Diss. (sammanfattning) Stockholm : Karolinska institutet, 2006. / Härtill 4 uppsatser.

Zugl.: Saarbrücken, Univ., Diss., 2008

Thesis (M.S.)--Miami University, Dept. of Physics, 2007. / Title from first page of PDF document. Includes bibliographical references (p. 49-50).

abstract: Immunosignaturing is a new immunodiagnostic technology that uses random-sequence peptide microarrays to profile the humoral immune response. Though the peptides have little sequence homology to any known protein, binding of serum antibodies may be detected, and the pattern correlated to disease states. The aim of my dissertation is to analyze the factors affecting the binding patterns using monoclonal antibodies and determine how much information may be extracted from the sequences. Specifically, I examined the effects of antibody concentration, competition, peptide density, and antibody valence. Peptide binding could be detected at the low concentrations relevant to immunosignaturing, and a monoclonal's signature could even be detected in the presences of 100 fold excess naive IgG. I also found that peptide density was important, but this effect was not due to bivalent binding. Next, I examined in more detail how a polyreactive antibody binds to the random sequence peptides compared to protein sequence derived peptides, and found that it bound to many peptides from both sets, but with low apparent affinity. An in depth look at how the peptide physicochemical properties and sequence complexity revealed that there were some correlations with properties, but they were generally small and varied greatly between antibodies. However, on a limited diversity but larger peptide library, I found that sequence complexity was important for antibody binding. The redundancy on that library did enable the identification of specific sub-sequences recognized by an antibody. The current immunosignaturing platform has little repetition of sub-sequences, so I evaluated several methods to infer antibody epitopes. I found two methods that had modest prediction accuracy, and I developed a software application called GuiTope to facilitate the epitope prediction analysis. None of the methods had sufficient accuracy to identify an unknown antigen from a database. In conclusion, the characteristics of the immunosignaturing platform observed through monoclonal antibody experiments demonstrate its promise as a new diagnostic technology. However, a major limitation is the difficulty in connecting the signature back to the original antigen, though larger peptide libraries could facilitate these predictions. / Dissertation/Thesis / Ph.D. Molecular and Cellular Biology 2011

This study provides new insights into the historical language contact between Classical Armenian and West Middle Iranian, specifically Parthian. Next to an up-to-date account of known lexical, morphological, and phraseological Iranian loans in Armenian, the discussion focuses on one major and three minor syntactic patterns which, it is argued, are the result of pattern replication. The major pattern, the Classical Armenian periphrastic perfect, has previously been the focus of numerous papers owing to its unusual construction: while intransitive verbs construe with nominative subjects and an optional form of the copula in subject agreement, transitive verbs exhibit genitive agents, accusative objects and an optional copula in a invariable 3.sg form. Based on a discussion of morphosyntactic alignment patterns in general, and of Armenian and West Middle Iranian in particular, it is shown that previous accounts cannot satisfactorily explain the syntax of the perfect. In a new approach, it is argued that Armenian exhibits tripartite morphosyntactic alignment as the result of 'copying' and adapting the ergative alignment pattern of the West Middle Iranian past tense. This analysis is supported both by the historical morphology of the perfect participle and by a corpus analysis of five major works of Armenian 5^th-century historiography. The minor patterns - ezāfe-like nominal relative clauses, subject resumption and switch-reference marking using the anaphoric pronoun Arm. ink'n, and the quotative use of Arm. (e)t'ē - are equally linked to parallel constructions in West Middle Iranian, which may have served as syntactic models for their Armenian counterparts. The final part of the study discusses the Armenian-Iranian relationship from a language contact point of view and, making use of historical, epigraphic, and literary sources, proposes that a superstrate shift of the Parthian-speaking ruling class of Armenia to Armenian as their primary language best explains the amount of Parthian linguistic material and patterns in Armenian.

There is a wide variety of drivers for business process modelling initiatives, reaching from organisational redesign to the development of information systems. Consequently, a common business process is often captured in multiple models that overlap in content due to serving different purposes. Business process management aims at exible adaptation to changing business needs. Hence, changes of business processes occur frequently and have to be incorporated in the respective process models. Once a process model is changed, related process models have to be updated accordingly, despite the fact that those process models may only be loosely coupled. In this article, we introduce an approach that supports change propagation between related process models. Given a change in one process model, we leverage the behavioural abstraction of behavioural profiles for corresponding activities in order to determine a change region in another model. Our approach is able to cope with changes in pairs of models that are not related by hierarchical refinement and show behavioural inconsistencies. We evaluate the applicability of our approach with two real-world process model collections. To this end, we either deduce change operations from different model revisions or rely on synthetic change operations.

Viral sequence data are increasingly being used to estimate evolutionary and epidemiological parameters to understand the dynamics of viral diseases. This thesis focuses on developing novel and improved computational methods for high-throughput analysis of large viral sequence datasets. I have developed a novel computational pipeline, Pipelign, to detect potentially unrelated sequences from groups of viral sequences during sequence alignment. Pipelign detected a large number of unrelated and mis-annotated sequences from several viral sequence datasets collected from GenBank. I subsequently developed ANVIL, a machine learning-based recombination detection and subtyping framework for pathogen sequences. ANVIL's performance was benchmarked using two large HIV datasets collected from the Los Alamos HIV Sequence Database and the UK HIV Drug Resistance Database, as well as on simulated data. Finally, I present a computational pipeline named Phlow, for rapid phylodynamic inference of heterochronous pathogen sequence data. Phlow is implemented with specialised and published analysis tools to infer important phylodynamic parameters from large datasets. Phlow was run with three empirical viral datasets and their outputs were compared with published results. These results show that Phlow is suitable for high-throughput exploratory phylodynamic analysis of large viral datasets. When combined, these three novel computational tools offer a comprehensive system for large scale viral sequence analysis addressing three important aspects: 1) establishing accurate evolutionary history, 2) recombination detection and subtyping, and 3) inferring phylodynamic history from heterochronous sequence datasets.

Submitted by Juliano Farias da Nobrega null (juliano@e8.com.br) on 2016-04-13T15:21:20Z No. of bitstreams: 1 dissert_juliano_unesp.pdf: 1652677 bytes, checksum: 2d05540d73450af0ce70d07689eeac2a (MD5) / Rejected by Felipe Augusto Arakaki (arakaki@reitoria.unesp.br), reason: Solicitamos que realize uma nova submissão seguindo as orientações abaixo: O arquivo submetido está sem a ficha catalográfica. A versão submetida por você é considerada a versão final da dissertação/tese, portanto não poderá ocorrer qualquer alteração em seu conteúdo após a aprovação. Corrija esta informação e realize uma nova submissão contendo o arquivo correto. Agradecemos a compreensão. on 2016-04-14T20:43:40Z (GMT) / Submitted by Juliano Farias da Nobrega null (juliano@e8.com.br) on 2016-04-15T13:45:15Z No. of bitstreams: 1 Dissertacao_Juliano_Unesp.pdf: 1798501 bytes, checksum: 97b5fd5aa56bbac1dd28b2e73b516bd4 (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-04-18T13:22:17Z (GMT) No. of bitstreams: 1 nobrega_jf_me_sjrp.pdf: 1798501 bytes, checksum: 97b5fd5aa56bbac1dd28b2e73b516bd4 (MD5) / Made available in DSpace on 2016-04-18T13:22:17Z (GMT). No. of bitstreams: 1 nobrega_jf_me_sjrp.pdf: 1798501 bytes, checksum: 97b5fd5aa56bbac1dd28b2e73b516bd4 (MD5) Previous issue date: 2016-02-29 / Recentemente, a bioinformática tornou-se um recurso imprescindível para a análise e interpretação da grande quantidade de informação biológica gerada pela biologia molecular e pelos sequenciadores de última geração. O processo de comparação dessas biossequências é o ponto de partida para o estudo da evolução e diferenciação dos organismos vivos, além de ser uma das tarefas mais importantes na biologia computacional. Neste trabalho apresenta-se uma abordagem baseada na heurística de Cadeias de Markov para otimização de um algoritmo de alinhamento múltiplo de sequências biológicas, proporcionando resultados com mais qualidade e sem o comprometimento do desempenho da ferramenta MUSCLE, escolhida para dar suporte ao trabalho. As cadeias de Markov foram escolhidas como técnica de otimização devido sua eficiente aplicabilidade em diversos problemas, sobretudo na biologia computacional, pois sua metodologia probabilística torna a aplicação computacionalmente viável, contornando os problemas NP-difícil e apresentando resultados significamente precisos. / Recently, bioinformatics has become an indispensable tool for analyzing and interpreting large amounts of information biological generated by molecular biology and the next-generation sequencers. The comparison process these sequences is the starting point for the study of evolution and differentiation of living organisms as well as being one of the most important tasks in computational biology. This work presents an approach based on Markov chains heuristics for optimization of a multiple alignment algorithm of biological sequences, provides improved quality results and without compromising the performance of MUSCLE tool chosen to support the work.. Markov chains were chosen as optimization technique due to its efficient applicability in various other problems, especially in computational biology, as its probabilistic methodology makes applying computationally feasible, bypassing the NP-hard problems and stating significantly accurate results.

This dissertation shows a model of Strategic Personal Planning and its link with the Organizational Strategic Planning. It s an exploratory study, qualitative nature with utilization of bibliographic research that allowed the analysis of Organizational Strategic Planning Models, Personal Planning and Aligment, so to build a Personal Strategic Planning model that was possible to harmonize with the Strategic Planning of the organization. The developed Personal Strategic Planning Model is built by five areas of act and performance: Individual Planning, Professional Planning, Family Planning, Personal Business Planning and Social Participation Planning. It was applied on nine people to validate it, and after the application it was done an interview about the effects and benefits of it. The developed Personal Strategic Planning aligned with the Organizational Planning allowed the integration of the personnel aspirations with the organizational in a synergy and equally balanced way. / Esta dissertação apresenta um Modelo de Planejamento Estratégico Pessoal e sua ligação com o Planejamento Estratégico Organizacional. É um estudo exploratório, de natureza qualitativa, com utilização de pesquisa bibliográfica, que permitiu a análise de modelos de Planejamento Estratégico Organizacional, Planejamento Pessoal e alinhamento, para, então, construir um Modelo de Planejamento Estratégico Pessoal, que fosse possível harmonizar com o Planejamento Estratégico da organização. O Modelo de Planejamento Estratégico Pessoal desenvolvido é composto por cinco áreas de atuação, ou desempenho: Planejamento Individual, Planejamento Profissional, Planejamento Familiar, Planejamento de Negócios Pessoais e Planejamento da Participação Social. Ele foi aplicado a nove pessoas, para validá-lo, sendo que, após a aplicação, foram feitas entrevistas sobre os efeitos e benefícios do mesmo. O alinhamento do Planejamento Estratégico Pessoal, desenvolvido, com o Planejamento Organizacional, possibilitou a integração das aspirações pessoais com as organizacionais, de forma sinérgica e equilibrada.

abstract: In this dissertation, the interface chemistry and electronic structure of plasma-enhanced atomic layer deposited (PEALD) dielectrics on GaN are investigated with x-ray and ultraviolet photoemission spectroscopy (XPS and UPS). Three interrelated issues are discussed in this study: (1) PEALD dielectric growth process optimization, (2) interface electronic structure of comparative PEALD dielectrics on GaN, and (3) interface electronic structure of PEALD dielectrics on Ga- and N-face GaN. The first study involved an in-depth case study of PEALD Al2O3 growth using dimethylaluminum isopropoxide, with a special focus on oxygen plasma effects. Saturated and self-limiting growth of Al2O3 films were obtained with an enhanced growth rate within the PEALD temperature window (25-220 ºC). The properties of Al2O3 deposited at various temperatures were characterized to better understand the relation between the growth parameters and film properties. In the second study, the interface electronic structures of PEALD dielectrics on Ga-face GaN films were measured. Five promising dielectrics (Al2O3, HfO2, SiO2, La2O3, and ZnO) with a range of band gap energies were chosen. Prior to dielectric growth, a combined wet chemical and in-situ H2/N2 plasma clean process was employed to remove the carbon contamination and prepare the surface for dielectric deposition. The surface band bending and band offsets were measured by XPS and UPS for dielectrics on GaN. The trends of the experimental band offsets on GaN were related to the dielectric band gap energies. In addition, the experimental band offsets were near the calculated values based on the charge neutrality level model. The third study focused on the effect of the polarization bound charge of the Ga- and N-face GaN on interface electronic structures. A surface pretreatment process consisting of a NH4OH wet chemical and an in-situ NH3 plasma treatment was applied to remove carbon contamination, retain monolayer oxygen coverage, and potentially passivate N-vacancy related defects. The surface band bending and polarization charge compensation of Ga- and N-face GaN were investigated. The surface band bending and band offsets were determined for Al2O3, HfO2, and SiO2 on Ga- and N-face GaN. Different dielectric thicknesses and post deposition processing were investigated to understand process related defect formation and/or reduction. / Dissertation/Thesis / Ph.D. Physics 2014