Miracle-dz/UniFAR-FTUs huggingface dataset:
Further empirical studies of test effectiveness

This paper reports on an empirical evaluation of the fault-detecting ability of two white-box software testing techniques: decision coverage (branch testing) and the all-uses data flow testing criterion. Each subject program was tested using a very large number of randomly generated test sets. For each test set, the extent to which it satisfied the given testing criterion was measured and it was determined whether or not the test set detected a program fault. These data were used to explore the relationship between the coverage achieved by test sets and the likelihood that they will detect a fault.Previous experiments of this nature have used relatively small subject programs and/or have used programs with seeded faults. In contrast, the subjects used here were eight versions of an antenna configuration program written for the European Space Agency, each consisting of over 10,000 lines of C code.For each of the subject programs studied, the likelihood of detecting a fault increased sharply as very high coverage levels were reached. Thus, this data supports the belief that these testing techniques can be more effective than random testing. However, the magnitudes of the increases were rather inconsistent and it was difficult to achieve high coverage levels.
Inference of Pathway Decomposition Across Multiple Species Through Gene Clustering

In the wake of gene-oriented data analysis in large-scale bioinformatics studies, focus in research is currently shifting towards the analysis of the functional association of genes, namely the metabolic pathways in which genes participate. The goal of this paper is to attempt to identify the core genes in a specific pathway, based on a user-defined selection of genomes. To this end, a novel algorithm has been developed that uses data from the KEGG database, and through the application of the MCL clustering algorithm, identifies clusters that correspond to different “layers” of genes, either on a phylogenetic or a functional level. The algorithm's complexity, evaluated experimentally, is presented and the results on three characteristic case studies are discussed.
Cholesterol Metabolism and Weight Reduction in Subjects with Mild Obstructive Sleep Apnoea: A Randomised, Controlled Study

To evaluate whether parameters of obstructive sleep apnoea (OSA) associate with cholesterol metabolism before and after weight reduction, 42 middle-aged overweight subjects with mild OSA were randomised to intensive lifestyle intervention (N = 23) or to control group (N = 18) with routine lifestyle counselling only. Cholesterol metabolism was evaluated with serum noncholesterol sterol ratios to cholesterol, surrogate markers of cholesterol absorption (cholestanol and plant sterols) and synthesis (cholestenol, desmosterol, and lathosterol) at baseline and after 1-year intervention. At baseline, arterial oxygen saturation (SaO2) was associated with serum campesterol (P < 0.05) and inversely with desmosterol ratios (P < 0.001) independently of gender, BMI, and homeostasis model assessment index of insulin resistance (HOMA-IR). Apnoea-hypopnoea index (AHI) was not associated with cholesterol metabolism. Weight reduction significantly increased SaO2and serum cholestanol and decreased AHI and serum cholestenol ratios. In the groups combined, the changes in AHI were inversely associated with changes of cholestanol and positively with cholestenol ratios independent of gender and the changes of BMI and HOMA-IR (P < 0.05). In conclusion, mild OSA seemed to be associated with cholesterol metabolism independent of BMI and HOMA-IR. Weight reduction increased the markers of cholesterol absorption and decreased those of cholesterol synthesis in the overweight subjects with mild OSA.
Spatialization Design: Comparing Points and Landscapes

Spatializations represent non-spatial data using a spatial layout similar to a map. We present an experiment comparing different visual representations of spatialized data, to determine which representations are best for a non-trivial search and point estimation task. Primarily, we compare point-based displays to 2D and 3D information landscapes. We also compare a colour (hue) scale to a grey (lightness) scale. For the task we studied, point-based spatializations were far superior to landscapes, and 2D landscapes were superior to 3D landscapes. Little or no benefit was found for redundantly encoding data using colour or greyscale combined with landscape height. 3D landscapes with no colour scale (height-only) were particularly slow and inaccurate. A colour scale was found to be better than a greyscale for all display types, but a greyscale was helpful compared to height-only. These results suggest that point-based spatializations should be chosen over landscape representations, at least for tasks involving only point data itself rather than derived information about the data space.
Insulation for Daydreams: A Role for Tonic Norepinephrine in the Facilitation of Internally Guided Thought

Although consciousness can be brought to bear on both perceptual and internally generated information, little is known about how these different cognitive modes are coordinated. Here we show that between-participant variance in thoughts unrelated to the task being performed (known as task unrelated thought, TUT) is associated with longer response times (RT) when target presentation occurs during periods when baseline Pupil Diameter (PD) is increased. As behavioral interference due to high baseline PD can reflect increased tonic activity in the norepinephrine system (NE), these results might implicate high tonic NE activity in the facilitation of TUTs. Based on these findings, it is hypothesised that high tonic mode NE leads to a generalised de-amplification of task relevant information that prioritses internally generated thought and insulates it from the potentially disruptive events taking place in the external environment.
Predictive Factors for Failure of Isotretinoin Treatment in Acne Patients: Results from a Cohort of 237 Patients

Background: The efficacy of oral isotretinoin in acne has been established, though the role of the mean daily dose (MDD) is still unclear. Objective: To determine the predictive factors of resistance to oral isotretinoin and the role of the MDD of isotretinoin on relapse of acne while taking into account patient characteristics and the total cumulative dose (TCD). Methods: Two hundred and thirty-seven patients treated with oral isotretinoin for the first time were enrolled by a single dermatologist. Patients with closed comedonal acne and with hyperandrogenism received adequate therapy prior to isotretinoin. Results: Closed comedonal acne was the only predictive factor of resistance to isotretinoin with an adjusted OR = 2.7 (95% CI: 1.0–7.3). The estimated rates of relapse at 1, 3 and 5 years were 14, 40 and 48%, respectively. Age and grade of facial acne were the only predictive factors for relapse with adjusted relative risks of 0.6 (95% CI: 0.4–0.8) for age ≥ 20 and 1.5 (95% CI: 1.0–2.2) for grade > 3. Conclusion: MDD, TCD, closed comedonal acne and hyperandrogenism that have been adequately treated prior to isotretinoin treatment had no prognostic value for relapse.
Risk Based Testing: Technique for Risk-based Test Case Generation and Prioritization

Nowadays, there are more projects, more competitive pressures and greater failure risk which needs to be managed with fewer resources with tighter timelines. Instead of doing more with less and risking late projects, increased costs or low quality, we need to find ways to achieve better with less. The focus of testing has to be placed on aspects of software that matter most with an aim of reducing the risk of failure as well as ensuring the quality and stability of the business applications. This can be achieved by applying the principle of Risk Based Prioritization of tests, known as Risk-based testing (RBT). The aim of Risk Based testing approach is to ensure that appropriate testing activities are identified and prioritized based on risk. The primary role of risk-based testing is to optimize available resources and time without affecting the quality of the product. In this light, this paper presents the progress different risk-based testing metrics to measure and control test cases and test activities progress, efforts and costs. In risk-based testing, the probability of a fault and the damage that this fault can cause when leading to a failure is considered for test case prioritization. Existing approaches for risk based testing provide guidelines for deriving test cases. However, those guidelines lack the level of detail and precision needed for automation. In this contribution, we introduce the risk-based testing technique RiteDAP, which automatically generates system test cases from activity diagrams and prioritizes those test cases based on risk.
Plumbagin Mediates Cardioprotection Against Myocardial Ischemia/Reperfusion Injury Through Nrf-2 Signaling

Background Plumbagin is a potent antioxidant with anti-inflammatory and anti-carcinogenic action. Myocardial ischemia/reperfusion injury results in organ damage through oxidative stress and inflammatory mechanisms. In this study, we analyzed the potential role of plumbagin against myocardial I/R injury in Wistar rats. Material/Methods Oxidative stress was measured through ROS, lipid peroxide content, and antioxidant enzyme activities. The expression of redox signaling and inflammatory proteins was analyzed through Western blotting. Inflammatory cytokine expressions were determined through ELISA. Results Oxidative stress status was reduced by plumbagin by decreasing ROS and lipid peroxide levels in rats with myocardial I/R (MI/R) injury. Plumbagin regulated redox imbalance induced by I/R injury by modulating the transcription factors NF-κB and Nrf-2. Further, downstream targets of NF-κB (COX-2, iNOS) and Nrf-2 (HO-1, NQO1 and GST) expression were significantly downregulated by plumbagin treatment. Pro-inflammatory cytokine expressions were significantly abrogated by plumbagin treatment. Conclusions This study shows the protective role of plumbagin against myocardial I/R injury by regulating antioxidant and inflammatory mechanisms.
Inclusion of endogenous hormone levels in risk prediction models of postmenopausal breast cancer.

PURPOSE Endogenous hormones are risk factors for postmenopausal breast cancer, and their measurement may improve our ability to identify high-risk women. Therefore, we evaluated whether inclusion of plasma estradiol, estrone, estrone sulfate, testosterone, dehydroepiandrosterone sulfate, prolactin, and sex hormone-binding globulin (SHBG) improved risk prediction for postmenopausal invasive breast cancer (n = 437 patient cases and n = 775 controls not using postmenopausal hormones) in the Nurses' Health Study. METHODS We evaluated improvement in the area under the curve (AUC) for 5-year risk of invasive breast cancer by adding each hormone to the Gail and Rosner-Colditz risk scores. We used stepwise regression to identify the subset of hormones most associated with risk and assessed AUC improvement; we used 10-fold cross validation to assess model overfitting. RESULTS Each hormone was associated with breast cancer risk (odds ratio doubling, 0.82 [SHBG] to 1.37 [estrone sulfate]). Individual hormones improved the AUC by 1.3 to 5.2 units relative to the Gail score and 0.3 to 2.9 for the Rosner-Colditz score. Estrone sulfate, testosterone, and prolactin were selected by stepwise regression and increased the AUC by 5.9 units (P = .003) for the Gail score and 3.4 (P = .04) for the Rosner-Colditz score. In cross validation, the average AUC change across the validation data sets was 6.0 (P = .002) and 3.0 units (P = .03), respectively. Similar results were observed for estrogen receptor-positive disease (selected hormones: estrone sulfate, testosterone, prolactin, and SHBG; change in AUC, 8.8 [P < .001] for Gail score and 5.8 [P = .004] for Rosner-Colditz score). CONCLUSION Our results support that endogenous hormones improve risk prediction for invasive breast cancer and could help identify women who may benefit from chemoprevention or more screening.
Performance analysis of the extended binaural MVDR beamformer with partial noise estimation in a homogeneous noise field

Besides noise reduction an important objective of a binaural speech enhancement algorithm is the preservation of the binaural cues of both the desired speech source as well as the undesired noise sources. Recently, it has been shown that by combining a binaural hearing system with an external microphone it is possible to improve both the noise reduction performance as well as the binaural cue preservation for a directional noise source. In this paper, we consider the binaural minimum variance distortionless response beamformer with partial noise estimation (MVDR-N), which aims at preserving the speech component and a scaled version of the noise component. For a homogeneous noise field, we theoretically analyze the influence of an external microphone on the performance of the binaural MVDR-N beamformer, showing that a larger SNR improvement can be achieved and a smaller scaling parameter is required to achieve a desired interaural coherence for the residual noise. Experimental simulation results in a realistic acoustic scenario confirm these theoretical findings.
Frequency and properties of bars in cluster and field galaxies at intermediate redshifts

We present a study of large-scale bars in field and cluster environments out to redshifts of ~0.8 using a final sample of 945 moderately inclined disk galaxies drawn from the EDisCS project. We characterize bars and their host galaxies and look for relations between the presence of a bar and the properties of the underlying disk. We investigate whether the fraction and properties of bars in clusters are different from their counterparts in the field. The properties of bars and disks are determined by ellipse fits to the surface brightness distribution of the galaxies using HST/ACS images in the F814W filter. The bar identification is based on quantitative criteria after highly inclined (> 60°) systems have been excluded. The total optical bar fraction in the redshift range z = 0.4-0.8 (median z = 0.60), averaged over the entire sample, is 25% (20% for strong bars). For the cluster and field subsamples, we measure bar fractions of 24% and 29%, respectively. We find that bars in clusters are on average longer than in the field and preferentially found close to the cluster center, where the bar fraction is somewhat higher (~31%) than at larger distances (~18%). These findings however rely on a relatively small subsample and might be affected by small number statistics. In agreement with local studies, we find that disk-dominated galaxies have a higher optical bar fraction (~45%) than bulge-dominated galaxies (~15%). This result is based on Hubble types and effective radii and does not change with redshift. The latter finding implies that bar formation or dissolution is strongly connected to the emergence of the morphological structure of a disk and is typically accompanied by a transition in the Hubble type. The question whether internal or external factors are more important for bar formation and evolution cannot be answered definitely. On the one hand, the bar fraction and properties of cluster and field samples of disk galaxies are quite similar, indicating that internal processes are crucial for bar formation. On the other hand, we find evidence that cluster centers are favorable locations for bars, which suggests that the internal processes responsible for bar growth are supported by the typical interactions taking place in such environments.
Temporal-Pattern Recognition by Single Neurons in a Sensory Pathway Devoted to Social Communication Behavior

Sensory systems often encode stimulus information into the temporal pattern of action potential activity. However, little is known about how the information contained within these patterns is extracted by postsynaptic neurons. Similar to temporal coding by sensory neurons, social information in mormyrid fish is encoded into the temporal patterning of an electric organ discharge. In the current study, sensitivity to temporal patterns of electrosensory stimuli was found to arise within the midbrain posterior exterolateral nucleus (ELp). Whole-cell patch recordings from ELp neurons in vivo revealed three patterns of interpulse interval (IPI) tuning: low-pass neurons tuned to long intervals, high-pass neurons tuned to short intervals, and bandpass neurons tuned to intermediate intervals. Many neurons within each class also responded preferentially to either increasing or decreasing IPIs. Playback of electric signaling patterns recorded from freely behaving fish revealed that the IPI and direction tuning of ELp neurons resulted in selective responses to particular social communication displays characterized by distinct IPI patterns. The postsynaptic potential responses of many neurons indicated a combination of excitatory and inhibitory synaptic input, and the IPI tuning of ELp neurons was directly related to rate-dependent changes in the direction and amplitude of postsynaptic potentials. These results suggest that differences in the dynamics of short-term synaptic plasticity in excitatory and inhibitory pathways may tune central sensory neurons to particular temporal patterns of presynaptic activity. This may represent a general mechanism for the processing of behaviorally relevant stimulus information encoded into temporal patterns of activity by sensory neurons.
Ezetimibe therapy: mechanism of action and clinical update

The lowering of low-density lipoprotein cholesterol (LDL-C) is the primary target of therapy in the primary and secondary prevention of cardiovascular events. Although statin therapy is the mainstay for LDL-C lowering, a significant percentage of patients prescribed these agents either do not achieve targets with statin therapy alone or have partial or complete intolerance to them. For such patients, the use of adjuvant therapy capable of providing incremental LDL-C reduction is advised. One such agent is ezetimibe, a cholesterol absorption inhibitor that targets uptake at the jejunal enterocyte brush border. Its primary target of action is the cholesterol transport protein Nieman Pick C1 like 1 protein. Ezetimibe is an effective LDL-C lowering agent and is safe and well tolerated. In response to significant controversy surrounding the use and therapeutic effectiveness of this drug, we provide an update on the biochemical mechanism of action for ezetimibe, its safety and efficacy, as well as the results of recent randomized studies that support its use in a variety of clinical scenarios.
Predicting Grammatical Classes from Phonological Cues: An Empirical Test

This paper investigates to what extent the grammatical class(es) of a word can be predicted on the basis of phonological and prosodic information only. We report on several experiments with an artificial learning system which has to assign English word forms to their appropriate grammatical class, using various types of phonological and prosodic information. First of all, we examine several phonological cues which were claimed by Kelly (1996) to be particularly good for distinguishing English nouns from verbs. Our results indicate that these cues are indeed partially predictive for the problem at hand and reveal that a combination of cues yields significantly better results than those obtained for each cue individually. We then show experimentally that ‘raw’ segmental information, augmented with word stress, allows the learning system to improve considerably upon those results . Secondly, we investigate several generalizations of the approach: basic segmental information also proves to be more predictive when the task is extended to encompass all open class words in English, and these findings can be replicated for a different (though related) language such as Dutch.
Effects of the antioxidants curcumin or selenium on cisplatin-induced nephrotoxicity and lipid peroxidation in rats.

A large number of natural products and dietary components have been evaluated as potential chemoprotective agents. In the present investigation we report the effects of pre-treatment with two dietary antioxidants, curcumin (8 mg kg-1 body wt.) or selenium (1 mg kg-1 body wt.), on cisplatin-induced lipid peroxidation and nephrotoxicity in Wistar rats. Adult male rats were divided into six treatment and control groups of six rats each. The animals were pre-treated by gavage with two doses of each antioxidant, one dose 24 h and the second 10 min before cisplatin intraperitoneal injection (5 mg kg-1 body wt.). The rats were killed 3 days after cisplatin injection and serum, urine and kidney were isolated and analysed. Cisplatin administration resulted in significant reduction of body weight and higher urinary volumes were observed in all groups treated with this antitumor drug (P< 0.05). The animals treated with cisplatin showed a depletion of renal glutathione, increased lipid peroxidation, and an increase in serum creatinine levels (P< 0.05). The administration of curcumin or selenium alone did not increase lipid peroxidation compared to the control group (P> 0.05). Three days after curcumin or selenium plus cisplatin treatments, the renal damage induced by cisplatin did not recover at a significant statistically level. This study suggests that the natural antioxidants curcumin or selenium did not offer protection against cisplatin-induced nephrotoxicity and lipid peroxidation in adult Wistar rats.
ε Subunit of Bacillus subtilis F1-ATPase Relieves MgADP Inhibition

MgADP inhibition, which is considered as a part of the regulatory system of ATP synthase, is a well-known process common to all F1-ATPases, a soluble component of ATP synthase. The entrapment of inhibitory MgADP at catalytic sites terminates catalysis. Regulation by the ε subunit is a common mechanism among F1-ATPases from bacteria and plants. The relationship between these two forms of regulatory mechanisms is obscure because it is difficult to distinguish which is active at a particular moment. Here, using F1-ATPase from Bacillus subtilis (BF1), which is strongly affected by MgADP inhibition, we can distinguish MgADP inhibition from regulation by the ε subunit. The ε subunit did not inhibit but activated BF1. We conclude that the ε subunit relieves BF1 from MgADP inhibition.
Molecular Pathways Molecular Pathways : BRAF Induces Bioenergetic Adaptation by Attenuating Oxidative Phosphorylation

Cancers acquire mutations in cooperating pathways that sustain their growth and survival. To support continued proliferation, tumor cells adapt their metabolism to balance energy production with their augmented biosynthetic needs. Although most normal differentiated cells use mitochondrial oxidative phosphorylation (OXPHOS) as the bioenergetic source, cancer cells have been proposed to rely principally on cytoplasmic glycolysis. The molecular basis for this shift, termed the Warburg effect, is the subject of intense investigation, because mechanistic understanding may lead to novel approaches to target the altered metabolism of cancer cells. Recently, mutations BRAF(V600E) have emerged as a major regulator of metabolic homeostasis. Melanoma cells may use a metabolic shift to circumvent BRAF(V600E)-induced senescence though limiting their reliance on OXPHOS and promote proliferation. Furthermore, BRAF(V600E) acts to suppress expression of the melanocyte master regulator microphthalmia-associated transcription factor (MITF) and the mitochondrial biogenesis coactivator PGC1a. Accordingly, therapeutic inhibition of BRAF(V600E) reverses metabolic reprogramming in melanoma cells and elevates OXPHOS through increased MITF–PGC1a levels. BRAF-targeted drugs modulate the metabolic state of malignant melanoma cells, and counteracting these adaptive responses using pharmacologic agents may prove useful in combinatorial therapeutic strategies. Clin Cancer Res; 20(9); 1–7. 2014 AACR.