This thesis argues that General Abdul Haris Nasution, the most influential military strategist that Indonesia has produced, developed an elective affinity between his strategies for 'people�s resistance' and an organicist vision of the proper relations between the state (including the military) and society that led to the Indonesian Army�s formulation of a unique, pervasive and highly durable means of military intervention in politics, the economy and society. Organicism is a stream of political thinking that views state and society as a single organic unity. Corporatist / functional modes of interest representation are often associated with organicist thinking. Nasution�s 'people�s resistance' strategies emerged during the armed struggle for national independence (from the Dutch) in the second half of the 1940s. The thesis argues that unlike the 'people�s war' strategies that emanated from the political left at roughly the same time, Nasution�s concepts were designed to uphold organic 'traditional' authority structures and depoliticise the national struggle. Associated with these strategies was a system of territorial commands that shadowed and supervised the aristocratically led civilian administration. The form of military intervention that grew out of this elective affinity reached its peak during the New Order regime of former President Suharto (1966 � 1998), when the army used its 'people�s resistance' doctrines and their associated territorial commands to control the population and the regime championed state-sanctioned corporatist / functional modes of interest representation. The identification of this elective affinity is a major point of departure from previous political biographies of Nasution. Another is the emphasis placed on Nasution�s family and personal life, particularly in the early chapters. This thesis explains how personal and family influences encouraged Nasution towards organicist thinking. It identifies how, in the early 1950s, Nasution idealised his 'people�s resistance' strategies and the support given to him during the armed struggle by organic 'traditional' authority figures. It shows how Nasution�s elective affinity between organicist thinking and 'people�s resistance' infused the interventionist doctrines that the army began to develop in the mid-to-late 1950s. In recent years the Indonesian Army has distanced itself from corporatist / functional forms of interest representation and has largely retreated from an active involvement in politics. Nevertheless, the thesis identifies a continuing adherence within the Army leadership to Nasution�s system of territorial commands and concepts of 'people�s resistance' that cannot readily be reconciled with democratic processes.

Oestrogens are produced by aromatisation of androgens by the aromatase enzyme. In the vertebrate brain this synthesis has vital functions in nerve protection, cell proliferation and nerve development during injury respectively brain development. Brain oestrogens are also crucial in activating certain reproductive and aggressive behaviours in mammals and birds. Teleosts have remarkably high activity of brain aromatase (bAA) compared to mammals and birds; 100-1000 times higher in brain regions like the hypothalamus, pre-optic area and optic tectum. The role of brain oestrogens in teleost behaviour is, however, less clear than in e.g. songbirds and rodents. This thesis studies the potential role of brain aromatase and brain oestrogens in the reproductive behaviour of the guppy male (Poecilia reticulata), how guppy brain aromatase responds to steroids and is distributed in the adult brain. The thesis shows that male behaviour can be affected by brain aromatase. Reduction of bAA by aromatase inhibitor treatment reduced the sexual behaviours sigmoid display and gonopodium swinging (I) and oestrogen receptor blocking with an oestrogen antagonist reduced the number of successful mating attempts (II). The anatomical study (IV) showed that brain aromatase is distributed in areas of the adult guppy brain that are connected to reproductive control and behaviour in vertebrates. Guppy bAA is stimulated by both androgens and oestrogens (III) but is more sensitive to oestrogens, especially in males, and could thus be used as an indicator of endocrine disruption at low concentrations found in the environment. The thesis can also conclude that females possess more brain aromatase than males, and that although it is expressed in the same pattern throughout the brain in both genders the enzymatic activity is differently distributed between the sexes. / Aromatase and androgens in fish reproductive behaviour

No description available.

Hypoxia is frequently detected during summer in Corpus Christi Bay, Texas, and causes significant harm to benthic organism population and diversity. Hypoxia is associated with the density stratification in the Bay but the cause of stratification is uncertain. To support the study of hypoxia and stratification, a cyberinfrastructure based on the CUAHSI (Consortium of Universities for the Advancement of Hydrologic Science, Inc) Hydrologic Information System (HIS) is implemented. HIS unites the sensor networks in the Bay by providing a standard data language and protocol for transferring data. Thus hypoxia-related data from multiple sources can be compiled into a structured database. In Corpus Christi Bay, salinity data collected from many locations and times are synthesized into a three-dimensional space-time continuum using geostatistical methods. The three dimensions are the depth, the distance along a transect line, and time. The kriged salinity concentration in space and time illuminates the pattern of movement of a saline gravity current along the bottom of the Bay. The travel time of a gravity current in the Bay is estimated to be on the order of one week and the speed is on the order of 1 km per day. Statistical study of high-resolution wind data shows that the stratification pattern in the Bay is related to the occurrence of strong, southeasterly winds in the 5 days prior to the observation. This relationship supports the hypothesis that stratification is caused by the wind initiating hypersaline gravity currents which flow from Laguna Madre into Corpus Christi Bay. An empirical physical hypoxia model is created that tracks the fate and transport of the gravity currents. The model uses wind and water quality data from real-time sensors published by HIS to predict the extent and duration of hypoxic regions in the Bay. Comparison of model results with historical data from 2005 to 2008 shows that wind-driven gravity currents can explain the spatially heterogeneous patterns of hypoxic zones in Corpus Christi Bay. / text

To determine the relationship between the abundance and density of benthic invertebrates, and the critical shear stress of individual grain sizes, a reach along Smith Creek, was divided into ten 2m x 2m quadrants. Within each quadrant, five randomly selected clasts for each grain size ranging from 2.26 to 25.6 cm were cleaned for benthic invertebrates. Wolman pebble counts for each quadrant were also conducted and used to determine the critical Shields stress per grain size fraction from the model given by Wiberg and Smith (1987) that explicitly accounts for particle hiding/sheltering effects in mixed-bed rivers. Particle entrainment values were then compared with estimated bankfull Shields stress values to determine sediment transport potential during bankfull flow. Invertebrate abundance was strongly positively correlated with critical Shields stress up to the 18.0 cm grain size, indicating a preference for certain grain sizes; while density was positively correlated with all grain sizes present.

A current trend in biological science is the increased use of computational tools for both the production and analysis of experimental data. This is especially true in the field of genomics, where advancements in DNA sequencing technology have dramatically decreased the time and cost associated with DNA sequencing resulting in increased pressure on the time required to prepare and analyze data generated during these experiments. As a result, the role of computational science in such biological research is increasing. This thesis seeks to address several major questions with respect to the development and application of single nucleotide polymorphism (SNP) resources in non-model organisms. Traditional SNP discovery using polymerase chain reaction (PCR) amplification and low-throughput DNA sequencing is a time consuming and laborious process, which is often limited by the time required to design intron-spanning PCR primers. While next-generation DNA sequencing (NGS) has largely supplanted low-throughput sequencing for SNP discovery applications, the PCR based SNP discovery method remains in use for cost effective, targeted SNP discovery. This thesis seeks to develop an automated method for intron-spanning PCR design which would remove a significant bottleneck in this process. This work develops algorithms for combining SNP data from multiple individuals, independent of the DNA sequencing platforms, for the purpose of developing SNP genotyping arrays. Additionally, tools for the filtering and selection of SNPs will be developed, providing start to finish support for the development of SNP genotyping arrays in complex polyploids using NGS. The result of this work includes two automated pipelines for the design of intron-spanning PCR primers, one which designs a single primer pair per target and another that designs multiple primer pairs per target. These automated pipelines are shown to reduce the time required to design primers from one hour per primer pair using the semi-automated method to 10 minutes per 100 primer pairs while maintaining a very high efficacy. Efficacy is tested by comparing the number of successful PCR amplifications of the semi- automated method with that of the automated pipelines. Using the Chi-squared test, the semi-automated and automated approaches are determined not to differ in efficacy. Three algorithms for combining SNP output from NGS data from multiple individuals are developed and evaluated for their time and space complexities. These algorithms were found to be computationally efficient, requiring time and space linear to the size of the input. These algorithms are then implemented in the Perl language and their time and memory performance profiled using experimental data. Profiling results are evaluated by applying linear models, which allow for predictions of resource requirements for various input sizes. Additional tools for the filtering of SNPs and selection of SNPs for a SNP array are developed and applied to the creation of two SNP arrays in the polyploid crop Brassica napus. These arrays, when compared to arrays in similar species, show higher numbers of polymorphic markers and better 3-cluster genotype separation, a viable method for determining the efficacy of design in complex genomes.

Eliminative materialism is a view that has been sparsely acknowledged and often overlooked when it comes to providing us with a criterion of what it takes for you and me to persist over time. This owes much to its counterintuitive belief in the non-existence of folk-psychological notions, such as persons. Against a backdrop of philosophical and scientific inquiry, this paper amounts to providing such a criterion in the form of f-organisms, taking a different route based on emergent descriptions, instead of conventional reductive explanations. The temporal plasticity (change over time) of such f-organisms display stable persistence conditions despite their constant state of reconstruction. What informs the question of identity in such a paradigm is dealt with accordingly, and the notion of the self is put in a context in which it can no longer be said to be the self we are familiar with – a context in which the center fails to hold. The imperative question for any of such criteria will be to accommodate the concept of identity as unconstrained and far away from uncertainty as possible. The main theme will thus be to reassess the general notion of diachronic identity to include our identity over time, and make explicit the various implications for such a view.

Thesis (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2005. / Not embargoed. Vita. References located at the end of each chapter.

Nous avons l’habitude de penser que l’organisme pluricellulaire, comme un certain homme et un certain cheval, est un modèle de l’individu. Toutefois, la philosophie contemporaine des sciences de la vie propose un certain nombre de définitions de l’individualité biologique qui provoquent des débats sans fin. Nous proposons une analyse historique des modifications de la notion d’individu qui ne vise pas à régler les débats, mais à comprendre la diversité des pensées portant sur cette notion. Nous commençons par analyser la découverte de la régénération du polype d’eau douce, faite au milieu du XVIIIe siècle par Abraham Trembley. Nous arrivons à mettre en lumière la rénovation philosophique effectuée au début de XXe siècle par Henri Bergson. L’histoire de la notion d’individu biologique présente des pensées qui transforment l’évidence en problématique. L’invention et la réinterprétation des concepts biologiques comme l’organisme, la cellule, la division du travail, le milieu, la sélection naturelle et la vie, permettent à la pensée biologique de remettre en cause la définition étymologique du terme d’individu, l’identification de l’individu et de l’organisme et la possibilité même de déterminer le niveau d’organisation correspondant à l’individu. La pluralité des concepts d’individu ne signifie pas qu’il faille renoncer à l’usage du terme en biologie. Au contraire, elle permet de mettre au jour l’ontologie impliquée dans les théories biologiques pour poser en termes précis les problèmes biologiques et philosophiques. La pensée de l’individualité biologique ouvre un vaste champ de recherche où les philosophes et les biologistes ont à travailler ensemble. / From a commonsense perspective, the multicellular organisms such as men and horses are thought of as typical examples of biological individuals. But contemporary philosophers of biology present a number of definitions of biological individuality which stimulate an intense debate over deciding the level of organization to which the biological individuality corresponds. This research proposes a historical analysis, which doesn’t aim to solve the conceptual issues, but to understand the diversity of biological thinking about individuality. From the regeneration of the polyp discovered by Abraham Trembley in the middle of the 18th century to the philosophical renovation achieved by Henri Bergson at the beginning of the 20th century, the biological thinking called into question the basis on which the notion of biological individuality was built. The invention and the reinterpretation of the concepts such as the organism, the cell, the division of labor, the milieu, the natural selection and the life, allowed to ask if the biological individuality can be defined as indivisibility, secondly if it can be identified with the organism, and finally if one can determine the level of organization to which the biological individuality corresponds. The diversity of concepts of biological individuality doesn’t mean that this term is dispensable for the biological research. It allows to present the biological and philosophical problems in more precise terms, so that the biologists and philosophers can cooperate to tackle them.

Resumo: Na descrição hierárquica do conhecimento biológico, o ser vivo é considerado como ponto central nas relações engendradas pelos seguintes níveis: ambiente externo (ecológico/evolutivo), organismo e ambiente interno (genético/ molecular). O organismo compreendido como nível focal da discussão biológica pode ressaltar a autonomia da Biologia em relação às outras áreas do conhecimento científico. No contexto do ensino, assume-se que as discussões epistemológicas do conhecimento biológico podem promover uma compreensão mais integrada dos fenômenos biológicos. Assim, organizou-se um grupo de pesquisa com graduandos de um curso de Ciências Biológicas para discutir conceitos centrais do conhecimento biológico, entre eles, o conceito de organismo. Esta pesquisa teve como objetivos: 1) Elaborar uma caracterização do conceito de organismo, partindo de uma abordagem hierárquica, integrando as discussões advindas da Filosofia da Biologia contemporânea referentes aos conceitos de auto-organização, autonomia agencial, propriedades emergentes e níveis hierárquicos; 2) Analisar como o conceito de organismo se impõe frente às explicações de vida presentes na literatura contemporânea da Filosofia da Biologia; 3) Utilizar a discussão teórica relativa ao conceito de organismo como fundamentação de um grupo de "Pesquisas em Epistemologia da Biologia", verificando as contribuições desse aporte teórico para a formação de alunos de Licenciatura em Ciências Biológicas na área de Epistemologia da Biologia e Ensino de Ciências; 4) Analisar as discussões e produções escritas ocorridas no desenvolvimento do grupo de "Pesquisas em Epistemologia da Biologia" que abordaram o conceito de organismo, com a finalidade de verificar se uma abordagem hierárquica tendo o organismo como nível focal contribui para uma visão integrada do conhecimento biológico pelos... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: In the hierarchical of biological knowledge, the living being could be considered as central point in the relations produced by three levels: external environment (ecological/evolution), organism and environment intern (genetic/molecular). The comprehension of the organism as a focal level in the biological debate can underline the autonomy of Biology among the other areas of the scientific knowledge. In the education context it is assumed that the epistemological discussions of the biological knowledge can promote an integrated understanding of the biological phenomena. Thus, a research group consisting of Biological Sciences undergraduates was organized to debate central concepts of the biological knowledge in which the discussions of the organism concept are included. This research aimed to: 1) develop a characterization of the concept of organism from a hierarchical approach by integrating the resulting discussions from contemporary philosophy of biology that are related to the concepts of self-organization, autonomy agents, emergent properties and hierarchical levels; 2) to analyze how the concept of organism is placed in front of the explications of life in the contemporary literature of philosophy of biology; 3) to use the theoretical discussion on the concept of organism as fundamentation for a group of "Studies in Epistemology of Biology," noting the help of this theoretical contribution to the Biological Sciences students training in the Biology and Epistemology in Science Teaching; 4) to analyze discussions and written productions that occurred in the development of the 'Research in Epistemology of Biology's group which addressed the concept the organism in order to verify if a hierarchical approach in which the organism is the focal level contributes to an integrated view of biological knowledge for biology students. On the basis of the theoretical referential... (Complete abstract click electronic access below) / Orientador: Ana Maria de Andrade Caldeira / Coorientador: Charbel Niño El-Hani / Banca: Fernando Bastos / Banca: Maurício de Carvalho Ramos / Banca: Luzia Marta Bellini / Banca: Marcelo Carbone Carneiro / Doutor