Replication Cost Research Articles

A Remote File Possession Checking Protocol in a Cloud Storage

Outsourcing a file to a remote cloud storage provides several benefits, including scalability, accessibility, data replication and considerable cost saving. Unfortunately, when we send a file to a remote cloud storage server, we do not know if this file is intact. To address this problem, we present a remote file possession checking protocol. In this protocol, we use three technologies: Firstly, we design a kind of file block tag whose security is based on the discrete logarithm problem (DLP); secondly, we use probability checking method to improve its effectiveness; thirdly, we use tag aggregation method to reduce its communication cost. Our theory analysis and experiment results show that our protocol is practical and secure.

Data partitioning for distributed web service transactions

In this paper we propose a database partitioning method that provides efficient response times for distributed web services transaction executions. Our partitioning and allocation approach aims at finding the optimal response time by reducing the cost of distributed data accesses, the cost of data replication, and using parallel execution as a cost-savings technique. We also seek to make the strategy work with dynamic workloads and distributed environments. For this, we develop a framework with a three-phased approach, which we outline in this paper.

Consequences of HLA-B*13-Associated Escape Mutations on HIV-1 Replication and Nef Function.

HLA-B*13 is associated with superior in vivo HIV-1 viremia control. Protection is thought to be mediated by sustained targeting of key cytotoxic T lymphocyte (CTL) epitopes and viral fitness costs of CTL escape in Gag although additional factors may contribute. We assessed the impact of 10 published B*13-associated polymorphisms in Gag, Pol, and Nef, in 23 biologically relevant combinations, on HIV-1 replication capacity and Nef-mediated reduction of cell surface CD4 and HLA class I expression. Mutations were engineered into HIV-1NL4.3, and replication capacity was measured using a green fluorescent protein (GFP) reporter T cell line. Nef-mediated CD4 and HLA-A*02 downregulation was assessed by flow cytometry, and T cell recognition of infected target cells was measured via coculture with an HIV-specific luciferase reporter cell line. When tested individually, only Gag-I147L and Gag-I437L incurred replicative costs (5% and 17%, respectively), consistent with prior reports. The Gag-I437L-mediated replication defect was rescued to wild-type levels by the adjacent K436R mutation. A novel B*13 epitope, comprising 8 residues and terminating at Gag147, was identified in p24(Gag) (GQMVHQAIGag140-147). No other single or combination Gag, Pol, or Nef mutant impaired viral replication. Single Nef mutations did not affect CD4 or HLA downregulation; however, the Nef double mutant E24Q-Q107R showed 40% impairment in HLA downregulation with no evidence of Nef stability defects. Moreover, target cells infected with HIV-1-NefE24Q-Q107R were recognized better by HIV-specific T cells than those infected with HIV-1NL4.3 or single Nef mutants. Our results indicate that CTL escape in Gag and Nef can be functionally costly and suggest that these effects may contribute to long-term HIV-1 control by HLA-B*13. Protective effects of HLA-B*13 on HIV-1 disease progression are mediated in part by fitness costs of CTL escape mutations in conserved Gag epitopes, but other mechanisms remain incompletely known. We extend our knowledge of the impact of B*13-driven escape on HIV-1 replication by identifying Gag-K436R as a compensatory mutation for the fitness-costly Gag-I437L. We also identify Gag-I147L, the most rapidly and commonly selected B*13-driven substitution in HIV-1, as a putative C-terminal anchor residue mutation in a novel B*13 epitope. Most notably, we identify a novel escape-driven fitness defect: B*13-driven substitutions E24Q and Q107R in Nef, when present together, substantially impair this protein's ability to downregulate HLA class I. This, in turn, increases the visibility of infected cells to HIV-specific T cells. Our results suggest that B*13-associated escape mutations impair HIV-1 replication by two distinct mechanisms, that is, by reducing Gag fitness and dampening Nef immune evasion function.

A single-residue change in the HIV-1 V3 loop associated with maraviroc resistance impairs CCR5 binding affinity while increasing replicative capacity.

BackgroundMaraviroc (MVC) is an allosteric CCR5 inhibitor used against HIV-1 infection. While MVC-resistant viruses have been identified in patients, it still remains incompletely known how they adjust their CD4 and CCR5 binding properties to resist MVC inhibition while preserving their replicative capacity. It is thought that they maintain high efficiency of receptor binding. To date however, information about the binding affinities to receptors for inhibitor-resistant HIV-1 remains limited.ResultsHere, we show by means of viral envelope (gp120) binding experiments and virus-cell fusion kinetics that a MVC-resistant virus (MVC-Res) that had emerged as a dominant viral quasispecies in a patient displays reduced affinities for CD4 and CCR5 either free or bound to MVC, as compared to its MVC-sensitive counterpart isolated before MVC therapy. An alanine insertion within the GPG motif (G310_P311insA) of the MVC-resistant gp120 V3 loop is responsible for the decreased CCR5 binding affinity, while impaired binding to CD4 is due to sequence changes outside V3. Molecular dynamics simulations of gp120 binding to CCR5 further emphasize that the Ala insertion alters the structure of the V3 tip and weakens interaction with CCR5 ECL2. Paradoxically, infection experiments on cells expressing high levels of CCR5 also showed that Ala allows MVC-Res to use CCR5 efficiently, thereby improving viral fusion and replication efficiencies. Actually, although we found that the V3 loop of MVC-Res is required for high levels of MVC resistance, other regions outside V3 are sufficient to confer a moderate level of resistance. These sequence changes outside V3, however, come with a replication cost, which is compensated for by the Ala insertion in V3.ConclusionThese results indicate that changes in the V3 loop of MVC-resistant viruses can augment the efficiency of CCR5-dependent steps of viral entry other than gp120 binding, thereby compensating for their decreased affinity for entry receptors and improving their fusion and replication efficiencies. This study thus sheds light on unsuspected mechanisms whereby MVC-resistant HIV-1 could emerge and grow in treated patients.Electronic supplementary materialThe online version of this article (doi:10.1186/s12977-015-0177-1) contains supplementary material, which is available to authorized users.

A Joint Online Transcoding and Delivery Approach for Dynamic Adaptive Streaming

Dynamic adaptive streaming has emerged as a popular approach for video services in today’s Internet. To date, the two important components in dynamic adaptive streaming, video transcoding that generates the adaptive bitrates of a video and video delivery that streams the videos to users, have been separately studied, resulting in a huge waste of computation and storage resource due to producing and caching different versions of videos regardless of their demands. We conduct extensive measurement studies of video sharing systems, including an IPTV service which streams regular, professionally made videos and an instant video clip sharing service which provides extremely short user-generated videos, as well as the availability of computation resource in conventional content delivery networks (CDNs). Based on the measurement insights, we propose an online joint transcoding and delivery approach for adaptive video streaming. We formulate optimization problems to enable high streaming quality for the users, and low computation and replication costs for the system. In particular, our strategy connects video transcoding and video delivery based on users’ preferences of CDN regions and regional preferences of video versions. We analyze hardness of these problems and design distributed solutions. Extensive trace-driven experiments further demonstrate the superiority of our design.

Costs of implementing a behavioral weight-loss and lifestyle-change program for individuals with serious mental illnesses in community settings.

Little research has examined costs of adopting a successful lifestyle intervention for people with serious mental illnesses in community clinics. The study aims to calculate the real-world costs of implementing a group-based weight-loss and lifestyle intervention in community settings. We used empirically derived costs to estimate implementation costs and conducted sensitivity analyses to estimate costs: (1) when implementing the intervention in high/low resource-intensive environments and (2) assuming variability in participant enrollment. To implement the STRIDE program for 15 individuals with serious mental illnesses, we estimated costs for the 12-month (30-session) intervention, with materials available in the public domain, at $16,427 or $1095 per participant. The majority of costs, $12,767, were associated with direct labor costs. Replication costs are largely associated with labor. Community health centers offer an untapped resource for implementing behavioral-lifestyle interventions, particularly under the Affordable Care Act, though additional payment reforms or incentives may be needed.

Mojim

Next-generation non-volatile memories (NVMs) promise DRAM-like performance, persistence, and high density. They can attach directly to processors to form non-volatile main memory (NVMM) and offer the opportunity to build very low-latency storage systems. These high-performance storage systems would be especially useful in large-scale data center environments where reliability and availability are critical. However, providing reliability and availability to NVMM is challenging, since the latency of data replication can overwhelm the low latency that NVMM should provide. We propose Mojim, a system that provides the reliability and availability that large-scale storage systems require, while preserving the performance of NVMM. Mojim achieves these goals by using a two-tier architecture in which the primary tier contains a mirrored pair of nodes and the secondary tier contains one or more secondary backup nodes with weakly consistent copies of data. Mojim uses highly-optimized replication protocols, software, and networking stacks to minimize replication costs and expose as much of NVMM?s performance as possible. We evaluate Mojim using raw DRAM as a proxy for NVMM and using an industrial NVMM emulation system. We find that Mojim provides replicated NVMM with similar or even better performance than un-replicated NVMM (reducing latency by 27% to 63% and delivering between 0.4 to 2.7X the throughput). We demonstrate that replacing MongoDB's built-in replication system with Mojim improves MongoDB's performance by 3.4 to 4X.

Mojim

Next-generation non-volatile memories (NVMs) promise DRAM-like performance, persistence, and high density. They can attach directly to processors to form non-volatile main memory (NVMM) and offer the opportunity to build very low-latency storage systems. These high-performance storage systems would be especially useful in large-scale data center environments where reliability and availability are critical. However, providing reliability and availability to NVMM is challenging, since the latency of data replication can overwhelm the low latency that NVMM should provide. We propose Mojim, a system that provides the reliability and availability that large-scale storage systems require, while preserving the performance of NVMM. Mojim achieves these goals by using a two-tier architecture in which the primary tier contains a mirrored pair of nodes and the secondary tier contains one or more secondary backup nodes with weakly consistent copies of data. Mojim uses highly-optimized replication protocols, software, and networking stacks to minimize replication costs and expose as much of NVMM?s performance as possible. We evaluate Mojim using raw DRAM as a proxy for NVMM and using an industrial NVMM emulation system. We find that Mojim provides replicated NVMM with similar or even better performance than un-replicated NVMM (reducing latency by 27% to 63% and delivering between 0.4 to 2.7X the throughput). We demonstrate that replacing MongoDB's built-in replication system with Mojim improves MongoDB's performance by 3.4 to 4X.

Liquidity risk and the term structure of interest rates

This paper develops an arbitrage-free pricing theory for a term structure of fixed income securities that incorporates liquidity risk. In our model, there is a quantity impact on the term structure of zero-coupon bond prices from the trading of any single zero-coupon bond. We derive a set of conditions under which the term structure evolution is arbitrage-free. These no arbitrage conditions constrain both the risk premia and the term structure’s volatility. In addition, we also provide conditions under which the market is complete, and we show that the replication cost of an interest rate derivative is the solution to a backward stochastic differential equation.

Selecting Stopping Rules for Confidence Interval Procedures

The sample size decision is crucial to the success of any sampling experiment. More samples imply better confidence and precision in the results, but require higher costs in terms of time, computing power, and money. Analysts often choose sequential stopping rules on an ad hoc basis to obtain confidence intervals with desired properties without requiring large sample sizes. However, the choice of stopping rule can affect the quality of the interval produced in terms of the coverage, precision, and replication cost. This article introduces methods for choosing and evaluating stopping rules for confidence interval procedures. We develop a general framework for assessing the quality of a broad class of stopping rules applied to independent and identically distributed data. We introduce coverage profiles that plot the coverage according to the stopping time and reveal situations when the coverage could be unexpectedly low. Finally, we recommend simple techniques for obtaining acceptable or optimal rules.

Frequency-dependent selection can lead to evolution of high mutation rates.

Theoretical and experimental studies have shown that high mutation rates can be advantageous, especially in novel or fluctuating environments. Here we examine how frequency-dependent competition may lead to fluctuations in trait frequencies that exert upward selective pressure on mutation rates. We use a mathematical model to show that cyclical trait dynamics generated by "rock-paper-scissors" competition can cause the mutation rate in a population to converge to a high evolutionarily stable mutation rate, reflecting a trade-off between generating novelty and reproducing past success. Introducing recombination lowers the evolutionarily stable mutation rate but allows stable coexistence between mutation rates above and below the evolutionarily stable rate. Even considering strong mutational load and ignoring the costs of faithful replication, evolution favors positive mutation rates if the selective advantage of prevailing in competition exceeds the ratio of recombining to nonrecombining offspring. We discuss a number of genomic mechanisms that may meet our theoretical requirements for the adaptive evolution of mutation. Overall, our results suggest that local mutation rates may be higher on genes influencing cyclical competition and that global mutation rates in asexual species may be higher in populations subject to strong cyclical competition.

FansyRoute

We consider the problem of routing in a highly and variably intermittent wireless network to support delay-intolerant as well as delay tolerant applications. Specifically, the links in such a network are too volatile to maintain a consistent topology, rendering most MANET protocols ineffective. At the same time, store-andforward (DTN) techniques are not an option due to the need for ndelay intolerance, and may be unnecessary due to the likely availability of contemporaneous, albeit rapidly changing, paths.We present a novel routing mechanism called FansyRoute, aimed at this challenged region between MANETs and DTNs. Fansy- Route adaptively adjusts the number of replications (fan-out) on a per-node basis, taking into account the level of intermittency along the path to the destination and a user-specified tradeoff between delivery expectation and the cost of replication. We study the performance of two FansyRoute schemes on a prime example of such variably intermittently connected networks, namely asynchronously duty-cycled sensor networks. Using ns-3, we compare FansyRoute to OLSR, AODV and Flooding. The results show that in an intermittent network, FansyRoute can deliver 50% more packets than the single path protocols, with less than 5% of the replication incurred by flooding. FansyRoute replicates only when needed and the replication is restricted to the challenged regions of the network.

Distributed replica placement algorithms for correlated data

In distributed systems, data may be correlated due to accesses from clients and the correlation has some impact on date placement, and existing research works focus on independent data objects. In this paper, we address both the scalability and the stability of the data placement solutions in internet environment. We first show that replica allocation decisions can be made locally for each replica site in a tree network, with data access knowledge of its neighbors. We then develop a new replication cost model for correlated data objects in Internet environment. Based on the cost model and the algorithms in previous research, we develop a distributed optimal replica allocation algorithm (DOPR) for correlated data in internet environment. A distributed heuristic algorithm (DHPR) is then developed to efficiently make replica placement decisions. The algorithm obtains sub-optimal solutions for the correlated data model and yields significant performance gains. Experimental studies show that the distributed heuristic allocation algorithm significantly outperforms the general frequency-based replication schemes (in which the replication decision of each data object is made based on the number of accesses on that data object).

A Lightweight and Cooperative Multifactor Considered File Replication Method in Structured P2P Systems

File replication is widely used in structured P2P systems to avoid hot spots in servers and enhance file availability. The number of replicas and replication distance affect the file replication cost. These two elements and the replica update frequency determined in the file replication stage also affect the cost of subsequent consistency maintenance. However, most existing file replication protocols focus on improving file lookup efficiency without considering its cost and its subsequent influence on consistency maintenance. This paper studies the problem about how a server chooses files to replicate and where to replicate files to achieve low cost in both file replication and consistency maintenance stages without compromising the effectiveness of file replication. This paper presents a lightweight and Cooperative multifactOr considered file Replication Protocol (CORP) to achieve this goal. CORP simultaneously takes into account multiple factors including file popularity, update rate, node available capacity, file load, and node locality, aiming to minimize the number of replicas, update frequency, and replication distance. CORP also dynamically adjusts the number of replicas based on ever-changing file popularity and visit pattern. Extensive experimental results from simulation and PlanetLab real-world testbed demonstrate the efficiency and effectiveness of CORP in comparison with other file replication protocols. It dramatically reduces the overhead of both file replication and consistency maintenance. In addition, it exhibits high adaptiveness to skewed lookups and yields significant improvement in reducing overloaded nodes. Specifically, compared to the other replication protocols, CORP can reduce more than 71 percent of file replicas, 84 percent of overloaded nodes, 94 percent of consistency maintenance cost, and 72 percent of file replication and consistency maintenance latency.

Single assay-wide variance experimental (SAVE) design for high-throughput screening

Advantages of statistical testing of high-throughput screens include P-values, which provide objective benchmarks of compound activity, and false discovery rate estimation. The cost of replication required for statistical testing, however, may often be prohibitive. We introduce the single assay-wide variance experimental (SAVE) design whereby a small replicated subset of an entire screen is used to derive empirical Bayes random error estimates, which are applied to the remaining majority of unreplicated measurements. The SAVE design is able to generate P-values comparable with those generated with full replication data. It performs almost as well as the random variance model t-test with duplicate data and outperforms the commonly used Z-scores with unreplicated data and the standard t-test. We illustrate the approach with simulated data and with experimental small molecule and small interfering RNA screens. The SAVE design provides substantial performance improvements over unreplicated screens with only slight increases in cost.

QoS-aware replica placement for data intensive applications

In recent years, with the rapid development of data intensive applications, data replication has become an enabling technology for the data grid to improve data availability, and reduce file transfer time and bandwidth consumption. The placement of replicas has been proven to be the most difficult problem that must be solved to realize the process of data replication. This paper addresses the quality of service (QoS) aware replica placement problem in data grid, and proposes a dynamic programming based replica placement algorithm that not only has a QoS requirement guarantee, but also can minimize the overall replication cost, including storage cost and communication cost. By simulation, experiments show that the replica placement algorithm outperforms an existing popular replica placement technique in data grid.

Highlight: Bacteria Shed DNA as They Adapt to Hot Temperatures

Highlight: Bacteria Shed DNA as They Adapt to Hot Temperatures

Performance-Driven Load Balancing with a Primary-Backup Approach for Computational Grids with Low Communication Cost and Replication Cost

Computational grids provide a massive source of processing power, providing the means to support processor intensive applications. The strong burstiness and unpredictability of the available resources raise the need to make applications robust against the dynamics of grid environment. The two main techniques that are most suitable to cope with the dynamic nature of the grid are load balancing and job replication. In this work, we develop a load-balancing algorithm by juxtaposes the strong points of neighbor-based and cluster-based load-balancing methods. We then integrate the proposed load-balancing approach with fault-tolerant scheduling namely MinRC and develop a performance-driven fault-tolerant load-balancing algorithm or PD_MinRC for independent jobs. In order to improve system flexibility, reliability, and save system resource, PD_MinRC employs passive replication scheme. Our main objective is to arrive at job assignments that could achieve minimum response time, maximum resource utilization, and a well-balanced load across all the resources involved in a grid. Experiments were conducted to show the applicability of PD_MinRC. One advantage of our approach is the relatively low overhead and robust performance against resource failures and inaccuracies in performance prediction information.

Connection Frequency Buffer Aware Routing Protocol for Delay Tolerant Network

DTN flooding based routing protocol replicate the message copy to increase the delivery like hood that overloads the network resources. The probabilistic routing protocols reduce replication cost by forwarding the message to a node that holds high predictability value to meet its destination. However, the network traffic converges to high probable nodes and produce congestion that triggers the drop of previously stored messages. In this paper, we have proposed a routing protocol called as Connection frequency Buffer Aware Routing Protocol (CFBARP) that uses an adaptive method to maintain the information about the available buffer space at the receiver before message transmission. Furthermore, a frequency based method has been employed to determine the connection recurrence among nodes. The proposed strategy has performed well in terms of reducing message drop, message relay while increases the delivery probability.

Retrieval-Guaranteed Location-Aware Information Brokerage Scheme in 3D Wireless Ad Hoc Networks

We address the problem of information brokerage, where information consumers search for the data acquired by information producers. To the best of our knowledge, there exists no retrieval-guaranteed location-aware information brokerage scheme with a bounded data retrieval path length and bounded replication and retrieval message overhead costs available for use in 3D wireless ad hoc networks to date. In this paper, we propose a novel location-aware information brokerage scheme, termed LAIB, where the network area is divided into cube grids, and data are replicated and retrieved in the hashed geographic location in each grid designated by the producer and the consumer, respectively. In LAIB, a polylogarithmic number of grids are designated by the producer and by the consumer, and at least one grid, whose distance from the grid of the consumer is smaller than the distance from the grid of the consumer to the grid of the producer, is designated by both the producer and the consumer. Simulations show that, as the network area is divided into a moderate number of grids, LAIB has good performance in term of retrieval latency stretch while ensuring moderate replication memory, replication message, and retrieval message overhead costs.