On the design of high-performance algorithms for aligning multiple protein sequences on mesh-based multiprocessor architectures

In this paper, we address the problem of multiple sequence alignment (MSA) for handling very large number of proteins sequences on mesh-based multiprocessor architectures. As the problem has been conclusively shown to be computationally complex, we employ divisible load paradigm (also, referred to as divisible load theory, DLT) to handle such large number of sequences. We design an efficient computational engine that is capable of conducting MSAs by exploiting the underlying parallelism embedded in the computational steps of multiple sequence algorithms. Specifically, we consider the standard Smith–Waterman (SW) algorithm in our implementation, however, our approach is by no means restrictive to SW class of algorithms alone. The treatment used in this paper is generic to a class of similar dynamic programming problems. Our approach is recursive in the sense that the quality of solutions can be refined continuously till an acceptable level of quality is achieved. After first phase of computation, we design a heuristic scheme that renders the final solution for MSA. We conduct rigorous simulation experiments using several hundreds of homologous protein sequences derived from the Rattus Norvegicus and Mus Musculus databases of olfactory receptors. We quantify the performance based on speed-up metric. We compare our algorithms to serial or single machine processing approaches. We testify our findings by comparing with conventional equal load partitioning (ELP) strategy that is commonly used in the parallel processing literature. Based on our extensive simulation study, we observe that DLT paradigm offers an excellent speed-up characteristics and provides avenues for its use in several other biological sequence processing related problem. This study is a first time attempt in using the DLT paradigm to devise efficient strategies to handle large scale multiple protein sequence alignment problem on mesh-based multiprocessor systems.     

Cognitive load in hypertext reading: A review

A process model of hypertext reading was used to generate predictions about the effects of hypertext features on cognitive processing during text navigation and comprehension. We evaluated the predictions of the model with respect to the extant literature, focusing on studies in which versions of hypertexts were compared. Consistent with our predictions, the increased demands of decision-making and visual processing in hypertext impaired reading performance. Individual differences in readers, such as working memory capacity and prior knowledge, mediated the impact of hypertext features. For example, readers with low working memory and low prior knowledge were usually disadvantaged in hypertext. Some benefits were observed for learners with low prior knowledge, however, if the hypertext structure was hierarchical and consistent with that of the knowledge domain. We also surveyed the effectiveness of structural features designed to reduce cognitive load, including graphical overviews, restricted access to links, and visible link types. Complex graphical overviews did not reliably enable learning and navigation, whereas navigational support from restricted access and visible link types were helpful. We identified gaps in the empirical literature and suggested future studies to investigate cognitive processes in hypertext reading.     

Movement abnormalities and the progression of prodromal symptomatology in adolescents at risk for psychotic disorders.

The link between movement abnormalities and psychotic disorders is presumed to reflect common neural mechanisms that influence both motor functions and vulnerability to psychosis. The prodromal period leading to psychotic disorders represents both a viable point for intervention and a developmental period that, if studied, could shed light on etiology; however, no published studies have examined the temporal progression of this link. A group with high levels of prodromal symptomatology (i.e., adolescents with schizotypal personality disorder [SPD]; n = 42) and both psychiatric controls (with other personality disorders or conduct disorder [OD]; n = 30) and nonpsychiatric controls ([NC]; n = 49) were recruited. Videotapes of structured psychiatric interviews were coded for movement abnormalities by raters blind to participants' diagnostic status, and follow-up assessments were conducted 1 year later. Controlling for psychotropic medications, the authors found that adolescents with SPD exhibited significantly more motor abnormalities in the face and upper body than did OD and NC controls. At baseline, movement abnormalities were positively correlated with the severity of positive, negative, and total prodromal symptoms. Within the SPD group, baseline movement abnormalities predicted symptom severity 1 year later. Movement abnormalities represent an early risk indicator that may be predictive of later symptom severity and potentially of psychosis onset. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Minimizing test-point allocation to improve diagnosability in business process models

Diagnosability analysis aims to determine whether observations available during the execution of a system are sufficient to precisely locate the source of a problem. Previous work deals with the diagnosability problem in contexts such as circuits and systems, but no with the adaptation of the diagnosability problem to business processes. In order to improve the diagnosability, a set of test points needs to be allocated. Therefore, the aim of this contribution is to determine a test-point allocation to obtain sufficient observable data in the dataflow to allow the discrimination of faults for a later diagnosis process. The allocation of test points depends on the strategies of the companies, for this reason we defined two possibilities: to improve the diagnosability of a business process for a fixed number of test points and the minimization of the number of test points for a given level of diagnosability. Both strategies have been implemented in the Test-Point Allocator tool in order to facilitate the integration of the test points in the business process model life cycle. Experimental results indicate that diagnosability of business processes can be improved by allocating test points in an acceptable time.     

热处理对4Cr5MoSiVl钢热疲劳裂纹扩展驱动力的影响

利用自制的高频感应加热、吹风冷却式试验机,对4Cr5MoSiVl钢缺口板状试样进行了Coffin型热疲劳试验。记录了热循环次数、热疲劳裂纹长度、试样中热应力变化之间的关系。分析了热循环过程中试样中应力的变化及热处理的影响。结果表明:热疲劳裂纹扩展驱动力为循环下限温度时的拉应力,驱动力的产生起源于循环上限温度时的压缩塑性应变,主要受钢的组织循环稳定性和钢的高温屈服强度所控制。4Cr5MoSiV1钢淬火后,经较高温度回火,使组织较为稳定时,可以得到较低的热疲劳裂纹扩展驱动力,从而具有较低的裂纹扩展速度。     

A unified and flexible solution for integrating CRL and OCSP into PKI applications

Public key certificates (PKCs) are used nowadays in several security protocols and applications, so as to secure data exchange via transport layer security channels, or to protect data at the application level by means of digital signatures. However, many security applications often fail to manage properly the PKCs, in particular when checking their validity status. These failures are partly due to the lack of experience (or training) of the users who configure these applications or protocols, and partly due to the scarce support offered by some common cryptographic libraries to the application developers. This paper describes the design and implementation of a light middleware dealing with certificate validation in a unified way. Our middleware exploits on one side the libraries that have already been defined or implemented for certificate validation, and it constructs a thin layer, which provides flexibility and security features to the upper layer applications. In our current approach, this layer boasts an integrated approach to support various certificate revocation mechanisms, it protects the applications from some common security attacks, and offers several configuration and performance options to the programmers and to the end users. We describe the architecture of this approach as well as its practical implementation in the form of a library based on the famous OpenSSL security library, and that can be easily integrated with other certificate‐aware security applications. Copyright © 2009 John Wiley & Sons, Ltd.     

Therapeutic Effects of hiPSC-Derived Glial and Neuronal Progenitor Cells-Conditioned Medium in Experimental Ischemic Stroke in Rats

Transplantation of various types of stem cells as a possible therapy for stroke has been tested for years, and the results are promising. Recent investigations have shown that the administration of the conditioned media obtained after stem cell cultivation can also be effective in the therapy of the central nervous system pathology (hypothesis of their paracrine action). The aim of this study was to evaluate the therapeutic effects of the conditioned medium of hiPSC-derived glial and neuronal progenitor cells in the rat middle cerebral artery occlusion model of the ischemic stroke. Secretory activity of the cultured neuronal and glial progenitor cells was evaluated by proteomic and immunosorbent-based approaches. Therapeutic effects were assessed by overall survival, neurologic deficit and infarct volume dynamics, as well as by the end-point values of the apoptosis- and inflammation-related gene expression levels, the extent of microglia/macrophage infiltration and the numbers of formed blood vessels in the affected area of the brain. As a result, 31% of the protein species discovered in glial progenitor cells-conditioned medium and 45% in neuronal progenitor cells-conditioned medium were cell type specific. The glial progenitor cell-conditioned media showed a higher content of neurotrophins (BDNF, GDNF, CNTF and NGF). We showed that intra-arterial administration of glial progenitor cells-conditioned medium promoted a faster decrease in neurological deficit compared to the control group, reduced microglia/macrophage infiltration, reduced expression of pro-apoptotic gene Bax and pro-inflammatory cytokine gene Tnf, increased expression of anti-inflammatory cytokine genes (Il4, Il10, Il13) and promoted the formation of blood vessels within the damaged area. None of these effects were exerted by the neuronal progenitor cell-conditioned media. The results indicate pronounced cytoprotective, anti-inflammatory and angiogenic properties of soluble factors secreted by glial progenitor cells.     

Evaluation and enhancement of COBRA-TF efficiency for LWR calculations

Detailed representations of the reactor core generate computational meshes with a high number of cells where the fluid dynamics equations must be solved. An exhaustive analysis of the CPU times needed by the thermal-hydraulic subchannel code COBRA-TF for different stages in the solution process has revealed that the solution of the linear system of pressure equations is the most time consuming process. To improve code efficiency two optimized matrix solvers, Super LU library and Krylov non-stationary iterative methods have been implemented in the code and their performance has been tested using a suite of five test cases. The results of performed comparative analyses have demonstrated that for large cases, the implementation of the Bi-Conjugate Gradient Stabilized (Bi-CGSTAB) Krylov method combined with the incomplete LU factorization with dual truncation strategy (ILUT) pre-conditioner reduced the time used by the code for the solution of the pressure matrix by a factor of 20. Both new solvers converge smoothly regardless of the nature of simulated cases and the mesh structures and improve the stability and accuracy of results compared to the classic Gauss–Seidel iterative method. The obtained results indicate that the direct inversion method is the best option for small cases.     

Whispering gallery modes in photoluminescence and Raman spectra of a spherical microcavity with CdTe quantum dots: anti-Stokes emission and interference effects

We have studied the photoluminescence and Raman spectra of a system consisting of a polystyrene latex microsphere coated by CdTe colloidal quantum dots. The cavity-induced enhancement of the Raman scattering allows the observation of Raman spectra from only a monolayer of CdTe quantum dots. Periodic structure with very narrow peaks in the photoluminescence spectra of a single microsphere was detected both in the Stokes and anti-Stokes spectral regions, arising from the coupling between the emission of quantum dots and spherical cavity modes.     

Magnetic response of soils and vegetation to heavy metal pollution--a case study

Fast and cost-effective detection of industrial pollution can significantly promote its ecological, economic, and social assessment. A magnetometric method, used for qualitative determination of anthropogenic contamination, meets these requirements but needs further development in more quantitative terms. It could be used successfully in numerous cases when the heavy metals coexist with strongly magnetic iron oxide particles in the source dust. We present an integrated magnetic and geochemical study that examines the utility of magnetometric techniques for rapid, qualitative detection of metallic pollutants in soils and vegetation. The new aspect of our approach, in comparison with previously published articles on this subject, is the combined investigation (magnetic and geochemical) of both soils and vegetation, thus using an additional medium for employing the magnetometry as a pollution proxy at a site. The study area is a small (approximately 3 km2) region in the suburbs of Sofia (Bulgaria), with the main pollution source being a metallurgical factory. Soil samples have been taken from the topmost 20 cm from private gardens, located at different distances from the factory. Vegetation samples were taken from ryegrass (both leaves and roots) and leaves from two kinds of deciduous trees (maple and acacia). The results show that both vegetation and soils are characterized by enhanced magnetic properties, compared to background material, which is due to the presence of magnetite particles of anthropogenic origin accompanying heavy metal emissions. SEM images and microprobe analyses reveal the presence of a significant amount of particles, containing heavy metals (including iron) in vegetation samples taken close to the main pollution source. Correlation analyses show a statistically significant link (correlation coefficients ranging from 0.6 to 0.7) between magnetic susceptibility and the main heavy metals (Cu, Zn, Pb) in soil samples, indicating that the magnetic susceptibility can provide a proxy method for identifying the relative contribution of industrial pollution in soils and vegetation, that is reliable, inexpensive, and less time-consuming than standard chemical analyses.