Multiscale analysis of protein functions and stochastic modelling of gene transcriptional regulatory networks

Genomic and proteomic analyses have attracted a great deal of interests in biological research in recent years. Many methods have been applied to discover useful information contained in the enormous databases of genomic sequences and amino acid sequences. The results of these investigations inspire further research in biological fields in return. These biological sequences, which may be considered as multiscale sequences, have some specific features which need further efforts to characterise using more refined methods. This project aims to study some of these biological challenges with multiscale analysis methods and stochastic modelling approach. The first part of the thesis aims to cluster some unknown proteins, and classify their families as well as their structural classes. A development in proteomic analysis is concerned with the determination of protein functions. The first step in this development is to classify proteins and predict their families. This motives us to study some unknown proteins from specific families, and to cluster them into families and structural classes. We select a large number of proteins from the same families or superfamilies, and link them to simulate some unknown large proteins from these families. We use multifractal analysis and the wavelet method to capture the characteristics of these linked proteins. The simulation results show that the method is valid for the classification of large proteins. The second part of the thesis aims to explore the relationship of proteins based on a layered comparison with their components. Many methods are based on homology of proteins because the resemblance at the protein sequence level normally indicates the similarity of functions and structures. However, some proteins may have similar functions with low sequential identity. We consider protein sequences at detail level to investigate the problem of comparison of proteins. The comparison is based on the empirical mode decomposition (EMD), and protein sequences are detected with the intrinsic mode functions. A measure of similarity is introduced with a new cross-correlation formula. The similarity results show that the EMD is useful for detection of functional relationships of proteins. The third part of the thesis aims to investigate the transcriptional regulatory network of yeast cell cycle via stochastic differential equations. As the investigation of genome-wide gene expressions has become a focus in genomic analysis, researchers have tried to understand the mechanisms of the yeast genome for many years. How cells control gene expressions still needs further investigation. We use a stochastic differential equation to model the expression profile of a target gene. We modify the model with a Gaussian membership function. For each target gene, a transcriptional rate is obtained, and the estimated transcriptional rate is also calculated with the information from five possible transcriptional regulators. Some regulators of these target genes are verified with the related references. With these results, we construct a transcriptional regulatory network for the genes from the yeast Saccharomyces cerevisiae. The construction of transcriptional regulatory network is useful for detecting more mechanisms of the yeast cell cycle.

Intrusion detection framework for encrypted networks

Network-based Intrusion Detection Systems (NIDSs) monitor network traffic for signs of malicious activities that have the potential to disrupt entire network infrastructures and services. NIDS can only operate when the network traffic is available and can be extracted for analysis. However, with the growing use of encrypted networks such as Virtual Private Networks (VPNs) that encrypt and conceal network traffic, a traditional NIDS can no longer access network traffic for analysis. The goal of this research is to address this problem by proposing a detection framework that allows a commercial off-the-shelf NIDS to function normally in a VPN without any modification. One of the features of the proposed framework is that it does not compromise on the confidentiality afforded by the VPN. Our work uses a combination of Shamir’s secret-sharing scheme and randomised network proxies to securely route network traffic to the NIDS for analysis. The detection framework is effective against two general classes of attacks – attacks targeted at the network hosts or attacks targeted at framework itself. We implement the detection framework as a prototype program and evaluate it. Our evaluation shows that the framework does indeed detect these classes of attacks and does not introduce any additional false positives. Despite the increase in network overhead in doing so, the proposed detection framework is able to consistently detect intrusions through encrypted networks.

Online environmental information systems

In today’s information society, electronic tools, such as computer networks for the rapid transfer of data and composite databases for information storage and management, are critical in ensuring effective environmental management. In particular environmental policies and programs for federal, state, and local governments need a large volume of up-to-date information on the quality of water, air, and soil in order to conserve and protect natural resources and to carry out meteorology. In line with this, the utilization of information and communication technologies (ICTs) is crucial to preserve and improve the quality of life. In handling tasks in the field of environmental protection a range of environmental and technical information is often required for a complex and mutual decision making in a multidisciplinary team environment. In this regard e-government provides a foundation of the transformative ICT initiative which can lead to better environmental governance, better services, and increased public participation in environmental decision- making process.

Information accountability for online healthcare social networks

Online social networking has become one of the most popular Internet applications in the modern era. They have given the Internet users, access to information that other Internet based applications are unable to. Although many of the popular online social networking web sites are focused towards entertainment purposes, sharing information can benefit the healthcare industry in terms of both efficiency and effectiveness. But the capability to share personal information; the factor which has made online social networks so popular, is itself a major obstacle when considering information security and privacy aspects. Healthcare can benefit from online social networking if they are implemented such that sensitive patient information can be safeguarded from ill exposure. But in an industry such as healthcare where the availability of information is crucial for better decision making, information must be made available to the appropriate parties when they require it. Hence the traditional mechanisms for information security and privacy protection may not be suitable for healthcare. In this paper we propose a solution to privacy enhancement in online healthcare social networks through the use of an information accountability mechanism.

Stakeholder engagement by governance networks

Public awareness of large infrastructure projects, many of which are delivered through networked arrangements is high for several reasons. These projects often involve significant public investment; they may involve multiple and conflicting stakeholders and can potentially have significant environmental impacts (Lim and Yang, 2008). To produce positive outcomes from infrastructure delivery it is imperative that stakeholder “buy in” be obtained particularly about decisions relating to the scale and location of infrastructure. Given the likelihood that stakeholders will have different levels of interest and investment in project outcomes, failure to manage this dynamic could potentially jeopardise project delivery by delaying or halting the construction of essential infrastructure. Consequently, stakeholder engagement has come to constitute a critical activity in infrastructure development delivered through networks. This paper draws on stakeholder theory and governance network theory and provides insights into how three multi-level networks within the Roads Alliance in Queensland engage with stakeholders in the delivery of road infrastructure. New knowledge about stakeholders has been obtained by testing a model of Stakeholder Salience and Engagement which combines and extends the stakeholder identification and salience theory and the ladder of stakeholder management and engagement. By applying this model, the broad research question: “How do governance networks engage with stakeholders?” has been addressed. A multiple embedded case study design was selected as the overall approach to explore, describe, explain and evaluate how stakeholder engagement occurred in three governance networks delivering road infrastructure in Queensland. The outcomes of this research contribute to and extend stakeholder theory by showing how stakeholder salience impacts on decisions about the types of engagement processes implemented. Governance network theory is extended by showing how governance networks interact with stakeholders. From a practical perspective this research provides governance networks with an indication of how to more effectively undertake engagement with different types of stakeholders.

How can soil monitoring networks be used to improve predictions of organic carbon pool dynamics and CO2 fluxes in agricultural soils?

Abstract As regional and continental carbon balances of terrestrial ecosystems become available, it becomes clear that the soils are the largest source of uncertainty. Repeated inventories of soil organic carbon (SOC) organized in soil monitoring networks (SMN) are being implemented in a number of countries. This paper reviews the concepts and design of SMNs in ten countries, and discusses the contribution of such networks to reducing the uncertainty of soil carbon balances. Some SMNs are designed to estimate country-specific land use or management effects on SOC stocks, while others collect soil carbon and ancillary data to provide a nationally consistent assessment of soil carbon condition across the major land-use/soil type combinations. The former use a single sampling campaign of paired sites, while for the latter both systematic (usually grid based) and stratified repeated sampling campaigns (5–10 years interval) are used with densities of one site per 10–1,040 km². For paired sites, multiple samples at each site are taken in order to allow statistical analysis, while for the single sites, composite samples are taken. In both cases, fixed depth increments together with samples for bulk density and stone content are recommended. Samples should be archived to allow for re-measurement purposes using updated techniques. Information on land management, and where possible, land use history should be systematically recorded for each site. A case study of the agricultural frontier in Brazil is presented in which land use effect factors are calculated in order to quantify the CO2 fluxes from national land use/management conversion matrices. Process-based SOC models can be run for the individual points of the SMN, provided detailed land management records are available. These studies are still rare, as most SMNs have been implemented recently or are in progress. Examples from the USA and Belgium show that uncertainties in SOC change range from 1.6–6.5 Mg C ha−1 for the prediction of SOC stock changes on individual sites to 11.72 Mg C ha−1 or 34% of the median SOC change for soil/land use/climate units. For national SOC monitoring, stratified sampling sites appears to be the most straightforward attribution of SOC values to units with similar soil/land use/climate conditions (i.e. a spatially implicit upscaling approach). Keywords Soil monitoring networks - Soil organic carbon - Modeling - Sampling design

Design of decoupling networks for circulant symmetric antenna arrays

Small element spacing in compact arrays results in strong mutual coupling between array elements. Performance degradation associated with the strong coupling can be avoided through the introduction of a decoupling network consisting of interconnected reactive elements. We present a systematic design procedure for decoupling networks of symmetrical arrays with more than three elements and characterized by circulant scattering parameter matrices. The elements of the decoupling network are obtained through repeated decoupling of the characteristic eigenmodes of the array, which allows the calculation of element values using closed-form expressions.

Bayesian methodology for genetics of complex diseases

Genetic research of complex diseases is a challenging, but exciting, area of research. The early development of the research was limited, however, until the completion of the Human Genome and HapMap projects, along with the reduction in the cost of genotyping, which paves the way for understanding the genetic composition of complex diseases. In this thesis, we focus on the statistical methods for two aspects of genetic research: phenotype definition for diseases with complex etiology and methods for identifying potentially associated Single Nucleotide Polymorphisms (SNPs) and SNP-SNP interactions. With regard to phenotype definition for diseases with complex etiology, we firstly investigated the effects of different statistical phenotyping approaches on the subsequent analysis. In light of the findings, and the difficulties in validating the estimated phenotype, we proposed two different methods for reconciling phenotypes of different models using Bayesian model averaging as a coherent mechanism for accounting for model uncertainty. In the second part of the thesis, the focus is turned to the methods for identifying associated SNPs and SNP interactions. We review the use of Bayesian logistic regression with variable selection for SNP identification and extended the model for detecting the interaction effects for population based case-control studies. In this part of study, we also develop a machine learning algorithm to cope with the large scale data analysis, namely modified Logic Regression with Genetic Program (MLR-GEP), which is then compared with the Bayesian model, Random Forests and other variants of logic regression.

Single-layer decoupling networks for circulant symmetric arrays

Reduced element spacing in antenna arrays gives rise to strong mutual coupling between array elements and may cause significant performance degradation. These effects can be alleviated by introducing a decoupling network consisting of interconnected reactive elements. The existing design approach for the synthesis of a decoupling network for circulant symmetric arrays allows calculation of element values using closed-form expressions, but the resulting circuit configuration requires multilayer technology for implementation. In this paper, a new structure for the decoupling of circulant symmetric arrays of more than four elements is presented. Element values are no longer obtained in closed form, but the resulting circuit is much simpler and can be implemented on a single layer.