Large Scale Verification of MPI Programs Using Lamport Clocks with Lazy Update

We propose a dynamic verification approach for large-scale message passing programs to locate correctness bugs caused by unforeseen nondeterministic interactions. This approach hinges on an efficient protocol to track the causality between nondeterministic message receive operations and potentially matching send operations. We show that causality tracking protocols that rely solely on logical clocks fail to capture all nuances of MPI program behavior, including the variety of ways in which nonblocking calls can complete. Our approach is hinged on formally defining the matches-before relation underlying the MPI standard, and devising lazy update logical clock based algorithms that can correctly discover all potential outcomes of nondeterministic receives in practice. can achieve the same coverage as a vector clock based algorithm while maintaining good scalability. LLCP allows us to analyze realistic MPI programs involving a thousand MPI processes, incurring only modest overheads in terms of communication bandwidth, latency, and memory consumption. © 2011 IEEE.

Prediction and Verification of miRNA Expression in Human and Rat Retinas.

PURPOSE: MicroRNAs (miRNAs) play a global role in regulating gene expression and have important tissue-specific functions. Little is known about their role in the retina. The purpose of this study was to establish the retinal expression of those miRNAs predicted to target genes involved in vision. METHODS: miRNAs potentially targeting important "retinal" genes, as defined by expression pattern and implication in disease, were predicted using a published algorithm (TargetScan; Envisioneering Medical Technologies, St. Louis, MO). The presence of candidate miRNAs in human and rat retinal RNA was assessed by RT-PCR. cDNA levels for each miRNA were determined by quantitative PCR. The ability to discriminate between miRNAs varying by a single nucleotide was assessed. The activity of miR-124 and miR-29 against predicted target sites in Rdh10 and Impdh1 was tested by cotransfection of miRNA mimics and luciferase reporter plasmids. RESULTS: Sixty-seven miRNAs were predicted to target one or more of the 320 retinal genes listed herein. All 11 candidate miRNAs tested were expressed in the retina, including miR-7, miR-124, miR135a, and miR135b. Relative levels of individual miRNAs were similar between rats and humans. The Rdh10 3'UTR, which contains a predicted miR-124 target site, mediated the inhibition of luciferase activity by miR-124 mimics in cell culture. CONCLUSIONS: Many miRNAs likely to regulate genes important for retinal function are present in the retina. Conservation of miRNA retinal expression patterns from rats to humans supports evidence from other tissues that disruption of miRNAs is a likely cause of a range of visual abnormalities.

Cytotoxic alkaloids motuporamines A-C: Synthesis and structural verification

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Bimodal biometric verification based on face and lips

In this paper, we present a novel approach to person verification by fusing face and lip features. Specifically, the face is modeled by the discriminative common vector and the discrete wavelet transform. Our lip features are simple geometric features based on a lip contour, which can be interpreted as multiple spatial widths and heights from a center of mass. In order to combine these features, we consider two simple fusion strategies: data fusion before training and score fusion after training, working with two different face databases. Fusing them together boosts the performance to achieve an equal error rate as low as 0.4% and 0.28%, respectively, confirming that our approach of fusing lips and face is effective and promising.

Computational Verification of Two Universal Relations for Simple Ionic Liquids. Kinetic Properties of a Model 2:1 Molten Salt

Two semianalytical relations [Nature, 1996, 381, 137 and Phys. Rev. Lett. 2001, 87, 245901] predicting dynamical coefficients of simple liquids on the basis of structural properties have been tested by extensive molecular dynamics simulations for an idealized 2:1 model molten salt. In agreement with previous simulation studies, our results support the validity of the relation expressing the self-diffusion coefficient as a Function of the radial distribution functions for all thermodynamic conditions such that the system is in the ionic (ie., fully dissociated) liquid state. Deviations are apparent for high-density samples in the amorphous state and in the low-density, low-temperature range, when ions condense into AB(2) molecules. A similar relation predicting the ionic conductivity is only partially validated by our data. The simulation results, covering 210 distinct thermodynamic states, represent an extended database to tune and validate semianalytical theories of dynamical properties and provide a baseline for the interpretation of properties of more complex systems such as the room-temperature ionic liquids.

Reasoning about orchestrations of web services using partial correctness

A service is a remote computational facility which is made available for general use by means of a wide-area network. Several types of service arise in practice: stateless services, shared state services and services with states which are customised for individual users. A service-based orchestration is a multi-threaded computation which invokes remote services in order to deliver results back to a user (publication). In this paper a means of specifying services and reasoning about the correctness of orchestrations over stateless services is presented. As web services are potentially unreliable the termination of even finite orchestrations cannot be guaranteed. For this reason a partial-correctness powerdomain approach is proposed to capture the semantics of recursive orchestrations.

Verification of McCabe's Delta L Law for Growth of Lysozyme Crystals by Hanging Drop Method

Lysozyme is a naturally occurring enzyme in egg white and has high commercial importance due to its antimicrobial properties. The main objective of this work was to study the growth rate of lysozyme crystals isolated from egg for the first 72 hours and verify the results with McCabe’s constant crystal growth theory. Hanging drop crystallization method was used to form high purity lysozyme crystals from the embryonic stage. To this end, this work differs from an earlier work of Forsythe et al., who used seed crystals in the size range of 10 µm - 40 µm for face growth measurements at different pH values. The maximum crystal size recorded in the present work was 392.86 µm, which is within the typical size range of 50 µm - 500 µm for which constant crystal growth is expected to hold according to McCabe’s ?L law. Electron micrographs (SEM) revealed the structure and dimensions of the crystals while SDS-Page was used to measure the purity of the crystals. The SEM results showed that that lysozyme growth rate was linear and agreed with McCabe’s constant growth theory, producing a growth rate of 1.77 x 10-3 µm .s-1

Preparation of planar retinal specimens:verification by histology, mRNA profiling, and proteome analysis

Elucidation of the transcriptome and proteome of the normal retina will be difficult since it is comprised of at least 55 different cell types. However the characteristic layered cellular anatomy of the retina makes it amenable to planar sectioning, enabling the generation of enriched retinal cell populations. The aim of this study was to validate a reproducible method for preparing enriched retinal layers from porcine retina.