Metagenomic systems biology: frameworks for modeling and characterizing the gut microbiome

Thesis (Ph.D.)--University of Washington, 2014

Critical autopoiesis and the materiality of law

Autopoietic theory is increasingly seen as a candidate for a radical theory of law, both in relation to its theoretical credentials and its relevance in terms of new and emerging forms of law. An aspect of the theory that has remained less developed, however, is its material side, and more concretely the theory’s accommodation of bodies, space, objects and their claim to legal agency. The present article reads Luhmann’s theory of autopoietic systems in a radical and material manner, linking it on the one hand to current post-structural theorisations of law and society, and on the other hand extending its ambit to accommodate the influx of material considerations that have been working their way through various other disciplines. The latter comprises both a materialisation of the theory itself and ways of conceptualising the legal system as material through and through. This I do by further developing what I have called Critical Autopoiesis, namely an acentric, topological, post-ecological and posthuman understanding of Luhmann’s theory, that draws on Deleuzian thought, feminist theory, geography, non-representational theory, and new material and object-oriented ontologies. These are combined with some well-rehearsed autopoietic concepts, such as distinction, environment and boundaries; Luhmann’s earlier work on materiality continuum; more recent work on bodies and space; as well as his work on form and medium in relation to art. The article concludes with five suggestions for an understanding of what critical autopoietic materiality might mean for law.

Personality and performance on digit span tests in online and offline settings.

This paper describes two studies examining links between personality and performance on a cognitive test in online and laboratory settings. Study 1 was completed online. 345 participants passively recruited through a personality assessment website completed a Five Factor Model personality inventory derived from the International Personality Item Pool. They then completed an online text-based digit span test. This required participants to repeat increasingly longer strings of digits, either in the same order (forward) or in the opposite of the presentation order (reverse). Conventional digit span tasks ask participants to respond verbally; in this instance they responded by typing the digits. Agreeableness and Openness to Experience each had small but significant associations with forward and reverse digit span. In a second, laboratory based, study, 103 participants completed paper versions of the IPIP Five Factor inventory, the NEO-FFI, and a battery of cognitive tests including the WAIS 4 digit span test. In this instance, Agreeableness and Openness to Experience were not significantly correlated with digit span measures. Taken together, these studies suggest that personality characteristics may influence performance on an online cognitive test. This effect was not seen in an offline version of the study. The paper will consider potential implications for online testing, for equivalence of online and offline methods, and for links between personality and performance on this cognitive test.

Cappadocia: where Greek prepositions come to die

The Cappadocian variety of Ulaghátsh is unique among the Greek-speaking world in having lost the inherited preposition ‘se’. The innovation is found with both locative and allative uses and has af-ected both syntactic contexts in which ‘se’ was originally found, that is, as a simple preposition (1) and as the left-occurring member of circumpositions of the type ‘se’ + NP + spatial adverb (2). (1) a. tránse ci [to meidán] en ávʝa see.PST.3SG COMP ART.DEF.SG.ACC yard.SG.ACC COP.3 game.PL.NOM ‘he saw that in the yard is some game’ (Dawkins 1916: 348) b. ta erʝó da qardáʃa évɣan [to qonáq] ART.DEF.PL.NOM two ART.DEF.PL.NOM friend.PL.NOM ascend.PST.3PL ART.DEF.SG.ACC house.SG.ACC ‘the two friends went up to the house’ (Dawkins 1916: 354) (2) émi [ta qonáca mésa], kiríʃde [to ʝasdɯ́q píso] enter.PST.3SG ART.DEF.PL.NOM house.PL.ACC inside hide.PST.3SG. ART.DEF.SG.ACC cushion.SG.ACC behind ‘he went into the houses and hid behind the cushions’ (Dawkins 1916: 348) In this paper, we set out to provide (a) a diachronic account of the loss of ‘se’ in Asia Minor Greek, and (b) a synchronic analysis of its ramifications for the encoding of the semantic and grammatical functions it had prior to its loss. The diachronic development of ‘se’ is traced by comparing the Ulaghátsh data with those obtained from Cappadocian varieties that have neither lost it nor do they show signs of losing it and, crucially, also from varieties in which ‘se’ is in the process of being lost. The comparative analysis shows that the loss first became manifest in circumpositions in which ‘se’ was preposed to the complement to which in turn a wide range of adverbs expressing topological relations were postposed (émi sa qonáca mésa > émi ta qonáca mésa). This finding is accounted for in terms of Sinha and Kuteva’s (1995) distributed spatial semantics framework, which accepts that the elements involved in the constructions under investigation—the verb (émi), ‘se’ and the spatial adverb (mésa)—all contribute to the expression of the spatial relational meaning but with differences in weighting. Of the three, ‘eis’ made the most minimal contribution, the bulk of it being distributed over the verb and the adverb. This allowed for it to be optionally dropped from circumpositions, a stage attested in Phlo-tá Cappadocian and Silliot, and to be later completely abandoned, originally in allative and subsequently in locative contexts (earlier: évɣan so qonáq > évɣan to qonáq; later: so meidán en ávʝa > to meidán en ávʝa). The earlier loss in allative contexts is also dealt with in distributed semantics terms as verbs of motion such as έβγαν are semantically more loaded than vacuous verbs like the copula and therefore the preposition could be left out in the former context more easily than in the latter. The analysis also addresses the possibility that the loss of ‘se’ may ultimately originate in substandard forms of Medieval Greek, which according to Tachibana (1994) displayed SPATIAL ADVERB + NP constructions. Applying the semantic map model (Croft 2003, Haspelmath 2003), the synchronic analysis of the varieties that retain ‘se’ reveals that—like many other allative markers crosslinguistically—it displays a pattern of multifunctionality in expressing nine different functions (among others allative, locative, recipient, addressee, experiencer), which can be mapped against four domains, viz. the spatiotemporal, the social, the mental and the logicotextual (cf. Rice & Kabata 2007). In Ulaghátsh Cappadocian, none of these functions is overtly marked as such. In cases like (1), the intended spatial relational meaning is arrived at through the combination of the syntax and the inherent semantics of the verb and the zero-marked NP as well as from the context. In environments of the type exemplified by (2), the adverb contributes further to the correct interpretation. The analysis additionally shows that, despite the loss of ‘se’, Ulaghátsh patterns with all other Cappadocian varieties in one important aspect: Goal and Location are expressed similarly (by zero in Ulaghátsh, by ‘se’ in the other varieties) whereas Source is being kept distinct (expressed by ‘apó’ in all varieties). Goal-Location polysemy is very common across the world’s languages and, most crucially, prevails over other possible polysemies in the tripartite distinction Source—Location—Goal (Lestrade 2010, Nikitina 2009). Taking into account this empirical observation, our findings suggest that the reor-anisation of spatial systems can have a local effect—in our case the loss of a member of the prepositional paradigm—but will keep the original global picture intact, thus conforming to crosslinguistically robust tendencies.  References Croft, W. 2001. Radical Construction Grammar: Syntactic Theory in Typological Perspective. Oxford: Oxford University Press. Dawkins, R. M. 1916. Modern Greek in Asia Minor: A Study of the Dialects of Sílli, Cappadocia and Phárasa with Grammar, Texts, Translations and Glossary. Cambridge: Cambridge University Press. Haspelmath, M. 2003. The geometry of grammatical meaning: semantic maps and cross-linguistic comparison. In M. Tomasello (Ed.), The New Psychology of Language, Volume 2. New York: Erlbaum, 211–243. Lestrade, S. 2010. The Space of Case. Doctoral dissertation. Radboud University Nijmegen. Nikitina, T. 2009. Subcategorization pattern and lexical meaning of motion verbs: a study of the source/goal ambiguity. Linguistics 47, 1113–1141. Rice, S. & K. Kabata. 2007. Cross-linguistic grammaticalization patterns of the allative. Linguistic Typology 11, 451–514. Sinha, C. & T. Kuteva. 1995. Distributed spatial semantics. Nordic Journal of Linguistics 18:2, 167–199. Tachibana, T. 1994. Syntactic structure of spatial expressions in the “Late Byzantine Prose Alexander Romance”. Propylaia 6, 35–51.

Principais dificuldades que os alunos de viola de arco apresentam quando ingressam no ensino superior português: relatório de estágio

A maioria dos instrumentistas de cordas friccionadas apresentam problemas ou dificuldades ao longo de toda a sua aprendizagem musical. Como professora e violetista, realizei este relatório de estágio com o intuito de pesquisar onde se focam a maioria desses problemas. Este relatório de estágio está dividido em duas diferentes secções, a primeira apresenta todo o trabalho pedagógico efectuado com três diferentes alunos, de diferentes níveis ao longo do ano lectivo de 2012/13 na Fundação Musical dos Amigos das Crianças (FMAC), e a segunda apresenta toda a investigação que realizei para concluir quais as principais dificuldades que os alunos de viola de arco apresentam quando ingressam no Ensino Superior. A investigação apresenta uma vasta pesquisa literária e o testemunho dos professores de várias instituições, como a Universidade do Minho, Escola Superior de Música e Artes de Espectáculo, Universidade de Aveiro, Escola Superior das Artes Aplicadas de Castelo Branco e Escola Superior de Música de Lisboa que ajudaram à profunda análise deste tema. Os resultados revelaram que os principais problemas apresentados nos estudantes de viola de arco são de origem técnica, ou seja, postura (posição do corpo, distribuição do peso correcto pelas pernas e escolha adequada do instrumento de acordo com a fisionomia do aluno); mão direita (pega correcta dos dedos no arco, distribuição de arco e contracção muscular); mão esquerda (posição do polegar, ombro e braço que afectam a afinação, flexibilidade, mudanças de posição e vibrato); influência da escolha do repertório por parte de um professor e autonomia do aluno.

Positive radial solutions of the Dirichlet problem for the Minkowski-Curvature equation in a ball

We study the existence and multiplicity of positive radial solutions of the Dirichlet problem for the Minkowski-curvature equation { -div(del upsilon/root 1-vertical bar del upsilon vertical bar(2)) in B-R, upsilon=0 on partial derivative B-R,B- where B-R is a ball in R-N (N >= 2). According to the behaviour off = f (r, s) near s = 0, we prove the existence of either one, two or three positive solutions. All results are obtained by reduction to an equivalent non-singular one-dimensional problem, to which variational methods can be applied in a standard way.

Definition of Distribution Network Tariffs Considering Distribution Generation and Demand Response

The use of distribution networks in the current scenario of high penetration of Distributed Generation (DG) is a problem of great importance. In the competitive environment of electricity markets and smart grids, Demand Response (DR) is also gaining notable impact with several benefits for the whole system. The work presented in this paper comprises a methodology able to define the cost allocation in distribution networks considering large integration of DG and DR resources. The proposed methodology is divided into three phases and it is based on an AC Optimal Power Flow (OPF) including the determination of topological distribution factors, and consequent application of the MW-mile method. The application of the proposed tariffs definition methodology is illustrated in a distribution network with 33 buses, 66 DG units, and 32 consumers with DR capacity.

A Playful Glance at Hierarchical Questions for Two-Way Alternating Automata

Two-way alternating automata were introduced by Vardi in order to study the satisfiability problem for the modal μ-calculus extended with backwards modalities. In this paper, we present a very simple proof by way of Wadge games of the strictness of the hierarchy of Motowski indices of two-way alternating automata over trees.

3D movement and muscle activity patterns in a violin bowing task

Objective: Overuse injuries in violinists are a problem that has been primarily analyzed through the use of questionnaires. Simultaneous 3D motion analysis and EMG to measure muscle activity has been suggested as a quantitative technique to explore this problem by identifying movement patterns and muscular demands which may predispose violinists to overuse injuries. This multi-disciplinary analysis technique has, so far, had limited use in the music world. The purpose of this study was to use it to characterize the demands of a violin bowing task. Subjects: Twelve injury-free violinists volunteered for the study. The subjects were assigned to a novice or expert group based on playing experience, as determined by questionnaire. Design and Settings: Muscle activity and movement patterns were assessed while violinists played five bowing cycles (one bowing cycle = one down-bow + one up-bow) on each string (G, D, A, E), at a pulse of 4 beats per bow and 100 beats per minute. Measurements: An upper extremity model created using coordinate data from markers placed on the right acromion process, lateral epicondyle of the humerus and ulnar styloid was used to determine minimum and maximum joint angles, ranges of motion (ROM) and angular velocities at the shoulder and elbow of the bowing arm. Muscle activity in right anterior deltoid, biceps brachii and triceps brachii was assessed during maximal voluntary contractions (MVC) and during the playing task. Data were analysed for significant differences across the strings and between experience groups. Results: Elbow flexion/extension ROM was similar across strings for both groups. Shoulder flexion/extension ROM increaslarger for the experts. Angular velocity changes mirrored changes in ROM. Deltoid was the most active of the muscles assessed (20% MVC) and displayed a pattern of constant activation to maintain shoulder abduction. Biceps and triceps were less active (4 - 12% MVC) and showed a more periodic 'on and off pattern. Novices' muscle activity was higher in all cases. Experts' muscle activity showed a consistent pattern across strings, whereas the novices were more irregular. The agonist-antagonist roles of biceps and triceps during the bowing motion were clearly defined in the expert group, but not as apparent in the novice group. Conclusions: Bowing movement appears to be controlled by the shoulder rather than the elbow as shoulder ROM changed across strings while elbow ROM remained the same. Shoulder injuries are probably due to repetition as the muscle activity required for the movement is small. Experts require a smaller amount of muscle activity to perform the movement, possibly due to more efficient muscle activation patterns as a result of practice. This quantitative multidisciplinary approach to analysing violinists' movements can contribute to fuller understanding of both playing demands and injury mechanisms .

Properties and algorithms of the (n, k)-star graphs

The (n, k)-star interconnection network was proposed in 1995 as an attractive alternative to the n-star topology in parallel computation. The (n, k )-star has significant advantages over the n-star which itself was proposed as an attractive alternative to the popular hypercube. The major advantage of the (n, k )-star network is its scalability, which makes it more flexible than the n-star as an interconnection network. In this thesis, we will focus on finding graph theoretical properties of the (n, k )-star as well as developing parallel algorithms that run on this network. The basic topological properties of the (n, k )-star are first studied. These are useful since they can be used to develop efficient algorithms on this network. We then study the (n, k )-star network from algorithmic point of view. Specifically, we will investigate both fundamental and application algorithms for basic communication, prefix computation, and sorting, etc. A literature review of the state-of-the-art in relation to the (n, k )-star network as well as some open problems in this area are also provided.

Properties and algorithms of the (n, k)-arrangement graphs

The (n, k)-arrangement interconnection topology was first introduced in 1992. The (n, k )-arrangement graph is a class of generalized star graphs. Compared with the well known n-star, the (n, k )-arrangement graph is more flexible in degree and diameter. However, there are few algorithms designed for the (n, k)-arrangement graph up to present. In this thesis, we will focus on finding graph theoretical properties of the (n, k)- arrangement graph and developing parallel algorithms that run on this network. The topological properties of the arrangement graph are first studied. They include the cyclic properties. We then study the problems of communication: broadcasting and routing. Embedding problems are also studied later on. These are very useful to develop efficient algorithms on this network. We then study the (n, k )-arrangement network from the algorithmic point of view. Specifically, we will investigate both fundamental and application algorithms such as prefix sums computation, sorting, merging and basic geometry computation: finding convex hull on the (n, k )-arrangement graph. A literature review of the state-of-the-art in relation to the (n, k)-arrangement network is also provided, as well as some open problems in this area.

Properties and algorithms of the hyper-star graph and its related graphs

The hyper-star interconnection network was proposed in 2002 to overcome the drawbacks of the hypercube and its variations concerning the network cost, which is defined by the product of the degree and the diameter. Some properties of the graph such as connectivity, symmetry properties, embedding properties have been studied by other researchers, routing and broadcasting algorithms have also been designed. This thesis studies the hyper-star graph from both the topological and algorithmic point of view. For the topological properties, we try to establish relationships between hyper-star graphs with other known graphs. We also give a formal equation for the surface area of the graph. Another topological property we are interested in is the Hamiltonicity problem of this graph. For the algorithms, we design an all-port broadcasting algorithm and a single-port neighbourhood broadcasting algorithm for the regular form of the hyper-star graphs. These algorithms are both optimal time-wise. Furthermore, we prove that the folded hyper-star, a variation of the hyper-star, to be maixmally fault-tolerant.

Generating Relation Algebras for Qualitative Spatial Reasoning

Basic relationships between certain regions of space are formulated in natural language in everyday situations. For example, a customer specifies the outline of his future home to the architect by indicating which rooms should be close to each other. Qualitative spatial reasoning as an area of artificial intelligence tries to develop a theory of space based on similar notions. In formal ontology and in ontological computer science, mereotopology is a first-order theory, embodying mereological and topological concepts, of the relations among wholes, parts, parts of parts, and the boundaries between parts. We shall introduce abstract relation algebras and present their structural properties as well as their connection to algebras of binary relations. This will be followed by details of the expressiveness of algebras of relations for region based models. Mereotopology has been the main basis for most region based theories of space. Since its earliest inception many theories have been proposed for mereotopology in artificial intelligence among which Region Connection Calculus is most prominent. The expressiveness of the region connection calculus in relational logic is far greater than its original eight base relations might suggest. In the thesis we formulate ways to automatically generate representable relation algebras using spatial data based on region connection calculus. The generation of new algebras is a two pronged approach involving splitting of existing relations to form new algebras and refinement of such newly generated algebras. We present an implementation of a system for automating aforementioned steps and provide an effective and convenient interface to define new spatial relations and generate representable relational algebras.

Properties and Algorithms of the KCube Graphs

The KCube interconnection topology was rst introduced in 2010. The KCube graph is a compound graph of a Kautz digraph and hypercubes. Compared with the at- tractive Kautz digraph and well known hypercube graph, the KCube graph could accommodate as many nodes as possible for a given indegree (and outdegree) and the diameter of interconnection networks. However, there are few algorithms designed for the KCube graph. In this thesis, we will concentrate on nding graph theoretical properties of the KCube graph and designing parallel algorithms that run on this network. We will explore several topological properties, such as bipartiteness, Hamiltonianicity, and symmetry property. These properties for the KCube graph are very useful to develop efficient algorithms on this network. We will then study the KCube network from the algorithmic point of view, and will give an improved routing algorithm. In addition, we will present two optimal broadcasting algorithms. They are fundamental algorithms to many applications. A literature review of the state of the art network designs in relation to the KCube network as well as some open problems in this field will also be given.

Surfaces de Riemann compactes et formule de trace d'Eichler

Dans ce mémoire, nous étudierons quelques propriétés algébriques, géométriques et topologiques des surfaces de Riemann compactes. Deux grand sujets seront traités. Tout d'abord, en utilisant le fait que toute surface de Riemann compacte de genre g plus grand ou égal à 2 possède un nombre fini de points de Weierstrass, nous allons pouvoir conclure que ces surfaces possèdent un nombre fini d'automorphismes. Ensuite, nous allons étudier de plus près la formule de trace d'Eichler. Ce théorème nous permet de trouver le caractère d'un automorphisme agissant sur l'espace des q-différentielles holomorphes. Nous commencerons notre étude en utilisant la quartique de Klein. Nous effectuerons un exemple de calcul utilisant le théorème d'Eichler, ce qui nous permettra de nous familiariser avec l'énoncé du théorème. Finalement, nous allons démontrer la formule de trace d'Eichler, en prenant soin de traiter le cas où l'automorphisme agit sans point fixe séparément du cas où l'automorphisme possède des points fixes.