The impact of CCT on driving safety in the normal and accident situation: A VR-based experimental study

Correlated color temperature (CCT) of the light source inside the road tunnel plays a crucial role in ensuring driving safety, which is demonstrated by previous studies that CCT influences not only visual effects but also non-visual effects. Although conventional laboratory experiments could simulate the CCT environment inside the tunnel to some extent, they fail to restore driving experience, let alone simulate driving behavior in the accident situation. It has largely remained unclear whether and how CCT would influence visual/non-visual performance of the subjects who are performing driving tasks, especially in the accident situation. Motivated by this gap, a virtual-reality-based framework for assessing the influence of CCT on the visual and non/visual performance in normal driving situation and in accident situation was proposed. In this study, tunnel models under seven different CCTs were created and a rear-end accident was designed in the tunnel. By integrating analog driving equipment, all participants were required to perform virtual driving tasks both in the normal situation and in the accident situation. The non-visual performance (driving fatigue) and the visual performance (reaction time) of the participants were collected and analyzed. Results show that the CCT of light source inside the tunnel was significant on the driving fatigue of the driver who was performing driving task, and it also had a significant impact on the visual performance when the driver was faced with a rear-end accident. Detailed experimental methodology, behavioral explanations underlying these findings, validity of results and practical implications are also discussed in the paper.     

Structural and dynamic insights into the C-terminal extension of cysteine proteinase B from Leishmania amazonensis

Cysteine proteinase B (CPB) is a significant virulence factor for Leishmania infections. Upon processing from its zymogen form, it happens a release of the immunomodulatory CPB C-terminal extension (cyspep) into the cytoplasm of the macrophage. Epitopes derived from this fragment were shown to influence the proportion of lymphocytes CD8+ upon infection, favoring the parasite escaping from the host́s immune system. At present, there is no available structural data of cyspep, which impairs a proper understanding of its biological functions. Here, we attempted to build molecular models for this fragment and subsequently evaluate their stabilities in aqueous solution from molecular dynamics simulations analysis. Characterization of our models obtained with distinct techniques (comparative modeling, threading, and ab initio) indicates a prevalence of β−sheets in agreement with consensus secondary structure predictions. Simulation data supported this finding since the formation of new strands, along with a rapid disruption of helical content, were observed. Overall, this study provides a rationalization of epitope mapping data and an improved understanding of cyspep antigenicity.     

High throughput processing of the structural information in the protein data bank

The protein data bank (PDB) is the largest, most comprehensive, freely available depository of protein structural information, containing more than 37 500 deposited structures. On one hand, the form and the organization of the PDB seems to be perfectly adequate for gathering information from specific protein structures, by using the bibliographic references and the informative remark fields. On the other hand, however, it seems to be impossible to automatically review remark fields and journal references for processing hundreds or thousands of PDB files.

We present here a family of combinatorial algorithms to solve some of these problems. Our algorithms are capable to automatically analyze PDB structural information, identify missing atoms, repair chain ID information, and most importantly, the algorithms are capable of identifying ligands with their respective binding sites.     

Overexpression and elevated plasma level of tumor-associated antigen 90K/Mac-2 binding protein in colorectal carcinoma

The cancer cell secretome may contain potentially useful biomarkers. Previously, we have analyzed the colorectal carcinoma (CRC) cell secretome. In this study, tumor‐associated antigen 90K (TAA90K)/Mac‐2 binding protein (Mac‐2BP), one of the CRC cell secreted proteins, was chosen for evaluation as a potential CRC biomarker because its mRNA level was also found to be significantly elevated in CRC tissues and in a more metastatic CRC cell line from the analysis of two public domain array‐based datasets. Immunohistochemical analysis of 241 CRC specimens showed that TAA90K/Mac‐2BP was positively detected in 52.7% of the tumors, but weakly or not detected in over 95% of the adjacent nontumor epithelial cells. The plasma TAA90K/Mac‐2BP levels were significantly higher in CRC patients (N = 280) versus healthy controls (N = 147) (7.77 ± 3.49 vs. 5.72 ± 2.67 μg/mL, p<0.001). Moreover, combination of TAA90K/Mac‐2BP and carcinoembryonic antigen (CEA) could outperform CEA alone in discriminating CRC patients from healthy persons in this case‐control study. Our results collectively indicate that analysis of cancer cell secretome is a feasible strategy for identifying cancer biomarker candidates, and the TAA90K/Mac‐2BP may be a potential CRC biomarker.     

蚁群算法研究与应用的新进展

蚁群算法是一种源于大自然生物界的仿生进化算法,具有自组织性、正反馈性、较强的鲁棒性和分布式计算等特性,且易于与其它算法相结合,在众多的复杂组合优化领域中有着广阔的应用前景。首先对蚁群算法的理论及其重要参数进行了阐述,继而分析了其在参数优化和智能融合方面的改进与应用;然后对其在车间作业调度问题、车辆路径问题、图像处理、电力系统优化等领域的应用进展进行了综述;最后对其理论研究和应用领域可能存在的问题及对策进行了探讨和展望。     

An alternative approach to characterize the topology of complex networks and its application in epidemic spreading

Based on the mean-field approach, epidemic spreading has been well studied. However, the mean-field approach cannot show the detailed contagion process, which is important in the control of epidemic. To fill this gap, we present a novel approach to study how the topological structure of complex network influences the concrete process of epidemic spreading. After transforming the network structure into hierarchical layers, we introduce a set of new parameters, i.e., the average fractions of degree for outgoing, ingoing, and remaining in the same layer, to describe the infection process. We find that this set of parameters are closely related to the degree distribution and the clustering coefficient but are more convenient than them in describing the process of epidemic spreading. Moreover, we find that the networks with exponential distribution have slower spreading speed than the networks with power-law degree distribution. Numerical simulations have confirmed the theoretical predictions.     

Glycoproteomics using fluid-based specimens in the discovery of lung cancer protein biomarkers: Promise and challenge

Lung cancer is the leading cancer in the United States and worldwide. In spite of the rapid progression in personalized treatments, the overall survival rate of lung cancer patients is still suboptimal. Over the past decade, tremendous efforts have been focused on the discovery of protein biomarkers to facilitate the early detection and monitoring of lung cancer progression during treatment. In addition to tumor tissues and cancer cell lines, a variety of biological material has been studied. Particularly in recent years, studies using fluid-based specimen or so-called “fluid-biopsy” specimens have progressed rapidly. Fluid specimens are relatively easier to collect than tumor tissue, and they can be repeatedly sampled during the disease progression. Glycoproteins are the major content of fluid specimens and have long been recognized to play fundamental roles in many physiological and pathological processes. In this review, we focus the discussion on recent advances of glycoproteomics, particularly in the identification of potential glyco protein biomarkers using fluid-based specimens in lung cancer. The purpose of this review is to summarize current strategies, achievements, and perspectives in the field. This insight will highlight the discovery of tumor-associated glycoprotein biomarkers in lung cancer and their potential clinical applications.     

An alternative approach to characterize the topology of complex networks and its application in epidemic spreading

Based on the mean-field approach, epidemic spreading has been well studied. However, the mean-field approach cannot show the detailed contagion process, which is important in the control of epidemic. To fill this gap, we present a novel approach to study how the topological structure of complex network influences the concrete process of epidemic spreading. After transforming the network structure into hierarchical layers, we introduce a set of new parameters, i.e., the average fractions of degree for outgoing, ingoing, and remaining in the same layer, to describe the infection process. We find that this set of parameters are closely related to the degree distribution and the clustering coefficient but are more convenient than them in describing the process of epidemic spreading. Moreover, we find that the networks with exponential distribution have slower spreading speed than the networks with power-law degree distribution. Numerical simulations have confirmed the theoretical predictions.     

The Role of Modeling and Asynchronous Distributed Simulation in Analyzing Complex Systems of the Future

The word simulate implies to imitate or to mimic while the word modeling refers to a small object, usually built to scale, that represents some existing object. Although the art of mimicking and modeling may be traced back to the beginning of civilization, with the emergence of computers, a few decades ago, the art of modeling and simulation experienced a remarkable transformation. The computational intelligence of the computer imparted the ability to encapsulate and simulate specific characteristics of not only living and inanimate objects but abstract concepts. While the human brain is equally capable of simulating abstract concepts, the precision and speed of the computers are unparalleled and they impart computer modeling and simulation a qualitative jump in its capability and fidelity. Also, while intimately connected to each other, modeling refers to the notion of representing the desired behavior of the target object or idea in the host computer and simulation refers to the execution of the model on a host computer. Today, towards the end of the twentieth century, the nature of modeling and simulation is undergoing another radical transformation. The emergence of economical and powerful computers coupled with the ability to network a large number of computers, promises the ability to model and simulate complex, real-world systems, that are rapidly becoming commonplace in the society, successfully and with a high degree of fidelity. Already, today's real-world systems including complex banking, credit-card transaction, transportation, ground-based communication, and space-based tele-communication systems defy the analytical modeling that had characterized the efforts over the past three decades. Virtually all analytical studies are severely restricted in the number of variables and the number of interacting units that may be modeled. Tomorrow's systems are expected to be far more complex, implying that modeling and large-scale simulation may be the most logical and, often, the only vehicle to study them objectively. This paper presents a fundamental analysis of the nature of complex physical and natural processes that will increasingly constitute the challenging problems of the future. It then develops a set of principles for modeling complex systems. Finally, it examines the role of asynchronous, distributed simulation in the study of a number of real-world systems. In general, modeling and simulation enables one to detect design errors, prior to developing a prototype, in a cost effective manner, identify potential problems during system operation, detect rare and elusive errors, and investigate hypothetical concepts that do not exist in nature. Upon execution, the simulation provides greater quantitative and qualitative insight into the behavior of the actual system. In addition, an asynchronous, distributed simulation, executing on a loosely-coupled parallel processor, closely resembles the actual, operational system, yielding results that potentially reflect reality, as close as possible. Furthermore, elements of the simulation code that emulate the system behavior may be transferred directly onto the operational system with minimal modifications. The knowledge encapsulated in this paper, has been derived from a number of actual case studies involving the modeling and simulation of a number of real-world problems.     

Using differential solubilization and 2-D gel electrophoresis to visualize increased numbers of proteins in the human cortex and caudate nucleus and putamen

The aim of this study was to determine if differential solubilization of human CNS proteins would increase the total number of proteins that could be visualized using 2-D gel electrophoresis. Hence, proteins were solubilized into Tris, CHAPS and SB3-10 before separation across a pH 4-7 IEF gradient and a 12-14% SDS polyacrylamide gel, which could be achieved with a run-to-run variation of 35% in spot intensity. Because Western blot analyses suggested proteins could be in more than one detergent fraction, we completed a conservative analyses of our 2-D gels assuming spots that appeared on multiple gels at the same molecular weight and pI were the same protein. These analyses show that we had visualized over 3000 unique protein spots across three 2-D gels generated from each sample of human frontal cortex and caudate-putamen. This represented, at worst, a significant increase in the number of spots visualized in the acidic protein spectrum compared to what has been reported in other studies of human CNS. This study, therefore, supports the proposal that the analysis of the human CNS proteome using 2-D gel electrophoresis, combined with appropriate sample preparation, can be used to expand the studies on the pathologies of neurological and psychiatric diseases.     

新时代高校图书馆数字参考咨询服务探微

数字参考咨询服务是当前高校图书馆参考咨询发展的必然趋势。本文在分析数字参考咨询服务的基本概念及特点基础上,详细剖析高校图书馆参考咨询服务的服务方式,提出发展策略包括加大图书馆数字参考咨询服务的宣传和推广力度,为数字参考咨询服务更好地展开奠定基础;优化人员配置,加强数字参考咨询服务的人才队伍建设;加大数字资源建设,为数字参考咨询服务做好资源保障等,推进高校图书馆数字参考咨询服务的可持续发展。     

Fibroblast protein profile analysis highlights the role of oxidative stress and vitamin K recycling in the pathogenesis of pseudoxanthoma elasticum

Pseudoxanthoma elasticum (PXE) is a genetic disorder associated to mutations in the ABCC6 gene; however, the pathogenetic mechanisms leading to elastic fibre calcifications and to clinical manifestations are still unknown. Dermal fibroblasts, directly involved in the production of the extracellular milieu, have been isolated from healthy subjects and from patients affected by PXE, cultured in vitro and characterized for their ability to produce reactive oxygen species, for structural and functional properties of their cell membranes, for changes in their protein profile. Data demonstrate that oxidative stress has profound and endurable consequences on PXE fibroblast phenotype being responsible for: reduced levels of global DNA methylation, increased amount of carbonylated proteins and of lipid peroxidation products, altered structural properties of cell membranes, modified protein expression. Data shed new light on the pathogenetic pathways in PXE, by identifying a network of proteins affecting elastic fibre calcification through inefficient vitamin K recycling, and highlight the role of differentially expressed proteins as targets for validating the efficacy of future therapeutic strategies aiming to delay and/or revert the pathologic phenotype of PXE fibroblasts. Moreover, data open new perspectives for investigating PXE-like phenotypes in the absence of ABCC6 mutations.     

Experimental decomposition of the positive bias temperature stress‐induced instability in self‐aligned coplanar InGaZnO thin‐film transistors and its modeling based on the multiple stretched‐exponential functions

Decomposition of the positive gate‐bias temperature stress (PBTS)‐induced instability into contributions of distinct mechanisms is experimentally demonstrated at several temperatures in top‐gate self‐aligned coplanar amorphous InGaZnO thin‐film transistors by combining the stress‐time‐divided measurements and the subgap density‐of‐states (DOS) extraction. It is found that the PBTS‐induced threshold voltage shift (ΔV_T) consists of three mechanisms: (1) increase of DOS due to excess oxygen in the active region; (2) shallow; and (3) deep charge trapping in the gate insulator components. Corresponding activation energy is 0.75, 0.4, and 0.9 eV, respectively. The increase of DOS is physically identified as the electron‐capture by peroxide. Proposed decomposition is validated by reproducing the PBTS time‐evolution of I–V characteristics through the technology computer‐aided design simulation into which the extracted DOS and charge trapping are incorporated. It is also found that the quantitative decomposition of PBTS‐induce ΔV_T accompanied with the multiple stretched‐exponential models enables an effective assessment of the complex degradation nature of multiple PBTS physical processes occurring simultaneously. Our results can be easily applied universally to any device with any stress conditions, along with guidelines for process optimization efforts toward ultimate PBTS stability.     

新时期档案管理人员应具备素质及培养途径探析

加强档案管理人员的素质建设,是新时期档案工作的重要任务径。新时期赋予档案管理者新的素质内涵,选好用好人才,加强教育培训,开展好经常性的思想政治教育,是提高档案管理者素质的有效途径。     

The binomial decomposition of OWA functions,the 2‐additive and 3‐additive cases in n dimensions

In the context of the binomial decomposition of ordered weighted averaging (OWA) functions, we investigate the constraints associated with the 2‐additive and 3‐additive cases in n dimensions. The 2‐additive case depends on one coefficient whose feasible region does not depend on the dimension n. On the other hand, the feasible region of the 3‐additive case depends on two coefficients and is explicitly dependent on the dimension n. This feasible region is a convex polygon with n vertices and n edges, which is strictly expanding in the dimension n. The orness of the OWA functions within the feasible region is linear in the two coefficients, and the vertices associated with maximum and minimum orness are identified. Finally, we discuss the 3‐additive binomial decomposition in the asymptotic infinite dimensional limit.     

KANTBP 2.0: New version of a program for computing energy levels, reaction matrix and radial wave functions in the coupled-channel hyperspherical adiabatic approach

A FORTRAN 77 program for calculating energy values, reaction matrix and corresponding radial wave functions in a coupled-channel approximation of the hyperspherical adiabatic approach is presented. In this approach, a multi-dimensional Schrödinger equation is reduced to a system of the coupled second-order ordinary differential equations on a finite interval with homogeneous boundary conditions: (i) the Dirichlet, Neumann and third type at the left and right boundary points for continuous spectrum problem, (ii) the Dirichlet and Neumann type conditions at left boundary point and Dirichlet, Neumann and third type at the right boundary point for the discrete spectrum problem. The resulting system of radial equations containing the potential matrix elements and first-derivative coupling terms is solved using high-order accuracy approximations of the finite element method. As a test desk, the program is applied to the calculation of the reaction matrix and radial wave functions for 3D-model of a hydrogen-like atom in a homogeneous magnetic field. This version extends the previous version 1.0 of the KANTBP program [O. Chuluunbaatar, A.A. Gusev, A.G. Abrashkevich, A. Amaya-Tapia, M.S. Kaschiev, S.Y. Larsen, S.I. Vinitsky, Comput. Phys. Commun. 177 (2007) 649-675].

Program summary

Program title: KANTBPCatalogue identifier: ADZH_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZH_v2_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 20 403No. of bytes in distributed program, including test data, etc.: 147 563Distribution format: tar.gzProgramming language: FORTRAN 77Computer: Intel Xeon EM64T, Alpha 21264A, AMD Athlon MP, Pentium IV Xeon, Opteron 248, Intel Pentium IVOperating system: OC Linux, Unix AIX 5.3, SunOS 5.8, Solaris, Windows XPRAM: This depends on

1.

the number of differential equations;

2.

the number and order of finite elements;

3.

the number of hyperradial points; and

4.

the number of eigensolutions required.

The test run requires 2 MBClassification: 2.1, 2.4External routines: GAULEG and GAUSSJ [2]Nature of problem: In the hyperspherical adiabatic approach [3-5], a multidimensional Schrödinger equation for a two-electron system [6] or a hydrogen atom in magnetic field [7-9] is reduced by separating radial coordinate ρ from the angular variables to a system of the second-order ordinary differential equations containing the potential matrix elements and first-derivative coupling terms. The purpose of this paper is to present the finite element method procedure based on the use of high-order accuracy approximations for calculating approximate eigensolutions of the continuum spectrum for such systems of coupled differential equations on finite intervals of the radial variable ρ∈[ρmin,ρmax]. This approach can be used in the calculations of effects of electron screening on low-energy fusion cross sections [10-12].Solution method: The boundary problems for the coupled second-order differential equations are solved by the finite element method using high-order accuracy approximations [13]. The generalized algebraic eigenvalue problem AF=EBF with respect to pair unknowns (E,F) arising after the replacement of the differential problem by the finite-element approximation is solved by the subspace iteration method using the SSPACE program [14]. The generalized algebraic eigenvalue problem (A−EB)F=λDF with respect to pair unknowns (λ,F) arising after the corresponding replacement of the scattering boundary problem in open channels at fixed energy value, E, is solved by the LDLT factorization of symmetric matrix and back-substitution methods using the DECOMP and REDBAK programs, respectively [14]. As a test desk, the program is applied to the calculation of the reaction matrix and corresponding radial wave functions for 3D-model of a hydrogen-like atom in a homogeneous magnetic field described in [9] on finite intervals of the radial variable ρ∈[ρmin,ρmax]. For this benchmark model the required analytical expressions for asymptotics of the potential matrix elements and first-derivative coupling terms, and also asymptotics of radial solutions of the boundary problems for coupled differential equations have been produced with help of a MAPLE computer algebra system.Restrictions: The computer memory requirements depend on:

1.

the number of differential equations;

2.

the number and order of finite elements;

3.

the total number of hyperradial points; and

4.

the number of eigensolutions required.

Restrictions due to dimension sizes may be easily alleviated by altering PARAMETER statements (see Section 3 and [1] for details). The user must also supply subroutine POTCAL for evaluating potential matrix elements. The user should also supply subroutines ASYMEV (when solving the eigenvalue problem) or ASYMS0 and ASYMSC (when solving the scattering problem) which evaluate asymptotics of the radial wave functions at left and right boundary points in case of a boundary condition of the third type for the above problems.Running time: The running time depends critically upon:

1.

the number of differential equations;

2.

the number and order of finite elements;

3.

the total number of hyperradial points on interval [ρmin,ρmax]; and

4.

the number of eigensolutions required.

The test run which accompanies this paper took 2 s without calculation of matrix potentials on the Intel Pentium IV 2.4 GHz.References:[1] O. Chuluunbaatar, A.A. Gusev, A.G. Abrashkevich, A. Amaya-Tapia, M.S. Kaschiev, S.Y. Larsen, S.I. Vinitsky, Comput. Phys. Commun. 177 (2007) 649-675; http://cpc.cs.qub.ac.uk/summaries/ADZHv10.html.[2] W.H. Press, S.A. Teukolsky, W.T. Vetterling, B.P. Flannery, Numerical Recipes: The Art of Scientific Computing, Cambridge University Press, Cambridge, 1986.[3] J. Macek, J. Phys. B 1 (1968) 831-843.[4] U. Fano, Rep. Progr. Phys. 46 (1983) 97-165.[5] C.D. Lin, Adv. Atom. Mol. Phys. 22 (1986) 77-142.[6] A.G. Abrashkevich, D.G. Abrashkevich, M. Shapiro, Comput. Phys. Commun. 90 (1995) 311-339.[7] M.G. Dimova, M.S. Kaschiev, S.I. Vinitsky, J. Phys. B 38 (2005) 2337-2352.[8] O. Chuluunbaatar, A.A. Gusev, V.L. Derbov, M.S. Kaschiev, L.A. Melnikov, V.V. Serov, S.I. Vinitsky, J. Phys. A 40 (2007) 11485-11524.[9] O. Chuluunbaatar, A.A. Gusev, V.P. Gerdt, V.A. Rostovtsev, S.I. Vinitsky, A.G. Abrashkevich, M.S. Kaschiev, V.V. Serov, Comput. Phys. Commun. 178 (2007) 301 330; http://cpc.cs.qub.ac.uk/summaries/AEAAv10.html.[10] H.J. Assenbaum, K. Langanke, C. Rolfs, Z. Phys. A 327 (1987) 461-468.[11] V. Melezhik, Nucl. Phys. A 550 (1992) 223-234.[12] L. Bracci, G. Fiorentini, V.S. Melezhik, G. Mezzorani, P. Pasini, Phys. Lett. A 153 (1991) 456-460.[13] A.G. Abrashkevich, D.G. Abrashkevich, M.S. Kaschiev, I.V. Puzynin, Comput. Phys. Commun. 85 (1995) 40-64.[14] K.J. Bathe, Finite Element Procedures in Engineering Analysis, Englewood Cliffs, Prentice-Hall, New York, 1982.