Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii

We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of noncharged polar amino acids, particularly Gin and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15degrees-98degreesC) were used to generate IIII modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gin, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60degreesC, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes. from psychrophiles to hyperthermophiles

Online Video as a Tool for Planning Education and Engagement: A Content Analysis of U.S. City Planning Departments’ YouTube Channels

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

Dynamic response: Real-time adaptation for music emotion

Music plays an enormous role in today's computer games; it serves to elicit emotion, generate interest and convey important information. Traditional gaming music is fixed at the event level, where tracks loop until a state change is triggered. This behaviour however does not reflect musically the in-game state between these events. We propose a dynamic music environment, where music tracks adjust in real-time to the emotion of the in-game state. We are looking to improve the affective response to symbolic music through the modification of structural and performative characteristics through the application of rule-based techniques. In this paper we undertake a multidiscipline approach, and present a series of primary music-emotion structural rules for implementation. The validity of these rules was tested in small study involving eleven participants, each listening to six permutations from two musical works. Preliminary results indicate that the environment was generally successful in influencing the emotion of the musical works for three of the intended four directions (happier, sadder & content/dreamier). Our secondary aim of establishing that the use of music-emotion rules, sourced predominantly from Western classical music, could be applied with comparable results to modern computer gaming music was also largely successfully.

Capabilities for strategic flexibility:a cognitive content framework

Different forms of strategic flexibility allow for reactive adaptation to different changing environments and the proactive driving of change. It is therefore becoming increasingly important for decision makers to not only possess marketing capabilities, but also the capabilities for strategic flexibility in its various forms. However, our knowledge of the relationships between decision makers’ different ways of thinking and their capabilities for strategic flexibility is limited. This limitation is constraining research and understanding. In this article we develop a theoretical cognitive content framework that postulates relationships between different ways of thinking about strategy and different information-processing demands. We then outline how the contrasting beliefs of decision makers may influence their capabilities to generate different hybrid forms of strategic flexibility at the cognitive level. Theoretically, the framework is embedded in resource-based theory, personal construct theory and schema theory. The implications for research and theory are discussed.

Meta level component-based framework for distributed computing applications

Adaptability for distributed object-oriented enterprise frameworks is a critical mission for system evolution. Today, building adaptive services is a complex task due to lack of adequate framework support in the distributed computing environment. In this thesis, we propose a Meta Level Component-Based Framework (MELC) which uses distributed computing design patterns as components to develop an adaptable pattern-oriented framework for distributed computing applications. We describe our novel approach of combining a meta architecture with a pattern-oriented framework, resulting in an adaptable framework which provides a mechanism to facilitate system evolution. The critical nature of distributed technologies requires frameworks to be adaptable. Our framework employs a meta architecture. It supports dynamic adaptation of feasible design decisions in the framework design space by specifying and coordinating meta-objects that represent various aspects within the distributed environment. The meta architecture in MELC framework can provide the adaptability for system evolution. This approach resolves the problem of dynamic adaptation in the framework, which is encountered in most distributed applications. The concept of using a meta architecture to produce an adaptable pattern-oriented framework for distributed computing applications is new and has not previously been explored in research. As the framework is adaptable, the proposed architecture of the pattern-oriented framework has the abilities to dynamically adapt new design patterns to address technical system issues in the domain of distributed computing and they can be woven together to shape the framework in future. We show how MELC can be used effectively to enable dynamic component integration and to separate system functionality from business functionality. We demonstrate how MELC provides an adaptable and dynamic run time environment using our system configuration and management utility. We also highlight how MELC will impose significant adaptability in system evolution through a prototype E-Bookshop application to assemble its business functions with distributed computing components at the meta level in MELC architecture. Our performance tests show that MELC does not entail prohibitive performance tradeoffs. The work to develop the MELC framework for distributed computing applications has emerged as a promising way to meet current and future challenges in the distributed environment.

Modulation of SERCA in the chronic phase of adjuvant arthritis as a possible adaptation mechanism of redox imbalance

Adjuvant arthritis (AA) is a condition that involves systemic oxidative stress. Unexpectedly, it was found that sarcoplasmic reticulum Ca2 +-ATPase (SERCA) activity was elevated in muscles of rats with AA compared to controls, suggesting possible conformational changes in the enzyme. There was no alteration in the nucleotide binding site but rather in the transmembrane domain according to the tryptophan polar/non-polar fluorescence ratio. Higher relative expression of SERCA, higher content of nitrotyrosine but no increase in phospholipid oxidation in AA SR was found. In vitro treatments of SR with HOCl showed that in AA animals SERCA activity was more susceptible to oxidative stress, but SR phospholipids were more resistant and SERCA could also be activated by phosphatidic acid. It was concluded that increased SERCA activity in AA was due to increased levels of SERCA protein and structural changes to the protein, probably induced by direct and specific oxidation involving reactive nitrogen species.

Demonstration of 10 Gbit/s transmission over 900 km SMF with <400 ns adaptation time using full-field EDC

This reported work significantly extends the reach of 10Gbit/s on-off keying singlemode fibre (SMF) transmission using full-field based electronic dispersion compensation (EDC) to 900 km. In addition, the EDC balances the complexity and the adaptation capability by employing a simple dispersive transmission line with static parameters for coarse dispersion compensation and 16-state maximum likelihood sequence estimation with Gaussian approximation based channel training for adaptive impairment trimming. Improved adaptation times of less than 400 ns for a bit error rate target of 10-3 over distances ranging from 0 to 900 km are reported.

Governance of open content creation:a conceptualization and analysis of control and guiding mechanisms in the open content domain

The open content creation process has proven itself to be a powerful and influential way of developing text-based content, as demonstrated by the success of Wikipedia and related sites. Distributed individuals independently edit, revise, or refine content, thereby creating knowledge artifacts of considerable breadth and quality. Our study explores the mechanisms that control and guide the content creation process and develops an understanding of open content governance. The repertory grid method is employed to systematically capture the experiences of individuals involved in the open content creation process and to determine the relative importance of the diverse control and guiding mechanisms. Our findings illustrate the important control and guiding mechanisms and highlight the multifaceted nature of open content governance. A range of governance mechanisms is discussed with regard to the varied levels of formality, the different loci of authority, and the diverse interaction environments involved. Limitations and opportunities for future research are provided.

An information foraging theory based user study of an adaptive user interaction framework for content-based image retrieval

This paper presents the design and results of a task-based user study, based on Information Foraging Theory, on a novel user interaction framework - uInteract - for content-based image retrieval (CBIR). The framework includes a four-factor user interaction model and an interactive interface. The user study involves three focused evaluations, 12 simulated real life search tasks with different complexity levels, 12 comparative systems and 50 subjects. Information Foraging Theory is applied to the user study design and the quantitative data analysis. The systematic findings have not only shown how effective and easy to use the uInteract framework is, but also illustrate the value of Information Foraging Theory for interpreting user interaction with CBIR. © 2011 Springer-Verlag Berlin Heidelberg.

Communicating Cuneiform:The Evolution of a Multimedia Cuneiform Database

Our paper presents the work of the Cuneiform Digital Forensic Project (CDFP), an interdisciplinary project at The University of Birmingham, concerned with the development of a multimedia database to support scholarly research into cuneiform, wedge-shaped writing imprinted onto clay tablets and indeed the earliest real form of writing. We describe the evolutionary design process and dynamic research and developmental cycles associated with the database. Unlike traditional publications, the electronic publication of resources offers the possibility of almost continuous revisions with the integration and support of new media and interfaces. However, if on-line resources are to win the favor and confidence of their respective communities there must be a clear distinction between published and maintainable resources, and, developmental content. Published material should, ideally, be supported via standard web-browser interfaces with fully integrated tools so that users receive a reliable, homogenous and intuitive flow of information and media relevant to their needs. We discuss the inherent dynamics of the design and publication of our on-line resource, starting with the basic design and maintenance aspects of the electronic database, which includes photographic instances of cuneiform signs, and shows how the continuous review process identifies areas for further research and development, for example, the “sign processor” graphical search tool and three-dimensional content, the results of which then feedback into the maintained resource.

Nondestructive measurement of water content and moisture migration of unsaturated red clays in South China

To reveal the moisture migration mechanism of the unsaturated red clays, which are sensitive to water content change and widely distributed in South China, and then rationally use them as a filling material for highway embankments, a method to measure the water content of red clay cylinders using X-ray computed tomography (CT) was proposed and verified. Then, studies on the moisture migrations in the red clays under the rainfall and ground water level were performed at different degrees of compaction. The results show that the relationship between dry density, water content, and CT value determined from X-ray CT tests can be used to nondestructively measure the water content of red clay cylinders at different migration time, which avoids the error reduced by the sample-to-sample variation. The rainfall, ground water level, and degree of compaction are factors that can significantly affect the moisture migration distance and migration rate. Some techniques, such as lowering groundwater table and increasing degree of compaction of the red clays, can be used to prevent or delay the moisture migration in highway embankments filled with red clays.

CamSim:a distributed smart camera network simulator

Smart cameras allow pre-processing of video data on the camera instead of sending it to a remote server for further analysis. Having a network of smart cameras allows various vision tasks to be processed in a distributed fashion. While cameras may have different tasks, we concentrate on distributed tracking in smart camera networks. This application introduces various highly interesting problems. Firstly, how can conflicting goals be satisfied such as cameras in the network try to track objects while also trying to keep communication overhead low? Secondly, how can cameras in the network self adapt in response to the behavior of objects and changes in scenarios, to ensure continued efficient performance? Thirdly, how can cameras organise themselves to improve the overall network's performance and efficiency? This paper presents a simulation environment, called CamSim, allowing distributed self-adaptation and self-organisation algorithms to be tested, without setting up a physical smart camera network. The simulation tool is written in Java and hence allows high portability between different operating systems. Relaxing various problems of computer vision and network communication enables a focus on implementing and testing new self-adaptation and self-organisation algorithms for cameras to use.

Towards Content-Sensitive Access to the Artefacts of the Bulgarian Iconography

his paper presents an ontological model of the knowledge about Bulgarian iconographical artefacts. It also describes content-sensitive services for access, browse, search and group iconographical objects, based on the presented ontology that will be implemented in the multimedia digital library “Virtual encyclopedia of Bulgarian iconography”.

A Semantic-Oriented Architecture of a Functional Module for Personalized and Adaptive Access to the Knowledge in a Multimedia Digital Library

This article presents the principal results of the doctoral thesis “Semantic-oriented Architecture and Models for Personalized and Adaptive Access to the Knowledge in Multimedia Digital Library” by Desislava Ivanova Paneva-Marinova (Institute of Mathematics and Informatics), successfully defended before the Specialised Academic Council for Informatics and Mathematical Modelling on 27 October, 2008.

Services for Content Creation and Presentation in an Iconographical Digital Library

Content creation and presentation are key activities in a multimedia digital library (MDL). The proper design and intelligent implementation of these services provide a stable base for overall MDL functionality. This paper presents the framework and the implementation of these services in the latest version of the “Virtual Encyclopaedia of Bulgarian Iconography” multimedia digital library. For the semantic description of the iconographical objects a tree-based annotation template is implemented. It provides options for autocompletion, reuse of values, bilingual entering of data, automated media watermarking, resizing and conversing. The paper describes in detail the algorithm for automated appearance of dependent values for different characteristics of an iconographical object. An algorithm for avoiding duplicate image objects is also included. The service for automated appearance of new objects in a collection after their entering is included as an important part of the content presentation. The paper also presents the overall service-based architecture of the library, covering its main service panels, repositories and their relationships. The presented vision is based on a long-term observation of the users’ preferences, cognitive goals, and needs, aiming to find an optimal functionality solution for the end users.