Hox transcription factors are extensively investigated in diverse fields of molecular and evolutionary biology. Hox genes belong to the family of homeobox transcription factors characterised by a 60 amino acids region called homeodomain. These genes are evolutionary conserved and play crucial roles in the development of animals. In particular, they are involved in the specification of segmental identity, and in the tetrapod limb differentiation. In vertebrates, this family of genes can be divided into 14 groups of homology. Common methods to classify Hox proteins focus on the homeodomain. Classification is however hampered by the high conservation of this short domain. Since phylogenetic tree reconstruction is time-consuming, it is not suitable to classify the growing number of Hox sequences. The first goal of this thesis is therefore to design an automated approach to classify vertebrate Hox proteins in their groups of homology. This approach classifies Hox proteins on the basis of their scores for a combination of protein generalised profiles. The resulting program, HoxPred, combines predictive accuracy and time efficiency. We used this program to detect and classify Hox genes in several teleost fish genomes. In particular, it allowed us to clarify the evolutionary history of the HoxC1a genes in teleosts. Overall, HoxPred could efficiently contribute to the bioinformatics toolbox commonly used to annotate vertebrate Hox sequences. This program was then evaluated in non-vertebrate species. Although not intended for the classification of Hox proteins in distantly related species, HoxPred showed a high accuracy in bilaterians. It has also given insights into the evolutionary relationships between bilaterian posterior Hox genes, which are notoriously difficult to classify with phylogenetic trees. As transcription factors, Hox proteins regulate target genes by specifically binding DNA on cis-regulatory elements. Only a few of these target genes have been identified so far. The second goal of this work was to evaluate whether it is possible to apply computational approaches to detect Hox cis-regulatory elements in genomic sequences. Regulatory Sequence Analysis Tools (RSAT) is a suite of bioinformatics tools dedicated to the detection of cis-regulatory elements in genomes. We participated to the development of matrix-based pattern matching approaches in RSAT. After having performed a statistical validation of the pattern-matching scores, we focused on a study case based on the vertebrate HoxB1 protein, which binds DNA with its cofactors Pbx and Meis. This study aimed at predicting combinations of cis-regulatory elements for these three transcription factors.

Extracellular microenvironment, including its components and biophysical parameters such as matrix structure and stiffness, is a crucial determinant of cellular function. There exists interdependency between cellular behaviors and the extracellular matrix (ECM), whereby cells are constantly sensing and modifying their surroundings in response to physical stress or during processes like wound repair, cancer cell invasion, and morphogenesis, to create an environment which supports adaptation. To date, knowledge of the distinct regulatory mechanisms of this complex relationship is little, while the urge is evident as it plays a significant role in understanding tissue remodeling. Cells are observed to align with the parallel arrays of collagen fibrils found in tissues such as bone, tendon, and cornea, suggesting the importance of ordered matrices in defining cell functions. In this study, epitaxial growths of ordered two-dimensional collagen matrices were created, with parallelly aligned fibrils on muscovite mica, and novel triangular pattern matrix on phlogopite mica. Using Fluorescence and Atomic Force Microscopy, we were able to observe cell polarization along with stress fiber formation and matrix deformation at high resolution. Cells were observed to be able to penetrate between collagen fibrils and generate traction anisotropically to polarize. These ordered collagen matrices serve as an excellent model to study cellular remodeling of ECM in vitro, in which this fundamental apprehension of cell-matrix relationship is of crucial importance to manipulate the system and obtain desired cell functions.

Mitt syfte med undersökningen är att konstruera en modell för bedömning av elevtexter. Bedömningsmodellen ska vara kapabel att ge både en helhetsbild och en detaljbild av elevers diskursiva analytiska förmåga. Min utgångspunkt vid konstruktionen av bedömningsmodellen var bland annat Judith Langers föreställningsvärld och John Biggs SOLO-taxonomi. För att testa min bedömningsmodell samlade jag in elevtexter från naturvetarprogrammet på en gymnasieskola i Södertälje kommun. Texterna är inhämtade från två ämnen, Svenska A och Svenska C, och består av essäer. Resultatet av min undersökning blev en bedömningsmatris som granskar texterna utifrån fyra aspekter; struktur, språk och stil, argumentation och reflektion. Bedömningsmatrisen fungerar emellertid bättre som ett vertyg för uppskattning av texter än som ett vertyg för bedömning. Den ger tillräcklig information hur eleverna ligger till enligt kursplanerna för Svenska A respektive C inom dessa fyra aspekter, och utifrån de resultaten kan läraren se vad varje enskild elev klarar av och inte klarar av och kan planera lektionerna därefter.

In this thesis we revisit two classical definitions of angle in an inner product space: real-part angle and Hermitian angle. Special attention is paid to Krein’s inequality and its analogue. Some applications are given, leading to a simple proof of a basic lemma for a trace inequality of unitary matrices and also its extension. A brief survey on recent results of angles between subspaces is presented. This naturally brings us to the world of majorization. After introducing the notion of majorization, we present some classical as well as recent results on eigenvalue majorization. Several new norm inequalities are derived by making use of a powerful decomposition lemma for positive semidefinite matrices. We also consider coneigenvalue majorization. Some discussion on the possible generalization of the majorization bounds for Ritz values is presented. We then turn to a basic notion in convex analysis, the Legendre-Fenchel conjugate. The convexity of a function is important in finding the explicit expression of the transform for certain functions. A sufficient convexity condition is given for the product of positive definite quadratic forms. When the number of quadratic forms is two, the condition is also necessary. The condition is in terms of the condition number of the underlying matrices. The key lemma in our derivation is found to have some connection with the generalized Wielandt inequality. A new inequality between angles in inner product spaces is formulated and proved. This leads directly to a concise statement and proof of the generalized Wielandt inequality, including a simple description of all cases of equality. As a consequence, several recent results in matrix analysis and inner product spaces are improved.

Metal Matrix Composites (MMC) offer several thermo-mechanical advantages over standard materials and alloys which make them better candidates in different applications. Their light weight, high stiffness, and strength have attracted several industries such as automotive, aerospace, and defence for their wide range of products. However, the wide spread application of Meal Matrix Composites is still a challenge for industry. The hard and abrasive nature of the reinforcement particles is responsible for rapid tool wear and high machining costs. Fracture and debonding of the abrasive reinforcement particles are the considerable damage modes that directly influence the tool performance. It is very important to find highly effective way to machine MMCs. So, it is important to predict forces when machining Metal Matrix Composites because this will help to choose perfect tools for machining and ultimately save both money and time. This research presents an analytical force model for predicting the forces generated during machining of Metal Matrix Composites. In estimating the generated forces, several aspects of cutting mechanics were considered including: shearing force, ploughing force, and particle fracture force. Chip formation force was obtained by classical orthogonal metal cutting mechanics and the Johnson-Cook Equation. The ploughing force was formulated while the fracture force was calculated from the slip line field theory and the Griffith theory of failure. The predicted results were compared with previously measured data. The results showed very good agreement between the theoretically predicted and experimentally measured cutting forces. / UOIT

The graph model for conflict resolution (GMCR) provides a convenient and effective means to model and analyze a strategic conflict. Standard practice is to carry out a stability analysis of a graph model, and then to follow up with a post-stability analysis, two critical components of which are status quo analysis and coalition analysis. In stability analysis, an equilibrium is a state that is stable for all decision makers (DMs) under appropriate stability definitions or solution concepts. Status quo analysis aims to determine whether a particular equilibrium is reachable from a status quo (or an initial state) and, if so, how to reach it. A coalition is any subset of a set of DMs. The coalition stability analysis within the graph model is focused on the status quo states that are equilibria and assesses whether states that are stable from individual viewpoints may be unstable for coalitions. Stability analysis began within a simple preference structure which includes a relative preference relationship and an indifference relation. Subsequently, preference uncertainty and strength of preference were introduced into GMCR but not formally integrated. In this thesis, two new preference frameworks, hybrid preference and multiple-level preference, and an integrated algebraic approach are developed for GMCR. Hybrid preference extends existing preference structures to combine preference uncertainty and strength of preference into GMCR. A multiple-level preference framework expands GMCR to handle a more general and flexible structure than any existing system representing strength of preference. An integrated algebraic approach reveals a link among traditional stability analysis, status quo analysis, and coalition stability analysis by using matrix representation of the graph model for conflict resolution. To integrate the three existing preference structures into a hybrid system, a new preference framework is proposed for graph models using a quadruple relation to express strong or mild preference of one state or scenario over another, equal preference, and an uncertain preference. In addition, a multiple-level preference framework is introduced into the graph model methodology to handle multiple-level preference information, which lies between relative and cardinal preferences in information content. The existing structure with strength of preference takes into account that if a state is stable, it may be either strongly stable or weakly stable in the context of three levels of strength. However, the three-level structure is limited in its ability to depict the intensity of relative preference. In this research, four basic solution concepts consisting of Nash stability, general metarationality, symmetric metarationality, and sequential stability, are defined at each level of preference for the graph model with the extended multiple-level preference. The development of the two new preference frameworks expands the realm of applicability of the graph model and provides new insights into strategic conflicts so that more practical and complicated problems can be analyzed at greater depth. Because a graph model of a conflict consists of several interrelated graphs, it is natural to ask whether well-known results of Algebraic Graph Theory can help analyze a graph model. Analysis of a graph model involves searching paths in a graph but an important restriction of a graph model is that no DM can move twice in succession along any path. (If a DM can move consecutively, then this DM's graph is effectively transitive. Prohibiting consecutive moves thus allows for graph models with intransitive graphs, which are sometimes useful in practice.) Therefore, a graph model must be treated as an edge-weighted, colored multidigraph in which each arc represents a legal unilateral move and distinct colors refer to different DMs. The weight of an arc could represent some preference attribute. Tracing the evolution of a conflict in status quo analysis is converted to searching all colored paths from a status quo to a particular outcome in an edge-weighted, colored multidigraph. Generally, an adjacency matrix can determine a simple digraph and all state-by-state paths between any two vertices. However, if a graph model contains multiple arcs between the same two states controlled by different DMs, the adjacency matrix would be unable to track all aspects of conflict evolution from the status quo. To bridge the gap, a conversion function using the matrix representation is designed to transform the original problem of searching edge-weighted, colored paths in a colored multidigraph to a standard problem of finding paths in a simple digraph with no color constraints. As well, several unexpected and useful links among status quo analysis, stability analysis, and coalition analysis are revealed using the conversion function. The key input of stability analysis is the reachable list of a DM, or a coalition, by a legal move (in one step) or by a legal sequence of unilateral moves, from a status quo in 2-DM or $n$-DM ($n > 2$) models. A weighted reachability matrix for a DM or a coalition along weighted colored paths is designed to construct the reachable list using the aforementioned conversion function. The weight of each edge in a graph model is defined according to the preference structure, for example, simple preference, preference with uncertainty, or preference with strength. Furthermore, a graph model and the four basic graph model solution concepts are formulated explicitly using the weighted reachability matrix for the three preference structures. The explicit matrix representation for conflict resolution (MRCR) that facilitates stability calculations in both 2-DM and $n$-DM ($n > 2$) models for three existing preference structures. In addition, the weighted reachability matrix by a coalition is used to produce matrix representation of coalition stabilities in multiple-decision-maker conflicts for the three preference frameworks. Previously, solution concepts in the graph model were traditionally defined logically, in terms of the underlying graphs and preference relations. When status quo analysis algorithms were developed, this line of thinking was retained and pseudo-codes were developed following a similar logical structure. However, as was noted in the development of the decision support system (DSS) GMCR II, the nature of logical representations makes coding difficult. The DSS GMCR II, is available for basic stability analysis and status quo analysis within simple preference, but is difficult to modify or adapt to other preference structures. Compared with existing graphical or logical representation, matrix representation for conflict resolution (MRCR) is more effective and convenient for computer implementation and for adapting to new analysis techniques. Moreover, due to an inherent link between stability analysis and post-stability analysis presented, the proposed algebraic approach establishes an integrated paradigm of matrix representation for the graph model for conflict resolution.

I argue for the Expanded Cluster Account of art (ECA) by first inquiring as to whether “art” is best described by a cluster account and where ECA fits into the current landscape of theories of concepts. Second, I explicate the relevant aspects of Boyd’s theory of natural kinds and argue that his concepts of “disciplinary matrices” and “homeostatic property clusters” (roughly analogous to Gaut’s criterial properties for characterizing art, particularized for each individual kind) have relevant roles in a proper cluster account of art, thus explicating and expanding Gaut’s account in the process. Third, I defend the thesis that Boyd’s concept of “disciplinary matrix,” when applied to “art,” is fulfilled by George Dickie’s notion of “the Artworld.” Lastly, I consider objections to ECA and positively explain its heuristic and explanatory efficacy above and beyond other contemporary “anti-definitional” accounts.

The reactions and photochemistry of atomic and diatomic transition metals with methanol, water, hydrogen, and carbon monoxide in noble gas matrices at cryogenic temperatures have been studied with the use of Fourier Transform infrared inert matrix spectroscopy. Atoms and dimers of iron and cobalt reacted with methanol to form the adducts, M(CH30H) and M2(CH30H), respectively. M(CH30H) underwent metal insertion into the 0-H bond of methanol to yield methoxymetal hydride, CH3OMH, with irradiation of the matrix in the violet (400 nm < λ < 500 nm) region. Ultraviolet (280 nm < λ < 360 nm) photolysis of the matrix rearranged CH30MH to yield the methylmetal hydroxide species, CH3MOH. CH30MH dissociated into carbon monoxide and hydrogen after prolonged irradiation in the ultraviolet region. Surprisingly, nickel atoms reacted spontaneously to insert into the 0-H bonds of methanol and water to form CH30NiH and HONiH, respectively. Violet photolysis caused CH30NiH to rearrange to form methylnickel hydroxide, CH3NiOH. This is effectively a two step process of the C-0 activation of methanol by a nickel atom. In addition to rearrangement, CH30NiH dissociates into carbon monoxide and hydrogen with violet photolysis. Nickel dimers also reacted spontaneously with water to form both an adduct and insertion products. Atomic nickel spontaneously inserts into the H-H bond of molecular hydrogen to yield a bent nickel dihydride, NiH2, in krypton and xenon matrices. Nickel dimers and trimers insert into the H-H bond of hydrogen to form Nix(H)2. In addition to the insertion products, nickel atoms, dimers, and trimers form adducts molecularly with hydrogen to yield complexes of the form Nix(H2)y, where x or y = 1-3. Reactions of iron with carbon monoxide in an argon matrix yielded the iron-carbonyl complexes, Fex(CO)y, where x = 1-3 and y = 1-2.

The Collaborative Synchronization Management Tool (CSMT) is an analysis tool that enables morphological and statistical analysis of plans. Input to the CSMT consists of a Cross Impact Matrix (CIM) where the relationships between the different activities of a plan are reflected as its values. This thesis proposes Modeling and Simulation as an alternative method of generating the CIM-values. The usage of this method will hopefully increase traceability and limit subjectivity, and it will also be less time-consuming. Determining the level of detail of the models was shown to be a challenge, as well as finding a suitable case scenario to validate the generation method more thoroughly. The results have provided positive indicators to the usefulness of the generation method of input to the CSMT but the evaluation remains somewhat inconclusive.

In this paper we consider optimal design of experiments in the case of correlated observations, when no replications are possible. This situation is typical when observing a random process or random field with known covariance structure. We present a theorem which demonstrates that the computation of optimum exact designs corresponds to solving minimization problems in terms of design measures. (author's abstract) / Series: Forschungsberichte / Institut für Statistik