Priorities for representation : Task settings and object interaction both influence object memory

Portions of this research were presented at the Experimental Psychological Society conference at the University of Kent (May, 2014).The first author is supported by a studentship provided by the University of Dundee. This study was conducted as part of the requirements for the degree of Doctor of Philosophy by the first author.

Priorities for representation : Task settings and object interaction both influence object memory

Portions of this research were presented at the Experimental Psychological Society conference at the University of Kent (May, 2014).The first author is supported by a studentship provided by the University of Dundee. This study was conducted as part of the requirements for the degree of Doctor of Philosophy by the first author.

The Influence of Gene Environment Interaction on the Risk of Cognitive Impairment: Reducing Sexual Risk Behaviors and Alcohol Use in HIV-infected Adults

Memory deficits and executive dysfunction are highly prevalent among HIV-infected adults. These conditions can affect their quality of life, antiretroviral adherence, and HIV risk behaviors. Several factors have been suggested including the role of genetics in relation to HIV disease progression. This dissertation aimed to determine whether genetic differences in HIV-infected individuals were correlated with impaired memory, cognitive flexibility and executive function and whether cognitive decline moderated alcohol use and sexual transmission risk behaviors among HIV-infected alcohol abusers participating in an NIH-funded clinical trial comparing the efficacy of the adapted Holistic Health Recovery Program (HHRP-A) intervention to a Health Promotion Control (HPC) condition in reducing risk behaviors. A total of 267 individuals were genotyped for polymorphisms in the dopamine and serotonin gene systems. Results yielded significant associations for TPH2, GALM, DRD2 and DRD4 genetic variants with impaired executive function, cognitive flexibility and memory. SNPs TPH2 rs4570625 and DRD2 rs6277 showed a risk association with executive function (odds ratio = 2.5, p = .02; 3.6, p = .001). GALM rs6741892 was associated with impaired memory (odds ratio = 1.9, p = .006). At the six-month follow-up, HHRP-A participants were less likely to report trading sex for food, drugs and money (20.0%) and unprotected insertive or receptive oral (11.6%) or vaginal and/or anal sex (3.2%) than HPC participants (49.4%, p

High-performance parallel systems for data-intensive computing

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

Memory effects and geometrical considerations in open quantum systems

This thesis discusses memory effects in open quantum systems with an emphasis on the Breuer, Laine, Piilo (BLP) measure of non-Markovianity. It is shown how the calculation of the measure can be simplifed and how quantum information protocols can bene t from memory e ects. The superdense coding protocol is used as an example of this. The quantum Zeno effect will also be studied from the point of view of memory e ects. Finally the geometric ideas used in simplifying the calculation of the BLP measure are applied in studying the amount of resources needed for detecting bipartite quantum correlations. It is shown that to decide without prior information if an unknown quantum state is entangled or not, an informationally complete measurement is required. The first part of the thesis contains an introduction to the theoretical ideas such as quantum states, closed and open quantum systems and necessary mathematical tools. The theory is then applied in the second part of the thesis as the results obtained in the original publications I-VI are presented and discussed.

Mesh partitioning and load balancing for distributed memory parallel systems

A method is outlined for optimising graph partitions which arise in mapping unstructured mesh calculations to parallel computers. The method employs a relative gain iterative technique to both evenly balance the workload and minimise the number and volume of interprocessor communications. A parallel graph reduction technique is also briefly described and can be used to give a global perspective to the optimisation. The algorithms work efficiently in parallel as well as sequentially and when combined with a fast direct partitioning technique (such as the Greedy algorithm) to give an initial partition, the resulting two-stage process proves itself to be both a powerful and flexible solution to the static graph-partitioning problem. Experiments indicate that the resulting parallel code can provide high quality partitions, independent of the initial partition, within a few seconds. The algorithms can also be used for dynamic load-balancing, reusing existing partitions and in this case the procedures are much faster than static techniques, provide partitions of similar or higher quality and, in comparison, involve the migration of a fraction of the data.

Interaction techniques with novel multimodal feedback for addressing gesture-sensing systems

Users need to be able to address in-air gesture systems, which means finding where to perform gestures and how to direct them towards the intended system. This is necessary for input to be sensed correctly and without unintentionally affecting other systems. This thesis investigates novel interaction techniques which allow users to address gesture systems properly, helping them find where and how to gesture. It also investigates audio, tactile and interactive light displays for multimodal gesture feedback; these can be used by gesture systems with limited output capabilities (like mobile phones and small household controls), allowing the interaction techniques to be used by a variety of device types. It investigates tactile and interactive light displays in greater detail, as these are not as well understood as audio displays. Experiments 1 and 2 explored tactile feedback for gesture systems, comparing an ultrasound haptic display to wearable tactile displays at different body locations and investigating feedback designs. These experiments found that tactile feedback improves the user experience of gesturing by reassuring users that their movements are being sensed. Experiment 3 investigated interactive light displays for gesture systems, finding this novel display type effective for giving feedback and presenting information. It also found that interactive light feedback is enhanced by audio and tactile feedback. These feedback modalities were then used alongside audio feedback in two interaction techniques for addressing gesture systems: sensor strength feedback and rhythmic gestures. Sensor strength feedback is multimodal feedback that tells users how well they can be sensed, encouraging them to find where to gesture through active exploration. Experiment 4 found that they can do this with 51mm accuracy, with combinations of audio and interactive light feedback leading to the best performance. Rhythmic gestures are continuously repeated gesture movements which can be used to direct input. Experiment 5 investigated the usability of this technique, finding that users can match rhythmic gestures well and with ease. Finally, these interaction techniques were combined, resulting in a new single interaction for addressing gesture systems. Using this interaction, users could direct their input with rhythmic gestures while using the sensor strength feedback to find a good location for addressing the system. Experiment 6 studied the effectiveness and usability of this technique, as well as the design space for combining the two types of feedback. It found that this interaction was successful, with users matching 99.9% of rhythmic gestures, with 80mm accuracy from target points. The findings show that gesture systems could successfully use this interaction technique to allow users to address them. Novel design recommendations for using rhythmic gestures and sensor strength feedback were created, informed by the experiment findings.

DIFFUSE-INTERFACE FIELD APPROACH TO MODELING SELF-ASSEMBLY OF HETEROGENEOUS COLLOIDAL SYSTEMS AND RELATED DIPOLE-DIPOLE INTERACTION PHENOMENA

Colloid self-assembly under external control is a new route to fabrication of advanced materials with novel microstructures and appealing functionalities. The kinetic processes of colloidal self-assembly have attracted great interests also because they are similar to many atomic level kinetic processes of materials. In the past decades, rapid technological progresses have been achieved on producing shape-anisotropic, patchy, core-shell structured particles and particles with electric/magnetic charges/dipoles, which greatly enriched the self-assembled structures. Multi-phase carrier liquids offer new route to controlling colloidal self-assembly. Therefore, heterogeneity is the essential characteristics of colloid system, while so far there still lacks a model that is able to efficiently incorporate these possible heterogeneities. This thesis is mainly devoted to development of a model and computational study on the complex colloid system through a diffuse-interface field approach (DIFA), recently developed by Wang et al. This meso-scale model is able to describe arbitrary particle shape and arbitrary charge/dipole distribution on the surface or body of particles. Within the framework of DIFA, a Gibbs-Duhem-type formula is introduced to treat Laplace pressure in multi-liquid-phase colloidal system and it obeys Young-Laplace equation. The model is thus capable to quantitatively study important capillarity related phenomena. Extensive computer simulations are performed to study the fundamental behavior of heterogeneous colloidal system. The role of Laplace pressure is revealed in determining the mechanical equilibrium of shape-anisotropic particles at fluid interfaces. In particular, it is found that the Laplace pressure plays a critical role in maintaining the stability of capillary bridges between close particles, which sheds light on a novel route to in situ firming compact but fragile colloidal microstructures via capillary bridges. Simulation results also show that competition between like-charge repulsion, dipole-dipole interaction and Brownian motion dictates the degree of aggregation of heterogeneously charged particles. Assembly and alignment of particles with magnetic dipoles under external field is studied. Finally, extended studies on the role of dipole-dipole interaction are performed for ferromagnetic and ferroelectric domain phenomena. The results reveal that the internal field generated by dipoles competes with external field to determine the dipole-domain evolution in ferroic materials.

Shear bond strength of self-etch and total-etch bonding systems at different dentin depths

The purpose of this study was to evaluate the dentin shear bond strength of four adhesive systems (Adper Single Bond 2, Adper Prompt L-Pop, Magic Bond DE and Self Etch Bond) in regards to buccal and lingual surfaces and dentin depth. Forty extracted third molars had roots removed and crowns bisected in the mesiodistal direction. The buccal and lingual surfaces were fixed in a PVC/acrylic resin ring and were divided into buccal and lingual groups assigned to each selected adhesive. The same specimens prepared for the evaluation of superficial dentin shear resistance were used to evaluate the different depths of dentin. The specimens were identified and abraded at depths of 0.5, 1.0, 1.5 and 2.0 mm. Each depth was evaluated by ISO TR 11405 using an EMIC-2000 machine regulated at 0.5 mm/min with a 200 Kgf load cell. We performed statistical analyses on the results (ANOVA, Tukey and Scheffé tests). Data revealed statistical differences (p < 0.01) in the adhesive and depth variation as well as adhesive/depth interactions. The Adper Single Bond 2 demonstrated the highest mean values of shear bond strength. The Prompt L-Pop product, a self-etching adhesive, revealed higher mean values compared with Magic Bond DE and Self Etch Bond adhesives, a total and self-etching adhesive respectively. It may be concluded that the shear bond strength of dentin is dependent on material (adhesive system), substrate depth and adhesive/depth interaction.

Effect of different polishing systems on the surface roughness of microhybrid composites

The use of composite resins in dentistry is well accepted for restoring anterior and posterior teeth. Many polishing protocols have been evaluated for their effect on the surface roughness of restorative materials. This study compared the effect of different polishing systems on the surface roughness of microhybrid composites. Thirty-six specimens were prepared for each composite $#91;Charisma® (Heraeus Kulzer), Fill Magic® (Vigodent), TPH Spectrum® (Dentsply), Z100® (3M/ESPE) and Z250® (3M/ESPE)] and submitted to surface treatment with Enhance® and PoGo® (Dentsply) points, sequential Sof-Lex XT® aluminum oxide disks (3M/ESPE), and felt disks (TDV) combined with Excel® diamond polishing paste (TDV). Average surface roughness (Ra) was measured with a mechanical roughness tester. The data were analyzed by two-way ANOVA with repetition of the factorial design and the Tukey-Kramer test (p<0.01). The F-test result for treatments and resins was high (p<0.0001 for both), indicating that the effect of the treatment applied to the specimen surface and the effect of the type of resin on surface roughness was highly significant. Regarding the interaction between polishing system and type of resin used, a p value of 0.0002 was obtained, indicating a statistically significant difference. A Ra of 1.3663 was obtained for the Sof-Lex/TPH Spectrum interaction. In contrast, the Ra for the felt disk+paste/Z250 interactions was 0.1846. In conclusion, Sof-Lex polishing system produced a higher surface roughness on TPH Spectrum resin when compared to the other interactions.

Complex networks: the key to systems biology

Though introduced recently, complex networks research has grown steadily because of its potential to represent, characterize and model a wide range of intricate natural systems and phenomena. Because of the intrinsic complexity and systemic organization of life, complex networks provide a specially promising framework for systems biology investigation. The current article is an up-to-date review of the major developments related to the application of complex networks in biology, with special attention focused on the more recent literature. The main concepts and models of complex networks are presented and illustrated in an accessible fashion. Three main types of networks are covered: transcriptional regulatory networks, protein-protein interaction networks and metabolic networks. The key role of complex networks for systems biology is extensively illustrated by several of the papers reviewed.

Alluvial-eolian interaction in a Cambrian rift margin: the Pedra das Torrinhas and Pedra Pintada formations (Guaritas Group, RS)

This work presents a study of selected outcrops from the Pedra das Torrinhas Formation of the Guaritas Group (Cambrian, Camaquã Basin), near the basin bordering Encantadas Fault Zone. The studied succession includes alluvial fan deposits that pass laterally into eolian deposits. Sedimentary facies and architectural element analysis were performed, followed by sedimentary petrography and microscopic porosity analysis, aiming to characterize the porosity of the deposits and its spatial distribution. The main objective was to contribute to a better understanding of the porosity spatial distribution in depositional systems characterized by the interaction between alluvial and eolian processes, with special reference to deposits formed prior to the development of terrestrial plants. Porosity values are related to depositional processes, with higher porosities associated to eolian dune deposits (mean of 8.4%), and lower porosity related to interdunes (mean of 3.4%) and alluvial fans (mean of 4.3%). Architectural elements analysis revealed the spatial relationships of these deposits, a response to the interplay of the eolian and alluvial processes. The integration of porosity data reveals that the interaction of alluvial and eolian processes results in heterogeneous distribution of porosity at the facies association scale. Eolian reworking of alluvial facies increases porosity whereas sheet-flood and other alluvial processes in the interdune areas reduce porosity.

Crossover between the extended and localized regimes in stochastic partially self-avoiding walks in one-dimensional disordered systems

Consider N sites randomly and uniformly distributed in a d-dimensional hypercube. A walker explores this disordered medium going to the nearest site, which has not been visited in the last mu (memory) steps. The walker trajectory is composed of a transient part and a periodic part (cycle). For one-dimensional systems, travelers can or cannot explore all available space, giving rise to a crossover between localized and extended regimes at the critical memory mu(1) = log(2) N. The deterministic rule can be softened to consider more realistic situations with the inclusion of a stochastic parameter T (temperature). In this case, the walker movement is driven by a probability density function parameterized by T and a cost function. The cost function increases as the distance between two sites and favors hops to closer sites. As the temperature increases, the walker can escape from cycles that are reminiscent of the deterministic nature and extend the exploration. Here, we report an analytical model and numerical studies of the influence of the temperature and the critical memory in the exploration of one-dimensional disordered systems.

Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.