A comparative analysis of dynamic grids vs. virtual grids using the A3pviGrid framework

With the proliferation of Quad/Multi-core micro-processors in mainstream platforms such as desktops and workstations; a large number of unused CPU cycles can be utilized for running virtual machines (VMs) as dynamic nodes in distributed environments. Grid services and its service oriented business broker now termed cloud computing could deploy image based virtualization platforms enabling agent based resource management and dynamic fault management. In this paper we present an efficient way of utilizing heterogeneous virtual machines on idle desktops as an environment for consumption of high performance grid services. Spurious and exponential increases in the size of the datasets are constant concerns in medical and pharmaceutical industries due to the constant discovery and publication of large sequence databases. Traditional algorithms are not modeled at handing large data sizes under sudden and dynamic changes in the execution environment as previously discussed. This research was undertaken to compare our previous results with running the same test dataset with that of a virtual Grid platform using virtual machines (Virtualization). The implemented architecture, A3pviGrid utilizes game theoretic optimization and agent based team formation (Coalition) algorithms to improve upon scalability with respect to team formation. Due to the dynamic nature of distributed systems (as discussed in our previous work) all interactions were made local within a team transparently. This paper is a proof of concept of an experimental mini-Grid test-bed compared to running the platform on local virtual machines on a local test cluster. This was done to give every agent its own execution platform enabling anonymity and better control of the dynamic environmental parameters. We also analyze performance and scalability of Blast in a multiple virtual node setup and present our findings. This paper is an extension of our previous research on improving the BLAST application framework using dynamic Grids on virtualization platforms such as the virtual box.     

From grids to places

Hafting et al. (2005) described grid cells in the dorsocaudal region of the medial entorhinal cortex (dMEC). These cells show a strikingly regular grid-like firing-pattern as a function of the position of a rat in an enclosure. Since the dMEC projects to the hippocampal areas containing the well-known place cells, the question arises whether and how the localized responses of the latter can emerge based on the output of grid cells. Here, we show that, starting with simulated grid-cells, a simple linear transformation maximizing sparseness leads to a localized representation similar to place fields. Action Editor: Alessandro Treves     

Hybrid genes in the analysis of transformation conditions

Direct gene transfer into plant protoplasts has been recently developed, and conditions for high frequency transformation of SR₁ tobacco protoplasts established. In this paper we analyse numerous transformation parameters in a comparative study on SR₁ Nicotiana tabacum and N. plumbaginifolia, and report on a simple chemical technique for very efficient protoplast transformation. It is based on the synergistic interaction of MgCl₂ and PEG. The technique yielded up to 1400 transformants per 3×10⁵ treated N. tabacum protoplasts (up to 4.8% of the survivors, late selected clones). Using N. plumbaginifolia, the frequencies were 10-fold lower, indicating that the competence for transformation has a species-specific component.Abbreviations PEG polyethyleneglycol - RTF relative transformation frequency - ATF absolute transformation frequency     

Schistosoma mansoni: analysis of cercarial transformation methods

Four methods of transforming cercariae to schistosomulae in vitro in ELAC buffer (pH 7.2, 37 C, 0-6 hr incubation) were compared in relation to biochemical and ultrastructural characteristics. The transformation methods used were chemical (3 mM linoleate), mechanical (centrifuge/vortex), mechanical/chemical, and heat (incubation at 37 C). Ultrastructural characteristics examined were based on the presence or absence of glycocalyx, heptalaminate membrane, cyton granules, and nuclear condition. Two EM fixation methods were used. Biochemical parameters assayed were loss of water tolerance (uptake of trypan blue dye), eicosanoid biosynthesis (PGE, LTB4, and 5-HETE), protein synthesis (leucine uptake), RNA synthesis (uracil and orotic acid uptake), and DNA synthesis (thymidine uptake). EM characteristics were remarkably similar for all transformation methods except heat incubation, with transformed cercariae evidencing the characteristics of schistosomulae (cyton granule migration, absence of glycocalyx and heptalaminate membrane); however, euchromatic nuclei could not be demonstrated using in vivo or in vitro transformation methods. Despite the ultrastructural similarities between transformation methods, biochemical data demonstrated that the resultant organisms were quite different. The chemical transformation method gave the highest rate of loss of water tolerance and eicosanoid production. RNA and protein synthesis were not correlated to ultrastructural changes and were highest in those organisms undergoing mechanical transformation methods, significantly higher than in those cercariae transformed by the chemical method. DNA synthesis was not demonstrated using any transformation method, although thymidine uptake did occur. Our data indicate substantial biochemical differences exist between morphologically similar organisms. Thus, experiments using any type of artificially transformed schistosomule must be interpreted with caution until additional biochemical and physiological studies on cercarial transformation are undertaken.     

A kinetic analysis of the estrogen receptor transformation.

The rate of the 4 to 5 S estrogen-binding protein (EBP) in vitro transformation was measured by sucrose gradient centrifugation analysis. The temperature-activated 4 to 5 S EBP transformation is found to be highly reproducible without loss of [3H]estradiol-binding activity in a buffer containing an excess of [3H]estradiol, 40 mM Tris, 1 mM dithiothreitol, and 1 M urea at pH 7.4. The presence of [3H]estradiol is necessary for the 4 to 5 EBP transformation. A kinetic analysis of the 4 to 5 EBP transformation shows that it is a bimolecular reaction, the dimerization of the 4 S EBP with a second (similar or dissimilar) monomer or subunit. In buffers containing 0.4 M KCl the apparent second order rate constant is 2.3 plus or minus 0-2 times 10-7 M minus 1 min minus 1 at 28 degrees. The reaction is independent of the initial receptor concentration, suggesting that the 4 S EBP is dissociated into monomeric units in buffers of high ionic strength. In buffers without KCl or with 0.1 M KCl the apparent second order rate constant of receptor transformation increases with decreasing receptor concentration. This suggests that the 4 S EBP is associated weakly with another macromolecule (or macromolecules) in buffers of low ionic strength. The rate of 4 to 5 S EBP transformation shows a 200-fold increase between 0 and 35 degrees. The Arrhenius energy of activation is 21.3 kcal mol minus 1 in buffer without KCl and 19.1 kcal mol minus 1 in buffer with 0.4 M KCl. Following the temperature-activated dimerization, the avidity of binding between the 4 S EBP and its complementary subunit is increased, 0.4 M KCl can no longer cause dissociation, and the 5 S EBP dimer appears. This kinetic analysis indicates that the avidity of binding between the subunits of the estrogen receptor is modulated by estradiol, temperature, and ionic strength. We propose that these interactions of the estrogen receptor's subunits reflect conformational changes involved in receptor activation.     

Molecular analysis of genomic DNA-mediated transformation in Zea mays

Total genomic DNA isolated from maize hygromycin B resistant cell line(hygr-G204) was used to transform the maize hygromycin B sensitive cell line(hygs-G204) to the hygr-phenotype using polyethyleneglycol treatment and the transformed calli were selected using hygromycin B. The primary transformant maize plants were regenerated and analysed at the molecular level using DNA hybridization, transgenome rescue and histochemical β-glucuronidase assay. The results indicated that genomic DNA-mediated transformation can lead to transfer, expression and stable integration of a DNA fragment into the host genome. This revised version was published online in July 2006 with corrections to the Cover Date.     

The transformation of local lesion counts for statistical analysis

An analysis of the frequency distribution of local lesions, produced by viruses on half-leaves of a number of plants, shows that their standard error increases with increasing mean. Hence analysis of variance and statistical tests of significance should not be applied to lesion numbers unless they are suitably transformed. The transformation into logarithms over-corrects so that the standard error decreases with increasing mean. A satisfactory transformation is y = log₁₀ ( x + c ), where x is the number of lesions and c is a constant. A method is given of assessing c for different experiments. Great accuracy is not needed; in an experiment discussed in detail a satisfactory transformation is obtained with any value for c between 15 and 80.
On individual plants the numbers of lesions formed on half-leaves are distributed more or less normally, whereas their distribution about the common mean for many plants is skew and 'leptokurtic'. The distribution of the transformed numbers is almost normal, both for individual plants and about the common mean for a number of plants.     

Genetic transformation of Populus genotypes with different chimaeric gene constructs: transformation efficiency and molecular analysis

Aspen (Populus tremula) and hybrid aspen (P. tremula × P. tremuloides) were transformed with different gene constructs using two types of promoter. The aim was to determine the influence of the reporter gene rolC, controlled by promoters of viral or plant origin, on genetic and morphologic expression of different transgenic aspen clones. An improved transformation method using leaf discs was developed, by which putative transgenic plantlets were regenerated at high efficiencies (up to 34%) on kanamycin-containing medium. Transgenic aspen carrying the rolC gene from Agrobacterium rhizogenes under control of the cauliflower-35S-promoter are reduced in size with smaller leaves, whereas aspen transgenic for the same rolC gene, but under control of the light inducible rbcS promoter from potato, are only slightly reduced in size compared to untransformed controls. However, all clones carrying 35S-rolC and rbcS-rolC genes revealed light-green colouration of leaves when compared to untransformed aspen. Owing to this special feature, constructs were used in which expression of the rolC gene was inhibited by insertion of a transposable element, Ac, from maize. Transgenic aspen transformed with the 35S-Ac-rolC and rbcS-Ac-rolC genes were morphologically similar to untransformed aspen, but out of 54 independently regenerated 35S-Ac-rolC transgenic aspen clones, 30 clones showed light-green/dark green variegated leaves. In contrast, out of 19 independently transformed rbcS-Ac-rolC aspen clones, only two clones revealed light-green/dark green variegated leaves. The role of bacterial strains in transformation, and molecular genetics of transgenic aspen plants (including the function of the transposable element, Ac, in the aspen genome) are discussed     

Model selection and logarithmic transformation in allometric analysis

The standard approach to most allometric research is to gather data on a biological function and a measure of body size, convert the data to logarithms, display the new values in a bivariate plot, and then fit a straight line to the transformations by the method of least squares. The slope of the fitted line provides an estimate for the allometric (or scaling) exponent, which often is interpreted in the context of underlying principles of structural and functional design. However, interpretations of this sort are based on the implicit assumption that the original data conform with a power function having an intercept of 0 on a plot with arithmetic coordinates. Whenever this assumption is not satisfied, the resulting estimate for the allometric exponent may be seriously biased and misleading. The problem of identifying an appropriate function is compounded by the logarithmic transformations, which alter the relationship between the original variables and frequently conceal the presence of outliers having an undue influence on properties of the fitted equation, including the estimate for the allometric exponent. Much of the current controversy in allometric research probably can be traced to substantive biases introduced by investigators who followed standard practice. We illustrate such biases with examples taken from the literature and outline a general methodology by which the biases can be minimized in future research.     

XC302的微生物转化及其产物研究

筛选可转化抗肿瘤新药XC302的微生物菌种,并对转化产物和活性进行研究。利用保藏的植物内生真菌进行转化筛选,获得了一株具有转化XC302能力的真菌HCCB07927,经过分子生物学鉴定,该茵属于丝核茵属（Rh＆octonia）,该茵株可转化XC302生成两个转化产物LYBXYl、LY-BXY2。经MS．MS分析初步确定了两个化合物的结构。抗肿瘤活性测定表明,两个产物均对PANC一1细胞具有较高的抑制作用,其抑制率高于对照品XC302。通过微生物转化技术,成功获得两个转化产物,其均对PANC．1细胞具有较高抑制活性。     

Linear relaxation analysis of the mechanochemical transformation of collagen fibers

The isometric tensile stress generation observed when collagen fibers are immersed in aqueous solutions of lithium bromide ranging in molar concentration up to 7 was studied at 23°C. The reverse process, namely, isometric stress relaxation of the fiber occurring by subsequent immersion in distilled water, was also studied. We find that the data in the region of LiBr concentration up to about 2.5 moles/liter are adequately represented by a superposition integral where σ(t) is the time-dependent stress generated by the collagen fiber held at fixed length, c(t) is the history of LiBr molar concentration, and K(t) is the isometric contractility function, expressed as stress per unit salt concentration. We conclude that, within a limited range of salt concentration, a collagen fiber in a LiBr bath behaves as if it were a linear, time-invariant system defined mechanochemically by a single function K(t) which depends on the structural characteristics of the fiber while being independent of salt concentration. An analysis is presented of isometric mechanochemical data obtained under conditions of equilibrium by other workers who studied the behavior of collagen fibers in aqueous solutions either of urea, LiBr, or KCNS. The analysis shows that these independent (equilibrium) data confirm the linarity of the relation between isometric contractile stress and salt concentration on which our superposition integral representation is based. We also find that the asymptotic (infinite-time) value of the isometric stress is linearly related to the chemical potential of the salt as well, in agreement with the equilibrium thermodynamic treatment of mechanochemical processes by Katchalsky and Oplatka.     

Similarity transformation approach to identifiability analysis of nonlinear compartmental models

Through use of the local state isomorphism theorem instead of the algebraic equivalence theorem of linear systems theory, the similarity transformation approach is extended to nonlinear models, resulting in finitely verifiable sufficient and necessary conditions for global and local identifiability. The approach requires testing of certain controllability and observability conditions, but in many practical examples these conditions prove very easy to verify. In principle the method also involves nonlinear state variable transformations, but in all of the examples presented in the paper the transformations turn out to be linear. The method is applied to an unidentifiable nonlinear model and a locally identifiable nonlinear model, and these are the first nonlinear models other than bilinear models where the reason for lack of global identifiability is nontrivial. The method is also applied to two models with Michaelis-Menten elimination kinetics, both of considerable importance in pharmacokinetics, and for both of which the complicated nature of the algebraic equations arising from the Taylor series approach has hitherto defeated attempts to establish identifiability results for specific input functions.     

Proteomics analysis reveals insight into the mechanism of H-Ras-mediated transformation

We implemented a proteomics approach to the systematical analysis of the alterations in the proteome of NIH3T3 cells transformed by oncogenic H-RasV12. Forty-four proteins associated with Ras-mediated transformation have been identified, and 28 proteins were not previously reported. RT-PCR analysis showed that approximately 44% of target proteins identified showed concomitant changes in mRNA abundance. A principal finding was the up-regulation of gankyrin, which was the first evidence to show that gankyrin pathway was implicated in Ras-activated transformation.     

Security-driven scheduling for data-intensive applications on grids

Security-sensitive applications that access and generate large data sets are emerging in various areas including bioinformatics and high energy physics. Data grids provide such data-intensive applications with a large virtual storage framework with unlimited power. However, conventional scheduling algorithms for data grids are unable to meet the security needs of data-intensive applications. In this paper we address the problem of scheduling data-intensive jobs on data grids subject to security constraints. Using a security- and data-aware technique, a dynamic scheduling strategy is proposed to improve quality of security for data-intensive applications running on data grids. To incorporate security into job scheduling, we introduce a new performance metric, degree of security deficiency, to quantitatively measure quality of security provided by a data grid. Results based on a real-world trace confirm that the proposed scheduling strategy significantly improves security and performance over four existing scheduling algorithms by up to 810% and 1478%, respectively.

Meta-communications in component-based communication frameworks for grids

Applications are faced with several network-related problems on current grids: heterogeneous networks, firewalls, NAT, private IP addresses, non-routed networks, performance problems on WAN. Moreover, the requirements concerning communications are varied and the acceptable tradeoffs highly depends on the applications. A solution to reach the flexibility regarding communication on grids is the use of a component-based communication framework. The users then compose their own protocol stacks by assembling building blocks in the way they want. However, a truly flexible and dynamic component-based communication framework needs a meta-communication channel for its out-of-band communications required by dynamic component assembly in a consistent way on multiple nodes. The meta-communication channel is useful for some “brokered” communication methods, too, and in particular those designed to cross firewalls. The meta-communication channel has often been the “weakest link” of component-based communication frameworks: bottleneck for the performance, back-door from the security point of view, and limited connectivity. In this article, we present an architecture for a meta-communication channel that suffers from none of the aforementioned limitations. It exhibits good properties regarding connectivity, security and performance. Thus, the gain in flexibility brought by software components may be fully exploited without trading anything against flexibility.