SimpleCAR: An Efficient Bug-Finding Tool Based on Approximate Reachability

We present a new safety hardware model checker SimpleCAR that serves as a reference implementation for evaluating Complementary Approximate Reachability (CAR), a new SAT-based model checking framework inspired by classical reachability analysis. The tool gives a “bottom-line” performance measure for comparing future extensions to the framework. We demonstrate the performance of SimpleCAR on challenging benchmarks from the Hardware Model Checking Competition. Our experiments indicate that SimpleCAR is particularly suited for unsafety checking, or bug-finding; it is able to solve 7 unsafe instances within 1 h that are not solvable by any other state-of-the-art techniques, including BMC and IC3/PDR, within 8 h. We also identify a bug (reports safe instead of unsafe) and 48 counterexample generation errors in the tools compared in our analysis

Intersection and Rotation of Assumption Literals Boosts Bug-Finding

SAT-based techniques comprise the state-of-the-art in functional verification of safety-critical hardware and software, including IC3/PDR-based model checking and Bounded Model Checking (BMC). BMC is the incontrovertible best method for unsafety checking, aka bug-finding. Complementary Approximate Reachability (CAR) and IC3/PDR complement BMC for bug-finding by detecting different sets of bugs. To boost the efficiency of formal verification, we introduce heuristics involving intersection and rotation of the assumption literals used in the SAT encodings of these techniques. The heuristics generate smaller unsat cores and diverse satisfying assignments that help in faster convergence of these techniques, and have negligible runtime overhead. We detail these heuristics, incorporate them in CAR, and perform an extensive experimental evaluation of their performance, showing a 25% boost in bug-finding efficiency of CAR.We contribute a detailed analysis of the effectiveness of these heuristics: their influence on SAT-based bug-finding enables detection of different bugs from BMCbased checking. We find the new heuristics are applicable to IC3/PDR-based algorithms as well, and contribute a modified clause generalization procedure

Conservation and divergence of known apicomplexan transcriptional regulons

<p>Abstract</p> <p>Background</p> <p>The apicomplexans are a diverse phylum of parasites causing an assortment of diseases including malaria in a wide variety of animals and lymphoproliferation in cattle. Little is known about how these varied parasites regulate their transcriptional regulons. Even less is known about how regulon systems, consisting of transcription factors and target genes together with their associated biological process, evolve in these diverse parasites.</p> <p>Results</p> <p>In order to obtain insights into the differences in transcriptional regulation between these parasites we compared the orthology profiles of putative malaria transcription factors across species and examined the enrichment patterns of four binding sites across eleven apicomplexans.</p> <p>About three-fifths of the factors are broadly conserved in several phylogenetic orders of sequenced apicomplexans. This observation suggests the existence of regulons whose regulation is conserved across this ancient phylum. Transcription factors not broadly conserved across the phylum are possibly involved in regulon systems that have diverged between species. Examining binding site enrichment patterns in light of transcription factor conservation patterns suggests a second mode via which regulon systems may diverge - rewiring of existing transcription factors and their associated binding sites in specific ways. Integrating binding sites with transcription factor conservation patterns also facilitated prediction of putative regulators for one of the binding sites.</p> <p>Conclusions</p> <p>Even though transcription factors are underrepresented in apicomplexans, the distribution of these factors and their associated regulons reflect common and family-specific transcriptional regulatory processes.</p

TLR2 and Nod2 Mediate Resistance or Susceptibility to Fatal Intracellular Ehrlichia Infection in Murine Models of Ehrlichiosis

Our murine models of human monocytic ehrlichiosis (HME) have shown that severe and fatal ehrlichiosis is due to generation of pathogenic T cell responses causing immunopathology and multi-organ failure. However, the early events in the liver, the main site of infection, are not well understood. In this study, we examined the liver transcriptome during the course of lethal and nonlethal infections caused by Ixodes ovatus Ehrlichia and Ehrlichia muris, respectively. On day 3 post-infection (p.i.), although most host genes were down regulated in the two groups of infected mice compared to naïve counterparts, lethal infection induced significantly higher expression of caspase 1, caspase 4, nucleotide binding oligomerization domain-containing proteins (Nod1), tumor necrosis factor-alpha, interleukin 10, and CCL7 compared to nonlethal infection. On day 7 p.i., lethal infection induced highly significant upregulation of type-1 interferon, several inflammatory cytokines and chemokines, which was associated with increased expression levels of Toll-like receptor-2 (TLR2), Nod2, MyD88, nuclear factor-kappa B (NF-kB), Caspase 4, NLRP1, NLRP12, Pycard, and IL-1β, suggesting enhanced TLR signals and inflammasomes activation. We next evaluated the participation of TLR2 and Nod2 in the host response during lethal Ehrlichia infection. Although lack of TLR2 impaired bacterial elimination and increased tissue necrosis, Nod2 deficiency attenuated pathology and enhanced bacterial clearance, which correlated with increased interferon-γ and interleukin-10 levels and a decreased frequency of pathogenic CD8+ T cells in response to lethal infection. Thus, these data indicate that Nod2, but not TLR2, contributes to susceptibility to severe Ehrlichia-induced shock. Together, our studies provide, for the first time, insight into the diversity of host factors and novel molecular pathogenic mechanisms that may contribute to severe HME. © 2013 Chattoraj et al

Identification of Intracellular and Plasma Membrane Calcium Channel Homologues in Pathogenic Parasites

Ca2+ channels regulate many crucial processes within cells and their abnormal activity can be damaging to cell survival, suggesting that they might represent attractive therapeutic targets in pathogenic organisms. Parasitic diseases such as malaria, leishmaniasis, trypanosomiasis and schistosomiasis are responsible for millions of deaths each year worldwide. The genomes of many pathogenic parasites have recently been sequenced, opening the way for rational design of targeted therapies. We analyzed genomes of pathogenic protozoan parasites as well as the genome of Schistosoma mansoni, and show the existence within them of genes encoding homologues of mammalian intracellular Ca2+ release channels: inositol 1,4,5-trisphosphate receptors (IP3Rs), ryanodine receptors (RyRs), two-pore Ca2+ channels (TPCs) and intracellular transient receptor potential (Trp) channels. The genomes of Trypanosoma, Leishmania and S. mansoni parasites encode IP3R/RyR and Trp channel homologues, and that of S. mansoni additionally encodes a TPC homologue. In contrast, apicomplexan parasites lack genes encoding IP3R/RyR homologues and possess only genes encoding TPC and Trp channel homologues (Toxoplasma gondii) or Trp channel homologues alone. The genomes of parasites also encode homologues of mammalian Ca2+ influx channels, including voltage-gated Ca2+ channels and plasma membrane Trp channels. The genome of S. mansoni also encodes Orai Ca2+ channel and STIM Ca2+ sensor homologues, suggesting that store-operated Ca2+ entry may occur in this parasite. Many anti-parasitic agents alter parasite Ca2+ homeostasis and some are known modulators of mammalian Ca2+ channels, suggesting that parasite Ca2+ channel homologues might be the targets of some current anti-parasitic drugs. Differences between human and parasite Ca2+ channels suggest that pathogen-specific targeting of these channels may be an attractive therapeutic prospect

Synthesizing Environment Invariants for Modular Hardware Verification

We automate synthesis of environment invariants for modular hardware verification in processors and application-specific accelerators, where functional equivalence is proved between a high-level specification and a low-level implementation. Invariants are generated and iteratively strengthened by reachability queries in a counterexample-guided abstraction refinement (CEGAR) loop. Within each iteration, we use a syntax-guided synthesis (SyGuS) technique for generating invariants, where we use novel grammars to capture high-level design insights and provide guidance in the search over candidate invariants. Our grammars explicitly capture the separation between control-related and data-related state variables in hardware designs to improve scalability of the enumerative search. We have implemented our SyGuS-based technique on top of an existing Constrained Horn Clause (CHC) solver and have developed a framework for hardware functional equivalence checking that can leverage other available tools and techniques for invariant generation. Our experiments show that our proposed SyGuS-based technique complements or outperforms existing property-directed reachability (PDR) techniques for invariant generation on practical hardware designs, including an AES block encryption accelerator, a Gaussian-Blur image processing accelerator and the PicoRV32 processor

A Bang into nowhere: Comments on the Universe Expansion Theory

Anaplasma marginale is the most prevalent tick-borne livestock pathogen and poses a significant threat to cattle industry. In contrast to currently available live blood-derived vaccines against A. marginale, alternative safer and better-defined subunit vaccines will be of great significance. Two proteins (VirB9-1 and VirB9-2) from the Type IV secretion system of A. marginale have been shown to induce humoral and cellular immunity. In this study, Escherichia coli were used to express VirB9-1 and VirB9-2 proteins. Silica vesicles having a thin wall of 6 nm and pore size of 5.8 nm were used as the carrier and adjuvant to deliver these two antigens both as individual or mixed nano-formulations. High loading capacity was achieved for both proteins, and the mouse immunisation trial with individual as well as mixed nano-formulations showed high levels of antibody titres over 107 and strong T-cell responses. The mixed nano-formulation also stimulated high-level recall responses in bovine T-cell proliferation assays. These results open a promising path towards the development of efficient A. marginale vaccines and provide better understanding on the role of silica vesicles to deliver multivalent vaccines as mixed nano-formulations able to activate both B-cell and T-cell immunity, for improved animal health