By integrating the simplicity of 18O-labeling and the low signal-to-noise of MS/MS spectra with supporting software and combining them with global shotgun protein identification, a robust quantitative pipeline has been created that avoids the disadvantages of other quantitative approaches. Test mixtures of labeled and unlabeled peptides were subjected to LC-MS/MS profiling experiments. Software programs were developed and applied to automatically determine protein ratios between two samples while applying a correction for incomplete labeling. The measurement of relative abundance at the product ion (MS/MS) level, instead of at the full scan (MS) level, is shown to provide excellent accuracy and sensitivity. Ratio distributions approached the expected means, allowing empirical derivation of confidence level cutoffs for determining statistically significant fold-changes in protein abundance. A set of stringent criteria for detecting spurious ratios based on consistency checking between unlabeled and labeled y-ion pairs was found to highlight putative false positive identifications.

Aquest treball és una contribució a l'estudi de diferents problemes que sorgeixen de dues àrees fortament connexes de la Teoria de Grafs: etiquetaments i descomposicions. Molts etiquetaments de grafs deuen el seu origen als presentats l'any 1967 per Rosa. Un d'aquests etiquetaments, àmpliament conegut com a etiquetament graceful, va ser definit originalment com a eina per atacar la conjectura de Ringel, la qual diu que el graf complet d'ordre 2m+1 pot ser descompost en m copies d'un arbre donat de mida m. Aquí, estudiem etiquetaments relacionats que ens donen certes aproximacions a la conjectura de Ringel, així com també a una altra conjectura de Graham i Häggkvist que, en una forma dèbil, demana la descomposició d'un graf bipartit complet per un arbre donat de mida apropiada. Les principals contribucions que hem fet en aquest tema són la prova de la darrera conjectura per grafs bipartits complets del doble de mida essent descompostos per arbres de gran creixement i un nombre primer d'arestes, i la prova del fet que cada arbre és un subarbre gran de dos arbres pels quals les dues conjectures es compleixen respectivament. Aquests resultats estan principalment basats en una aplicació del mètode polinomial d'Alon. Un altre tipus d'etiquetaments, els etiquetaments magic, també són tractats aquí. Motivats per la noció de quadrats màgics de Teoria de Nombres, en aquest tipus d'etiquetaments volem asignar nombres enters a parts del graf (vèrtexs, arestes, o vèrtexs i arestes) de manera que la suma de les etiquetes assignades a certes subestructures del graf sigui constant. Desenvolupem tècniques basades en particions de certs conjunts d'enters amb algunes condicions additives per construir etiquetaments cycle-magic, un nou tipus d'etiquetament introduït en aquest treball i que estén la noció clàssica d'etiquetament magic. Els etiquetaments magic no donen cap descomposició de grafs, però les tècniques usades per obtenir-los estan al nucli d'un altre problema de descomposició, l'ascending subgraph decomposition (ASD). Alavi, Boals, Chartrand, Erdös i Oellerman, van conjecturar l'any 1987 que tot graf té un ASD. Aquí, estudiem l'ASD per grafs bipartits, una classe de grafs per la qual la conjectura encara no ha estat provada. Donem una condició necessària i una de suficient sobre la seqüència de graus d'un estable del graf bipartit de manera que admeti un ASD en que cada factor sigui un star forest. Les tècniques utilitzades estan basades en l'existència de branca-acoloriments en multigrafs bipartits. També tractem amb el sumset partition problem, motivat per la conjectura ASD, que demana una partició de [n] de manera que la suma dels elements de cada part sigui igual a un valor prescrit. Aquí donem la millor condició possible per la versió modular del problema que ens permet provar els millors resultats ja coneguts en el cas enter per n primer. La prova està de nou basada en el mètode polinomial. / This work is a contribution to the study of various problems that arise from two strongly connected areas of the Graph Theory: graph labelings and graph decompositions. Most graph labelings trace their origins to the ones presented in 1967 by Rosa. One of these labelings, widely known as the graceful labeling, originated as a means of attacking the conjecture of Ringel, which states that the complete graph of order 2m+1 can be decomposed into m copies of a given tree of size m. Here, we study related labelings that give some approaches to Ringel's conjecture, as well as to another conjecture by Graham and Häggkvist that, in a weak form, asks for the decomposition of a complete bipartite graph by a given tree of appropriate size. Our main contributions in this topic are the proof of the latter conjecture for double sized complete bipartite graphs being decomposed by trees with large growth and prime number of edges, and the proof of the fact that every tree is a large subtree of two trees for which both conjectures hold respectively. These results are mainly based on a novel application of the so-called polynomial method by Alon. Another kind of labelings, the magic labelings, are also treated. Motivated by the notion of magic squares in Number Theory, in these type of labelings we want to assign integers to the parts of a graph (vertices, edges, or vertices and edges) in such a way that the sums of the labels assigned to certain substructures of the graph remain constant. We develop techniques based on partitions of certain sets of integers with some additive conditions to construct cycle-magic labelings, a new brand introduced in this work that extends the classical magic labelings. Magic labelings do not provide any graph decomposition, but the techniques that we use to obtain them are the core of another decomposition problem, the ascending subgraph decomposition (ASD). In 1987, was conjectured by Alavi, Boals. Chartrand, Erdös and Oellerman that every graph has an ASD. Here, we study ASD of bipartite graphs, a class of graphs for which the conjecture has not been shown to hold. We give a necessary and a sufficient condition on the one sided degree sequence of a bipartite graph in order that it admits an ASD by star forests. Here the techniques are based on the existence of edge-colorings in bipartite multigraphs. Motivated by the ASD conjecture we also deal with the sumset partition problem, which asks for a partition of [n] in such a way that the sum of the elements of each part is equal to a prescribed value. We give a best possible condition for the modular version of the sumset partition problem that allows us to prove the best known results in the integer case for n a prime. The proof is again based on the polynomial method.

Kunskap gällande barn och ungdomar som har olika funktionsnedsättningar är underutvecklad både i skolsituationen och i det sociala arbetet. Därmed är syftet med studien att studera hur kunskapsläget ser ut bland kuratorer respektive lärare som arbetar i särskilda klasser för elever som har Asperger syndrom. Vidare syftar studien till att granska vilka riktlinjer som finns uppsatta för kuratorer och lärare som möter ungdomar med särskilda behov samt hur ett professionellt bemötande beskrivs och tillämpas i praktiken. En kvalitativ metod har använts och studien omfattar sju intervjuer med kuratorer och lärare från två olika särskilda gymnasier. Resultatet visar att skolpersonalen lägger ett stort fokus på bemötandet av dessa elever och detta är en central del i det sociala arbetet med eleverna. För ett gynnsamt utfall hjälper inte enbart Skolverkets riktlinjer gällande hur arbetet med eleverna ska se ut. De båda verksamheterna har valt att utforma ytterligare riktlinjer för att skapa en god miljö där eleverna ska utvecklas och stärkas i sig själva. Detta arbetssätt går i linje med empowerment som tillsammans med stämplingsteorin har varit analysverktyg i studien. I diskussionen gällande vilka för- och nackdelar som finns med särskilda klasser för elever med Asperger syndrom kan ses att fördelarna väger tyngre än de nackdelar som råder. / The knowledge in children and adolescents who have various disabilities are under-developed both in school as well as in social work. Thus, the purpose of this study is to examine how the state of knowledge appears among social workers and teachers working in special classes for students with Asperger syndrome. Furthermore, the study aims to examine the guidelines that are set for counselors and teachers who work with adolescents with special needs and how a professional approach is described and applied in practice. A qualitative method was used and the study includes seven interviews with counselors and teachers from two special schools. The result shows that school staff places a strong focus on treatment of these students and this is a central part in social work with adolescents. To achieve a favorable outcome for the students with Asperger syndrome not only the Agency's guidelines are helpful for work with these students. The two schools have therefor chosen to develop their own additional guidelines for creating a good environment in which students will be developed and strengthened in themselves. This approach is in line with empowerment along with labeling theory, and these two have been research tools in the study. The discussion shows that the advantages of special classes for students with Asperger syndrome outweigh the few disadvantages that exist.

<p>We show topological priors play an important role in solving the inverse problem of shape reconstruction. We classify the applications into 1D, 2D, and 3D cases:</p><p>In 1D, we show that the persistent extrema of the curvature function of a closed curve are useful for shape simplication. In 2D, we study how to label a scene into multiple tiers to approximate the actual scene layout. We use the number of extrema as a topological prior to bound the complexity of the shape of tiers and study 2D labeling under symmetry shape priors. In 3D, we recover the detailed 3D root shape using multiple 2D images. Three novel ideas are presented. First, we propose the use of harmonic images for background subtraction. Second, we develop the regularized visual hull to preserve the details of an example image in reconstruction. Third, we enforce the topological connectedness by an ecient algorithm that is inspired by the recent development of persistent homology.</p><p>Computational efficiency is emphasized throughout the thesis. We show that 1D topological persistence can be computed in O(n) time on a closed curve of n nodes. For 2D tiered labeling, we give an approximation algorithm to compute it in O(nK) time for K tiers on an image of n pixels. For 3D root reconstruction, we accelerate the computation using oct-trees and minimal spanning trees. With these ingredients, it takes only a few seconds to reconstruct a detailed root shape from 40 images of resolution 1600*1200 on a laptop.</p> / Dissertation

The cytoskeleton is a diverse, multi-protein framework that plays a fundamental role in many cellular activities including mitosis, cell division, intracellular transport, cell motility, muscle contraction, and the regulation of cell polarity and organization. Furthermore, cytoskeletal filaments have been implicated in the pathogenesis of a wide variety of diseases including cancer, blood disease, cardiovascular disease, inflammatory disease, neurodegenerative disease, and problems with skin, nail, cornea, hair, liver and colon. Increasing evidence suggests that the distribution and organization of the cytoskeleton in living cells are affected by mechanical stresses and the cytoskeleton determines cell stiffness. We developed a fully nonlinear, constrained mixture model for adherent cells that allows one to account separately for the contributions of the primary structural constituents of the cytoskeleton and extended a prior solution from the finite elasticity literature for use in a sub-class of atomic force microscopy (AFM) studies of cell mechanics. The model showed that the degree of substrate stretch and the geometry of the AFM tip dramatically affect the measured cell stiffness. Consistent with previous studies, the model showed that disruption of the actin filaments can reduce the stiffness substantially, whereas there can be little contribution to the overall cell stiffness by the microtubules or intermediate filaments. To investigate the effect of mechanical stretching on cytoskeletal remodeling and cell stiffness, we developed a simple cell-stretching device that can be combined with an AFM and confocal microscopy. Results demonstrate that cyclic stretching significantly and rapidly alters both cell stiffness and focal adhesion associated vinculin and paxillin, suggesting that focal adhesion remodeling plays a critical role in cell stiffness by recruiting and anchoring F-actin. Finally, we estimated cytoskeletal remodeling by synthesizing data on stretch-induced dynamic changes in cell stiffness and focal adhesion area using constrained mixture approach. Results suggest that the acute increase in stiffness in response to an increased cyclic stretch was probably due to an increased stretch of the original filaments whereas the subsequent decrease back towards normalcy was consistent with a replacement of the highly stretched original filaments with less stretched new filaments.

A set of three through-bond energy transfer cassettes based on BODIPY as a donor and cyanine dyes as acceptors has been prepared via Sonogashira couplings, and their photophysical properties were examined. These cassettes fluoresce around 600 to 800 nm and are resolved by approximately 100 nm. This property is an important factor for multiplexing study in cellular imaging. Several useful fluorescent probes such as 5- and 6-carboxyfluorescein, water-soluble BODIPY, and water-soluble Nile Blue dyes, have also been synthesized and their photophysical properties studied. We have also attempted to develop a method for protein mono-labeling via a solidphase approach. The labeling of protein with one fluorescent dye facilitates quantification and single molecule imaging in biological applications. Various solidsupports such as PEGA, CPG, and BSA-coated CPG, were tested. Photolabile and chemically cleavable linkers were prepared to connect solid-supports and fluorophores. Unfortunately, our approach to the fluorescent mono-labeling of native proteins did not give us any conclusive results.

New methodologies for the efficient syntheses of 4,4-difluoro-4-bora-3a,4adiaza- s-indacenes (BODIPYs) and rosamines were developed. A serendipitous discovery led to a new reaction which afforded BODIPYs in high yields. Systematic studies of the kinetics and mechanisms of the new reaction were performed. A series of BODIPYs were successfully prepared using the new approach. A simple and efficient synthesis of rosamines with cyclic-amine substituents was devised. These new rosamines showed interesting anti-tumor activities. Several types of novel fluorescent compounds were prepared. Highly fluorescent GFP-chromophore analogs were designed and synthesized. The correlation between the optical properties and the structures was investigated. New pyronin dyes with mesoheteroatom substituents were efficiently prepared. The fluorescence properties of these compounds were highly dependent on the nature of the meso-substituents. A set of BODIPY dyes that fluoresce brightly above 600 nm were made. They were then used as acceptors to prepare water-soluble through-bond energy transfer cassettes. All the cassettes had complete energy transfer and high quantum yields in MeOH. A few also had good fluorescence properties in aqueous media and even on proteins. The through-bond energy transfer cassettes were used to monitor protein-protein interactions. In order to test our hypothesis, an artificial protein interaction system was built by utilizing the biotin/(strept)avidin interactions. Thus Atto425-BSA-biotin, streptavidin-cassette1 and avidin-cassette2 were prepared. The interactions between Atto425-BSA-biotin and cassette labeled (strept)avidin were successfully detected in vitro and in living cells by fluorescence techniques.

A specific number sociological theories and empirical studies suggest that deviant identity is the result of being formally or informally sanctioned by social audiences. The process by which individuals develop a deviant identity has been well documented by the literature. Most of this literature has linked the development of a deviant identity to the performance of deviant behavior. There is less evidence documenting the maleficent effects of bearing personal deviant characteristics such as stigmatizing health conditions, and/or being an involuntary member of a group socially defined as deviant (e.g. being the child of an alcoholic parent) in the development of a deviant identity. It is also noteworthy that, although parenting has been the focus of hundreds of studies examining deviant behavior and its consequences for individuals and their families, researchers rarely have been concerned with the effects of parenting in the development of a deviant self-concept. This dissertation examines the effects of parental emotional support on the development of a deviant identity by using a longitudinal data set that incorporates information of adolescents aged 12-19 who report their race, gender, level of selfesteem, parental relations, parental deviant behavior/characteristics, and peers and teacher stigmatization. Various models were estimated to test whether the relationship between deviance and deviant identity was significant, the mediating effects of stigmatization by peers and by teachers, and the moderating effect of both maternal and paternal emotional support on the development of a deviant identity. The results indicate that both maternal and paternal emotional support moderated the effect of maternal deviance but not the effect of paternal deviance. In the case of personal deviance, however, maternal deviance tended to increase as opposed to decrease deviant identity. Paternal emotional support did not moderate the effect of health limitations but it did diminish the effect of contact with the police. These findings were independent of the effects of gender, race, socioeconomic status, age, family structure, and earlier deviant identity. The implications and significance of these findings are discussed.

Fluorescent labeling can improve the detection sensitivity in capillary electrophoretic (CE) separations down to attomolar concentrations. However, most fluorescent labels are not compatible with CE because their fluorescence properties and charge states are pH-dependent, they are often hydrophobic and they have a tendency to significantly change the properties of the analytes after labeling. A group of fluorescent labeling reagents have been prepared whose fluorophores have properties that are optimized for CE separations. These fluorophores have fluorescence properties and charge states that are independent of pH in the 2 < pH < 11 range. Their excitation maxima are also compatible with the 488 nm line of the Argon ion laser. A mono-cationic acridine-based fluorescent label was prepared and was found to not shift the pI of a labeled model protein in capillary isoelectric focusing separation (cIEF). Lower loading, due to increased sensitivity, led to better resolution of closely spaced isoform peaks having a pI = 0.05. A tri-anionic pyrene-based fluorescent labeling reagent was also synthesized and was used in the sodium dodecyl sulfate capillary gel electrophoresis (SDS-CGE) separation of proteins. The fluorophore led to an LOQ in the nM range, and did not alter the migration behavior of proteins in the sieving matrix. A third fluorescent labeling reagent was developed as a solid phase reagent (SPR) where the fluorophore was immobilized on a solid surface through a cleavable anchor. The fluorophore is di-anionic and is based on pyrene. The SPR was designed to allow the simultaneous capture and labeling of an analyte and the efficient release of the label-analyte conjugate under mild acidic conditions. The use of the SPR allowed the labeling of a diamine whose concentration was in the low nanomolar range. The SPR opens up the possibility for mono-labeling and proportional multiple labeling of proteins.

The final implementation of Mandatory Country-of-Origin Labeling has caused some U.S. packing plants and finishing operations to discontinue using Canadian live hogs and feeder pigs in their operations thereby reducing trade. Using a system of simultaneous equations representing U.S. import demand and U.S. price, this thesis estimates the reduction in trade and any possible price effects in both live hogs and feeder pigs associated with the implementation of the final rule of Mandatory Country of Origin Labeling in the United States. It was found that the implementation of Mandatory Country of Origin Labeling reduced the trade of live hogs between the United States and Canada by 37.8 percent. The reduction in feeder pigs was 24.1 percent. It was also found that the implementation of Mandatory Country of Origin Labeling had no effect on the price of both live hogs and feeder pigs in the U.S. market.