Search

The computing power of graphics processing units (GPU) has increased rapidly, and there has been extensive research on general-purpose computing on GPU (GPGPU) for cryptographic algorithms such as RSA, Elliptic Curve Cryptosystem (ECC), NTRU, and Advanced Encryption Standard. With the rise of GPGPU, commodity computers have become complex heterogeneous GPU+CPU systems. This new architecture poses new challenges and opportunities in high-performance computing. In this paper, we present highspeed parallel implementations of the rainbow method based on perfect tables, which is known as the most efficient time-memory trade-off, in the heterogeneous GPU+CPU system. We give a complete analysis of the effect of multiple checkpoints on reducing the cost of false alarms and take advantage of it for load balancing between GPU and CPU. For GTX460, our implementation is about 1.86 and 3.25 times faster than other GPU-accelerated implementations, RainbowCrack and Cryptohaze, respectively, and for GTX580, 1.53 and 2.40 times faster. [ABSTRACT FROM AUTHOR]

Abstract: A series of three-dimensional finite element analyses was conducted to evaluate the combined horizontal-moment bearing capacities of tripod bucket foundations for offshore wind turbines in undrained clay. The tripod bucket foundation consists of three single bucket foundations, which enhance the bearing capacities because of the effect of the interaction among individual buckets. A linear-elastic perfectly plastic model, which obeys the Tresca failure criterion, was used to simulate the stress–strain response of clay, in which Young׳s modulus and undrained shear strength were assumed to increase linearly with depth. The effects of bucket spacing, embedment depth, vertical load, and non-homogeneity of clay on the combined horizontal-moment capacities were analyzed. Finally, the design equation of the combined horizontal-moment capacities was developed as a function of the aspect ratios (skirt length/diameter) of the foundations. [Copyright &y& Elsevier]

Background: Exacerbation of COPD is a major risk factor for bad prognosis of COPD. A few plasma proteins have been discovered to associate with hospital admission due to exacerbation up to date. We tried to find new plasma biomarkers to predict the exacerbation of COPD. Methods: We examined the plasma of normal control (n = 8) and COPD stable (n = 8) and exacerbation (n = 8) using 2-Dimentional Electrophoresis. The differentially expressed protein spots were identified by MALDI-TOF. ELISA were performed for quantitative measurement of RARα in plasma from normal control (n = 37) and COPD (n = 35). Results: 17 proteins were differentially expressed in plasma between stable and exacerbation state in the subjects with COPD. Identification using MALDI-TOF showed that retinoic acid receptor alpha, ninein, isoform CRA_a, alpha-1 antitrypsin, fibrinogen gamma, tyrosyl-DNA phosphodiesterase 2, and T cell receptor delta chain were increased in exacerbation of COPD, while fibrin beta, Crystal Structure Of An Autoimmune Complex Between A Human Igm RF* And Igg1 Fc, transferrin, serpin peptidase inhibitor member 6, complement factor B preproprotein, Chain B, Crig Bound To C3c, and WD repeat-containing protein 1 isoform 1 were decreased. Quantitative measurement showed that RARα plasma levels significantly increased in exacerbation state compared to stable state of COPD (n = 14). In the plasma of stable state, the COPD subjects (n = 14) having more than 0.4 time/yr of admission had very high levels of RAR alpha protein and those (n = 11) having less than 0.4 times/yr of admission had the intermediate levels compared to those having no exacerbation (n = 10). ROC analysis of RAR alpha levels to frequency of admission showed an area under the curve of 0.844. A cut-off of 0.154 ng/ml of RAR alpha predicted hospital admission with a sensitivity of 71.4% and a specificity of 92.8%. Conclusion: The proteomic analysis of plasma indicates that alteration of several proteins may be associated with admission of COPD. Among them, plasma RAR alpha level may predict hospital admission with a sensitivity of 71.4% and a specificity of 92.8%. [ABSTRACT FROM AUTHOR]

Chromosomal abnormalities are important prognostic factors for patients diagnosed with multiple myeloma ( MM). We retrospectively reviewed the clinical and laboratory data of 525 MM patients to assess the abnormalities frequently found by conventional cytogenetic analysis and to determine their relationship to prognosis and clinical parameters. Samples from 222 (42.3%) patients had abnormal karyotypes. Hyperdiploidy-1 (>50 chromosomes), hyperdiploidy-2 (47-50 chromosomes), pseudodiploidy (46 with abnormalities), and hypodiploidy (<46 chromosomes) were found in 55, 44, 42, and 81 patients, respectively. The median overall survival ( OS) was significantly shorter in patients with hyperdiploidy-2 (20.9 months), pseudodiploidy (19.9 months), and hypodiploidy (18.3 months) compared with patients with normal karyotype (66 months) and hyperdiploidy-1 (55.4 months) ( P < 0.001). Among patients with chromosomal abnormalities, those with 1q amplification had a shorter median OS (17 vs. 25.1 months, P = 0.018). Patients with a chromosome 13 deletion in the pseudodiploidy group also had a shorter OS. A karyotype with more than six structural abnormalities was found to have the most significant independent prognostic value by multivariate analysis. These data show that hyperdiploidy with 47-50 chromosomes should be recategorized as an unfavorable risk group, and the number of structural abnormalities needs to be considered as an important factor for prognosis. In conclusion, our findings imply that subclassification of chromosomal abnormalities by conventional cytogenetics could be applied to the prognostic assessment of MM. [ABSTRACT FROM AUTHOR]

Abstract: Tripod bucket foundations are being used as alternative foundations to resist large horizontal and moment loadings from offshore wind turbines. The bearing capacity of the tripod bucket foundation differs particularly from that of the single bucket foundation due to the interaction among individual buckets of the tripod. This paper investigated the group effect of tripod bucket foundations in clay by three-dimensional finite element analysis. Parametric studies were performed varying the spacing between each bucket foundation, embedded depth of the bucket foundation, and loading directions. Normally consolidated clay under an undrained condition was modeled using a linear elastic-perfectly plastic model obeying the Tresca failure criterion. The undrained shear strength and Young's modulus of clay were assumed to linearly increase with depth. The group efficiency factor, which is the ratio of the bearing capacity of the tripod bucket foundation to that of the single bucket foundation, was evaluated based on finite element analysis for vertical, horizontal and moment loadings. Results showed that the efficiency factors were functions of the bucket spacing and embedment depth of the foundations. [Copyright &y& Elsevier]

DDoS (distributed denial of service) attacks have gradually increased and have become more sophisticated. There have been several methods for defending against these attacks. However, because the types and scales of DDoS attacks have been diversified, it has become important to defend against DDoS attacks not only in main networks, but also in small scale networks such as AS (autonomous system). We have designed a DDoS defense system working inside AS without either changing the network structure or modifying the router. For this purpose, we have applied the Shield mechanism, which deals with the location problem in DDoS defense, and utilizes the routing updates protocol called RIP (routing information protocol), a representative protocol of IGP (interior gateway protocol). Moreover, we have also conducted experiments by using simulations to find the optimal number and locations of deployed systems. [ABSTRACT FROM AUTHOR]

A series of three-dimensional finite element analyses was conducted to investigate the effects of the embedment depth, the non-homogeneity of clay, and combined loads on the undrained bearing capacities of bucket foundations. The undrained shear strength and Young's modulus of clay were assumed to vary linearly with depth. Meanwhile, the stress-strain response of clay was simulated using the Tresca criterion. The numerical modeling adopted in this study was verified by comparing the calculated capacities with those from previous studies. Based on the results of the finite element analyses over 1400 cases, new equations were proposed to calculate the vertical, horizontal, and moment bearing capacities as well as to define the capacity envelopes under general combined loads. Comparisons with the capacity envelopes of previous studies showed that the proposed equations properly predicted the bearing capacities of the bucket foundation by considering the effects of the non-homogeneity of clay and embedment depth. [ABSTRACT FROM AUTHOR]

The heat shock protein 70 (HSP70) gene family plays a key role in protecting plant cells or tissues from thermal or oxidative stress. Although many studies have elucidated the molecular functions of individual family members, genome-wide analysis of this family is still limited, especially for crop species. Our objective was to integrate various meta-profiling data into the context of a phylogenetic tree, which would enable us to perform fine evaluation of functional dominancy or redundancy within this family. Our data indicated that a loss-of-function mutant of a rice cytosolic HSP70 gene ( OsctHSP70-1) did not show a clear defective phenotype in response to high temperature because of the existence of another gene family member that was closely clustered with OsctHSP70-1 and had similar expression patterns. Moreover, the second gene showed much stronger anatomical expression. We indirectly analyzed the function of OsctHSP70-1 by studying GUS activity under the control of the endogenous promoter. We also designed a probable interaction network mediated by OsctHSP70-1 and used co-expression analysis among its components to refine the network, suggesting more probable model to explain the function of OsctHSP70-1. [ABSTRACT FROM AUTHOR]

Abstract: Heat is a primary abiotic stress that reduces crop yields. At the seedling stage, we identified heat-sensitive mutants that carried T-DNA inserted into a heat shock protein 70 gene, OsHsp70CP1. When grown under a constant high temperature (40°C), the seedling leaves developed severe chlorosis whereas plants grown at a constant 27°C showed a normal phenotype. This indicated that OsHsp70CP1 is essential for chloroplast differentiation from the proplastids under high temperatures. Transient expression analyses revealed that OsHsp70CP1 was localized to the stroma. OsHsp70CP1 was dominantly expressed in photosynthetic tissues; transcripts were greatly increased by heat stress. Some transcripts for plastid RNA metabolism were impaired in the mutant while others were not, demonstrating that a subset of nuclear-encoded proteins are substrates of OsHsp70CP1. [Copyright &y& Elsevier]

Grass cell wall properties influence food, feed, and biofuel feedstock usage efficiency. The glucuronoarabinoxylan of grass cell walls is esterified with the phenylpropanoid-derived hydroxycinnamic acids ferulic acid (FA) and para-coumaric acid (p-CA). Feruloyl esters undergo oxidative coupling with neighboring phenylpropanoids on glucuronoarabinoxylan and lignin. Examination of rice (Oryza sativa) mutants in a grass-expanded and -diverged clade of BAHD acyl-coenzyme A-utilizing transferases identified four mutants with altered cell wall FA or p-CA contents. Here, we report on the effects of overexpressing one of these genes, OsAt10 (LOC_OsO6g39390), in rice. An activation-tagged line, OsAT10-D1, shows a 60% reduction in matrix polysaccharide-bound FA and an approximately 300% increase in p-CA in young leaf tissue but no discernible phenotypic alterations in vegetative development, lignin content, or lignin composition. Two additional independent OsAt10 overexpression lines show similar changes in FA and p-CA content. Cell wall fractionation and liquid chromatography-mass spectrometry experiments isolate the cell wall alterations in the mutant to ester conjugates of a five- carbon sugar with p-CA and FA. These results suggest that OsAT10 is a p-coumaroyl coenzyme A transferase involved in glucuronoarabinoxylan modification. Biomass from OsAT10-D1 exhibits a 20% to 40% increase in saccharification yield depending on the assay. Thus, OsAt10 is an attractive target for improving grass cell wall quality for fuel and animal feed. [ABSTRACT FROM AUTHOR]

Flowering is exquisitely regulated by both promotive and inhibitory factors. Molecular genetic studies with Arabidopsis have verified several epigenetic repressors that regulate flowering time. However, the roles of chromatin remodeling factors in developmental processes have not been well explored in Oryza sativa (rice). We identified a chromatin remodeling factor Os VIL2 ( O. sativa VIN3- LIKE 2) that promotes flowering. Os VIL2 contains a plant homeodomain ( PHD) finger, which is a conserved motif of histone binding proteins. Insertion mutations in O s VIL 2 caused late flowering under both long and short days. In osvil2 mutants O s LFL 1 expression was increased, but that of E hd1, H d3a and RFT 1 was reduced. We demonstrated that Os VIL2 is bound to native histone H3 in vitro. Chromatin immunoprecipitation analyses showed that Os VIL2 was directly associated with O s LFL 1 chromatin. We also observed that H3 K27me3 was significantly enriched by O s LFL 1 chromatin in the wild type, but that this enrichment was diminished in the osvil2 mutants. These results indicated that Os VIL2 epigenetically represses O s LFL 1 expression. We showed that Os VIL2 physically interacts with Os EMF2b, a component of polycomb repression complex 2. As observed from osvil2, a null mutation of O s EMF 2b caused late flowering by increasing O s LFL 1 expression and decreasing Ehd1 expression. Thus, we conclude that Os VIL2 functions together with PRC2 to induce flowering by repressing O s LFL 1. [ABSTRACT FROM AUTHOR]

To overcome the challenges presented by predicted climate change, it is important to understand how crops perceive and respond to high temperatures. In this paper, we performed genome-wide transcriptome analysis of rice to identify immediate early genes strongly induced by high temperature. We compared the effects of high temperature (37°C) treatments (for 0.5 or 1h) of seedlings relative to untreated controls (28°C) using the NSF45K array. We then identified 710 genes exhibiting at least 2-fold up-regulation at both time points. From the comparison of this dataset with other publicly available rice datasets under heat stress [i.e., for 10 and 30 min (early heat response), and 10 h at 42°C (late heat response)], we identified 244 genes and 238 genes at least 2 fold upregulated during the early and late heat responses, respectively. We defined 244 genes as early heat stress responsive group and 238 genes as prolonged heat stress responsive group. Gene ontology (GO) enrichment analysis revealed that a chaperone-mediated protein folding cofactor was the most significantly over-represented GO term associated with the prolonged heat response. Processes involved in cellular protein metabolism, protein folding, response to stress, small GTPase mediated signal transduction, and glycolysis are enriched in both early and prolonged heat responses, suggesting a role for these genes in the general heat stress response. Enrichment of processes involved in cell redox homeostasis, intracellular protein transport, electron transport chain, and regulation of transcription (DNA-dependent) were only identified in the early heat response. In addition, we observed that a large portion of the genes relating to the prolonged heat response were also associated with responses to other abiotic stresses such as drought, salt, cold, and submergence. Our data contribute to a better understanding the molecular mechanism of heat stress response in rice. [ABSTRACT FROM AUTHOR]

The increasing use of bi-directional (Osterberg cell) load tests in piles necessitates a reliable evaluation of the load-movement relationship equivalent to the head-down load test. In this study, the existing evaluation methods were reviewed, and a new method for evaluating the equivalent head-down curve was proposed. This method considers possible situations, such as non-measured axial load distribution along the pile and the existence of residual load distribution. Three cases, in which bi-directional and head-down load tests were performed at the same site, were analyzed in order to validate the proposed method. The results of the case studies showed that the equivalent load-movement curves obtained either without assuming unit shaft resistance distribution or by considering the effect of residual load agreed well with the measured curves obtained from the head-down test. Therefore, the proposed method is recommended for practical use. [ABSTRACT FROM AUTHOR]

Abstract: The present paper presents the results of three-dimensional finite element analyses of bucket foundations in normally consolidated uniform clay under undrained conditions. The stress–strain response of clay was simulated using the Tresca criterion. The bearing capacities were calculated and found to be largely dependent on the aspect ratio of the bucket foundation. Based on the results of the analyses, new equations were proposed for calculating vertical and horizontal bearing capacities. In the proposed equations, the vertical capacity consisted of an end-bearing resistance and a skin friction resistance, whereas the horizontal capacity consisted of a normal resistance, a radial shear resistance, and a base shear resistance. Comparison of the numerical results showed that the proposed equations properly predicted the capacities of the bucket foundations in uniform or non-uniform clays. [Copyright &y& Elsevier]

Summary Tapetum development and meiosis play crucial roles in anther development. Here we identified a rice gene, DEFECTIVE TAPETUM AND MEIOCYTES 1 ( DTM1), which controls the early stages of that development. This gene encodes for an endoplasmic reticulum (ER) membrane protein that is present only in cereals. Our T-DNA insertion mutations gave rise to abnormal tapetal formation. Cellular organelles, especially the ER, were underdeveloped, which led to hampered differentiation and degeneration of the tapetum. In addition, the development of pollen mother cells was arrested at the early stages of meiotic prophase I. RNA in-situ hybridization analyses showed that DTM1 transcripts were most abundant in tapetal cells at stages 6 and 7, and moderately in the pollen mother cells and meiocytes. Transcripts of UDT1, which functions in tapetum development during early meiosis, were reduced in dtm1 anthers, as were those of PAIR1, which is involved in chromosome pairing and synapsis during meiosis. However, expression of MSP1 and MEL1, which function in anther wall specification and germ cell division, respectively, was not altered in the dtm1 mutant. Moreover, transcripts of DTM1 were reduced in msp1 mutant anthers, but not in udt1 and pair1 mutants. These results, together with their mutant phenotypes, suggest that DTM1 plays important roles in the ER membrane during early tapetum development, functioning after MSP1 and before UDT1, and also in meiocyte development, after MEL1 and before PAIR1. [ABSTRACT FROM AUTHOR]