Analysis of multiple crystal forms of Bacillus subtilis BacB suggests a role for a metal ion as a nucleant for crystallization

Bacillus subtilis BacB is an oxidase that is involved in the production of the antibiotic bacilysin. This protein contains two double-stranded beta-helix (cupin) domains fused in a compact arrangement. BacB crystallizes in three crystal forms under similar crystallization conditions. An interesting observation was that a slight perturbation of the crystallization droplet resulted in the nucleation of a different crystal form. An X-ray absorption scan of BacB suggested the presence of cobalt and iron in the crystal. Here, a comparative analysis of the different crystal forms of BacB is presented in an effort to identify the basis for the different lattices. It is noted that metal ions mediating interactions across the asymmetric unit dominate the different packing arrangements. Furthermore, a normalized B-factor analysis of all the crystal structures suggests that the solvent-exposed metal ions decrease the flexibility of a loop segment, perhaps influencing the choice of crystal form. The residues coordinating the surface metal ion are similar in the triclinic and monoclinic crystal forms. The coordinating ligands for the corresponding metal ion in the tetragonal crystal form are different, leading to a tighter packing arrangement. Although BacB is a monomer in solution, a dimer of BacB serves as a template on which higher order symmetrical arrangements are formed. The different crystal forms of BacB thus provide experimental evidence for metal-ion-mediated lattice formation and crystal packing.

Inventory Routing - A Strategic Management Accounting Perspective

This dissertation develops a strategic management accounting perspective of inventory routing. The thesis studies the drivers of cost efficiency gains by identifying the role of the underlying cost structure, demand, information sharing, forecasting accuracy, service levels, vehicle fleet, planning horizon and other strategic factors as well as the interaction effects among these factors with respect to performance outcomes. The task is to enhance the knowledge of the strategic situations that favor the implementation of inventory routing systems, understanding cause-and-effect relationships, linkages and gaining a holistic view of the value proposition of inventory routing. The thesis applies an exploratory case study design, which is based on normative quantitative empirical research using optimization, simulation and factor analysis. Data and results are drawn from a real world application to cash supply chains. The first research paper shows that performance gains require a common cost component and cannot be explained by simple linear or affine cost structures. Inventory management and distribution decisions become separable in the absence of a set-dependent cost structure, and neither economies of scope nor coordination problems are present in this case. The second research paper analyzes whether information sharing improves the overall forecasting accuracy. Analysis suggests that the potential for information sharing is limited to coordination of replenishments and that central information do not yield more accurate forecasts based on joint forecasting. The third research paper develops a novel formulation of the stochastic inventory routing model that accounts for minimal service levels and forecasting accuracy. The developed model allows studying the interaction of minimal service levels and forecasting accuracy with the underlying cost structure in inventory routing. Interestingly, results show that the factors minimal service level and forecasting accuracy are not statistically significant, and subsequently not relevant for the strategic decision problem to introduce inventory routing, or in other words, to effectively internalize inventory management and distribution decisions at the supplier. Consequently the main contribution of this thesis is the result that cost benefits of inventory routing are derived from the joint decision model that accounts for the underlying set-dependent cost structure rather than the level of information sharing. This result suggests that the value of information sharing of demand and inventory data is likely to be overstated in prior literature. In other words, cost benefits of inventory routing are primarily determined by the cost structure (i.e. level of fixed costs and transportation costs) rather than the level of information sharing, joint forecasting, forecasting accuracy or service levels.

Molecular methods for the epidemiological analysis of methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pneumoniae

Methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pneumoniae are major health problems worldwide, both found in symptomless carriage but also causing even life-threatening infections. The aim of this thesis was to characterise MRSA and S. pneumoniae in detail by using several molecular typing methods for various epidemiological purposes: clonality analysis, epidemiological surveillance, outbreak investigation, and virulence factor analysis. The characteristics of MRSA isolates from the strain collection of the Finnish National Infectious Disease Register (NIDR) and pneumococcal isolates collected from military recruits and children with acute otitis media (AOM) were analysed using various typing techniques. Antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), spa typing, staphylococcal cassette chromosome mec (SCCmec) typing, and the detection of Panton-Valentine leukocidin (PVL) genes were performed for MRSA isolates. Pneumococcal isolates were analysed using antimicrobial susceptibility testing, serotyping, MLST, and by detecting pilus islet 1 (PI-1) and 2 (PI-2) genes. Several international community- and hospital-associated MRSA clones were recognised in Finland. The genetic diversity among MRSA FIN-4 isolates and among FIN-16 isolates was low. Overall, MRSA blood isolates from 1997 to 2006 were genetically diverse. spa typing was found to be a highly discriminatory, rapid and accurate typing method and it also qualifies as the primary typing method in countries with a long history of PFGE-based MRSA strain nomenclature. However, additional typing by another method, e.g. PFGE, is needed in certain situations to be able to provide adequate discrimination for epidemiological surveillance and outbreak investigation. An outbreak of pneumonia was associated with one pneumococcal strain among military recruits, previously healthy young men living in a crowded setting. The pneumococcal carriage rate after the outbreak was found to be exceptionally high. PI-1 genes were detected at a rather low prevalence among pneumococcal isolates from children with AOM. However, the study demonstrated that PI-1 has existed among pneumococcal isolates prior to pneumococcal conjugate vaccine and the increased antimicrobial resistance era. Moreover, PI-1 was found to associate with the serotype rather than the genotype. This study adds to our understanding of the molecular epidemiology of MRSA strains in Finland and the importance of an appropriate genotyping method to be able to perform high-level laboratory-based surveillance of MRSA. Epidemiological and molecular analyses of S. pneumoniae add to our knowledge of the characteristics of pneumococcal strains in Finland.

Physiological modules for generating discrete and rhythmic movements: Component analysis of EMG signals

A central question in Neuroscience is that of how the nervous system generates the spatiotemporal commands needed to realize complex gestures, such as handwriting. A key postulate is that the central nervous system (CNS) builds up complex movements from a set of simpler motor primitives or control modules. In this study we examined the control modules underlying the generation of muscle activations when performing different types of movement: discrete, point-to-point movements in eight different directions and continuous figure-eight movements in both the normal, upright orientation and rotated 90 degrees. To test for the effects of biomechanical constraints, movements were performed in the frontal-parallel or sagittal planes, corresponding to two different nominal flexion/abduction postures of the shoulder. In all cases we measured limb kinematics and surface electromyographic activity (EMB) signals for seven different muscles acting around the shoulder. We first performed principal component analysis (PCA) of the EMG signals on a movement-by-movement basis. We found a surprisingly consistent pattern of muscle groupings across movement types and movement planes, although we could detect systematic differences between the PCs derived from movements performed in each sholder posture and between the principal components associated with the different orientations of the figure. Unexpectedly we found no systematic differences between the figute eights and the point-to-point movements. The first three principal components could be associated with a general co-contraction of all seven muscles plus two patterns of reciprocal activatoin. From these results, we surmise that both "discrete-rhythmic movements" such as the figure eight, and discrete point-to-point movement may be constructed from three different fundamental modules, one regulating the impedance of the limb over the time span of the movement and two others operating to generate movement, one aligned with the vertical and the other aligned with the horizontal.

Percepção sobre o papel do Código de Ética Profissional na solução de dilemas éticos: um estudo empírico na Controladoria Geral do Município do Rio de Janeiro (CGM)

O grande impacto dos escândalos que afetam organizações das mais diversas áreas, inclusive as públicas, tem difundido um interesse generalizado em comportamentos éticos e antiéticos. A administração ideal baseia-se em um modelo de gestão, cujo processo utiliza mecanismos que assegurem sua eficiência e eficácia e, conseqüentemente, propiciem a redução de conflitos dentro da organização. A observância de um código de ética profissional favorece essa redução de conflitos, pois seu objetivo central é a formação da consciência sobre padrões de conduta. Nesse contexto, os servidores públicos devem constituir e observar determinadas regras de conduta que norteiam seu exercício profissional, pois a consciência dos princípios morais, seja no exercício do cargo ou função, ou fora dele, refletirá no exercício vocacional do poder do estado. Seus atos, comportamentos e atitudes deverão preservar a honra e a tradição do Funcionalismo Público diante da sociedade. Entretanto, a efetividade do cumprimento de um Código de Ética não se baseia nas leis administrativas e nem com estas se confunde, mas se apóia no sentimento de adesão moral e de convicção íntima de cada servidor público. Diante dos desafios encontrados na gestão de organizações públicas e de sua importância para a sociedade em geral, o objetivo desta pesquisa é verificar os fatores que influenciam a percepção dos servidores públicos civis municipais quanto ao valor do Código de Ética Profissional da Prefeitura do Rio de Janeiro como auxiliar na solução de dilemas éticos. A amostra foi constituída por 90 (noventa) servidores lotados na Controladoria Geral do Município (CGM). A metodologia utilizada para a análise exploratória e confirmatória dos dados, necessitou de técnicas de análise fatorial na redução de dados e regressão linear múltipla para testar as cinco hipóteses oriundas do problema de pesquisa. Os resultados obtidos evidenciaram que a percepção dos servidores sobre os valores morais professados no Código de Ética e o conhecimento deles sobre o Código influenciam a percepção sobre o seu valor como auxiliar na resolução de dilemas éticos. Os resultados também sugerem que o servidor municipal percebe, em um nível baixo, o compromisso da Administração com o código.

Nonparametric Bayesian sparse factor models with application to gene expression modeling

A nonparametric Bayesian extension of Factor Analysis (FA) is proposed where observed data $\mathbf{Y}$ is modeled as a linear superposition, $\mathbf{G}$, of a potentially infinite number of hidden factors, $\mathbf{X}$. The Indian Buffet Process (IBP) is used as a prior on $\mathbf{G}$ to incorporate sparsity and to allow the number of latent features to be inferred. The model's utility for modeling gene expression data is investigated using randomly generated data sets based on a known sparse connectivity matrix for E. Coli, and on three biological data sets of increasing complexity.

The adoption of sustainable remediation behaviour in the US and UK: a cross country comparison and determinant analysis.

The sustainable remediation concept, aimed at maximizing the net environmental, social, and economic benefits in contaminated site remediation, is being increasingly recognized by industry, governments, and academia. However, there is limited understanding of actual sustainable behaviour being adopted and the determinants of such sustainable behaviour. The present study identified 27 sustainable practices in remediation. An online questionnaire survey was used to rank and compare them in the US (n=112) and the UK (n=54). The study also rated ten promoting factors, nine barriers, and 17 types of stakeholders' influences. Subsequently, factor analysis and general linear models were used to determine the effects of internal characteristics (i.e. country, organizational characteristics, professional role, personal experience and belief) and external forces (i.e. promoting factors, barriers, and stakeholder influences). It was found that US and UK practitioners adopted many sustainable practices to similar extents. Both US and UK practitioners perceived the most effectively adopted sustainable practices to be reducing the risk to site workers, protecting groundwater and surface water, and reducing the risk to the local community. Comparing the two countries, we found that the US adopted innovative in-situ remediation more effectively; while the UK adopted reuse, recycling, and minimizing material usage more effectively. As for the overall determinants of sustainable remediation, the country of origin was found not to be a significant determinant. Instead, organizational policy was found to be the most important internal characteristic. It had a significant positive effect on reducing distant environmental impact, sustainable resource usage, and reducing remediation cost and time (p<0.01). Customer competitive pressure was found to be the most extensively significant external force. In comparison, perceived stakeholder influence, especially that of primary stakeholders (site owner, regulator, and primary consultant), did not appear to have as extensive a correlation with the adoption of sustainability as one would expect.

Development of a general internet attitude scale and internet self-efficacy scale

The measurement of users’ attitudes towards and confidence with using the Internet is an important yet poorly researched topic. Previous research has encountered issues that serve to obfuscate rather than clarify. Such issues include a lack of distinction between the terms ‘attitude’ and ‘self-efficacy’, the absence of a theoretical framework to measure each concept, and failure to follow well-established techniques for the measurement of both attitude and self-efficacy. Thus, the primary aim of this research was to develop two statistically reliable scales which independently measure attitudes towards the Internet and Internet self-efficacy. This research addressed the outlined issues by applying appropriate theoretical frameworks to each of the constructs under investigation. First, the well-known three component (affect, behaviour, cognition) model of attitudes was applied to previous Internet attitude statements. The scale was distributed to four large samples of participants. Exploratory factor analyses revealed four underlying factors in the scale: Internet Affect, Internet Exhilaration, Social Benefit of the Internet and Internet Detriment. The final scale contains 21 items, demonstrates excellent reliability and achieved excellent model fit in the confirmatory factor analysis. Second, Bandura’s (1997) model of self-efficacy was followed to develop a reliable measure of Internet self-efficacy. Data collected as part of this research suggests that there are ten main activities which individuals can carry out on the Internet. Preliminary analyses suggested that self-efficacy is confounded with previous experience; thus, individuals were invited to indicate how frequently they performed the listed Internet tasks in addition to rating their feelings of self-efficacy for each task. The scale was distributed to a sample of 841 participants. Results from the analyses suggest that the more frequently an individual performs an activity on the Internet, the higher their self-efficacy score for that activity. This suggests that frequency of use ought to be taken into account in individual’s self-efficacy scores to obtain a ‘true’ self-efficacy score for the individual. Thus, a formula was devised to incorporate participants’ previous experience of Internet tasks in their Internet self-efficacy scores. This formula was then used to obtain an overall Internet self-efficacy score for participants. Following the development of both scales, gender and age differences were explored in Internet attitudes and Internet self-efficacy scores. The analyses indicated that there were no gender differences between groups for Internet attitude or Internet self-efficacy scores. However, age group differences were identified for both attitudes and self-efficacy. Individuals aged 25-34 years achieved the highest scores on both the Internet attitude and Internet self-efficacy measures. Internet attitude and self-efficacy scores tended to decrease with age with older participants achieving lower scores on both measures than younger participants. It was also found that the more exposure individuals had to the Internet, the higher their Internet attitude and Internet self-efficacy scores. Examination of the relationship between attitude and self-efficacy found a significantly positive relationship between the two measures suggesting that the two constructs are related. Implication of such findings and directions for future research are outlined in detail in the Discussion section of this thesis.

Bayesian Gaussian Copula Factor Models for Mixed Data.

Gaussian factor models have proven widely useful for parsimoniously characterizing dependence in multivariate data. There is a rich literature on their extension to mixed categorical and continuous variables, using latent Gaussian variables or through generalized latent trait models acommodating measurements in the exponential family. However, when generalizing to non-Gaussian measured variables the latent variables typically influence both the dependence structure and the form of the marginal distributions, complicating interpretation and introducing artifacts. To address this problem we propose a novel class of Bayesian Gaussian copula factor models which decouple the latent factors from the marginal distributions. A semiparametric specification for the marginals based on the extended rank likelihood yields straightforward implementation and substantial computational gains. We provide new theoretical and empirical justifications for using this likelihood in Bayesian inference. We propose new default priors for the factor loadings and develop efficient parameter-expanded Gibbs sampling for posterior computation. The methods are evaluated through simulations and applied to a dataset in political science. The models in this paper are implemented in the R package bfa.

Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies.

BACKGROUND: Nonparametric Bayesian techniques have been developed recently to extend the sophistication of factor models, allowing one to infer the number of appropriate factors from the observed data. We consider such techniques for sparse factor analysis, with application to gene-expression data from three virus challenge studies. Particular attention is placed on employing the Beta Process (BP), the Indian Buffet Process (IBP), and related sparseness-promoting techniques to infer a proper number of factors. The posterior density function on the model parameters is computed using Gibbs sampling and variational Bayesian (VB) analysis. RESULTS: Time-evolving gene-expression data are considered for respiratory syncytial virus (RSV), Rhino virus, and influenza, using blood samples from healthy human subjects. These data were acquired in three challenge studies, each executed after receiving institutional review board (IRB) approval from Duke University. Comparisons are made between several alternative means of per-forming nonparametric factor analysis on these data, with comparisons as well to sparse-PCA and Penalized Matrix Decomposition (PMD), closely related non-Bayesian approaches. CONCLUSIONS: Applying the Beta Process to the factor scores, or to the singular values of a pseudo-SVD construction, the proposed algorithms infer the number of factors in gene-expression data. For real data the "true" number of factors is unknown; in our simulations we consider a range of noise variances, and the proposed Bayesian models inferred the number of factors accurately relative to other methods in the literature, such as sparse-PCA and PMD. We have also identified a "pan-viral" factor of importance for each of the three viruses considered in this study. We have identified a set of genes associated with this pan-viral factor, of interest for early detection of such viruses based upon the host response, as quantified via gene-expression data.

Species diversity structure analysis at two sites in the tropical rain forest of Sumatra

Data from a hilly forest study site at Batang Ule, Sumatra, are organized into 30 100-m × 10-m subplots lying perpendicular to the line of maximal topographic gradient, from the valley to the plateau/ridge. The following methodological question is addressed: what species diversity measures are best used in order to reveal the ecologically distinct regions in the site. The main tool used to answer this question is the α-diversity curve (Hα). Graphical examination of tree and species densities, and α-diversity curves identifies an anomalous species diversity behaviour of the ‘ridge above the slope’ subplots which may have implications on land-facet class definitions. Factor analysis of the α-diversity curves indicates that the diversity space is two-dimensional: i.e. two diversity measures are sufficient to characterize the site; the species density (H0), and the Berger-Parker index (H[infty infinity]). In the two-dimensional diversity-space three distinct species diversity groups are found which relate to the topographic gradient at the Batang Ule site. The results are compared with those for a flat homogeneous site at Pasirmayang, Sumatra. The implications of the results on land-classifications in species-diversity mapping and conservation strategy are discussed.

Investigation of the permeation of model formulations and a commercial ibuprofen formulation in Carbosil® and human skin using ATR-FTIR and multivariate spectral analysis

The purpose of the present study was to use attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) and target factor analysis (TFA) to investigate the permeation of model drugs and formulation components through Carbosil® membrane and human skin. Diffusion studies of saturated solutions in 50:50 water/ethanol of methyl paraben (MP), ibuprofen (IBU) and caffeine (CF) were performed on Carbosil® membrane. The spectroscopic data were analysed by target factor analysis, and evolution profiles of the signal for each component (i.e. the drug, water, ethanol and membrane) over time were obtained. Results showed that the data were successfully deconvoluted as correlations between factors from the data and reference spectra of the components, were above 0.8 in all cases. Good reproducibility over three runs for the evolution profiles was obtained. From the evolution profiles it was observed that water diffused better through the Carbosil® membrane than ethanol, confirming the hydrophilic properties of the Carbosil® membrane used. IBU diffused slower compared with MP and CF. The evolution profile of CF was very similar to that of water, probably because of the high solubility of CF in water, indicating that both compounds are diffusing concurrently. The second part of the work involved a study of the evolution profiles of the components of a commercial topical gel containing 5% (w/w) of ibuprofen as it permeated through human skin. Although the system was much more complex, data were still successfully deconvoluted and the different components of the formulation identified except for benzyl alcohol which might be attributed to the low concentrations of benzyl alcohol used in topical formulations. (C) 2009 Elsevier B.V. All rights reserved.

Expression of vascular endothelial growth factor (VEGF) and its receptors is regulated in eyes with intra-ocular tumours

The immunolocalization and gene expression of vascular endothelial growth factor (VEGF) and its cognate tyrosine kinase receptors, Flt-1 and KDR, has been studied in ocular melanomas and retinoblastomas using in situ hybridization and immunohistochemistry. Tumour-related alterations in VEGF/VEGF-receptor expression have also been examined in separate and uninvolved iris, retina and choroid of the same eyes. Although VEGF immunoreactivity in the normal retina was virtually absent, low-level VEGF expression was evident in the ganglion cell-bodies, Müller cells and in a distinct population of amacrine cells. VEGF gene expression was absent in the iris and choroid of normal eyes. In tumour-bearing eyes, high levels of VEGF protein and gene expression were observed within the vascularized regions of the tumours, while the adjacent retina and choroid showed increased VEGF levels when compared with normals. Flt-1 and KDR gene expression and immunolocalization occurred in VEGF-expressing ganglion, Müller and amacrine cells in normal eyes. Within the intra-ocular tumours, VEGF-receptor gene expression and protein was evident in the endothelial cells and also in cells close to the vessels, while in the adjacent retina, Flt-1 and KDR levels were elevated over normal, especially in the blood vessels. Flt-1 and KDR were both observed at elevated levels in the choroid and iris blood vessels. This study suggests that VEGF, Flt-1 and KDR are expressed by neural, glial and vascular elements within normal human retina. Intra-ocular tumours demonstrate a high level of VEGF and VEGF-receptor expression; within uninvolved, spatially separate retina, choroid and iris in the same eyes, expression is also elevated, especially within the vasculature. Retinal vascular endothelia may respond to high intra-ocular levels of VEGF by increasing expression of their VEGF receptors, a phenomenon which could have relevance to neoplasm-related ocular neovascularization.

Adaptation of a questionnaire to assess the epistemological beliefs of mathematics in secondary school teachers

The objective of the study is to determine the psychometric properties of the Epistemological Beliefs Questionnaire on Mathematics. 171 Secondary School Mathematics Teachers of the Central Region of Cuba participated. The results show acceptable internal consistency. The factorial structure of the scale revealed three major factors, consistent with the Model of the Three Constructs: beliefs about knowledge, about learning and teaching. Irregular levels in the development of the epistemological belief system about mathematics of these teachers were shown, with a tendency among naivety and sophistication poles. In conclusion, the questionnaire is useful for evaluating teacher’s beliefs about mathematics.