Do Bugs Propagate? An Empirical Analysis of Temporal Correlations Among Software Bugs

The occurrences of bugs are not isolated events, rather they may interact, affect each other, and trigger other latent bugs. Identifying and understanding bug correlations could help developers localize bug origins, predict potential bugs, and design better architectures of software artifacts to prevent bug affection. Many studies in the defect prediction and fault localization literature implied the dependence and interactions between multiple bugs, but few of them explicitly investigate the correlations of bugs across time steps and how bugs affect each other. In this paper, we perform social network analysis on the temporal correlations between bugs across time steps on software artifact ties, i.e., software graphs. Adopted from the correlation analysis methodology in social networks, we construct software graphs of three artifact ties such as function calls and type hierarchy and then perform longitudinal logistic regressions of time-lag bug correlations on these graphs. Our experiments on four open-source projects suggest that bugs can propagate as observed on certain artifact tie graphs. Based on our findings, we propose a hybrid artifact tie graph, a synthesis of a few well-known software graphs, that exhibits a higher degree of bug propagation. Our findings shed light on research for better bug prediction and localization models and help developers to perform maintenance actions to prevent consequential bugs

Effect of WeiJia on carbon tetrachloride induced chronic liver injury

Aim: To study the effect of WeiJia on chronic liver injury using carbon tetrachloride (CCl 4) induced liver injury animal model. Methods: Wista r rats weighing 180-220g were randomly divided into three groups: normal control group (Group A), CCl 4 induced liver injury control group (Group B) and CCl 4 induction with WeiJia treatment group (Group C). Each group consisted of 14 rats. Liver damage and fibrosis was induced by subcutaneous injection with 40% CCl 4 in olive oil at 3 mL/kg body weight twice a week for eight weeks for Groups B and C rats whereas olive oil was used for Group A rats. Starting from the third week, Group C rats also received daily intraperitoneal injection of WeiJia at a dose of 1.25 μg/kg body weight. Animals were sacrificed at the fifth week (4 male, 3 female), and eighth week (4 male, 3 female) respectively. Degree of fibrosis were measured and serological markers for liver fibrosis and function including hyaluronic acid (HA), type IV collagen (CIV), γ-glutamyl transferase (γ-GT), alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were determined. Alpha smooth muscle actin (α-SMA) and proliferating cell nuclear antigen (PCNA) immunohistochemistry were also performed. Results: CCl 4 induction led to the damage of liver and development of fibrosis in Group B and Group C rats when compared to Group A rats. The treatment of WeiJia in Group C rats could reduce the fibrosis condition significantly compared to Group B rats. The effect could be observed after three weeks of treatment and was more obvious after eight weeks of treatment. Serum HA, CIV, ALT, AST and γ-GT levels after eight weeks of treatment for Group C rats were 58±22 μg/L (P 0.05) respectively, similar to normal control group (Group A), but significantly different from CCl 4 induced liver injury control group (Group B). An increase in PCNA and decrease in α-SMA expression level was also observed. Conclusion: WeiJia could improve liver function and reduce liver fibrosis which might be through the inhibition of stellate cell activity. © 2006 The WJG Press. All rights reserved.published_or_final_versio

Highly Efficient Multiview Depth Coding Based on Histogram Projection and Allowable Depth Distortion

The file attached to this record is the author's final peer reviewed version.Mismatches between the precisions of representing the disparity, depth value and rendering position in 3D video systems cause redundancies in depth map representations. In this paper, we propose a highly efficient multiview depth coding scheme based on Depth Histogram Projection (DHP) and Allowable Depth Distortion (ADD) in view synthesis. Firstly, DHP exploits the sparse representation of depth maps generated from stereo matching to reduce the residual error from INTER and INTRA predictions in depth coding. We provide a mathematical foundation for DHP-based lossless depth coding by theoretically analyzing its rate-distortion cost. Then, due to the mismatch between depth value and rendering position, there is a many-to-one mapping relationship between them in view synthesis, which induces the ADD model. Based on this ADD model and DHP, depth coding with lossless view synthesis quality is proposed to further improve the compression performance of depth coding while maintaining the same synthesized video quality. Experimental results reveal that the proposed DHP based depth coding can achieve an average bit rate saving of 20.66% to 19.52% for lossless coding on Multiview High Efficiency Video Coding (MV-HEVC) with different groups of pictures. In addition, our depth coding based on DHP and ADD achieves an average depth bit rate reduction of 46.69%, 34.12% and 28.68% for lossless view synthesis quality when the rendering precision varies from integer, half to quarter pixels, respectively. We obtain similar gains for lossless depth coding on the 3D-HEVC, HEVC Intra coding and JPEG2000 platforms

Comparative Cytotoxicity of Glycyrrhiza glabra Roots from Different Geographical Origins Against Immortal Human Keratinocyte (HaCaT), Lung Adenocarcinoma (A549) and Liver Carcinoma (HepG2) Cells

Glycyrrhiza glabra L. (Fabaceae), commonly known as 'liquorice', is a well-known medicinal plant. Roots of this plant have long been used as a sweetening and flavouring agent in food and pharmaceutical products, and also as a traditional remedy for cough, upper and lower respiratory ailments, kidney stones, hepatitis C, skin disorder, cardiovascular diseases, diabetes, gastrointestinal ulcers and stomach ache. Previous pharmacological and clinical studies have revealed its antitussive, antiinflammatory, antiviral, antimicrobial, antioxidant, immunomodulatory, hepatoprotective and cardioprotective properties. While glycyrrhizin, a sweet-tasting triterpene saponin, is the principal bioactive compound, several bioactive flavonoids and isoflavonoids are also present in the roots of this plant. In the present study, the cytotoxicity of the methanol extracts of nine samples of the roots of G.-glabra, collected from various geographical origins, was assessed against immortal human keratinocyte (HaCaT), lung adenocarcinoma (A549) and liver carcinoma (HepG2) cell lines using the in vitro 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazoliumbromide cell toxicity/viability assay. Considerable variations in levels of cytotoxicity were observed among various samples of G.-glabra

Topoisomer Differentiation of Molecular Knots by FTICR MS: Lessons from Class II Lasso Peptides

Lasso peptides constitute a class of bioactive peptides sharing a knotted structure where the C-terminal tail of the peptide is threaded through and trapped within an N-terminalmacrolactamring. The structural characterization of lasso structures and differentiation from their unthreaded topoisomers is not trivial and generally requires the use of complementary biochemical and spectroscopic methods. Here we investigated two antimicrobial peptides belonging to the class II lasso peptide family and their corresponding unthreaded topoisomers: microcin J25 (MccJ25), which is known to yield two-peptide product ions specific of the lasso structure under collisioninduced dissociation (CID), and capistruin, for which CID does not permit to unambiguously assign the lasso structure. The two pairs of topoisomers were analyzed by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) upon CID, infrared multiple photon dissociation (IRMPD), and electron capture dissociation (ECD). CID and ECDspectra clearly permitted to differentiate MccJ25 from its non-lasso topoisomer MccJ25-Icm, while for capistruin, only ECD was informative and showed different extent of hydrogen migration (formation of c\bullet/z from c/z\bullet) for the threaded and unthreaded topoisomers. The ECD spectra of the triply-charged MccJ25 and MccJ25-lcm showed a series of radical b-type product ions {\eth}b0In{\TH}. We proposed that these ions are specific of cyclic-branched peptides and result from a dual c/z\bullet and y/b dissociation, in the ring and in the tail, respectively. This work shows the potentiality of ECD for structural characterization of peptide topoisomers, as well as the effect of conformation on hydrogen migration subsequent to electron capture

Slow-wave sleep is controlled by a subset of nucleus accumbens core neurons in mice

Sleep control is ascribed to a two-process model, a widely accepted concept that posits homoeostatic drive and a circadian process as the major sleep-regulating factors. Cognitive and emotional factors also influence sleep–wake behaviour; however, the precise circuit mechanisms underlying their effects on sleep control are unknown. Previous studies suggest that adenosine has a role affecting behavioural arousal in the nucleus accumbens (NAc), a brain area critical for reinforcement and reward. Here, we show that chemogenetic or optogenetic activation of excitatory adenosine A2A receptor-expressing indirect pathway neurons in the core region of the NAc strongly induces slow-wave sleep. Chemogenetic inhibition of the NAc indirect pathway neurons prevents the sleep induction, but does not affect the homoeostatic sleep rebound. In addition, motivational stimuli inhibit the activity of ventral pallidum-projecting NAc indirect pathway neurons and suppress sleep. Our findings reveal a prominent contribution of this indirect pathway to sleep control associated with motivation

Whole-Genome Cartography of Estrogen Receptor α Binding Sites

Using a chromatin immunoprecipitation-paired end diTag cloning and sequencing strategy, we mapped estrogen receptor α (ERα) binding sites in MCF-7 breast cancer cells. We identified 1,234 high confidence binding clusters of which 94% are projected to be bona fide ERα binding regions. Only 5% of the mapped estrogen receptor binding sites are located within 5 kb upstream of the transcriptional start sites of adjacent genes, regions containing the proximal promoters, whereas vast majority of the sites are mapped to intronic or distal locations (>5 kb from 5′ and 3′ ends of adjacent transcript), suggesting transcriptional regulatory mechanisms over significant physical distances. Of all the identified sites, 71% harbored putative full estrogen response elements (EREs), 25% bore ERE half sites, and only 4% had no recognizable ERE sequences. Genes in the vicinity of ERα binding sites were enriched for regulation by estradiol in MCF-7 cells, and their expression profiles in patient samples segregate ERα-positive from ERα-negative breast tumors. The expression dynamics of the genes adjacent to ERα binding sites suggest a direct induction of gene expression through binding to ERE-like sequences, whereas transcriptional repression by ERα appears to be through indirect mechanisms. Our analysis also indicates a number of candidate transcription factor binding sites adjacent to occupied EREs at frequencies much greater than by chance, including the previously reported FOXA1 sites, and demonstrate the potential involvement of one such putative adjacent factor, Sp1, in the global regulation of ERα target genes. Unexpectedly, we found that only 22%–24% of the bona fide human ERα binding sites were overlapping conserved regions in whole genome vertebrate alignments, which suggest limited conservation of functional binding sites. Taken together, this genome-scale analysis suggests complex but definable rules governing ERα binding and gene regulation