“CHOODRAW”—an interactive molecular graphics program (PC/XT/AT) to display small molecules complexed with protein fragments selected from the protein data bank

CHOODRAW is a two-part interactive molecular graphics program to display small-molecule-protein complexes. Fragments of structural data of a protein can be displayed from protein data bank data files together with binding of small molecules to the protein. The software consists of two separate programs written in Borland Turbo Basic.     

Supervised ranking in the weka environment

Software for solving the supervised ranking problem is presented. Four variants of the Ordinal Stochastic Dominance Learner (OSDL) are given, together with the space and time complexity of their implementations. It is shown that the described software, which includes two further algorithms for supervised ranking, fits seamlessly into the weka environment.     

Optimal multilevel organization modelling for active contributions of principals

A model of the optimal multilevel organization is described. Its originality is determined by its multilevel character, the optimal hierarchy structure being the internal parameter examined together with the “classical” organization theory parameters, such as technology, number of agents and principals, their types and effort levels, stimulation mechanisms. The key assumption is the additivity of principals’ contributions to the total profit of the organization. A particular case of the model with the logarithmic profit function is examined in detail.     

Scheduling satellite launch missions: an MILP approach

The paper deals with an MILP model to schedule satellite launches with alternative launchers and different mission profiles, subject to resource constraints. The model is part of a simulation tool developed within a joint research project with the European space agency. The focus is on geostationary transfer orbit (GTO) launches of payloads, which are associated with a given time window for launch, a payload mass, and a potential revenue. A launch requires the payload, a launcher compatible with both payload mass and mission profile, a launch complex for that launcher, and a launch range (i.e., resources that are shared by the launch complexes, including a mission control station). We consider three launcher types, which differ in cost and performance, are produced at a limited rate, and cannot be stocked in large amounts. One of the launchers is also able to carry out dual launch missions, i.e., missions in which two payloads are launched together, provided that their joint mass does not exceed launcher’s mass capacity and their time windows overlap. After each launch, the launch complexes and the launch range need some latency time to be reset. Two natural objectives are minimizing the number of lost payloads and maximizing profit. Here we report experiences with a discrete-time MILP model formulation, which is rather flexible and can be extended to cope with additional problem features. Natural concerns, such as computational effort and the effect of time discretization, are addressed in the paper.     

CPL: Detecting Protein Complexes by Propagating Labels on Protein-Protein Interaction Network

Proteins usually bind together to form complexes, which play an important role in cellular activities. Many graph clustering methods have been proposed to identify protein complexes by finding dense regions in protein-protein interaction networks. We present a novel framework （CPL） that detects protein complexes by propagating labels through interactions in a network, in which labels denote complex identifiers. With proper propagation in CPL, proteins in the same complex will be assigned with the same labels. CPL does not make any strong assumptions about the topological structures of the complexes, as in previous methods. Tile CPL algorithm is tested on several publicly available yeast protein-protein interaction networks and compared with several state-of-the-art methods. The results suggest that CPL performs better than the existing methods. An analysis of the functional homogeneity based on a gene ontology analysis shows that the detected complexes of CPL are highly biologically relevant.     

三唑烯醇手性分离的密度泛函研究

利用密度泛函B3LYP/6-31G*方法,分别将E-三唑烯醇的对应异构体ER、ES,Z-三唑烯醇的对应异构体ZR、ZS,手性固定相(CSP)以及三唑烯醇的4个异构体与手性固定相(CSP)络合后的分子结构构型全优化.计算结果,三唑烯醇的这4个异构体均能以氢键的形式,与CSP形成复合体;计算表明由于空间效应,E-三唑烯醇的2个手性异构体分子与CSP的结合能力各不相同,因可以通过手型固定相去分离,而Z-三唑烯醇的2个手性异构体分子都能与CSP形成双氢键,结合能相近,却不能通过手性固定相去分离;实验可以证明.     

Dimension-independent simplification and refinement of Morse complexes

Ascending and descending Morse complexes, determined by a scalar field f defined over a manifold M, induce a subdivision of M into regions associated with critical points of f, and compactly represent the topology of M. We define two simplification operators on Morse complexes, which work in arbitrary dimensions, and we define their inverse refinement operators. We describe how simplification and refinement operators affect Morse complexes on M, and we show that these operators form a complete set of atomic operators to create and update Morse complexes on M. Thus, any operator that modifies Morse complexes on M can be expressed as a suitable sequence of the atomic simplification and refinement operators we have defined. The simplification and refinement operators also provide a suitable basis for the construction of a multi-resolution representation of Morse complexes.     

PH—电位法测定多元配合物稳定常数的计算程序

本文扩展了应用于测定二元配合物稳定常数的 TITFIT 程序,使之适用于形成多元配合物的平衡体系。通常滴定曲线的函数误差(滴定 NaOH 的总体积 ml)σ_(ml)<0.5%。适合曲线的最好参数与文献值列于表,我们的结果与文献上的相符较好。     

In the mind and in the technology: The vicarious presence of the teacher in pupil’s learning of science in collaborative group activity at the interactive whiteboard

The focus of research into the use of the interactive whiteboard (IWB) in the classroom has been largely in relation to teacher–pupil interaction, with very little consideration of its possible use as a tool for pupils’ collaborative endeavour. This paper is based upon an ESRC-funded project,¹ which considers how pupils use the interactive whiteboard when working together on science-related activities. It provides an analysis of video and other data from science lessons in UK Years 4 and 5 primary classrooms (pupils aged 8–10 years). Concentrating on a series of lessons constructed by three (out of 12) of the project teachers, together with their written and spoken commentaries, it takes each set of lessons as a case for study and comparison.     

Conformational analysis of alkali metal complexes of anionic species of aspartic acid, their interconversion and deprotonation: a DFT investigation

Gas-phase geometry-optimized structures of aspartate complexes of anionic species (Hasp(-)) with lithium, sodium and potassium metal cations and transition-state structures for their interconversions were obtained using the density functional theory computations at the B3LYP/6-311++G(d,p) level of theory. The metal ion affinities of Hasp(-) species and deprotonation energies of [Hasp-M] complexes, M=Li+, Na+ and K+, and their conformers were obtained. Relative energies of the [Hasp-M] complex conformers, reaction energies, thermodynamic properties, rate and equilibrium constants of their complexation are reported. Binding energies of the most stable complexes with Li+, Na+ and K+ are -168.53, -133.34 and -117.68kcal/mol, respectively. The most stable complex conformer as a tri-coordinated form for aspartate complex with Li(+) and bi-coordinated form for aspartate complexes with Na+ and K+ were found.     

Synthesis of an information channel in planning goal functioning of space remote sensing systems according to quality criteria

Quality criteria for an image received from optic-electronic complexes of space remote sensing systems and methods of evaluating these quality criteria that allow one to choose parameters of elements of a ground space information channel together with orbital design of space remote sensing systems are considered.     

设计中抽象思维和形象思维的作用

通过分析抽象思维和形象思维在设计构思过程中的特点,研究两种思维能力在设计中的联系,从而理解其发挥的作用。本文力求寻找形象思维和抽象思维两种能力的有效结合的途径,从而促进设计发展,真正提高设计者的能力。     

Deterministic and stochastic P systems for modelling cellular processes

This paper presents two approaches based on metabolic and stochastic P systems, together with their associated analysis methods, for modelling biological systems and illustrates their use through two case studies.     

Efficient parallel algorithm for the two-dimensional diffusion equation subject to specification of mass

An efficient L ₀-stable parallel algorithm is developed for the two-dimensional diffusion equation with non-local time-dependent boundary conditions. The algorithm is based on subdiagonal Padé approximation to the matrix exponentials arising from the use of the method of lines and may be implemented on a parallel architecture using two processors running concurrently with each processor employing the use of tridiagonal solvers at every time-step. The algorithm is tested on two model problems from the literature for which discontinuities between initial and boundary conditions exist. The CPU times together with the associated error estimates are compared.     

Monitoring healthcare performance by analytic hierarchy process: a developing-country perspective

The formulation and solution of multi‐criteria healthcare decision problems is of critical importance to the health and socio‐economic betterment of developing countries. The study shows how the multi‐criteria decision‐making method could facilitate implementation of healthcare performance analysis, especially for the public healthcare system of Bangladesh, which operates mainly through thana health complexes (THCs). We include outreach services and rural facilities together with ongoing THC activities, and analyze their relative performance. The methodology uses a phase of the Delphi method and of the analytic hierarchy process (AHP) approach. The outcome of Delphi is used as input for the hierarchical processing procedure in AHP and determines performance order of the healthcare activities. Results from AHP are discussed for implementation in decision‐making and the managerial policymaking process, towards improvement of overall healthcare performance.     

RFN-B+树索引文件及其有效性

在对比传统的B树和B⁺树的定义和操作算法的基础上,定义了一种新的B⁺树:RFN-B⁺树,以获得更高的空间利用率和可用性.首先比较和分析了RFN-B⁺树与传统B⁺树的空间效率,然后讨论了RFN-B⁺树索引文件的有效性以及支持这种有效性的全链接指针结构和两个备用模块:基于虚拟根结点的随机检索算法和重构结点的算法.     

Predicting overlapping protein complexes in weighted interactome networks

Protein complexes play important roles in integrating individual gene products to perform useful cellular functions.The increasing mount of protein–protein interaction(PPI)data has enabled us to predict protein complexes.In spite of the advances in these computational approaches and experimental techniques,it is impossible to construct an absolutely reliable PPI network.Taking into account the reliability of interactions in the PPI network,we have constructed a weighted protein–protein interaction(WPPI)network,in which the reliability of each interaction is represented as a weight using the topology of the PPI network.As overlaps are likely to have biological importance,we proposed a novel method named WN-PC(weighted network-based method for predicting protein complexes)to predict overlapping protein complexes on the WPPI network.The proposed algorithm predicts neighborhood graphs with an aggregation coefficient over a threshold as candidate complexes,and binds attachment proteins to candidate complexes.Finally,we have filtered redundant complexes which overlap other complexes to a very high extent in comparison to their density and size.A comprehensive comparison between competitive algorithms and our WN-PC method has been made in terms of the F-measure,coverage rate,and P-value.We have applied WN-PC to two different yeast PPI data sets,one of which is a huge PPI network consisting of over 6000 proteins and 200000 interactions.Experimental results show that WN-PC outperforms the state-of-the-art methods.We think that our research may be helpful for other applications in PPI networks.     

Differential pulse voltammetric determination of N-acetylcysteine by the electrocatalytic oxidation at the surface of carbon nanotube-paste electrode modified with cobalt salophen complexes

The preparation and electrochemical performance of the carbon nanotube-paste electrode modified with salophen complexes of cobalt(III) perchlorate, with various substituents on the salophen ligand, as well as their electrocatalytic activity toward the oxidation of N-acetylcysteine (NAC) is investigated. Several Schiff base complexes containing various nucleophilic and electrophilic functional groups were prepared, and their electrochemical characteristics for the electro-oxidation of NAC were evaluated using cyclic and differential pulse voltammetry (CV and DPV). The results revealed, the modified electrodes show an efficient and selective electrocatalytic activity toward the anodic oxidation of NAC among biologically important compounds in buffered solutions at pH of 7.0. The best voltammetric responses were obtained for a carbon-paste electrode (CPE) modified with a salophen complex containing para-methoxy groups on its salicylaldehyde ring. The analytical response of the modified electrode for response to other sulfhydryl compounds (e.g., cysteine, penicillamine, captopril and mercaptopropionyl glycine) in comparison to NAC was investigated by CV and DPV methods. The DPV method was applied as a sensitive method for the quantitative detection of the trace amounts of NAC. A linear dynamic range from 1 × 10⁻⁷ to 1 × 10⁻⁴ M with calibration sensitivity of 0.0646 μA/μM is resulted for NAC in DPV measurements. The detection limit was 5 × 10⁻⁸ M, which is remarkably lower than those reported previously for NAC using other modified electrodes. The results of voltammetric determinations show a very good reproducibility, and the R.S.D. for the slope of the calibration curve, based on 10 measurements in a period of two months, was <3.9%. The detection system provides very stable electrochemical responses toward NAC, makes it very suitable for using in pharmaceutical and clinical measurements.     

Two algorithms for the construction of product formulas

By using formulas already known in the literature, we present two algorithms, together with their Fortran implementations, for the numerical construction of product quadrature rules.