Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm

Total DNA isolated from Rhizobium leguminosarum VF39SM cells is resistant to cleavage by the restriction endonuclease PstI. Plasmid curing and transfer studies localized this phenotype to pRleVF39b, the second smallest of six plasmids found in this bacterium. In vitro selection for vector modification was employed to isolate a presumptive methylase gene (M.Rle39BI) from a plasmid gene library. Total and plasmid DNAs isolated from E. coli containing M.RleBI were resistant to digestion by PstI. Sequence data suggested that a putative restriction endonuclease (R.Rle39BI) was also encoded on the same fragment. The two genes were flanked by identical copies of a putative insertion sequence, which was also present in several copies elsewhere in the VF39SM genome. The presence of this element in other strains examined suggested that this element is indeed an insertion sequence. The differences in G/C content between the DNA coding for the R/M system and that of the IS element suggest that this DNA region may have been acquired by horizontal transfer.     

A genetic algorithm based molecular modeling technique for RNA stem-loop structures

A new modeling technique for arriving at the three dimensional (3-D) structure of an RNA stem-loop has been developed based on a conformational search by a genetic algorithm and the following refinement by energy minimization. The genetic algorithm simultaneously optimizes a population of conformations in the predefined conformational space and generates 3-D models of RNA. The fitness function to be optimized by the algorithm has been defined to reflect the satisfaction of known conformational constraints. In addition to a term for distance constraints, the fitness function contains a term to constrain each local conformation near to a prepared template conformation. The technique has been applied to the two loops of tRNA, the anticodon loop and the T-loop, and has found good models with small root mean square deviations from the crystal structure. Slightly different models have also been found for the anticodon loop. The analysis of a collection of alternative models obtained has revealed statistical features of local variations at each base position.     

二次半定规划的原始对偶预估校正内点算法

将半定规划(Semidefinite Programming,SDP)的内点算法推广到二次半定规划(QuadraticSemidefinite Programming,QSDP),重点讨论了AHO搜索方向的产生方法.首先利用Wolfe对偶理论推导得到了求解二次半定规划的非线性方程组,利用牛顿法求解该方程组,得到了求解QSDP的内点算法的AHO搜索方向,证明了该搜索方向的存在唯一性,最后给出了求解二次半定规划的预估校正内点算法的具体步骤,并对基于不同搜索方向的内点算法进行了数值实验,结果表明基于NT方向的内点算法最为稳健.     

A graph-theoretic algorithm for comparative modeling of protein structure

The interconnected nature of interactions in protein structures appears to be the major hurdle in preventing the construction of accurate comparative models. We present an algorithm that uses graph theory to handle this problem. Each possible conformation of a residue in an amino acid sequence is represented using the notion of a node in a graph. Each node is given a weight based on the degree of the interaction between its side-chain atoms and the local main-chain atoms. Edges are then drawn between pairs of residue conformations/nodes that are consistent with each other (i.e. clash-free and satisfying geometrical constraints). The edges are weighted based on the interactions between the atoms of the two nodes. Once the entire graph is constructed, all the maximal sets of completely connected nodes (cliques) are found using a clique-finding algorithm. The cliques with the best weights represent the optimal combinations of the various main-chain and side-chain possibilities, taking the respective environments into account. The algorithm is used in a comparative modeling scenario to build side-chains, regions of main chain, and mix and match between different homologs in a context-sensitive manner. The predictive power of this method is assessed by applying it to cases where the experimental structure is not known in advance.     

A novel algorithm for Ethernet-passive-optical-network dynamic bandwidth allocation based on threshold

The Ethernet passive optical network (EPON) is the next generation of broad-band network technique.A crucial issue in EPONs is the sharing of uplink bandwidth among optical network units (ONUs).This article provides a novel dynamic bandwidth allocation algorithm,i.e.threshold dynamic bandwidth allocation (TDBA),which is based on adaptive threshold,to increase resource utilization.The algorithm uses ONU data-transmitting rate to adjust optical line terminal (OLT) receiving data threshold from an ONU.Simulation results show that this algorithm can decrease average packet delay and increase network throughput in a 10G EPON system.     

基于列生成与线性规划的炼钢组炉优化算法

针对考虑钢级"以优充次"的炼钢组炉问题,构建了以炼钢成本最小化与炼钢余材最小化为目标的多目标优化模型,基于目标优先级不同,首先以降低炼钢成本为目标,利用列生成算法给出具有最低炼钢成本的组炉方案;在此基础上,建立余材优化线性规划模型,通过缩减炉重和增加合同量的方式,进一步降低炼钢余材,得到最终的组炉方案。实例表明,该算法具有良好的优化性能和实用性。     

Improved parameters for the prediction of RNA hairpin stability

Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequences of the type GGXANmAYCC, where XY is the set of four Watson-Crick base pairs and the underlined loop sequences are three to nine nucleotides. A nearest neighbor analysis of the data indicates the free energy of loop formation at 37 degrees C is dependent upon loop size and closing base pair. The model previously developed to predict the stability for RNA hairpin loops (n > 3) includes contributions from the size of the loop, the identity of the closing base pair, the free energy increment (deltaGo(37mm)) for the interaction of the closing base pair with the first mismatch and an additional stabilization term for GA and UU first mismatches [Serra, M. J., Axenson, T. J., & Turner, D. H. (1994) Biochemistry 33, 14289]. The results presented here allow improvements in the parameters used to predict RNA hairpin stability. For hairpin loops of n = 4-9, deltaGo(37iL)(n) is 4.9, 5.0, 5.0, 5.0, 4.9, and 5.5 kcal/mol, respectively, and the penalty for hairpin closure by AU or UA is +0.6 kcal/mol. deltaGo(37iL)(n) is the free energy for initiating a loop of n nucleotides. The model for predicting hairpin loop stability for loops larger than three becomes deltaGo(37L)(n) = deltaGo(37iL)(n) + deltaGo(37mm) + 0.6(if closed by AU or UA) - 0.7(if first mismatch is GA or UU). Hairpin loops of three are modeled as independent of loop sequence with deltaGo(37iL)(3) = 4.8 and the penalty for AU closure of +0.6 kcal/mol. Thermodynamic parameters for hairpin formation in 1 M NaCl for 11 naturally occurring RNA hairpin sequences are reported. The model provides good agreement with the measured values for both T(M) (within 10 degrees C of the measured value) and deltaGo(37) (within 0.8 kcal/mol of the measured value) for hairpin formation. In general, the nearest neighbor model allows prediction of RNA hairpin stability to within 5-10% of the experimentally measured values.     

A logistic regression model including DNA status and morphology of spermatozoa for prediction of fertilization in vitro

To determine predictive values of routine semen analysis, sperm morphology evaluation using strict criteria and DNA status for in-vitro fertilization (IVF), 66 consecutive couples undergoing IVF in a university hospital IVF programme were prospectively investigated. Semen samples from 66 men were evaluated by routine semen analysis, morphology evaluation using strict criteria and acridine orange staining for determination of DNA status. A new technique is described for acridine orange scoring which consisted of evaluation of two smears per case, with and without heat treatment. Resistance to heat-provoked denaturation was determined by the difference between two evaluations. A logistic regression model was built and receiver operating characteristic curves were constructed to determine the threshold values and to compare diagnostic properties. Morphology evaluation using strict criteria and concentration of progressively motile spermatozoa were found to be the principal parameters determining the sperm fertilizing capacity in vitro. The logistic regression model composed of morphology evaluation using strict criteria and acridine orange score had a powerful diagnostic capability for prediction of fertilization in vitro.     

A polyhedral approach to RNA sequence structure alignment

Ribonucleic acid (RNA) is a polymer composed of four bases denoted A, C, G, and U. It generally is a single-stranded molecule where the bases form hydrogen bonds within the same molecule leading to structure formation. In comparing different homologous RNA molecules it is important to consider both the base sequence and the structure of the molecules. Traditional alignment algorithms can only account for the sequence of bases, but not for the base pairings. Considering the structure leads to significant computational problems because of the dependencies introduced by the base pairings. In this paper we address the problem of optimally aligning a given RNA sequence of unknown structure to one of known sequence and structure. We phrase the problem as an integer linear program and then solve it using methods from polyhedral combinatorics. In our computational experiments we could solve large problem instances--23S ribosomal RNA with more than 1400 bases--a size intractable for former algorithms.     

一种动态的时延约束费用优化多播路由算法

对动态环境下满足时延约束且费用最优的多播路由算法进行了研究.改进了一种触发重组算法,该算法根据一个区域内的节点加入或退出次数来确定对多播树的损害程度,若达到所给定平衡因子的值则触发重组.仿真表明,该算法具有较好的性能,能满足某些特殊的场合的要求.     

A dynamic model of outer hair cell motility including intracellular and extracellular fluid viscosity

The deformation response of a guinea pig outer hair cell is modeled for mechanical and electrical stimulation up to 25 kHz. The analysis uses a Fourier series technique for a finite length cell surrounded internally and externally by a much larger continuum of viscous fluid. The analytical solution predicts that outer hair cell length changes occur due to applied mechanical or electrical stimulation without significant resonance, characteristic of a highly damped system. The deformation is found to have little attenuation up to a corner frequency of about 2 kHz for long cells and 10 kHz for short cells, in agreement with published experimental results. For electrical loading of 1 mV across the lateral cell wall, deformation for short cells is calculated to be greater than 1 nm for frequencies up to 20 kHz. These results support the proposition that in vivo the outer hair cell modifies the character of basilar membrane deformation on a cycle-by-cycle basis. An estimate of the capability of the cell to supply energy to the basilar membrane is given based on published values of outer hair cell material properties.     

一类二层多目标规划的混沌遗传优化算法及其应用

针对求解一类二层多目标规划问题,首先将其转化为等价的单目标规划问题,然后利用遗传算法优化的反演性和混沌优化方法的遍历性,并结合精确罚函数求解非线性约束优化问题,提出了求解此类问题的混沌遗传算法.该方法能够有效改善遗传算法的局部搜索能力和搜索精度,求解精度和可靠性较高.实际算例表明,算法是有效可行的.     

一种基于AHP的海上待泊区动态编排算法

为保障海上安全形势稳定,提高船舶进出港交通效率,海上交通相关管理部门研究建立了待泊区并投入使用.待泊区的使用需要提前进行申请,海事局进行编排和调度.针对船舶待泊区申请的编排需求,提出了一种基于AHP的待泊区动态编排算法,首先确立待泊区编排算法的主要影响因素,并为各因素依次建立隶属度函数,结合采用AHP层次分析法确定各影响因素的动态权系数,进而得到综合隶属度函数值,从而完成待泊区申请的动态智能编排,大大提升了海上船舶的通航效率.该算法具有编排过程高效、编排结果精准等优点,还能应对编排因素多变的特点,结合各个港口的实际情况和独特特征,对不同影响因素进行个性化配置,大大提升用户体验.     

一种快速的动态属性约简矩阵算法

针对实际决策表中对象动态变化的情况,首先引入简化决策表概念,剔除决策表中大量重复的对象,并构造了基于正区域的简化矩阵,有效地缩小了算法的搜索空间;然后从理论上阐述了基于简化矩阵的属性约简和基于矩阵的属性约简的一致性,并仅需扫描一遍简化矩阵便可求解出属性约简;最后在原属性约简的基础上,提出一种快速的动态属性约简矩阵算法.通过算例分析和实验对比验证了算法的有效性和可行性.     

A functional ribosomal RNA tertiary structure involves a base triple interaction

Comparative sequence analysis reveals a coordinated set of nucleotide exchanges between the base pair 1092/1099 and the unpaired position 1072 [(1092/1099)1072] in the L11 binding domain of 23S ribosomal RNA. This set of exchanges has occurred at least 4 times during evolution, suggesting that these positions form a base triple. The analysis further suggests an important role for positions (1065/1073), adjacent to 1072. The covariation at positions (1092/1099)1072 is studied here by analysis of RNA variants using UV melting and binding of ribosomal protein L11 and thiostrepton to assay for tertiary folding of this domain. The tertiary structure of the RNA is eliminated by alteration of the unpaired nucleotide (C1072 to U mutation), and binding of L11 and thiostrepton are reduced 10-fold compared to the wild type. In contrast, substitution of the base pair (CG1092/1099 to UA mutation) allows formation of the tertiary structure but dramatically alters the pH dependence of tertiary folding. The fully compensated set of mutations, (CG)C to (UA)U, restores the tertiary structure of the RNA to a state almost identical to the wild type. The nature of this base triple and its implications for the folding of the RNA and ligand interactions are discussed.     

STRUCTURELAB: a heterogeneous bioinformatics system for RNA structure analysis

STRUCTURELAB is a computational system that has been developed to permit the use of a broad array of approaches for the analysis of the structure of RNA. The goal of the development is to provide a large set of tools that can be well integrated with experimental biology to aid in the process of the determination of the underlying structure of RNA sequences. The approach taken views the structure determination problem as one of dealing with a database of many computationally generated structures and provides the capability to analyze this data set from different perspectives. Many algorithms are integrated into one system that also utilizes a heterogeneous computing approach permitting the use of several computer architectures to help solve the posed problems. These different computational platforms make it relatively easy to incorporate currently existing programs as well as newly developed algorithms and to best match these algorithms to the appropriate hardware. The system has been written in Common Lisp running on SUN or SGI Unix workstations, and it utilizes a network of participating machines defined in reconfigurable tables. A window-based interface makes this heterogeneous environment as transparent to the user as possible.     

GeneGenerator--a flexible algorithm for gene prediction and its application to maize sequences

MOTIVATION: We developed GeneGenerator because of the need for a tool to predict gene structure without knowing in advance how to score potential exons and introns in order to obtain the best results, pertinent in particular to less well-studied organisms for which suitable training sets are small. GeneGenerator is a very flexible algorithm which for a given genomic sequence generates a number of feasible gene structures satisfying user-defined constraints. The specific implementation described in detail requires minimum scoring for translation start and donor and acceptor splice sites according to previously trained logitlinear models. In addition, potential exons and introns are required to exceed specified minimal lengths and threshold scores for coding or non-coding potential derived as log-likelihood ratios of appropriate Markov sequence models. RESULTS: A database of 46 non-redundant genomic sequences from maize is used for illustration. It is shown that the correct gene structures do not always maximize the considered target function. However, in most cases, the correct or nearly correct structures are found in a small set of high-scoring structures. A critical review of the generated structures sometimes allows the choices to be narrowed by considering additional variables such as predicted splice site strength or local optimality of splice site scores. Summary statistics for prediction accuracy over all 46 maize genes are derived under cross-validation and non-cross-validation training conditions for the Markov sequence models. The algorithm achieved exon sensitivity of 0.81 and specificity of 0.75 on an independent set of 14 novel maize genomic segments. AVAILABILITY: GeneGenerator runs under Borland-Pascal 7.0 using MS-DOS and C on UNIX work stations. The source code is available upon request. CONTACT: jkleffe@euler.grumed.fu-berlin-de     

Evaluation of a programming algorithm for the third tachycardia zone in a fourth-generation implantable cardioverter-defibrillator

Lungs from eight goats of mixed sexes and breeds (Cashmere, Nubian and Toggenburg) aged between 10 and 48 months were used in this study. Tissues from lung parenchyma were minced and routinely prepared for transmission electron microscopy (TEM) after using different methods of fixation. Thick sections were examined with a light microscope and samples, to include terminal bronchioles, respiratory bronchioles, alveolar ducts and alveolar membrane, were selected for ultrathin sectioning. Six cell types, ciliated, non-ciliated bronchiolar epithelial, mucus-producing, alveolar Type I, alveolar Type II and capillary endothelial cell were identified and characterised cytologically. It was established that the cell population in the distal airways is similar to that observed in other domestic mammals. The mucus-producing cell, which appears to be a common cell type in the distal airways of man and Rhesus monkey, was encountered particularly in adult goats in the present study. This study has also established that the Clara cell of the goat shows some cytological differences from those of some other mammalian species by having a large amount of SER, particularly in the apical region. Lipid vacuoles were seen to be a feature of the alveolar Type II cells; these do not appear to have been reported in other mammalian species. The study has provided a basic understanding of the morphological features of the cell population of the epithelium lining the distal airways in the goat's respiratory tract. The difference in junctional complexes between the various alveolar epithelial cells perhaps signify a different pattern of intercellular transport, thus influencing the pathogenesis and resolution of alveolar pulmonary edema.     

A model for dynamic embrittlement

A model is presented to calculate the rate of crack advance in the stepwise decohesion process which can result from the stress-induced penetration of a surface-adsorbed element into a solid, usually along grain boundaries. We call this process dynamic embrittlement. The model employs a diffusion equation containing both the usual random-mixing term and a term reflecting the work done by a tensile stress when surface atoms diffuse inward. Given the diffusion constant of the surface species and the stress profile at the crack tip, the concentration build-up ahead of the crack as a function of time can be calculated. This can be combined with an empirical relationship between the interfacial concentration of the surface species and the stress to cause decohesion to give the crack-growth rate. This model is applied to the case of sulfur-induced cracking of an alloy steel in the process known as stress-relief cracking.