1,294 research outputs found

    Metabolic Network Alignments and their Applications

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    The accumulation of high-throughput genomic and proteomic data allows for the reconstruction of the increasingly large and complex metabolic networks. In order to analyze the accumulated data and reconstructed networks, it is critical to identify network patterns and evolutionary relations between metabolic networks. But even finding similar networks becomes computationally challenging. The dissertation addresses these challenges with discrete optimization and the corresponding algorithmic techniques. Based on the property of the gene duplication and function sharing in biological network,we have formulated the network alignment problem which asks the optimal vertex-to-vertex mapping allowing path contraction, vertex deletion, and vertex insertions. We have proposed the first polynomial time algorithm for aligning an acyclic metabolic pattern pathway with an arbitrary metabolic network. We also have proposed a polynomial-time algorithm for patterns with small treewidth and implemented it for series-parallel patterns which are commonly found among metabolic networks. We have developed the metabolic network alignment tool for free public use. We have performed pairwise mapping of all pathways among five organisms and found a set of statistically significant pathway similarities. We also have applied the network alignment to identifying inconsistency, inferring missing enzymes, and finding potential candidates

    Research on Financing Efficiencies of Strategic Emerging Listed Companies by Six-Stage DEA Model

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    Accounting for the information of input slack variables, as well as the effects of external environment and stochastic factors, a six-stage DEA model was proposed based on four-stage DEA model. It was employed to assess the financing efficiencies of 689 strategic emerging listed companies in 2015. By isolating the environmental and stochastic factors, the final efficiencies can reflect the actual financing level of these companies. The empirical results show that most financing efficiencies are still at a low level relatively. The scales of these strategic emerging companies are the main constraint on their development. And the special technical level also has an impact on these efficiencies. In addition, the efficiency difference among provinces in China gives another support to environmental influence on the strategic emerging industry. Therefore, a strategic emerging company should pay attention to expanding its scale of production and heighten its special technical level and it should improve its financing efficiencies with the help of local government power

    Structural and electronic properties of Al nanowires: an ab initio pseudopotential study

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    The stability and electronic structure of a single monatomic Al wire has been studied using the ab initio pseudopotential method. The Al wire undergoes two structural rearrangements under compression, i.e., zigzag configurations at angles of 140o140^o and 60o60^o. The evolution of electronic structures of the Al chain as a function of structural phase transition has been investigated. The relationship between electronic structure and geometric stability is also discussed. The 2p bands in the Al nanowire are shown to play a critical role in its stability. The effects of density functionals (GGA and LDA) on cohesive energy and bond length of Al nanostructures (dimmer, chains, and monolayers) are also examined. The link between low dimensional 0D structure (dimmer) to high dimensional 3D bulk Al is estimated. An example of optimized tip-suspended finite atomic chain is presented to bridge the gap between hypothetical infinite chains and experimental finite chains.Comment: 11 pages, 5 figure

    Nanoparticle manipulation by thermal gradient

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    A method was proposed to manipulate nanoparticles through a thermal gradient. The motion of a fullerene molecule enclosed inside a (10, 10) carbon nanotube with a thermal gradient was studied by molecular dynamics simulations. We created a one-dimensional potential valley by imposing a symmetrical thermal gradient inside the nanotube. When the temperature gradient was large enough, the fullerene sank into the valley and became trapped. The escaping velocities of the fullerene were evaluated based on the relationship between thermal gradient and thermophoretic force. We then introduced a new way to manipulate the position of nanoparticles by translating the position of thermostats with desirable thermal gradients. Compared to nanomanipulation using a scanning tunneling microscope or an atomic force microscope, our method for nanomanipulation has a great advantage by not requiring a direct contact between the probe and the object

    A catalog of collected debris disks: properties, classifications and correlations between disks and stars/planets

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    We have collected a catalog of 1095 debris disks with properties and classification (resolved, planet, gas) information. From the catalog, we defined a less biased sample with 612 objects and presented the distributions of their stellar and disk properties to search for correlations between disks and stars. We found debris disks were widely distributed from B to M-type stars while planets were mostly found around solar-type stars, gases were easier to detect around early-type stars and resolved disks were mostly distributed from A to G- type stars. The fractional luminosity dropped off with stellar age and planets were mostly found around old stars while gas-detected disks were much younger. The dust temperature of both one-belt systems and cold components in two-belt systems increased with distance while decreasing with stellar age. In addition, we defined a less biased planet sample with 211 stars with debris disks but no planets and 35 stars with debris disks and planets and found the stars with debris disks and planets had higher metallicities than stars with debris disks but no planets. Among the 35 stars with debris disks and planets, we found the stars with disks and cool Jupiters were widely distributed with age from 10 Myr to 10 Gyr and metallicity from -1.56 to 0.28 while the other three groups tended to be old (> 4Gyr) and metal-rich (> -0.3). Besides, the eccentricities of cool Jupiters are distributed from 0 to 0.932 wider than the other three types of planets (< 0.3).Comment: 34 pages, 12 figures, 3 tables, Accepted for publication in RA

    Direct pulsed laser crystallization of nanocrystals for absorbent layers in photovoltaics: Multiphysics simulation and experiment

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    Direct pulsed laser crystallization (DPLC) of nanoparticles of photoactive material-Copper Indium Selenide (nanoCIS) is investigated by multiphysics simulation and experiments. Laser interaction with nanoparticles is fundamentally different from their bulk counterparts. A multiphysics electromagnetic-heat transfer model is built to simulate DPLC of nanoparticles. It is found smaller photoactive nanomaterials (e.g., nanoCIS) require less laser fluence to accomplish the DPLC due to their stronger interactions with incident laser and lower melting point. The simulated optimal laser fluence is validated by experiments observation of ideal microstructure. Selectivity of DPLC process is also confirmed by multiphysics simulation and experiments. The combination effects of pulse numbers and laser intensity to trigger laser ablation are investigated in order to avoid undesired results during multiple laser processing. The number of pulse numbers is inversely proportional to the laser fluence to trigger laser ablation. (C) 2013 AIP Publishing LLC

    Ultraviolet laser crystallized ZnO:Al films on sapphire with high Hall mobility for simultaneous enhancement of conductivity and transparency

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    One of the most challenging issues in transparent conductive oxides (TCOs) is to improve their conductivity without compromising transparency. High conductivity in TCO films often comes from a high carrier concentration, which is detrimental to transparency due to free carrier absorption. Here we show that UV laser crystallization (UVLC) of aluminum-doped ZnO (AZO) films prepared by pulsed laser deposition on sapphire results in much higher Hall mobility, allowing relaxation of the constraints of the conductivity/transparency trade-off. X-ray diffraction patterns and morphological characterizations show grain growth and crystallinity enhancement during UVLC, resulting in less film internal imperfections. Optoelectronic measurements show that UVLC dramatically improves the electron mobility, while the carrier concentration decreases which in turn simultaneously increases conductivity and transparency. AZO films under optimized UVLC achieve the highest electron mobility of 79 cm(2)/V s at a low carrier concentration of 7.9 x 10(+19) cm(-3). This is realized by a laser crystallization induced decrease of both grain boundary density and electron trap density at grain boundaries. The infrared (IR) to mid-IR range transmittance spectrum shows UVLC significantly enhances the AZO film transparency without compromising conductivity. (C) 2014 AIP Publishing LLC

    Acute lung injury inhibition by juglone in LPS induced sepsis mouse model involves Sirt1 activation

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    Purpose: To investigate the effect of juglone on LPS induced lung injury in a mouse model and in TC 1cell line.Methods: Edema formation in lungs were measured by determination of lung wet/dry weight. Expressions of various proteins were assessed by western blot assay, while Sirt1 level was assessed using immunohistochemistry. Mice were randomly assigned to nine groups of 10 mice each: normal control, untreated and seven juglone treatment groups. Acute lung injury was induced in mice by injecting LPS (10 mg/kg) via intraperitoneal route (ip). The treatment groups were given 10, 20, 30, 40, 50, 60 and 100 ╬╝M of juglone, ip, respectively.Results: The levels of MMP-9, IL-6, IL-1╬▓ and iNOS were significantly higher in acute lung injury induced mice compared than the control group (p &lt; 0.05). Treatment of the mice with juglone significantly decreased LPS-induced up-regulation of inflammatory cytokines in a dose-dependentmanner. The production of inflammatory cytokines was almost completely inhibited in the mice treated with 100 mg/kg dose of juglone, while treatment of the LPS-stimulated TC 1 cells with juglone upregulated the expression of Sirt1 mRNA. Down-regulation of Sirt1 expression by siRNA inhibited the effect of juglone on LPS-induced increase in inflammatory cytokine production.Conclusion: Juglone prevents lung injury in mice via up-regulation of Sirt1 expression. Therefore, juglone might be useful for the development of a treatment strategy for lung injury. Keywords: Inflammatory, Sirtuin, Edema, Cytokines, Lung injury, TC 1 lung alveolar epithelial cells, Sirt
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