Placement of file replicas in data grid environments

In this paper, we address the problem of file replica placement in Data Grids given a certain traffic pattern. We propose a new file replica placement algorithm and compare its performance with a standard replica placement algorithm using simulation. The results show that file replication improve the performance of the data access but the gains depend on several factors including where the file replicas are located, burstness of the request arrival, packet loses and file sizes.

The design and implementation of an active replication scheme for distributing services in a cluster of workstations

Replication is the key to providing high availability, fault tolerance, and enhanced performance in a cluster of workstations (COWs). However, building such a system remains as a difficult and challenging task, mainly due to the difficulty of maintaining data consistency among replicas and the lack of easy and efficient tools supporting the development procedure. In this paper we propose an active replication scheme in which data consistency can be maintained. Based on the active replication scheme, we present an object-oriented design pattern and a constructing tool to simplify the design and implementation of service replications in COWs.

Effects of replication on measured S-N curves of metals

Replication, or repeated tests at the same stress amplitude, is used to provide statistical confidence in life data during the development of S-N curves. This paper discusses the effects of replication on the measurement of S-N curves and presents an alternative to traditional replication methods for the determination of S-N curves, particularly for the development of preliminary S-N curves. Using specimens made out of the extruded bars of a magnesium alloy, it is demonstrated that the S-N curve estimated using the data from non-replication tests is almost same as that from replication tests. The advantage of using non-replication fatigue tests is that it uses fewer specimens, in this instance, only half of that required for 50% replication fatigue test, to achieve the same estimation as that of the replication fatigue tests. Another advantage of using non-replication fatigue tests is that it can detect the non-linearity using limited specimens.

Effects of replication on measured S-N curves of metals

Replication, or repeated tests at the same stress amplitude, is used to provide statistical confidence in life data during the development of S-N curves. This paper discusses the effects of replication on the measurement of S-N curves and presents an alternative to traditional replication methods for the determination of S-N curves, particularly for the development of preliminary S-N curves. Using specimens made out of the extruded bars of a magnesium alloy, it is demonstrated that the S-N curve estimated using the data from non-replication tests is almost same as that from replication tests. The advantage of using non-replication fatigue tests is that it uses fewer specimens, in this instance, only half of that required for 50% replication fatigue test, to achieve the same estimation as that of the replication fatigue tests. Another advantage of using non-replication fatigue tests is that it can detect the non-linearity using limited specimens.

The dimer initiation sequence stem-loop of human immunodeficiency virus type 1 is dispensable for viral replication in peripheral blood mononuclear cells

Human immunodeficiency virus type 1 (HIV-1) contains two copies of genomic RNA that are noncovalently linked via a palindrome sequence within the dimer initiation site (DIS) stem-loop. In contrast to the current paradigm that the DIS stem or stem-loop is critical for HIV-1 infectivity, which arose from studies using T-cell lines, we demonstrate here that HIV-1 mutants with deletions in the DIS stem-loop are replication competent in peripheral blood mononuclear cells (PBMCs). The DIS mutants contained either the wild-type (5′GCGCGC3′) or an arbitrary (5′ACGCGT3′) palindrome sequence in place of the 39-nucleotide DIS stem-loop (NLCGCGCG and NLACGCGT). These DIS mutants were replication defective in SupT1 cells, concurring with the current model in which DIS mutants are replication defective in T-cell lines. All of the HIV-1 DIS mutants were replication competent in PBMCs over a 40-day infection period and had retained their respective DIS mutations at 40 days postinfection. Although the stability of the virion RNA dimer was not affected by our DIS mutations, the RNA dimers exhibited a diffuse migration profile when compared to the wild type. No defect in protein processing of the Gag and GagProPol precursor proteins was found in the DIS mutants. Our data provide direct evidence that the DIS stem-loop is dispensable for viral replication in PBMCs and that the requirement of the DIS stem-loop in HIV-1 replication is cell type dependent.

Human immunodeficiency virus type 1 protease regulation of tat activity is essential for efficient reverse transcription and replication

The human immunodeficiency virus type 1 (HIV-1) Tat protein enhances reverse transcription, but it is not known whether Tat acts directly on the reverse transcription complex or through indirect mechanisms. Since processing of Tat by HIV protease (PR) might mask its presence and, at least in part, explain this lack of data, we asked whether Tat can be cleaved by PR. We used a rabbit reticulocyte lysate (RRL) system to make Tat and PR. HIV-1 PR is expressed as a Gag-Pol fusion protein, and a PR-inactivated Gag-Pol is also expressed as a control. We showed that Tat is specifically cleaved in the presence of PR, producing a protein of approximately 5 kDa. This result suggested that the cleavage site was located in or near the Tat basic domain (amino acids 49 to 57), which we have previously shown to be important in reverse transcription. We created a panel of alanine-scanning mutations from amino acids 45 to 54 in Tat and evaluated functional parameters, including transactivation, reverse transcription, and cleavage by HIV-1 PR. We showed that amino acids 49 to 52 (RKKR) are absolutely required for Tat function in reverse transcription, that mutation of this domain blocks cleavage by HIV-1 PR, and that other pairwise mutations in this region modulate reverse transcription and proteolysis in strikingly similar degrees. Mutation of Tat Y47G48 to AA also down-regulated Tat-stimulated reverse transcription but had little effect on transactivation or proteolysis by HIV PR, suggesting that Y47 is critical for reverse transcription. We altered the tat gene of the laboratory strain NL4-3 to Y47D and Y47N so that overlapping reading frames were not affected and showed that Y47D greatly diminished virus replication and conveyed a reverse transcription defect. We hypothesize that a novel, cleaved form of Tat is present in the virion and that it requires Y47 for its role in support of efficient reverse transcription.

Nef binds p6* in gagpol during replication of human immunodeficiency virus type 1

The atypical Nef protein (NefF12) from human immunodeficiency virus type 1 strain F12 (HIV-1F12) interferes with virion production and infectivity via a mysterious mechanism. The correlation of these effects with the unusual perinuclear subcellular localization of NefF12 suggested that the wild-type Nef protein could bind to assembly intermediates in late stages of viral replication. To test this hypothesis, Nef from HIV-1NL4-3 was fused to an endoplasmic reticulum (ER) retention signal (NefKKXX). This mutant NefKKXX protein recapitulated fully the effects of NefF12 on Gag processing and virion production, either alone or as a CD8 fusion protein. Importantly, the mutant NefKKXX protein also localized to the intermediate compartment, between the ER and the trans-Golgi network. Furthermore, Nef bound the GagPol polyprotein in vitro and in vivo. This binding mapped to the C-terminal flexible loop in Nef and the transframe p6* protein in GagPol. The significance of this interaction was demonstrated by a genetic assay in which the release of a mutant HIV-1 provirus lacking the PTAP motif in the late domain that no longer binds Tsg101 was rescued by a Nef.Tsg101 chimera. Importantly, this rescue as well as incorporation of Nef into HIV-1 virions correlated with the ability of Nef to interact with GagPol. Our data demonstrate that the retention of Nef in the intermediate compartment interferes with viral replication and suggest a new role for Nef in the production of HIV-1.

Primary T-lymphocytes rescue the replication of HIV-1 DIS RNA mutants in part by facilitating reverse transcription

The dimerization initiation site (DIS) stem-loop within the HIV-1 RNA genome is vital for the production of infectious virions in T-cell lines but not in primary cells. In comparison to peripheral blood mononuclear cells (PBMCs), which can support the replication of both wild type and HIV-1 DIS RNA mutants, we have found that DIS RNA mutants are up to 100 000-fold less infectious than wild-type HIV-1 in T-cell lines. We have also found that the cell-type-dependent replication of HIV-1 DIS RNA mutants is largely producer cell-dependent, with mutants displaying a greater defect in viral cDNA synthesis when viruses were not derived from PBMCs. While many examples exist of host–pathogen interplays that are mediated via proteins, analogous examples which rely on nucleic acid triggers are limited. Our data provide evidence to illustrate that primary T-lymphocytes rescue, in part, the replication of HIV-1 DIS RNA mutants through mediating the reverse transcription process in a cell-type-dependent manner. Our data also suggest the presence of a host cell factor that acts within the virus producer cells. In addition to providing an example of an RNA-mediated cell-type-dependent block to viral replication, our data also provides evidence which help to resolve the dilemma of how HIV-1 genomes with mismatched DIS sequences can recombine to generate chimeric viral RNA genomes.

Detecting the impact of invasive species on native fauna: Cane toads (Bufo marinus), frillneck lizards (Chlamydosaurus kingii) and the importance of spatial replication

An understanding of which native species are severely impacted by an anthropogenic change (such as the arrival of an invasive species) and which are not is critical to prioritizing conservation efforts. However, it is difficult to detect such impacts if the native taxa exhibit strong stochastic variations in abundance; a ‘natural’ population decline might be wrongly interpreted as an impact of the invader. Frillneck lizards (Chlamydosaurus kingii) are large iconic Australian agamids, and have been reported to decline following the invasion of toxic cane toads. We monitored three populations of the species in the savanna woodland of tropical Australia over a 7-year period bracketing toad arrival. One population crashed, one remained stable and one increased. Hence, studies on any single population might have inferred that cane toads have negative, negligible or positive effects on frillneck lizards. With the benefit of spatial replication, and in combination with observations of prey choice by captive lizards, our data suggest that invasive cane toads have had little or no effect on frillneck abundance.

A framework for implementing asynchronous replication scheme in utility-based computing environment

This paper addresses a problem on implementing an asynchronous replication scheme in utility-based computing environment. The problem needs a special attention as most of the existing replication scheme in this computing system whether implicitly support synchronous replication and/or only consider read-only job. Therefore, we propose an intelligent framework that can reinforce an effective resource selection scheme by allowing the components that give impact on the performance such as resource/data freshness of the replicated system in such environment to be considered. We exploit an Update Ordering (UO) approach and reconcile these components in designing the framework. Important issues such as job propagation delay and job propagation rules are especially addressed. Our experiments show that the proposed framework is capable to become a platform of an effective resource selection scheme and achieve a good result with good system performance as compared to existing algorithms.

Boosting imbalanced data learning with Wiener process oversampling

Learning from imbalanced data is a challenging task in a wide range of applications, which attracts significant research efforts from machine learning and data mining community. As a natural approach to this issue, oversampling balances the training samples through replicating existing samples or synthesizing new samples. In general, synthesization outperforms replication by supplying additional information on the minority class. However, the additional information needs to follow the same normal distribution of the training set, which further constrains the new samples within the predefined range of training set. In this paper, we present the Wiener process oversampling (WPO) technique that brings the physics phenomena into sample synthesization. WPO constructs a robust decision region by expanding the attribute ranges in training set while keeping the same normal distribution. The satisfactory performance of WPO can be achieved with much lower computing complexity. In addition, by integrating WPO with ensemble learning, the WPOBoost algorithm outperformsmany prevalent imbalance learning solutions.