Semaphorin–plexin signalling genes associated with human breast tumourigenesis

Introduction Gene expression profiling has enabled us to demonstrate the heterogeneity of breast cancers. The potential of a tumour to grow and metastasise is partly dependant on its ability to initiate angiogenesis or growth and remodelling of new blood vessels, usually from a pre-existing vascular network, to ensure delivery of oxygen, nutrients, and growth factors to rapidly dividing transformed cells along with access to the systemic circulation. Cell–cell signalling of semaphorin ligands through interaction with their plexin receptors is important for the homeostasis and morphogenesis of many tissues and has been widely studied for a role in neural connectivity, cancer, cell migration and immune responses. This study investigated the role of four semaphorin/plexin signalling genes in human breast cancers in vivo and in vitro. Materials and methods mRNA was extracted from formalin fixed paraffin embedded archival breast invasive ductal carcinoma tissue samples of progressive grades (grades I–III) and compared to tissue from benign tumours. Gene expression profiles were determined by microarray using the Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and validated by Q-PCR using a Corbett RotorGene 6000. Following validation, the gene expression profile of the identified targets was correlated with those of the human breast cancer cell lines MCF-7 and MDA-MD-231. Results The array data revealed that 888 genes were found to be significantly (p ≤ 0.05) differentially expressed between grades I and II tumours and 563 genes between grade III and benign tumours. From these genes, we identified four genes involved in semaphorin–plexin signalling including SEMA4D which has previously been identified as being involved in increased angiogenesis in breast cancers, and three other genes, SEMA4F, PLXNA2 and PLXNA3, which in the literature were associated with tumourigenesis, but not directly in breast tumourigenesis. The microarray analysis revealed that SEMA4D was significantly (P = 0.0347) down-regulated in the grade III tumours compared to benign tumours; SEMA4F, was significantly (P = 0.0159) down-regulated between grades I and II tumours; PLXNA2 was significantly (P = 0.036) down-regulated between grade III and benign tumours and PLXNA3 significantly (P = 0.042) up-regulated between grades I and II tumours. Gene expression of SEMA4D was validated using Q-PCR, demonstrating the same expression profile in both data sets. When the sample set was increased to incorporate more cases, SEMA4D continued to follow the same expression profile, including statistical significance for the differences observed and small standard deviations. In vitro the same pattern was present where expression for SEMA4D was significantly higher in MDA-MB-231 cells when compared to MCF-7 cells. The expression of SEMA4F, PLXNA2 and PLXNA3 could not be validated using Q-PCR, however in vitro analysis of these three genes revealed that both SEMA4F and PLXNA3 followed the microarray trend in expression, although they did not reach significance. In contrast, PLXNA2 demonstrated statistical significance and was in concordance with the literature. Discussion We, and others, have proposed SEMA4D to be a gene with a potentially protective effect in benign tumours that contributes to tumour growth and metastatic suppression. Previous data supports a role for SEMA4F as a tumour suppressor in the peripheral nervous system but our data seems to indicate that the gene is involved in tumour progression in breast cancer. Our in vitro analysis of PLXNA2 revealed that the gene has higher expression in more aggressive breast cancer cell types. Finally, our in vitro analysis on PLXNA3 also suggest that this gene may have some form of growth suppressive role in breast cancer, in addition to a similar role for the gene previously reported in ovarian cancer. From the data obtained in this study, SEMA4D may have a role in more aggressive and potentially metastatic breast tumours. Conclusions Semaphorins and their receptors, the plexins, have been implicated in numerous aspects of neural development, however their expression in many other epithelial tissues suggests that the semaphorin–plexin signalling system also contributes to blood vessel growth and development. These findings warrant further investigation of the role of semaphorins and plexins and their role in normal and tumour-induced angiogenesis in vivo and in vitro. This may represent a new front of attack in anti-angiogenic therapies of breast and other cancers.

Significant differences in gene expression of GABA receptors in peripheral blood leukocytes of migraineurs

Migraine is a debilitating neurovascular disorder, with a substantial genetic component. The exact cause of a migraine attack is unknown; however cortical hyperexcitability is thought to play a role. As Gamma-aminobutyric Acid (GABA) is the major inhibitory neurotransmitter in the brain, malfunctioning of this system may be a cause of the hyperexcitability. To date, there has been limited research examining the gene expression or genetics of GABA receptors in relation to migraine. The aim of our study was to determine if GABA receptors play a role in migraine by investigating their gene expression using profile in migraine affected individuals and non-affected controls by Q-PCR. Gene expression of GABA(A) receptor subunit isoforms (GABRA3, GABRB3, GABRQ) and GABA(B) receptor 2 (GABBR2) was quantified in mRNA obtained from peripheral blood leukocytes from 28 migraine subjects and 22 healthy control subjects. Analysis of results showed that two of the tested genes, GABRA3 and GABBR2, were significantly down regulated in migraineurs (P=0.018; P=0.017), compared to controls. Results from the other tested genes did not show significant gene expression variation. The results indicate that there may be specific GABA receptor gene expression variation in migraine, particularly involving the GABRA3 and GABBR2 genes. This study also identifies GABRA3 and GABBR2 as potential biomarkers to select migraineurs that may be more responsive to GABA agonists with future investigations in this area warranted.

Examining the stability of transport behaviours for high-risk early adolescents

Transport related injury is a leading cause of death and disability for adolescents and represents a substantial burden on public health and the community as a whole. Adolescents appear to have a growing risk of harm due to the co-existence of increasing alcohol use and engagement in risky transport behaviours. Understanding more about the development and stability of these behaviours by young adolescents over time could be beneficial in targeting transport injury prevention interventions for high-risk adolescents. In Australia alcohol use begins to increase significantly through the early and middle adolescent years even though the majority of these young people are still in school. Aim This paper reports on changes over a six month period in alcohol use, anger management experiences and transport risk taking behaviours including riding a bicycle without a helmet and under-age driving for high-risk adolescents and non high-risk early adolescents. Year 9 students (N=1,005) from 20 schools in Queensland, Australia completed a baseline survey in the first half of 2012 and at a six month follow up. Respondents at both times were asked about their engagement in risk taking behaviours measured by Mak’s adolescent delinquency scale, which included five transport related items. They were also asked to rate their alcohol use for the preceding three month period. The stability of these risk taking indicators was measured by comparing baseline results with the six month follow up. Results High-risk adolescents were more likely to report change in their alcohol use and transport behaviours when compared with non high-risk adolescents over a six month period. There were no significant changes in control of anger for either group. Demographic characteristics were not shown to have any significant effect on the stability of risk indicators for high-risk adolescents and non high-risk adolescents. Differences were found in the stability of risk taking indicators for high-risk adolescents and non high-risk adolescents. The findings of this paper have implications in targeting transport risk behaviour change interventions to meet the needs of high-risk adolescents.

Shorter telomere length in peripheral blood cells associated with migraine in women

Objective To evaluate relative telomere length of female migraine patients. Background Migraine is a debilitating disorder affecting 6-28% of the population. Studies on the mechanisms of migraine have demonstrated genetic causes but the pathophysiology and subcellular effects of the disease remain poorly understood. Shortened telomere length is associated with age-related or chronic diseases, and induced stresses. Migraine attacks may impart significant stress on cellular function, thus this study investigates a correlation between shortening of telomeres and migraine. Methods Relative telomere length was measured using a previously described quantitative polymerase chain reaction method. A regression analysis was performed to assess differences in mean relative telomere length between migraine patients and healthy controls. Results The leukocyte telomeres of a cohort of 142 Caucasian female migraine subjects aged 18-77 years and 143 matched 17-77-year-old healthy control Caucasian women were examined.A significantly shorter relative telomere length was observed in the migraine group compared with the control group after adjusting for age and body mass index (P = .001). In addition, age of onset was observed to associate with the loss of relative telomere length, especially at early age of onset (<17 years old). No association was observed between relative telomere length and the severity and frequency of migraine attacks and the duration of migraine. Conclusion Telomeres are shorter in migraine patients and there is more variation in telomere length in migraine patients.

Developing targets and strategies for school-based injury prevention programs to reduce alcohol associated transport risks

Background There is considerable and ongoing debate about the role and effectiveness of school-based injury prevention programs in reducing students’ later involvement in alcohol associated transport injuries. Most relevant literature is concerned with pre-driving and licensing programs for middle age range adolescents (15-17 years). This research team is concerned with prevention at an earlier stage by targeting interventions to young adolescents (13-14 years). There is strong evidence that young adolescents who engage in unsafe and illegal alcohol associated transport risks are significantly likely to incur serious related injuries in longitudinal follow up. For example, a state-wide representative sample of male adolescents (mean age 14.5 years) who reported being passengers of drink drivers were significantly more likely to have incurred a hospitalised injury related to traffic events at a 20 year follow up. Aim This paper reports on first aid training integrated with peer protection and school connectedness within the Skills for Preventing Injury in Youth (SPIY) program. A component of the intervention is concerned with providing strategies to reduce the likelihood of being a passenger of a drink driver and effectiveness is followed up at six months post-intervention. Method In early 2012 the study was undertaken in 35 high schools throughout Queensland that were randomly assigned to intervention and control conditions. A total of 2,521 Year 9 students (mean age 13.5years, 43% male) completed surveys prior to the intervention. Results Of these students 316 (13.7%) reported having ridden in a car with someone who has been drinking. This is a traffic safety behaviour that is particularly relevant to a peer protection intervention and the findings of the six month follow up will be reported. Discussion and conclusions This research will provide evidence as to whether this approach to the introduction of first aid skills within a school-based health education curriculum has traffic safety implications.

Fundamental understanding on the use of Bluetooth scanner as a complementary transport data

Literature is limited in its knowledge of the Bluetooth protocol based data acquisition process and in the accuracy and reliability of the analysis performed using the data. This paper extends the body of knowledge surrounding the use of data from the Bluetooth Media Access Control Scanner (BMS) as a complementary traffic data source. A multi layer simulation model named Traffic and Communication Simulation (TCS) is developed. TCS is utilised to model the theoretical properties of the BMS data and analyse the accuracy and reliability of travel time estimation using the BMS data.

Empirical evaluation of public transport travel time variability

Although transit travel time variability is essential for understanding the deterioration of reliability, optimising transit schedule and route choice; it has not attracted enough attention from the literature. This paper proposes public transport-oriented definitions of travel time variability and explores the distributions of public transport travel time using the Transit Signal Priority data. First, definitions of public transport travel time variability are established by extending the common definitions of variability in the literature and by using route and services data of public transport vehicles. Second, the paper explores the distribution of public transport travel time. A new approach for analysing the distributions involving all transit vehicles as well as vehicles from a specific route is proposed. The Lognormal distribution is revealed as the descriptors for public transport travel time from the same route and service. The methods described in this study could be of interest for both traffic managers and transit operators for planning and managing the transit systems.

The B subunit of coagulation factor XIII is linked to renin and the Duffy blood group to α-spectrin on human chromosome 1

Family linkage studies were used to detect two linkage relationships on human chromosome 1. The B subunit of coagulation factor XIII showed significant linkage to renin with a maximum lod score of 5.071 at a distance of 10 cM. Significant linkage was also shown between the Duffy blood group and α-spectrin with linkage results giving a combined lod score of 3.194 at 5 cM.

Effects of hyperbaric oxygen and inducible nitric oxide synthase inhibitor treatment on femoral head osteonecrosis in a rat model

Introduction: Apoptosis is the final destiny of many cells in the body, though this process has been observed in some pathological processes. One of these pathological processes is femoral head non-traumatic osteonecrosis. Among many pro/anti-apoptotic factors, nitric oxide has recently been an area of further interest. Osteocyte apoptosis and its relation to pro-apoptotic action invite further research, and the inducible form of nitric oxide synthase (iNOS)—which produces a high concentration of nitric oxide—has been flagged. The aim of this study was to investigate the effect of hyperbaric oxygen (HBO) and inducible NOS suppressor (Aminoguanidine) in prevention of femoral head osteonecrosis in an experimental model of osteonecrosis in spontaneous hypertensive rats (SHRs). Methods: After animal ethic approval 34 SHR rats were divided into four groups. Ten rats were allocated to the control group without any treatment, and eight rats were allocated to three treatment groups namely: HBO, Aminoguanidine (AMG), and the combination of HBO and AMG treatments (HBO+AMG). The HBO group received 250 kPa of oxygen via hyperbaric chamber for 30 days started at their 5th week of life; the AMG group received 1mg/ml of AMG in drinking water from the fifth week till the 17th week of life; and the last group received a combination of these treatments. Rats were sacrificed at the end of the 17th week of life and both femurs were analysed for evidence of osteonecrosis using Micro CT scan and H&E staining. Also, osteocyte apoptosis and the presence of two different forms of NOS (inducible (iNOS) and endothelial (eNOS)) were analysed by immunostaining and apoptosis staining (Hoechst and TUNEL). Results: Bone morphology of metaphyseal and epiphyseal area of all rats were investigated and analysed. Micro CT findings revealed significantly higher mean fractional trabecular bone volume (FBV) of metaphyseal area in untreated SHRs compared with all other treatments (HBO, P<0.05, HBO+AMG, P<0.005, and AMG P<0.001). Bone surface to volume ratio also significantly increased with HBO+AMG and AMG treatments when compared with the control group (18.7 Vs 20.8, P<0.05, and 18.7 Vs 21.1, P<0.05). Epiphyseal mean FBV did not change significantly among groups. In the metaphyseal area, trabecular thickness and numbers significantly decreased with AMG treatment, while trabecular separation significantly increased with both AMG and HBO+AMG treatment. Histological ratio of no ossification and osteonecrosis was 37.5%, 43.7%, 18.7% and 6.2% of control, HBO, HBO+AMG and AMG groups respectively with only significant difference observed between HBO and AMG treatment (P<0.01). High concentration of iNOS was observed in the region of osteonecrosis while there was no evidence of eNOS activity around that region. In comparison with the control group, the ratio of osteocyte apoptosis significantly reduced in AMG treatment (P<0.005). We also observed significantly fewer apoptotic osteocytes in AMG group comparing with HBO treatment (P<0.05). Conclusion: None of our treatments prevents osteonecrosis at the histological or micro CT scan level. High concentration of iNOS in the region of osteonecrosis and significant reduction of osteocyte apoptosis with AMG treatment were supportive of iNOS modulating osteocyte apoptosis in SHRs.

Mapping local solutions to entrenched transport problems: Key lessons regarding the use of geographical information technologies in community mapping with disadvantaged communities

There is an increasing interest in the use of information technology as a participatory planning tool, particularly the use of geographical information technologies to support collaborative activities such as community mapping. However, despite their promise, the introduction of such technologies does not necessarily promote better participation nor improve collaboration. In part this can be attributed to a tendency for planners to focus on the technical considerations associated with these technologies at the expense of broader participation considerations. In this paper we draw on the experiences of a community mapping project with disadvantaged communities in suburban Australia to highlight the importance of selecting tools and techniques which support and enhance participatory planning. This community mapping project, designed to identify and document community-generated transport issues and solutions, had originally intended to use cadastral maps extracted from the government’s digital cadastral database as the foundation for its community mapping approach. It was quickly discovered that the local residents found the cadastral maps confusing as the maps lacked sufficient detail to orient them to their suburb (the study area). In response to these concerns and consistent with the project’s participatory framework, a conceptual base map based on resident’s views of landmarks of local importance was developed to support the community mapping process. Based on this community mapping experience we outline four key lessons learned regarding the process of community mapping and the place of geographical information technologies within this process.

Planning for sustainability of non motorised public transport in a developing city

Most large cities around the world are undergoing rapid transport sector development to cater for increased urbanization. Subsequently the issues of mobility, access equity, congestion, operational safety and above all environmental sustainability are becoming increasingly crucial in transport planning and policy making. The popular response in addressing these issues has been demand management, through improvement of motorised public transport (MPT) modes (bus, train, tram) and non-motorized transport (NMT) modes (walk, bicycle); improved fuel technology. Relatively little attention has however been given to another readily available and highly sustainable component of the urban transport system, non-motorized public transport (NMPT) such as the pedicab that operates on a commercial basis and serves as an NMT taxi; and has long standing history in many Asian cities; relatively stable in existence in Latin America; and reemerging and expanding in Europe, North America and Australia. Consensus at policy level on the apparent benefits, costs and management approach for NMPT integration has often been a major transport planning problem. Within this context, this research attempts to provide a more complete analysis of the current existence rationale and possible future, or otherwise, of NMPT as a regular public transport system. The analytical process is divided into three major stages. Stage 1 reviews the status and role condition of NMPT as regular public transport on a global scale- in developing cities and developed cities. The review establishes the strong ongoing and future potential role of NMPT in major developing cities. Stage 2 narrows down the status review to a case study city of a developing country in order to facilitate deeper role review and status analysis of the mode. Dhaka, capital city of Bangladesh, has been chosen due to its magnitude of NMPT presence. The review and analysis reveals the multisectoral and dominant role of NMPT in catering for the travel need of Dhaka transport users. The review also indicates ad-hoc, disintegrated policy planning in management of NMPT and the need for a planning framework to facilitate balanced integration between NMPT and MT in future. Stage 3 develops an integrated, multimodal planning framework (IMPF), based on a four-step planning process. This includes defining the purpose and scope of the planning exercise, determining current deficiencies and preferred characteristics for the proposed IMPF, selection of suitable techniques to address the deficiencies and needs of the transport network while laying out the IMPF and finally, development of a delivery plan for the IMPF based on a selected layout technique and integration approach. The output of the exercise is a planning instrument (decision tool) that can be used to assign a road hierarchy in order to allocate appropriate traffic to appropriate network type, particularly to facilitate the operational balance between MT and NMT. The instrument is based on a partial restriction approach of motorised transport (MT) and NMT, structured on the notion of functional hierarchy approach, and distributes/prioritises MT and NMT such that functional needs of the network category is best complemented. The planning instrument based on these processes and principles offers a six-level road hierarchy with a different composition of network-governing attributes and modal priority, for the current Dhaka transport network, in order to facilitate efficient integration of NMT with MT. A case study application of the instrument on a small transport network of Dhaka also demonstrates the utility, flexibility and adoptability of the instrument in logically allocating corridors with particular positions in the road hierarchy paradigm. Although the tool is useful in enabling balanced distribution of NMPT with MT at different network levels, further investigation is required with reference to detailed modal variations, scales and locations of a network to further generalise the framework application.

Controlling whole blood activation and resultant clot properties on various material surfaces : a possible therapeutic approach for enhancing bone healing

Injured bone initiates the healing process by forming a blood clot at the damaged site. However, in severe damage, synthetic bone implants are used to provide structural integrity and restore the healing process. The implant unavoidably comes into direct contact with whole blood, leading to a blood clot formation on its surface. Despite this, most research in bone tissue engineering virtually ignores the important role of a blood clot in supporting healing. Surface chemistry of a biomaterial is a crucial property in mediating blood-biomaterials interactions, and hence the formation of the resultant blood clot. Surfaces presenting mixtures of functional groups carboxyl (–COOH) and methyl (–CH3) have been shown to enhance platelet response and coagulation activation, leading to the formation of fibrin fibres. In addition, it has been shown that varying the compositions of these functional groups and the length of alkyl groups further modulate the immune complement response. In this study, we hypothesised that a biomaterial surface with mixture of –COOH/–CH3(methyl), –CH2CH3 (ethyl) or –(CH2)3CH3 (butyl) groups at different ratios would modulate blood coagulation and complement activation, and eventually tailor the structural and functional properties of the blood clot formed on the surface, which subsequently impacts new bone formation. Firstly, we synthesised a series of materials composed of acrylic acid (AA), and methyl (MMA), ethyl (EMA) or butyl methacrylates (BMA) at different ratios and coated on the inner surfaces of incubation vials. Our surface analysis showed that the amount of –COOH groups on the surface coatings was lower than the ratios of AA prepared in the materials even though the surface content of –COOH groups increased with increasing in AA ratios. It was indicated that the surface hydrophobicity increased with increasing alkyl chain length: –CH 3 > –CH2CH3 > –(CH2)3CH3, and decreased with increasing –COOH groups. No significant differences in surface hydrophobicity was found on surfaces with –CH3 and –CH2CH3 groups in the presence of –COOH groups. The material coating was as smooth as uncoated glass and without any major flaws. The average roughness of material-coated surface (3.99 ± 0.54 nm) was slightly higher than that of uncoated glass surface (2.22 ± 0.29 nm). However, no significant differences in surface average roughness was found among surfaces with the same functionalities at different –COOH ratios nor among surfaces with different alkyl groups but the same –COOH ratios. These suggested that the surface functional groups and their compositions had a combined effect on modulating surface hydrophobicity but not surface roughness. The second part of our study was to investigate the effect of surface functional groups and their compositions on blood cascade activation and structural properties of the formed clots. It was found that surfaces with –COOH/–(CH2)3CH3 induced a faster coagulation activation than those with –COOH/–CH3 and –CH2CH3, regardless of the –COOH ratios. An increase in –COOH ratios on –COOH/–CH3 and –CH2CH3 surfaces decreased the rate of activation. Moreover, all material-coated surfaces markedly reduced the complement activation compared to uncoated glass surfaces, and the pattern of complement activation was entirely similar to that of surface-induced coagulation, suggesting there is an interaction between two cascades. The clots formed on material-coated surfaces had thicker fibrin with a tighter network at the exterior when compared to uncoated glass surfaces. Compared to the clot exteriors, thicker fibrins with a loose network were found in clot interiors. Coated surfaces resulted in more rigid clots with a significantly slower fibrinolysis after 1 h of lysis when compared to uncoated glass surfaces. Significant differences in fibrinolysis after 1 h of lysis among clots on material-coated surfaces correlated well with the differences in fibrin thickness and density at clot exterior. In addition, more growth factors were released during clot formation than during clot lysis. From an intact clot, there was a correlation between the amount of PDGF-AB release and fibrin density. Highest amount of PDGF-AB was released from clots formed on surfaces with 40% –COOH/60% –CH 3 (i.e. 65MMA). During clot lysis, the release of PDGF-AB also correlated with the fibrinolytic rate while the release of TGF-â1 was influenced by the fibrin thickness. This suggested that different clot structures led to different release profiles of growth factors in clot intact and degrading stages. We further validated whether the clots formed on material-coatings provide the microenvironment for improved bone healing by using a rabbit femoral defect model. In this pilot study, the implantation of clots formed on 65MMA coatings significantly increased new bone formation with enhanced chondrogenesis, osteoblasts activity and vascularisation, but decreased inflammatory macrophage number at the defects after 4 weeks when compared to commercial bone grafts ChronOSTM â-TCP granules. Empty defects were observed when blood clot formation was inhibited. In summary, our study demonstrated that surface functional groups and their relative ratios on material coatings synergistically modulate activation of blood cascades, resultant fibrin architecture, rigidity, susceptibility to fibrinolysis as well as growth factor release of the formed clots, which ultimately alter the healing microenvironment of injured bones.

Corporate social responsibility in Japanese firms in transport sector

Corporate Social Responsibility (CSR) reporting has become common practice for large organisations globally, yet there is variance in the CSR related activities claimed in disclosures. CSR researchers argue that cultural and historical backgrounds are the influential drivers of CSR behaviour. However, the links between actual activities claimed in CSR reports and the cultural systems that underpin these reported activities is an under-explored area. This thesis discusses the uniqueness of Japanese socio-cultural aspects. While Japan is well-known for having the most advanced energy efficient technologies in the world, it is also known for being below international standards for gender equality in the workplace. Therefore, this thesis aims to explore and examine organisational behaviours through the lens of relativism in order to understand what organisations are reporting and how and why managers prioritise these activities. This thesis is based on longitudinal qualitative research focusing on the Japanese transport companies that published CSR reports between 2005 and 2009. The findings from manually coded content analysis revealed: (1) that activities related to providing public safety, waste management and the 3Rs (reduce, reuse and recycle), and environmental innovation were the top three most frequently reported CSR activities; and (2) complying with laws, career planning, flexible work practices, and providing public safety were the three categories that showed the most significant increase in reporting frequency from 2005-2009. This thesis extends the previous literature. Takagaki (2010b) identified that the transport industry, particularly the air and water sub-sectors, is the industry where the environmental problems are serious and require urgent attention. Takagaki (2010b) chose to explore the electronics industry as this industry is considered to be middle ground for its level of seriousness and urgency. This research: (1) examines the transport industry; (2) investigates the links between the actual activities reported, and the activities reported to be influential drivers of these activities.

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 methodology to develop an urban transport disadvantage framework : the case of Brisbane, Australia

Most individuals travel in order to participate in a network of activities which are important for attaining a good standard of living. Because such activities are commonly widely dispersed and not located locally, regular access to a vehicle is important to avoid exclusion. However, planning transport system provisions that can engage members of society in an acceptable degree of activity participation remains a great challenge. The main challenges in most cities of the world are due to significant population growth and rapid urbanisation which produces increased demand for transport. Keeping pace with these challenges in most urban areas is difficult due to the widening gap between supply and demand for transport systems which places the urban population at a transport disadvantage. The key element in mitigating the issue of urban transport disadvantage is to accurately identify the urban transport disadvantaged. Although wide-ranging variables and multi-dimensional methods have been used to identify this group, variables are commonly selected using ad-hoc techniques and unsound methods. This poses questions of whether the current variables used are accurately linked with urban transport disadvantage, and the effectiveness of the current policies. To fill these gaps, the research conducted for this thesis develops an operational urban transport disadvantage framework (UTDAF) based on key statistical urban transport disadvantage variables to accurately identify the urban transport disadvantaged. The thesis develops a methodology based on qualitative and quantitative statistical approaches to develop an urban transport disadvantage framework designed to accurately identify urban transport disadvantage. The reliability and the applicability of the methodology developed is the prime concern rather than the accuracy of the estimations. Relevant concepts that impact on urban transport disadvantage identification and measurement and a wide range of urban transport disadvantage variables were identified through a review of the existing literature. Based on the reviews, a conceptual urban transport disadvantage framework was developed based on the causal theory. Variables identified during the literature review were selected and consolidated based on the recommendations of international and local experts during the Delphi study. Following the literature review, the conceptual urban transport disadvantage framework was statistically assessed to identify key variables. Using the statistical outputs, the key variables were weighted and aggregated to form the UTDAF. Before the variable's weights were finalised, they were adjusted based on results of correlation analysis between elements forming the framework to improve the framework's accuracy. The UTDAF was then applied to three contextual conditions to determine the framework's effectiveness in identifying urban transport disadvantage. The development of the framework is likely to be a robust application measure for policy makers to justify infrastructure investments and to generate awareness about the issue of urban transport disadvantage.