The application of DArTseq technology to pineapple

DArTseq technology is potentially the most appropriate system to discover hundreds of polymorphic genomic loci, scoring thousands of unique genomic-wide DNA fragments in one single experiment, without requiring existing DNA sequence information. The DArT complexity reduction approach in combination with Illumina short read sequencing (Hiseq2000) was applied. To test the application of DArTseq technology in pineapple, a reference population of 13 Ananas genotypes from primitive wild accessions to modern cultivars was used. In a comparison of 3 systems, the combination of restriction enzymes PstI and MseI performed the best producing 18,900 DArT markers and close to 20,000 SNPs. Based on these markers genetic relationships between the samples were identified and a dendrogram was generated. The topography of the tree corresponds with our understanding of the genetic relationships between the genotypes. Importantly, the replicated samples of all genotypes have a dissimilarity of close to 0.0 and occupy the same positions on the tree, confirming high reproducibility of the markers detected. Eventually it is planned that molecular markers will be identified that are associated with resistance to Phytophthora cinnamomi (Pc), the most economically important pathogen of pineapple in Australia, as genetic resistance is known to exist within the Ananas. Marker assisted selection can then be utilized in a pineapple breeding program to develop cultivars resistant to Pc.

Spectral unmixing with estimated adaptive endmember index using Extended Support Vector Machine

The most difficult operation in the flood inundation mapping using optical flood images is to separate fully inundated areas from the ‘wet’ areas where trees and houses are partly covered by water. This can be referred as a typical problem the presence of mixed pixels in the images. A number of automatic information extraction image classification algorithms have been developed over the years for flood mapping using optical remote sensing images. Most classification algorithms generally, help in selecting a pixel in a particular class label with the greatest likelihood. However, these hard classification methods often fail to generate a reliable flood inundation mapping because the presence of mixed pixels in the images. To solve the mixed pixel problem advanced image processing techniques are adopted and Linear Spectral unmixing method is one of the most popular soft classification technique used for mixed pixel analysis. The good performance of linear spectral unmixing depends on two important issues, those are, the method of selecting endmembers and the method to model the endmembers for unmixing. This paper presents an improvement in the adaptive selection of endmember subset for each pixel in spectral unmixing method for reliable flood mapping. Using a fixed set of endmembers for spectral unmixing all pixels in an entire image might cause over estimation of the endmember spectra residing in a mixed pixel and hence cause reducing the performance level of spectral unmixing. Compared to this, application of estimated adaptive subset of endmembers for each pixel can decrease the residual error in unmixing results and provide a reliable output. In this current paper, it has also been proved that this proposed method can improve the accuracy of conventional linear unmixing methods and also easy to apply. Three different linear spectral unmixing methods were applied to test the improvement in unmixing results. Experiments were conducted in three different sets of Landsat-5 TM images of three different flood events in Australia to examine the method on different flooding conditions and achieved satisfactory outcomes in flood mapping.

Identifying Genetic Risk Factors in Canine Autoimmune Disorders

Autoimmune diseases are more common in dogs than in humans and are already threatening the future of some highly predisposed dog breeds. Susceptibility to autoimmune diseases is controlled by environmental and genetic factors, especially the major histocompatibility complex (MHC) gene region. Dogs show a similar physiology, disease presentation and clinical response as humans, making them an excellent disease model for autoimmune diseases common to both species. The genetic background of canine autoimmune disorders is largely unknown, but recent annotation of the dog genome and subsequent development of new genomic tools offer a unique opportunity to map novel autoimmune genes in various breeds. Many autoimmune disorders show breed-specific enrichment, supporting a strong genetic background. Furthermore, the presence of hundreds of breeds as genetic isolates facilitates gene mapping in complex autoimmune disorders. Identification of novel predisposing genes establishes breeds as models and may reveal novel candidate genes for the corresponding human disorders. Genetic studies will eventually shed light on common biological functions and interactions between genes and the environment. This study aimed to identify genetic risk factors in various autoimmune disorders, including systemic lupus erythematosus (SLE)-related diseases, comprising immune-mediated rheumatic disease (IMRD) and steroid-responsive meningitis arteritis (SMRA) as well as Addison s disease (AD) in Nova Scotia Duck Tolling Retrievers (NSDTRs) and chronic superficial keratitis (CSK) in German Shepherd dogs (GSDs). We used two different approaches to identify genetic risk factors. Firstly, a candidate gene approach was applied to test the potential association of MHC class II, also known as a dog leukocyte antigen (DLA) in canine species. Secondly, a genome-wide association study (GWAS) was performed to identify novel risk loci for SLE-related disease and AD in NSDTRs. We identified DLA risk haplotypes for an IMRD subphenotype of SLE-related disease, AD and CSK, but not in SMRA, and show that the MHC class II gene region is a major genetic risk factor in canine autoimmune diseases. An elevated risk was found for IMRD in dogs that carried the DLA-DRB1*00601/DQA1*005011/DQB1*02001 haplotype (OR = 2.0, 99% CI = 1.03-3.95, p = 0.01) and for ANA-positive IMRD dogs (OR = 2.3, 99% CI = 1.07-5.04, p-value 0.007). We also found that DLA-DRB1*01502/DQA*00601/DQB1*02301 haplotype was significantly associated with AD in NSDTRs (OR = 2.1, CI = 1.0-4.4, P = 0.044) and the DLA-DRB1*01501/DQA1*00601/DQB1*00301 haplotype with the CSK in GSDs (OR=2.67, CI=1.17-6.44, p= 0.02). In addition, we found that homozygosity for the risk haplotype increases the risk for each disease phenotype and that an overall homozygosity for the DLA region predisposes to CSK and AD. Our results have enabled the development of genetic tests to improve breeding practices by avoiding the production of puppies homozygous for risk haplotypes. We also performed the first successful GWAS for a complex disease in dogs. With less than 100 cases and 100 controls, we identified five risk loci for SLE-related disease and AD and found strong candidate genes involved in a novel T-cell activation pathway. We show that an inbred dog population has fewer risk factors, but each of them has a stronger genetic risk. Ongoing studies aim to identify the causative mutations and bring new knowledge to help diagnostics, treatment and understanding of the aetiology of SLE-related diseases.

Seismic reflection experiments imaging the physical nature of crustal structures in southern California

Seismic reflection methods have been extensively used to probe the Earth's crust and suggest the nature of its formative processes. The analysis of multi-offset seismic reflection data extends the technique from a reconnaissance method to a powerful scientific tool that can be applied to test specific hypotheses. The treatment of reflections at multiple offsets becomes tractable if the assumptions of high-frequency rays are valid for the problem being considered. Their validity can be tested by applying the methods of analysis to full wave synthetics.

Three studies illustrate the application of these principles to investigations of the nature of the crust in southern California. A survey shot by the COCORP consortium in 1977 across the San Andreas fault near Parkfield revealed events in the record sections whose arrival time decreased with offset. The reflectors generating these events are imaged using a multi-offset three-dimensional Kirchhoff migration. Migrations of full wave acoustic synthetics having the same limitations in geometric coverage as the field survey demonstrate the utility of this back projection process for imaging. The migrated depth sections show the locations of the major physical boundaries of the San Andreas fault zone. The zone is bounded on the southwest by a near-vertical fault juxtaposing a Tertiary sedimentary section against uplifted crystalline rocks of the fault zone block. On the northeast, the fault zone is bounded by a fault dipping into the San Andreas, which includes slices of serpentinized ultramafics, intersecting it at 3 km depth. These interpretations can be made despite complications introduced by lateral heterogeneities.

In 1985 the Calcrust consortium designed a survey in the eastern Mojave desert to image structures in both the shallow and the deep crust. Preliminary field experiments showed that the major geophysical acquisition problem to be solved was the poor penetration of seismic energy through a low-velocity surface layer. Its effects could be mitigated through special acquisition and processing techniques. Data obtained from industry showed that quality data could be obtained from areas having a deeper, older sedimentary cover, causing a re-definition of the geologic objectives. Long offset stationary arrays were designed to provide reversed, wider angle coverage of the deep crust over parts of the survey. The preliminary field tests and constant monitoring of data quality and parameter adjustment allowed 108 km of excellent crustal data to be obtained.

This dataset, along with two others from the central and western Mojave, was used to constrain rock properties and the physical condition of the crust. The multi-offset analysis proceeded in two steps. First, an increase in reflection peak frequency with offset is indicative of a thinly layered reflector. The thickness and velocity contrast of the layering can be calculated from the spectral dispersion, to discriminate between structures resulting from broad scale or local effects. Second, the amplitude effects at different offsets of P-P scattering from weak elastic heterogeneities indicate whether the signs of the changes in density, rigidity, and Lame's parameter at the reflector agree or are opposed. The effects of reflection generation and propagation in a heterogeneous, anisotropic crust were contained by the design of the experiment and the simplicity of the observed amplitude and frequency trends. Multi-offset spectra and amplitude trend stacks of the three Mojave Desert datasets suggest that the most reflective structures in the middle crust are strong Poisson's ratio (σ) contrasts. Porous zones or the juxtaposition of units of mutually distant origin are indicated. Heterogeneities in σ increase towards the top of a basal crustal zone at ~22 km depth. The transition to the basal zone and to the mantle include increases in σ. The Moho itself includes ~400 m layering having a velocity higher than that of the uppermost mantle. The Moho maintains the same configuration across the Mojave despite 5 km of crustal thinning near the Colorado River. This indicates that Miocene extension there either thinned just the basal zone, or that the basal zone developed regionally after the extensional event.

Estudo de crenças e preconceito linguístico em alunos do sexto ano de uma escola do município de Paracambi (RJ)

A necessidade de basear as aulas de Língua Portuguesa na gramática normativa é muito defendida no ambiente escolar. As universidades, por outro lado, aceitam a ideia de que os princípios da Sociolinguística laboviana devem ser introduzidos na educação básica. Dessa maneira, há uma lacuna entre o que se aprende na teoria pedagógica e o que, de fato, ocorre em sala de aula. Buscando encurtar a distância existente entre a teoria linguística e a prática pedagógica, esta pesquisa teve como objetivo apresentar um roteiro de atividades que se relacionam à reflexão por parte dos alunos no que tange a suas crenças linguísticas, principalmente as que apresentam uma vertente preconceituosa. Para isso, foi aplicado um teste de crenças linguísticas com alunos do sexto ano do ensino fundamental de uma escola pública, localizada no município de Paracambi, RJ. Depois foram ministradas quatro aulas a fim de demonstrar aos alunos que a norma popular apresenta uma regularidade, portanto, não é linguisticamente inferior à norma de prestígio. Para finalizar, o mesmo teste de crenças linguísticas foi aplicado nos mesmos alunos. Essa pesquisa, baseada em Cyranka (2007), verificou a viabilidade de um trabalho com a Sociolinguística na escola, procurando avaliar a capacidade de os alunos refletirem sociolinguisticamente

Fabrication of test structures for 4×4 InP/InGaAsP integrated optical matrix

A novel optical switching matrix measuring 1×2 mm2 in size is fabricated. The switching matrix is composed of waveguides, four 1×4 multimode interference (MMI) splitters, 32 total internal refraction mirrors and four 4×1 MMI combiners with the extremely compact size of 1×2 mm2. This integrated device are assessed and loss contribution measured from test structure is presented.

Beyond words: Testing alignment among inter-organizational performance measures

Purpose: This paper seeks to measure in a quantitative way the degree of alignment among a set of performance measures between two organizations. Design/methodology/approach: This paper extends Venkatraman's test of coalignment to assess the alignment of a set of performance measures governing a contractual inter-organizational relationship. The authors applied the test and present coefficients of misalignment across three sets of measures: those used by a service provider involved in the research, those used by customers contracting the services, and those documented in 11 contracts studied. Findings: Results confirmed a high degree of alignment between target and actual operational performance in the contracts. The alignment of customers' financial objectives and contracts' operational metrics was low. Calculations show poor alignment between the objectives of the provider and the contribution received from the contracts. Research limitations/implications: Some limitations of the conclusions include the small sample of contracts used in the calculations. Further research should include not only actual contracts, but also failed ones. Practical implications: It is possible that misaligned goals, represented in misaligned performance measures, lead to tensions in intra-firm relationships. If these tensions are not addressed properly the relationship could be unstable or terminated prematurely. This method of measuring alignment could detect early potential dangers in intra-firm relationships. Originality/value: This paper extends Venkatraman's test of coalignment to assess the alignment of a set of performance measures governing a contractual inter-organizational relationship. Management researchers and business professionals may use this methodology when exploring degrees of alignment of performance measures in intra-functional and inter-firm relationships. © Emerald Group Publishing Limited.

A validation of commercial flow solver performance on hybridised octree meshes

In recent years we have been developing a meshing system which is aimed at eliminating the bottleneck represented by building meshes for real-world, complex turbomachinery configurations. This system is based on a rapid octree meshing technology which is then made conformal to the bodies present. The objective of this paper is to demonstrate that this class of mesh is not only very fast to produce but also fit-for-purpose in the sense that simulations generated with third-party commercial flow solvers like Fluent have the same accuracy as those performed on more conventional meshes. A range of standard examples and test cases will be presented. Copyright © 2011 by ASME.

A influência do nível socioeconómico na leitura

Trabalho apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Licenciada em Terapêutica da Fala

Can metaphors and analogies improve communication with seriously ill patients?

OBJECTIVE: It is not known how often physicians use metaphors and analogies, or whether they improve patients' perceptions of their physicians' ability to communicate effectively. Therefore, the objective of this study was to determine whether the use of metaphors and analogies in difficult conversations is associated with better patient ratings of their physicians' communication skills. DESIGN: Cross-sectional observational study of audio-recorded conversations between patients and physicians. SETTING: Three outpatient oncology practices. PATIENTS: Ninety-four patients with advanced cancer and 52 physicians. INTERVENTION: None. MAIN OUTCOME MEASURES: Conversations were reviewed and coded for the presence of metaphors and analogies. Patients also completed a 6-item rating of their physician's ability to communicate. RESULTS: In a sample of 101 conversations, coders identified 193 metaphors and 75 analogies. Metaphors appeared in approximately twice as many conversations as analogies did (65/101, 64% versus 31/101, 31%; sign test p < 0.001). Conversations also contained more metaphors than analogies (mean 1.6, range 0-11 versus mean 0.6, range 0-5; sign rank test p < 0.001). Physicians who used more metaphors elicited better patient ratings of communication (rho = 0.27; p = 0.006), as did physicians who used more analogies (Spearman rho = 0.34; p < 0.001). CONCLUSIONS: The use of metaphors and analogies may enhance physicians' ability to communicate.

Improving the generation of decision objectives

Real decision makers exhibit significant shortcomings in the generation of objectives for decisions that they face. Prior research has illustrated the magnitude of this shortcoming but not its causes. In this paper, we identify two distinct impediments to the generation of decision objectives: not thinking broadly enough about the range of relevant objectives, and not thinking deeply enough to articulate every objective within the range that is considered. To test these explanations and explore ways of stimulating a more comprehensive set of objectives, we present three experiments involving a variety of interventions: the provision of sample objectives, organization of objectives by category, and direct challenges to do better, with or without a warning that important objectives are missing. The use of category names and direct challenges with a warning both led to improvements in the quantity of objectives generated without impacting their quality; other interventions yielded less improvement. We conclude by discussing the relevance of our findings to decision analysis and offering prescriptive implications for the elicitation of decision objectives. © 2010 INFORMS.

Modelling technologies and applications

Numerical modelling technology and software is now being used to underwrite the design of many microelectronic and microsystems components. The demands for greater capability of these analysis tools are increasing dramatically, as the user community is faced with the challenge of producing reliable products in ever shorter lead times. This leads to the requirement for analysis tools to represent the interactions amongst the distinct phenomena and physics at multiple length and timescales. Multi-physics and Multi-scale technology is now becoming a reality with many code vendors. This chapter discusses the current status of modelling tools that assess the impact of nano-technology on the fabrication/packaging and testing of microsystems. The chapter is broken down into three sections: Modelling Technologies, Modelling Application to Fabrication, and Modelling Application to Assembly/Packing and Modelling Applied for Test and Metrology.

An interlaboratory comparison for the quantification of aqueous dimethylsulfide

An interlaboratory comparison (ILC) was conducted to evaluate the proficiency of multiple laboratories to quantify dimethylsulfide (DMS) in aqueous solution. Ten participating laboratories were each supplied with blind duplicate test solutions containing dimethylsulfoniopropionate hydrochloride (DMSP HCl) dissolved in acidified artificial seawater. The test solutions were prepared by the coordinating laboratory from a DMSP HCl reference material that was synthesized and purity certified for this purpose. A concentration range was specified for the test solutions and the participating laboratories were requested to dilute them as required for their analytical procedure, together with the addition of excess alkali under gas-tight conditions to convert the DMSP to DMS. Twenty-two DMS concentrations and their estimated expanded measurement uncertainties (95% confidence level) were received from the laboratories. With two exceptions, the within-laboratory variability was 5% or less and the between-laboratory variability was ~ 25%. The magnitude of expanded measurement uncertainties reported from all participants ranged from 1% to 33% relative to the result. The information gained from this pilot ILC indicated the need for further test sample distribution studies of this type so that participating laboratories can identify systematic errors in their analysis procedures and realistically evaluate their measurement uncertainty. The outcome of ILC studies provides insights into the comparability of data in the global surface seawater DMS database.

The effect of anisotropic elasticity on the yielding characteristics of overconsolidated natural clay

Quantitative application of elastoplastic theory to the yielding behaviour of natural soils has always been uncertain. Part of the reason is that the theory was developed for reconstituted materials with isotropic structure, in contrast to natural soils that are usually anisotropic. The approach considered in this study assumes that pre-yielding behaviour is governed by the theory of linear anisotropic elasticity and that yield loci in the mean effective stress ( p') – deviator stress (q) plane are aligned approximately along the coefficient of earth pressure (K0) line. The assumption of a rotated yield locus associated with anisotropic elastic behaviour within the state boundary surface indicates that the elastic wall within the state boundary surface is inclined. The form of the state boundary surface has been determined mathematically in terms of anisotropic elastic and Cam-Clay soil parameters. Stress path tests were conducted on samples of Belfast Upper Boulder Clay removed from a depth of 28 m below ground surface. Good agreement was found between predicted and measured yield loci. The study also examined the influence of subsequent isotropic compression on the yielding characteristics of the natural clay. The indications are that the anisotropy developed during deposition disappears when the sample is loaded to a stress level at least twice the stress generated during the original deposition process. The methods developed in the paper have also been applied to test results reported previously on Winnipeg clay, and good agreement was obtained.

Pricing of Liquidity Risks in London Stock Exchange

This thesis aims to investigate pricing of liquidity risks in London Stock Exchange. Liquidity Adjusted Capital Asset Pricing Model i.e. LCAPM developed by Acharya and Pedersen (2005) is being applied to test the influence of various liquidity risks on stock returns in London Stock Exchange. The Liquidity Adjusted Capital Asset Pricing model provides a unified framework for the testing of liquidity risks. All the common stocks listed and delisted for the period of 2000 to 2014 are included in the data sample. The study has incorporated three different measures of liquidity – Percent Quoted Spread, Amihud (2002) and Turnover. The reason behind the application of three different liquidity measures is the multi-dimensional nature of liquidity. Firm fixed effects panel regression is applied for the estimation of LCAPM. However, the results are robust according to Fama-Macbeth regressions. The results of the study indicates that liquidity risks in the form of (i) level of liquidity, (ii) commonality in liquidity (iii) flight to liquidity, (iv) depressed wealth effect and market return as well as aggregate liquidity risk are priced at London Stock Exchange. However, the results are sensitive to the choice of liquidity measures.