Modeling of protein signaling networks in clinical proteomics

Molecular interactions that underlie pathophysiological states are being elucidated using techniques that profile proteomicend points in cellular systems. Within the field of cancer research, protein interaction networks play pivotal roles in the establishment and maintenance of the hallmarks of malignancy, including cell division, invasion, and migration. Multiple complementary tools enable a multifaceted view of how signal protein pathway alterations contribute to pathophysiological states.One pivotal technique is signal pathway profiling of patient tissue specimens. This microanalysis technology provides a proteomic snapshot at one point in time of cells directly procured from the native context of a tumor micro environment. To study the adaptive patterns of signal pathway events over time, before and after experimental therapy, it is necessary to obtain biopsies from patients before, during, and after therapy. A complementary approach is the profiling of cultured cell lines with and without treatment. Cultured cell models provide the opportunity to study short-term signal changes occurring over minutes to hours. Through this type of system, the effects of particular pharmacological agents may be used to test the effects of signal pathway inhibition or activation on multiple endpoints within a pathway. The complexity of the data generated has necessitated the development of mathematical models for optimal interpretation of interrelated signaling pathways. In combination,clinical proteomic biopsy profiling, tissue culture proteomic profiling, and mathematical modeling synergistically enable a deeper understanding of how protein associations lead to disease states and present new insights into the design of therapeutic regimens.

Security and Privacy in Vehicular Ad-Hoc Networks : Survey and the Road Ahead

Vehicular Ad-hoc Networks (VANETs) can make roads safer, cleaner, and smarter. It can offer a wide range of services, which can be safety and non-safety related. Many safety-related VANETs applications are real-time and mission critical, which would require strict guarantee of security and reliability. Even non-safety related multimedia applications, which will play an important role in the future, will require security support. Lack of such security and privacy in VANETs is one of the key hindrances to the wide spread implementations of it. An insecure and unreliable VANET can be more dangerous than the system without VANET support. So it is essential to make sure that “life-critical safety” information is secure enough to rely on. Securing the VANETs along with appropriate protection of the privacy drivers or vehicle owners is a very challenging task. In this work we summarize the attacks, corresponding security requirements and challenges in VANETs. We also present the most popular generic security policies which are based on prevention as well detection methods. Many VANETs applications require system-wide security support rather than individual layer from the VANETs’ protocol stack. In this work we will review the existing works in the perspective of holistic approach of security. Finally, we will provide some possible future directions to achieve system-wide security as well as privacy-friendly security in VANETs.

Introspective service interface synthesis in business networks

Service mismatches involve the adaptation of structural and behavioural interfaces of services, which in practice incurs long lead times through manual, coding e ort. We propose a framework, complementary to conventional service adaptation, to extract comprehensive and seman- tically normalised service interfaces, useful for interoperability in large business networks and the Internet of Services. The framework supports introspection and analysis of large and overloaded operational signa- tures to derive focal artefacts, namely the underlying business objects of services. A more simpli ed and comprehensive service interface layer is created based on these, and rendered into semantically normalised in- terfaces, given an ontology accrued through the framework from service analysis history. This opens up the prospect of supporting capability comparisons across services, and run-time request backtracking and ad- justment, as consumers discover new features of a service's operations through corresponding features of similar services. This paper provides a rst exposition of the service interface synthesis framework, describing patterns having novel requirements for unilateral service adaptation, and algorithms for interface introspection and business object alignment. A prototype implementation and analysis of web services drawn from com- mercial logistic systems are used to validate the algorithms and identify open challenges and future research directions.

Surviving (thriving) in academia : feminist support networks and women ECRs

In this paper, we reflect upon our experiences and those of our peers as doctoral students and early career researchers in an Australian political science department. We seek to explain and understand the diverse ways that participating in an unofficial Feminist Reading Group in our department affected our experiences. We contend that informal peer support networks like reading groups do more than is conventionally assumed, and may provide important avenues for sustaining feminist research in times of austerity, as well as supporting and enabling women and emerging feminist scholars in academia. Participating in the group created a community of belonging and resistance, providing women with personal validation, information and material support, as well as intellectual and political resources to understand and resist our position within the often hostile spaces of the University. While these experiences are specific to our context, time and location, they signal that peer networks may offer critical political resources for responding to the ways that women’s bodies and concerns are marginalised in increasingly competitive and corporatised university environments.

Physical mechanism of the compressive response of F-actin networks : significance of crosslinker unbinding events

A model of crosslinker unbinding is implemented in a highly coarsegrained granular model of F-actin cytoskeleton. We employ this specific granular model to study the mechanisms of the compressive responses of F-actin networks. It is found that the compressive response of F-actin cytoskeleton has dependency on the strain rate. The evolution of deformation energy in the network indicates that crosslinker unbinding events can induce the remodelling of F-actin cytoskeleton in response to external loadings. The internal stress in F-actin cytoskeleton can efficiently dissipate with the help of crosslinker unbinding, which could lead to the spontaneous relaxation of living cells.

Peripheral, central and coercive routes for promoting Enterprise Social Networks

Organisations employ Enterprise Social Networks (ESNs) (such as Yammer) expecting better intra-organisational communication and collaboration. However, ESNs are struggling to gain momentum and wide adoption among users. Promoting user participation is a challenge, particularly in relation to lurkers – the silent ESN members who do not contribute any content. Building on behaviour change research, we propose a three-route model consisting of the central, peripheral and coercive routes of influence that depict users’ cognitive strategies, and we examine how management interventions (e.g. sending promotional emails) impact users’ beliefs and (consequent) posting and lurking behaviours in ESNs. Furthermore, we identify users’ salient motivations to lurk or post. We employ a multi-method research design to conceptualise, operationalise and validate the research model. This study has implications for academics and practitioners regarding the nature, patterns and outcomes of management interventions in prompting ESN.

Do good things and talk about them : a theory of academics usage of enterprise social networks for impression management tactics

Enterprise social networks provide benefits especially for knowledge-intensive work as they enable communication, collaboration and knowledge exchange. These platforms should therefore lead to increased adoption and use by knowledge-intensive workers such as consultants or indeed researchers. Our interest is in ascertaining whether scientific researchers use enterprise social networks as part of their work practices. This focus is motivated by an apparent schism between a need for researchers to exchange knowledge and profile themselves, and the aversion to sharing breakthrough ideas and joining in an ever-increasing publishing and marketing game. We draw on research on academic work practices and impression management to develop a model of academics’ ESN usage for impression management tactics. We describe important constructs of our model, offer strategies for their operationalization and give an outlook to our ongoing empirical study of the use of an ESN platform by 20 schools across six faculties at an Australian university.

Anomaly detection in online social networks : using data-mining techniques and fuzzy logic

This research is a step forward in improving the accuracy of detecting anomaly in a data graph representing connectivity between people in an online social network. The proposed hybrid methods are based on fuzzy machine learning techniques utilising different types of structural input features. The methods are presented within a multi-layered framework which provides the full requirements needed for finding anomalies in data graphs generated from online social networks, including data modelling and analysis, labelling, and evaluation.

Combining opinions for use in Bayesian networks: A measurement error approach

Bayesian networks (BNs) are graphical probabilistic models used for reasoning under uncertainty. These models are becoming increasing popular in a range of fields including ecology, computational biology, medical diagnosis, and forensics. In most of these cases, the BNs are quantified using information from experts, or from user opinions. An interest therefore lies in the way in which multiple opinions can be represented and used in a BN. This paper proposes the use of a measurement error model to combine opinions for use in the quantification of a BN. The multiple opinions are treated as a realisation of measurement error and the model uses the posterior probabilities ascribed to each node in the BN which are computed from the prior information given by each expert. The proposed model addresses the issues associated with current methods of combining opinions such as the absence of a coherent probability model, the lack of the conditional independence structure of the BN being maintained, and the provision of only a point estimate for the consensus. The proposed model is applied an existing Bayesian Network and performed well when compared to existing methods of combining opinions.

Recent advances in modeling the vulnerability of transportation networks

It is well known that, for major infrastructure networks such as electricity, gas, railway, road, and urban water networks, disruptions at one point have a knock on effect throughout the network. There is an impressive amount of individual research projects examining the vulnerability of critical infrastructure network. However, there is little understanding of the totality of the contribution made by these projects and their interrelationships. This makes their review a difficult process for both new and existing researchers in the field. To address this issue, a two-step literature review process is used, to provide an overview of the vulnerability of the transportation network in terms of four main themes - research objective, transportation mode, disruption scenario and vulnerability indicator –involving the analysis of related articles from 2001 to 2013. Two limitations of existing research are identified: (1) the limited amount of studies relating to multi-layer transportation network vulnerability analysis, and (2) the lack of evaluation methods to explore the relationship between structure vulnerability and dynamical functional vulnerability. In addition to indicating that more attention needs to be paid to these two aspects in future, the analysis provides a new avenue for the discovery of knowledge, as well as an improved understanding of transportation network vulnerability.

Human vs. machine : identification of bat species from their echolocation calls by humans and by artificial neural networks

Automated remote ultrasound detectors allow large amounts of data on bat presence and activity to be collected. Processing of such data involves identifying bat species from their echolocation calls. Automated species identification has the potential to provide more consistent, predictable, and potentially higher levels of accuracy than identification by humans. In contrast, identification by humans permits flexibility and intelligence in identification, as well as the incorporation of features and patterns that may be difficult to quantify. We compared humans with artificial neural networks (ANNs) in their ability to classify short recordings of bat echolocation calls of variable signal to noise ratios; these sequences are typical of those obtained from remote automated recording systems that are often used in large-scale ecological studies. We presented 45 recordings (1–4 calls) produced by known species of bats to ANNs and to 26 human participants with 1 month to 23 years of experience in acoustic identification of bats. Humans correctly classified 86% of recordings to genus and 56% to species; ANNs correctly identified 92% and 62%, respectively. There was no significant difference between the performance of ANNs and that of humans, but ANNs performed better than about 75% of humans. There was little relationship between the experience of the human participants and their classification rate. However, humans with <1 year of experience performed worse than others. Currently, identification of bat echolocation calls by humans is suitable for ecological research, after careful consideration of biases. However, improvements to ANNs and the data that they are trained on may in future increase their performance to beyond those demonstrated by humans.

Evaluation of channel congestion in dedicated short-range communication networks

This thesis presents a novel idea for an adaptive prioritized cross-layer design (APCLD) control algorithm to achieve comprehensive channel congestion control for vehicular safety communication based on DSRC technology. An appropriate evaluation metric and two control parameters have been established. Simulation studies have evaluated the DSRC network performance in different traffic scenario and under different channel conditions. The APCLD algorithm is derived from the results of the simulation analysis.

Bayesian networks for information synthesis in complex systems

This thesis introduces a method of applying Bayesian Networks to combine information from a range of data sources for effective decision support systems. It develops a set of techniques in development, validation, visualisation, and application of Complex Systems models, with a working demonstration in an Australian airport environment. The methods presented here have provided a modelling approach that produces highly flexible, informative and applicable interpretations of a system's behaviour under uncertain conditions. These end-to-end techniques are applied to the development of model based dashboards to support operators and decision makers in the multi-stakeholder airport environment. They provide highly flexible and informative interpretations and confidence in these interpretations of a system's behaviour under uncertain conditions.

MIMO enhanced slotted cooperation in urban vehicular networks

The requirement of isolated relays is one of the prime obstacles in utilizing sequential slotted cooperative protocols for Vehicular Ad-hoc Networks (VANET). Significant research advancement has taken place to improve the diversity multiplexing trade-off (DMT) of cooperative protocols in conventional mobile networks without much attention on vehicular ad-hoc networks. We have extended the concept of sequential slotted amplify and forward (SAF) protocols in the context of urban vehicular ad-hoc networks. Multiple Input Multiple Output (MIMO) reception is used at relaying vehicular nodes to isolate the relays effectively. The proposed approach adds a pragmatic value to the sequential slotted cooperative protocols while achieving attractive performance gains in urban VANETs. We have analysed the DMT bounds and the outage probabilities of the proposed scheme. The results suggest that the proposed scheme can achieve an optimal DMT similar to the DMT upper bound of the sequential SAF. Furthermore, the outage performance of the proposed scheme outperforms the SAF protocol by 2.5 dB at a target outage probability of 10-4.

Multi-objective models and techniques for analysing the absolute capacity of railway networks

Railway capacity determination and expansion are very important topics. In prior research, the competition between different entities such as train services and train types, on different network corridors however have been ignored, poorly modelled, or else assumed to be static. In response, a comprehensive set of multi-objective models have been formulated in this article to perform a trade-off analysis. These models determine the total absolute capacity of railway networks as the most equitable solution according to a clearly defined set of competing objectives. The models also perform a sensitivity analysis of capacity with respect to those competing objectives. The models have been extensively tested on a case study and their significant worth is shown. The models were solved using a variety of techniques however an adaptive E constraint method was shown to be most superior. In order to identify only the best solution, a Simulated Annealing meta-heuristic was implemented and tested. However a linearization technique based upon separable programming was also developed and shown to be superior in terms of solution quality but far less in terms of computational time.