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Next-generation sequencing has generated enormous amount of DNA and RNA sequences that potentially carry volumes of genetic information, e.g. protein-coding genes. The thesis is divided into three main parts describing i) GeneMarkS-2, ii) GeneMarkS-T, and iii) MetaGeneTack. In prokaryotic genomes, ab initio gene finders can predict genes with high accuracy. However, the error rate is not negligible and largely species-specific. Most errors in gene prediction are made in genes located in genomic regions with atypical GC composition, e.g. genes in pathogenicity islands. We describe a new algorithm GeneMarkS-2 that uses local GC-specific heuristic models for scoring individual ORFs in the first step of analysis. Predicted atypical genes are retained and serve as ‘external’ evidence in subsequent runs of self-training. GeneMarkS-2 also controls the quality of training process by effectively selecting optimal orders of the Markov chain models as well as duration parameters in the hidden semi-Markov model. GeneMarkS-2 has shown significantly improved accuracy compared with other state-of-the-art gene prediction tools. Massive parallel sequencing of RNA transcripts by the next generation technology (RNA-Seq) provides large amount of RNA reads that can be assembled to full transcriptome. We have developed a new tool, GeneMarkS-T, for ab initio identification of protein-coding regions in RNA transcripts. Unsupervised estimation of parameters of the algorithm makes unnecessary several steps in the conventional gene prediction protocols, most importantly the manually curated preparation of training sets. We have demonstrated that the GeneMarkS-T self-training is robust with respect to the presence of errors in assembled transcripts and the accuracy of GeneMarkS-T in identifying protein-coding regions and, particularly, in predicting gene starts compares favorably to other existing methods. Frameshift prediction (FS) is important for analysis and biological interpretation of metagenomic sequences. Reads in metagenomic samples are prone to sequencing errors. Insertion and deletion errors that change the coding frame impair the accurate identification of protein coding genes. Accurate frameshift prediction requires sufficient amount of data to estimate parameters of species-specific statistical models of protein-coding and non-coding regions. However, this data is not available; all we have is metagenomic sequences of unknown origin. The challenge of ab initio FS detection is, therefore, twofold: (i) to find a way to infer necessary model parameters and (ii) to identify positions of frameshifts (if any). We describe a new tool, MetaGeneTack, which uses a heuristic method to estimate parameters of sequence models used in the FS detection algorithm. It was shown on several test sets that the performance of MetaGeneTack FS detection is comparable or better than the one of earlier developed program FragGeneScan.

Thesis (MScEng (Civil Engineering))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: Pre-cast sections have the advantages of structural efficiency, better quality control and less construction time, which enable them to be widely used in building structures. The connections of pre-cast buildings play a vital role for the stability and strength of structures. Nowadays, more attention is drawn to the aesthetical appearance of building structures, especially by architects. The Hidden Corbel Connection (HCC) was then developed to make the building structures stable and aesthetically pleasing. A modified HCC was designed and investigated in this study. Amongst all the mechanisms in the connection zone, the mechanism of the end anchorage length of tension reinforcement plays a key role in the economy of the connection and is hence further investigated. In order to investigate whether the end anchorage length of tension reinforcement can be reduced for a simply supported beam, a 2D non-linear finite element model is used to analyze the stress distribution inside the connection zone. Based on the stress distribution in the connection zone, the tensile force was calculated at the face of the support, which directly correlates to the required end anchorage length of tension reinforcement. The confinement in the connection zone increases the bond stress, which in turn reduces the required anchorage length of tension reinforcement. Therefore, a 3D model is used to analyze the region inside the modified HCC to find the position of the best confinement. By comparing the finite element (FE) results with Eurocode 2 (2004), and SABS 0100-1 (2000), it is demonstrated that the FE results require the shortest anchorage length, while the longest anchorage length is specified in SABS 0100-1 (2000). Based on the comparison between the FE results and the design codes, a laboratory experiment was then performed to determine if the end anchorage length of tension reinforcement can be reduced. Four beams with different support conditions and with different end anchorage length of tension reinforcement were tested. The results of the laboratory experiment indicate that the end anchorage length for simply supported beams can be shortened from the specification of SABS 0100-1 (2000).

Coronal Mass Ejections (CMEs) and solar flares are energetic events taking place at the Sun that can affect the space weather or the near-Earth environment by the release of vast quantities of electromagnetic radiation and charged particles. Solar active regions are the areas where most flares and CMEs originate. Studying the associations among sunspot groups, flares, filaments, and CMEs is helpful in understanding the possible cause and effect relationships between these events and features. Forecasting space weather in a timely manner is important for protecting technological systems and human life on earth and in space. The research presented in this thesis introduces novel, fully computerised, machine learning-based decision rules and models that can be used within a system design for automated space weather forecasting. The system design in this work consists of three stages: (1) designing computer tools to find the associations among sunspot groups, flares, filaments, and CMEs (2) applying machine learning algorithms to the associations' datasets and (3) studying the evolution patterns of sunspot groups using time-series methods. Machine learning algorithms are used to provide computerised learning rules and models that enable the system to provide automated prediction of CMEs, flares, and evolution patterns of sunspot groups. These numerical rules are extracted from the characteristics, associations, and time-series analysis of the available historical solar data. The training of machine learning algorithms is based on data sets created by investigating the associations among sunspots, filaments, flares, and CMEs. Evolution patterns of sunspot areas and McIntosh classifications are analysed using a statistical machine learning method, namely the Hidden Markov Model (HMM).

Arabic text recognition was not researched as thoroughly as other natural languages. The need for automatic Arabic text recognition is clear. In addition to the traditional applications like postal address reading, check verification in banks, and office automation, there is a large interest in searching scanned documents that are available on the internet and for searching handwritten manuscripts. Other possible applications are building digital libraries, recognizing text on digitized maps, recognizing vehicle license plates, using it as first phase in text readers for visually impaired people and understanding filled forms. This research work aims to contribute to the current research in the field of optical character recognition (OCR) of printed Arabic text by developing novel techniques and schemes to advance the performance of the state of the art Arabic OCR systems. Statistical and analytical analysis for Arabic Text was carried out to estimate the probabilities of occurrences of Arabic character for use with Hidden Markov models (HMM) and other techniques. Since there is no publicly available dataset for printed Arabic text for recognition purposes it was decided to create one. In addition, a minimal Arabic script is proposed. The proposed script contains all basic shapes of Arabic letters. The script provides efficient representation for Arabic text in terms of effort and time. Based on the success of using HMM for speech and text recognition, the use of HMM for the automatic recognition of Arabic text was investigated. The HMM technique adapts to noise and font variations and does not require word or character segmentation of Arabic line images. In the feature extraction phase, experiments were conducted with a number of different features to investigate their suitability for HMM. Finally, a novel set of features, which resulted in high recognition rates for different fonts, was selected. The developed techniques do not need word or character segmentation before the classification phase as segmentation is a byproduct of recognition. This seems to be the most advantageous feature of using HMM for Arabic text as segmentation tends to produce errors which are usually propagated to the classification phase. Eight different Arabic fonts were used in the classification phase. The recognition rates were in the range from 98% to 99.9% depending on the used fonts. As far as we know, these are new results in their context. Moreover, the proposed technique could be used for other languages. A proof-of-concept experiment was conducted on English characters with a recognition rate of 98.9% using the same HMM setup. The same techniques where conducted on Bangla characters with a recognition rate above 95%. Moreover, the recognition of printed Arabic text with multi-fonts was also conducted using the same technique. Fonts were categorized into different groups. New high recognition results were achieved. To enhance the recognition rate further, a post-processing module was developed to correct the OCR output through character level post-processing and word level post-processing. The use of this module increased the accuracy of the recognition rate by more than 1%.

In this paper, we argue that shadow activities and different levels of marketization of household production systematically distort international comparisons of aggregate gross household saving rates (HSRs): Higher shares of hidden income increase observed HSRs. Panel data for 18 (24) OECD-countries covering a period of a decade show that gross HSRs are positively related to the degree of corruption(used as a proxy for the propensity to shift economic activities into the shadow) and to the share of income from property and self employment. At the same time, gross HSRs are negatively related to the female employment rate, the ratio of indirect taxes to direct taxes, and to the tax wedge. One plausible story behind these phenomena might be that unobserved consumption and wages in the shadow labor market induce an upward bias in observed HSRs and profit shares, while the price level effects of a higher share of indirect taxes and a 'welfare state' effect lower observed HSRs. (authors' abstract) / Series: Department of Economics Working Paper Series

<p>Det övergripande syftet med min C-uppsats är att granska lärarens bedömning och perceptio-ner för elever i behov av särskilt stöd och vidare belysa vilka möjligheter och begränsningar de anser sig ha för att kunna ta hänsyn till elever i behov av särskilt stöd samt få en syn på de skolsituationer som barn och elever med dolda funktionshinder och i behov av särskilt stöd kan befinna sig i.</p><p>För att få svar på mina frågor har sex lärare inklusive en special lärare intervjuats och samti-digt diskuterades de psykologiska och biologiska faktorer kring barns och ungdomars utveck-ling. Den historiska återblicken ger oss en uppfattning på hur begreppet ”en skola för alla” har utvecklats inom loppet av tiden och vilka syn på barn i behov av särskilt stöd har pedagogerna idag. De centrala frågorna rörde sig om pedagogernas uppfattning om barn med koncentra-tionssvårigheter och deras syn på diagnostisering av barn med problem. En inkluderande inte-grering i jämförelse med segregering diskuterades också samt hur pedagogerna kan hjälpa dessa barn.</p><p>Eleverna i skolan är olika och deras olikheter måste mötas med omtanke. För att uppfylla de-ras behov krävs kunniga och kompetenta personal i skolan. Skolan måste ha en fungerande och tillfredställande elevvård för att kunna nå skolans mål. Skolornas neddragningar på grund av ekonomiska problem gör att barn med dolda funktionshinder misslyckas allt oftare i da-gens skola. Dessa orsakar att barn får ett dåligt självförtroende med upprepade misslyckande och försämrar deras problem.</p><p>Allmänt finns det en del olika faktorer som ligger bakom barn med koncentrations svårighe-ter. De biologisk och ärftliga faktorer samt tillväxtmiljön och deras samhällsställning kan ge-nerellt nämnas. Brist på tid, ekonomi och kunskap i skolorna är det en barriär för att kunna hjälpa barn med svårigheter.</p> / <p>The comprehensive purpose with this paper is to have a look at teacher’s assessment and per-ception of pupils with special educational needs. And further illustrate which possibilities and restrictions they believe to have, to take children with special educational needs into consid-eration and get a view of school situations who children with hidden functional disability and with special educations needs are at the present.</p><p>To get answer to my questions, six teachers inclusive a special teacher for pupils with im-paired disabilities have been interviewed and discussed the psychological and biological fac-tors around children’s development. The historical review gave us a perceptive on how defini-tion of “school for all” has been developed during the time and what is teacher’s opinion on children with special needs today. The central questions were concentrating on teachers un-derstanding of children with concentration difficulty and their opinion on diagnostic of chil-dren with problems. An “including integration” compared to segregating been discussed as well and finally discussed how teachers can help these children.</p><p>Pupils in school are not comparable and these differences must meets carefully. To meet chil-dren’s requirements schools have need of personnel’s competence and proficiency. Schools required having functioning and satisfactory pupil welfare to achieve the aim. Lowering of school resources due to economical problems do that child with hidden functional disability fails more often in schools these days. These effects cause that children get a horrific self-confidence and worsen their problems. Generally, there are different factors behind the con-centrations difficulty. The biological and hereditary factors as well as home environment and their class society can points out in general. Lacking of time, economy and knowledge stops teachers to helping children in school.</p>

Cette thèse vise à développer une méthode générique de modélisation des dynamiques passées et actuelles de l'organisation territoriale de l'activité agricole (OTAA). Nous avons développé une méthode de modélisation stochastique fondée sur des modèles de Markov cachés qui permet de fouiller un corpus de données spatio-temporelles d'occupations du sol (OCS) en vue de le segmenter et de révéler des dynamiques agricoles cachées. Nous avons testé cette méthode sur des corpus d'OCS issus de sources variées et appartenant à des territoires agricoles de dimensions. Cette méthode apporte 3 contributions à la modélisation de l'OTAA : (i) la description de l'OTAA suivant une approche temporo-spatiale qui identifie des régularités temporelles, puis les localise en segmentant le territoire agricole en zones compactes de régularités temporelles similaires; (ii) la fouille des voisinages des successions d'OCS et de leurs dynamiques; (iii) l'articulation des régularités révélées par notre approche de fouille de données à l'échelle régionale avec des règles identifiées par des experts en agronomie et en écologie à des échelles plus locales en vue d'expliquer les régularités et de valider les hypothèses des experts. Nos résultats valident l'hypothèse que l'OTAA se prête bien à la représentation par un champs de Markov de successions. Cette thèse ouvre la voie à une nouvelle approche de modélisation de l'OTAA explorant le couplage entre régularités et règles, et exploitant davantage les outils d'intelligence artificielle. Elle constituerait les prémices de ce qui pourrait devenir une agronomie numérique des territoires / The purpose of this thesis is to develop a generic method for modelling the past and current dynamics of Landscape Organization of Farming Activity (LOFA). We developed a stochastic modelling method based on Hidden Markov Models that allows data mining within a corpus of spatio-temporal land use data to segment the corpus and reveal hidden agricultural dynamics. We applied this method to land use corpora from various sources belonging to two agricultural landscapes of regional dimension. This method provides three contributions to the modeling of LOFA : (i) LOFA description following a temporo-spatial approach that first identifies temporal regularities and then localizes them by segmenting the agricultural landscape into compact areas having similar temporal regularities; (ii) data mining of the neighborhood of land use successions and their dynamics; (iii) combining of the regularities revealed by our data mining approach at the regional level with rules identified by agronomy and ecology experts at more local scales to explain the regularities and validate the experts' hypotheses. Our results validate the hypothesis according to which LOFA fits well a Markov field of land-use successions. This thesis opens the door to a new LOFA modelling approach that investigates the combining of regularities and rules and that further exploits artificial intelligence tools. This work could serve as the beginning of what could become a numerical landscape agronomy

Os vírus são as entidades biológicas mais abundantes encontradas na natureza. O método clássico de estudo dos vírus requerem seu isolamento e propagação in vitro. Contudo, necessita-se ter um conhecimento prévio sobre as condições necessárias para seu cultivo em células, sendo assim a maior parte dos vírus existentes não é conhecida. Análises metagenômicas são uma alternativa para a detecção e caracterização de novos vírus, uma vez que não requerem um cultivo prévio e as amostras podem conter material genético de múltiplos organismos. Uma vez obtidas as sequências montadas a partir das leituras metagenômicas, o método mais utilizado para a identificação e classificação dos organismos é a busca de similaridade com o programa BLAST contra bancos de sequências conhecidas. Contudo, métodos de alinhamento pareado são capazes de identificar apenas sequências com identidade superior a 20-30%. Uma alternativa a essa limitação é o uso de métodos baseados no uso de perfis, que podem aumentar a sensibilidade de detecção de homólogos filogeneticamente distantes. HMMs de perfil são modelos probabilísticos capazes de representar a diversidade de caracteres em posições-específicas de um alinhamento de múltiplas sequências. Nosso grupo desenvolveu a ferramenta TABAJARA, utilizada neste projeto, para a identificação de blocos que podem ser conservados em todas as sequências do alinhamento ou discriminativos entre grupos de sequências. Esses blocos são utilizados para a geração de HMMs de perfil, os quais podem ser usados, no contexto da virologia, para a identificação de grupos taxonômicos amplos como famílias virais ou, ainda, taxa mais restritos como gêneros ou mesmo espécies de vírus. O presente projeto teve como objetivos aplicar e otimizar o programa TABAJARA em diferentes grupos taxonômicos de vírus, construir modelos específicos para cada um desses grupos e validar esses modelos em dados metagenômicos. O primeiro modelo de estudo escolhido foi a ordem Bunyavirales, composta de vírus de ssRNA (-) majoritariamente envelopados e esféricos, com genoma segmentado e pertencentes ao grupo 5 da classificação de Baltimore. Este grupo inclui vírus causadores de várias doenças em humanos, animais e plantas. O segundo modelo de estudo escolhido foi a família Togaviridae, composta de vírus de ssRNA (+) envelopados e esféricos, cujo genoma expressa uma poliproteína e pertencem ao grupo 4 da classificação de Baltimore. Este grupo inclui o vírus Chikungunya e outras espécies que causam diversas patologias ao homem. O terceiro modelo de estudo escolhido foi a subfamília Spounavirinae, compreendendo bacteriófagos que infectam vários hospedeiros bacterianos e em alguns casos possuem potencial terapêutico comprovado contra infecções bacterianas que afetam o homem. Estes fagos apresentam partículas virais com estrutura cabeça-cauda, não são envelopados, apresentam genoma de dsDNA e pertencem ao grupo 1 da classificação de Baltimore. Todos os modelos construídos foram validados quanto à sensibilidade e especificidade de detecção e, ao final, foram utilizados em análises de prospecção de vírus em dados metagenômicos obtidos na base SRA do NCBI. Os HMMs de perfil apresentaram excelente desempenho, comprovando a viabilidade da metodologia proposta neste projeto. Os resultados apresentados neste trabalho abrem a perspectiva da ampla utilização de HMMs de perfil como ferramentas universais para a detecção e classificação de vírus em dados metagenômicos. / Viruses are the most widely biological entities found in nature. Most of the information that can be obtained from these organisms requires viral in vitro isolation and cultivation. However, most of the existing viruses are still unknown because the biological requirements for their successful propagation have not been identified so far. Metagenomic analyses offer an interesting alternative for the detection and characterization of novel viruses, since previous cultivation is not required, and the samples may contain genetic material of multiple organisms. Once assembled sequences are obtained from individual reads, the most widely used method for viral identification and classification is the use of BLAST similarity searches against databases of known sequences. However, pairwise alignment methods are only able to identify sequences that present identity greater than 20-30%. Profile-based methods may increase the sensitivity of detection of remote homologues. Profile HMMs are probabilistic models capable of representing the diversity of amino acid residues at specific positions of a multiple sequence alignment. Our group is developing TABAJARA, a tool for the identification of alignment blocks that are conserved across all sequences of the alignment or discriminative between groups of sequences. These blocks are used to generate profile HMMs, which can in turn be used, in the context of virology, to identify broad taxonomic groups, such as viral families, or narrower taxa as genera or viral species. The present project aimed to apply and standardize the use of TABAJARA in different taxonomic groups of viruses, to build specific models for each of these groups and to validate these models in metagenomic data. We used three viral models for this study. The first chosen model was the Bunyavirales order, composed of mostly enveloped and spherical ssRNA(-) viruses with a segmented genome belonging to group 5 of the Baltimore classification. This group includes viruses that cause several important diseases in humans, animals and plants. The second chosen model was the Togaviridae family, composed of enveloped and spherical ssRNA(+) viruses, with a genome coding for a polyprotein, and belonging to group 4 of the Baltimore classification. This group includes the Chikungunya virus and some other viral species that cause relevant pathologies to humans and animals. Finally, we used the Spounavirinae subfamily, comprising viruses that infect a variety of bacterial hosts and that can potentially be used for phage therapy of some human bacterial diseases. These phages present non-enveloped virions with a head-to-tail structure, a dsDNA genome, and belong to group 1 of the Baltimore classification. All constructed profile HMMs were evaluated in regard to their sensitivity and specificity of detection, as well as tested in viral surveys using metagenomic data from the SRA database. The profile HMMs presented excellent performance, proving the viability of the methodology proposed in this project. The results presented in this work open the perspective of the wide use of profile HMMs as universal tools for the detection and classification of viruses in metagenomic data.