A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis

Background Several lines of evidence suggests that transcription factors are involved in the pathogenesis of Multiple Sclerosis (MS) but a complete mapping the whole network has been elusive. One of the reasons is that there are several clinical subtypes of MS and transcription factors which may be involved in one subtype may not be in others. We investigated the possibility that this network could be mapped using microarray technologies and modern bioinformatics methods on a dataset from whole blood in 99 untreated MS patients (36 Relapse Remitting MS, 43 Primary Progressive MS, and 20 Secondary Progressive MS) and 45 age-matched healthy controls, Methodology/Principal Findings We have used two different analytical methodologies: a differential expression analysis and a differential co-expression analysis, which have converged on a significant number of regulatory motifs that seem to be statistically overrepresented in genes which are either differentially expressed (or differentially co-expressed) in cases and controls (e.g. V$KROX_Q6, p-value < 3.31E-6; V$CREBP1_Q2, p-value < 9.93E-6, V$YY1_02, p-value < 1.65E-5). Conclusions/significance: Our analysis uncovered a network of transcription factors that potentially dysregulate several genes in MS or one or more of its disease subtypes. Analysing the published literature we have found that these transcription factors are involved in the early T-lymphocyte specification and commitment as well as in oligodendrocytes dedifferentiation and development. The most significant transcription factors motifs were for the Early Growth response EGR/KROX family, ATF2, YY1 (Yin and Yang 1), E2F-1/DP-1 and E2F-4/DP-2 heterodimers, SOX5, and CREB and ATF families.

A Hybrid Queue-based Bayesian Network Framework for passenger facilitation modelling

This paper presents a novel framework for the modelling of passenger facilitation in a complex environment. The research is motivated by the challenges in the airport complex system, where there are multiple stakeholders, differing operational objectives and complex interactions and interdependencies between different parts of the airport system. Traditional methods for airport terminal modelling do not explicitly address the need for understanding causal relationships in a dynamic environment. Additionally, existing Bayesian Network (BN) models, which provide a means for capturing causal relationships, only present a static snapshot of a system. A method to integrate a BN complex systems model with stochastic queuing theory is developed based on the properties of the Poisson and Exponential distributions. The resultant Hybrid Queue-based Bayesian Network (HQBN) framework enables the simulation of arbitrary factors, their relationships, and their effects on passenger flow and vice versa. A case study implementation of the framework is demonstrated on the inbound passenger facilitation process at Brisbane International Airport. The predicted outputs of the model, in terms of cumulative passenger flow at intermediary and end points in the inbound process, are found to have an $R^2$ goodness of fit of 0.9994 and 0.9982 respectively over a 10 hour test period. The utility of the framework is demonstrated on a number of usage scenarios including real time monitoring and `what-if' analysis. This framework provides the ability to analyse and simulate a dynamic complex system, and can be applied to other socio-technical systems such as hospitals.

Modeling the viability of the free-ranging cheetah population in Namibia : an object-oriented Bayesian network approach

Conservation of free-ranging cheetah (Acinonyx jubatus) populations is multi faceted and needs to be addressed from an ecological, biological and management perspective. There is a wealth of published research, each focusing on a particular aspect of cheetah conservation. Identifying the most important factors, making sense of various (and sometimes contrasting) findings, and taking decisions when little or no empirical data is available, are everyday challenges facing conservationists. Bayesian networks (BN) provide a statistical modeling framework that enables analysis and integration of information addressing different aspects of conservation. There has been an increased interest in the use of BNs to model conservation issues, however the development of more sophisticated BNs, utilizing object-oriented (OO) features, is still at the frontier of ecological research. We describe an integrated, parallel modeling process followed during a BN modeling workshop held in Namibia to combine expert knowledge and data about free-ranging cheetahs. The aim of the workshop was to obtain a more comprehensive view of the current viability of the free-ranging cheetah population in Namibia, and to predict the effect different scenarios may have on the future viability of this free-ranging cheetah population. Furthermore, a complementary aim was to identify influential parameters of the model to more effectively target those parameters having the greatest impact on population viability. The BN was developed by aggregating diverse perspectives from local and independent scientists, agents from the national ministry, conservation agency members and local fieldworkers. This integrated BN approach facilitates OO modeling in a multi-expert context which lends itself to a series of integrated, yet independent, subnetworks describing different scientific and management components. We created three subnetworks in parallel: a biological, ecological and human factors network, which were then combined to create a complete representation of free-ranging cheetah population viability. Such OOBNs have widespread relevance to the effective and targeted conservation management of vulnerable and endangered species.

INFORMAS (International Network for Food and Obesity/non-communicable diseases Research, Monitoring and Action Support) : overview and key principles

Non-communicable diseases (NCDs) dominate disease burdens globally and poor nutrition increasingly contributes to this global burden. Comprehensive monitoring of food environments, and evaluation of the impact of public and private sector policies on food environments is needed to strengthen accountability systems to reduce NCDs. The International Network for Food and Obesity/NCDs Research, Monitoring and Action Support (INFORMAS) is a global network of public-interest organizations and researchers that aims to monitor, benchmark and support public and private sector actions to create healthy food environments and reduce obesity, NCDs and their related inequalities. The INFORMAS framework includes two ‘process’ modules, that monitor the policies and actions of the public and private sectors, seven ‘impact’ modules that monitor the key characteristics of food environments and three ‘outcome’ modules that monitor dietary quality, risk factors and NCD morbidity and mortality. Monitoring frameworks and indicators have been developed for 10 modules to provide consistency, but allowing for stepwise approaches (‘minimal’, ‘expanded’, ‘optimal’) to data collection and analysis. INFORMAS data will enable benchmarking of food environments between countries, and monitoring of progress over time within countries. Through monitoring and benchmarking, INFORMAS will strengthen the accountability systems needed to help reduce the burden of obesity, NCDs and their related inequalities.

Measuring global economic interdependence : a hierarchical network approach

This paper investigates the business cycle co-movement across countries and regions since 1950 as a measure for quantifying the economic interdependence in the ongoing globalisation process. Our methodological approach is based on analysis of a correlation matrix and the networks it contains. Such an approach summarises the interaction and interdependence of all elements, and it represents a more accurate measure of the global interdependence involved in an economic system. Our results show (1) the dynamics of interdependence has been driven more by synchronisation in regional growth patterns than by the synchronisation of the world economy, and (2) world crisis periods dramatically increase the global co-movement in the world economy.

Effects of wireless sensor network uncertainties on output-only modal-based damage identification

The use of Wireless Sensor Networks (WSNs) for Structural Health Monitoring (SHM) has become a promising approach due to many advantages such as low cost, fast and flexible deployment. However, inherent technical issues such as data synchronization error and data loss have prevented these distinct systems from being extensively used. Recently, several SHM-oriented WSNs have been proposed and believed to be able to overcome a large number of technical uncertainties. Nevertheless, there is limited research examining effects of uncertainties of generic WSN platform and verifying the capability of SHM-oriented WSNs, particularly on demanding SHM applications like modal analysis and damage identification of real civil structures. This article first reviews the major technical uncertainties of both generic and SHM-oriented WSN platforms and efforts of SHM research community to cope with them. Then, effects of the most inherent WSN uncertainty on the first level of a common Output-only Modal-based Damage Identification (OMDI) approach are intensively investigated. Experimental accelerations collected by a wired sensory system on a benchmark civil structure are initially used as clean data before being contaminated with different levels of data pollutants to simulate practical uncertainties in both WSN platforms. Statistical analyses are comprehensively employed in order to uncover the distribution pattern of the uncertainty influence on the OMDI approach. The result of this research shows that uncertainties of generic WSNs can cause serious impact for level 1 OMDI methods utilizing mode shapes. It also proves that SHM-WSN can substantially lessen the impact and obtain truly structural information without having used costly computation solutions.

The tertiary debate : a case study analysis of factors considered when applying for university entry by traditional age school leavers in Brisbane

Many interacting factors contribute to a student's choice of a university. This study takes a systems perspective of the choice and develops a Bayesian Network to represent and quantify these factors and their interactions. The systems model is illustrated through a small study of traditional school leavers in Australia, and highlights similarities and differences between universities' perceptions of student choices, students' perceptions of factors that they should consider and how students really make choices. The study shows the range of information that can be gained from this approach, including identification of important factors and scenario assessment.

Observability analysis of electric networks considering branch impedance

This paper presents an analytical method to analyze the effect of X to R ratio as well as impedance value of branches on observability of a network based on un-decoupled formulation of state estimation (SE) and null space of matrices. The results showed that the X to R ratio of branches had no effect on the observability of networks. In addition, it was shown that observability of some networks was affected by impedance values while some others were not affected. In addition, for branch observability analysis of radial network, a simple and quick method is developed. Illustrative examples of the network under transmission and distribution voltages demonstrate the effectiveness of the proposed methods.

Truncated differential analysis of reduced-round LBlock

In this paper we present truncated differential analysis of reduced-round LBlock by computing the differential distribution of every nibble of the state. LLR statistical test is used as a tool to apply the distinguishing and key-recovery attacks. To build the distinguisher, all possible differences are traced through the cipher and the truncated differential probability distribution is determined for every output nibble. We concatenate additional rounds to the beginning and end of the truncated differential distribution to apply the key-recovery attack. By exploiting properties of the key schedule, we obtain a large overlap of key bits used in the beginning and final rounds. This allows us to significantly increase the differential probabilities and hence reduce the attack complexity. We validate the analysis by implementing the attack on LBlock reduced to 12 rounds. Finally, we apply single-key and related-key attacks on 18 and 21-round LBlock, respectively.

Security analysis of Australian and E.U. e-passport implementation

This paper makes a formal security analysis of the current Australian e-passport implementation using model checking tools CASPER/CSP/FDR. We highlight security issues in the current implementation and identify new threats when an e-passport system is integrated with an automated processing system like SmartGate. The paper also provides a security analysis of the European Union (EU) proposal for Extended Access Control (EAC) that is intended to provide improved security in protecting biometric information of the e-passport bearer. The current e-passport specification fails to provide a list of adequate security goals that could be used for security evaluation. We fill this gap; we present a collection of security goals for evaluation of e-passport protocols. Our analysis confirms existing security weaknesses that were previously identified and shows that both the Australian e-passport implementation and the EU proposal fail to address many security and privacy aspects that are paramount in implementing a secure border control mechanism. ACM Classification C.2.2 (Communication/Networking and Information Technology – Network Protocols – Model Checking), D.2.4 (Software Engineering – Software/Program Verification – Formal Methods), D.4.6 (Operating Systems – Security and Privacy Protection – Authentication)

Critical analysis of spam prevention techniques

E-mail spam has remained a scourge and menacing nuisance for users, internet and network service operators and providers, in spite of the anti-spam techniques available; and spammers are relentlessly circumventing these anti-spam techniques embedded or installed in form of software products on both client and server sides of both fixed and mobile devices to their advantage. This continuous evasion degrades the capabilities of these anti-spam techniques as none of them provides a comprehensive reliable solution to the problem posed by spam and spammers. Major problem for instance arises when these anti-spam techniques misjudge or misclassify legitimate emails as spam (false positive); or fail to deliver or block spam on the SMTP server (false negative); and the spam passes-on to the receiver, and yet this server from where it originates does not notice or even have an auto alert service to indicate that the spam it was designed to prevent has slipped and moved on to the receiver’s SMTP server; and the receiver’s SMTP server still fail to stop the spam from reaching user’s device and with no auto alert mechanism to inform itself of this inability; thus causing a staggering cost in loss of time, effort and finance. This paper takes a comparative literature overview of some of these anti-spam techniques, especially the filtering technological endorsements designed to prevent spam, their merits and demerits to entrench their capability enhancements, as well as evaluative analytical recommendations that will be subject to further research.

Personal media and wireless cities : towards an urban spatial analysis

For the past decade, at least, varieties of small, hand held networked instruments have appeared on the global scene, selling in record numbers, and being utilized by all manner of persons from the old to the young; children, women, men, the wealthy and the poor and in all countries. Their presences bespeak a radical shift in telecommunications infrastructure and the future of communications. They are particularly visible in urban areas where mobile transmission network infrastructure (3G, 4G, cellular and Wi-Fi) is more established and substantial, options more plentiful, and density of populations more dramatic. These end user products—I phones, cell phones, Blackberries, DSi, DS, IPads, Zooms, and others – of the mobile communications industry are the latest, hottest globalized commodities. At the same time, wirelessness, or the state of being wireless, and therefore capable of taking along one's networks, communicating from unlikely spaces, and navigating with GPS, is a complex social, political and economic communications phenomenon of early 21st century life. This thesis examines the specter of being wireless in cities. It lends the entire idea an experimentally envisioned, historical and planned context wherein personalization of media tools is seen both as a design development of corporate, artistic, and military imagination, as well as a profound social phenomenon enabling new forms of sharing, belonging, and urban community. In doing that it asserts the parameters of a new mobile space which, aside from clear benefits to humankind by way of mobility, has reinscribed numerous categories including gender. Moreover, it posits the recognition of other, more nuanced theoretical spaces for complex readings of gender and gendered use, including some instantiation of the notion of 'network' itself as a cyborgian and gendered social form. Additionally, cities are studied as places where technology is not only quickly popularized, but is connected to larger political interests, such as the reading of data, tracking of information, and the new security culture. In so doing the work has been undertaken as an urban spatial analysis and experimental ethnography, utilizing architectural, feminist, techno-utopian, industrial and theoretical literatures as discursive underpinnings from whence understandings and interpretations of mobile space, the mobile office, networked mobility, and personal media have come, linking the space of cities to specific, pioneering urban public art projects in which voice, texting and MMS have been utilized in expressions of ubiquitous networks and urban history. Through numerous examples of techno art, the thesis discusses the 'wireless city' as an emerging cultural, socially constructed economic and spatial entity, both conceived and formed through historic processes of urbanization.

Analysis of the needs of the East Coast cluster regional natural resource management bodies in relation to planning for climate change adaptation

The Climate Change Adaptation for Natural Resource Management (NRM) in East Coast Australia Project aims to foster and support an effective “community of practice” for climate change adaptation within the East Coast Cluster NRM regions that will increase the capacity for adaptation to climate change through enhancements in knowledge and skills and through the establishment of long‐term collaborations. It is being delivered by six consortium research partners: * The University of Queensland (project lead) * Griffith University * University of the Sunshine Coast * CSIRO * New South Wales Office of Environment and Heritage * Queensland Department of Science, IT, Innovation and the Arts (Queensland Herbarium). The project relates to the East Coast Cluster, comprising the six coastal NRM regions and regional bodies between Rockhampton and Sydney: * Fitzroy Basin Association (FBA) * Burnett‐Mary Regional Group (BMRG) * SEQ Catchments (SEQC) * Northern Rivers Catchment Management Authority (CMA) (NRCMA) * Hunter‐Central Rivers CMA (HCRCMA) * Hawkesbury Nepean CMA (HNCMA). The aims of this report are to summarise the needs of the regional bodies in relation to NRM planning for climate change adaptation, and provide a basis for developing the detailed work plan for the research consortium. Two primary methods were used to identify the needs of the regional bodies: (1) document analysis of the existing NRM/ Catchment Action Plans (CAPs) and applications by the regional bodies for funding under Stream 1 of the Regional NRM Planning for Climate Change Fund, and; (2) a needs analysis workshop, held in May 2013 involving representatives from the research consortium partners and the regional bodies. The East Coast Cluster includes five of the ten largest significant urban areas in Australia, world heritage listed natural environments, significant agriculture, mining and extensive grazing. The three NSW CMAs have recently completed strategic level CAPs, with implementation plans to be finalised in 2014/2015. SEQC and FBA are beginning a review of their existing NRM Plans, to be completed in 2014 and 2015 respectively; while BMRG is aiming to produce a NRM and Climate Variability Action Strategy. The regional bodies will receive funding from the Australian Government through the Regional NRM Planning for Climate Change Fund (NRM Fund) to improve regional planning for climate change and help guide the location of carbon and biodiversity activities, including wildlife corridors. The bulk of the funding will be available for activities in 2013/2014, with smaller amounts available in subsequent years. Most regional bodies aim to have a large proportion of the planning work complete by the end of 2014. In addition, NSW CMAs are undergoing major structural change and will be incorporated into semi‐autonomous statutory Local Land Services bodies from 2014. Boundaries will align with local government boundaries and there will be significant change in staff and structures. The regional bodies in the cluster have a varying degree of climate knowledge. All plans recognise climate change as a key driver of change, but there are few specific actions or targets addressing climate change. Regional bodies also have varying capacity to analyse large volumes of spatial or modelling data. Due to the complex nature of natural resource management, all regional bodies work with key stakeholders (e.g. local government, industry groups, and community groups) to deliver NRM outcomes. Regional bodies therefore require project outputs that can be used directly in stakeholder engagement activities, and are likely to require some form of capacity building associated with each of the outputs to maximise uptake. Some of the immediate needs of the regional bodies are a summary of information or tools that are able to be used immediately; and a summary of the key outputs and milestone dates for the project, to facilitate alignment of planning activities with research outputs. A project framework is useful to show the linkages between research elements and the relevance of the research to the adaptive management cycle for NRM planning in which the regional bodies are engaged. A draft framework is proposed to stimulate and promote discussion on research elements and linkages; this will be refined during and following the development of the detailed project work plan. The regional bodies strongly emphasised the need to incorporate a shift to a systems based resilience approach to NRM planning, and that approach is included in the framework. The regional bodies identified that information on climate projections would be most useful at regional and subregional scale, to feed into scenario planning and impact analysis. Outputs should be ‘engagement ready’ and there is a need for capacity building to enable regional bodies to understand and use the projections in stakeholder engagement. There was interest in understanding the impacts of climate change projections on ecosystems (e.g. ecosystem shift), and the consequent impacts on the production of ecosystem services. It was emphasised that any modelling should be able to be used by the regional bodies with their stakeholders to allow for community input (i.e. no black box models). The online regrowth benefits tool was of great interest to the regional bodies, as spatial mapping of carbon farming opportunities would be relevant to their funding requirements. The NSW CMAs identified an interest in development of the tool for NSW vegetation types. Needs relating to socio‐economic information included understanding the socio‐economic determinants of carbon farming uptake and managing community expectations. A need was also identified to understand the vulnerability of industry groups as well as community to climate change impacts, and in particular understanding how changes in the flow of ecosystem services would interact with the vulnerability of these groups to impact on the linked ecologicalsocio‐economic system. Responses to disasters (particularly flooding and storm surge) and recovery responses were also identified as being of interest. An ecosystem services framework was highlighted as a useful approach to synthesising biophysical and socioeconomic information in the context of a systems based, resilience approach to NRM planning. A need was identified to develop processes to move towards such an approach to NRM planning from the current asset management approach. Examples of best practice in incorporating climate science into planning, using scenarios for stakeholder engagement in planning and processes for institutionalising learning were also identified as cross‐cutting needs. The over‐arching theme identified was the need for capacity building for the NRM bodies to best use the information available at any point in time. To this end a planners working group has been established to support the building of a network of informed and articulate NRM agents with knowledge of current climate science and capacity to use current tools to engage stakeholders in NRM planning for climate change adaptation. The planners working group would form the core group of the community of practice, with the broader group of stakeholders participating when activities aligned with their interests. In this way, it is anticipated that the Project will contribute to building capacity within the wider community to effectively plan for climate change adaptation.

Security analysis of the non-aggressive challenge response of the DNP3 Protocol using a CPN Model

Distributed Network Protocol Version 3 (DNP3) is the de-facto communication protocol for power grids. Standard-based interoperability among devices has made the protocol useful to other infrastructures such as water, sewage, oil and gas. DNP3 is designed to facilitate interaction between master stations and outstations. In this paper, we apply a formal modelling methodology called Coloured Petri Nets (CPN) to create an executable model representation of DNP3 protocol. The model facilitates the analysis of the protocol to ensure that the protocol will behave as expected. Also, we illustrate how to verify and validate the behaviour of the protocol, using the CPN model and the corresponding state space tool to determine if there are insecure states. With this approach, we were able to identify a Denial of Service (DoS) attack against the DNP3 protocol.

Formal analysis of card-based payment systems in mobile devices

To provide card holder authentication while they are conducting an electronic transaction using mobile devices, VISA and MasterCard independently proposed two electronic payment protocols: Visa 3D Secure and MasterCard Secure Code. The protocols use pre-registered passwords to provide card holder authentication and Secure Socket Layer/ Transport Layer Security (SSL/TLS) for data confidentiality over wired networks and Wireless Transport Layer Security (WTLS) between a wireless device and a Wireless Application Protocol (WAP) gateway. The paper presents our analysis of security properties in the proposed protocols using formal method tools: Casper and FDR2. We also highlight issues concerning payment security in the proposed protocols.