Radiologists' workload has been steadily increasing for decades. As digital technology matures it improves the workflow for radiology departments and decreases the time necessary to examine patients. Computer systems are widely used in health care and are for example used to view radiology images. To simplify this, display protocols based on examination data are used to automatically create a layout and hang images for the user. To cover a wide variety of examinations hundreds of protocols must be created, which is a time-consuming task and the system can still fail to hang series if strict requirements on the protocols are not met. To remove the need for this manual step we propose to use machine learning based on past manually corrected presentations. The classifiers are trained on the metadata in the examination and how the radiologist preferred to hang the series. The chosen approach was to create classifiers for different layout rules and then use these predictions in an algorithm for assigning series types to individual image slots according to categories based on metadata, similar to how display protocol works. The resulting presentations shows that the system is able to learn, but must increase its prediction accuracy if it is to be used commercially. Analyses of the different parts show that increased accuracy in early steps should improve overall success. / Röntgenläkares arbetsbörda har under flera årtionden ökat. Den digitala sjukvårdsteknologin utvecklas ständigt vilket bidrar till ett förbättrat arbetsflöde och kortare undersökningstider i radiologiavdelningar. Datorsystem används idag överallt inom sjukvården och används bland annat för att visa bilder åt röntgenläkare. För att underlätta visningen används display protocol som automatiskt skapar layouts och hänger bilder åt användaren. För att täcka ett stort antal olika undersökningstyper krävs att användaren skapar hundratals protokoll vilket är en tidskrävande uppgift, och systemet kan ändå misslyckas med att hänga upp bilder om de strikta kraven protokollen ställer inte uppfylls. För att ta bort detta manuella steg föreslår vi att man använder maskininlärning baserat på tidigare sparade presentationer.  Klassificerarna tränas på undersökningens metadata och radiologens preferenser på hängning av serier. Den valda metoden går ut på att skapa klassificerare för olika layout-regler och att sedan använda deras output i en algoritm som placerar ut series-typer till individuella bildplatser enligt kategorier baserade på metadata. Denna metod liknar den process de nuvarande display protokollen utför. De presentationer som skapats visar att systemet kan läras upp, men kräver högre precision om det ska användas kommersiellt. Analys av de olika delarna tyder på att ökad precision tidigt i systemet skulle öka den totala precision.

Angiogênese é a formação de novos vasos sanguíneos a partir de vasos já existentes e é importante em processos fisiológicos, que em adultos é restrita ao reparo tecidual e ao ciclo reprodutivo feminino. Entretanto, doenças, como câncer ou retinopatias, induzem a formação da angiogênese patológica, necessária para a progressão destas patologias. Anticorpos monoclonais constituem uma das classes de biofármacos que mais cresce e com impacto importante nas doenças dependentes de angiogênese. Entre as diversas metodologias para a identificação de anticorpos monoclonais contra alvos terapêuticos, está o phage display. Por causa do fator de crescimento endotelial vascular (VEGF) ser o principal fator responsável pela formação de novos vasos, o principal biofármaco anti-angiogênico disponível na clínica atualmente é um anticorpo monoclonal (bevacizumab) direcionadas contra o VEGF. Embora terapias anti-VEGF sejam eficazes, ainda não são ideais devido a efeitos colaterais indesejados e a resistência medicamentosa. Novas alternativas são necessárias a fim de aperfeiçoar as terapias angiogênicas. O objetivo do nosso estudo é identificar novos alvos moleculares e desenvolver novos agentes terapêuticos para doenças dependentes de angiogênese. Para atingirmos nossa meta escolhemos o sistema de phage display para selecionarmos anticorpos com propriedades angiogênicas. Uma biblioteca de de anticorpos foi desenvolvida em nosso laboratório, dirigida contra a molécula VEGF, em particular uma de suas isoformas. Os animais imunizados desenvolveram anticorpos específicos, detectados por ELISA e Western-blot. A amplificação do pool de genes das cadeias leve e pesada de imunoglobulinas foi realizada para produzir os fragmentos single-chain (ScFv) que foram então clonados no vetor para a construção da biblioteca. A biblioteca de display de anticorpos ScFv será, portanto, analisada em plataformas angiogênicas para isolar anticorpos específicos contra isoformas de VEGF e novos marcadores moleculares de superfície celular expressos por células endoteliais ativadas. / Angiogenesis is the formation of new blood vessels from pre-existing ones and is an important physiological process, which in adults is mostly restricted to wound healing or the female reproductive cycle. However, different illnesses, such as cancer or retinopathies, induce the formation of pathological angiogenesis, necessary for disease progression. Monoclonal antibodies are one of the fastest growing class of biopharmaceuticals with important implications in angiogenesis dependent diseases. Among various methods for the identification of monoclonal antibodies against therapeutic targets is phage display technology. Because the vascular endothelial growth factor (VEGF) is the main molecular factor responsible for the formation of new blood vessels, the major anti-angiogenic drug available in the clinic today is a monoclonal antibody (bevacizumab) directed against VEGF. However, although anti-VEGF therapies are effective, they are not yet ideal due to undesirable side effects and drug resistance. Novel alternatives are necessary to improve on angiogenic therapies. The aim of our study is to identify novel molecular targets and to develop new therapeutic agents for angiogenic dependent diseases. To achieve our goal we have chosen the phage display system in order to select for antibodies with angiogenic properties. An antibody phage library has been developed in our laboratory, directed against VEGF molecule, particularly one of it isoforms. The animals were immunized and developed specific antibodies, detected by ELISA and Western-blot. Amplification of the pool of light and heavy chain Ig genes was performed to produce the single chain (ScFv) fragments for library construction. The ScFv antibody display libraries will be then screened in angiogenic settings to isolate antibodies against specific VEGF isoforms and novel cell surface molecular markers expressed by activated human endothelial cells

Leptospirose é uma doença infecciosa emergente cujos agentes etiológicos são espécies patogênicas do gênero Leptospira. Leptospiras patogênicas possuem inúmeros genes específicos codificando proteínas com funções desconhecidas, sugerindo que as leptospiras apresentam fatores de virulência únicos. Adesinas bacterianas são importantes fatores de virulência e, assim, a identificação de adesinas conservadas em espécies patogênicas de Leptospira pela construção de bibliotecas genômicas expostas na superfície de bacteriófagos (shotgun phage display), seguida por seleção em células e/ou componentes da matriz extracelular (biopanning), pode revelar novos antígenos e alvos para o tratamento e prevenção da leptospirose. Bibliotecas foram construídas com o DNA genômico de L. interrogans fragmentado e o fagomídeo pG8SAET, sendo testadas algumas abordagens para clonagem como a ligação entre extremidades cegas (blunt-end) e técnicas baseadas em ligação entre extremidades coesivas, incluindo a obtenção de ORESTES e a utilização de adaptadores em grampo. Apesar de serem encontradas algumas limitações, a clonagem por ligação blunt-end se mostrou a mais eficiente para a construção de bibliotecas, sendo adotada para a construção de três bibliotecas em maior escala. A seleção de novas possíveis adesinas a partir das bibliotecas construídas foi realizada em células eucarióticas através da metodologia BRASIL. A primeira biblioteca (BBT1) exibiu 106 clones totais, a partir da qual foram selecionados quatro proteínas em fase apenas com a proteína VIII do fago (pVIII). No entanto, nenhuma delas seria exposta por programas de predição na bactéria. Outras duas bibliotecas foram construídas (BBT2 e BBT3), as quais obtiveram um número ideal de clones para uma ampla cobertura do genoma (>2x107 clones). Por apresentar maior proporção de clones válidos, a BBT2 foi utilizada para a seleção de adesinas, resultando em onze clones em fase com pVIII e/ou sequência sinal do fago. Análises por programas de predição revelaram três proteínas hipotéticas, denominadas LepA962, LepA069 e LepA388, as quais poderiam estar expostas ou ser secretadas pela bactéria, sugerindo uma possível função de adesina. O estudo da proteína LepA388 levou ao reconhecimento de outras doze proteínas semelhantes e pertencentes a uma família paráloga contendo um domínio denominado DUF_61, motivo de função desconhecida presente em proteínas compartilhadas somente entre as espécies patogênicas mais virulentas de Leptospira. Por esta razão, a proteína LepA388 foi a mais estudada. A clonagem de três porções da proteína (LepA388P, LepA388NR e LepA388F) para expressão heteróloga resultou em proteínas recombinantes insolúveis e, considerando a riqueza em resíduos de cisteína presente em sua estrutura, não foi possível renaturá-las adequadamente. Diante dos obstáculos encontrados, apenas a porção contendo a sequência apresentada pelo fago (LepA388P) foi utilizada para obtenção de antissoros em camundongos, os quais apresentaram altos títulos, demonstrando a alta imunogenicidade da proteína LepA388P. O reconhecimento de proteínas nativas da família paráloga DUF_61 em extratos de diferentes sorovares de Leptospira não foi observado, assim como sua expressão in vitro a partir de bactérias em diferentes condições de cultivo. Estudos adicionais sobre a expressão in vivo e funções dos membros desta família são necessários para uma compreensão mais ampla de seu papel na biologia de leptospiras e, possivelmente, na patogênese da leptospirose. / Leptospirosis is an emerging infectious disease whose etiologic agents are pathogenic species of the genus Leptospira. Pathogenic leptospires have countless specific genes encoding proteins with unknown functions, suggesting that leptospires have unique virulence factors. Bacterial adhesins are important virulence factors and so the identification of conserved adhesins in pathogenic Leptospira species from shotgun phage display libraries, followed by selection (biopanning) in cells and/or extracellular matrix components, can reveal new antigens and strategies for leptospirosis treatment and prevention. Libraries were constructed using fragmented genomic DNA from L. interrogans and pG8SAET phagemid vector. Cloning approaches included blunt-end ligation and techniques based in cohesive-end ligation, such as ORESTES strategy and hairpin linkers. Despite some limitations, cloning by blunt-end ligation was the most efficient for library construction, being adopted for the construction of three libraries on a larger scale. Selection of new possible adhesins was performed by biopanning of the libraries in eukaryotic cells through BRASIL methodology. The first library called BBT1 exhibited approximately 106 total clones, and its biopanning resulted in four proteins fused to phage protein VIII, but none of them were expected to be exposed by the bacteria. Other libraries were built (BBT2 and BBT3) which reached the expected number of clones to obtain a larger genome representation (> 2x107 clones). Since it showed the highest proportion of positive clones, BBT2 was selected to perform a second biopanning, resulting in eleven proteins fused to phage protein VIII and/or signal peptide. In silico analysis revealed three hypothetical proteins, named LepA962, LepA069 and LepA388, that would be exposed or secreted by the bacteria, suggesting a possible adhesin function. The study of LepA388 protein led to the recognition of twelve other similar proteins belonging to a paralogous family that contains a domain called DUF_61, domain of unknown function that is present in proteins shared only among the most virulent pathogenic species of Leptospira. For this reason, the LepA388 protein was the most studied. The cloning of three portions of the protein (LepA388P, LepA388NR and LepA388F) for heterologous expression resulted in insoluble recombinant proteins, and given the presence of many cysteine residues in its structure, it was not possible to renature them appropriately. In face of the imposed obstacles, only the portion containing the sequence presented by the bacteriophage (LepA388P) was used to obtain antisera in mice, which showed high titers, demonstrating the high immunogenicity of the protein LepA388P. Recognition of native DUF_61 paralogous family proteins in extracts from distinct Leptospira serovars was not observed, as well as its in vitro expression from bacteria cultured in different conditions. Additional studies on the in vivo expression and functions of members of this family are needed for a broader understanding of their role in leptospiral biology and possibly in the pathogenesis of leptospirosis.

This work describes design interface between matrix with controller HD44780 and graphic LCD. This device replace 2x20, 4x20, 4x40 character display. Character which should be displayed are send through a parallel interface, such as matrix display, or send through SPI bus. Communication line RS-485 are used for set language character set. Language character sets are saved into external flash memory.

Proteases are important enzymes in the biotechnology due to their specific cleavage of substrates. HRV 3C, sortase A and TEV are some examples of cysteine proteases which become more of use lately in applications as removal of affinity tags (3C/TEV) and labelling of proteins (sortase). Here an investigation was made on the proteases by displaying them on two different prokaryotic hosts; E. coli and S. carnosus and to use these to cleave away affinity proteins (Affibody molecule) from other cells with an incorporated cleavage site. Constructs were cloned and incorporated into expressing strains which were then cultivated and induced. Analysis of surface expression was done by flow cytometer. Cleavage was made by cultivating combinations with cleavable bacteria and bacteria displaying proteases. A functional protease would lead to the presence of Affibody molecules in the supernatant. Flow cytomtery analysis was first made to inevstigate signal difference in Affibody binding by the addition of flurophores. Secondly SDS-PAGE was made on the centrifuged supernatant to investigate the presence of a product. Finally analysis of the bacteria was made by examining the reaction with soluble substrate and comparing activity with soluble enzyme. All of the enzymes were able to be displayed on the surface of bacteria with a clear separation from control. The cleavage analysis showed however varying results yet no clear evidence of product. Best flow cytometer results were seen for 3C but SDS-PAGE/MS did not show any cleaved product. For Sortase SDS-PAGE showed positive result but analysis with MS showed no product. TEV was concluded not to be funcional at all hence the failing to cleave soluble substrate  when condition seemed near optimal and faulty flow cytometer data. Even though the lack of success there is still many further studies that can be done on the proteases in order to prove its absence/presence  of activity.

Le cancer représente la second cause de décès au monde. Le développement de traitements innovants contre le cancer repose aujourd’hui sur l’identification de biomarqueurs des tumeurs et le développement de produits thérapeutiques capables de reconnaitre ces marqueurs de façon spécifique. Ces produits thérapeutiques de nouvelles générations ont le potentiel d’éliminer spécifiquement les cellules tumorales et donc de réduire les effets secondaires des traitements ainsi que les risques de rechute. Malheureusement, un certain nombre de patients ne peuvent bénéficier de ces traitements, du fait de l’absence de biomarqueurs connus à la surface de leur tumeur. Ce projet a ainsi pour ambition de développer de nouvelles thérapies ciblées en exploitant une nouvelle classe de biomarqueurs et ainsi de venir enrichir l’arsenal thérapeutique disponible pour le traitement des cancers. / Cancer is the second cause of death worldwide. Recent advance in cancer treatments involved the identification of cancer biomarkers and the development of efficient therapeutic products able to specifically recognize them. This new class of products has the ability to specifically target tumor cells, with the major advantages to decrease or abolish treatments side effects and relapses of the disease. Unfortunately, a certain number of patients do not respond to those treatments lacking the expression of those biomarkers on their tumor. This project aims at developing new targeted therapies by exploiting a new class of cancer biomarkers, which would potentially extend the therapeutics options against cancer.

The process of capturing solid geometry as 3 dimensional data requires the use of laser based reverse engineering hardware, known as a digitizer. Many digitizers exist as articulated coordinate measuring machines augmented with a laser, which forces the operator into many postures that are not ergonomically sound, particularly in the operator's upper body. This study analyzes the traditional method of laser digitizing using modern methods and technologies. An alternative user interface using a head-mounted monocular display is hypothesized and evaluated.

The current study investigated the task performance and subjective preference for two color displays with differing image generation technologies, the standard cathode ray tube shadow mask (CRT) display and the newer liquid crystal/cathode ray tube (LC/CRT) display. Six subjects performed three different information processing tasks using each of the two color display technologies and expressed their display preference via evaluation questionnaires. Ambient illumination measurements were obtained to determine preferred conditions for each display. A four-way factorial design was used to collect task performance data and ambient illumination preferences; performance data were collected as errors per unit task quantity for each of the task types. Subjective evaluations consisted of 20 five-interval bipolar adjective scales and a forced choice rating on eight display parameters. An analysis of variance procedure and post-hoc Newman-Keuls analyses were employed in the analyses of the performance and subjective bipolar adjective scale data; the forced choice rating scales were evaluated using the Sign Test. The task performance results indicate that neither display produced better task performance. The subjective data revealed mixed results; while the bipolar adjective scales indicate no differences between the two display technologies, the forced choice rating shows a preference for the LC/CRT display on some display parameters. A significant difference between the two displays was demonstrated for ambient illumination preferences; the LC/CRT was viewed in greater ambient illumination than the CRT display. / Master of Science

M. S.

Since the introduction of graphical user interfaces (GUI), input control devices have become an integral part of desktop computing. When interfacing with GUIs, these input control devices have become the human's primary means of communicating with the computer. Although there have been a number of experiments conducted on pointing devices for desktop machine, there is little research on pointing devices for wearable computer technology. This is surprising because pointing devices are a major component of a wearable computer system, allowing the wearer to select and manipulate objects on the screen. The design of these pointing devices will have a major impact on the ease with which the operator can interact with information being displayed (Card, English, and Burr, 1978). As a result, this research is the first in a series to investigate design considerations for pointing devices and visual displays that will support wearable computer users. Twenty soldiers participated in an experiment using target acquisition software with five pointing devices and two visual displays. The findings of the research strongly support the use of a relative mode-pointing device with rotational characteristics (i.e. trackball or thumbwheel) over other designs. Furthermore, the results also suggest that there is little difference between pointing devices operated with the thumb and index finger for target acquisition tasks. This study has also showed that there were little differences in pointing and homing time for pointing devices across the two visual displays. Finally, the study demonstrated that the Fitts' law model could be applied to hand-operated pointing devices for wearable computers. This is important because it allows the future development of pointing devices to be compared with the devices tested in this research using the Fitts' Law Index of Performance calculations. / Master of Science