Separation of Test-Free Propositional Dynamic Logics over Context-Free Languages

For a class L of languages let PDL[L] be an extension of Propositional Dynamic Logic which allows programs to be in a language of L rather than just to be regular. If L contains a non-regular language, PDL[L] can express non-regular properties, in contrast to pure PDL. For regular, visibly pushdown and deterministic context-free languages, the separation of the respective PDLs can be proven by automata-theoretic techniques. However, these techniques introduce non-determinism on the automata side. As non-determinism is also the difference between DCFL and CFL, these techniques seem to be inappropriate to separate PDL[DCFL] from PDL[CFL]. Nevertheless, this separation is shown but for programs without test operators.Comment: In Proceedings GandALF 2011, arXiv:1106.081

Recovery From Monocular Deprivation Using Binocular Deprivation: Experimental Observations and Theoretical Analysis

Ocular dominance (OD) plasticity is a robust paradigm for examining the functional consequences of synaptic plasticity. Previous experimental and theoretical results have shown that OD plasticity can be accounted for by known synaptic plasticity mechanisms, using the assumption that deprivation by lid suture eliminates spatial structure in the deprived channel. Here we show that in the mouse, recovery from monocular lid suture can be obtained by subsequent binocular lid suture but not by dark rearing. This poses a significant challenge to previous theoretical results. We therefore performed simulations with a natural input environment appropriate for mouse visual cortex. In contrast to previous work we assume that lid suture causes degradation but not elimination of spatial structure, whereas dark rearing produces elimination of spatial structure. We present experimental evidence that supports this assumption, measuring responses through sutured lids in the mouse. The change in assumptions about the input environment is sufficient to account for new experimental observations, while still accounting for previous experimental results

Molecular Model of Dynamic Social Network Based on E-mail communication

In this work we consider an application of physically inspired sociodynamical model to the modelling of the evolution of email-based social network. Contrary to the standard approach of sociodynamics, which assumes expressing of system dynamics with heuristically defined simple rules, we postulate the inference of these rules from the real data and their application within a dynamic molecular model. We present how to embed the n-dimensional social space in Euclidean one. Then, inspired by the Lennard-Jones potential, we define a data-driven social potential function and apply the resultant force to a real e-mail communication network in a course of a molecular simulation, with network nodes taking on the role of interacting particles. We discuss all steps of the modelling process, from data preparation, through embedding and the molecular simulation itself, to transformation from the embedding space back to a graph structure. The conclusions, drawn from examining the resultant networks in stable, minimum-energy states, emphasize the role of the embedding process projecting the non–metric social graph into the Euclidean space, the significance of the unavoidable loss of information connected with this procedure and the resultant preservation of global rather than local properties of the initial network. We also argue applicability of our method to some classes of problems, while also signalling the areas which require further research in order to expand this applicability domain

Display of a Maize cDNA library on baculovirus infected insect cells

<p>Abstract</p> <p>Background</p> <p>Maize is a good model system for cereal crop genetics and development because of its rich genetic heritage and well-characterized morphology. The sequencing of its genome is well advanced, and new technologies for efficient proteomic analysis are needed. Baculovirus expression systems have been used for the last twenty years to express in insect cells a wide variety of eukaryotic proteins that require complex folding or extensive posttranslational modification. More recently, baculovirus display technologies based on the expression of foreign sequences on the surface of <it>Autographa californica </it>(AcMNPV) have been developed. We investigated the potential of a display methodology for a cDNA library of maize young seedlings.</p> <p>Results</p> <p>We constructed a full-length cDNA library of young maize etiolated seedlings in the transfer vector pAcTMVSVG. The library contained a total of 2.5 × 10⁵independent clones. Expression of two known maize proteins, calreticulin and auxin binding protein (ABP1), was shown by western blot analysis of protein extracts from insect cells infected with the cDNA library. Display of the two proteins in infected insect cells was shown by selective biopanning using magnetic cell sorting and demonstrated proof of concept that the baculovirus maize cDNA display library could be used to identify and isolate proteins.</p> <p>Conclusion</p> <p>The maize cDNA library constructed in this study relies on the novel technology of baculovirus display and is unique in currently published cDNA libraries.</p> <p>Produced to demonstrate proof of principle, it opens the way for the development of a eukaryotic <it>in vivo </it>display tool which would be ideally suited for rapid screening of the maize proteome for binding partners, such as proteins involved in hormone regulation or defence.</p

Synthesizing SystemC Code from Delay Hybrid CSP

Delay is omnipresent in modern control systems, which can prompt oscillations and may cause deterioration of control performance, invalidate both stability and safety properties. This implies that safety or stability certificates obtained on idealized, delay-free models of systems prone to delayed coupling may be erratic, and further the incorrectness of the executable code generated from these models. However, automated methods for system verification and code generation that ought to address models of system dynamics reflecting delays have not been paid enough attention yet in the computer science community. In our previous work, on one hand, we investigated the verification of delay dynamical and hybrid systems; on the other hand, we also addressed how to synthesize SystemC code from a verified hybrid system modelled by Hybrid CSP (HCSP) without delay. In this paper, we give a first attempt to synthesize SystemC code from a verified delay hybrid system modelled by Delay HCSP (dHCSP), which is an extension of HCSP by replacing ordinary differential equations (ODEs) with delay differential equations (DDEs). We implement a tool to support the automatic translation from dHCSP to SystemC

Back to the "Gold Standard": How Precise is Hematocrit Detection Today?

Introduction: The commonly used method for hematocrit detection, by visual examination of microcapillary tube, known as "micro-HCT", is subjective but remains one of the key sources for fast hematocrit evaluation. Analytical automation techniques have increased the standardization of RBC index detection; however, indirect hematocrit measurements by blood analyzer, the automated HCT, do not correlate well with "micro-HCT" results in patients with hematological pathologies. We aimed to overcome those disadvantages in "micro-HCT" analysis using "ImageJ" processing software. Methods: 223 blood samples from the "general population" and 19 from sickle cell disease patients were examined in parallel for hematocrit values using the automated HCT, standard "micro-HCT," and "ImageJ" micro-HCT methods. Results: For the "general population" samples, the "ImageJ" values were significantly higher than the corresponding values evaluated by standard "micro-HCT" and automated HCT, except for the 0 to 2 month old newborns, in which the automated HCT results were similar to the "ImageJ" evaluated HCT. Similar to the "general population" cohort, we found significantly higher values measured by "ImageJ" compared to either "micro-HCT" or the automated HCT in SCD patients. Correspondent differences for the MCV and MCHC were also found. Discussion: This study introduces the "micro-HCT" assessment technique using the image-analysis module of "ImageJ" software. This procedure allows overcoming most of the data errors associated with the standard "micro-HCT" evaluation and can replace the use of complicated and expensive automated equipment. The presented results may also be used to develop new standards for calculating hematocrit and associated parameters for routine clinical practice. Keywords: Image analysis; Microcapillary hematocrit; RBC indices

A Distributed Multilevel Force-directed Algorithm

The wide availability of powerful and inexpensive cloud computing services naturally motivates the study of distributed graph layout algorithms, able to scale to very large graphs. Nowadays, to process Big Data, companies are increasingly relying on PaaS infrastructures rather than buying and maintaining complex and expensive hardware. So far, only a few examples of basic force-directed algorithms that work in a distributed environment have been described. Instead, the design of a distributed multilevel force-directed algorithm is a much more challenging task, not yet addressed. We present the first multilevel force-directed algorithm based on a distributed vertex-centric paradigm, and its implementation on Giraph, a popular platform for distributed graph algorithms. Experiments show the effectiveness and the scalability of the approach. Using an inexpensive cloud computing service of Amazon, we draw graphs with ten million edges in about 60 minutes.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016