Miracle-dz/UniFAR-FTUs huggingface dataset:
A Semantic Framework for Test Coverage (Extended Version)

Since testing is inherently incomplete, test selection is of vital importance. Coverage measures evaluate the quality of a test suite and help the tester select test cases with maximal impact at minimum cost. Existing coverage criteria for test suites are usually defined in terms of syntactic characteristics of the implementation under test or its specification. Typical black-box coverage metrics are state and transition coverage of the specification. White-box testing often considers statement, condition and path coverage. A disadvantage of this syntactic approach is that different coverage figures are assigned to systems that are behaviorally equivalent, but syntactically different. Moreover, those coverage metrics do not take into account that certain failures are more severe than others, and that more testing effort should be devoted to uncover the most important bugs, while less critical system parts can be tested less thoroughly. This paper introduces a semantic approach to test coverage. Our starting point is a weighted fault model, which assigns a weight to each potential error in an implementation. We define a framework to express coverage measures that express how well a test suite covers such a specification, taking into account the error weight. Since our notions are semantic, they are insensitive to replacing a specification by one with equivalent behaviour.We present several algorithms that, given a certain minimality criterion, compute a minimal test suite with maximal coverage. These algorithms work on a syntactic representation of weighted fault models as fault automata. They are based on existing and novel optimization problems. Finally, we illustrate our approach by analyzing and comparing a number of test suites for a chat protocol.
Localization of nitric oxide synthase isoforms in porcine ocular tissues.

PURPOSE To determine by immunohistochemistry the distribution of different nitric oxide synthases (NOS) isoforms in the porcine eye. METHODS By light microscopy (immunofluorescence), porcine ocular tissues were investigated using monoclonal antibodies against neuronal NOS (nNOS; NOS I), endothelial NOS (ecNOS; NOS III), and macrophage NOS (macNOS; NOS II). RESULTS Specific nNOS immunoreactivity was detected along the apical cytoplasmic portions of the non-pigmented and pigmented ciliary epithelial cells, in the endothelial lining of the corneoscleral meshwork and the uveal cords of the iridocorneal angle tissue, as well as in the photoreceptor layer of the sensory retina. Immunoreactivity for ecNOS was confined to the vascular endothelium of the vessels of the conjunctiva, iris, ciliary body, retina, choroid and optic nerve. A mild immunostaining for macNOS was present in the cytoplasm of some non-pigmented ciliary epithelial cells. CONCLUSIONS The predominant localization of nNOS in ciliary epithelial and trabecular endothelial cells suggests a possible involvement of nNOS in both the production and outflow of aqueous humor in porcine eyes.
Gastroprotective Effect of Selenium on Ethanol-Induced Gastric Damage in Rats

In the present study, we examined the gastroprotective effect of selenium against ethanol-induced gastric mucosal lesions in rats. The gastric mucosal lesions were produced by oral administration with various concentrations of ethanol for three days, and 80% ethanol treatment was determined to be the optimal condition for induction of gastric damage. To identify the protective effect of selenium on ethanol-induced gastric damage, various doses of selenium were given as pretreatment for three days, and then gastric damage was induced by 80% ethanol treatment. Selenium showed a protective effect against ethanol-induced gastric mucosal lesions in a dose dependent manner. Specifically, 100 μg/kg selenium showed the highest level of gastroprotection. In addition, selenium markedly attenuated ethanol-induced lipid peroxidation in gastric mucosa and increased activities of radical scavenging enzymes, such as superoxide dismutase (SOD), catalase, and glutathione peroxidase in a dose-dependent manner. Histological data showed that 100 μg/kg selenium distinctly reduced the depth and severity of the ethanol induced gastric lesion. These results clearly demonstrate that selenium inhibits the formation of ethanol-induced gastric mucosal lesions through prevention of lipid peroxidation and activation of enzymatic radical scavenging.
Data Balancing for Efficient Training of Hybrid ANN/HMM Automatic Speech Recognition Systems

Hybrid speech recognizers, where the estimation of the emission pdf of the states of hidden Markov models (HMMs), usually carried out using Gaussian mixture models (GMMs), is substituted by artificial neural networks (ANNs) have several advantages over the classical systems. However, to obtain performance improvements, the computational requirements are heavily increased because of the need to train the ANN. Departing from the observation of the remarkable skewness of speech data, this paper proposes sifting out the training set and balancing the amount of samples per class. With this method, the training time has been reduced 18 times while obtaining performances similar to or even better than those with the whole database, especially in noisy environments. However, the application of these reduced sets is not straightforward. To avoid the mismatch between training and testing conditions created by the modification of the distribution of the training data, a proper scaling of the a posteriori probabilities obtained and a resizing of the context window need to be performed as demonstrated in this paper.
Stress Potentiates Early and Attenuates Late Stages of Visual Processing

Stress can fundamentally alter neural responses to incoming information. Recent research suggests that stress and anxiety shift the balance of attention away from a task-directed mode, governed by prefrontal cortex, to a sensory-vigilance mode, governed by the amygdala and other threat-sensitive regions. A key untested prediction of this framework is that stress exerts dissociable effects on different stages of information processing. This study exploited the temporal resolution afforded by event-related potentials to disentangle the impact of stress on vigilance, indexed by early perceptual activity, from its impact on task-directed cognition, indexed by later postperceptual activity in humans. Results indicated that threat of shock amplified stress, measured using retrospective ratings and concurrent facial electromyography. Stress also double-dissociated early sensory-specific processing from later task-directed processing of emotionally neutral stimuli: stress amplified N1 (184–236 ms) and attenuated P3 (316–488 ms) activity. This demonstrates that stress can have strikingly different consequences at different processing stages. Consistent with recent suggestions, stress amplified earlier extrastriate activity in a manner consistent with vigilance for threat (N1), but disrupted later activity associated with the evaluation of task-relevant information (P3). These results provide a novel basis for understanding how stress can modulate information processing in everyday life and stress-sensitive disorders.
Textual Entailment Recognition Based on Inversion Transduction Grammars

The PASCAL Challenge’s textual entailment recognition (RTE) task presents intriguing opportunities to test various implications of the strong language universal constraint posited by Wu’s (1995, 1997) Inversion Transduction Grammar (ITG) hypothesis. The ITG Hypothesis provides a strong inductive bias, and has been repeatedly shown empirically to yield both efficiency and accuracy gains for numerous language acquisition tasks. Since the RTE challenge abstracts over many tasks, it invites meaningful analysis of the ITG Hypothesis across tasks including information retrieval, comparable documents, reading comprehension, question answering, information extraction, machine translation, and paraphrase acquisition. We investigate two new models for the RTE problem that employ simple generic Bracketing ITGs. Experimental results show that, even in the absence of any thesaurus to accommodate lexical variation between the Text and the Hypothesis strings, surprisingly strong results for a number of the task subsets are obtainable from the Bracketing ITG’s structure matching bias alone.
Memory Systems 1994

Current thinking on memory systems of 1994, D.L. Schacter, E. Tulving multiple memory systems - what and why - an update, L. Nadel variations in synaptic plasticity and types of memory in corticohippocampal networks, G. Lynch, R. Granger hippocampal function and interference, M.L. Shapiro, D.S. Olton the memory coherence problem - configured associations and the hippocampal system, J.W. Rudy, R.J. Sutherland the hippocampal system and declarative memory in humans and animals - experimental analysis and historical origins, H. Eichenbaum declarative and non-declarative memory - multiple brain systems supporting learning and memory, L.R. Squire priming and multiple memory systems - perceptual mechanisms of implicit memory, D.L. Schacter memory and working with memory - evaluation of a component process model and comparisons with other models, M. Moscovitch binding complex memories - the role of reactivation and the hippocampus, M.K. Johnson, B.L. Chalfonte working interface - the interface between memory and cognition, A. Baddeley cognitive binding, J. Metcalfe, W.E. Mencl, G.W Cottrell.
The OX-44 molecule couples to signaling pathways and is associated with CD2 on rat T lymphocytes and a natural killer cell line

The MRC OX-44 molecule, which is expressed on all peripheral leukocytes, identifies the subset of thymocytes capable of proliferating in response to alloantigens and lectins (Paterson, D.J., J.R. Green, W.A. Jefferies, M. Puklavec, and A.F. Williams. 1987. J. Exp. Med. 165:1). When we isolated monoclonal antibodies (mAbs) on the basis of their ability to activate the phosphatidylinositol signaling pathway in RNK-16 cells (a rat leukemia line with natural killer activity), three of the resulting mAbs recognized the OX-44 molecule. Addition of these mAbs to RNK-16 elicits protein tyrosine phosphorylation, generates inositol phosphates, and increases the concentration of cytoplasmic free calcium. These responses require the addition of intact mAb and are not observed with F(ab')2 fragments. One of these mAbs (7D2) is mitogenic for freshly isolated rat splenic T cells and synergizes with a mAb to the T cell antigen receptor in this activation. A 50-60-kD glycoprotein coprecipitates with the OX-44 molecule from RNK-16 cells and rat splenic T cells. Peptide mapping and reprecipitation studies indicate that the coprecipitating molecule is CD2. Thus, the OX-44 molecule can couple to multiple signaling pathways and associates with CD2 on both RNK-16 and rat T cells.
Adaptive Robust Kalman Filtering via Krein Space Estimation

This paper is concerned with the design of an adaptive robust Kalman filter for the discrete-time system with norm-bounded parametric uncertainty. A set of covariance-dependent forgetting factors is introduced into the design of robust filtering algorithm in Krein space. Here, the forgetting is non-uniform in time and in space. It is shown, via a simulation example, that the proposed filter achieves robustness against parameter variation and improvement in performance when compared with a conventional Kalman filter and an existing robust Kalman filter, respectively
BCL2 Predicts Survival in Germinal Center B-cell–like Diffuse Large B-cell Lymphoma Treated with CHOP-like Therapy and Rituximab

Purpose: We have previously shown the prognostic significance of BCL2 expression in the activated B-cell–like diffuse large B-cell lymphoma (ABC-DLBCL) patients treated with cyclophosphamide-Adriamycin-vincristine-prednisone (CHOP) or CHOP-like therapy. However, after the inclusion of rituximab (R) in the CHOP regimen, several conflicting observations about the prognostic value of BCL2 expression have been reported. Experimental Design: We evaluated the R-CHOP cohort of 221 DLBCL cases with gene expression profiling data. BCL2 protein (n = 169), mRNA (n = 221) expression, and t(14;18) (n = 144) were correlated with clinical outcome. The CHOP cohort (n = 181) was used for comparative analysis. Results: BCL2 protein expression has significant impact on overall survival (OS) and event-free survival (EFS) in DLBCL (OS, P = 0.009; EFS, P = 0.001) and GCB-DLBCL (OS, P = 0.03; EFS, P = 0.002) but not in ABC-DLBCL in the R-CHOP cohort. The survival differences for EFS in GCB-DLBCL were still observed in multivariate analysis. At the mRNA level, this correlation was observed in EFS in DLBCL (P = 0.006), but only a trend was observed in GCB-DLBCL (P = 0.09). The t(14;18) was detected in 34% of GCB-DLBCL but was not associated with significant differences in survival. Gene enrichment analysis identified significant enrichment of the DLBCL “stromal-1” signatures and hypoxia-inducible factor 1 (HIF1-α) signature in BCL2(−)GCB-DLBCL, whereas TFH cell signatures were enriched in BCL2(+)GCB-DLBCL. Conclusion: The prognostic significance of BCL2 has changed after inclusion of rituximab in the treatment protocol and is observed in the GCB-DLBCL rather than the ABC-DLBCL. Although rituximab has benefited patients in both DLBCL subgroups, the BCL2(+)GCB-DLBCL seems to receive less benefit from this treatment and may require other novel therapeutic intervention. Clin Cancer Res; 17(24); 7785–95. ©2011 AACR.
Joint space controller design for electrohydraulic servos

This paper focuses on the joint space control of mechanical systems with electrohydraulic servos. Using mechanism inverse kinematics, desired Cartesian trajectories yield desired actuator trajectories, which are fed to a novel model-based controller. Rigid body equations of motion and hydraulics dynamics, including friction and servovalve models are employed. The developed feedback controller uses the system dynamic and hydraulic model to yield servovalve currents. As an example, the developed controller is applied to a single degree-of-freedom (dof) servomechanism. Identification procedures employed in estimating the physical parameters of the experimental single dof servomechanism are discussed. In contrast to other approaches, here, force, pressure or acceleration feedback is not required. Simulations with typical desired trajectory inputs are presented and a good performance of the controller is obtained.
Autophagy Deficiency Diminishes Indomethacin-Induced Intestinal Epithelial Cell Damage through Activation of the ERK/Nrf2/HO-1 Pathway

Nonsteroidal anti-inflammatory drugs (NSAIDs) can cause epithelial cell damage in the stomach, intestine, and colon. NSAIDs are reported to induce autophagy and apoptosis in intestinal epithelial cells; however, their role in cell damage is poorly understood. To examine the role of autophagy in cell damage, we used autophagy-related gene Atg5-conditional knockout mice, in which the Atg5 gene is only knocked out in intestinal epithelial cells. In an indomethacin (IM)–induced gastrointestinal ulcer mouse model, intestinal epithelium damage was reduced in Atg5-conditional knockout mice compared with wild-type mice. IM-induced damage in IEC6 rat intestinal epithelial cells was reduced when Atg5 was silenced (IEC6shAtg5 cells). Western blot analyses indicated that IM-induced apoptosis decreased, and the potent, oxidative stress–related extracellular signal–regulated kinase (ERK)/nuclear factor-erythroid2-like2 (Nrf2)/heme oxygenase-1 (HO-1) signaling pathway was upregulated in IEC6shAtg5 cells. An experiment using a reactive oxygen species (ROS)-sensitive fluorescent dye in IEC6shAtg5 cells revealed that the amount of ROS at the baseline and the rate of increase after IM treatment were lower than in intact IEC6 cells. The mitochondrial membrane potential at the baseline and the reduction rate in IM-treated IEC6shAtg5 cells were lower than in intact IEC6 cells, indicating that autophagy deficiency increased ROS production caused by mitochondrial disturbance. Furthermore, MnTMPyP, a manganese–superoxide dismutase mimetic, significantly inhibited IM-induced autophagy and subsequent apoptosis as well as activation of the ERK/Nrf2/HO-1 pathway. These data suggest that autophagy deficiency and subsequent activation of the ERK/Nrf2/HO-1 pathway diminished IM-induced, apoptosis-mediated intestinal epithelial cell damage, and genetic analyses of single nucleotide polymorphisms in autophagy-related genes could predict NSAID-induced intestinal injury.
Meta‐Analysis of Genome‐Wide Association Studies with Correlated Individuals: Application to the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

Investigators often meta‐analyze multiple genome‐wide association studies (GWASs) to increase the power to detect associations of single nucleotide polymorphisms (SNPs) with a trait. Meta‐analysis is also performed within a single cohort that is stratified by, e.g., sex or ancestry group. Having correlated individuals among the strata may complicate meta‐analyses, limit power, and inflate Type 1 error. For example, in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), sources of correlation include genetic relatedness, shared household, and shared community. We propose a novel mixed‐effect model for meta‐analysis, “MetaCor,” which accounts for correlation between stratum‐specific effect estimates. Simulations show that MetaCor controls inflation better than alternatives such as ignoring the correlation between the strata or analyzing all strata together in a “pooled” GWAS, especially with different minor allele frequencies (MAFs) between strata. We illustrate the benefits of MetaCor on two GWASs in the HCHS/SOL. Analysis of dental caries (tooth decay) stratified by ancestry group detected a genome‐wide significant SNP (rs7791001, P‐value = 3.66×10−8 , compared to 4.67×10−7 in pooled), with different MAFs between strata. Stratified analysis of body mass index (BMI) by ancestry group and sex reduced overall inflation from λGC=1.050 (pooled) to λGC=1.028 (MetaCor). Furthermore, even after removing close relatives to obtain nearly uncorrelated strata, a naïve stratified analysis resulted in λGC=1.058 compared to λGC=1.027 for MetaCor.
Modeling and analysis of loading effect on leakage of nanoscaled bulk-CMOS logic circuits

In nanoscale complementary metal-oxide-semiconductor (CMOS) devices, a significant increase in subthreshold, gate, and reverse-biased junction band-to-band-tunneling (BTBT) leakage results in large leakage power in logic circuits. Leakage components interact with each other at the device level (through device geometry and the doping profile) and at the circuit level (through the node voltages). Due to the circuit-level interaction of the different leakage components, the leakage of a logic gate depends on the circuit topology, i.e., the number and the nature of the other logic gates connected to its input and output. In this paper, the effect of loading on a leakage of a circuit is analyzed for the first time. The authors have also proposed a method to accurately estimate the total leakage in a logic circuit from its logic-level description considering the impact of loading and transistor stacking.
Sub-Lethal Effects of Pesticide Residues in Brood Comb on Worker Honey Bee (Apis mellifera) Development and Longevity

Background Numerous surveys reveal high levels of pesticide residue contamination in honey bee comb. We conducted studies to examine possible direct and indirect effects of pesticide exposure from contaminated brood comb on developing worker bees and adult worker lifespan. Methodology/Principal Findings Worker bees were reared in brood comb containing high levels of known pesticide residues (treatment) or in relatively uncontaminated brood comb (control). Delayed development was observed in bees reared in treatment combs containing high levels of pesticides particularly in the early stages (day 4 and 8) of worker bee development. Adult longevity was reduced by 4 days in bees exposed to pesticide residues in contaminated brood comb during development. Pesticide residue migration from comb containing high pesticide residues caused contamination of control comb after multiple brood cycles and provided insight on how quickly residues move through wax. Higher brood mortality and delayed adult emergence occurred after multiple brood cycles in contaminated control combs. In contrast, survivability increased in bees reared in treatment comb after multiple brood cycles when pesticide residues had been reduced in treatment combs due to residue migration into uncontaminated control combs, supporting comb replacement efforts. Chemical analysis after the experiment confirmed the migration of pesticide residues from treatment combs into previously uncontaminated control comb. Conclusions/Significance This study is the first to demonstrate sub-lethal effects on worker honey bees from pesticide residue exposure from contaminated brood comb. Sub-lethal effects, including delayed larval development and adult emergence or shortened adult longevity, can have indirect effects on the colony such as premature shifts in hive roles and foraging activity. In addition, longer development time for bees may provide a reproductive advantage for parasitic Varroa destructor mites. The impact of delayed development in bees on Varroa mite fecundity should be examined further.
Adaptive Bilateral Filter for Sharpness Enhancement and Noise Removal

In this paper, we present an adaptive bilateral filter (ABF) for sharpness enhancement and noise removal. ABF sharpens an image by increasing the slope of the edges without producing overshoot or undershoot. Our new approach to slope restoration significantly differs from the previous slope restoration algorithms in that ABF does not involve detecting edge orientations or edge profiles. Compared with the bilateral filter, ABF restored images are significantly sharper. Compared with an unsharp mask (USM) based sharpening method the optimal USM (OUM), ABF restored edges are as sharp as those rendered by the OUM, but without halo. ABF also outperforms the bilateral filter and the OUM in noise removal.