Domain-based distributes mediation system for large-scale data integration

The increasing use of computers and the development of communication infrastructures resulted in abundance of information on the networks and extremely need for querying and integrating data from large number of data sources, especially for scientific applications. Distributed mediation system performs this task fragmentally, where each mediator in the system architecture responsible for querying subset of data sources.To make such type of systems success in large scale, we must deal with two issues: logical distribution of the data sources and mediators in the system architecture, and logical interaction between the mediators.To handle these issues, this paper proposes a domain based distributed mediation system called Multi-Mediators System for Large scale Data Integration (MMSLDI).MMSLDI enables the reducing of the general query response time by eliminating unnecessary visits to the data sources that do not contribute to the answer of the query.Moreover, it satisfies the requirements of adaptation to various kinds of domains, decentralized control, and automation of its processes

File management in a mobile DHT-based P2P environment

The emergence of mobile P2P systems is largely due to the evolution of mobile devices into powerful information processing units. The relatively structured context that results from the mapping of mobile patterns of behaviour onto P2P models is however constrained by the vulnerabilities of P2P networks and the inherent limitations of mobile devices. Whilst the implementation of P2P models gives rise to security and reliability issues, the deployment of mobile devices is subject to efficiency constraints. This paper presents the development and deployment of a mobile P2P system based on distributed hash tables (DHT). The secure, reliable and efficient dispersal of files is taken as an application. Reliability was addressed by providing two methods for file dispersal: replication and erasure coding. Security constraints were catered for by incorporating an authentication mechanism and three encryption schemes. Lightweight versions of various algorithms were selected in order to attend to efficiency requirements

Allosteric Conversation in the Androgen Receptor Ligand-Binding Domain Surfaces

Androgen receptor (AR) is a major therapeutic target that plays pivotal roles in prostate cancer (PCa) and androgen insensitivity syndromes. Wepreviously proposed that compounds recruited to ligand-binding domain (LBD) surfaces could regulate AR activity in hormone-refractory PCa and discovered several surface modulators of AR function. Surprisingly, the most effective compounds bound preferentially to a surface of unknown function [binding function 3 (BF-3)] instead of the coactivator-binding site [activation function 2 (AF-2)]. Different BF-3 mutations have been identified in PCa or androgen insensitivity syndrome patients, and they can strongly affect AR activity. Further, comparison of AR x-ray structures with and without bound ligands at BF-3 and AF-2 showed structural coupling between both pockets. Here, we combine experimental evidence and molecular dynamic simulations to investigate whether BF-3 mutations affect AR LBD function and dynamics possibly via allosteric conversation between surface sites. Our data indicate that AF-2 conformation is indeed closely coupled to BF-3 and provide mechanistic proof of their structural interconnection. BF-3 mutations may function as allosteric elicitors, probably shifting the AR LBD conformational ensemble toward conformations that alter AF-2 propensity to reorganize into subpockets that accommodate N-terminal domain and coactivator peptides. The induced conformation may result in either increased or decreased AR activity. Activating BF-3 mutations also favor the formation of another pocket (BF-4) in the vicinity of AF-2 and BF-3, which we also previously identified as a hot spot for a small compound. We discuss the possibility that BF-3 may be a protein-docking site that binds to the N-terminal domain and corepressors. AR surface sites are attractive pharmacological targets to develop allosteric modulators that might be alternative lead compounds for drug design. © 2012 by The Endocrie Society

Implementing and evaluating an ICON orchestrator

The cloud computing paradigm has risen, during the last 20 years, to the task of bringing powerful computational services to the masses. Centralizing the computer hardware to a few large data centers has brought large monetary savings, but at the cost of a greater geographical distance between the server and the client. As a new generation of thin clients have emerged, e.g. smartphones and IoT-devices, the larger latencies induced by these greater distances, can limit the applications that could benefit from using the vast resources available in cloud computing. Not long after the explosive growth of cloud computing, a new paradigm, edge computing has risen. Edge computing aims at bringing the resources generally found in cloud computing closer to the edge where many of the end-users, clients and data producers reside. In this thesis, I will present the edge computing concept as well as the technologies enabling it. Furthermore I will show a few edge computing concepts and architectures, including multi- access edge computing (MEC), Fog computing and intelligent containers (ICON). Finally, I will also present a new edge-orchestrator, the ICON Python Orchestrator (IPO), that enables intelligent containers to migrate closer to the users. The ICON Python orchestrator tests the feasibility of the ICON concept and provides per- formance measurements that can be compared to other contemporary edge computing im- plementations. In this thesis, I will present the IPO architecture design including challenges encountered during the implementation phase and solutions to specific problems. I will also show the testing and validation setup. By using the artificial testing and validation network, client migration speeds were measured using three different cases - redirection, cache hot ICON migration and cache cold ICON migration. While there is room for improvements, the migration speeds measured are on par with other edge computing implementations

Leveraging Resources on Anonymous Mobile Edge Nodes

Smart devices have become an essential component in the life of mankind. The quick rise of smartphones, IoTs, and wearable devices enabled applications that were not possible few years ago, e.g., health monitoring and online banking. Meanwhile, smart sensing laid the infrastructure for smart homes and smart cities. The intrusive nature of smart devices granted access to huge amounts of raw data. Researchers seized the moment with complex algorithms and data models to process the data over the cloud and extract as much information as possible. However, the pace and amount of data generation, in addition to, networking protocols transmitting data to cloud servers failed short in touching more than 20% of what was generated on the edge of the network. On the other hand, smart devices carry a large set of resources, e.g., CPU, memory, and camera, that sit idle most of the time. Studies showed that for plenty of the time resources are either idle, e.g., sleeping and eating, or underutilized, e.g. inertial sensors during phone calls. These findings articulate a problem in processing large data sets, while having idle resources in the close proximity. In this dissertation, we propose harvesting underutilized edge resources then use them in processing the huge data generated, and currently wasted, through applications running at the edge of the network. We propose flipping the concept of cloud computing, instead of sending massive amounts of data for processing over the cloud, we distribute lightweight applications to process data on users\u27 smart devices. We envision this approach to enhance the network\u27s bandwidth, grant access to larger datasets, provide low latency responses, and more importantly involve up-to-date user\u27s contextual information in processing. However, such benefits come with a set of challenges: How to locate suitable resources? How to match resources with data providers? How to inform resources what to do? and When? How to orchestrate applications\u27 execution on multiple devices? and How to communicate between devices on the edge? Communication between devices at the edge has different parameters in terms of device mobility, topology, and data rate. Standard protocols, e.g., Wi-Fi or Bluetooth, were not designed for edge computing, hence, does not offer a perfect match. Edge computing requires a lightweight protocol that provides quick device discovery, decent data rate, and multicasting to devices in the proximity. Bluetooth features wide acceptance within the IoT community, however, the low data rate and unicast communication limits its use on the edge. Despite being the most suitable communication protocol for edge computing and unlike other protocols, Bluetooth has a closed source code that blocks lower layer in front of all forms of research study, enhancement, and customization. Hence, we offer an open source version of Bluetooth and then customize it for edge computing applications. In this dissertation, we propose Leveraging Resources on Anonymous Mobile Edge Nodes (LAMEN), a three-tier framework where edge devices are clustered by proximities. On having an application to execute, LAMEN clusters discover and allocate resources, share application\u27s executable with resources, and estimate incentives for each participating resource. In a cluster, a single head node, i.e., mediator, is responsible for resource discovery and allocation. Mediators orchestrate cluster resources and present them as a virtually large homogeneous resource. For example, two devices each offering either a camera or a speaker are presented outside the cluster as a single device with both camera and speaker, this can be extended to any combination of resources. Then, mediator handles applications\u27 distribution within a cluster as needed. Also, we provide a communication protocol that is customizable to the edge environment and application\u27s need. Pushing lightweight applications that end devices can execute over their locally generated data have the following benefits: First, avoid sharing user data with cloud server, which is a privacy concern for many of them; Second, introduce mediators as a local cloud controller closer to the edge; Third, hide the user\u27s identity behind mediators; and Finally, enhance bandwidth utilization by keeping raw data at the edge and transmitting processed information. Our evaluation shows an optimized resource lookup and application assignment schemes. In addition to, scalability in handling networks with large number of devices. In order to overcome the communication challenges, we provide an open source communication protocol that we customize for edge computing applications, however, it can be used beyond the scope of LAMEN. Finally, we present three applications to show how LAMEN enables various application domains on the edge of the network. In summary, we propose a framework to orchestrate underutilized resources at the edge of the network towards processing data that are generated in their proximity. Using the approaches explained later in the dissertation, we show how LAMEN enhances the performance of applications and enables a new set of applications that were not feasible

Bioartificial scaffolds fabrication and their use for in vitro testing of wound healing devices

In the last decades Negative Pressure Wound Therapy (NPWT) has shown its efficacy in wound healing, applying continuous or intermittent subatmospheric pressure to the wound surface by means of dressing systems. While there is general consensus that positive effects originate from a complex interplay of mechanisms such as deformations and exudate removal, uncertainty persists about the optimal mode of application and the consequences of this therapy at a cellular level. A better understanding of the skin mechanobiology in response to therapeutic stimuli using a bioreactor system can help to individualize future wound therapies in a reproducible and controlled environment. This thesis proposed the fabrication of in vitro 3D skin models aiming to reproduce the relationship that occurs between cell types and skin substrate and investigated their use in a bioreactor in order to obtain new knowledge of NPWT mechanisms. Freeze-drying and electrospinning were considered to be the best methodologies to obtain homogenous and standardized 3D structures that were favourable for the purpose. Highly porous pure collagen and collagen-based scaffolds were firstly created using the freeze-drying technique. Various cross-linking methods were assessed and directly compared to establish the most suitable to improve mechanical stability and physical properties. Meanwhile, fibrous structures that could resemble the topography of the extra cellular matrix (ECM) were produced with the electrospinning system using toxic-free solutions and an in-house-developed rotating collector. The prospect to fabricate a hybrid bilayer scaffold, combining the two techniques was also investigated and discussed. Primary human skin fibroblasts were cultured on these structures and cell interaction and viability were evaluated through assays and microscopy techniques. Lastly, a proof-of-concept bioreactor for NPWT investigation was designed and tested on the freeze-dried scaffolds demonstrating the feasibility of this research approach. Results showed that blending methodology used in the freeze-drying can lead to scaffolds with unique physical properties while cross-linking has influence on substrate stiffness that guides cell response. With regard to the electrospinning, the use of the rotating collector was found to be promising in obtaining a bimodal fibre distribution resulting in porous and orientated membranes that simulate the orientation of collagen fibres in the dermis of human skin and could be beneficial for cell infiltration.To conclude, this study laid the groundwork for further development of these bioartificial scaffolds with improved properties that could be used as skin models and combined in a negative-pressure cell culture system with the aim to advance the understanding of NPWT biological mechanism and its clinical efficacy

Grid service discovery with rough sets

Copyright [2008] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to [email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.The computational grid is evolving as a service-oriented computing infrastructure that facilitates resource sharing and large-scale problem solving over the Internet. Service discovery becomes an issue of vital importance in utilising grid facilities. This paper presents ROSSE, a Rough sets based search engine for grid service discovery. Building on Rough sets theory, ROSSE is novel in its capability to deal with uncertainty of properties when matching services. In this way, ROSSE can discover the services that are most relevant to a service query from a functional point of view. Since functionally matched services may have distinct non-functional properties related to Quality of Service (QoS), ROSSE introduces a QoS model to further filter matched services with their QoS values to maximise user satisfaction in service discovery. ROSSE is evaluated in terms of its accuracy and efficiency in discovery of computing services

SDSF : social-networking trust based distributed data storage and co-operative information fusion.

As of 2014, about 2.5 quintillion bytes of data are created each day, and 90% of the data in the world was created in the last two years alone. The storage of this data can be on external hard drives, on unused space in peer-to-peer (P2P) networks or using the more currently popular approach of storing in the Cloud. When the users store their data in the Cloud, the entire data is exposed to the administrators of the services who can view and possibly misuse the data. With the growing popularity and usage of Cloud storage services like Google Drive, Dropbox etc., the concerns of privacy and security are increasing. Searching for content or documents, from this distributed stored data, given the rate of data generation, is a big challenge. Information fusion is used to extract information based on the query of the user, and combine the data and learn useful information. This problem is challenging if the data sources are distributed and heterogeneous in nature where the trustworthiness of the documents may be varied. This thesis proposes two innovative solutions to resolve both of these problems. Firstly, to remedy the situation of security and privacy of stored data, we propose an innovative Social-based Distributed Data Storage and Trust based co-operative Information Fusion Framework (SDSF). The main objective is to create a framework that assists in providing a secure storage system while not overloading a single system using a P2P like approach. This framework allows the users to share storage resources among friends and acquaintances without compromising the security or privacy and enjoying all the benefits that the Cloud storage offers. The system fragments the data and encodes it to securely store it on the unused storage capacity of the data owner\u27s friends\u27 resources. The system thus gives a centralized control to the user over the selection of peers to store the data. Secondly, to retrieve the stored distributed data, the proposed system performs the fusion also from distributed sources. The technique uses several algorithms to ensure the correctness of the query that is used to retrieve and combine the data to improve the information fusion accuracy and efficiency for combining the heterogeneous, distributed and massive data on the Cloud for time critical operations. We demonstrate that the retrieved documents are genuine when the trust scores are also used while retrieving the data sources. The thesis makes several research contributions. First, we implement Social Storage using erasure coding. Erasure coding fragments the data, encodes it, and through introduction of redundancy resolves issues resulting from devices failures. Second, we exploit the inherent concept of trust that is embedded in social networks to determine the nodes and build a secure net-work where the fragmented data should be stored since the social network consists of a network of friends, family and acquaintances. The trust between the friends, and availability of the devices allows the user to make an informed choice about where the information should be stored using `k\u27 optimal paths. Thirdly, for the purpose of retrieval of this distributed stored data, we propose information fusion on distributed data using a combination of Enhanced N-grams (to ensure correctness of the query), Semantic Machine Learning (to extract the documents based on the context and not just bag of words and also considering the trust score) and Map Reduce (NSM) Algorithms. Lastly we evaluate the performance of distributed storage of SDSF using era- sure coding and identify the social storage providers based on trust and evaluate their trustworthiness. We also evaluate the performance of our information fusion algorithms in distributed storage systems. Thus, the system using SDSF framework, implements the beneficial features of P2P networks and Cloud storage while avoiding the pitfalls of these systems. The multi-layered encrypting ensures that all other users, including the system administrators cannot decode the stored data. The application of NSM algorithm improves the effectiveness of fusion since large number of genuine documents are retrieved for fusion

Registry composition in ambient networks

Ambient Networks (AN) is a new networking concept for beyond 3G. It is a product of the European Union's Sixth Framework Program (FP6). Network composition is a core concept of ANs. It allows dynamic, scalable and uniform cooperation between heterogeneous networks. ANs can host various registries. These registries may be of different types (e.g. centralized, distributed), store heterogeneous types of information (e.g. raw data vs. aggregated data), and rely on different interfaces to access the stored information (i.e. protocols or programming interfaces). When ANs compose, the hosted registries need to compose. Registry composition is a sub-process of network composition. It provides seamless and autonomous access to the content of all of the registries in the composed network. This thesis proposes a new architecture for registry composition in ANs. This overall architecture is made up of four components: interface interworking, data interworking, negotiation and signaling. Interface interworking enables dynamic intercommunication between registries with heterogeneous interfaces. Data interworking involves dynamically overcoming data heterogeneity (e.g. format and granularity). Interface and data interworking go beyond static interworking using gateways, as done today. The negotiation component allows the negotiation of the composition agreement. Signaling coordinates and regulates the negotiation and the execution of the composition agreement. Requirements are derived and related work is reviewed. We propose a new functional entity and a new procedure to orchestrate the composition process. We also propose a new architecture for interface interworking, based on a peer to peer overlay network. We have built a proof-of-concept prototype. The interface-interworking component is used as the basis of our new architecture to data interworking. This architecture reuses mechanisms and algorithms from the federated data base area. The thesis proposes as well a new architecture for on-line negotiation. The architecture includes a template for composition agreement proposals, and a negotiation protocol that was validated using SPIN. A new signaling framework is also proposed. It is based on the IETF Next Step in Signaling (NSIS) framework and was validated using OPNET. Most of these contributions are now part of the AN concept, as defined by the European Union's Sixth Framework Progra