The Costs of Ecosystem Adaptation: Methodology and Estimates for Indian Forests

34 p.

Functional evaluation of noncovalent interactions in neuroreceptors and progress toward the expansion of unnatural amino acid methodology

This dissertation primarily describes chemical-scale studies of G protein-coupled receptors and Cys-loop ligand-gated ion channels to better understand ligand binding interactions and the mechanism of channel activation using recently published crystal structures as a guide. These studies employ the use of unnatural amino acid mutagenesis and electrophysiology to measure subtle changes in receptor function.

In chapter 2, the role of a conserved aromatic microdomain predicted in the D3 dopamine receptor is probed in the closely related D2 and D4 dopamine receptors. This domain was found to act as a structural unit near the ligand binding site that is important for receptor function. The domain consists of several functionally important noncovalent interactions including hydrogen bond, aromatic-aromatic, and sulfur-π interactions that show strong couplings by mutant cycle analysis. We also assign an alternate interpretation for the linear fluorination plot observed at W6.48, a residue previously thought to participate in a cation-π interaction with dopamine.

Chapter 3 outlines attempts to incorporate chemically synthesized and in vitro acylated unnatural amino acids into mammalian cells. While our attempts were not successful, method optimizations and data for nonsense suppression with an in vivo acylated tRNA are included. This chapter is aimed to aid future researchers attempting unnatural amino acid mutagenesis in mammalian cells.

Chapter 4 identifies a cation-π interaction between glutamate and a tyrosine residue on loop C in the GluClβ receptor. Using the recently published crystal structure of the homologous GluClα receptor, other ligand-binding and protein-protein interactions are probed to determine the similarity between this invertebrate receptor and other more distantly related vertebrate Cys-loop receptors. We find that many of the interactions previously observed are conserved in the GluCl receptors, however care must be taken when extrapolating structural data.

Chapter 5 examines inherent properties of the GluClα receptor that are responsible for the observed glutamate insensitivity of the receptor. Chimera synthesis and mutagenesis reveal the C-terminal portion of the M4 helix and the C-terminus as contributing to formation of the decoupled state, where ligand binding is incapable of triggering channel gating. Receptor mutagenesis was unable to identify single residue mismatches or impaired protein-protein interactions within this domain. We conclude that M4 helix structure and/or membrane dynamics are likely the cause of ligand insensitivity in this receptor and that the M4 helix has an role important in the activation process.

The Uniform World Model: A Methodology for Predicting the Health Impacts of Air Pollution

47 p.

San Francisco : a city reinvented by creative innovation

The aim of this paper is to analyse the recent evolution of the city of San Francisco to outline the major features that have made it possible this continuing process of creative innovation in the city. In order to meet this objective, the project is framed around answering two key research questions: (1) what are the main economic and social elements that characterise urban change in the city of San Francisco and (2) which is the role of public strategies in the continuing economic success of San Francisco. The paper concludes that the successful performance of San Francisco is the result of the actions taken by many agents in the city, but the role of public authorities, especially the City and County, must be stressed, both through direct intervention and by coordinating, fostering and supporting the private and non-profit sectors. This is especially relevant in a country like the US where private initiative has been seen in many occasions as the greatest driver of economic and social success. Yet, the performance of San Francisco City cannot be explained without the role played by the public sector, in coordination with the civil society

Towards a standard methodology to evaluate internal cluster validity indices

The evaluation and comparison of internal cluster validity indices is a critical problem in the clustering area. The methodology used in most of the evaluations assumes that the clustering algorithms work correctly. We propose an alternative methodology that does not make this often false assumption. We compared 7 internal cluster validity indices with both methodologies and concluded that the results obtained with the proposed methodology are more representative of the actual capabilities of the compared indices.

Methodology of the Lake Victoria Fisheries Research Project's Co-management survey

In this book section, the theoretical background to the methodology is outlined, questionnaire development described, sample selection outlined and biases and shortcomings to the survey noted.

Record of a colloquium organised by IUBS on the methodology of radiation measurement under water. [Translation from: Mem. Inst. Ital. Idrobiol. 17, 57-79, 1964]

These minutes report on colloquium on the methodology of radiation measurement under water. The meeting was held on 3-5 January 1957, at the Biological Station, Lunz, Austria. The participants of the colloquium discussed various methodologies of radiation measurements, basic methods such as Secchi Disc and underwater photometer as well as specialist equipment like the absolute radiation apparatus.

NEW METHODOLOGY FOR FEEDER RECONFIGURATION IN DISTRIBUTION NETWORKS WITH DISTRIBUTED ENERGY RESOURCES

This doctoral Thesis defines and develops a new methodology for feeder reconfiguration in distribution networks with Distributed Energy Resources (DER). The proposed methodology is based on metaheuristic Ant Colony Optimization (ACO) algorithms. The methodology is called Item Oriented Ant System (IOAS) and the doctoral Thesis also defines three variations of the original methodology, Item Oriented Ant Colony System (IOACS), Item Oriented Max-min Ant System (IOMMAS) y Item Oriented Max-min Ant Colony System (IOACS). All methodologies pursue a twofold objective, to minimize the power losses and maximize DER penetration in distribution networks. The aim of the variations is to find the algorithm that adapts better to the present optimization problem, solving it most efficiently. The main feature of the methodology lies in the fact that the heuristic information and the exploitation information (pheromone) are attached to the item not to the path. Besides, the doctoral Thesis proposes to use feeder reconfiguration in order to increase the distribution network capacity of accepting a major degree of DER. The proposed methodology and its three variations have been tested and verified in two distribution networks well documented in the existing bibliography. These networks have been modeled and used to test all proposed methodologies for different scenarios with various DER penetration degrees.

Compliance verification methodology for renewable generation integration. Application to island power grids

261 p.

Application of Entropy and Fractal Dimension Analyses to the Pattern Recognition of Contaminated Fish Responses in Aquaculture

The objective of the work was to develop a non-invasive methodology for image acquisition, processing and nonlinear trajectory analysis of the collective fish response to a stochastic event. Object detection and motion estimation were performed by an optical flow algorithm in order to detect moving fish and simultaneously eliminate background, noise and artifacts. The Entropy and the Fractal Dimension (FD) of the trajectory followed by the centroids of the groups of fish were calculated using Shannon and permutation Entropy and the Katz, Higuchi and Katz-Castiglioni's FD algorithms respectively. The methodology was tested on three case groups of European sea bass (Dicentrarchus labrax), two of which were similar (C1 control and C2 tagged fish) and very different from the third (C3, tagged fish submerged in methylmercury contaminated water). The results indicate that Shannon entropy and Katz-Castiglioni were the most sensitive algorithms and proved to be promising tools for the non-invasive identification and quantification of differences in fish responses. In conclusion, we believe that this methodology has the potential to be embedded in online/real time architecture for contaminant monitoring programs in the aquaculture industry.

Apaf-1 Inhibitors Protect from Unwanted Cell Death in In Vivo Models of Kidney Ischemia and Chemotherapy Induced Ototoxicity

Background: Excessive apoptosis induces unwanted cell death and promotes pathological conditions. Drug discovery efforts aimed at decreasing apoptotic damage initially targeted the inhibition of effector caspases. Although such inhibitors were effective, safety problems led to slow pharmacological development. Therefore, apoptosis inhibition is still considered an unmet medical need. Methodology and Principal Findings: The interaction between Apaf-1 and the inhibitors was confirmed by NMR. Target specificity was evaluated in cellular models by siRNa based approaches. Cell recovery was confirmed by MTT, clonogenicity and flow cytometry assays. The efficiency of the compounds as antiapoptotic agents was tested in cellular and in vivo models of protection upon cisplatin induced ototoxicity in a zebrafish model and from hypoxia and reperfusion kidney damage in a rat model of hot ischemia. Conclusions: Apaf-1 inhibitors decreased Cytc release and apoptosome-mediated activation of procaspase-9 preventing cell and tissue damage in ex vivo experiments and in vivo animal models of apoptotic damage. Our results provide evidence that Apaf-1 pharmacological inhibition has therapeutic potential for the treatment of apoptosis-related diseases.