strong</i> <i>CC</i>, both C<sub>R</sub> and C<sub>I</sub> are met. In this work we first show that CC is prevalent in both of its forms and demonstrate that it is a safety reducing factor for <i>Coverage-Based Fault Localization</i> (CBFL). We then propose two techniques for cleansing test suites from coincidental correctness to enhance CBFL, given that the test cases have already been classified as failing or passing. We evaluated the effectiveness of our techniques by empirically quantifying their accuracy in identifying weak CC tests. The results were promising, for example, the better performing technique, using 105 test suites and statement coverage, exhibited 9% false negatives, 30% false positives, and no false negatives nor false positives in 14.3% of the test suites. Also using 73 test suites and more complex coverage, the numbers were 12%, 19%, and 15%, respectively.
Development of a Configurable Growth Chamber with a Computer Vision System to Study Circadian Rhythm in Plants

Plant development is the result of an endogenous morphogenetic program that integrates environmental signals. The so-called circadian clock is a set of genes that integrates environmental inputs into an internal pacing system that gates growth and other outputs. Study of circadian growth responses requires high sampling rates to detect changes in growth and avoid aliasing. We have developed a flexible configurable growth chamber comprising a computer vision system that allows sampling rates ranging between one image per 30 s to hours/days. The vision system has a controlled illumination system, which allows the user to set up different configurations. The illumination system used emits a combination of wavelengths ensuring the optimal growth of species under analysis. In order to obtain high contrast of captured images, the capture system is composed of two CCD cameras, for day and night periods. Depending on the sample type, a flexible image processing software calculates different parameters based on geometric calculations. As a proof of concept we tested the system in three different plant tissues, growth of petunia- and snapdragon (Antirrhinum majus) flowers and of cladodes from the cactus Opuntia ficus-indica. We found that petunia flowers grow at a steady pace and display a strong growth increase in the early morning, whereas Opuntia cladode growth turned out not to follow a circadian growth pattern under the growth conditions imposed. Furthermore we were able to identify a decoupling of increase in area and length indicating that two independent growth processes are responsible for the final size and shape of the cladode.
Total Enantioselective Synthesis and In Vivo Biological Evaluation of a Novel Fluorescent BODIPY α‐Galactosylceramide

Natural killer T (NKT) cells are a distinct subset of mature lymphocytes endowed with features of activated and regulatory T cells. α‐Galactosylceramides (α‐GalCers), the synthetic prototype of which is KRN7000, are the only natural reagents recognised by the T‐cell receptor of NKT cells. The α‐GalCer‐activated NKT cells promptly release IFNγ and IL‐4 (IFN=interferon; IL=interleukin) and undergo apoptotic death within hours. In mice, activated NKT cells are responsible for antitumour activity and protection against autoimmune diseases. KRN7000 can thus be considered as the root of a family of novel immunoregulatory drugs. To get insights into the in vivo behaviour of α‐galactosylceramides, an original fluorescent derivative has been prepared by following a convergent synthetic scheme. This strategy allows the introduction of different acyl chains, carbohydrate residues and various labels in the final steps of the synthesis. The fluorescent BODIPY probe derived from a versatile glycolipid precursor is as active as KRN7000 for inducing apoptosis of liver NKT cells. Fluorescence was detected in peritoneal macrophages and splenic antigen‐presenting cells, in Kupffer‐like cells in the liver, but not in lymphocytes.
Anti-Glutamate Receptor Antibodies in Pediatric Enteroviral Encephalitis

ABSTRACT In order to better understand enteroviral encephalitis we investigated the clinical symptoms and several disease markers. Between 2000 and 2005 eight patients aged between 9 months and 5 years were admitted to our hospital with one case having sequela. Glutamic oxaloacetic transaminase (GOT), serum IL-6, and ferritin were elevated in most of the cases. Their IL-6 and diacron-reactive oxygen metabolites (d-ROM) in cerebral spinal fluid (CSF) were also high (86%%). However, pleocytosis and high protein levels in CSF were rarely found. In viral loads of the first CSF, there were no differences between the patient with sequela and the ones without sequela. However, anti-glutamate receptor IgMδ2 was only detected in the CSF of the patient with sequela. These findings suggest that the immunological phenomenon is more closely related to the development of sequela related to enteroviral encephalitis than other disease markers, such as inflammatory cytokine, free radicals, and viral loads. Therefore, a specific therapy against immunological status might decrease the sequela; however, further research is necessary to confirm this.
A novel autophagy modulator 6-Bio ameliorates SNCA/α-synuclein toxicity

ABSTRACT Parkinson disease (PD) is a life-threatening neurodegenerative movement disorder with unmet therapeutic intervention. We have identified a small molecule autophagy modulator, 6-Bio that shows clearance of toxic SNCA/α-synuclein (a protein implicated in synucleopathies) aggregates in yeast and mammalian cell lines. 6-Bio induces autophagy and dramatically enhances autolysosome formation resulting in SNCA degradation. Importantly, neuroprotective function of 6-Bio as envisaged by immunohistology and behavior analyses in a preclinical model of PD where it induces autophagy in dopaminergic (DAergic) neurons of mice midbrain to clear toxic protein aggregates suggesting that it could be a potential therapeutic candidate for protein conformational disorders.
Monoclonal B-cell Lymphocytosis in a Patient with Wegener Granulomatosis: A Case Report and Update on 2016 World Health Organization Classification

The association between autoimmune disease and risk of monoclonal malignancy is well studied. However, monoclonal B-cell lymphocytosis (MBL) in patients with autoimmune diseases has rarely been reported. The newly published 2016 revision of the World Health Organization (WHO) classification of lymphoid neoplasms has officially accepted MBL as an independent disease entity. [1] Herein, we present a case of Wegener granulomatosis (WG) with MBL. Through this case, the diagnosis and management of MBL as a less known condition to rheumatologists, especially under the background of an autoimmune disorder, is reviewed. Moreover, the association between autoimmune disease and risk of monoclonal malignancy is discussed.
Comparison of Neuroretinal Rim Area Measurements Made by the Heidelberg Retina Tomograph I and the Heidelberg Retina Tomograph II

Purpose:To investigate the agreement between neuroretinal rim area (RA) measurements using the Heidelberg Retina Tomograph I (HRT Classic) and Heidelberg Retina Tomograph II (HRT II). To compare apparent RA changes in follow-up series of HRT II topographies when using either an HRT Classic or HRT II mean topography as baseline. Design:Cross-sectional study and “no-change,” short time series study. Participants:Forty-three ocular hypertensive and 31 primary open angle glaucoma subjects. Methods:Five HRT Classic and 5 HRT II examinations were acquired from 1 eye of each subject, across 2 visits within 6 weeks. For the cross-sectional study, follow-up RA measurements from HRT Classic and HRT II were compared, using the same HRT Classic mean topography as the baseline. The linear rates of RA change were compared in 2 short time series with either an HRT Classic or an HRT II mean topography as baseline, and 4 follow-up HRT II mean topographies. Intervals between topographies were arbitrarily set at 1 year for meaningful comparisons of rates. Rates of RA change over time were calculated by linear regression. Separate analyses were performed using 3 available reference planes (RP). Main Outcome Measures:Global and sectoral RA measurements in HRT Classic and HRT II mean topographies; linear rates of RA change. Results:HRT Classic minus HRT II mean differences (95% limits of agreement) were 0.09 (−0.17, 0.35) mm2, 0.09 (−0.13, 0.32) mm2, and 0.11 (−0.24, 0.46) mm2 for the Moorfields, 320 µm, and standard RPs, respectively (P<0.001 for all RPs, Wilcoxon rank sum test). In the time series, the mean differences (95% limits of agreement) of RA rates of change (HRT Classic baseline minus HRT II baseline) were −0.01 (−0.06, 0.03) mm2/y, −0.01 (−0.06, 0.04) mm2/y, and −0.02 (−0.09, 0.05) mm2/y using the Moorfields, 320 µm, and standard RPs, respectively. Conclusion:Although HRT software is backward-compatible, follow-up RA measurements made in the same eye using HRT Classic and HRT II devices display statistically and clinically meaningful systematic differences when HRT Classic topographies are used as a baseline.
A systematic review and critical appraisal of gene polymorphism association studies in medication-overuse headache

Purpose of review Medication-overuse headache is a secondary chronic headache disorder, evolving from an episodic primary headache type, caused by the frequent and excessive use of headache symptomatic drugs. While gene polymorphisms have been deeply investigated as susceptibility factors for migraine, little attention has been paid to medication-overuse headache genetics. In the present study we conducted a systematic review to identify, appraise and summarize the current findings of gene polymorphism association studies in medication-overuse headache. Methods A comprehensive literature search was conducted on PubMed and Web of Knowledge databases of primary studies that met the diagnostic criteria for medication-overuse headache according to the temporally-relevant Classification of Headache Disorder of the International Headache Society. Results A total of 17 candidate gene association studies focusing on medication-overuse headache were finally included in the qualitative review. Among these, 12 studies investigated the role of common gene polymorphisms as risk factors for medication-overuse headache susceptibility, six studies focused on the relationship with clinical features of medication-overuse headache patients, and four studies evaluated their role as determinants of clinical outcomes in medication-overuse headache patients. Conclusion Results of single studies show a potential role of polymorphic variants of the dopaminergic gene system or of other genes related to drug-dependence pathways as susceptibility factors for disease or as determinants of monthly drug consumption, respectively. In this systematic review, we summarize the findings of gene polymorphism association studies in medication-overuse headache and discuss the methodological issues that need to be addressed in the design of future studies.
How does a biopsy of endoscopically normal terminal ileum contribute to the diagnosis? Which patients should undergo biopsy?

Background Terminal ileum endoscopy and biopsy are the diagnostic tools of diseases attacking the ileum. However, abnormal histological findings can be found in endoscopically normal terminal ileum. Objective This study was performed to evaluate the histopathological results of biopsies from endoscopically normal terminal ileum in order to determine pre-procedure clinical and laboratory factors predicting abnormal histopathological results, if any. Methods A total of 297 patients who underwent colonoscopy and terminal ileum biopsy and had normal terminal ileum or a few aphthous ulcers in the terminal ileum together with completely normal colon mucosa were included in the study. The patients were grouped into two arms as normal cases and cases with aphthous ulcers. Histopathological and pre-procedural laboratory results of patients were analyzed according to their indications. Results The terminal ileum was endoscopically normal in 200 patients, and 97 patients had aphthous ulcers. Chronic ileitis rate was present in 5.5% of those with endoscopically normal terminal ileum and in 39.2% of the patients with aphthous ulcers. In both groups, the highest rate of chronic ileitis was detected in the patients with known inflammatory bowel disease (IBD) (15.4 and 50%, respectively), anemia (9.5 and 43.5%, respectively), and in the patients having chronic diarrhea together with abdominal pain (7.7 and 44.8%, respectively). We found that the sensitivity of mean platelet volume for predicting chronic ileitis was 87% and the specificity was 45% at a cut-off value lower than 9.35 fl. Conclusion In anemia indication or chronic diarrhea together with abdominal pain, the frequency of aphthous ulcers detected by ileoscopy and the frequency of chronic ileitis detected histopathologically despite a normal-appearing ileum were elevated.
Benzodiazepine Effects on Arousal Threshold during Sleep.

Abstract : In a series of studies, the effects of benzodiazepines on arousal threshold during sleep have been investigated. Two studies, one using flurazepam, 30 mg, over 10 nights and one using triazolam, . 5 mg, over 6 nights were conducted in the authors' laboratory. A third study at the University of Florida measured the effects of flurazepam, 30 mg, and pentobarbital, 100 mg, each administered on two nights. All drug threshold levels were compared to placebo values. All three studies found that the sedative hypnotics increased arousal threshold to an intermittent pure tone. The placebo groups' highest mean arousal threshold was 70-75dB, compared to 100-110dB threshold values for the hypnoptic group. The increase in arousal threshold occurred during the first hours of sleep, reaching a peak around 120-150 minutes post-ingestion. Return to sleep was also more rapid in medicated subjects, and the reduction in sleep latency followed the same time course as did the change in arousal threshold. Arousal threshold and sleep latency did not differ between drug and placebo groups after 3 hours post-administration. The short acting benzodiazepine, triazolam, and flurazepam with its long acting metabolite did not differ in the magnitude of the elevation of arousal threshold, time course of effects across the night, or type of change over nights of consecutive use.
Combined Automatic Speech Recognition and Machine Translation in Business Correspondence Domain for English-Croatian

The paper presents combined automatic speech recognition (ASR) of English and machine translation (MT) for English and Croatian and Croatian-English language pairs in the domain of business correspondence. The first part presents results of training the ASR commercial system on English data sets, enriched by error analysis. The second part presents results of machine translation performed by free online tool for English and Croatian and Croatian- English language pairs. Human evaluation in terms of usability is conducted and internal consistency calculated by Cronbach's alpha coefficient, enriched by error analysis. Automatic evaluation is performed by WER (Word Error Rate) and PER (Position-independent word Error Rate) metrics, followed by investigation of Pearson’s correlation with human evaluation.
Modeling and Analysis of a Stable Direction-Based Routing Protocol in Vehicle Mobile Ad Hoc Networks

Considering the specific characteristics of vehicular ad hoc networks (VANETs), such as high mobility, variable density, and non-uniform distribution, it is a challenging task to find a stable and efficient routing path in VANETs. In addition, analytical models are rarely existed which can quantificationally evaluate routing protocols from an algorithmic perspective. In this paper, a novel analytical model was proposed for the evaluation of routing breakage in urban environment. Furthermore, a Direction Based AODV Routing Protocol (DBAP), which concerns vehicle's moving direction as an assistant ingredient was presented to enhance the performance of AODV. The simulation results show the validity of the proposed model, as well as the improved performance of DBAP in link-breakage and drop ratio.
Psychometric properties of the Chinese version of the Positive Empathy Scale among undergraduates

We translated and examined the psychometric properties of a Chinese version of the Positive Empathy Scale (PES). Exploratory factor analysis ( N = 428) and confirmatory factor analysis ( N = 503) were performed on data from 2 undergraduate samples to examine the scale’s construct validity, and the convergent, divergent, and concurrent validity, and test–retest reliability were also assessed ( n = 87). The analyses showed that the PES had a single factor, a Cronbach’s alpha of . 837, and a test–retest reliability coefficient (4-week interval) of . 78. Confirmatory factor analysis showed that the scale’s structure was satisfactory. It was strongly correlated with measures of similar constructs (e.g., empathic concern, positive affect), but not with measures of dissimilar psychological constructs (e.g., personal distress). The scale also had a positive correlation with prosocial behavior and well-being. Thus, the Chinese version of the PES is a suitable measure of positive empathy for Chinese undergraduates.
Uptake of Apolipoprotein E‐Containing High Density Lipoproteins by Hepatic Parenchymal Cells

Cholesterol-enriched, apolipoprotein E-containing high density lipoproteins (apo E HDLc), which were Isolated from the plasma of cholesterol-fed dogs by using agarose column chromatography or ultracentrlfugatlon, possessed essentially Identical biochemical and metabolic characteristics. Radlolodlnated (125I) apo E HDIc Isolated by either method gave identical rates of clearance from the plasma, I.e., >50% of the Injected dose was cleared from the plasma within 5 to 10 minutes, principally by the liver. Detailed studies localizing apo E HDLc uptake to specific cell types within the liver were performed in both normal and cholesterol-fed rats. The validity of using the canine apo E HDLc In the rat was supported by observations of marked similarities In plasma clearance, I.e., a rapid acute phase of disappearance, and a near-quantitative hepatic uptake of lipoproteins In both species. Canine apo E HDLc (fluorescently labeled with 1,1′-dloctadecyl-3,3,3′, 3-tetramethylindocarbocyanine), which were Injected into normal rats, appeared to be taken up primarily by parenchymal cells, as determined by fluorescence microscopy. Light microscopic autoradlography also revealed that the uptake of 129I apo E HDLc was principally carried out by parenchymal cells In rat Ilver. Likewise, the uptake of apo E HDLc by the Ilver of cholesterol-fed rats was extensively localized to parenchymal cells. An In situ, single-pass perfusion of a lobule of the Ilver of a normal dog with lodlnated and fluorescently labeled apo E HDLc confirmed that the uptake of the lipoproteins was principally carried out by parenchymal cells. The plasma clearance of apo E HDLc by hepatic parenchymal cells, even In cholesterol-fed animals In which the apo B,E (LDL) receptors were markedly downregulated (undetectable), suggests that the apo E receptor, presumably the remnant receptor, Is localized In the parenchymal cells.
The serum 25-hydroxyvitamin D levels and hip fracture risk: a meta-analysis of prospective cohort studies

Hip fracture has increasingly become a social and economic burden. The relationship between serum 25-hydroxyvitamin D levels and the risk of hip fracture reported by previous studies remains controversial. We searched Pubmed and Embase to identify studies reporting the relationship between serum 25-hydroxyvitamin D levels and risk of hip fracture. Fifteen prospective cohort studies with a total of 51239 participants and 3386 hip fracture cases were included. By pooling the Relative Risk of the lowest vs. the highest categories indicated that lower levels of serum 25-hydroxyvitamin D were more likely to be a risk factor for hip fracture with adjusted Relative Risk (95%Confidence Interval) of 1.58 (1.41, 1.77). Subgroup meta-analysis examining the stability of the primary results achieved the same results. A dose-response meta-analysis showed that the risk of hip fracture was a descending curve below the line of RR=1. The descending trend was obvious when serum 25-hydroxyvitamin D levels were less than 60 nmol/L and was flat when serum 25-hydroxyvitamin D levels were more than 60 nmol/L. We found that individuals with low levels of serum 25-hydroxyvitamin D have an increased risk of hip fracture, and this effect was evident when the serum 25-hydroxyvitamin D levels were less than 60 nmol/L.
Development of three different cell types is associated with the activity of a specific MYB transcription factor in the ventral petal of Antirrhinum majus flowers

Petal tissue comprises several different cell types, which have specialised functions in pollination in different flowering plant species. In Antirrhinum majus, the MIXTA protein directs the formation of conical epidermal cells in petals. Transgenic experiments have indicated that MIXTA activity can also initiate trichome development, dependent on the developmental timing of its expression. MIXTA is normally expressed late in petal development and functions only in conical cell differentiation. However, an R2R3 MYB transcription factor very similar to MIXTA (AmMYBML1), which induces both trichome and conical cell formation in transgenic plants, is expressed very early during the development of the ventral petal. Its cellular expression pattern suggests that it fulfils three functions: trichome production in the corolla tube, conical cell development in the petal hinge epidermis and reinforcement of the hinge through differential mesophyll cell expansion. The DIVARICATA (DIV) gene is required for ventral petal identity. In div mutants, the ventral petal assumes the identity of lateral petals lacking these three specialised cell types, and expression of AmMYBML1 is significantly reduced compared with wild type, supporting the proposed role of AmMYBML1 in petal cell specification. We suggest that AmMYBML1 is regulated by DIV in association with the B-function proteins DEFICIENS and GLOBOSA, and, consequently, controls specification of particular cells within the ventral petal which adapt the corolla to specialised functions in pollination.
Biomimetic centering behavior [mobile robots with panoramic sensors]

A reactive robotic centering behavior based on panoramic vision is presented. It is inspired by the way insects exploit visual information in analogous navigation tasks. By employing a panoramic camera, the development of the centering behavior is simplified both from a theoretical and from an implementation point of view. The proposed method relies on the extraction of primitive visual information from appropriately selected areas of a panoramic visual field and its direct use in the control law. Experimental results from an implementation of this method on a robotic platform demonstrate a centering behavior which can be achieved in real-time and with high accuracy. The proposed technique circumvents the need to address complex problems of 3D structure estimation and the resulting control laws were shown to possess the required stability properties.