Byzantine Attack and Defense in Cognitive Radio Networks: A Survey

The Byzantine attack in cooperative spectrum sensing (CSS), also known as the spectrum sensing data falsification (SSDF) attack in the literature, is one of the key adversaries to the success of cognitive radio networks (CRNs). In the past couple of years, the research on the Byzantine attack and defense strategies has gained worldwide increasing attention. In this paper, we provide a comprehensive survey and tutorial on the recent advances in the Byzantine attack and defense for CSS in CRNs. Specifically, we first briefly present the preliminaries of CSS for general readers, including signal detection techniques, hypothesis testing, and data fusion. Second, we analyze the spear and shield relation between Byzantine attack and defense from three aspects: the vulnerability of CSS to attack, the obstacles in CSS to defense, and the games between attack and defense. Then, we propose a taxonomy of the existing Byzantine attack behaviors and elaborate on the corresponding attack parameters, which determine where, who, how, and when to launch attacks. Next, from the perspectives of homogeneous or heterogeneous scenarios, we classify the existing defense algorithms, and provide an in-depth tutorial on the state-of-the-art Byzantine defense schemes, commonly known as robust or secure CSS in the literature. Furthermore, we highlight the unsolved research challenges and depict the future research directions.Comment: Accepted by IEEE Communications Surveys and Tutoiral

Untangling Cycles for Contour Grouping

We introduce a novel topological formulation for contour grouping. Our grouping criterion, called untangling cycles, exploits the inherent topological 1D structure of salient contours to extract them from the otherwise 2D image clutter. To define a measure for topological classification robust to clutter and broken edges, we use a graph formulation instead of the standard computational topology. The key insight is that a pronounced 1D contour should have a clear ordering of edgels, to which all graph edges adhere, and no long range entanglements persist. Finding the contour grouping by optimizing these topological criteria is challenging. We introduce a novel concept of circular embedding to encode this combinatorial task. Our solution leads to computing the dominant complex eigenvectors/ eigenvalues of the random walk matrix of the contour grouping graph. We demonstrate major improvements over state-of-the-art approaches on challenging real images

Saliency Based Opportunitstic Search for Object Part Extraction and Labeling

We study the task of object part extraction and labeling, which seeks to understand objects beyond simply identifiying their bounding boxes. We start from bottom-up segmentation of images and search for correspondences between object parts in a few shape models and segments in images. Segments comprising different object parts in the image are usually not equally salient due to uneven contrast, illumination conditions, clutter, occlusion and pose changes. Moreover, object parts may have different scales and some parts are only distinctive and recognizable in a large scale. Therefore, we utilize a multi-scale shape representation of objects and their parts, figural contextual information of the whole object and semantic contextual information for parts. Instead of searching over a large segmentation space, we present a saliency based opportunistic search framework to explore bottom-up segmentation by gradually expanding and bounding the search domain.We tested our approach on a challenging statue face dataset and 3 human face datasets. Results show that our approach significantly outperforms Active Shape Models using far fewer exemplars. Our framework can be applied to other object categories

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs.

Variable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. In this work, we solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We develop software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We use this to discover VNTRs with length stratified by continental population, and expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease

Expression and characterization of the UL31 protein from duck enteritis virus

<p>Abstract</p> <p>Background</p> <p>Previous studies indicate that the UL31 protein and its homology play similar roles in nuclear egress of all <it>herpesviruses</it>. However, there is no report on the UL31 gene product of DEV. In this study, we expressed and presented the basic properties of the DEV UL31 product.</p> <p>Results</p> <p>The entire ORF of the UL31 was cloned into pET 32a (+) prokaryotic expression vector. <it>Escherichia coli </it>BL21(DE3) competent cells were transformed with the construct followed by the induction of protein expression by the addition of IPTG. Band corresponding to the predicted sizes (55 kDa) was produced on the SDS-PAGE. Over expressed 6×His-UL31 fusion protein was purified by nickel affinity chromatography. The DEV UL31 gene product has been identified by using a rabbit polyclonal antiserum raised against the purified protein. A protein of approximate 35 kDa that reacted with the antiserum was detected in immunoblots of DEV-infected cellular lysates, suggesting that the 35 kDa protein was the primary translation product of the UL31 gene. RT-PCR analyses revealed that the UL31 gene was transcribed most abundantly during the late phase of replication. Subsequently, Immunofluorescence analysis revealed that the protein was widespread speckled structures in the nuclei of infected cells. Western blotting of purified virion preparations showed that UL31 was a component of intracellular virions but was absent from mature extracellular virions. Finally, an Immunofluorescence assay was established to study the distribution of the UL31 antigen in tissues of artificially DEV infected ducks. The results showed that the UL31 antigen was primarily located in the cells of digestive organs and immunological organs.</p> <p>Conclusion</p> <p>In this work, we present the basic properties of the DEV UL31 product. The results indicate that DEV UL31 shares many similarities with its HSV or PRV homolog UL31 and suggest that functional cross-complementation is possible between members of the <it>Alpha</it>herpesvirus subfamily. Furthermore, in vivo experiments with ducks infected with UL31-defective isolates of DEV will also be of importance in order to assess the possible role of the UL31 protein in viral pathogenesis. These properties of the UL31 protein provide a prerequisite for further functional analysis of this gene.</p

Characterization of the duck enteritis virus UL55 protein

<p>Abstract</p> <p>Background</p> <p>Characteration of the newly identified duck enteritis virus UL55 gene product has not been reported yet. Knowledge of the protein UL55 can provide useful insights about its function.</p> <p>Results</p> <p>The newly identified duck enteritis virus UL55 gene was about 561 bp, it was amplified and digested for construction of a recombinant plasmid pET32a(+)/UL55 for expression in Escherichia coli. SDS-PAGE analysis revealed the recombinant protein UL55(pUL55) was overexpressed in Escherichia coli BL21 host cells after induction by 0.2 mM IPTG at 37°C for 4 h and aggregated as inclusion bodies. The denatured protein about 40 KDa named pUL55 was purified by washing five times, and used to immune rabbits for preparation of polyclonal antibody. The prepared polyclonal antibody against pUL55 was detected and determined by Agar immundiffusion and Neutralization test. The results of Wstern blotting assay and intracellular analysis revealed that pUL55 was expressed most abundantly during the late phase of replication and mainly distributed in cytoplasm in duck enteritis virus infected cells.</p> <p>Conclusions</p> <p>In this study, the duck enteritis virus UL55 protein was successfully expressed in prokaryotic expression system. Besides, we have prepared the polyclonal antibody against recombinant prtein UL55, and characterized some properties of the duck enteritis virus UL55 protein for the first time. The research will be useful for further functional analysis of this gene.</p

Induction of immune responses in ducks with a DNA vaccine encoding duck plague virus glycoprotein C

<p>Abstract</p> <p>Background</p> <p>A DNA vaccine expressing glycoprotein C (gC) of duck plague virus (DPV) was evaluated for inducing immunity in ducks. The plasmid encoding gC of DPV was administered via intramuscular (IM) injection and gene gun bombardment.</p> <p>Results</p> <p>After immunization by both routes virus-specific serum antibody and T-cell responses developed. Vaccination of ducks by IM injection induced a stronger humoral, but weaker cell-mediated immune response. In contrast, a better cell-mediated immune response was achieved by using a gene gun to deliver DNA-coated gold beads to the epidermis with as little as 6 μg of DNA.</p> <p>Conclusions</p> <p>This demonstrated that both routes of DNA inoculation can be used for eliciting virus-specific immune responses. Although DNA vaccine containing DPV gC is effective in both intramuscular injection and gene gun bombardment, the latter could induce significantly higher cell-mediated responses against DPV.</p

TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.

The Long interspersed nuclear element 1 (LINE-1) is a primary source of genetic variation in humans and other mammals. Despite its importance, LINE-1 activity remains difficult to study because of its highly repetitive nature. Here, we developed and validated a method called TeXP to gauge LINE-1 activity accurately. TeXP builds mappability signatures from LINE-1 subfamilies to deconvolve the effect of pervasive transcription from autonomous LINE-1 activity. In particular, it apportions the multiple reads aligned to the many LINE-1 instances in the genome into these two categories. Using our method, we evaluated well-established cell lines, cell-line compartments and healthy tissues and found that the vast majority (91.7%) of transcriptome reads overlapping LINE-1 derive from pervasive transcription. We validated TeXP by independently estimating the levels of LINE-1 autonomous transcription using ddPCR, finding high concordance. Next, we applied our method to comprehensively measure LINE-1 activity across healthy somatic cells, while backing out the effect of pervasive transcription. Unexpectedly, we found that LINE-1 activity is present in many normal somatic cells. This finding contrasts with earlier studies showing that LINE-1 has limited activity in healthy somatic tissues, except for neuroprogenitor cells. Interestingly, we found that the amount of LINE-1 activity was associated with the with the amount of cell turnover, with tissues with low cell turnover rates (e.g. the adult central nervous system) showing lower LINE-1 activity. Altogether, our results show how accounting for pervasive transcription is critical to accurately quantify the activity of highly repetitive regions of the human genome