Molecular analysis of evolutionary relationships of Phaseolus dumosus with the gene pool of common bean

Valuable genetic variation for bean breeding programs is held within the common bean secondary gene pool which consists of Phaseolus albescens, P. coccineus, P. costaricensis, and P. dumosus. However, the use of close relatives for bean improvement is limited due to the lack of knowledge about genetic variation and genetic plasticity of many of these species. Characterisation and analysis of the genetic diversity is necessary among beans' wild relatives; in addition, conflicting phylogenies and relationships need to be understood and a hypothesis of a hybrid origin of P. dumosus needs to be tested. This thesis research was orientated to generate information about the patterns of relationships among the common bean secondary gene pool, with particular focus on the species Phaseolus dumosus. This species displays a set of characteristics of agronomic interest, not only for the direct improvement of common bean but also as a source of valuable genes for adaptation to climate change. Here I undertake the first comprehensive study of the genetic diversity of P. dumosus as ascertained from both nuclear and chloroplast genome markers. A germplasm collection of the ancestral forms of P. dumosus together with wild, landrace and cultivar representatives of all other species of the common bean secondary gene pool, were used to analyse genetic diversity, phylogenetic relationships and structure of P. dumosus. Data on molecular variation was generated from sequences of cpDNA loci accD-psaI spacer, trnT-trnL spacer, trnL intron and rps14-psaB spacer and from the nrDNA the ITS region. A whole genome DArT array was developed and used for the genotyping of P. dumosus and its closes relatives. 4208 polymorphic markers were generated in the DArT array and from those, 742 markers presented a call rate >95% and zero discordance. DArT markers revealed a moderate genetic polymorphism among P. dumosus samples (13% of polymorphic loci), while P. coccineus presented the highest level of polymorphism (88% of polymorphic loci). At the cpDNA one ancestral haplotype was detected among all samples of all species in the secondary genepool. The ITS region of P. dumosus revealed high homogeneity and polymorphism bias to P. coccineus genome. Phylogenetic reconstructions made with Maximum likelihood and Bayesian methods confirmed previously reported discrepancies among the nuclear and chloroplast genomes of P. dumosus. The outline of relationships by hybridization networks displayed a considerable number of interactions within and between species. This research provides compelling evidence that P. dumosus arose from hybridisation between P. vulgaris and P. coccineus and confirms that P. costaricensis has likely been involved in the genesis or backcrossing events (or both) in the history of P. dumosus. The classification of the specie P. persistentus was analysed based on cpDNA and ITS sequences, the results found this species to be highly related to P. vulgaris but not too similar to P. leptostachyus as previously proposed. This research demonstrates that wild types of the secondary genepool carry a significant genetic variation which makes this a valuable genetic resource for common bean improvement. The DArT array generated in this research is a valuable resource for breeding programs since it has the potential to be used in several approaches including genotyping, discovery of novel traits, mapping and marker-trait associations. Efforts should be made to search for potential populations of P. persistentus and to increase the collection of new populations of P. dumosus, P. albescens and P. costaricensis that may provide valuable traits for introgression into common bean and other Phaseolus crops.

Formal Modeling and Analysis Techniques for High Level Petri Nets

Petri Nets are a formal, graphical and executable modeling technique for the specification and analysis of concurrent and distributed systems and have been widely applied in computer science and many other engineering disciplines. Low level Petri nets are simple and useful for modeling control flows but not powerful enough to define data and system functionality. High level Petri nets (HLPNs) have been developed to support data and functionality definitions, such as using complex structured data as tokens and algebraic expressions as transition formulas. Compared to low level Petri nets, HLPNs result in compact system models that are easier to be understood. Therefore, HLPNs are more useful in modeling complex systems. There are two issues in using HLPNs - modeling and analysis. Modeling concerns the abstracting and representing the systems under consideration using HLPNs, and analysis deals with effective ways study the behaviors and properties of the resulting HLPN models. In this dissertation, several modeling and analysis techniques for HLPNs are studied, which are integrated into a framework that is supported by a tool. For modeling, this framework integrates two formal languages: a type of HLPNs called Predicate Transition Net (PrT Net) is used to model a system's behavior and a first-order linear time temporal logic (FOLTL) to specify the system's properties. The main contribution of this dissertation with regard to modeling is to develop a software tool to support the formal modeling capabilities in this framework. For analysis, this framework combines three complementary techniques, simulation, explicit state model checking and bounded model checking (BMC). Simulation is a straightforward and speedy method, but only covers some execution paths in a HLPN model. Explicit state model checking covers all the execution paths but suffers from the state explosion problem. BMC is a tradeoff as it provides a certain level of coverage while more efficient than explicit state model checking. The main contribution of this dissertation with regard to analysis is adapting BMC to analyze HLPN models and integrating the three complementary analysis techniques in a software tool to support the formal analysis capabilities in this framework. The SAMTools developed for this framework in this dissertation integrates three tools: PIPE+ for HLPNs behavioral modeling and simulation, SAMAT for hierarchical structural modeling and property specification, and PIPE+Verifier for behavioral verification.

Quantifying and Modeling the Influence of Forest on the Magnitude and Duration of Mountain Snow Storage in the Pacific Northwest, USA

Thesis (Ph.D.)--University of Washington, 2016-08

Value and proportions of intangible assets : A comparison between the private- and the public sector

Organizations within the public- and the private sector have different aims with their accounting. Privately held organizations often have the intention to make profit, while authorities within the public sector aim to provide citizens with different services. The difference between these two sectors is also visible in the legislation, where International Accounting Standards Board set the standards for privately held organizations and Ekonomistyrningsverket do the same for the public sector. Because of the larger demand by the society for knowledge and technology, included in the category intangible assets, these are more emphasized in the accounting for organizations. Intangible assets are although linked with complexity which is associated with the measurement. The purpose of this study is therefore to see whether there are any existing differences in how to measure and value intangible assets and internally generated ones between listed companies in the private sector and authorities operating in the public sector. This study is conducted with both a qualitative and quantitative perspective. The data collected for this study is secondary, and is gathered through samples of annual reports from different companies in order to be representative for the whole population. The main results of this study is that there are differences in the measurement and valuation of intangible assets dependent on which sector an organization operates within and this is not due to the standards and regulations. The differences are visible in the percentage change in value of intangible assets since they fluctuate more heavily in the private sector than in the public sector. Simultaneously, the proportions of internally generated intangible assets compared to intangible assets in general differ between the two sectors.

Aspects of Land Take in the Metropolitan Area of Naples

Land take is a phenomenon of great concern nowadays because of the large number of its negative impacts regarding biological, economic and social balance. In Italy, the development of urban and other artificial land has been irreversibly transforming a nonrenewable resource such as soil, regardless the almost constant population rate, with different speed depending of the region considered. The aim of this paper is to analyze the phenomenon in the metropolitan area of Naples, which is an area highly affected by territorial aggression of human matrix. The data used are both by the Institute for Environmental Protection and Research (ISPRA) Report 2015 on the usage of the land and by ISTAT relating to the resident population up to the 1st of January 2015 and the extension of land for agricultural use (Census 2010). The mathematical combination of this data creates a new indicator that can be referred to as “residual land”; this residual area is of great extension with many different characteristics and it could represent the area where the phenomenon of land take most occurs. The identification, measurement and analysis of “residual land” provide new insights on the evolution of land take and this new indicator can represent a critical element to work on to prevent future land transformation and protect natural and agricultural areas within the Italian context.

Assessing a Methodological Proposal for the Design, Creation and Evaluation of Learning Objects Oriented to Educators with Diverse Educational and Technological Competencies

This paper describes a methodological proposal for the design, creation and evaluation of Learning Objects (LOs). This study arises from the compilation and analysis of several LO design methodologies currently used in Ibero-America. This proposal, which has been named DICREVOA, defines five different phases: analysis, design (instructional and multimedia), implementation (LO and metadata), evaluation (from the perspective of both the producer and the consumer of the LO), and publishing. The methodology focuses not only on the teaching inexperienced, but also on those having a basic understanding of the technological and educational aspects related to LO design; therefore, the study emphasizes LO design activities centered around the Kolb cycle and the use of the ExeLearning tool in order to implement the LO core. Additionally, DICREVOA was used in a case study, which demonstrates how it provides a feasible mechanism for LO design and implementation within different contexts. Finally, DICREVOA, the case study to which it was applied, and the results obtained are presented

Identification and characterisation of telomere regulatory and signalling pathways after induction of telomere dysfunction

Telomeres are DNA-protein complexes which cap the ends of eukaryotic linear chromosomes. In normal somatic cells telomeres shorten and become dysfunctional during ageing due to the DNA end replication problem. This leads to activation of signalling pathways that lead to cellular senescence and apoptosis. However, cancer cells typically bypass this barrier to immortalisation in order to proliferate indefinitely. Therefore enhancing our understanding of telomere dysfunction and pathways involved in regulation of the process is essential. However, the pathways involved are highly complex and involve interaction between a wide range of biological processes. Therefore understanding how telomerase dysfunction is regulated is a challenging task and requires a systems biology approach. In this study I have developed a novel methodology for visualisation and analysis of gene lists focusing on the network level rather than individual or small lists of genes. Application of this methodology to an expression data set and a gene methylation data set allowed me to enhance my understanding of the biology underlying a senescence inducing drug and the process of immortalisation respectively. I then used the methodology to compare the effect of genetic background on induction of telomere uncapping. Telomere uncapping was induced in HCT116 WT, p21-/- and p53-/- cells using a viral vector expressing a mutant variant of hTR, the telomerase RNA template. p21-/- cells showed enhanced sensitivity to telomere uncapping. Analysis of a candidate pathway, Mismatch Repair, revealed a role for the process in response to telomere uncapping and that induction of the pathway was p21 dependent. The methodology was then applied to analysis of the telomerase inhibitor GRN163L and synergistic effects of hypoglycaemia with this drug. HCT116 cells were resistant to GRN163L treatment. However, under hypoglycaemic conditions the dose required for ablation of telomerase activity was reduced significantly and telomere shortening was enhanced. Overall this new methodology has allowed our group and collaborators to identify new biology and improve our understanding of processes regulating telomere dysfunction.

Bioaccumulation and effects of TBT on molluscs from southern Portugal

Tese de dout. Ciências e Tecnologias do Ambiente, Faculdade de Ciências do Mar e do Ambiente, Univ. do Algarve, 2004

Tailored mesoporous silica nanoparticles for controlled drug delivery: platform fabrication, targeted delivery, and computational design and analysis

Mesoporous silica nanoparticles (MSNs) are exceptionally promising drug carriers for controlled drug delivery systems because their morphology, pore structure, pore volume and pore size can be well tailored to obtain certain drug release profiles. Moreover, they possess the ability to specifically transport and deliver anti-cancer drugs when targeting molecules are properly grafted onto their surface. MSNs based drug delivery systems have the potential to revolutionize cancer therapy. This review provides a comprehensive overview of the fabrication, modification of MSNs and their applications in tumour-targeted delivery. In addition, the characterization and analysis of MSNs with computer aided strategies were described. The existing issues and future prospective concerning the applications of MSNs as drug carriers for controlled drug delivery systems were discussed.

Computation and fabrication of scaled prototypes

The formal, functional, and material attributes of design are routinely investigated through the construction of physical models and scaled prototypes. With the increasing adoption of computational workflows, the digital to physical translation process is central to the construction of scaled prototypes. However, the choice of methods, tools and materials for computational prototyping is a developing area. Therefore a systematic body of knowledge on the benefits and costs of multiple methods of computational prototyping for the construction of physical prototypes need to be identified. This paper addresses the prototyping process through the comparison of three computational methods of fabrication through the modelling, analysis and construction of a Gaussian Vault. It reports on the process of digital to physical construction using additive manufacturing, surface fabrication and structural component models. The Gaussian Vault offers a unique set of geometric, structural and physical characteristics for testing all three methods of prototyping. The size, shape and proportion of vault prototypes are rapidly generated and tested. The design geometry, material properties and physical construction of the Gaussian Vault are realised using commonly used practice workflows comprising parametric modelling and analysis of geometry, model rationalisation with material characteristics and finally the use of digital fabrication methods. Comparison of the results identifies the characteristics, benefits and limitations of the three approaches. Finally the paper discusses the digital to physical translation processes and summarises the characteristics, benefits and issues encountered in each.

Control and Supervision of Wind Energy Conversion Systems

This paper is about a PhD thesis and includes the study and analysis of the performance of an onshore wind energy conversion system. First, mathematical models of a variable speed wind turbine with pitch control are studied, followed by the study of different controller types such as integer-order controllers, fractional-order controllers, fuzzy logic controllers, adaptive controllers and predictive controllers and the study of a supervisor based on finite state machines is also studied. The controllers are included in the lower level of a hierarchical structure composed by two levels whose objective is to control the electric output power around the rated power. The supervisor included at the higher level is based on finite state machines whose objective is to analyze the operational states according to the wind speed. The studied mathematical models are integrated into computer simulations for the wind energy conversion system and the obtained numerical results allow for the performance assessment of the system connected to the electric grid. The wind energy conversion system is composed by a variable speed wind turbine, a mechanical transmission system described by a two mass drive train, a gearbox, a doubly fed induction generator rotor and by a two level converter.

Social audit: A mess or means in CSR assessment?

Social Audits play an important role in the measurement and analysis of a company's social performance. They provide corporations with a tool to plan and manage their social responsibility activities. Similarly, they provide stakeholders with a tool which they could use when monitoring, assessing and analysing concrete and accurate company data. Whilst the topic of social audits has been raised and discussed by a number of scholars, industry representatives and government institutions over the years, such contributions have mostly revolved around the general notion and importance of social audit, rather than addressing the most effective ways to achieve a widespread and reliable adoption of the practice through the implementation of specific legal regulation and other methods. This matter is of significant importance as corporations can exert a considerable amount control over the entire social audit process, allowing them to disclose only information deemed beneficial to their own corporate image instead of releasing all relevant social and environmental data. In order to achieve a truly transparent system promoting corporate accountability, there is an obvious need for social audits to be regulated. One of the purposes of this book is to provide an overview of the development of social audit practices and regulation. It also sets out to explore the issues and challenges which have arisen relating to this matter around the world.

Medida socioeducativa de internação no Maranhão: uma visão de seus atores

O presente trabalho apresentado ao Programa de Pós-Graduação em Psicologia Social da Universidade do Estado do Rio de Janeiro (UERJ), no Curso de Doutorado Interinstitucional (DINTER) realizado em parceria com a Universidade Federal do Maranhão (UFMA), teve como proposta pesquisar a visão dos atores sociais envolvidos diretamente com a medida socioeducativa de internação no Maranhão. O objetivo da pesquisa foi identificar a visão dos atores sociais sobre aspectos relacionados ao processo de aplicação, execução e cumprimento da medida socioeducativa de privação de liberdade. Com o propósito de compreender a percepção das pessoas que atuam nas três etapas da medida socioeducativa de internação, realizou-se uma pesquisa de campo com três grupos sendo que, cada grupo foi representado por indivíduos que estavam vinculados a cada uma das etapas da referida medida. Os dados foram coletados por intermédio de entrevistas com os respectivos sujeitos, utilizando-se como apoio um roteiro semiestruturado, elaborado em consonância com os objetivos da pesquisa. Para categorização, dimensionamento e análise dos dados e dos registros do diário de campo utilizou-se a técnica de Análise de Conteúdo. Os resultados alcançados com a pesquisa proporcionam subsídios para uma reflexão sobre o processo e as condições em que se dão a execução e o cumprimento da medida socioeducativa de internação no Centro da Juventude Esperança (CJE) da Fundação da Criança e do Adolescente (FUNAC) no Maranhão (MA). Os resultados da pesquisa apontam para uma incongruência entre o que estabelece a Lei n 8.069/1990, que instituiu o Estatuto da Criança e do Adolescente (ECA), o que preconiza o Sistema Nacional de Atendimento Socioeducativo (SINASE) e o que, de fato tem sido efetivado pela unidade (CJE) de internação e execução da medida de privação de liberdade. Além destas questões, os resultados da pesquisa também indicam que o Sistema de Garantias de Direitos da Criança e do Adolescente (SGDCA), no Maranhão não vem funcionando em conformidade com os princípios e diretrizes previstos pelo ECA, cujo objetivo principal da medida socioeducativa de internação, abrangendo aspectos educativos, formativos e sociais, não estaria acontecendo no Estado do Maranhão.

Diretrizes para o planejamento de experimentos em jogos educacionais voltados para o ensino de Engenharia de Software

Jogos educacionais constituem em uma importante ferramenta de ensino na área de Engenharia de Software, onde, muitas vezes, os alunos não passam por nenhum mecanismo de treinamento prático. Um jogo educacional de qualidade tem que ter objetivos educacionais bem definidos, motivar os alunos e efetivar a aprendizagem dos conteúdos. A aplicação de jogos no Ensino de Engenharia de Software deve ser realizada de forma sistemática e controlada com base em avaliação. A técnica Estatística de Experimentação permite a medição e a análise das variáveis envolvidas no processo de aplicação de jogos para que estes possam ser aplicados com qualidade. Para definir melhor os experimentos no uso de jogos para o ensino de Engenharia de Software, este trabalho propõe diretrizes para o planejamento de experimentos em jogos educacionais, de forma que permita verificar a influência e a significância da utilização desses jogos no ensino e aprendizado dos conceitos de Engenharia de Software. Um experimento com o SimulES-W foi realizado seguindo essas diretrizes, onde foi possível ser demonstrada sua aplicabilidade e simplicidade em sua definição. A experiência de uso do SimulES-W mostra que aprender com jogos de computador é divertido, interativo e que, apesar dos resultados obtidos não serem significativos estatisticamente, de certa forma contribui para o ensino da Engenharia de Software, não sendo necessariamente um conhecimento prévio do conteúdo.

高塬沟壑区董志塬沟头溯源侵蚀典型调查研究

详细调查了董志塬地区的西峰区、宁县以及庆城县的沟头溯源侵蚀情况,并对近年来发生前进的沟头进行了详细的实地测量和地形地貌特点分析,对董志塬沟头溯源侵蚀整体情况做出概括。在此基础上将溯源侵蚀的发生类型划分:水力冲刷型、陷穴诱发型、裂缝诱发型和人为诱发型。针对每种类型进行了典型的实例分析。