A grid-based infrastructure for distributed retrieval

In large-scale distributed retrieval, challenges of latency, heterogeneity, and dynamicity emphasise the importance of infrastructural support in reducing the development costs of state-of-the-art solutions. We present a service-based infrastructure for distributed retrieval which blends middleware facilities and a design framework to ‘lift’ the resource sharing approach and the computational services of a European Grid platform into the domain of e-Science applications. In this paper, we give an overview of the DILIGENT Search Framework and illustrate its exploitation in the field of Earth Science

Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1

With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this study, we investigate the epidemiological characteristics of 5,675 HIV-1 pol gene sequences sampled from distinct infections in the United Kingdom. These sequences were phylogenetically analyzed in conjunction with 976 complete-genome and 3,201 pol gene reference sequences sampled globally and representing the broad range of HIV-1 genetic diversity, allowing us to estimate the probable geographic origins of the various strains present in the United Kingdom. A statistical analysis of phylogenetic clustering in this data set identified several independent transmission chains within the United Kingdom involving recently introduced strains and indicated that strains more commonly associated with infections acquired heterosexually in East Africa are spreading among men who have sex with men. Coalescent approaches were also used and indicated that the transmission chains that we identify originated in the late 1980s to early 1990s. Similar changes in the epidemiological structuring of HIV epidemics are likely to be taking in place in other industrialized nations with large immigrant populations. The framework implemented here takes advantage of the vast amount of routinely generated HIV-1 sequence data and can provide epidemiological insights not readily obtainable through standard surveillance methods

Object Distribution Networks for World-wide Document Circulation

This paper presents an Object Distribution System (ODS), a distributed system inspired by the ultra-large scale distribution models used in everyday life (e.g. food or newspapers distribution chains). Beyond traditional mechanisms of approaching information to readers (e.g. caching and mirroring), this system enables the publication, classification and subscription to volumes of objects (e.g. documents, events). Authors submit their contents to publication agents. Classification authorities provide classification schemes to classify objects. Readers subscribe to topics or authors, and retrieve contents from their local delivery agent (like a kiosk or library, with local copies of objects). Object distribution is an independent process where objects circulate asynchronously among distribution agents. ODS is designed to perform specially well in an increasingly populated, widespread and complex Internet jungle, using weak consistency replication by object distribution, asynchronous replication, and local access to objects by clients. ODS is based on two independent virtual networks, one dedicated to the distribution (replication) of objects and the other to calculate optimised distribution chains to be applied by the first network

Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes

Human cytomegalovirus (HCMV) infects most of the population worldwide, persisting throughout the host's life in a latent state with periodic episodes of reactivation. While typically asymptomatic, HCMV can cause fatal disease among congenitally infected infants and immunocompromised patients. These clinical issues are compounded by the emergence of antiviral resistance and the absence of an effective vaccine, the development of which is likely complicated by the numerous immune evasins encoded by HCMV to counter the host's adaptive immune responses, a feature that facilitates frequent super-infections. Understanding the evolutionary dynamics of HCMV is essential for the development of effective new drugs and vaccines. By comparing viral genomes from uncultivated or low-passaged clinical samples of diverse origins, we observe evidence of frequent homologous recombination events, both recent and ancient, and no structure of HCMV genetic diversity at the whole-genome scale. Analysis of individual gene-scale loci reveals a striking dichotomy: while most of the genome is highly conserved, recombines essentially freely and has evolved under purifying selection, 21 genes display extreme diversity, structured into distinct genotypes that do not recombine with each other. Most of these hyper-variable genes encode glycoproteins involved in cell entry or escape of host immunity. Evidence that half of them have diverged through episodes of intense positive selection suggests that rapid evolution of hyper-variable loci is likely driven by interactions with host immunity. It appears that this process is enabled by recombination unlinking hyper-variable loci from strongly constrained neighboring sites. It is conceivable that viral mechanisms facilitating super-infection have evolved to promote recombination between diverged genotypes, allowing the virus to continuously diversify at key loci to escape immune detection, while maintaining a genome optimally adapted to its asymptomatic infectious lifecycle

Document replication strategies for geographically distributed web search engines

Cataloged from PDF version of article.Large-scale web search engines are composed of multiple data centers that are geographically distant to each other. Typically, a user query is processed in a data center that is geographically close to the origin of the query, over a replica of the entire web index. Compared to a centralized, single-center search engine, this architecture offers lower query response times as the network latencies between the users and data centers are reduced. However, it does not scale well with increasing index sizes and query traffic volumes because queries are evaluated on the entire web index, which has to be replicated and maintained in all data centers. As a remedy to this scalability problem, we propose a document replication framework in which documents are selectively replicated on data centers based on regional user interests. Within this framework, we propose three different document replication strategies, each optimizing a different objective: reducing the potential search quality loss, the average query response time, or the total query workload of the search system. For all three strategies, we consider two alternative types of capacity constraints on index sizes of data centers. Moreover, we investigate the performance impact of query forwarding and result caching. We evaluate our strategies via detailed simulations, using a large query log and a document collection obtained from the Yahoo! web search engine. (C) 2012 Elsevier Ltd. All rights reserved

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is however critical both for basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brain-wide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brain-wide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open access data repository; compatibility with existing resources, and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.Comment: 41 page

Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape.

Vaccination has essentially eradicated poliovirus. Yet, its mutation rate is higher than that of viruses like HIV, for which no effective vaccine exists. To investigate this, we infer a fitness model for the poliovirus viral protein 1 (vp1), which successfully predicts in vitro fitness measurements. This is achieved by first developing a probabilistic model for the prevalence of vp1 sequences that enables us to isolate and remove data that are subject to strong vaccine-derived biases. The intrinsic fitness constraints derived for vp1, a capsid protein subject to antibody responses, are compared with those of analogous HIV proteins. We find that vp1 evolution is subject to tighter constraints, limiting its ability to evade vaccine-induced immune responses. Our analysis also indicates that circulating poliovirus strains in unimmunized populations serve as a reservoir that can seed outbreaks in spatio-temporally localized sub-optimally immunized populations

An Efficient Holistic Data Distribution and Storage Solution for Online Social Networks

In the past few years, Online Social Networks (OSNs) have dramatically spread over the world. Facebook [4], one of the largest worldwide OSNs, has 1.35 billion users, 82.2% of whom are outside the US [36]. The browsing and posting interactions (text content) between OSN users lead to user data reads (visits) and writes (updates) in OSN datacenters, and Facebook now serves a billion reads and tens of millions of writes per second [37]. Besides that, Facebook has become one of the top Internet traffic sources [36] by sharing tremendous number of large multimedia files including photos and videos. The servers in datacenters have limited resources (e.g. bandwidth) to supply latency efficient service for multimedia file sharing among the rapid growing users worldwide. Most online applications operate under soft real-time constraints (e.g., ≤ 300 ms latency) for good user experience, and its service latency is negatively proportional to its income. Thus, the service latency is a very important requirement for Quality of Service (QoS) to the OSN as a web service, since it is relevant to the OSN’s revenue and user experience. Also, to increase OSN revenue, OSN service providers need to constrain capital investment, operation costs, and the resource (bandwidth) usage costs. Therefore, it is critical for the OSN to supply a guaranteed QoS for both text and multimedia contents to users while minimizing its costs. To achieve this goal, in this dissertation, we address three problems. i) Data distribution among datacenters: how to allocate data (text contents) among data servers with low service latency and minimized inter-datacenter network load; ii) Efficient multimedia file sharing: how to facilitate the servers in datacenters to efficiently share multimedia files among users; iii) Cost minimized data allocation among cloud storages: how to save the infrastructure (datacenters) capital investment and operation costs by leveraging commercial cloud storage services. Data distribution among datacenters. To serve the text content, the new OSN model, which deploys datacenters globally, helps reduce service latency to worldwide distributed users and release the load of the existing datacenters. However, it causes higher inter-datacenter communica-tion load. In the OSN, each datacenter has a full copy of all data, and the master datacenter updates all other datacenters, generating tremendous load in this new model. The distributed data storage, which only stores a user’s data to his/her geographically closest datacenters, simply mitigates the problem. However, frequent interactions between distant users lead to frequent inter-datacenter com-munication and hence long service latencies. Therefore, the OSNs need a data allocation algorithm among datacenters with minimized network load and low service latency. Efficient multimedia file sharing. To serve multimedia file sharing with rapid growing user population, the file distribution method should be scalable and cost efficient, e.g. minimiza-tion of bandwidth usage of the centralized servers. The P2P networks have been widely used for file sharing among a large amount of users [58, 131], and meet both scalable and cost efficient re-quirements. However, without fully utilizing the altruism and trust among friends in the OSNs, current P2P assisted file sharing systems depend on strangers or anonymous users to distribute files that degrades their performance due to user selfish and malicious behaviors. Therefore, the OSNs need a cost efficient and trustworthy P2P-assisted file sharing system to serve multimedia content distribution. Cost minimized data allocation among cloud storages. The new trend of OSNs needs to build worldwide datacenters, which introduce a large amount of capital investment and maintenance costs. In order to save the capital expenditures to build and maintain the hardware infrastructures, the OSNs can leverage the storage services from multiple Cloud Service Providers (CSPs) with existing worldwide distributed datacenters [30, 125, 126]. These datacenters provide different Get/Put latencies and unit prices for resource utilization and reservation. Thus, when se-lecting different CSPs’ datacenters, an OSN as a cloud customer of a globally distributed application faces two challenges: i) how to allocate data to worldwide datacenters to satisfy application SLA (service level agreement) requirements including both data retrieval latency and availability, and ii) how to allocate data and reserve resources in datacenters belonging to different CSPs to minimize the payment cost. Therefore, the OSNs need a data allocation system distributing data among CSPs’ datacenters with cost minimization and SLA guarantee. In all, the OSN needs an efficient holistic data distribution and storage solution to minimize its network load and cost to supply a guaranteed QoS for both text and multimedia contents. In this dissertation, we propose methods to solve each of the aforementioned challenges in OSNs. Firstly, we verify the benefits of the new trend of OSNs and present OSN typical properties that lay the basis of our design. We then propose Selective Data replication mechanism in Distributed Datacenters (SD3) to allocate user data among geographical distributed datacenters. In SD3,a datacenter jointly considers update rate and visit rate to select user data for replication, and further atomizes a user’s different types of data (e.g., status update, friend post) for replication, making sure that a replica always reduces inter-datacenter communication. Secondly, we analyze a BitTorrent file sharing trace, which proves the necessity of proximity-and interest-aware clustering. Based on the trace study and OSN properties, to address the second problem, we propose a SoCial Network integrated P2P file sharing system for enhanced Efficiency and Trustworthiness (SOCNET) to fully and cooperatively leverage the common-interest, geographically-close and trust properties of OSN friends. SOCNET uses a hierarchical distributed hash table (DHT) to cluster common-interest nodes, and then further clusters geographically close nodes into a subcluster, and connects the nodes in a subcluster with social links. Thus, when queries travel along trustable social links, they also gain higher probability of being successfully resolved by proximity-close nodes, simultaneously enhancing efficiency and trustworthiness. Thirdly, to handle the third problem, we model the cost minimization problem under the SLA constraints using integer programming. According to the system model, we propose an Eco-nomical and SLA-guaranteed cloud Storage Service (ES3), which finds a data allocation and resource reservation schedule with cost minimization and SLA guarantee. ES3 incorporates (1) a data al-location and reservation algorithm, which allocates each data item to a datacenter and determines the reservation amount on datacenters by leveraging all the pricing policies; (2) a genetic algorithm based data allocation adjustment approach, which makes data Get/Put rates stable in each data-center to maximize the reservation benefit; and (3) a dynamic request redirection algorithm, which dynamically redirects a data request from an over-utilized datacenter to an under-utilized datacenter with sufficient reserved resource when the request rate varies greatly to further reduce the payment. Finally, we conducted trace driven experiments on a distributed testbed, PlanetLab, and real commercial cloud storage (Amazon S3, Windows Azure Storage and Google Cloud Storage) to demonstrate the efficiency and effectiveness of our proposed systems in comparison with other systems. The results show that our systems outperform others in the network savings and data distribution efficiency