File and Object Replication in Data Grids

Data replication is a key issue in a Data Grid and can be managed in different ways and at different levels of granularity: for example, at the file level or object level. In the High Energy Physics community, Data Grids are being developed to support the distributed analysis of experimental data. We have produced a prototype data replication tool, the Grid Data Mirroring Package (GDMP) that is in production use in one physics experiment, with middleware provided by the Globus Toolkit used for authentication, data movement, and other purposes. We present here a new, enhanced GDMP architecture and prototype implementation that uses Globus Data Grid tools for efficient file replication. We also explain how this architecture can address object replication issues in an object-oriented database management system. File transfer over wide-area networks requires specific performance tuning in order to gain optimal data transfer rates. We present performance results obtained with GridFTP, an enhanced version of FTP, and discuss tuning parameters.     

Structure-activity relationship study of β-oxidation resistant indole-based 5-oxo-6,8,11,14-eicosatetraenoic acid (5-oxo-ETE) receptor antagonists

5-Oxo-6,8,11,14-eicosatetraenoic acid (5-oxo-ETE) is formed from 5S-hydroxy-6,8,11,14-eicosatetraenoic acid (5-HETE) by the 5-lipoxygenase (5-LO) pathway under conditions associated with oxidative stress. 5-Oxo-ETE is an important pro-inflammatory mediator, which stimulates the migration of eosinophils via a selective G-protein coupled receptor, known as the OXE receptor (OXE-R). Previously, we designed and synthesized structural mimics of 5-oxo-ETE such as 1 using an indole scaffold. In the present work, we added various substituents at C-3 of this moiety to block potential β-oxidation of the 5-oxo-valerate side chain, and investigated the structure-activity relationships of the resulting novel β-oxidation-resistant antagonists. Cyclopropyl and cyclobutyl substituents were well tolerated in this position, but were less potent as the highly active 3S-methyl compound. It seems likely that 3-alkyl substituents can affect the conformation of the 5-oxovalerate side chain containing the critical keto and carboxyl groups, thereby affecting interaction with the OXE-receptor.     

A resource-sharing model based on a repeated game in fog computing

With the rapid development of cloud computing techniques, the number of users is undergoing exponential growth. It is difficult for traditional data centers to perform many tasks in real time because of the limited bandwidth of resources. The concept of fog computing is proposed to support traditional cloud computing and to provide cloud services. In fog computing, the resource pool is composed of sporadic distributed resources that are more flexible and movable than a traditional data center. In this paper, we propose a fog computing structure and present a crowd-funding algorithm to integrate spare resources in the network. Furthermore, to encourage more resource owners to share their resources with the resource pool and to supervise the resource supporters as they actively perform their tasks, we propose an incentive mechanism in our algorithm. Simulation results show that our proposed incentive mechanism can effectively reduce the SLA violation rate and accelerate the completion of tasks.     

An HPLC-CAD/fluorescence lipidomics platform using fluorescent fatty acids as metabolic tracers

Fluorescent lipids are important tools for live imaging in cell culture and animal models, yet their metabolism has not been well-characterized. Here we describe a novel combined HPLC and LC-MS/MS method developed to characterize both total lipid profiles and the products of fluorescently labeled lipids. Using this approach, we found that lipids labeled with the fluorescent tags, 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene (BODIPY FL), 4,4-difluoro-5-(2-thienyl)-4-bora-3a,4a-diaza-s-indacene [BODIPY(558/568)], and dipyrrometheneboron difluoride undecanoic acid (TopFluor) are all metabolized into varying arrays of polar and nonpolar fluorescent lipid products when they are fed to larval zebrafish. Quantitative metabolic labeling experiments performed in this system revealed significant effects of total dietary lipid composition on fluorescent lipid partitioning. We provide evidence that cholesterol metabolism in the intestine is important in determining the metabolic fates of dietary FAs. Using this method, we found that inhibitors of dietary cholesterol absorption and esterification both decreased incorporation of dietary fluorescent FAs into cholesterol esters (CEs), suggesting that CE synthesis in enterocytes is primarily responsive to the availability of dietary cholesterol. These results are the first to comprehensively characterize fluorescent FA metabolism and to demonstrate their utility as metabolic labeling reagents, effectively coupling quantitative biochemistry with live imaging studies.     

Study of the metabolism of pyrazinamide using a high-performance liquid chromatographic analysis of urine samples

A reversed-phase high-performance liquid chromatographic method was developed for the simultaneous determination of pyrazinamide and its metabolites in urine. Study of the metabolism of pyrazinamide by this method demonstrated that 5-hydroxypyrazinamide excretion was compatible with pyrazinoic acid excretion and allopurinol decreased in vivo conversion of pyrazinamide to 5-hydroxypyrazinamide and blocked that of pyrazinoic acid to 5-hydroxypyrazinoic acid.     

Novel prostaglandin D2-derived activators of peroxisome proliferator-activated receptor-γ are formed in macrophage cell cultures

Incubation of RAW 264.7 murine macrophages with 9,15-dihydroxy-11-oxo-, (5Z,9α,13E,15(S))-Prosta-5,13-dien-1-oic acid [prostaglandin D₂ (PGD₂)] induced formation of considerable peroxisome proliferator-activated receptor-γ (PPARγ) activity [Nature 391 (1998) 79]. Because PGD₂ itself is a poor PPARγ ligand, we incubated RAW 264.7 macrophage cultures with prostaglandin D₂ for 24 h and studied the ability of the metabolites formed to activate PPARγ. PGD₂ products were extracted and fractionated by reverse phase high-performance liquid chromatography. Chemical identification was achieved by UV spectroscopy, gas–liquid chromatography/mass spectrometry and chemical syntheses of reference compounds. PGD₂ was converted to eight products, six of which were identified. Ligand-induced interaction of PPARγ with steroid receptor coactivator-1 was determined by glutathione-S-transferase pull-down assays and PPARγ activation was investigated by transient transfection of RAW 264.7 macrophages. In addition to the previously known ligand 11-oxo-(5Z,9,12E,14Z)-Prosta-5,9,12,14-tetraen-1-oic acid (15-deoxy-Δ^12,14-PGJ₂), a novel PPARγ ligand and activator viz. 9-hydroxy-11-oxo-, (5Z,9α,12E,14Z)-Prosta-5,12,14-trien-1-oic acid (15-deoxy-Δ^12,14-PGD₂) was identified. The biological significance of these results is currently under investigation.     

二维液相色谱法在羊草地上部总蛋白分离中的应用

取8周龄羊草的地上部分,用三氯乙酸-丙酮法沉淀总蛋白,沉淀裂解后将缓冲液置换为起始缓冲液,进行第一维色谱聚焦分离。将第一维分离收集的pH值为8.5至4.0之间的组分分别进行第二维无孔硅胶反相高效液相色谱分离,利用ProteoVue软件获得羊草植株总蛋白pI/UV图谱,即羊草植株总蛋白质表达谱。文中对二维液相色谱法分离羊草蛋白质进行了方法学的研究,在第二维分离中尝试用3种不同的洗脱梯度条件进行分离,优化二维液相色谱分离条件并与传统凝胶双向电泳进行了比较,另外还对二维液相色谱的重现性和准确性进行了检验。实验建立了利用二维液相色谱分离羊草总蛋白的技术方法。     

Solving the SAT problem using a DNA computing algorithm based on ligase chain reaction

A new DNA computing algorithm based on a ligase chain reaction is demonstrated to solve an SAT problem. The proposed DNA algorithm can solve an n-variable m-clause SAT problem in m steps and the computation time required is O (3m+n). Instead of generating the full-solution DNA library, we start with an empty test tube and then generate solutions that partially satisfy the SAT formula. These partial solutions are then extended step by step by the ligation of new variables using Taq DNA ligase. Correct strands are amplified and false strands are pruned by a ligase chain reaction (LCR) as soon as they fail to satisfy the conditions. If we score and sort the clauses, we can use this algorithm to markedly reduce the number of DNA strands required throughout the computing process. In a computer simulation, the maximum number of DNA strands required was 2(0.48n) when n=50, and the exponent ratio varied inversely with the number of variables n and the clause/variable ratio m/n. This algorithm is highly space-efficient and error-tolerant compared to conventional brute-force searching, and thus can be scaled-up to solve large and hard SAT problems.     

基于分子信标的DNA计算

DNA计算是解决一类难以计算问题的一种新方法,这种计算随着问题的增大可以呈指数增长．迄今为止,许多研究成果已经成功地提高了它的性能和增加了它的可行性,本文在基于表面的DNA计算中采用了分子信标编码策略,并对分子信标在与对应的补链杂交形成双链时的受力进行分析,给出3-SAT问题的另一种解法．这种方法比现有的方法更有效,更具发展前景．因为它具有编码简单;耗材底;操作时间短;技术先进等优点．本文尝试了分子生物学,光学和力学的结合．这一工作为DNA计算能解决NP一完全问题提供了更有力的依据．