Large improvements in application throughput of long-running multi-component applications using batch grids

Computational grids with multiple batch systems (batch grids) can be powerful infrastructures for executing long-running multi-component parallel applications. In this paper, we evaluate the potential improvements in throughput of long-running multi-component applications when the different components of the applications are executed on multiple batch systems of batch grids. We compare the multiple batch executions with executions of the components on a single batch system without increasing the number of processors used for executions. We perform our analysis with a foremost long-running multi-component application for climate modeling, the Community Climate System Model (CCSM). We have built a robust simulator that models the characteristics of both the multi-component application and the batch systems. By conducting large number of simulations with different workload characteristics and queuing policies of the systems, processor allocations to components of the application, distributions of the components to the batch systems and inter-cluster bandwidths, we show that multiple batch executions lead to 55% average increase in throughput over single batch executions for long-running CCSM. We also conducted real experiments with a practical middleware infrastructure and showed that multi-site executions lead to effective utilization of batch systems for executions of CCSM and give higher simulation throughput than single-site executions. Copyright (c) 2011 John Wiley & Sons, Ltd.

Expansions of tau hadronic spectral function moments in a nonpower QCD perturbation theory with tamed large order behavior

The moments of the hadronic spectral functions are of interest for the extraction of the strong coupling alpha(s) and other QCD parameters from the hadronic decays of the tau lepton. Motivated by the recent analyses of a large class of moments in the standard fixed-order and contour-improved perturbation theories, we consider the perturbative behavior of these moments in the framework of a QCD nonpower perturbation theory, defined by the technique of series acceleration by conformal mappings, which simultaneously implements renormalization-group summation and has a tame large-order behavior. Two recently proposed models of the Adler function are employed to generate the higher-order coefficients of the perturbation series and to predict the exact values of the moments, required for testing the properties of the perturbative expansions. We show that the contour-improved nonpower perturbation theories and the renormalization-group-summed nonpower perturbation theories have very good convergence properties for a large class of moments of the so-called ``reference model,'' including moments that are poorly described by the standard expansions. The results provide additional support for the plausibility of the description of the Adler function in terms of a small number of dominant renormalons.

Large-MIMO Receiver based on Linear Regression of MMSE Residual

Multiple input multiple output (MIMO) systems with large number of antennas have been gaining wide attention as they enable very high throughputs. A major impediment is the complexity at the receiver needed to detect the transmitted data. To this end we propose a new receiver, called LRR (Linear Regression of MMSE Residual), which improves the MMSE receiver by learning a linear regression model for the error of the MMSE receiver. The LRR receiver uses pilot data to estimate the channel, and then uses locally generated training data (not transmitted over the channel), to find the linear regression parameters. The proposed receiver is suitable for applications where the channel remains constant for a long period (slow-fading channels) and performs quite well: at a bit error rate (BER) of 10(-3), the SNR gain over MMSE receiver is about 7 dB for a 16 x 16 system; for a 64 x 64 system the gain is about 8.5 dB. For large coherence time, the complexity order of the LRR receiver is the same as that of the MMSE receiver, and in simulations we find that it needs about 4 times as many floating point operations. We also show that further gain of about 4 dB is obtained by local search around the estimate given by the LRR receiver.

Origin of 1/f noise in graphene produced for large-scale applications in electronics

The authors report a detailed investigation of the flicker noise (1/f noise) in graphene films obtained from chemical vapour deposition (CVD) and chemical reduction of graphene oxide. The authors find that in the case of polycrystalline graphene films grown by CVD, the grain boundaries and other structural defects are the dominant source of noise by acting as charged trap centres resulting in huge increase in noise as compared with that of exfoliated graphene. A study of the kinetics of defects in hydrazine-reduced graphene oxide (RGO) films as a function of the extent of reduction showed that for longer hydrazine treatment time strong localised crystal defects are introduced in RGO, whereas the RGO with shorter hydrazine treatment showed the presence of large number of mobile defects leading to higher noise amplitude.

Parametric studies of tension leg platform with large amplitude motions

Tension leg platform (TLP) is an important kind of working station for deep water exploration and development in ocean, whose dynamic responses deserve a serious thought. It is shown that for severe sea state, the effects of nonlinearities induced by large displacements of TLP may be noteworthy, and then employment of small displacements model should be restrained. In such situation, large amplitude motion model may be an appropriate alternative. The numerical experiments are performed to study the differences of dynamic responses between the two models. It is shown that for most cases, differences between results of the two models are significant. The variances of the differences vs. the wave period are the most remarkable, and that of the differences vs. wave heading angle are also apparent.

Diet composition of large striped bass (Morone saxatilis) in Chesapeake Bay

Large (>458 mm) striped bass (Morone saxatilis) are dominant predators in Chesapeake Bay. In recent years, the Chesapeake Bay stock of striped bass has increased dramatically, raising concerns about their predatory impact and their forage requirements. In response to these concerns and the need for more recent ecological studies, this investigation was conducted to characterize feeding habits of large striped bass in Chesapeake Bay. Stomach contents from 1225 striped bass from 458 to 1151 mm TL were examined in the spring and fall of 1997 and 1998. Striped bass consumed 52 different species of vertebrates and invertebrates; however, only a few species of clupeoid and sciaenid fishes dominated diets across both the seasons and size ranges of striped bass examined. Of finfish species, menhaden (Brevoortia tyrannus) was the dominant prey in most areas and gizzard shad (Dorosoma cepedianum) replaced menhaden in importance in lower salinity waters. Spot (Leiostomus xanthurus) and other sciaenid fishes and anadromous herrings (Alosa spp.) also contibuted large percentages of striped bass diet. Although pelagic schooling fishes formed the majority of the diet, benthic fishes contributed a higher percentage to the diet than in previous studies of striped bass diet composition.

Uncertainty management for on-line optimisation of a POMDP-based large-scale spoken dialogue system

The optimization of dialogue policies using reinforcement learning (RL) is now an accepted part of the state of the art in spoken dialogue systems (SDS). Yet, it is still the case that the commonly used training algorithms for SDS require a large number of dialogues and hence most systems still rely on artificial data generated by a user simulator. Optimization is therefore performed off-line before releasing the system to real users. Gaussian Processes (GP) for RL have recently been applied to dialogue systems. One advantage of GP is that they compute an explicit measure of uncertainty in the value function estimates computed during learning. In this paper, a class of novel learning strategies is described which use uncertainty to control exploration on-line. Comparisons between several exploration schemes show that significant improvements to learning speed can be obtained and that rapid and safe online optimisation is possible, even on a complex task. Copyright © 2011 ISCA.

Effects of turbulent reynolds number on the performance of algebraic flame surface density models for large eddy simulation in the thin reaction zones regime: A direct numerical simulation analysis

A direct numerical simulation (DNS) database of freely propagating statistically planar turbulent premixed flames with a range of different turbulent Reynolds numbers has been used to assess the performance of algebraic flame surface density (FSD) models based on a fractal representation of the flame wrinkling factor. The turbulent Reynolds number Ret has been varied by modifying the Karlovitz number Ka and the Damköhler number Da independently of each other in such a way that the flames remain within the thin reaction zones regime. It has been found that the turbulent Reynolds number and the Karlovitz number both have a significant influence on the fractal dimension, which is found to increase with increasing Ret and Ka before reaching an asymptotic value for large values of Ret and Ka. A parameterisation of the fractal dimension is presented in which the effects of the Reynolds and the Karlovitz numbers are explicitly taken into account. By contrast, the inner cut-off scale normalised by the Zel'dovich flame thickness ηi/δz does not exhibit any significant dependence on Ret for the cases considered here. The performance of several algebraic FSD models has been assessed based on various criteria. Most of the algebraic models show a deterioration in performance with increasing the LES filter width. © 2012 Mohit Katragadda et al.

Detection of serum and mucosal antibody production and antibody secreting cells (ASCs) in large yellow croaker (Pseudosciaena crocea) following vaccination with Vibrio harveyi via different routes

The kinetics of mucosal and serum antibody response is well as antibody secreting cells (ASCs) production were studied in large yellow croaker following vaccination with inactivated Vibrio harveyi by different routes: oral administration. intraperitoneal (IP) injection and immersion. Indirect ELISA was used to measure the antibody level in serum and cutaneous mucus, and ELISPOT was used to monitor the ASCs derived from gill, blood and head kidney. The data demonstrated that IP injection resulted in the highest antibody levels in the systemic circulation, whereas immersion induced significant antibody levels in mucous. As for the ASCs response, IP injection induced high numbers of ASCs in the head kidney and blood; oral intubation only induced a slight ASCs response in the head kidney: immersion induced a much stronger ASCs response in the gill. These results indicate that mucosal antibodies following immersion immunization are independent of a systemic response and more sensitive, since it could be triggered earlier than serum antibodies. The mucosal antibodies following IP injection immunization may depend oil a systemic immune response. The protective effects of the three vaccination methods were compared by challenging with live V. harveyi. Survival of the three groups of vaccinated fish varied front 40 to 60%. while 100% mortality was found in control fish. Compared with IP and oral vaccination, immersion stimulated higher specific antibody titers in the mucosal system and achieved similar protection, so it is in effective and efficient method for immunizing a large number of fish against V harveyi (C) 2008 Elsevier B.V. All rights reserved.

Top down scale-up of semiconducting nanostructures for large area electronics

In this paper, we present a study on electrical and optical characteristics of n-type tin-oxide nanowires integrated based on top-down scale-up strategy. Through a combination of contact printing and plasma based back-channel passivation, we have achieved stable electrical characteristics with standard deviation in mobility and threshold voltage of 9.1% and 25%, respectively, for a large area of 1× 1 cm2 area. Through use of contact printing, high alignment of nanowires was achieved thus minimizing the number of nanowire-nanowire junctions, which serve to limit carrier transport in the channel. In addition, persistent photoconductivity has been observed, which we attribute to oxygen vacancy ionization and subsequent elimination using a gate pulse driving scheme. © 2014 IEEE.

Progress of large-scale air-sea interaction studies in China

This paper summarizes the progress of large-scale air-sea interaction studies that has been achieved in China in the four-year period from July 1998 to July 2002, including seven aspects in the area of the air-sea interaction, namely air-sea interaction related to the tropical Pacific Ocean, monsoon-related air-sea interaction, air-sea interaction in the north Pacific Ocean, air-sea interaction in the Indian Ocean, air-sea interactions in the global oceans, field experiments, and oceanic cruise surveys. However more attention has been paid to the first and the second aspects because a large number of papers in the reference literature for preparing and organizing this paper are concentrated in the tropical Pacific Ocean, such as the ENSO process with its climatic effects and dynamics, and the monsoon-related air-sea interaction. The literature also involves various phenomena with their different time and spatial scales such as intraseasonal, annual, interannual, and interdecadal variabilities in the atmosphere/ocean interaction system, reflecting the contemporary themes in the four-year period at the beginning of an era from the post-TOGA to CLIVAR studies. Apparently, it is a difficult task to summarize the great progress in this area, as it is extracted from a large quantity of literature, although the authors tried very hard.

雨生红球藻Rubisco在虾青素积累过程中的表达分析

虾青素因其具有极强的抗氧化性及优越的着色作用，被广泛应用于营养保健和水产养殖中，备受国内外研究者的关注。红球藻是目前虾青素的生物来源中较有优势的一条途径。 我们选取雨生红球藻作为研究材料，收集其生长过程中四个不同的阶段，分别为绿色游动细胞阶段，绿色不动细胞阶段，绿褐色不动细胞阶段（开始积累虾青素），以及红色不动孢子阶段。本研究中提取了核酮糖-1,5-二磷酸羧化/加氧酶（Rubisco）的粗提液，并测定了酶活。其编码基因rbcL的mRNA表达量也被测定。另外，光合速率与呼吸速率的比值（P/R）通过测定与计算得出，各个阶段藻细胞中虾青素的含量由分析得出。本研究还应用了叶绿素荧光测定方法，确定了光系统II潜在最大活性（Fv / Fm），光系统II实际活性（ΦPSII），电子传递速率（ETR）和非光化学淬灭参数（NPQ）。 结果表明，绿色游动细胞的生长状态最佳，其P/R、Fv / Fm、ΦPSII均为最大，NPQ为最小。这说明在此状态的细胞中，光系统II的活性最强；但是其Rubisco活性与rbcL表达量均为最小。相比之下，在绿褐色不动细胞中，P/R和NPQ的值较低，Fv / Fm、ΦPSII和ETR值都最小，但Rubisco活性与rbcL表达量均为最高。 结合工业生产虾青素的方法，我们认为，Rubisco或许参与了虾青素的合成，而非Calvin循环为色素合成提供前体和能量。因此，在生产过程中适当加入碳源，比如CO2，可以有效增大虾青素的产量。

Regulacja karboksylazy/oksygenazy rybulozo-1,5-bisfosforanu (Rubisco) u Arabidopsis thaliana w odpowiedzi na zmianę natężenia światła z umiarkowanego na niskie

Wydział Biologii

Neuroprotection resulting from insufficiency of RANBP2 is associated with the modulation of protein and lipid homeostasis of functionally diverse but linked pathways in response to oxidative stress.

Oxidative stress is a deleterious stressor associated with a plethora of disease and aging manifestations, including neurodegenerative disorders, yet very few factors and mechanisms promoting the neuroprotection of photoreceptor and other neurons against oxidative stress are known. Insufficiency of RAN-binding protein-2 (RANBP2), a large, mosaic protein with pleiotropic functions, suppresses apoptosis of photoreceptor neurons upon aging and light-elicited oxidative stress, and promotes age-dependent tumorigenesis by mechanisms that are not well understood. Here we show that, by downregulating selective partners of RANBP2, such as RAN GTPase, UBC9 and ErbB-2 (HER2; Neu), and blunting the upregulation of a set of orphan nuclear receptors and the light-dependent accumulation of ubiquitylated substrates, light-elicited oxidative stress and Ranbp2 haploinsufficiency have a selective effect on protein homeostasis in the retina. Among the nuclear orphan receptors affected by insufficiency of RANBP2, we identified an isoform of COUP-TFI (Nr2f1) as the only receptor stably co-associating in vivo with RANBP2 and distinct isoforms of UBC9. Strikingly, most changes in proteostasis caused by insufficiency of RANBP2 in the retina are not observed in the supporting tissue, the retinal pigment epithelium (RPE). Instead, insufficiency of RANBP2 in the RPE prominently suppresses the light-dependent accumulation of lipophilic deposits, and it has divergent effects on the accumulation of free cholesterol and free fatty acids despite the genotype-independent increase of light-elicited oxidative stress in this tissue. Thus, the data indicate that insufficiency of RANBP2 results in the cell-type-dependent downregulation of protein and lipid homeostasis, acting on functionally interconnected pathways in response to oxidative stress. These results provide a rationale for the neuroprotection from light damage of photosensory neurons by RANBP2 insufficiency and for the identification of novel therapeutic targets and approaches promoting neuroprotection.

Glucocorticoid receptor β and histone deacetylase 1 and 2 expression in the airways of severe asthma.

Rationale Upregulation of glucocorticoid receptor ß (GRß) has been implicated in steroid resistance in severe asthma, although previous studies are conflicting. GRß has been proposed as a dominant negative isoform of glucocorticoid receptor a (GRa) but it has also been suggested that GRß can cause steroid resistance via reduced expression of histone deacetylase 2 (HDAC2), a key regulator of steroid responsiveness in the airway.


Objectives To examine GRß, GRa, HDAC1 and HDAC2 expression at transcript and protein levels in bronchial biopsies from a large series of patients with severe asthma, and to compare the findings with those of patients with mild to moderate asthma and healthy volunteers.


Methods Bronchoscopic study in two UK centres with real-time PCR and immunohistochemistry performed on biopsies, western blotting of bronchial epithelial cells and immunoprecipitation with anti-GRß antibody.


Measurements and main results Protein and mRNA expression for GRa and HDAC2 did not differ between groups. GRß mRNA was detected in only 13 of 73 samples (seven patients with severe asthma), however immunohistochemistry showed widespread epithelial staining in all groups. Western blotting of bronchial epithelial cells with GRß antibody detected an additional ‘cross-reacting’ protein, identified as clathrin. HDAC1 expression was increased in patients with severe asthma compared with healthy volunteers.


Conclusions GRß mRNA is expressed at low levels in a minority of patients with severe asthma. HDAC1 and HDAC2 expression was not downregulated in severe asthma. These data do not support upregulated GRß and resultant reduced HDAC expression as the principal mechanism of steroid resistance in severe asthma. Conflicting GRß literature may be explained in part by clathrin cross-reactivity with commercial antibodies.