Gene transcription in individual living cells is inevitably a stochastic and dynamic process. Little is known about how cells and organisms learn to balance the fidelity of transcriptional control and the stochasticity of transcription dynamics. In an effort to elucidate the contribution of environmental signals to this intricate balance, a Three State Model was recently proposed, and the transcription system was assumed to transit among three different functional states randomly. In this work, we employ this model to demonstrate how the stochastic dynamics of gene transcription can be characterized by the three transition parameters. We compute the probability distribution of a zero transcript event and its conjugate, the distribution of the time durations in gene on or gene off periods, the transition frequency between system states, and the transcriptional bursting frequency. We also exemplify the mathematical results by the experimental data on prokaryotic and eukaryotic transcription. The analysis reveals that no promoters will be definitely turned on to transcribe within a finite time period, no matter how strong the induction signals are applied, and how abundant the activators are available. Although stronger extrinsic signals could enhance promoter activation rate, the promoter creates an intrinsic ceiling that no signals could cross over in a finite time. Consequently, among a large population of isogenic cells, only a portion of the cells, but not the whole population, could be induced by environmental signals to express a particular gene within a finite time period. We prove that the gene on duration follows an exponential distribution, and the gene off intervals show a local maximum that is best described by assuming two sequential exponential process. The transition frequencies are determined by a system of stochastic differential equations, or equivalently, an iterative scheme of integral operators. We prove that for each positive integer n , there associates a unique time, called the peak instant, at which the nth transcript synthesis cycle since time zero proceeds most likely. These moments constitute a time series preserving the nature order of n.

Better understanding of urban travelers is necessary, as sustainable development is becoming an integral part of transportation policy and practice. A volume of research shows people’s expressed willingness to adopt more sustainable urban travel behaviours, but a general sense of resistance to change is often encountered. Current methods in transportation research are not able to fully grasp on individual motivations such as discontent with public transport. This gap of knowledge in qualitative transportation research calls for the development of new methods. James Scott’s concept of the hidden transcript allows for the assumption that there are expressions of dissatisfaction towards public transportation at grassroots level. In order to access hidden transcripts on public transportation in Stockholm there is a need for a new method, which is developed in this thesis. The proposed visual mixed method draws from principles of visual ethnography, virtual ethnography, nethnography and social media research. The methodology is then tested and assessed as a platform to give voice to hidden transcripts on public transportation. The choice of method for developing the method is meta-methodology. The discussion sheds light on the potential of the framework (1) to grant access to hidden transcripts; (2) to fill a knowledge gap in transportation qualitative research; (3) to assist planners towards sustainable development of urban transportation.

<p>In the modern world, Internet has become a popular place, people with speech hearing disabilities and search engines can't take part of speech content in podcast les. In order to solve the problem partially, the Sphinx decoders such as Sphinx-3, Sphinx-4 can be used to implement a Auto Transcript Generator application, by coupling already existing large acoustic model, language model and a existing dictionary, or by training your own large acoustic model, language model and creating your own dictionary to support continuous speaker independent speech recognition system.</p>

In this study, we assessed pirAB toxin transcription in Photorhabdus luminescens laumondii (strain TT01) (Enterobacteriaceae) by comparing mRNA abundance under in vivo and in vitro conditions. In vivo assays considered both natural and forced infections with two lepidopteran hosts: Galleria mellonella and Manduca sexta. Three portals of entry were utilized for the forced infection assays: (a) integument; (b) the digestive route (via mouth and anus); and (c) the tracheal route (via spiracles). We also assessed plu4093-2 transcription during the course of a natural infection; this is when the bacteria are delivered by Heterorhabditis bacteriophora nematodes. Transcript abundance in G. mellonella was higher than in M. sexta at two of the observed time points: 15 and 18 h. Expression of pirAB plu4093-2 reached above endogenous control levels at 22 h in G. mellonella but not in M. sexta. Overall, pirAB plu4093-2 transcripts were not as highly expressed in M. sexta as in G. mellonella, from 15 to 22 h. This is the first study to directly compare pirAB plu4093-2 toxin transcript production considering different portals of entry.

Esta dissertação apresenta uma edição anotada de um livro inédito de contos de Valdomiro Silveira, Mucufos. A introdução situa historicamente esse livro, expõe as visões críticas a respeito do conjunto da obra do escritor, que envolvem aspectos sociais, humanos, estéticos e lingüísticos. Descreve o conjunto de contos de Mucufos encontrados em duas pastas denominadas Mucufos e Originaes manuscriptos de Papae (preciosíssimos), no Arquivo Valdomiro Silveira, no IEB/ USP, e explicita os critérios adotados na edição. Tal edição tem por finalidade estabelecer, a partir do confronto entre o apógrafo de CLSD (Carmen Lydia de Souza Dias), os autógrafos, os datiloscritos e os impressos encontrados nas pastas e no Arquivo do Estado, uma edição fidedigna. Para tanto, além do confronto referido, foi escolhida a transcrição crítica dos contos, procurando preservar os arcaísmos e os regionalismos presentes neles. A partir da transcrição, foram estabelecidos dois tipos de notas de rodapé. O primeiro, denominado de Nota CLSD, indica jornais de época em que foi publicada a maior parte dos contos, local e data de publicação, assim como local e data da escritura dos contos. O segundo, denominado Nota da edição, indica a pasta onde foi encontrado o conto e explica algumas palavras de cunho regional. Nas análises dos contos, buscou-se problematizar o teor de realismo, com a contribuição da categoria do realismo, segundo Georg Lukács; também foram analisadas as características estéticas, o grau de descrição de elementos da natureza e os principais temas e motivos. Entre estes últimos, destaca-se a violência e seu tratamento estético. Das análises, depreende-se a visão de Brasil por parte do escritor. A presente dissertação, pelo que foi exposto, busca resgatar uma parte do legado artístico de um escritor que muito se preocupou em humanizar um sujeito até então marginalizado em nossa literatura, o caipira, e discutir as principais questões estéticas e ideológicas surgidas nas análises dos 24 contos que constituem a edição. / This dissertation focuses on the annotated edition of an unpublished book of short stories, Mucufos, by Valdomiro Silveira. The introduction situates this book in a historical context, explaining critical views on the collected works of the writer, involving social, human, esthetical and linguistic aspects. It describes the short story collection of Mucufos found in two files named Mucufos and Originaes manuscriptos de Papae (especially valuable) in the Valdomiro Silveira Archive (IEB/ USP), and explains the criteria adopted for the edition. The aim of this edition was to establish an authentic edition emanating from a comparison between a reproduction by CLSD (Carmen Lydia de Souza Dias), autographs, typewritten sheets and printed papers found in the files and in the Office of Public Records. Apart from this comparison, a critical transcript of the short stories was chosen, in an attempt to preserve archaisms and regionalisms in these stories. Two types of footnotes were established from the transcript. The first note, named CLSD Note, indicates newspapers of the time period when most of the short stories were published, with publication date and location, as well as location and date when the stories were written. The second note, named Edition Note, indicates the file where the story was found, explaining some words of regional character. In an analysis of the short stories, there was an attempt to put in doubt the tenor of realism, with contribution from the category of realism, according to Georg Lukács; esthetical features, description of the elements, and main topics and motives were also analyzed. In the latter, violence and its esthetical treatment are highlighted. The writer\'s view of Brazil can be inferred from the analyses. Therefore, the current dissertation seeks to salvage part of the artistic legacy of a writer who was very concerned with humanizing an individual who had been marginalized in our literature until then, i.e. the hillbilly, and discuss the main esthetical and ideological issues that appear in the analyses of the 24 short stories of the edition.

The purpose of this thesis is to develop a software application based on previous studies by 1997 Oak Ridge Design Studio Team that matches students' progress with major requirements in their college career. This study addresses the problems of previous studies and suggests a solution. A powerful new technique, XML, is used to model, store and process the data of major requirements and student records. This application produces an HTML file that provides detailed information of a student's academic progress towards graduation.

In spite of substantial investments in science, technology, engineering, and mathematics (STEM) education, low enrollment and high attrition rate among students in these fields remain an unmitigated challenge for higher education institutions. In particular, underrepresentation of women and minority students with STEM-related college degrees replicates itself in the makeup of the workforce, adding another layer to the challenge. While most studies examine the relationship between student characteristics and their outcomes, in this study, I take a new approach to understand academic pathways as a dynamic process of student curricular experiences that influence his/her decision about subsequent course-takings and major field of the study. I leverage data mining techniques to examine the processes leading to degree completion in STEM fields. Specifically, I apply Sequential Pattern Mining and Sequential Clustering to student transcript data from a four-year university to identify frequent academic major trajectories and also the most frequent course-taking patterns in STEM fields. I also investigate whether there are any significant differences between male and female students’ academic major and course-taking patterns in these fields. The findings suggest that non-STEM majoring paths are the most frequent academic pattern among students, followed by life science trajectories. Engineering and other hard science trajectories are much less frequent. The frequency of all STEM trajectories, however, declines over time as students switch to non-STEM majors. The switching rate from non-STEM to STEM fields overtime is, however, much lower. I also find that male and female students follow different academic pathways, and these gender-based differences are even more significant within STEM fields. Students’ course-taking patterns also suggest that taking engineering and computer science courses is predominantly a male course-taking behavior, while females are more likely to pursue academic pathways in life science. I also find that STEM introductory courses - particularly Calculus I, Calculus II and Chemistry I – are gateway courses, that serve as potential barriers to pursuing degrees in STEM-related fields for a large number of students who showed an initial interest in STEM courses. Female students were more likely to switch to non-STEM fields after taking these courses, while male students were more likely to drop out of college overall. In addition to the study’s findings on students’ academic pathways toward attaining a college degree in a STEM-related field, this study also shows how data mining techniques that leverage data about the sequence of courses students take can be used by higher education leaders and researchers to better understand students’ academic progress and explore how students navigate and interact with college curriculum. In particular, this study demonstrates how these analytic approaches might be used to design and structure more effective course taking pathways and develop interventions to improve student retention in STEM fields.

Ultra-deep RNA sequencing has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We develop MATS (Multivariate Analysis of Transcript Splicing), a Bayesian statistical framework for flexible hypothesis testing of differential alternative splicing patterns on RNA-Seq data. MATS uses a multivariate uniform prior to model the between-sample correlation in exon splicing patterns, and a Markov chain Monte Carlo (MCMC) method coupled with a simulation-based adaptive sampling procedure to calculate the P value and false discovery rate (FDR) of differential alternative splicing. Importantly, the MATS approach is applicable to almost any type of null hypotheses of interest, providing the flexibility to identify differential alternative splicing events that match a given user-defined pattern. We evaluated the performance of MATS using simulated and real RNA-Seq data sets. In the RNA-Seq analysis of alternative splicing events regulated by the epithelial-specific splicing factor ESRP1, we obtained a high RT-PCR validation rate of 86% for differential alternative splicing events with a MATS FDR of < 10%. Additionally, over the full list of RT-PCR tested exons, the MATS FDR estimates matched well with the experimental validation rate. Our results demonstrate that MATS is an effective and flexible approach for detecting differential alternative splicing from RNA-Seq data.

This research investigates the physiological and transcriptional responses of Nitrosomonas europaea when exposed to chlorinated aromatic compounds and heavy metals under varying environmental conditions. It was found that transcriptional responses of identified sentinel genes correlate well with nitrification inhibition. Sorption of metals to biomass was also investigated and found not to correlate well with N. europaea inhibition. Whole genome microarray experiments were performed to define the transcriptional response of N. europaea when exposed to chlorobenzene. 13 out of 2460 N. europaea genes were significantly up-regulated after a 1-hour exposure to 4 μM chlorobenzene. HPLC analysis revealed that chlorobenzene was being oxidized primarily into 4-chlorophenol, and further physiological studies revealed that the presence of 4-chlorophenol could account for the inhibitory responses observed. RT-qPCR analysis of several differentially regulated genes verified that similar transcriptional responses were occurring for both chlorobenzene and 4-chlorophenol. 50% inhibitory concentrations of chlorobenzene and 4-chlorophenol resulted in moderate up-regulation of studied genes, however, increasing the concentration of 4-chlorophenol to achieve nitrification inhibition of 93% or more dramatically increased the fold regulation of several of the identified up- and down- regulated genes of interest. Increasing the 4-chlorophenol exposure time to 3 hours at the higher inhibition levels led to a general decrease in amplitude of transcriptional response for all genes tested. Cultures of N. europaea were exposed to various amounts of cadmium in aqueous solution containing EDTA, a strong metal-chelating organic, to control free ionic cadmium²⁺ (Cd²⁺) concentrations. Inhibition of ammonia oxidation as well as transcriptional up-regulation of merA, an identified sentinel gene for exposure to cadmium was found to correlate well with the concentration of Cd²⁺. The concentration of Cd²⁺ required to significantly affect N. europaea cells was found to be in the nanomolar range, which is several orders of magnitude lower than values reported in the literature for cadmium inhibition to mixed-culture activated sludge systems. The sorption of cadmium to the cells was found to be proportional to both the concentration of total cadmium and the concentration of Cd²⁺. At the concentration of metals required to cause approximately 50% nitrification inhibition, specific oxygen uptake results indicate the inhibition is specific to AMO with HAO and downstream energy-generation processes intact. To investigate more closely the inhibitory interactions between heavy metals and AMO, N. europaea inhibition by cadmium, zinc and silver was studied under substrate-limiting conditions. Unlike incubation in oxic environments, 1 hour incubations of N. europaea with cadmium and silver under anoxic conditions did not cause inhibition of nitrification activity after re-suspension in oxic media. In contrast, zinc, which is normally considered an analogue of cadmium in terms of toxic effect and transport mechanisms, was non-inhibitory to N. europaea when exposed in media lacking ammonia. Transcriptional response of merA closely followed the inhibition patterns, with samples which were inhibited after the removal of the metal having significant up-regulation of the gene, and those samples which were uninhibited showing no significant change in merA transcript levels compared to controls. Although sorbed metal concentrations were not found to be predictive of either extent of inhibition or transcriptional response, significantly more cadmium, zinc and silver were sorbed to biomass when incubated in aerobic media compared to anoxic media. Sorption in oxic media was found to be independent of AMO activity and similar results were obtained using Deinococcus radiodurans, a non-nitrifying gram-positive extremophile. The results indicate that greater heavy metal sorption to biomass in oxic environments may be due to general membrane chemistry effects. / Graduation date: 2011 / Access restricted to the OSU Community at author's request from March 31, 2011 - March 31, 2012

Renewable fibers produced by forest trees provide excellentraw material of high economic value for industrialapplications. Despite this, the genes and corresponding enzymesinvolved in wood fiber biosynthesis in trees are poorlycharacterized. This thesis describes a functional genomicsapproach for the identification of carbohydrate-active enzymesinvolved in secondary cell wall (wood) formation in hybridaspen. First, a 3' target amplification method was developed toenable microarray-based gene expression analysis on minuteamounts of RNA. The amplification method was evaluated usingboth a smaller microarray containing 192 cDNA clones and alarger microarray containing 2995 cDNA clones that werehybridized with targets isolated from xylem and phloem.Moreover, a gene expression study of phloem differentiation wasperformed to show the usefulness of the amplificationmethod. A microarray containing 2995 cDNA clones representing aunigene set of a cambial region EST library was used to studygene expression during wood formation. Transcript populationsfrom thin tissue sections representing different stages ofxylem development were hybridized onto the microarrays. It wasdemonstrated that genes encoding lignin and cellulosebiosynthetic enzymes, as well as a number of genes withoutassigned function, were differentially expressed across thedevelopmental gradient. Microarrays were also used to track changes in geneexpression in the developing xylem of transgenic, GA-20 oxidaseoverexpressing hybrid aspens that had increased secondarygrowth. The study revealed that a number of genes encoding cellwall related enzymes were upregulated in the transgenic trees.Moreover, most genes with high transcript changes could beassigned a role in the early events of xylogenesis. Ten genes encoding putative cellulose synthases (CesAs) wereidentified in our ownPopulusESTdatabase. Full length cDNA sequences wereobtained for five of them. Expression analyses performed withreal-time PCR and microarrays in normal wood undergoingxylogenesis and in tension wood revealed xylem specificexpression of four putative CesA isoenzymes. Finally, an approach combining expressionprofiling,bioinformatics as well as EST and full length sequencing wasadopted to identify secondary cell wall related genes encodingcarbohydrate-active enzymes, such as glycosyltransferases andglycoside hydrolases. As expected, glycosyltransferasesinvolved in the carbohydrate biosynthesis dominated thecollection of the secondary cell wall related enzymes that wereidentified. Key words:Populus, xylogenesis, secondary cell wall,cellulose, hemicellulose, microarrays, transcript profiling,carbohydrate-active enzyme, glycosyltransferase, glycosidehydrolase