BackgroundIntegrating and analyzing heterogeneous genome-scale data is a huge algorithmic challenge for modern systems biology. Bipartite graphs can be useful for representing relationships across pairs of disparate data types, with the interpretation of these relationships accomplished through an enumeration of maximal bicliques. Most previously-known techniques are generally ill-suited to this foundational task, because they are relatively inefficient and without effective scaling. In this paper, a powerful new algorithm is described that produces all maximal bicliques in a bipartite graph. Unlike most previous approaches, the new method neither places undue restrictions on its input nor inflates the problem size. Efficiency is achieved through an innovative exploitation of bipartite graph structure, and through computational reductions that rapidly eliminate non-maximal candidates from the search space. An iterative selection of vertices for consideration based on non-decreasing common neighborhood sizes boosts efficiency and leads to more balanced recursion trees.ResultsThe new technique is implemented and compared to previously published approaches from graph theory and data mining. Formal time and space bounds are derived. Experiments are performed on both random graphs and graphs constructed from functional genomics data. It is shown that the new method substantially outperforms the best previous alternatives.ConclusionsThe new method is streamlined, efficient, and particularly well-suited to the study of huge and diverse biological data. A robust implementation has been incorporated into GeneWeaver, an online tool for integrating and analyzing functional genomics experiments, available at http://geneweaver.org. The enormous increase in scalability it provides empowers users to study complex and previously unassailable gene-set associations between genes and their biological functions in a hierarchical fashion and on a genome-wide scale. This practical computational resource is adaptable to almost any applications environment in which bipartite graphs can be used to model relationships between pairs of heterogeneous entities.
Using the quark mass density-and temperature dependent model, we have studied the thermodynamical properties and the stability of strangelet at finite temperature. The temperature, charge and strangeness dependences on the stability of strangelet are investigated. We find that the stable strangelets are only occured in the high strangeness and high negative charge region.
It is shown that the quark mass density-dependent model can not be used to explain the process of the quark deconfinement phase transition because the quark confinement is permanent in this model. A quark mass densityand temperature-dependent model in which the quark confinement is impermanent has been suggested. We argue that the vacuum energy density B is a function of temperature and satisfies B = B 0 1 − T T c 2 , where T c is the critical temperature of quark deconfinement. The dynamical and thermodynamical properties of bulk strange quark matter for quark mass density-and temperature-dependent model are discussed.
Aβ25-35, a proteolytic fragment of the Alzheimer amyloid beta (Aβ) peptide, is produced in the brains of Alzheimer's patients and retains the neurotoxicity of its full-length counterpart. The formation of pores/channels in membranes has been reported as one of the mechanisms responsible for Aβ25-35 toxicity. In addition, it has been proposed that pore/channel might be formed by the aggregation of Aβ25-35 in membranes into a β-barrel structure. However, the structure of the β-barrel and its perturbation on the ordering of lipid bilayer at atomic level remain elusive. In this study, we have investigated the interactions of three types of preformed Aβ25-35 β-barrels (labeled as barrels A, B, and C) with negatively charged palmitoyloleoylphosphatidylglycerol (POPG) lipid bilayers using all-atom molecular dynamics (MD) simulations. Each type of Aβ25-35 β-barrel consists of eight β-strands with positively charged side chains of lysine residues oriented toward the interior or exterior of the barrel. Barrels A, B, and C have respectively an out-of-register mixed parallel-antiparallel (taken from our previous study), in-register mixed parallel-antiparallel, and in-register antiparallel β-strand arrangements. Simulations have been performed by employing the initial configurations where the β-barrels are fully or partially inserted into the bilayer. On the basis of nine independent 150 ns MD runs for the full-insertion system, we found that barrels A and C slightly affect the local ordering of lipid bilayer, while barrel B perturbs the local structure of membrane and even causes membrane leakage for water by forming nanometer-sized hydrophilic pore when lysine residues on its inner side. Two 100 ns MD simulations on partial-insertion system show that partial insertion of Aβ25-35 β-barrel in the bilayer results in a tendency to stay inside for barrel B. These results suggest that barrel B with Lys residues on its inner side is the most likely Aβ25-35 pore structure leading to membrane leakage. Our MD simulations provide significant insight into the atomic resolution structure of Aβ25-35 β-sheet-rich pores and the membrane disruption mechanism induced by Aβ25-35 amyloid pores.
It is found that the radius of a stable strangelet decreases as the temperature increases in a quark mass density-dependent model. To overcome this difficulty, we extend this model to a quark mass density-and temperature-dependent model in which the vacuum energy density at zero baryon density limit B depends on temperature. An ansatz which reads] is introduced and the regions for the best choice of the parameters are studied.PACS number: 12.39. Ki,21.65.+f,25.75.Dw Typeset using REVT E X 1
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