Adaptive Sector Grouping to Reduce False Sharing in Distributed RAID

Distributed redundant array of inexpensive disks (RAID) is often embedded in a cluster architecture. In a centralized RAID subsystem, the false sharing problem does not exist, because the disk array allows only mutually exclusive access by one user at a time. However, the problem does exist in a distributed RAID architecture, because multiple accesses may occur simultaneously in a distributed environment. This problem will seriously limit the effectiveness of collective I/O operations in network-based, cluster computing. Traditional accesses to disks in a RAID are done at block level. The block granularity is large, say 32 KB, often resulting in false sharing among fragments in the block. The false sharing problem becomes worse when the block size or the stripe unit becomes too large. To solve this problem, we propose an adaptive sector grouping approach to accessing a distributed RAID. Each sector has a fine grain of 512 B. Multiple sectors are grouped together to match with the data block size. The grouped sector has a variable size that can be adaptively adjusted by software. Benchmark experiments reveal the positive effects of this adaptive access scheme on the performance of a RAID. Our scheme can reduce the collective I/O access time without increasing the buffer size. Both theoretical analysis and experimental results demonstrate the performance gain in using grouped sectors for fast access of distributed RAID.     

(Brady)Rhizobium-plant communications involved in infection and nodulation

Conclusion The interactions between(Brady)Rhizobium and legume plants involves many interesting problems. In the last ten years, there were remarkable experiments which have detected excreted flavonoid compounds at pmol levels from plant roots, which induce(Brady)Rhizobium nod gene expression (Long 1989, Nap and Bisseling 1990, Dénariéet al. 1992, Schlamanet al. 1992). The responses of rhizobial genes to the various kinds of chemical compound are different (Maxwellet al. 1989, Zaatet al. 1989, Davis and Johnston 1990, Hartwiget al. 1990, Hungriaet al. 1992). The resolution of pSym genes controlling those mechanisms makes way for the long-term goal of introducing nitrogen fixation ability into nonlegume plants. Recently, some experiments have shown thatRhizobium and other nitrogen fixing bacteria form nodule-like strutures on rice, barley or wheat (Al-Mallah 1989, Jinget al. 1990, Rolfe and Bender 1991). Some O₂ protection mechanism instead of leghemoglobin must be needed for nitrogen fixation byRhizobium or other N₂-fixing bacteria which have invaded in the nonlegume root tissue. The isolation of the plant mutants or preparation of transgenic plants capable of hyper-nodule formation having efficient nitrogen fixation ability may be major goals. For the attainment of these goals, transformation of a foreign genome (nif-ornod gene cassette) into the plant cell might be a good way to proceed (Barkeret al. 1990). It is also necessary to clarify the relationships between the level of relative endogenous plant hormones and the exchange of the differentiation of the root tissue to the nodule tissue. This phenomenon of redifferentiation of plant tissue by the results from(Brady)Rhizobium and legume communications will be an important approach likely to lead to solve the molecular basis of plant having “TOTIPOTENCY”.     

Peroxynitrite decay in the presence of hydrogen peroxide,mannitol and ethanol: A reappraisal

We have reported previously that the apparent rate of peroxynitrite (ONOO^-) decay, as followed from its absorbance at 302 nm, decreases in the presence of hydrogen peroxide, mannitol and ethanol (Alvarez et al., 1995, Chem. Res. Toxicol. 8:859-864; Alvarez et al., 1998, Free Radic. Biol. Med. 24:1331–1337). Recently, two papers confirmed the observation and proposed that this slowing effect was due to the formation of absorbing peroxynitrate (O₂NOO^-) as intermediate (Goldstein and Czapski, 1998, J. Am. Chem. Soc. 120:3458–3463; Hodges and Ingold, 1999, J. Am. Chem. Soc. 121:10695–10701). Peroxynitrate would be formed from the reaction of peroxynitrite-derived nitrogen dioxide with superoxide. Superoxide, in turn, would arise from the one-electron oxidation of hydrogen peroxide, or from the reaction of reductive radicals derived from mannitol and ethanol with dioxygen. In agreement with this concept, we show herein that under the conditions of our previous work, the slowing effect is prevented by superoxide dismutase and, in the case of mannitol and ethanol, by reducing the dioxygen concentration of the reaction solutions. Thus, superoxide formation is necessary for the decrease in the rate of absorbance decay. In addition, by simulations using known rate constants and absorption coefficients, we show that the slowing effect can be quantitatively accounted for by the formation of peroxynitrate.     

Making choices between rules or between actions

A new study by Klaes et al. in this issue of Neuron shows that the brain can simultaneously apply two rules to the same sensory information in order to specify two parallel potential action goals, which then compete for execution in the sensorimotor system.     

广东省南雄盆地白垩系—第三系交界恐龙绝灭问题

广东省南雄盆地中的红层可划分为三个群五个组,大致代表了晚白垩世—始新世的沉积.根据绝对年龄、古地磁测定结果和脊椎动物化石组合性质的综合分析,位于地磁极性带 29R 上部的坪岭组和上湖组之间的分界线被确定为 K/T 界线.对晚白垩世恐龙蛋的研究表明,不同"种"的恐龙蛋是在地磁极性带 29R 的中、下部,也就是说在白垩系—第三系交界之前20～30万年期间绝迹的.而且在这一时期内,所有已发现的蛋壳中,绝大多数蛋壳的厚度和显微结构都显示出明显的病理特征,例如根据随机取样统计,Macroolithus yaotunensis 蛋壳异常结构的出现率,最高可达75%.产生病态恐龙蛋壳的生理机制可以根据发生在现生鸟类的相同病理特征来解释.进一步分析恐龙蛋壳的微量元素和稳定同位素组成,结果显示, Pb, Cu, Mn 等9种元素丰度变化在这一时期达到最大峰值, δ~(18)O 也出现正异常.在这一基础上提出,微量元素的污染和气候突然的变化妨碍了正常蛋壳结构的形成,导致了恐龙的绝灭.这一绝灭过程大约经历了20～30万年.     

A new gene (madI) involved in the phototropic response of Phycomyces

Summary Only eight genes are known to be involved in the phototropic response of Phycomyces (madA-H). Mutants affected in these genes have played a major role in the analysis of photosensory transduction processes in this system. A set of new mutants isolated by Alvarez et al. (1989) that are unable to bend towards dim unilateral blue light were studied by complementation and recombination. Two of these mutants have mutations in madE, one has a mutation in madF and one is a double madE madF mutant. The three remaining mutants tested did not complement each other and showed positive complementation with strains carrying mutations in the genes madA, madB, and madC, indicating that they carried mutations in a new gene designated madI. Recombination analysis showed that madI is unlinked to madA, madB and madC.     

RAID level selection for heterogeneous disk arrays

Heterogeneous Disk Arrays (HDAs) allow resource sharing of their hardware by multiple RAID levels. RAID1 (mirrored disks) and RAID5 (distributed parity arrays) are the two RAID levels considered in this study. They are both single disk failure tolerant (1DFT), but differ significantly in their efficiency in processing database workloads. The goal of the study is to maximize the number of Virtual Array (VA) allocations in HDA. We develop an analysis to estimate the load per VA based on a few parameters: the fraction of accesses to small versus large blocks and the fraction of updates versus reads. A VA is allocated according to the RAID level, which minimizes the anticipated load based on input parameters. Operation in normal and degraded mode is considered for comparison purposes, but in fact allocations are carried out using the higher load in degraded mode to ensure that single disk failures will not result in overload. We report on parametric studies to gain insight into circumstances leading to a RAID1 or RAID5 classification. An allocation experiment with a synthetic workload is used to demonstrate the superiority of HDA with respect to purely RAID1 or RAID5 disk arrays. This analytic study can be extended to 2DFT arrays, namely RAID6 versus 3-way replication.     

Recent Advances in GFP Folding Reporter and Split-GFP Solubility Reporter Technologies. Application to Improving the Folding and Solubility of Recalcitrant Proteins from Mycobacterium tuberculosis

We have improved our green fluorescent protein (GFP) folding reporter technology [Waldo et al., (1999) Nat. Biotechnol. 17, 691–695] to evolve recalcitrant proteins from Mycobacterium tuberculosis. The target protein is inserted into the scaffolding of the GFP, eliminating false-positive artifacts caused by expression of truncated protein variants from internal cryptic ribosome binding sites in the target RNA. In parallel, we have developed a new quantitative fluorescent protein tagging and detection system based on micro-domains of GFP. This split-GFP system, which works both in vivo and in vitro, is amenable to high-throughput assays of protein expression and solubility [Cabantous et al., (2005) Nat. Biotechnol. 23, 102–107]. Together, the GFP folding reporter and split-GFP technologies offer a comprehensive system for manipulating and improving protein folding and solubility.     

Role of histone tails in the conformation and interactions of nucleosome core particles

The goal of this work was to test the role of the histone tails in the emergence of attractive interactions between nucleosomes above a critical salt concentration that corresponds to the complete tail extension outside the nucleosome [Mangenot, S., et al (2002) Biophys. J. 82, 345-356; Mangenot, S., et al (2002) Eur. Phys. J. E 7, 221-231]. Small angle X-ray scattering experiments were performed in parallel with intact and trypsin tail-deleted nucleosomes with 146 +/- 3 bp DNA. We varied the monovalent salt concentration from 10 to 300 monovalent salt concentration and followed the evolution of (i) the second virial coefficient that characterizes the interactions between particles and (ii) the conformation of the particle. The attractive interactions do not emerge in the absence of the tails, which validates the proposed hypothesis.     

Strategies in preflight for an optimal Yurchenko layout vault

An optimal Yurchenko layout vault of an elite female gymnast was identified by Koh et al. [2003. A predicted optimal performance of the Yurchenko layout vault in women's artistic gymnastics. Journal of Applied Biomechanics 19, 187-204] to require a combination of an increased body angle at horse contact and increased angular momentum for postflight than was recorded experimentally. However, the individual effect of each of these variables to producing the optimal vault is not known. The purpose of the study was to determine an appropriate strategy to teaching the optimal Yurchenko layout vault. Separate optimisations were carried out to investigate how each of these variables would change in order to produce the optimal vault identified by Koh et al. (2003). A combined optimal parameter selection and optimal control approach was used. The results suggest that when the body angle of attack at horse impact was kept low, pre-flight angular momentum had to be increased, with further gains during horse impact, to produce an optimal vault. This strategy of increasing solely the level of angular momentum needed for optimum postflight may not be attainable realistically. On the other hand, employing a larger body angle of attack required an increase in angular momentum during impact but which was attainable. Both optimisations show that increasing the vertical CM horse takeoff velocity is essential for postflight height and distance. The strategy to enhance performance should thus focus on maintaining an appropriate CM pre-flight velocity, a high level of angular momentum during pre-flight and to contact the horse with a large body angle of attack.     

A New Enzymatic Method for the Measurement of Creatinine Involving a Novel ATP-dependent Enzyme,N-Methylhydantoin Amidohydrolase

A new enzymatic method for the measurement of serum and urine creatinine is described. The method is based on a novel microbial creatinine degradation pathway via N-methylhydantoin [Shimizu et al., Clin. Chim. Acta, 185, 241–252 (1989)]. By using two novel enzymes, N-methylhydantoin amidohydrolase and N-carbamoylsarcosine amidohydrolase, as key enzymes, coupled with a colorimetric procedure for hydrogen peroxide detection, the creatinine level can be measured. The results obtained for human serum and urine show good correlation with those obtained by a standard chemical method based on the Jaffe reaction. The new method is simple and specific, and shows excellent sensitivity and reliability.     

Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers

Within the CHARMM polarizable force field based on the classical Drude oscillator, atomic polarizabilities are derived via fitting to ab initio calculated data on isolated gas phase molecules, with an empirical scaling factor applied to account for differences between the gas and condensed phases. In the development of polarizable models for the ethers, a polarizability scaling factor of 0.7 was previously applied [Vorobyov et al. J Comput Chem 3:1120–1133, 2007]. While the resulting force field models gave good agreement with a variety of experimental data, they systematically underestimated the liquid phase dielectric constants. Here, a new CHARMM polarizable model is developed for the ethers, employing a polarizability scaling factor of 0.85 and including atom-based Thole scale factors recently introduced into the CHARMM Drude polarizable force field [Harder et al. J Phys Chem B 112:3509-3521, 2008]. The new model offers a significant improvement in the reproduction of liquid phase dielectric constants, while maintaining the good agreement of the previous model with all other experimental and quantum mechanical data, highlighting the sensitivity of liquid phase properties to the choice of atomic polarizability parameters.     

An annealed chaotic maximum neural network for bipartite subgraph problem

In this paper, based on maximum neural network, we propose a new parallel algorithm that can help the maximum neural network escape from local minima by including a transient chaotic neurodynamics for bipartite subgraph problem. The goal of the bipartite subgraph problem, which is an NP- complete problem, is to remove the minimum number of edges in a given graph such that the remaining graph is a bipartite graph. Lee et al. presented a parallel algorithm using the maximum neural model (winner-take-all neuron model) for this NP- complete problem. The maximum neural model always guarantees a valid solution and greatly reduces the search space without a burden on the parameter-tuning. However, the model has a tendency to converge to a local minimum easily because it is based on the steepest descent method. By adding a negative self-feedback to the maximum neural network, we proposed a new parallel algorithm that introduces richer and more flexible chaotic dynamics and can prevent the network from getting stuck at local minima. After the chaotic dynamics vanishes, the proposed algorithm is then fundamentally reined by the gradient descent dynamics and usually converges to a stable equilibrium point. The proposed algorithm has the advantages of both the maximum neural network and the chaotic neurodynamics. A large number of instances have been simulated to verify the proposed algorithm. The simulation results show that our algorithm finds the optimum or near-optimum solution for the bipartite subgraph problem superior to that of the best existing parallel algorithms.     

Germicide capacity of macrophages (MØ) in the Antarctic fish Notothenia coriiceps (Richardson, 1844) at 0°C

The germicide capability of the macrophage (MØ) of the Antarctic fish Notothenia coriiceps is demonstrated using fluorescence microscopy for the first time. The MØs were able to kill microorganisms by intracellular mechanism and this killing can be stimulated by oyster-derived glycogen. Although the phagocytosis index is lower than in temperate water fish species, this work demonstrates that non-specific defence mechanism plays an important role in the polar environment. There are some studies on inflammation in N. coriiceps [Silva et al. (1998) Polar Biol 20:206–212], parasite–host relation [Silva et al. (1999) Polar Biol 22:417–424] and phagocytosis [Silva et al. (2002) J Fish Biol 60:466–478]. These previous studies have shown that the MØ were able to identify biotic and abiotic factors. However, it can be of interest to study the activity of MØ in microorganism killing, and this work adds new insights of this fundamental process under Antarctic temperatures.     

Peroxynitrite decay in the presence of hydrogen peroxide, mannitol and ethanol: a reappraisal

We have reported previously that the apparent rate of peroxynitrite (ONOO(-) ) decay, as followed from its absorbance at 302 nm, decreases in the presence of hydrogen peroxide, mannitol and ethanol (Alvarez et al., 1995, Chem. Res. Toxicol. 8:859-864; Alvarez et al., 1998, Free Radic. Biol. Med. 24:1331-1337). Recently, two papers confirmed the observation and proposed that this slowing effect was due to the formation of absorbing peroxynitrate (O(2) NOO(-) ) as intermediate (Goldstein and Czapski, 1998, J. Am. Chem. Soc. 120:3458-3463; Hodges and Ingold, 1999, J. Am. Chem. Soc. 121:10695-10701). Peroxynitrate would be formed from the reaction of peroxynitrite-derived nitrogen dioxide with superoxide. Superoxide, in turn, would arise from the one-electron oxidation of hydrogen peroxide, or from the reaction of reductive radicals derived from mannitol and ethanol with dioxygen. In agreement with this concept, we show herein that under the conditions of our previous work, the slowing effect is prevented by superoxide dismutase and, in the case of mannitol and ethanol, by reducing the dioxygen concentration of the reaction solutions. Thus, superoxide formation is necessary for the decrease in the rate of absorbance decay. In addition, by simulations using known rate constants and absorption coefficients, we show that the slowing effect can be quantitatively accounted for by the formation of peroxynitrate.     

Parametric and ensemble sequence alignment algorithms

Recently algorithms for parametric alignment (Watermanet al., 1992,Natl Acad. Sci. USA 89, 6090–6093; Gusfieldet al., 1992,Proceedings of the Third Annual ACM-SIAM Discrete Algorithms) find optimal scores for all penalty parameters, both for global and local sequence alignment. This paper reviews those techniques. Then in the main part of this paper dynamic programming methods are used to compute ensemble alignment, finding all alignment scores for all parameters. Both global and local ensemble alignments are studied, and parametric alignment is used to compute near optimal ensemble alignments.     

A java applet for exploring the new higher level classification of eukaryotes with emphasis on the taxonomy of protists

ABSTRACT. We have converted the hierarchically organized new higher level classification of eukaryotes with emphasis on the taxonomy of protists proposed by Adl et al. into an interactive and dynamic Java applet. The current version of the applet can be accessed via http://phylogenetics.bioapps.biozentrum.uni-wuerzburg.de/etv . We use the layout from a Degree-of-Interest tree (DOITree) that effectively displays all the taxonomic information as well as the phylogenetic relationships described in the original article by Adl et al. The tree was made using the Prefuse Toolkit for interactive information visualization. All browsers capable of using Java applets will be able to view the tree. The applet is freely available for scientists, teachers, and students.     

Index to Authors,Volume 6

Abstract

The refractive indices of wet-spun films of CsDNA have been measured for light polarized parallel and perpendicular to the helical axis as a function of relative humidity (RH). These data have been combined with previously published data (Biopolymers 30 (1990) 877–887) for the volume per base pair and water content as a function of RH in order to extract the optical polarizabilities. This work was motivated by the study of Weidlich et al. (Biopolymers 26 (1987) 439–453) who reported a ～35% increase at the A-to-B transition in the parallel and perpendicular polarizabilities of NaDNA. In contrast, a much smaller increase in the polarizabilities of CsDNA is found near the A-to-B transition: ～ 12% for the perpendicular direction and < 4% for the parallel direction.     

A nonlinear biphasic viscohyperelastic model for articular cartilage

Experiments on articular cartilage have shown nonlinear stress-strain curves under finite deformations as well as intrinsic viscous effects of the solid phase. The aim of this study was to propose a nonlinear biphasic viscohyperelastic model that combines the intrinsic viscous effects of the proteoglycan matrix with a nonlinear hyperelastic constitutive equation. The proposed equation satisfies objectivity and reduces for uniaxial loading to a solid type viscous model in which the actions of the springs are represented by the hyperelastic function proposed by Holmes and Mow [1990. J. Biomechanics 23, 1145-1156.]. Results of the model, that were efficiently implemented in an updated Lagrangian algorithm, were compared with experimental infinitesimal data reported by DiSilverstro and Suh [2001. J. Biomechanics 34, 519-525.] and showed acceptable fitting for the axial force (R(2)=0.991) and lateral displacement (R(2)=0.914) curves in unconfined compression as well as a good fitting of the axial indentation force curve (R(2)=0.982). In addition, the model showed an excellent fitting of finite-deformation confined compression stress relaxation data reported by Ateshian et al. [1997. J. Biomechanics 30, 1157-1164.] and Huang et al. [2005. J. Biomechanics 38, 799-809.] (R(2)=0.993 and R(2)=0.995, respectively). The constitutive equation may be used to represent the mechanical behavior of the proteoglycan matrix in a fiber reinforced model of articular cartilage.