Z2SAL: a translation-based model checker for Z

Despite being widely known and accepted in industry, the Z formal specification language has not so far been well supported by automated verification tools, mostly because of the challenges in handling the abstraction of the language. In this paper we discuss a novel approach to building a model-checker for Z, which involves implementing a translation from Z into SAL, the input language for the Symbolic Analysis Laboratory, a toolset which includes a number of model-checkers and a simulator. The Z2SAL translation deals with a number of important issues, including: mapping unbounded, abstract specifications into bounded, finite models amenable to a BDD-based symbolic checker; converting a non-constructive and piecemeal style of functional specification into a deterministic, automaton-based style of specification; and supporting the rich set-based vocabulary of the Z mathematical toolkit. This paper discusses progress made towards implementing as complete and faithful a translation as possible, while highlighting certain assumptions, respecting certain limitations and making use of available optimisations. The translation is illustrated throughout with examples; and a complete working example is presented, together with performance data

Gene expression profiling of oxidative stress response of C. elegans aging defective AMPK mutants using massively parallel transcriptome sequencing

<p>Abstract</p> <p>Background</p> <p>A strong association between stress resistance and longevity in multicellular organisms has been established as many mutations that extend lifespan also show increased resistance to stress. AAK-2, the <it>C. elegans </it>homolog of an alpha subunit of AMP-activated protein kinase (AMPK) is an intracellular fuel sensor that regulates cellular energy homeostasis and functions in stress resistance and lifespan extension.</p> <p>Findings</p> <p>Here, we investigated global transcriptional responses of <it>aak-2 </it>mutants to oxidative stress and in turn identified potential downstream targets of AAK-2 involved in stress resistance in <it>C. elegans</it>. We employed massively parallel Illumina sequencing technology and performed comprehensive comparative transcriptome analysis. Specifically, we compared the transcriptomes of <it>aak-2 </it>and wild type animals under normal conditions and conditions of induced oxidative stress. This research has presented a snapshot of genome-wide transcriptional activities that take place in <it>C. elegans </it>in response to oxidative stress both in the presence and absence of AAK-2.</p> <p>Conclusions</p> <p>The analysis presented in this study has enabled us to identify potential genes involved in stress resistance that may be either directly or indirectly under the control of AAK-2. Furthermore, we have extended our current knowledge of general defense responses of <it>C. elegans </it>against oxidative stress supporting the function for AAK-2 in inhibition of biosynthetic processes, especially lipid synthesis, under oxidative stress and transcriptional regulation of genes involved in reproductive processes.</p

Reactive oxygen production induced by near-infrared radiation in three strains of the Chl d-containing cyanobacterium Acaryochloris marina

Cyanobacteria in the genus Acaryochloris have largely exchanged Chl a with Chl d, enabling them to harvest near-infrared radiation (NIR) for oxygenic photosynthesis, a biochemical pathway prone to generate reactive oxygen species (ROS). In this study, ROS production under different light conditions was quantified in three Acaryochloris strains (MBIC11017, HICR111A and the novel strain CRS) using a real-time ethylene detector in conjunction with addition of 2-keto-4-thiomethylbutyric acid, a substrate that is converted to ethylene when reacting with certain types of ROS. In all strains, NIR was found to generate less ROS than visible light (VIS). More ROS was generated if strains MBIC11017 and HICR111A were adapted to NIR and then exposed to VIS, while strain CRS demonstrated the opposite behavior. To our knowledge, this is the first study of ROS generation associated with NIR-driven oxygenic photosynthesis and it suggests that Acaryochloris can avoid a considerable amount of light-induced stress by using NIR instead of VIS for its photosynthesis, adding further evolutionary arguments to their widespread appearance

Pulsar spins from an instability in the accretion shock of supernovae

Rotation-powered radio pulsars are born with inferred initial rotation periods of order 300 ms (some as short as 20 ms) in core-collapse supernovae. In the traditional picture, this fast rotation is the result of conservation of angular momentum during the collapse of a rotating stellar core. This leads to the inevitable conclusion that pulsar spin is directly correlated with the rotation of the progenitor star. So far, however, stellar theory has not been able to explain the distribution of pulsar spins, suggesting that the birth rotation is either too slow or too fast. Here we report a robust instability of the stalled accretion shock in core-collapse supernovae that is able to generate a strong rotational flow in the vicinity of the accreting proto-neutron star. Sufficient angular momentum is deposited on the proto-neutron star to generate a final spin period consistent with observations, even beginning with spherically symmetrical initial conditions. This provides a new mechanism for the generation of neutron star spin and weakens, if not breaks, the assumed correlation between the rotational periods of supernova progenitor cores and pulsar spin.Comment: To be published in Natur

High frequency diffraction of an electromagnetic plane wave by an imperfectly conducting rectangular cylinder

Copyright @ 2011 IEEEWe shall consider the the problem of determining the scattered far wave field produced when a plane E-polarized wave is incident on an imperfectly conducting rectangular cylinder. By using the the uniform asymptotic solution for the problem of the diffraction of a plane wave by a right-angled impedance wedge, in conjunction with Keller's method, the a high frequency far field solution to the problem is given

Categorizing facial expressions : a comparison of computational models

The original publication is available at www.springerlink.com Copyright SpringerRecognizing expressions is a key part of human social interaction, and processing of facial expression information is largely automatic for humans, but it is a non-trivial task for a computational system. The purpose of this work is to develop computational models capable of differentiating between a range of human facial expressions. Raw face images are examples of high-dimensional data, so here we use two dimensionality reduction techniques: principal component analysis and curvilinear component analysis. We also preprocess the images with a bank of Gabor filters, so that important features in the face images may be identified. Subsequently, the faces are classified using a support vector machine. We show that it is possible to differentiate faces with a prototypical expression from the neutral expression. Moreover, we can achieve this with data that has been massively reduced in size: in the best case the original images are reduced to just 5 components. We also investigate the effect size on face images, a concept which has not been reported previously on faces. This enables us to identify those areas of the face that are involved in the production of a facial expression.Peer reviewe

Comparison of patients undergoing switching versus augmentation of antipsychotic medications during treatment for schizophrenia

It is often difficult to determine whether a patient may best benefit by augmenting their current medication or switching them to another. This post-hoc analysis compares patients’ clinical and functional profiles at the time their antipsychotic medications were either switched or augmented. Adult outpatients receiving oral antipsychotic treatment for schizophrenia were assessed during a 12-month international observational study. Clinical and functional measures were assessed at the time of first treatment switch/augmentation (0–14 days prior) and compared between Switched and Augmented patient groups. Due to low numbers of patients providing such data, interpretations are based on effect sizes. Data at the time of change were available for 87 patients: 53 Switched and 34 Augmented. Inadequate response was the primary reason for treatment change in both groups, whereas lack of adherence was more prevalent in the Switched group (26.4% vs 8.8%). Changes in clinical severity from study initiation to medication change were similar, as indicated by Clinical Global Impressions–Severity scores. However, physical and mental component scores of the 12-item Short-Form Health Survey improved in the Augmented group, but worsened in the Switched group. These findings suggest that the patient’s worsening or lack of meaningful improvement prompts clinicians to switch antipsychotic medications, whereas when patients show some improvement, clinicians may be more likely to try bolstering the improvements through augmentation. Current findings are consistent with physicians’ stated reasons for switching versus augmenting antipsychotics in the treatment of schizophrenia. Confirmation of these findings requires further research

Superficial simplicity of the 2010 El Mayor–Cucapah earthquake of Baja California in Mexico

The geometry of faults is usually thought to be more complicated at the surface than at depth and to control the initiation, propagation and arrest of seismic ruptures. The fault system that runs from southern California into Mexico is a simple strike-slip boundary: the west side of California and Mexico moves northwards with respect to the east. However, the M_w 7.2 2010 El Mayor–Cucapah earthquake on this fault system produced a pattern of seismic waves that indicates a far more complex source than slip on a planar strike-slip fault. Here we use geodetic, remote-sensing and seismological data to reconstruct the fault geometry and history of slip during this earthquake. We find that the earthquake produced a straight 120-km-long fault trace that cut through the Cucapah mountain range and across the Colorado River delta. However, at depth, the fault is made up of two different segments connected by a small extensional fault. Both segments strike N130° E, but dip in opposite directions. The earthquake was initiated on the connecting extensional fault and 15 s later ruptured the two main segments with dominantly strike-slip motion. We show that complexities in the fault geometry at depth explain well the complex pattern of radiated seismic waves. We conclude that the location and detailed characteristics of the earthquake could not have been anticipated on the basis of observations of surface geology alone