Molecular cytogenetic analysis of basal cell carcinoma DNA using comparative genomic hybridization

In an attempt to define genomic copy number changes associated with the development of basal cell carcinoma, we investigated 15 sporadic tumors by comparative genomic hybridization. With the incorporation of tissue microdissection and degenerate oligonucleotide primed-polymerase chain reaction we were able to isolate, and then universally amplify, DNA from the tumor type. This combined approach allows the investigation of chromosomal imbalances within a histologically distinct region of tissue. Using comparative genomic hybridization we have observed novel and recurrent chromosomal gains at 6p (47%), 6q (20%), 9p (20%), 7 (13%), and X (13%). In addition comparative genomic hybridization revealed regional loss on 9q in 33% of tested tumors encompassing 9q22.3 to which the putative tumor suppressor gene, Patched, has been mapped. The deletion of Patched has been indicated in the development of hereditary and sporadic basal cell carcinomas. The identification of these recurrent genetic aberrations suggests that basal cell carcinomas may not be as genetically stable as previously thought. Further investigation of these regions may lead to the identification of other genes responsible for basal cell carcinoma formation.

Evaluating patient presentations for care delivered by emergency nurse practitioners : a retrospective analysis of 12 months

Background The delivery of quality patient care in the emergency department (ED) is emerging as one of the most important service indicators to be measured in health services today. The emergency nurse practitioner role was implemented as a service innovation in a Emergency & Trauma Centre (ETC), Melbourne, Australia, in July 2004 .The primary aim of the role was intended to enhance healthcare services, improve the efficiency and timely delivery of high quality care to patients. Aim To conduct a retrospective study of patient presentations at the ETC to obtain a profile of the characteristics of patients managed by emergency nurse practitioners. Specifically the objectives of the study were to: 1) examine the demographics of the patient population 2) evaluate data on emergency department service indicators for this patient cohort Method All patients presenting to the ETC from January 01 2011 to December 31 2011 and managed by emergency nurse practitioners were included in the review. Data collection included baseline demographics, waiting times to be seen, length of stay, emergency department discharge diagnoses and referral patterns. Data were extracted and imported directly from the emergency department Patient Information System (Cerner log), for the specified time frame. Results A total of 5212 patients were reviewed in the study period. The median age of patients was 35 years and 61% of patients were male. The most common discharge diagnosis was open wounds to hand/wrist. Waiting times to be seen by the emergency nurse practitioner were 14 minutes and length of stay for patients with a discharge disposition of home were 122 minutes. Conclusions This study has provided information on patient baseline characteristics and performance on important service indicators for this patient sample that will inform further research to evaluate specific outcomes of the emergency nurse practitioner service.

Analysis of organic aerosols collected on filters by Aerosol Mass Spectrometry for source identification

Aerosol mass spectrometers (AMS) are powerful tools in the analysis of the chemical composition of airborne particles, particularly organic aerosols which are gaining increasing attention. However, the advantages of AMS in providing on-line data can be outweighed by the difficulties involved in its use in field measurements at multiple sites. In contrast to the on-line measurement by AMS, a method which involves sample collection on filters followed by subsequent analysis by AMS could significantly broaden the scope of AMS application. We report the application of such an approach to field studies at multiple sites. An AMS was deployed at 5 urban schools to determine the sources of the organic aerosols at the schools directly. PM1 aerosols were also collected on filters at these and 20 other urban schools. The filters were extracted with water and the extract run through a nebulizer to generate the aerosols, which were analysed by an AMS. The mass spectra from the samples collected on filters at the 5 schools were found to have excellent correlations with those obtained directly by AMS, with r2 ranging from 0.89 to 0.98. Filter recoveries varied between the schools from 40 -115%, possibly indicating that this method provides qualitative rather than quantitative information. The stability of the organic aerosols on Teflon filters was demonstrated by analysing samples stored for up to two years. Application of the procedure to the remaining 20 schools showed that secondary organic aerosols were the main source of aerosols at the majority of the schools. Overall, this procedure provides accurate representation of the mass spectra of ambient organic aerosols and could facilitate rapid data acquisition at multiple sites where AMS could not be deployed for logistical reasons.

TUNEL analysis of DNA fragmentation in mouse unfertilized oocytes : the effect of microorganisms within human follicular fluid collected during IVF cycles

Recently we reported the presence of bacteria within follicular fluid. Previous studies have reported that DNA fragmentation in human spermatozoa after in vivo or in vitro incubation with bacteria results in early embryo demise and a reduced rate of ongoing pregnancy, but the effect of bacteria on oocytes is unknown. This study examined the DNA within mouse oocytes after 12 hours’ incubation within human follicular fluids (n = 5), which were collected from women undergoing in vitro fertilization (IVF) treatment. Each follicular fluid sample was cultured to detect the presence of bacteria. Terminal deoxynucleotidyl transferase mediated dUTP nick-end labeling (TUNEL) was used to label DNA fragmentation in ovulated, non-fertilized mouse oocytes following in vitro incubation in human follicular fluid. The bacteria Streptococcus anginosus and Peptoniphilus spp., Lactobacillus gasseri (low-dose), L. gasseri (high-dose), Enterococcus faecalis, or Propionibacterium acnes were detected within the follicular fluids. The most severe DNA fragmentation was observed in oocytes incubated in the follicular fluids containing P. acnes or L. gasseri (high-dose). No DNA fragmentation was observed in the mouse oocytes incubated in the follicular fluid containing low-dose L. gasseri or E. faecalis. Low human oocyte fertilization rates (<29%) were associated with extensive fragmentation in mouse oocytes (80–100%). Bacteria colonizing human follicular fluid in vivo may cause DNA fragmentation in mouse oocytes following 12 h of in vitro incubation. Follicular fluid bacteria may result in poor quality oocytes and/or embryos, leading to poor IVF outcomes.

Analysis of androgen and anti-androgen regulation of KLK-related peptidase 2, 3, and 4 alternative transcripts in prostate cancer

We assessed whether alternative transcripts (using KLK2, KLK3 and KLK4 as models) are differentially regulated by androgens and anti-androgens as an indicator of prostate cancers as they acquire treatment resistance. Using RNAseq of LNCaP cells treated with dihydrotestosterone, bicalutamide and enzalutamide, we show that the expression of variant KLK transcripts is markedly different to other variant transcripts at those loci. We also reveal that KLK variants are also over 2-fold more highly expressed in prostate cancers compared to their corresponding normal prostate. We propose that androgens and anti-androgens can activate specific variant transcripts of critical prostate cancer genes during treatment resistance

Analysis of Sdhd and Mmp12 in an affected solar keratosis and control cohort

The incidence of Squamous Cell Carcinoma (SCG) is growing in certain populations to the extent that it is now the most common skin lesion in young men and women in high ultraviolet exposure regions such as Queensland. In terms of incidence up to 40% of the Australian population over 40 years of age is thought to possess the precancerous Solar Keratosis (SK) lesion and with a small, but significant, chance of progression into SCC, understanding the genetic events that play a role in this process is essential. The major aims of this study were to analyse whole blood derived samples for DNA aberrations in genes associated with tumour development and cellular maintenance, with the ultimate aim of identifying genes associated with non-melanoma skin cancer development. More specifically the first aim of this project was to analyse the SDHD and MMP12 genes via Dual-Labelled Probe Real-Time PCR for copy number aberrations in an affected Solar Keratosis and control cohort. It was found that 12 samples had identifiable copy-number aberrations in either the SDHD or MMP12 gene (this means that a genetic section of either of these two genes is aberrantly amplified or deleted), with five of the samples exhibiting aberrations in both genes. The significance of this study is the contribution to the knowledge of the genetic pathways that are malformed in the progression and development of the pre-cancerous skin lesion Solar Keratosis. © 2008 Springer Science+Business Media, LLC.

Destination marketing organizations and destination marketing : a narrative analysis of the literature

This article presents the first narrative analysis of the areas of research that have developed within the destination marketing field since its commencement in 1973. Given the broad extent of the field, and the absence of any previous reviews in four decades, a key challenge is in providing a focus for such a disparate body of knowledge. The review is structured around one principal question: ‘To what extent is the Destination Marketing Organisation (DMO) responsible for the competitiveness of the destination’? In pursuit of this underlying question, we address a number of themes including nomenclature and the DMO, the evolution of the destination marketing literature, competitiveness as the DMO reason d’être, and DMO effectiveness including issues of branding and positioning, and future research themes in the field.

Analysis of nonlinear sequences and streamciphers

Streamciphers are common cryptographic algorithms used to protect the confidentiality of frame-based communications like mobile phone conversations and Internet traffic. Streamciphers are ideal cryptographic algorithms to encrypt these types of traffic as they have the potential to encrypt them quickly and securely, and have low error propagation. The main objective of this thesis is to determine whether structural features of keystream generators affect the security provided by stream ciphers.These structural features pertain to the state-update and output functions used in keystream generators. Using linear sequences as keystream to encrypt messages is known to be insecure. Modern keystream generators use nonlinear sequences as keystream.The nonlinearity can be introduced through a keystream generator's state-update function, output function, or both. The first contribution of this thesis relates to nonlinear sequences produced by the well-known Trivium stream cipher. Trivium is one of the stream ciphers selected in a final portfolio resulting from a multi-year project in Europe called the ecrypt project. Trivium's structural simplicity makes it a popular cipher to cryptanalyse, but to date, there are no attacks in the public literature which are faster than exhaustive keysearch. Algebraic analyses are performed on the Trivium stream cipher, which uses a nonlinear state-update and linear output function to produce keystream. Two algebraic investigations are performed: an examination of the sliding property in the initialisation process and algebraic analyses of Trivium-like streamciphers using a combination of the algebraic techniques previously applied separately by Berbain et al. and Raddum. For certain iterations of Trivium's state-update function, we examine the sets of slid pairs, looking particularly to form chains of slid pairs. No chains exist for a small number of iterations.This has implications for the period of keystreams produced by Trivium. Secondly, using our combination of the methods of Berbain et al. and Raddum, we analysed Trivium-like ciphers and improved on previous on previous analysis with regards to forming systems of equations on these ciphers. Using these new systems of equations, we were able to successfully recover the initial state of Bivium-A.The attack complexity for Bivium-B and Trivium were, however, worse than exhaustive keysearch. We also show that the selection of stages which are used as input to the output function and the size of registers which are used in the construction of the system of equations affect the success of the attack. The second contribution of this thesis is the examination of state convergence. State convergence is an undesirable characteristic in keystream generators for stream ciphers, as it implies that the effective session key size of the stream cipher is smaller than the designers intended. We identify methods which can be used to detect state convergence. As a case study, theMixer streamcipher, which uses nonlinear state-update and output functions to produce keystream, is analysed. Mixer is found to suffer from state convergence as the state-update function used in its initialisation process is not one-to-one. A discussion of several other streamciphers which are known to suffer from state convergence is given. From our analysis of these stream ciphers, three mechanisms which can cause state convergence are identified.The effect state convergence can have on stream cipher cryptanalysis is examined. We show that state convergence can have a positive effect if the goal of the attacker is to recover the initial state of the keystream generator. The third contribution of this thesis is the examination of the distributions of bit patterns in the sequences produced by nonlinear filter generators (NLFGs) and linearly filtered nonlinear feedback shift registers. We show that the selection of stages used as input to a keystream generator's output function can affect the distribution of bit patterns in sequences produced by these keystreamgenerators, and that the effect differs for nonlinear filter generators and linearly filtered nonlinear feedback shift registers. In the case of NLFGs, the keystream sequences produced when the output functions take inputs from consecutive register stages are less uniform than sequences produced by NLFGs whose output functions take inputs from unevenly spaced register stages. The opposite is true for keystream sequences produced by linearly filtered nonlinear feedback shift registers.

Computational analysis of laminated glass panels under blast loads: A comparison of two dimensional and three dimensional modelling approaches

This paper illustrates the use of finite element (FE) technique to investigate the behaviour of laminated glass (LG) panels under blast loads. Two and three dimensional (2D and 3D) modelling approaches available in LS-DYNA FE code to model LG panels are presented. Results from the FE analysis for mid-span deflection and principal stresses compared well with those from large deflection plate theory. The FE models are further validated using the results from a free field blast test on a LG panel. It is evident that both 2D and 3D LG models predict the experimental results with reasonable accuracy. The 3D LG models give slightly more accurate results but require considerably more computational time compared to the 2D LG models.

Failure analysis of laminated glass panels subjected to blast loads

This paper presents a rigorous and a reliable analytical procedure using finite element (FE) techniques to study the blast response of laminated glass (LG) panel and predict the failure of its components. The 1st principal stress (σ11) is used as the failure criterion for glass and the von mises stress (σv) is used for the interlayer and sealant joints. The results from the FE analysis for mid-span deflection, energy absorption and the stresses at critical locations of glass, interlayer and structural sealant are presented in the paper. These results compared well with those obtained from a free field blast test reported in the literature. The tensile strength (T) of the glass has a significant influence on the behaviour of the LG panel and should be treated carefully in the analysis. The glass panes absorb about 80% of the blast energy for the treated blast load and this should be minimised in the design.

A micro perspective analysis of capability renewal through knowledge integration within product innovation projects

The aim of this paper is examine how firms renew their organisational capabilities based on micro organisational processes. Organisational capability development literature points to firms’ failure in capability renewal process. To overcome this inefficiency, it is proposed to integrate dynamic capability and ambidexterity perspectives by studying knowledge integration within product innovation. In this relation, applying micro perspective in studying technology diffusion within Iranian Auto industry revealed micro co-evolutionary relationships between knowledge integration within product innovation and capability development. Furthermore, based on near decomposability principals, the analysis suggested relationships among modularity of product architecture, modularity of organisational modularity and modularity of industry architecture in downstream and upstream value chain. Based on these micro-macro co evolutionary effects, capability development process underlying successful corporate entrepreneurship may be verified.

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.

Ultimate flexural limit states analysis of prestressed concrete sleeper

Railway is one of the most important, reliable and widely used means of transportation, carrying freight, passengers, minerals, grains, etc. Thus, research on railway tracks is extremely important for the development of railway engineering and technologies. The safe operation of a railway track is based on the railway track structure that includes rails, fasteners, pads, sleepers, ballast, subballast and formation. Sleepers are very important components of the entire structure and may be made of timber, concrete, steel or synthetic materials. Concrete sleepers were first installed around the middle of last century and currently are installed in great numbers around the world. Consequently, the design of concrete sleepers has a direct impact on the safe operation of railways. The "permissible stress" method is currently most commonly used to design sleepers. However, the permissible stress principle does not consider the ultimate strength of materials, probabilities of actual loads, and the risks associated with failure, all of which could lead to the conclusion of cost-ineffectiveness and over design of current prestressed concrete sleepers. Recently the limit states design method, which appeared in the last century and has been already applied in the design of buildings, bridges, etc, is proposed as a better method for the design of prestressed concrete sleepers. The limit states design has significant advantages compared to the permissible stress design, such as the utilisation of the full strength of the member, and a rational analysis of the probabilities related to sleeper strength and applied loads. This research aims to apply the ultimate limit states design to the prestressed concrete sleeper, namely to obtain the load factors of both static and dynamic loads for the ultimate limit states design equations. However, the sleepers in rail tracks require different safety levels for different types of tracks, which mean the different types of tracks have different load factors of limit states design equations. Therefore, the core tasks of this research are to find the load factors of the static component and dynamic component of loads on track and the strength reduction factor of the sleeper bending strength for the ultimate limit states design equations for four main types of tracks, i.e., heavy haul, freight, medium speed passenger and high speed passenger tracks. To find those factors, the multiple samples of static loads, dynamic loads and their distributions are needed. In the four types of tracks, the heavy haul track has the measured data from Braeside Line (A heavy haul line in Central Queensland), and the distributions of both static and dynamic loads can be found from these data. The other three types of tracks have no measured data from sites and the experimental data are hardly available. In order to generate the data samples and obtain their distributions, the computer based simulations were employed and assumed the wheel-track impacts as induced by different sizes of wheel flats. A valid simulation package named DTrack was firstly employed to generate the dynamic loads for the freight and medium speed passenger tracks. However, DTrack is only valid for the tracks which carry low or medium speed vehicles. Therefore, a 3-D finite element (FE) model was then established for the wheel-track impact analysis of the high speed track. This FE model has been validated by comparing its simulation results with the DTrack simulation results, and with the results from traditional theoretical calculations based on the case of heavy haul track. Furthermore, the dynamic load data of the high speed track were obtained from the FE model and the distributions of both static and dynamic loads were extracted accordingly. All derived distributions of loads were fitted by appropriate functions. Through extrapolating those distributions, the important parameters of distributions for the static load induced sleeper bending moment and the extreme wheel-rail impact force induced sleeper dynamic bending moments and finally, the load factors, were obtained. Eventually, the load factors were obtained by the limit states design calibration based on reliability analyses with the derived distributions. After that, a sensitivity analysis was performed and the reliability of the achieved limit states design equations was confirmed. It has been found that the limit states design can be effectively applied to railway concrete sleepers. This research significantly contributes to railway engineering and the track safety area. It helps to decrease the failure and risks of track structure and accidents; better determines the load range for existing sleepers in track; better rates the strength of concrete sleepers to support bigger impact and loads on railway track; increases the reliability of the concrete sleepers and hugely saves investments on railway industries. Based on this research, many other bodies of research can be promoted in the future. Firstly, it has been found that the 3-D FE model is suitable for the study of track loadings and track structure vibrations. Secondly, the equations for serviceability and damageability limit states can be developed based on the concepts of limit states design equations of concrete sleepers obtained in this research, which are for the ultimate limit states.

Genetic susceptibility to complex traits : moving towards informed analysis of whole-genome screens

Susceptibility to complex traits, by definition, involves aetiological polymorphisms at multiple genetic loci combined with variable contributions by environmental factors. However, the approaches taken to identifying genetic loci implicated in susceptibility to complex traits frequently overlooks the compounding contribution of multiple loci in favour of highlighting a single gene solely responsible for predisposition. It is only in a small minority of cases that this has resulted in clear disease heritability associated with polymorphisms in a single gene. More often, this approach has led to an accumulation of single-gene associations with minor contributions to disease susceptibility. As the genomic era advances and genome-wide screens become higher in resolution and throughput, the need for simultaneous consideration of multiple loci is becoming more important. With special reference to non-Hodgkin’s lymphoma (NHL), this chapter will overview the current progress made in elucidating genetic polymorphisms associated with disease susceptibility. We also present novel data from a high-resolution single nucleotide polymorphism (SNP) microarray screen for susceptibility loci that are involved in NHL. Using an ‘informed approach’, the findings are highlighted within the context of cellular pathways, and provide insight and new ideas for methods of analysis for genome-wide screens for susceptibility.