INTRODUCTION: Spinal deformities, including adult spinal deformities (ASD) and adolescent idiopathic scoliosis (AIS), can cause significant pain and disability. Radiographic parameters are measured in order to establish quantitative relationships among spinal alignment and health related quality of life metrics. Various classification systems including the Scoliosis Research Society (SRS)-Schwab and Global Alignment Proportion (GAP) score have been developed to correlate radiographic parameters with relevant clinical outcomes. While the SRS-Schwab Classification is both a coronal and sagittal categorization that correlates to health related quality of life metrics, the GAP score is a newly developed 13-point scale that focuses on sagittal alignment to predict mechanical failure postoperatively. The study aims to evaluate the utility of the GAP score as a method of evaluating radiographic correction and maintenance over one year. METHODS: This was a retrospective analysis of ASD and AIS patients who underwent operative intervention. Patients were evaluated for GAP score changes from preoperative to postoperative and then to a one year follow up. Of the 285 screened patients, 73 had suitable radiographs for measurements. This included 45 ASD patients, 32 of which had one year follow up radiographs, and 28 AIS patients, of which only 19 had one year follow up radiographs. Measurements were obtained by three independent readers. These included pelvic incidence (PI), pelvic tilt (PT), L1-S1 lumbar lordosis (L1-S1 LL), L4-S1 lumbar lordosis (L4-S1 LL), sacral slope (SS), global tilt (GT), and sagittal vertical axis (SVA). GAP score subcategories were calculated and summed to produce the GAP score. RESULTS: The 73 included patients had an average age of 41.8 ± 24.1, BMI of 26.2 ±6.3, and consisted of 51 females (69.9%). All but one radiographic parameters exhibited an Intra Class Correlation (ICC) of over 0.66. PI had an ICC of 0.59 which was likely due to the incomplete visibility of the femoral heads in few radiographs. Among ASD patients, from pre to postoperative, PI-LL significantly decreased from 18° to 5°, PT significantly decreased from 26° to 19°, L1-S1 LL significantly increased from 37° to 47°, L4-S1 LL significantly increased from 28° to 31°, GT significantly decreased from 37° to 25°, SVA significantly decreased from 120 mm to 64 mm, and total GAP score significantly decreased from 8 to 6. For the 32 patients with long term data, the GAP score changed significantly from 9 to 6 to 7 at one year follow up. Of the 32 patients, 14 patients experienced a worsened score at the one year follow up. Among AIS patients, PI-LL increased from 0° to 3°, PT remained 13°, L1-S1 LL decreased from 56° to 53°, L4-S1 LL significantly decreased from 37° to 31°, GT increased from 14° to 16°, SVA decreased from 25 mm to 28 mm, and total GAP score increased from 3 to 4. For the 19 with long term data, the GAP score changed significantly from 3 to 3 to 2 and 2 patients experienced a worsened score at the one year follow up. DISCUSSION: The patient population showed a slight improvement in GAP score among both ASD and AIS groups. The improvement is more pronounced when evaluating with the SRS-Schwab Classification. The GAP score does not emphasize the same radiographic parameters and therefore does not correlate well with the SRS-Schwab Classification. Many patients also experienced a worsened GAP score by the one year follow up which can be attributed to the adjacent superior or inferior region (PJK), thoracolumbar region (construct failure), or compensation at the pelvis through hip flexion. Additionally, GAP is potentially oversensitive to measurement error and rounding differences. Thus, the utility of the GAP score in evaluating spinal deformity patients is questionable and requires further adjustment and evaluation based on prospective studies.

Made available in DSpace on 2016-04-29T14:23:42Z (GMT). No. of bitstreams: 1 Aline Rodrigheri Ioste.pdf: 3892568 bytes, checksum: d4b25a166ea46de0a3b7edfbfeab6923 (MD5) Previous issue date: 2016-03-04 / The objective of this study is to deeply understand the techniques currently used in optimal alignment of DNA sequences, focused on the strengths and limitations of these methods. Analyzing the feasibility of creating a new logical approach able to ensure optimal results , taking into account existing problems in optimal alignment as: (i ) the numerous alignment possibilities of two sequences , ( ii ) the great need for space and memory the machines, ( ii ) processing time to compute the optimal data and (iv ) exponential growth. This study allowed the beginning of the creation of a new logical approach to the global optimum alignment, showing promising results in higher scores with less need for calculations where the mastery of these new techniques can lead to use search of excellent results in the global alignment optimal in large data bases / O objetivo deste estudo é entender profundamente as técnicas utilizadas atualmente no alinhamento ótimo de sequências de DNA e analisar a viabilidade da criação de uma nova abordagem lógica capaz de garantir o resultado ótimo, levando em consideração os problemas existentes no alinhamento ótimo como: (i) as inúmeras possibilidades de alinhamento de duas sequências, (ii) a grande necessidade de espaço e memória das máquinas, (ii) o tempo de processamento para computar os dados ótimos e (iv) seu crescimento exponencial. O presente estudo permitiu o início da criação de uma nova abordagem lógica para o alinhamento ótimo global, demonstrando resultados promissores de maiores pontuações com menos necessidades de cálculos, onde o domínio destas novas técnicas pode conduzir à utilização da busca de resultados ótimos no alinhamento global de sequências biológicas em grandes bases de dados

This diploma thesis deals with the description of homologous genes and molecular biological databases that are used for their search and allow comparison. Among the most important institutions that deal with data management and analysis, include the EBI, NCBI and CIB. For searching homologous genes is the most fundamental NCBI - National Center for Biotechnology Information. More attention is paid to the search algorithms of homologous genes such as BLASTN and PatternHunter. The practical part of this thesis is the implementation of the algorithm comparing two sequences and locating homologous genes. The comparison is made on the basis of the nucleotide sequence and amino acid sequence. The results generated from the program will be further compared with results from commercially available programs.

Large scale image mosaicing methods are in great demand among scientists who study different aspects of the seabed, and have been fostered by impressive advances in the capabilities of underwater robots in gathering optical data from the seafloor. Cost and weight constraints mean that lowcost Remotely operated vehicles (ROVs) usually have a very limited number of sensors. When a low-cost robot carries out a seafloor survey using a down-looking camera, it usually follows a predetermined trajectory that provides several non time-consecutive overlapping image pairs. Finding these pairs (a process known as topology estimation) is indispensable to obtaining globally consistent mosaics and accurate trajectory estimates, which are necessary for a global view of the surveyed area, especially when optical sensors are the only data source. This thesis presents a set of consistent methods aimed at creating large area image mosaics from optical data obtained during surveys with low-cost underwater vehicles. First, a global alignment method developed within a Feature-based image mosaicing (FIM) framework, where nonlinear minimisation is substituted by two linear steps, is discussed. Then, a simple four-point mosaic rectifying method is proposed to reduce distortions that might occur due to lens distortions, error accumulation and the difficulties of optical imaging in an underwater medium. The topology estimation problem is addressed by means of an augmented state and extended Kalman filter combined framework, aimed at minimising the total number of matching attempts and simultaneously obtaining the best possible trajectory. Potential image pairs are predicted by taking into account the uncertainty in the trajectory. The contribution of matching an image pair is investigated using information theory principles. Lastly, a different solution to the topology estimation problem is proposed in a bundle adjustment framework. Innovative aspects include the use of fast image similarity criterion combined with a Minimum spanning tree (MST) solution, to obtain a tentative topology. This topology is improved by attempting image matching with the pairs for which there is the most overlap evidence. Unlike previous approaches for large-area mosaicing, our framework is able to deal naturally with cases where time-consecutive images cannot be matched successfully, such as completely unordered sets. Finally, the efficiency of the proposed methods is discussed and a comparison made with other state-of-the-art approaches, using a series of challenging datasets in underwater scenarios / Els mètodes de generació de mosaics de gran escala gaudeixen d’una gran demanda entre els científcs que estudien els diferents aspectes del fons submarí, afavorida pels impressionants avenços en les capacitats dels robots submarins per a l’obtenció de dades ptiques del fons. El cost i el pes constitueixen restriccions que impliquen que els vehicles operats remotament disposin habitualment d’un nombre limitat de sensors. Quan un robot de baix cost duu a terme una exploració del fons submarí utilitzant una càmera apuntant cap al terreny, aquest segueix habitualment una trajectòria que dóna com a resultat diverses parelles d’imatges amb superposició de manera sequencial. Trobar aquestes parelles (estimació de la topologia) és una tasca indispensable per a l’obtenció de mosaics globalment consistents així com una estimació de trajectòria precisa, necessària per disposar d’una visió global de la regió explorada, especialment en el cas en què els sensors òptics constitueixen la única font de dades. Aquesta tesi presenta un conjunt de mètodes robustos destinats a la creació de mosaics d’àrees de grans dimensions a partir de dades òptiques (imatges) obtingudes durant exploracions realitzades amb vehicles submarins de baix cost. En primer lloc, es presenta un mètode d’alineament global desenvolupat en el context de la generació de mosaics basat en característiques 2D, substituint una minimització no lineal per dues etapes lineals. Així mateix, es proposa un mètode simple de rectificació de mosaics basat en quatre punts per tal de reduir les distorsions que poden aparèixer a causa de la distorsió de les lents, l’acumulació d’errors i les dificultats d’adquisició d’imatges en el medi submarí. El problema de l’estimació de la topologia s’aborda mitjanant la combinació d’un estat augmentat amb un altre de Kalman estès, amb l’objectiu de minimitzar el nombre total d’intents de cerca de correspondències i obtenir simultàniament la millor trajectòria possible. La predicció de les parelles d’imatges potencials té en compte la incertesa de la trajectòria, i la contribució de l’obtenció de correspondències per a un parell d’imatges s’estudia d’acord amb principis de la teoria de la informació. Així mateix, el problema de l’estimació de la topologia és abordat en el context d’un alineament global. Les innovacions inclouen l’ús d’un criteri ràpid per a determinació de la similitud entre imatges combinat amb una solució basada en arbres d’expansió mínima, per tal d’obtenir una topologia provisional. Aquesta topologia és millorada mitjançant l’intent de cerca de correspondències entre parelles d’imatges amb major probabilitat de superposició. Contràriament al que succeïa en solucions prèvies per a la construcció de mosaics de grans àrees, el nostre entorn de treball és capaç de tractar amb casos en què imatges consecutives en el temps no han pogut ser relacionades satisfactòriament, com és el cas de conjunts d’imatges totalment desordenats. Finalment, es discuteix l’eficiència del mètode proposat i es compara amb altres solucions de l’estat de l’art, utilitzant una sèrie de conjunts de dades complexos en escenaris subaquàtics.

Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.