Bioinformatic analysis for exploring relationships between genes and gene products

To carry out their specific roles in the cell, genes and gene products often work together in groups, forming many relationships among themselves and with other molecules. Such relationships include physical protein-protein interaction relationships, regulatory relationships, metabolic relationships, genetic relationships, and much more. With advances in science and technology, some high throughput technologies have been developed to simultaneously detect tens of thousands of pairwise protein-protein interactions and protein-DNA interactions. However, the data generated by high throughput methods are prone to noise. Furthermore, the technology itself has its limitations, and cannot detect all kinds of relationships between genes and their products. Thus there is a pressing need to investigate all kinds of relationships and their roles in a living system using bioinformatic approaches, and is a central challenge in Computational Biology and Systems Biology. This dissertation focuses on exploring relationships between genes and gene products using bioinformatic approaches. Specifically, we consider problems related to regulatory relationships, protein-protein interactions, and semantic relationships between genes. A regulatory element is an important pattern or "signal", often located in the promoter of a gene, which is used in the process of turning a gene "on" or "off". Predicting regulatory elements is a key step in exploring the regulatory relationships between genes and gene products. In this dissertation, we consider the problem of improving the prediction of regulatory elements by using comparative genomics data. With regard to protein-protein interactions, we have developed bioinformatics techniques to estimate support for the data on these interactions. While protein-protein interactions and regulatory relationships can be detected by high throughput biological techniques, there is another type of relationship called semantic relationship that cannot be detected by a single technique, but can be inferred using multiple sources of biological data. The contributions of this thesis involved the development and application of a set of bioinformatic approaches that address the challenges mentioned above. These included (i) an EM-based algorithm that improves the prediction of regulatory elements using comparative genomics data, (ii) an approach for estimating the support of protein-protein interaction data, with application to functional annotation of genes, (iii) a novel method for inferring functional network of genes, and (iv) techniques for clustering genes using multi-source data.

Use of the DACUM process in the identification and verification of competencies for the medical administrative assistant

Medicine has changed in recent years. Medicare will all of its rules and regulations, worker's compensation laws, managed care and the trend toward more and larger group practices all contributed to the creation of an extremely structured regulatory environment which in turn demanded highly trained medical administrative assistants.^ The researcher noted three primary problems in the identification of competencies for the medical administrative assistant position: A lack of curricula, diverse roles, and a complex environment which has undergone radical change in recent years and will continue to evolve. Therefore, the purposes of the study were to use the DACUM process to develop a relevant list of competencies required by the medical administrative assistant practicing in physicians' offices in South Florida; determine the rank order of importance of each competency using a scale of one to five; cross-validate the DACUM group scores with a second population who did not participate in the DACUM process; and establish a basis for a curriculum framework for an occupational program.^ The DACUM process of curriculum development was selected because it seemed best suited to the need to develop a list of competencies for an occupation for which no programs existed. A panel of expert medical office administrative staff was selected to attend a 2-day workshop to describe their jobs in great detail. The panel, led by a trained facilitator, listed major duties and the respective tasks of their job. Brainstorming techniques were used to develop a consensus.^ Based upon the DACUM workshop, a survey was developed listing the 8 major duties and 71 tasks identified by the panel. The survey was mailed to the DACUM group and a second, larger population who did not participate in the DACUM. The survey results from the two groups were then compared. The non-DACUM group validated all but 3 of the 71 tasks listed by the DACUM panel. Because the three tasks were rated by the second group as at least "somewhat important" and rated "very important" by the DACUM group, the researcher recommended the inclusion of all 71 tasks in program development for this occupation. ^

Metacognitive Functions, Interest, and Student Engagement in the Writing Process: A Review of the Literature

The purpose of this paper is to draw on research that discusses the relationship between interest and metacognitive functions and its effect on engaging students in the writing process. Results indicate students who are interested in their writing activities engage in metacognitive strategies, remain focused, and complete their tasks.

Integration and querying of heterogeneous, autonomous, distributed database systems

Today, databases have become an integral part of information systems. In the past two decades, we have seen different database systems being developed independently and used in different applications domains. Today's interconnected networks and advanced applications, such as data warehousing, data mining & knowledge discovery and intelligent data access to information on the Web, have created a need for integrated access to such heterogeneous, autonomous, distributed database systems. Heterogeneous/multidatabase research has focused on this issue resulting in many different approaches. However, a single, generally accepted methodology in academia or industry has not emerged providing ubiquitous intelligent data access from heterogeneous, autonomous, distributed information sources. This thesis describes a heterogeneous database system being developed at Highperformance Database Research Center (HPDRC). A major impediment to ubiquitous deployment of multidatabase technology is the difficulty in resolving semantic heterogeneity. That is, identifying related information sources for integration and querying purposes. Our approach considers the semantics of the meta-data constructs in resolving this issue. The major contributions of the thesis work include: (i.) providing a scalable, easy-to-implement architecture for developing a heterogeneous multidatabase system, utilizing Semantic Binary Object-oriented Data Model (Sem-ODM) and Semantic SQL query language to capture the semantics of the data sources being integrated and to provide an easy-to-use query facility; (ii.) a methodology for semantic heterogeneity resolution by investigating into the extents of the meta-data constructs of component schemas. This methodology is shown to be correct, complete and unambiguous; (iii.) a semi-automated technique for identifying semantic relations, which is the basis of semantic knowledge for integration and querying, using shared ontologies for context-mediation; (iv.) resolutions for schematic conflicts and a language for defining global views from a set of component Sem-ODM schemas; (v.) design of a knowledge base for storing and manipulating meta-data and knowledge acquired during the integration process. This knowledge base acts as the interface between integration and query processing modules; (vi.) techniques for Semantic SQL query processing and optimization based on semantic knowledge in a heterogeneous database environment; and (vii.) a framework for intelligent computing and communication on the Internet applying the concepts of our work.

O slogan empresarial como construção discursiva: uma abordagem cognitivo-funcional

In this paper, we analyze corporate slogans, understanding them as a discursive construction that is, as a pairing of form and function able to unite the notions of textual type and discursive genre. In this way, we developed a qualitative and quantitative analysis, aimed specifically to analyze the formal properties (phonetic, morphological and syntactic) and functional (semantic, pragmatic and discursive) of slogans. Furthermore, we attempted at verifying and quantifying recurring aspects involved in their construction, in order to capture configurational patterns underlying their formation. The data come from slogans collected in products and / or service stores in the metropolitan area of Natal city, Rio Grande do Norte. This research is based on the Cognitive-Functional Linguistics, that conjugates the North American functionalist tradition, represented by researchers as Talmy Givón, Paul Hopper, Joan Bybee, Elizabeth Closs-Traugott, with Cognitive Linguistics, in particular, the chain linked to Construction Grammar, as postulated by Adele Goldberg, William Croft e Jan-Olla Östman, among others. The results ratified the importance of the interface between the formal and functional aspects in the analysis of linguistic uses. These results point to the idea of the slogan as the pairing of form and function on textual / discursive level, in other words, as a discursive construction, constituting as cognitive storage of a scheme / model of textual formation with a specific discursive-pragmatic function.

Design and implementation of a relative localization system for ground and aerial robotic teams

The main focus of this thesis is to address the relative localization problem of a heterogenous team which comprises of both ground and micro aerial vehicle robots. This team configuration allows to combine the advantages of increased accessibility and better perspective provided by aerial robots with the higher computational and sensory resources provided by the ground agents, to realize a cooperative multi robotic system suitable for hostile autonomous missions. However, in such a scenario, the strict constraints in flight time, sensor pay load, and computational capability of micro aerial vehicles limits the practical applicability of popular map-based localization schemes for GPS denied navigation. Therefore, the resource limited aerial platforms of this team demand simpler localization means for autonomous navigation. Relative localization is the process of estimating the formation of a robot team using the acquired inter-robot relative measurements. This allows the team members to know their relative formation even without a global localization reference, such as GPS or a map. Thus a typical robot team would benefit from a relative localization service since it would allow the team to implement formation control, collision avoidance, and supervisory control tasks, independent of a global localization service. More importantly, a heterogenous team such as ground robots and computationally constrained aerial vehicles would benefit from a relative localization service since it provides the crucial localization information required for autonomous operation of the weaker agents. This enables less capable robots to assume supportive roles and contribute to the more powerful robots executing the mission. Hence this study proposes a relative localization-based approach for ground and micro aerial vehicle cooperation, and develops inter-robot measurement, filtering, and distributed computing modules, necessary to realize the system. The research study results in three significant contributions. First, the work designs and validates a novel inter-robot relative measurement hardware solution which has accuracy, range, and scalability characteristics, necessary for relative localization. Second, the research work performs an analysis and design of a novel nonlinear filtering method, which allows the implementation of relative localization modules and attitude reference filters on low cost devices with optimal tuning parameters. Third, this work designs and validates a novel distributed relative localization approach, which harnesses the distributed computing capability of the team to minimize communication requirements, achieve consistent estimation, and enable efficient data correspondence within the network. The work validates the complete relative localization-based system through multiple indoor experiments and numerical simulations. The relative localization based navigation concept with its sensing, filtering, and distributed computing methods introduced in this thesis complements system limitations of a ground and micro aerial vehicle team, and also targets hostile environmental conditions. Thus the work constitutes an essential step towards realizing autonomous navigation of heterogenous teams in real world applications.

Differential activation in temporal, cingulate and prefrontal cortices during response inhibition in bipolar disorder

Background: Increased impulsivity and aberrant response inhibition have been observed in bipolar disorder (BD). This study examined the functional abnormalities and underlying neural processes during response inhibition in BD, and its relationship to impulsivity. Methods: We assessed impulsivity using the Barratt Impulsiveness Scale (BIS) and, using functional magnetic resonance imaging (fMRI), measured neural activity in response to an Affective Go-NoGo Task, consisting of emotional facial stimuli (fear, happy, anger faces) and non-emotional control stimuli (neutral female and male faces) in euthymic BD (n=23) and healthy individuals (HI; n=25). Results: BD patients were significantly more impulsive, yet did not differ from HI on accuracy or reaction time on the emotional go/no-go task. Comparing neural patterns of activation when processing emotional Go versus emotional NoGo trials yielded increased activation in BD within temporal and cingulate cortices and within prefrontal-cortical regions in HI. Furthermore, higher BIS scores for BD were associated with slower reaction times, and indicative of compensatory cognitive strategies to counter increased impulsivity. Conclusions: These findings illustrate cognition-emotion interference in BD and the observed differences in neural activation indicate potentially altered emotion modulation. Increased activation in brain regions previously shown in emotion regulation and response inhibition tasks could represent a disease-specific marker for BD

Talom Rukbo and the Donyipolo Yelam Kebang: restructuring Adi religious practices in Arunachal Pradesh, Northeast India

The purpose of this dissertation is to examine and contextualize the recent changes in the articulation of Donyipolo faith among the indigenous community of the Adi from the 1980s until the present. This is achieved by documenting both ‘non-formalized’ and ‘formalized’ belief and ritual within this Eastern Himalayan community. Since the mid-1980s, the Adi – led by indigenous activist Talom Rukbo and the Donyipolo Yelam Kebang (Donyipolo Faith Council) – have been restructuring Donyipolo to fit the model of more mainstream religions via a series of processes that could be called ‘formalization’ or ‘institutionalization’, a reformation blueprint that has subsequently spread to neighboring ethnic groups. This ethnography, exploring both folk practice and the modern reformation, is rooted in radical empiricism – in this context, meaning to collect data and allow analysis to arise organically. Radical empiricism is employed alongside vernacular theorizing to allow for the acknowledgement of indigenous theory through which we can trace indigenous agencies and the construction of indigenous lifeworlds. Facilitating this space for the acknowledgement of ‘religious re-imaginings’ as a means of cultural preservation – and as a representation of creativity – is significant particularly when viewed in the context of contemporary research on similar movements in Northeast India, which sometimes tends toward the negation of indigenous innovation by representing such religious revivals as conversion tools attributed to the Hindu right. It is hoped that the reader will come away from this dissertation with an understanding of the ‘constellations of faith’ that comprise ‘traditional’ Donyipolo and a comprehension of the innovative institutionalization processes that have shaped the new Adi praxis. Donyipolo should be viewed as a complex, nuanced, and independent indigenous faith, whether in its forms of folk expressions or in its new structure as expressed through the Donyipolo Yelam Kebang.

Traitement des émotions évoquées par les expressions faciales, vocales et musicales à la suite d’un traumatisme craniocérébral

Le traitement des émotions joue un rôle essentiel dans les relations interpersonnelles. Des déficits dans la reconnaissance des émotions évoquées par les expressions faciales et vocales ont été démontrés à la suite d’un traumatisme craniocérébral (TCC). Toutefois, la majorité des études n’ont pas différencié les participants selon le niveau de gravité du TCC et n’ont pas évalué certains préalables essentiels au traitement émotionnel, tels que la capacité à percevoir les caractéristiques faciales et vocales, et par le fait même, la capacité à y porter attention. Aucune étude ne s’est intéressée au traitement des émotions évoquées par les expressions musicales, alors que la musique est utilisée comme méthode d’intervention afin de répondre à des besoins de prise en charge comportementale, cognitive ou affective chez des personnes présentant des atteintes neurologiques. Ainsi, on ignore si les effets positifs de l’intervention musicale sont basés sur la préservation de la reconnaissance de certaines catégories d’émotions évoquées par les expressions musicales à la suite d’un TCC. La première étude de cette thèse a évalué la reconnaissance des émotions de base (joie, tristesse, peur) évoquées par les expressions faciales, vocales et musicales chez quarante et un adultes (10 TCC modéré-sévère, 9 TCC léger complexe, 11 TCC léger simple et 11 témoins), à partir de tâches expérimentales et de tâches perceptuelles contrôles. Les résultats suggèrent un déficit de la reconnaissance de la peur évoquée par les expressions faciales à la suite d’un TCC modéré-sévère et d’un TCC léger complexe, comparativement aux personnes avec un TCC léger simple et sans TCC. Le déficit n’est pas expliqué par un trouble perceptuel sous-jacent. Les résultats montrent de plus une préservation de la reconnaissance des émotions évoquées par les expressions vocales et musicales à la suite d’un TCC, indépendamment du niveau de gravité. Enfin, malgré une dissociation observée entre les performances aux tâches de reconnaissance des émotions évoquées par les modalités visuelle et auditive, aucune corrélation n’a été trouvée entre les expressions vocales et musicales. La deuxième étude a mesuré les ondes cérébrales précoces (N1, N170) et plus tardives (N2) de vingt-cinq adultes (10 TCC léger simple, 1 TCC léger complexe, 3 TCC modéré-sévère et 11 témoins), pendant la présentation d’expressions faciales évoquant la peur, la neutralité et la joie. Les résultats suggèrent des altérations dans le traitement attentionnel précoce à la suite d’un TCC, qui amenuisent le traitement ultérieur de la peur évoquée par les expressions faciales. En somme, les conclusions de cette thèse affinent notre compréhension du traitement des émotions évoquées par les expressions faciales, vocales et musicales à la suite d’un TCC selon le niveau de gravité. Les résultats permettent également de mieux saisir les origines des déficits du traitement des émotions évoquées par les expressions faciales à la suite d’un TCC, lesquels semblent secondaires à des altérations attentionnelles précoces. Cette thèse pourrait contribuer au développement éventuel d’interventions axées sur les émotions à la suite d’un TCC.

Semantic feature-based visual attention model for pedestrian detection

Objective
Pedestrian detection under video surveillance systems has always been a hot topic in computer vision research. These systems are widely used in train stations, airports, large commercial plazas, and other public places. However, pedestrian detection remains difficult because of complex backgrounds. Given its development in recent years, the visual attention mechanism has attracted increasing attention in object detection and tracking research, and previous studies have achieved substantial progress and breakthroughs. We propose a novel pedestrian detection method based on the semantic features under the visual attention mechanism.
Method
The proposed semantic feature-based visual attention model is a spatial-temporal model that consists of two parts: the static visual attention model and the motion visual attention model. The static visual attention model in the spatial domain is constructed by combining bottom-up with top-down attention guidance. Based on the characteristics of pedestrians, the bottom-up visual attention model of Itti is improved by intensifying the orientation vectors of elementary visual features to make the visual saliency map suitable for pedestrian detection. In terms of pedestrian attributes, skin color is selected as a semantic feature for pedestrian detection. The regional and Gaussian models are adopted to construct the skin color model. Skin feature-based visual attention guidance is then proposed to complete the top-down process. The bottom-up and top-down visual attentions are linearly combined using the proper weights obtained from experiments to construct the static visual attention model in the spatial domain. The spatial-temporal visual attention model is then constructed via the motion features in the temporal domain. Based on the static visual attention model in the spatial domain, the frame difference method is combined with optical flowing to detect motion vectors. Filtering is applied to process the field of motion vectors. The saliency of motion vectors can be evaluated via motion entropy to make the selected motion feature more suitable for the spatial-temporal visual attention model.
Result
Standard datasets and practical videos are selected for the experiments. The experiments are performed on a MATLAB R2012a platform. The experimental results show that our spatial-temporal visual attention model demonstrates favorable robustness under various scenes, including indoor train station surveillance videos and outdoor scenes with swaying leaves. Our proposed model outperforms the visual attention model of Itti, the graph-based visual saliency model, the phase spectrum of quaternion Fourier transform model, and the motion channel model of Liu in terms of pedestrian detection. The proposed model achieves a 93% accuracy rate on the test video.
Conclusion
This paper proposes a novel pedestrian method based on the visual attention mechanism. A spatial-temporal visual attention model that uses low-level and semantic features is proposed to calculate the saliency map. Based on this model, the pedestrian targets can be detected through focus of attention shifts. The experimental results verify the effectiveness of the proposed attention model for detecting pedestrians.

Bilingual Lexical Access in Reading : Analyzing the Effect of Semantic Context on Non-Selective Access in Bilingual Memory

Recent empirical studies about the neurological executive nature of reading in bilinguals differ in their evaluations of the degree of selective manifestation in lexical access as implicated by data from early and late reading measures in the eye-tracking paradigm. Currently two scenarios are plausible: (1) Lexical access in reading is fundamentally language non-selective and top-down effects from semantic context can influence the degree of selectivity in lexical access; (2) Cross-lingual lexical activation is actuated via bottom-up processes without being affected by top-down effects from sentence context. In an attempt to test these hypotheses empirically, this study analyzed reader-text events arising when cognate facilitation and semantic constraint interact in a 22 factorially designed experiment tracking the eye movements of 26 Swedish-English bilinguals reading in their L2. Stimulus conditions consisted of high- and low-constraint sentences embedded with either a cognate or a non-cognate control word. The results showed clear signs of cognate facilitation in both early and late reading measures and in either sentence conditions. This evidence in favour of the non-selective hypothesis indicates that the manifestation of non-selective lexical access in reading is not constrained by top-down effects from semantic context.

Lexical Interference in Semantic Processing of Simple Words: Implications for Brand Names

This study provides evidence for a Stroop-like interference effect in word recognition. Based on phonologic and semantic properties of simple words, participants who performed a same/different word-recognition task exhibited a significant response latency increase when word pairs (e.g., POLL, ROD) featured a comparison word (POLL) that was a homonym of a synonym (pole) of the target word (ROD). These results support a parallel-processing framework of lexical decision making, in which activation of the pathways to word recognition may occur at different levels automatically and in parallel. A subset of simple words that are also brand names was examined and exhibited this same interference. Implications for word recognition theory and practical implications for strategic marketing are discussed.

Convex Optimization Algorithms and Statistical Bounds for Learning Structured Models

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

Proof theory for hybrid(ised) logics

Hybridisation is a systematic process along which the characteristic features of hybrid logic, both at the syntactic and the semantic levels, are developed on top of an arbitrary logic framed as an institution. In a series of papers this process has been detailed and taken as a basis for a speci cation methodology for recon gurable systems. The present paper extends this work by showing how a proof calculus (in both a Hilbert and a tableau based format) for the hybridised version of a logic can be systematically generated from a proof calculus for the latter. Such developments provide the basis for a complete proof theory for hybrid(ised) logics, and thus pave the way to the development of (dedicated) proof support.

THREE AMERICAN INTERNATIONAL PIANO COMPETITIONS: THE PIANO WORKS THEY COMMISSIONED BETWEEN 1962 AND 2012

Over a period of 50 years—between 1962 and 2012—three preeminent American piano competitions, the Van Cliburn International Piano Competition, the University of Maryland International Piano Competition/William Kapell International Piano Competition and the San Antonio International Piano Competition, commissioned for inclusion on their required performance lists 26 piano works, almost all by American composers. These compositions, works of sufficient artistic depth and technical sophistication to serve as rigorous benchmarks for competition finalists, constitute a unique segment of the contemporary American piano repertoire. Although a limited number of these pieces have found their way into the performance repertoire of concert artists, too many have not been performed since their premières in the final rounds of the competitions for which they were designed. Such should not be the case. Some of the composers in question are innovative titans of 20th-century American music—Samuel Barber, Aaron Copland, Leonard Bernstein, John Cage, John Corigliano, William Schuman, Joan Tower and Ned Rorem, to name just a few—and many of the pieces themselves, as historical touchstones, deserve careful examination. This study includes, in addition to an introductory overview of the three competitions, a survey of all 26 compositions and an analysis of their expressive characteristics, from the point of view of the performing pianist. Numerous musical examples support the analysis. Biographical information about the composers, along with descriptions of their overall musical styles, place these pieces in historical context. Analytical and technical comprehension of this distinctive and rarely performed corner of the modern classical piano world could be of inestimable value to professional pianists, piano pedagogues and music educators alike.