Verification of Similar FSMs by Mixing Incremental Re-encoding, Reachability Analysis, and Combinational Checks

State space exploration is often used to prove properties about sequential behavior of Finite State Machines (FSMs). For example, equivalence of two machines is proved by analyzing the reachable state set of their product machine. Nevertheless, reachability analysis is infeasible on large practical examples. Combinational verification is far less expensive, but on the other hand its application is limited to combinational circuits, or particular design schemes. Finally, approximate techniques imply sufficient, not strictly necessary conditions.The purpose of this paper is to extend the applicability of purely combinational checks. This is generally achieved through state minimization, partitioning, and re-encoding the FSMs to factor out their differences. We focus on re-encoding. In particular, we present an incremental approach to re-encoding for verification that transforms the product machine traversal into a combinational verification in the best case, and into a computationally simpler product machine traversal in the general case.Experimental results demonstrate the effectiveness of this technique on medium-large circuits where other techniques may fail.     

The material basis for reduced mechanical properties in oim mice bones

Osteogenesis imperfecta (OI), a heritable disease caused by molecular defects in type I collagen, is characterized by skeletal deformities and brittle bones. The heterozygous and homozygous oim mice (oim/+ and oim/oim) exhibit mild and severe OI phenotypes, respectively, serving as controlled animal models of this disease. In the current study, bone geometry, mechanics, and material properties of 1-year-old mice were evaluated to determine factors that influence the severity of phenotype in OI. The oim/oim mice exhibited significantly smaller body size, femur length, and moment of area compared with oim/+ and wild-type (+/+) controls. The oim/oim femur mechanical properties of failure torque and stiffness were 40% and 30%, respectively, of the +/+ values, and 53% and 36% of the oim/+ values. Collagen content was reduced by 20% in the oim/oim compared with +/+ bone and tended to be intermediate to these values for the oim/+. Mineral content was not significantly different between the oim/oim and +/+ bones. However, the oim/oim ash content was significantly reduced compared with that of the oim/+. Mineral carbonate content was reduced by 23% in the oim/oim bone compared with controls. Mineral crystallinity was reduced in the oim/oim and oim/+ bone compared with controls. Overall, for the majority of parameters examined (geometrical, mechanical, and material), the oim/+ values were intermediate to those of the oim/oim and +/+, a finding that parallels the phenotypes of the mice. This provides evidence that specific material properties, such as mineral crystallinity and collagen content, are indicative and possibly predictive of bone fragility in this mouse model, and by analogy in human OI.     

Compositionally Progressive Solutions of Synchronous FSM Equations

The paper addresses the problem of designing a component that combined with a known part of a system, called the context FSM, is a reduction of a given specification FSM. We study compositionally progressive solutions of synchronous FSM equations. Such solutions, when combined with the context, do not block any input that may occur in the specification, so they are of practical use. We show that, if a synchronous FSM equation has a compositionally progressive solution, then there is a largest regular compositionally progressive solution including all of them. We provide two different algorithms to compute a largest regular compositionally progressive solution: one deletes all compositionally non-progressive strings from a largest solution, the other splits states of a largest solution and then removes those inducing a non-progressive composition.

Specification, synthesis, and verification of hazard-free asynchronous circuits

This article describes three aspects of asynchronous design from a Petri-net specification called asignal transition graph (STG). First, we show that the STG defined by Chu [1] is too restrictive for specifying general asynchronous behavior and propose extensions to the STG which allow for more general and compact representation. Second, we show that syntactic constraints on STGs are not sufficient to guarantee hazard-free implementations under the unbounded gate delay model, and present techniques to synthesize two-level implementations which are hazard-free under the multiple signal change condition. To remove all hazards under the multiple signal change condition, the initial specification may need to be modified. Finally, we show that behavior containment test using the event coordination model [2] is a powerful tool for the formal verification of asynchronous circuits. This verification method can provide sanity checks for all synthesis methods that use the unbounded gate delay model, and provides a mechanism for designers to validate some manual gate-level changes to the final design.     

Partial-Order Reduction in Symbolic State-Space Exploration

State-space explosion is a fundamental obstacle in the formal verification of designs and protocols. Several techniques for combating this problem have emerged in the past few years, among which two are significant: partial-order reduction and symbolic state-space search. In asynchronous systems, interleavings of independent concurrent events are equivalent, and only a representative interleaving needs to be explored to verify local properties. Partial-order methods exploit this redundancy and visit only a subset of the reachable states. Symbolic techniques, on the other hand, capture the transition relation of a system and the set of reachable states as boolean functions. In many cases, these functions can be represented compactly using binary decision diagrams (BDDs). Traditionally, the two techniques have been practiced by two different schools—partial-order methods with enumerative depth-first search for the analysis of asynchronous network protocols, and symbolic breadth-first search for the analysis of synchronous hardware designs. We combine both approaches and develop a method for using partial-order reduction techniques in symbolic BDD-based invariant checking. We present theoretical results to prove the correctness of the method, and experimental results to demonstrate its efficacy.     

Iron Reduction in Dermacentor andersoni Tick Cells Inhibits Anaplasma marginale Replication

Anaplasma spp. are obligate intracellular, tick-borne, bacterial pathogens that cause bovine and human anaplasmosis. We lack tools to prevent these diseases in part due to major knowledge gaps in our fundamental understanding of the tick–pathogen interface, including the requirement for and molecules involved in iron transport during tick colonization. We determine that iron is required for the pathogen Anaplasma marginale, which causes bovine anaplasmosis, to replicate in Dermacentor andersoni tick cells. Using bioinformatics and protein modeling, we identified three orthologs of the Gram-negative siderophore-independent iron uptake system, FbpABC. Am069, the A. marginale ortholog of FbpA, lacks predicted iron-binding residues according to the NCBI conserved domain database. However, according to protein modeling, the best structural orthologs of Am069 are iron transport proteins from Cyanobacteria and Campylobacter jejuni. We then determined that all three A. marginale genes are modestly differentially expressed in response to altered host cell iron levels, despite the lack of a Ferric uptake regulator or operon structure. This work is foundational for building a mechanistic understanding of iron uptake, which could lead to interventions to prevent bovine and human anaplasmosis.     

Influence of adhesion molecule expression by human brain microvessel endothelium on cancer cell adhesion

Cultures of endothelial (En) cells derived from human brain microvessels were established in order to characterize adhesion molecule expression and to assay the adhesion properties of neoplastic cell lines to monolayers of En cells. Low constitutive expression of beta1 integrin (CD29), and ICAM-2 (CD102) was detected on human brain microvessel En cells. The beta1 chain of the VLA integrin family, ICAM-1, E-selectin (CD62E) and VCAM-1 (CD106) but not ICAM-2 and PECAM-1 (CD31) expression was upregulated by IL1-alpha, and TNF-alpha proinflammatory cytokines. High expression of PECAM-1 was found on non-activated human brain EN cells. In order to study the potential role of adhesion molecules in neoplastic cell adhesion two tumor cell lines were chosen. Adhesion of a cell line (DU145) derived from a cerebral metastasis of prostate carcinoma to human brain microvessel En cell monolayers was less pronounced compared to adhesion of a primary prostate carcinoma cell line (ND1). Adhesion of cerebral metastatic neoplastic cell line (DU145) was not significantly influenced by incubation of endothelial cells with different proinflammatory cytokines. The adhesion capability of primary prostate carcinoma line (NDI) was significantly upregulated by TNF-alpha proinflammatory cytokine. Furthermore, the adhesion of ND1 was partly inhibited using anti-E-selectin and VCAM-1 monoclonal antibodies. There was no significant effect of anti-adhesion antibodies on the adhesion characteristics of the cerebral metastatic (DU145) cell line. Our data demonstrate that different mechanisms are involved in the adhesion of neoplastic cells to cerebral En cells and turn our attention to the importance of adhesion molecule expression in the formation of metastases.     

An environment for formal verification based on symbolic computations

We present an environment for formally verifying hardware, based on symbolic computations. This includes a new concurrency model, called the combinational/sequential or C/S concurrency model which has close ties to hardware. We allow fairness constraints and describe methods for specifying them and for formally verifying in their presence. Properties are specified by either CTL formulae or edge-Rabin automata. We give algorithms, in the presence of fairness constraints, for model checking CTL or for checking that the language of our system is contained in the language of a property automation. Finally, techniques are given for hierarchical verification and for detecting errors quickly (early failure detection).     

Formula-Dependent Equivalence for Compositional CTL Model Checking

We present a polytime computable state equivalence that is defined with respect to a given CTL formula. Since it does not attempt to preserve all CTL formulas, like bisimulation does, we can expect to compute coarser equivalences. This equivalence can be used to reduce the complexity of model checking a system of interacting FSMs. Additionally, we show that in some cases our techniques can detect if a formula passes or fails, without forming the entire product machine. The method is exact and fully automatic, and handles full CTL.