Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis

Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes. Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.

Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis

Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes, Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.

Comparison of pollinators and natural enemies: a meta-analysis of landscape and local effects on abundance and richness in crops

To manage agroecosystems for multiple ecosystem services, we need to know whether the management of one service has positive, negative, or no effects on other services. We do not yet have data on the interactions between pollination and pest-control services. However, we do have data on the distributions of pollinators and natural enemies in agroecosystems. Therefore, we compared these two groups of ecosystem service providers, to see if the management of farms and agricultural landscapes might have similar effects on the abundance and richness of both. In a meta-analysis, we compared 46 studies that sampled bees, predatory beetles, parasitic wasps, and spiders in fields, orchards, or vineyards of food crops. These studies used the proximity or proportion of non-crop or natural habitats in the landscapes surrounding these crops (a measure of landscape complexity), or the proximity or diversity of non-crop plants in the margins of these crops (a measure of local complexity), to explain the abundance or richness of these beneficial arthropods. Compositional complexity at both landscape and local scales had positive effects on both pollinators and natural enemies, but different effects on different taxa. Effects on bees and spiders were significantly positive, but effects on parasitoids and predatory beetles (mostly Carabidae and Staphylinidae) were inconclusive. Landscape complexity had significantly stronger effects on bees than it did on predatory beetles and significantly stronger effects in non-woody rather than in woody crops. Effects on richness were significantly stronger than effects on abundance, but possibly only for spiders. This abundance-richness difference might be caused by differences between generalists and specialists, or between arthropods that depend on non-crop habitats (ecotone species and dispersers) and those that do not (cultural species). We call this the ‘specialist-generalist’ or ‘cultural difference’ mechanism. If complexity has stronger effects on richness than abundance, it might have stronger effects on the stability than the magnitude of these arthropod-mediated ecosystem services. We conclude that some pollinators and natural enemies seem to have compatible responses to complexity, and it might be possible to manage agroecosystems for the benefit of both. However, too few studies have compared the two, and so we cannot yet conclude that there are no negative interactions between pollinators and natural enemies, and no trade-offs between pollination and pest-control services. Therefore, we suggest a framework for future research to bridge these gaps in our knowledge.

Comparative analysis of strut-and-tie models using Smooth Evolutionary Structural Optimization

The strut-and-tie models are widely used in certain types of structural elements in reinforced concrete and in regions with complexity of the stress state, called regions D, where the distribution of deformations in the cross section is not linear. This paper introduces a numerical technique to determine the strut-and-tie models using a variant of the classical Evolutionary Structural Optimization, which is called Smooth Evolutionary Structural Optimization. The basic idea of this technique is to identify the numerical flow of stresses generated in the structure, setting out in more technical and rational members of strut-and-tie, and to quantify their value for future structural design. This paper presents an index performance based on the evolutionary topology optimization method for automatically generating optimal strut-and-tie models in reinforced concrete structures with stress constraints. In the proposed approach, the element with the lowest Von Mises stress is calculated for element removal, while a performance index is used to monitor the evolutionary optimization process. Thus, a comparative analysis of the strut-and-tie models for beams is proposed with the presentation of examples from the literature that demonstrates the efficiency of this formulation. © 2013 Elsevier Ltd.

Comparative analysis of circular and triangular gold nanodisks for field enhancement applications

ABSTRACT: In this paper, we present a quantitative comparison of circular and triangular gold nanodisks with the same length and thickness. The method of moments is used to solve numerically the scattering problem. With this model, we investigate the spatial near field distribution, spectral response, far field diagrams, and bandwidth wavelength of these particles. Our results show that the resonant wavelength and the near field enhancement and confinement of the triangular particle are larger than those for the circular particle, but the resonance bandwidth and scattering cross section of the triangular particle are smaller.

Analysis of dispersive and dissipative media with optical resonances

In this paper we analyze the problem of light-matter interaction when absorptive resonances are imbedded in the material dispersion. We apply an improved approach to aluminum (Al) in the optical frequency range to investigate the impact of these resonances on the operating characteristics of Al-based nanoscale devices. Quantities such as group velocity, stored energy density, and energy velocity, normally obtained using a single resonance model [Wave Propagation and Group Velocity (Academic Press, 1960), Nat. Mater. 11, 208 (2012)], are now accurately calculated regardless of the medium adopted. We adapt the Loudon approach [Nat. Mater. 11, 208 (2012)] to media with several optical resonances and present the details of the extended model. We also show pertinent results for Al-based metal-dielectric-metal (MDM) waveguides, around spectral resonances. The model delineated here can be applied readily to any metal accurately characterized by Drude-Lorentz spectral resonance features. (C) 2012 Optical Society of America

Institutional Processes and Discursive Strategies: Rhetoric and Vocabulary Analysis of CSR and Sustainability

The candidate tackled an important issue in contemporary management: the role of CSR and Sustainability. The research proposal focused on a longitudinal and inductive research, directed to specify the evolution of CSR and contribute to the new institutional theory, in particular institutional work framework, and to the relation between institutions and discourse analysis. The documental analysis covers all the evolution of CSR, focusing also on a number of important networks and associations. Some of the methodologies employed in the thesis have been employed as a consequence of data analysis, in a truly inductive research process. The thesis is composed by two section. The first section mainly describes the research process and the analyses results. The candidates employed several research methods: a longitudinal content analysis of documents, a vocabulary research with statistical metrics as cluster analysis and factor analysis, a rhetorical analysis of justifications. The second section puts in relation the analysis results with theoretical frameworks and contributions. The candidate confronted with several frameworks: Actor-Network-Theory, Institutional work and Boundary Work, Institutional Logic. Chapters are focused on different issues: a historical reconstruction of CSR; a reflection about symbolic adoption of recurrent labels; two case studies of Italian networks, in order to confront institutional and boundary works; a theoretical model of institutional change based on contradiction and institutional complexity; the application of the model to CSR and Sustainability, proposing Sustainability as a possible institutional logic.

Essays on the Empirical Analysis of Economic and Political Development in Sub-Saharan Africa

In Sub-Saharan Africa, non-democratic events, like civil wars and coup d'etat, destroy economic development. This study investigates both domestic and spatial effects on the likelihood of civil wars and coup d'etat. To civil wars, an increase of income growth is one of common research conclusions to stop wars. This study adds a concern on ethnic fractionalization. IV-2SLS is applied to overcome causality problem. The findings document that income growth is significant to reduce number and degree of violence in high ethnic fractionalized countries, otherwise they are trade-off. Income growth reduces amount of wars, but increases its violent level, in the countries with few large ethnic groups. Promoting growth should consider ethnic composition. This study also investigates the clustering and contagion of civil wars using spatial panel data models. Onset, incidence and end of civil conflicts spread across the network of neighboring countries while peace, the end of conflicts, diffuse only with the nearest neighbor. There is an evidence of indirect links from neighboring income growth, without too much inequality, to reduce the likelihood of civil wars. To coup d'etat, this study revisits its diffusion for both all types of coups and only successful ones. The results find an existence of both domestic and spatial determinants in different periods. Domestic income growth plays major role to reduce the likelihood of coup before cold war ends, while spatial effects do negative afterward. Results on probability to succeed coup are similar. After cold war ends, international organisations seriously promote democracy with pressure against coup d'etat, and it seems to be effective. In sum, this study indicates the role of domestic ethnic fractionalization and the spread of neighboring effects to the likelihood of non-democratic events in a country. Policy implementation should concern these factors.

NONLINEAR TUBE-FITTING FOR THE ANALYSIS OF ANATOMICAL AND FUNCTIONAL STRUCTURES

We are concerned with the estimation of the exterior surface of tube-shaped anatomical structures. This interest is motivated by two distinct scientific goals, one dealing with the distribution of HIV microbicide in the colon and the other with measuring degradation in white-matter tracts in the brain. Our problem is posed as the estimation of the support of a distribution in three dimensions from a sample from that distribution, possibly measured with error. We propose a novel tube-fitting algorithm to construct such estimators. Further, we conduct a simulation study to aid in the choice of a key parameter of the algorithm, and we test our algorithm with validation study tailored to the motivating data sets. Finally, we apply the tube-fitting algorithm to a colon image produced by single photon emission computed tomography (SPECT)and to a white-matter tract image produced using diffusion tensor `imaging (DTI).

Individual patient data meta-analysis of diagnostic and prognostic studies in obstetrics, gynaecology and reproductive medicine

BACKGROUND: In clinical practice a diagnosis is based on a combination of clinical history, physical examination and additional diagnostic tests. At present, studies on diagnostic research often report the accuracy of tests without taking into account the information already known from history and examination. Due to this lack of information, together with variations in design and quality of studies, conventional meta-analyses based on these studies will not show the accuracy of the tests in real practice. By using individual patient data (IPD) to perform meta-analyses, the accuracy of tests can be assessed in relation to other patient characteristics and allows the development or evaluation of diagnostic algorithms for individual patients. In this study we will examine these potential benefits in four clinical diagnostic problems in the field of gynaecology, obstetrics and reproductive medicine. METHODS/DESIGN: Based on earlier systematic reviews for each of the four clinical problems, studies are considered for inclusion. The first authors of the included studies will be invited to participate and share their original data. After assessment of validity and completeness the acquired datasets are merged. Based on these data, a series of analyses will be performed, including a systematic comparison of the results of the IPD meta-analysis with those of a conventional meta-analysis, development of multivariable models for clinical history alone and for the combination of history, physical examination and relevant diagnostic tests and development of clinical prediction rules for the individual patients. These will be made accessible for clinicians. DISCUSSION: The use of IPD meta-analysis will allow evaluating accuracy of diagnostic tests in relation to other relevant information. Ultimately, this could increase the efficiency of the diagnostic work-up, e.g. by reducing the need for invasive tests and/or improving the accuracy of the diagnostic workup. This study will assess whether these benefits of IPD meta-analysis over conventional meta-analysis can be exploited and will provide a framework for future IPD meta-analyses in diagnostic and prognostic research.

Dynamic analysis of payloads and structures with intermediate modal density

La necesidad de desarrollar técnicas para predecir la respuesta vibroacústica de estructuras espaciales lia ido ganando importancia en los últimos años. Las técnicas numéricas existentes en la actualidad son capaces de predecir de forma fiable el comportamiento vibroacústico de sistemas con altas o bajas densidades modales. Sin embargo, ambos rangos no siempre solapan lo que hace que sea necesario el desarrollo de métodos específicos para este rango, conocido como densidad modal media. Es en este rango, conocido también como media frecuencia, donde se centra la presente Tesis doctoral, debido a la carencia de métodos específicos para el cálculo de la respuesta vibroacústica. Para las estructuras estudiadas en este trabajo, los mencionados rangos de baja y alta densidad modal se corresponden, en general, con los rangos de baja y alta frecuencia, respectivamente. Los métodos numéricos que permiten obtener la respuesta vibroacústica para estos rangos de frecuencia están bien especificados. Para el rango de baja frecuencia se emplean técnicas deterministas, como el método de los Elementos Finitos, mientras que, para el rango de alta frecuencia las técnicas estadísticas son más utilizadas, como el Análisis Estadístico de la Energía. En el rango de medias frecuencias ninguno de estos métodos numéricos puede ser usado con suficiente precisión y, como consecuencia -a falta de propuestas más específicas- se han desarrollado métodos híbridos que combinan el uso de métodos de baja y alta frecuencia, intentando que cada uno supla las deficiencias del otro en este rango medio. Este trabajo propone dos soluciones diferentes para resolver el problema de la media frecuencia. El primero de ellos, denominado SHFL (del inglés Subsystem based High Frequency Limit procedure), propone un procedimiento multihíbrido en el cuál cada subestructura del sistema completo se modela empleando una técnica numérica diferente, dependiendo del rango de frecuencias de estudio. Con este propósito se introduce el concepto de límite de alta frecuencia de una subestructura, que marca el límite a partir del cual dicha subestructura tiene una densidad modal lo suficientemente alta como para ser modelada utilizando Análisis Estadístico de la Energía. Si la frecuencia de análisis es menor que el límite de alta frecuencia de la subestructura, ésta se modela utilizando Elementos Finitos. Mediante este método, el rango de media frecuencia se puede definir de una forma precisa, estando comprendido entre el menor y el mayor de los límites de alta frecuencia de las subestructuras que componen el sistema completo. Los resultados obtenidos mediante la aplicación de este método evidencian una mejora en la continuidad de la respuesta vibroacústica, mostrando una transición suave entre los rangos de baja y alta frecuencia. El segundo método propuesto se denomina HS-CMS (del inglés Hybrid Substructuring method based on Component Mode Synthesis). Este método se basa en la clasificación de la base modal de las subestructuras en conjuntos de modos globales (que afectan a todo o a varias partes del sistema) o locales (que afectan a una única subestructura), utilizando un método de Síntesis Modal de Componentes. De este modo es posible situar espacialmente los modos del sistema completo y estudiar el comportamiento del mismo desde el punto de vista de las subestructuras. De nuevo se emplea el concepto de límite de alta frecuencia de una subestructura para realizar la clasificación global/local de los modos en la misma. Mediante dicha clasificación se derivan las ecuaciones globales del movimiento, gobernadas por los modos globales, y en las que la influencia del conjunto de modos locales se introduce mediante modificaciones en las mismas (en su matriz dinámica de rigidez y en el vector de fuerzas). Las ecuaciones locales se resuelven empleando Análisis Estadístico de Energías. Sin embargo, este último será un modelo híbrido, en el cual se introduce la potencia adicional aportada por la presencia de los modos globales. El método ha sido probado para el cálculo de la respuesta de estructuras sometidas tanto a cargas estructurales como acústicas. Ambos métodos han sido probados inicialmente en estructuras sencillas para establecer las bases e hipótesis de aplicación. Posteriormente, se han aplicado a estructuras espaciales, como satélites y reflectores de antenas, mostrando buenos resultados, como se concluye de la comparación de las simulaciones y los datos experimentales medidos en ensayos, tanto estructurales como acústicos. Este trabajo abre un amplio campo de investigación a partir del cual es posible obtener metodologías precisas y eficientes para reproducir el comportamiento vibroacústico de sistemas en el rango de la media frecuencia. ABSTRACT Over the last years an increasing need of novel prediction techniques for vibroacoustic analysis of space structures has arisen. Current numerical techniques arc able to predict with enough accuracy the vibro-acoustic behaviour of systems with low and high modal densities. However, space structures are, in general, very complex and they present a range of frequencies in which a mixed behaviour exist. In such cases, the full system is composed of some sub-structures which has low modal density, while others present high modal density. This frequency range is known as the mid-frequency range and to develop methods for accurately describe the vibro-acoustic response in this frequency range is the scope of this dissertation. For the structures under study, the aforementioned low and high modal densities correspond with the low and high frequency ranges, respectively. For the low frequency range, deterministic techniques as the Finite Element Method (FEM) are used while, for the high frequency range statistical techniques, as the Statistical Energy Analysis (SEA), arc considered as more appropriate. In the mid-frequency range, where a mixed vibro-acoustic behaviour is expected, any of these numerical method can not be used with enough confidence level. As a consequence, it is usual to obtain an undetermined gap between low and high frequencies in the vibro-acoustic response function. This dissertation proposes two different solutions to the mid-frequency range problem. The first one, named as The Subsystem based High Frequency Limit (SHFL) procedure, proposes a multi-hybrid procedure in which each sub-structure of the full system is modelled with the appropriate modelling technique, depending on the frequency of study. With this purpose, the concept of high frequency limit of a sub-structure is introduced, marking out the limit above which a substructure has enough modal density to be modelled by SEA. For a certain analysis frequency, if it is lower than the high frequency limit of the sub-structure, the sub-structure is modelled through FEM and, if the frequency of analysis is higher than the high frequency limit, the sub-structure is modelled by SEA. The procedure leads to a number of hybrid models required to cover the medium frequency range, which is defined as the frequency range between the lowest substructure high frequency limit and the highest one. Using this procedure, the mid-frequency range can be define specifically so that, as a consequence, an improvement in the continuity of the vibro-acoustic response function is achieved, closing the undetermined gap between the low and high frequency ranges. The second proposed mid-frequency solution is the Hybrid Sub-structuring method based on Component Mode Synthesis (HS-CMS). The method adopts a partition scheme based on classifying the system modal basis into global and local sets of modes. This classification is performed by using a Component Mode Synthesis, in particular a Craig-Bampton transformation, in order to express the system modal base into the modal bases associated with each sub-structure. Then, each sub-structure modal base is classified into global and local set, fist ones associated with the long wavelength motion and second ones with the short wavelength motion. The high frequency limit of each sub-structure is used as frequency frontier between both sets of modes. From this classification, the equations of motion associated with global modes are derived, which include the interaction of local modes by means of corrections in the dynamic stiffness matrix and the force vector of the global problem. The local equations of motion are solved through SEA, where again interactions with global modes arc included through the inclusion of an additional input power into the SEA model. The method has been tested for the calculation of the response function of structures subjected to structural and acoustic loads. Both methods have been firstly tested in simple structures to establish their basis and main characteristics. Methods are also verified in space structures, as satellites and antenna reflectors, providing good results as it is concluded from the comparison with experimental results obtained in both, acoustic and structural load tests. This dissertation opens a wide field of research through which further studies could be performed to obtain efficient and accurate methodologies to appropriately reproduce the vibro-acoustic behaviour of complex systems in the mid-frequency range.

San Antonio Alcohol Safety Action Project - analytic study no. 5-6: analysis of PDE and rehabilitation. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Analysis of algorithms for finding all spanning trees of a graph.

"Supported in part by the following grants: US NSF GJ 217, US NSF GJ 812, and project BUILD."

CYP2D6: a global analysis of phenotypic and genotypic variation in search of radical cure of Plasmodium vivax malaria

Thesis (Master's)--University of Washington, 2016-06