Morphometric analysis of telencephalic structure in a variety of neognath and paleognath bird species reveals regional differences associated with specific behavioral traits

Birds exhibit a huge array of behavior, ecology and physiology, and occupy nearly every environment on earth, ranging from the desert outback of Australia to the tropical rain forests of Panama. Some birds have adopted a fully nocturnal lifestyle, such as the barn owl and kiwi, while others, such as the albatross, spend nearly their entire life flying over the ocean. Each species has evolved unique adaptations over millions of years to function in their respective niche. In order to increase processing power or network efficiency, many of these adaptations require enlargements and/or specializations of the brain as a whole or of specific brain regions. In this study, we examine the relative size and morphology of 9 telencephalic regions in a number of Paleognath and Neognath birds and relate the findings to differences in behavior and sensory ecology. We pay particular attention to those species that have undergone a relative enlargement of the telencephalon to determine whether this relative increase in telencephalic size is homogeneous across different brain regions or whether particular regions have become differentially enlarged. The analysis indicates that changes in the relative size of telencephalic regions are not homogeneous, with every species showing hypertrophy or hypotrophy of at least one of them. The three-dimensional structure of these regions in different species was also variable, in particular that of the mesopallium in kiwi. The findings from this study provide further evidence that the changes in relative brain size in birds reflect a process of mosaic evolution.

Genetic characterisation and structural analysis of the O-specific polysaccharide of Yersinia pseudotuberculosis serotype O:1c

Many, but not all, of the current 21 serotypes of Yersinia pseudotuberculosis have been investigated with regard to the chemical structures of their O-specific polysaccharide (OPS) and the genetic basis of their biosynthesis. Completion of the genetics and structures of the remaining serotypes will enhance our understanding of the emerging relationship between genetics and structures within this species. Here, we present a structural and genetic analysis of the Y. pseudotuberculosis serotype O:1c OPS. Our results showed that this OPS has the same backbone as Y. pseudotuberculosis O:2b, but with a 3,6-dideoxy-D-ribo-hexofuranose (paratofuranose, Parf) side-branch instead of a 3,6-dideoxy-D-xylo-hexopyranose (abequopyranose, Abep). The 3'-end of the gene cluster is the same as for O:2b and has the genes for synthesis of the backbone and for processing the completed repeat unit. The 5'-end of the cluster consists of the same genes as O:1b for synthesis of Parf and a related gene for its transfer to the repeating unit backbone.

RNASeqBrowser: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks

Background Strand specific RNAseq data is now more common in RNAseq projects. Visualizing RNAseq data has become an important matter in Analysis of sequencing data. The most widely used visualization tool is the UCSC genome browser that introduced the custom track concept that enabled researchers to simultaneously visualize gene expression at a particular locus from multiple experiments. Our objective of the software tool is to provide friendly interface for visualization of RNAseq datasets. Results This paper introduces a visualization tool (RNASeqBrowser) that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks -- all being dynamically built from the BAM file. Paired reads are also connected in the browser to enable easier identification of novel exon/intron borders and chimaeric transcripts. Strand specific RNAseq data is also supported by RNASeqBrowser that displays reads above (positive strand transcript) or below (negative strand transcripts) a central line. Finally, RNASeqBrowser was designed for ease of use for users with few bioinformatic skills, and incorporates the features of many genome browsers into one platform. Conclusions The features of RNASeqBrowser: (1) RNASeqBrowser integrates UCSC genome browser and NGS visualization tools such as IGV. It extends the functionality of the UCSC genome browser by adding several new types of tracks to show NGS data such as individual raw reads, SNPs and InDels. (2) RNASeqBrowser can dynamically generate RNA secondary structure. It is useful for identifying non-coding RNA such as miRNA. (3) Overlaying NGS wiggle data is helpful in displaying differential expression and is simple to implement in RNASeqBrowser. (4) NGS data accumulates a lot of raw reads. Thus, RNASeqBrowser collapses exact duplicate reads to reduce visualization space. Normal PC’s can show many windows of NGS individual raw reads without much delay. (5) Multiple popup windows of individual raw reads provide users with more viewing space. This avoids existing approaches (such as IGV) which squeeze all raw reads into one window. This will be helpful for visualizing multiple datasets simultaneously. RNASeqBrowser and its manual are freely available at http://www.australianprostatecentre.org/research/software/rnaseqbrowser webcite or http://sourceforge.net/projects/rnaseqbrowser/ webcite

Flow pattern analysis in a highly stenotic patient-specific carotid bifurcation model using a turbulence model

The aim of this study is to investigate the blood flow pattern in carotid bifurcation with a high degree of luminal stenosis, combining in vivo magnetic resonance imaging (MRI) and computational fluid dynamics (CFD). A newly developed two-equation transitional model was employed to evaluate wall shear stress (WSS) distribution and pressure drop across the stenosis, which are closely related to plaque vulnerability. A patient with an 80% left carotid stenosis was imaged using high resolution MRI, from which a patient-specific geometry was reconstructed and flow boundary conditions were acquired for CFD simulation. A transitional model was implemented to investigate the flow velocity and WSS distribution in the patient-specific model. The peak time-averaged WSS value of approximately 73Pa was predicted by the transitional flow model, and the regions of high WSS occurred at the throat of the stenosis. High oscillatory shear index values up to 0.50 were present in a helical flow pattern from the outer wall of the internal carotid artery immediately after the throat. This study shows the potential suitability of a transitional turbulent flow model in capturing the flow phenomena in severely stenosed carotid arteries using patient-specific MRI data and provides the basis for further investigation of the links between haemodynamic variables and plaque vulnerability. It may be useful in the future for risk assessment of patients with carotid disease.

Normalized wall index specific and MRI-based stress analysis of atherosclerotic carotid plaques: A study comparing acutely symptomatic and asymptomatic patients

Background: Biomechanical stresses play an important role in determining plaque stability. Quantification of these simulated stresses can be potentially used to assess plaque vulnerability and differentiate different patient groups. Methods and Results: 54 asymptomatic and 45 acutely symptomatic patients underwent in vivo multicontrast magnetic resonance imaging (MRI) of the carotid arteries. Plaque geometry used for finite element analysis was derived from in vivo MRI at the sites of maximum and minimum plaque burden. In total, 198 slices were used for the computational simulations. A pre-shrink technique was used to refine the simulation. Maximum principle stress at the vulnerable plaque sites (ie, critical stress) was extracted for the selected slices and a comparison was performed between the 2 groups. Critical stress in the slice with maximum plaque burden is significantly higher in acutely symptomatic patients as compared to asymptomatic patients (median, inter quartile range: 198.0 kPa (119.8-359.0 kPa) vs 138.4 kPa (83.8-242.6 kPa), P=0.04). No significant difference was found in the slice with minimum plaque burden between the 2 groups (196.7 kPa (133.3-282.7 kPa) vs 182.4 kPa (117.2-310.6 kPa), P=0.82). Conclusions: Acutely symptomatic carotid plaques have significantly high biomechanical stresses than asymptomatic plaques. This might be potentially useful for establishing a biomechanical risk stratification criteria based on plaque burden in future studies.

A cyclostationary multi-domain analysis of fluid instability in Kaplan turbines

Hydraulic instabilities represent a critical problem for Francis and Kaplan turbines, reducing their useful life due to increase of fatigue on the components and cavitation phenomena. Whereas an exhaustive list of publications on computational fluid-dynamic models of hydraulic instability is available, the possibility of applying diagnostic techniques based on vibration measurements has not been investigated sufficiently, also because the appropriate sensors seldom equip hydro turbine units. The aim of this study is to fill this knowledge gap and to exploit fully, for this purpose, the potentiality of combining cyclostationary analysis tools, able to describe complex dynamics such as those of fluid-structure interactions, with order tracking procedures, allowing domain transformations and consequently the separation of synchronous and non-synchronous components. This paper will focus on experimental data obtained on a full-scale Kaplan turbine unit, operating in a real power plant, tackling the issues of adapting such diagnostic tools for the analysis of hydraulic instabilities and proposing techniques and methodologies for a highly automated condition monitoring system. © 2015 Elsevier Ltd.

Mutational analysis of the insulin‑like growth factor 1 receptor tyrosine kinase domain in non-small cell lung cancer patients

The insulin‑like growth factor 1 receptor (IGF1R) pathway plays an important role in the pathogenesis of non‑small cell lung cancer (NSCLC) and also provides a mechanism of resistance to targeted therapies. IGF1R is therefore an ideal therapeutic target and several inhibitors have entered clinical trials. However, thus far the response to these inhibitors has been poor, highlighting the importance of predictive biomarkers to identify patient cohorts who will benefit from these targeted agents. It is well‑documented that mutations and/or deletions in the epidermal growth factor receptor (EGFR) tyrosine kinase (TK) domain predict sensitivity of NSCLC patients to EGFR TK inhibitors. Single‑nucleotide polymorphisms (SNPs) in the IGF pathway have been associated with disease, including breast and prostate cancer. The aim of the present study was to elucidate whether the IGF1R TK domain harbours SNPs, somatic mutations or deletions in NSCLC patients and correlates the mutation status to patient clinicopathological data and prognosis. Initially 100 NSCLC patients were screened for mutations/deletions in the IGF1R TK domain (exons 16‑21) by sequencing analysis. Following the identification of SNP rs2229765, a further 98 NSCLC patients and 866 healthy disease‑free control patients were genotyped using an SNP assay. The synonymous SNP (rs2229765) was the only aberrant base change identified in the IGF1R TK domain of 100 NSCLC patients initially analysed. SNP rs2229765 was detected in exon 16 and was found to have no significant association between IGF1R expression and survival. The GA genotype was identified in 53.5 and 49.4% of NSCLC patients and control individuals, respectively. No significant difference was found in the genotype (P=0.5487) or allele (P=0.9082) frequencies between the case and control group. The present findings indicate that in contrast to the EGFR TK domain, the IGF1R TK domain is not frequently mutated in NSCLC patients. The synonymous SNP (rs2229765) had no significant association between IGF1R expression and survival in the cohort of NSCLC patients.

Detailed analysis of a conservative difference approximation for the time fractional diffusion equation

Diffusion equations that use time fractional derivatives are attractive because they describe a wealth of problems involving non-Markovian Random walks. The time fractional diffusion equation (TFDE) is obtained from the standard diffusion equation by replacing the first-order time derivative with a fractional derivative of order α ∈ (0, 1). Developing numerical methods for solving fractional partial differential equations is a new research field and the theoretical analysis of the numerical methods associated with them is not fully developed. In this paper an explicit conservative difference approximation (ECDA) for TFDE is proposed. We give a detailed analysis for this ECDA and generate discrete models of random walk suitable for simulating random variables whose spatial probability density evolves in time according to this fractional diffusion equation. The stability and convergence of the ECDA for TFDE in a bounded domain are discussed. Finally, some numerical examples are presented to show the application of the present technique.

Effective Cell-Centred Time-Domain Maxwell's Equations Numerical Solvers

This research work analyses techniques for implementing a cell-centred finite-volume time-domain (ccFV-TD) computational methodology for the purpose of studying microwave heating. Various state-of-the-art spatial and temporal discretisation methods employed to solve Maxwell's equations on multidimensional structured grid networks are investigated, and the dispersive and dissipative errors inherent in those techniques examined. Both staggered and unstaggered grid approaches are considered. Upwind schemes using a Riemann solver and intensity vector splitting are studied and evaluated. Staggered and unstaggered Leapfrog and Runge-Kutta time integration methods are analysed in terms of phase and amplitude error to identify which method is the most accurate and efficient for simulating microwave heating processes. The implementation and migration of typical electromagnetic boundary conditions. from staggered in space to cell-centred approaches also is deliberated. In particular, an existing perfectly matched layer absorbing boundary methodology is adapted to formulate a new cell-centred boundary implementation for the ccFV-TD solvers. Finally for microwave heating purposes, a comparison of analytical and numerical results for standard case studies in rectangular waveguides allows the accuracy of the developed methods to be assessed.

Critically evaluating rural women’s participation and empowerment : An interdisciplinary feminist framework for research and analysis

Community development is increasingly using participatory processes that aim to be inclusive and empowering. However, researchers have found that such processes can have contradictory effects. Australian research has highlighted the significant leadership of rural women in sustainable community and economic development and in the adoption of new communication technologies such as the Internet. A focus on gender in participatory development may therefore lead to more effective programs and policies. This chapter outlines an interdisciplinary feminist framework for critically evaluating the participation and empowerment of rural women. This framework was found effective in evaluating an Australian project that aimed to enhance rural women’s access to communication technologies and to empower its participants. Its multiple theoretical and methodological approaches are outlined. The framework advocates an analysis of diversity and difference and the macro and micro contexts. Some principles and strategies for rural women’s inclusion, participation, empowerment, and for participatory feminist evaluation are outlined.

Application of the analytic hierarchy process (AHP) in multi-criteria analysis of the selection of intelligent building systems

The availability of innumerable intelligent building (IB) products, and the current dearth of inclusive building component selection methods suggest that decision makers might be confronted with the quandary of forming a particular combination of components to suit the needs of a specific IB project. Despite this problem, few empirical studies have so far been undertaken to analyse the selection of the IB systems, and to identify key selection criteria for major IB systems. This study is designed to fill these research gaps. Two surveys: a general survey and the analytic hierarchy process (AHP) survey are proposed to achieve these objectives. The first general survey aims to collect general views from IB experts and practitioners to identify the perceived critical selection criteria, while the AHP survey was conducted to prioritize and assign the important weightings for the perceived criteria in the general survey. Results generally suggest that each IB system was determined by a disparate set of selection criteria with different weightings. ‘Work efficiency’ is perceived to be most important core selection criterion for various IB systems, while ‘user comfort’, ‘safety’ and ‘cost effectiveness’ are also considered to be significant. Two sub-criteria, ‘reliability’ and ‘operating and maintenance costs’, are regarded as prime factors to be considered in selecting IB systems. The current study contributes to the industry and IB research in at least two aspects. First, it widens the understanding of the selection criteria, as well as their degree of importance, of the IB systems. It also adopts a multi-criteria AHP approach which is a new method to analyse and select the building systems in IB. Further research would investigate the inter-relationship amongst the selection criteria.

Service analysis : A critical assessment of the state of the art

The service-orientation paradigm has not only become prevalent in the software systems domain in recent years, but is also increasingly applied on the business level to restructure organisational capabilities. In this paper, we present the results of an extensive literature review of 30 approaches related to service identification and analysis for both domains. Based on the consolidation of a superset of comparison criteria for service-oriented methodologies found in related literature, we compare and evaluate the different characteristics of service engineering methods with a focus on service analysis. Although a close business and IT alignment is regarded as one of the core beneficial promises of service-orientation, our analysis suggests that there is a lack of unified, comprehensive methodology for service identification and analysis integrating and addressing both domains. Thus, we discuss how our results can inform directions for future research in this area.

Report : enabling team collaboration with pervasive and mobile computing : cost benefit analysis methodology

Construction is an information intensive industry in which the accuracy and timeliness of information is paramount. It observed that the main communication issue in construction is to provide a method to exchange data between the site operation, the site office and the head office. The information needs under consideration are time critical to assist in maintaining or improving the efficiency at the jobsite. Without appropriate computing support this may increase the difficulty of problem solving. Many researchers focus their research on the usage of mobile computing devices in the construction industry and they believe that mobile computers have the potential to solve some construction problems that leads to reduce overall productivity. However, to date very limited observation has been conducted in terms of the deployment of mobile computers for construction workers on-site. By providing field workers with accurate, reliable and timely information at the location where it is needed, it will support the effectiveness and efficiency at the job site. Bringing a new technology into construction industry is not only need a better understanding of the application, but also need a proper preparation of the allocation of the resources such as people, and investment. With this in mind, an accurate analysis is needed to provide clearly idea of the overall costs and benefits of the new technology. A cost benefit analysis is a method of evaluating the relative merits of a proposed investment project in order to achieve efficient allocation of resources. It is a way of identifying, portraying and assessing the factors which need to be considered in making rational economic choices. In principle, a cost benefit analysis is a rigorous, quantitative and data-intensive procedure, which requires identification all potential effects, categorisation of these effects as costs and benefits, quantitative estimation of the extent of each cost and benefit associated with an action, translation of these into a common metric such as dollars, discounting of future costs and benefits into the terms of a given year, and summary of all cost and benefit to see which is greater. Even though many cost benefit analysis methodologies are available for a general assessment, there is no specific methodology can be applied for analysing the cost and benefit of the application of mobile computing devices in the construction site. Hence, the proposed methodology in this document is predominantly adapted from Baker et al. (2000), Department of Finance (1995), and Office of Investment Management (2005). The methodology is divided into four main stages and then detailed into ten steps. The methodology is provided for the CRC CI 2002-057-C Project: Enabling Team Collaboration with Pervasive and Mobile Computing and can be seen in detail in Section 3.