Herpes simplex virus is an important model in the study of temporally regulated gene expression in eukaryotic cells. Three classes of genes - immediate early, early, and late - are sequentially expressed during the course of lytic infection. One immediate early gene product, ICP4, is required for transactivation of most early and late genes; it is also implicated in repression of immediate early gene expression. ICP4's mechanism(s) of action is/are not yet understood; although ICP4 binds to specific sequences of DNA, whether this is necessary for transregulation by ICP4 is not clear. To gain a better understanding of how the ability of ICP4 to bind DNA relates to its transregulatory activities, I introduced ICP4 binding sites into a simple model promoter within the viral genome. Two sets of construct were made in which an ICP4 binding site (or mutant site) was placed either downstream or upstream of a TATA box, reproducing the spacing found in (i) the native 𝘐𝘊𝘗4 promoter and (ii) the native 𝘐𝘊𝘗0 promoter (respectively). The promoter of HSV-1 𝘜𝘓24𝘣 (a nonessential gene in tissue culture) was replaced with these model promoters and levels of transcripts accumulating from these constructs during lytic infection assayed by primer extension. I found that an ICP4 site placed either upstream or downstream of a TATA box shifted kinetics of expression from E/leaky L to true L. Neither the strength of the TATA box nor the helical orientation of the ICP4 binding site with respect to the TATA box affected this result. / Thesis / Master of Science (MS)

Previous studies have shown that a functional Ad 5 E1A protein from the 13 S mRNA is required during lytic infection for activation of early viral gene expression (Jones and Shenk, 1979b; Berk et al, 1979; Montell et al, 1982). The mechanism by which E1A exerts this regulatory function is still unclear and has been the subject of intense investigation (Persson et al, 1981a; Katze et al, 1981, 1983; Nevins, 1981; Shaw and Ziff, 1982). Most of these recent investigations have relied on the use of metabolic inhibitors such as cycloheximide to eliminate protein synthesis as a means of determining the role of viral and host proteins in the regulatory process. The results from these studies have been inconsistent. The purpose of this research project has been to re-examine the regulation of Ad 5 early gene expression without the use of drug inhibitors. In this study tsH1 cells, a mutant CHO cell line which at temperatures above 37°C are inhibited in protein synthesis, were used. At critical times during the course of wild type or host-range 1 infection of tsH1 cells, protein synthesis was inhibited and Early Region 4 expression was examined. In every case, efficient E4 expression was dependent on functional E1A protein and this requirement could not be replaced by simply inhibiting protein synthesis. The results are discussed in relation to models proposed to explain the regulation of Ad 5 Early Gene Expression. / Thesis / Master of Science (MS)

Ovarian secretions and growth hormone (GH) are major endocrine regulators of mammary growth and development in bovine mammary gland; but information on endocrine regulation during early prepubertal period is limited. Our overall objective was to study the regulation of mammary growth and development as well as transcript abundance in early prepubertal bovine mammary gland by ovarian secretions and exogenous bovine somatotropin (bST). In the first study, we determined the effect of staged ovariectomy on mammary growth and development in two to four month old Holstein heifers. In the second study, effects of bST on mammary growth and development, and also on putative stem cell population were evaluated by beginning bST treatment in one month old Holstein heifers. Mammary growth and development was determined by mass of mammary tissue, biochemical analyses, histological examination, transcript abundance and protein expression in mammary parenchyma (PAR) and fat pad (MFP). Ovariectomy reduced mass and lipid content of PAR without affecting the histological characteristics or rate of epithelial cell proliferation. There was a marked reduction in progesterone receptor expression both at the mRNA and protein level. Ovariectomy also reduced transcript abundance in GH receptor (R), insulin-like growth factor (IGF)-1, IGF binding protein -6, estrogen responsive and proliferation marker genes, but increased the mRNA abundance of IGF-1R in PAR. On the other hand, administration of bST did not have an impact on PAR growth, epithelial proliferation, putative stem cell population or transcript abundance of IGF-axis genes. However, bST reduced the relative abundance of GHR, signal transducers and activators of transcription-5b and suppressors of cytokine signaling-2 in mammary PAR. Transcript abundance of IGF-axis molecules, estrogen responsive genes and proliferation markers in MFP was not affected by ovariectomy or bST. Overall, our data suggest that ovary is a predominant regulator of mammary growth and development in prepubertal heifers and that exogenous bST is not effective as a mammary specific mitogen in very young prepubertal heifers. / Ph. D.

Classification of tissues and diseases based on gene expression data is a powerful application of DNA microarrays. Many popular classifiers like support vector machines, nearest-neighbour methods, and boosting have been applied successfully to this problem. However, it is difficult to determine from these classifiers which genes are responsible for the distinctions between the diseases. We propose a novel framework for classification of gene expression data based on notion of condition-specific clusters of co-expressed genes called xMotifs. Our xMotif-based classifier is biologically interpretable: we show how we can detect relationships between xMotifs and gene functional annotations. Our classifier achieves high-accuracy on leave-one-out cross-validation on both two-class and multi-class data. Our technique has the potential to be the method of choice for researchers interested in disease and tissue classification. / Master of Science

Diss. (sammanfattning) Stockholm : Karol. inst., 2006. / Härtill 4 uppsatser.

As a universal element of human nature, the experience, expression, and perception of emotions permeate our daily lives. Many emotions are thought to be basic and common to all humanity, irrespective of social or cultural background. Of these emotions, the corresponding facial expressions of a select few are known to be truly universal, in that they can be identified by most observers without the need for training. Facial expressions of emotion are subsequently used as a method of communication, whether through close face-to-face contact, or the use of emoticons online and in mobile texting. Facial expressions are fundamental to acting for stage and screen, and to animation for film and computer games. Expressions of emotion have been the subject of intense experimentation in psychology and computer science research, both in terms of their naturalistic appearance and the virtual replication of facial movements. From this work much is known about expression universality, anatomy, psychology, and synthesis. Beyond the realm of scientific research, animation practitioners have scrutinised facial expressions and developed an artistic understanding of movement and performance. However, despite the ubiquitous quality of facial expressions in life and research, our understanding of how to produce synthetic, dynamic imitations of emotional expressions which are perceptually valid remains somewhat limited. The research covered in this thesis sought to unite an artistic understanding of expression animation with scientific approaches to facial expression assessment. Acting as both an animation practitioner and as a scientific researcher, the author set out to investigate emotional facial expression dynamics, with the particular aim of identifying spatio-temporal configurations of animated expressions that not only satisfied artistic judgement, but which also stood up to empirical assessment. These configurations became known as emotional expression choreographies. The final work presented in this thesis covers the performative, practice-led research into emotional expression choreography, the results of empirical experimentation (where choreographed animations were assessed by observers), and the findings of qualitative studies (which painted a more detailed picture of the potential context of choreographed expressions). The holistic evaluation of expression animation from these three epistemological perspectives indicated that emotional expressions can indeed be choreographed in order to create refined performances which have empirically measurable effects on observers, and which may be contextualised by the phenomenological interpretations of both student animators and general audiences.

We study the tasks of transcript expression quantification and differential expression analysis based on data from high-throughput sequencing of the transcriptome (RNA-seq). In an RNA-seq experiment subsequences of nucleotides are sampled from a transcriptome specimen, producing millions of short reads. The reads can be mapped to a reference to determine the set of transcripts from which they were sequenced. We can measure the expression of transcripts in the specimen by determining the amount of reads that were sequenced from individual transcripts. In this thesis we propose a new probabilistic method for inferring the expression of transcripts from RNA-seq data. We use a generative model of the data that can account for read errors, fragment length distribution and non-uniform distribution of reads along transcripts. We apply the Bayesian inference approach, using the Gibbs sampling algorithm to sample from the posterior distribution of transcript expression. Producing the full distribution enables assessment of the uncertainty of the estimated expression levels. We also investigate the use of alternative inference techniques for the transcript expression quantification. We apply a collapsed Variational Bayes algorithm which can provide accurate estimates of mean expression faster than the Gibbs sampling algorithm. Building on the results from transcript expression quantification, we present a new method for the differential expression analysis. Our approach utilizes the full posterior distribution of expression from multiple replicates in order to detect significant changes in abundance between different conditions. The method can be applied to differential expression analysis of both genes and transcripts. We use the newly proposed methods to analyse real RNA-seq data and provide evaluation of their accuracy using synthetic datasets. We demonstrate the advantages of our approach in comparisons with existing alternative approaches for expression quantification and differential expression analysis. The methods are implemented in the BitSeq package, which is freely distributed under an open-source license. Our methods can be accessed and used by other researchers for RNA-seq data analysis.

O processamento e a identificação de emoções faciais constituem ações essenciais para estabelecer interação entre pessoas. Alguns transtornos psiquiátricos podem limitar a capacidade de um indivíduo em reconhecer emoções em expressões faciais. De modo a contribuir com a solução deste problema, técnicas computacionais podem ser utilizadas para compor ferramentas destinadas ao diagnóstico, avaliação e treinamento no reconhecimento de tais expressões. Com esta motivação, o objetivo deste trabalho é definir, implementar e avaliar um método para sintetizar expressões faciais que representam emoções em imagens de pessoas reais. Nos trabalhos encontrados na literatura a principal ideia é que a expressão facial da imagem de uma pessoa pode ser reconstituída na imagem de outra pessoa. Este estudo difere-se das abordagens apresentadas na literatura ao propor uma técnica que considera a similaridade entre imagens faciais para escolher aquela que será empregada como origem para a reconstituição. Desta maneira, pretende-se aumentar o realismo das imagens sintetizadas. A abordagem sugerida para resolver o problema, além de buscar as faces mais similares em banco de imagens, faz a deformação dos componentes faciais e o mapeamento das diferenças de iluminação na imagem destino. O realismo das imagens geradas foi mensurado de forma objetiva e subjetiva usando imagens disponíveis em bancos de imagens públicos. Uma análise visual mostrou que as imagens sintetizadas com base em faces similares apresentaram um grau de realismo adequado, principalmente quando comparadas com imagens sintetizadas a partir de faces aleatórias. Além de constituir uma contribuição para a geração de imagens a serem aplicadas em ferramentas de auxílio ao diagnóstico e terapia de distúrbios psiquiátricos, oferece uma contribuição para a área de Ciência da Computação, por meio da proposição de novas técnicas de síntese de expressões faciais / The ability to process and identify facial emotions are essential factors for an individual\'s social interaction. Some psychiatric disorders can limit an individual\'s ability to recognize emotions in facial expressions. This problem could be confronted by using computational techniques in order to develop learning environments for diagnosis, evaluation, and training in identifying facial emotions. With this motivation, the objective of this work is to define, implement and evaluate a method to synthesize realistic facial expression that represents emotions in images of real people. The main idea of the studies found in the literature is that a facial expression of one persons image can be reenacted in an another persons image. The study differs from the approaches presented in the literature when proposing a technique that considers the similarity between facial images to choose the one that will be used as the origin for reenactment. As a result, we intend to increase the realism of the synthesized images. Our approach to solve the problem, besides searching for the most similar facial components in the image dataset, also deforms the facial elements and maps the differences of illumination in the target image. A visual analysis showed that the images synthesized on the basis of similar faces presented an adequate degree of realism, especially when compared with images synthesized from random faces. The study will contribute to the generation of the images applied to tools for the diagnosis and therapy of psychiatric disorders, and also contribute to the computational field, through the proposition of new techniques for facial expression synthesis

O processamento e a identificação de emoções faciais constituem ações essenciais para estabelecer interação entre pessoas. Alguns transtornos psiquiátricos podem limitar a capacidade de um indivíduo em reconhecer emoções em expressões faciais. De modo a contribuir com a solução deste problema, técnicas computacionais podem ser utilizadas para compor ferramentas destinadas ao diagnóstico, avaliação e treinamento no reconhecimento de tais expressões. Com esta motivação, o objetivo deste trabalho é definir, implementar e avaliar um método para sintetizar expressões faciais que representam emoções em imagens de pessoas reais. Nos trabalhos encontrados na literatura a principal ideia é que a expressão facial da imagem de uma pessoa pode ser reconstituída na imagem de outra pessoa. Este estudo difere-se das abordagens apresentadas na literatura ao propor uma técnica que considera a similaridade entre imagens faciais para escolher aquela que será empregada como origem para a reconstituição. Desta maneira, pretende-se aumentar o realismo das imagens sintetizadas. A abordagem sugerida para resolver o problema, além de buscar as faces mais similares em banco de imagens, faz a deformação dos componentes faciais e o mapeamento das diferenças de iluminação na imagem destino. O realismo das imagens geradas foi mensurado de forma objetiva e subjetiva usando imagens disponíveis em bancos de imagens públicos. Uma análise visual mostrou que as imagens sintetizadas com base em faces similares apresentaram um grau de realismo adequado, principalmente quando comparadas com imagens sintetizadas a partir de faces aleatórias. Além de constituir uma contribuição para a geração de imagens a serem aplicadas em ferramentas de auxílio ao diagnóstico e terapia de distúrbios psiquiátricos, oferece uma contribuição para a área de Ciência da Computação, por meio da proposição de novas técnicas de síntese de expressões faciais / The ability to process and identify facial emotions are essential factors for an individual\'s social interaction. Some psychiatric disorders can limit an individual\'s ability to recognize emotions in facial expressions. This problem could be confronted by using computational techniques in order to develop learning environments for diagnosis, evaluation, and training in identifying facial emotions. With this motivation, the objective of this work is to define, implement and evaluate a method to synthesize realistic facial expression that represents emotions in images of real people. The main idea of the studies found in the literature is that a facial expression of one persons image can be reenacted in an another persons image. The study differs from the approaches presented in the literature when proposing a technique that considers the similarity between facial images to choose the one that will be used as the origin for reenactment. As a result, we intend to increase the realism of the synthesized images. Our approach to solve the problem, besides searching for the most similar facial components in the image dataset, also deforms the facial elements and maps the differences of illumination in the target image. A visual analysis showed that the images synthesized on the basis of similar faces presented an adequate degree of realism, especially when compared with images synthesized from random faces. The study will contribute to the generation of the images applied to tools for the diagnosis and therapy of psychiatric disorders, and also contribute to the computational field, through the proposition of new techniques for facial expression synthesis

This thesis is focused on mapping written expression among pupils at the fifth grade of basic schools. The thesis is divided into two parts - the theoretical part and the empirical part. The theoretical part of the thesis is devoted to the theoretical knowledge available about written expression and about disorder of written expression. Attention is paid here to the diagnosis of written expression and to the analysis of the available diagnostic tools that deal with testing of written expression. In the empirical part of the thesis, we are primarily focused on designing the test of written expression and its evaluation system. Our next goal was to verify the predictive value of the designed test of written expression on fifth grade pupils and to compare pupils' performance among themselves. Secondary goal of the thesis is to compare the results of the test by a statistical quantitative methodology and to subsequently discuss them in terms of gender, font pattern (Comenia Script font and bound font pattern) and the presence or absence of specific learning disorders. The partial goal is to verify the correlation of the results of the designed test. Data collection was conducted by a group administration. A total of six basic schools took part in research studies of the written expression. We have...