Integrative modeling of transcriptional regulation in response to antirheumatic therapy

<p>Abstract</p> <p>Background</p> <p>The investigation of gene regulatory networks is an important issue in molecular systems biology and significant progress has been made by combining different types of biological data. The purpose of this study was to characterize the transcriptional program induced by etanercept therapy in patients with rheumatoid arthritis (RA). Etanercept is known to reduce disease symptoms and progression in RA, but the underlying molecular mechanisms have not been fully elucidated.</p> <p>Results</p> <p>Using a DNA microarray dataset providing genome-wide expression profiles of 19 RA patients within the first week of therapy we identified significant transcriptional changes in 83 genes. Most of these genes are known to control the human body's immune response. A novel algorithm called TILAR was then applied to construct a linear network model of the genes' regulatory interactions. The inference method derives a model from the data based on the Least Angle Regression while incorporating DNA-binding site information. As a result we obtained a scale-free network that exhibits a self-regulating and highly parallel architecture, and reflects the pleiotropic immunological role of the therapeutic target TNF-alpha. Moreover, we could show that our integrative modeling strategy performs much better than algorithms using gene expression data alone.</p> <p>Conclusion</p> <p>We present TILAR, a method to deduce gene regulatory interactions from gene expression data by integrating information on transcription factor binding sites. The inferred network uncovers gene regulatory effects in response to etanercept and thus provides useful hypotheses about the drug's mechanisms of action.</p

Exploratory study to explore the role of ICT in the process of knowledge management in an Indian business environment

In the 21st century and the emergence of a digital economy, knowledge and the knowledge base economy are rapidly growing. To effectively be able to understand the processes involved in the creating, managing and sharing of knowledge management in the business environment is critical to the success of an organization. This study builds on the previous research of the authors on the enablers of knowledge management by identifying the relationship between the enablers of knowledge management and the role played by information communication technologies (ICT) and ICT infrastructure in a business setting. This paper provides the findings of a survey collected from the four major Indian cities (Chennai, Coimbatore, Madurai and Villupuram) regarding their views and opinions about the enablers of knowledge management in business setting. A total of 80 organizations participated in the study with 100 participants in each city. The results show that ICT and ICT infrastructure can play a critical role in the creating, managing and sharing of knowledge in an Indian business environment

Detecting Coordination Problems in Collaborative Software Development Environments

Software development is rarely an individual effort and generally involves teams of developers collaborating to generate good reliable code. Among the software code there exist technical dependencies that arise from software components using services from other components. The different ways of assigning the design, development, and testing of these software modules to people can cause various coordination problems among them. We claim\ud that the collaboration of the developers, designers and testers must be related to and governed by the technical task structure. These collaboration practices are handled in what we call Socio-Technical Patterns.\ud The TESNA project (Technical Social Network Analysis) we report on in this paper addresses this issue. We propose a method and a tool that a project manager can use in order to detect the socio-technical coordination problems. We test the method and tool in a case study of a small and innovative software product company

Can open-source projects (re-) shape the SDN/NFV-driven telecommunication market?

Telecom network operators face rapidly changing business needs. Due to their dependence on long product cycles they lack the ability to quickly respond to changing user demands. To spur innovation and stay competitive, network operators are investigating technological solutions with a proven track record in other application domains such as open source software projects. Open source software enables parties to learn, use, or contribute to technology from which they were previously excluded. OSS has reshaped many application areas including the landscape of operating systems and consumer software. The paradigmshift in telecommunication systems towards Software-Defined Networking introduces possibilities to benefit from open source projects. Implementing the control part of networks in software enables speedier adaption and innovation, and less dependencies on legacy protocols or algorithms hard-coded in the control part of network devices. The recently proposed concept of Network Function Virtualization pushes the softwarization of telecommunication functionalities even further down to the data plane. Within the NFV paradigm, functionality which was previously reserved for dedicated hardware implementations can now be implemented in software and deployed on generic Commercial Off-The Shelf (COTS) hardware. This paper provides an overview of existing open source initiatives for SDN/NFV-based network architectures, involving infrastructure to orchestration-related functionality. It situates them in a business process context and identifies the pros and cons for the market in general, as well as for individual actors

Building Programmable Wireless Networks: An Architectural Survey

In recent times, there have been a lot of efforts for improving the ossified Internet architecture in a bid to sustain unstinted growth and innovation. A major reason for the perceived architectural ossification is the lack of ability to program the network as a system. This situation has resulted partly from historical decisions in the original Internet design which emphasized decentralized network operations through co-located data and control planes on each network device. The situation for wireless networks is no different resulting in a lot of complexity and a plethora of largely incompatible wireless technologies. The emergence of "programmable wireless networks", that allow greater flexibility, ease of management and configurability, is a step in the right direction to overcome the aforementioned shortcomings of the wireless networks. In this paper, we provide a broad overview of the architectures proposed in literature for building programmable wireless networks focusing primarily on three popular techniques, i.e., software defined networks, cognitive radio networks, and virtualized networks. This survey is a self-contained tutorial on these techniques and its applications. We also discuss the opportunities and challenges in building next-generation programmable wireless networks and identify open research issues and future research directions.Comment: 19 page

A trustworthy mobile agent infrastructure for network management

Despite several advantages inherent in mobile-agent-based approaches to network management as compared to traditional SNMP-based approaches, industry is reluctant to adopt the mobile agent paradigm as a replacement for the existing manager-agent model; the management community requires an evolutionary, rather than a revolutionary, use of mobile agents. Furthermore, security for distributed management is a major concern; agent-based management systems inherit the security risks of mobile agents. We have developed a Java-based mobile agent infrastructure for network management that enables the safe integration of mobile agents with the SNMP protocol. The security of the system has been evaluated under agent to agent-platform and agent to agent attacks and has proved trustworthy in the performance of network management tasks