Robust Selection of the Most Discriminative Variables in the Dichotomous Problem with Application to Some Respiratory Disease Data

A robust method for selection of variables with the greatest discriminatory power is presented in the paper. The method deals with the two groups of data problem. An application of the method to some respiratory disease data and comparisons with classical procedures are given, also.     

Stoichiometric binding of diacylglycerol to the phorbol ester receptor

The major phorbol ester receptor is the Ca++-activated, phospholipid-dependent protein kinase C. Diacylglycerol stimulates protein kinase C in a fashion similar to the phorbol esters. Likewise, it inhibits phorbol ester binding competitively. Both results suggest that diacylglycerol is the/an endogenous phorbol ester analogue. Alternatively, the diacylglycerol might simply be acting to modify the phospholipid environment of the protein. If diacylglycerol were indeed functioning as an analogue, it should interact with the receptor stoichiometrically. This interaction can be quantitated by measuring the perturbation in apparent diacylglycerol binding affinity as a function of the ratio of diacylglycerol to receptor. We report here that 1,2-dioleoylglycerol interacts with the receptor with the predicted stoichiometry.     

A graph theoretic approach to the development of minimal phylogenetic trees

Summary The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the length of any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.     

On the limitations of standard statistical modeling in biological systems: A full Bayesian approach for biology

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist.     

Relations between grapevine replant disease and root colonization of grapevine (Vitis sp.) by fluorescent pseudomonads and endomycorrhizal fungi

In pot experiments cuttings of grapevine rootstock cultivar 5C were grown on a soil from a grapevine nursery affected with replant disease (replant soil) and on a similar soil that had not been planted with grapevines before (non-replant soil). Plants were also inoculated with the vesicular-arbuscular (VA) mycorrhizal fungus,Glomus mosseae, or left without mycorrhizal fungus inoculation. Shoot and root growth, mycorrhization of roots and numbers of total aerobic bacteria and fluorescent pseudomonads on the rhizoplane of grapevines were determined at several sampling dates. On replant soil, numbers of fluorescent pseudomonads on the rhizoplane were higher compared to non-replant soil, before differences in shoot and root weight between replant and non-replant soil occurred. Without inoculation withG. mosseae, the mycorrhization of roots was much lower on replant soil (13%) than on non-replant soil (51%). On replant soil, inoculation withG. mosseae increased mycorrhization to 39% and increased shoot length, leaf area and shoot weight. The beneficial effect of VA-fungus inoculation on replant soil was not due to increased nutrient concentrations in leaves. On replant soil, the inoculation withG. mosseae reduced the number of fluorescent pseudomonads on rhizoplane of grapevine, while the numbers of total aerobic bacteria were not influenced by inoculation withG. mosseae. These results suggest a direct or indirect role of fluorescent pseudomonads in replant disease of grapevine.     

Innovative problem solving by wild spotted hyenas

Innovative animals are those able to solve novel problems or invent novel solutions to existing problems. Despite the important ecological and evolutionary consequences of innovation, we still know very little about the traits that vary among individuals within a species to make them more or less innovative. Here we examine innovative problem solving by spotted hyenas (Crocuta crocuta) in their natural habitat, and demonstrate for the first time in a non-human animal that those individuals exhibiting a greater diversity of initial exploratory behaviours are more successful problem solvers. Additionally, as in earlier work, we found that neophobia was a critical inhibitor of problem-solving success. Interestingly, although juveniles and adults were equally successful in solving the problem, juveniles were significantly more diverse in their initial exploratory behaviours, more persistent and less neophobic than were adults. We found no significant effects of social rank or sex on success, the diversity of initial exploratory behaviours, behavioural persistence or neophobia. Our results suggest that the diversity of initial exploratory behaviours, akin to some measures of human creativity, is an important, but largely overlooked, determinant of problem-solving success in non-human animals.     

An efficient algorithm for DNA fragment assembly in MapReduce

Fragment assembly is one of the most important problems of sequence assembly. Algorithms for DNA fragment assembly using de Bruijn graph have been widely used. These algorithms require a large amount of memory and running time to build the de Bruijn graph. Another drawback of the conventional de Bruijn approach is the loss of information. To overcome these shortcomings, this paper proposes a parallel strategy to construct de Bruijin graph. Its main characteristic is to avoid the division of de Bruijin graph. A novel fragment assembly algorithm based on our parallel strategy is implemented in the MapReduce framework. The experimental results show that the parallel strategy can effectively improve the computational efficiency and remove the memory limitations of the assembly algorithm based on Euler superpath. This paper provides a useful attempt to the assembly of large-scale genome sequence using Cloud Computing.     

肽自动合成中有关问题探讨

讨论了肽自动合成中的方法选择、偶联技术、故障排除、肽－树脂裂解及肽的纯化等主要问题及策略。