Real-Time Gene-Expression Extraction with Fast Classification (FC) Networks

Fast Classification (FC) networks were inspired by a biologically plausible mechanism for short term memory where learning occurs instantaneously. Both weights and the topology for an FC network are mapped directly from the training samples by using a prescriptive training scheme. Only two presentations of the training data are required to train an FC network. Compared with iterative learning algorithms such as Back-propagation (which may require many hundreds of presentations of the training data), the training of FC networks is extremely fast and learning convergence is always guaranteed. Thus FC networks may be suitable for applications where real-time classification is needed. In this paper, the FC networks are applied for the real-time extraction of gene expressions for Chlamydia microarray data. Both the classification performance and learning time of the FC networks are compared with the Multi-Layer Proceptron (MLP) networks and support-vector-machines (SVM) in the same classification task. The FC networks are shown to have extremely fast learning time and comparable classification accuracy.

Efficient update and retrieval of objects in a multiresolution geospatial database

Many emerging applications benefit from the extraction of geospatial data specified at different resolutions for viewing purposes. Data must also be topologically accurate and up-to-date as it often represents real-world changing phenomena. Current multiresolution schemes use complex opaque data types, which limit the capacity for in-database object manipulation. By using z-values and B+trees to support multiresolution retrieval, objects are fragmented in such a way that updates to objects or object parts are executed using standard SQL (Structured Query Language) statements as opposed to procedural functions. Our approach is compared to a current model, using complex data types indexed under a 3D (three-dimensional) R-tree, and shows better performance for retrieval over realistic window sizes and data loads. Updates with the R-tree are slower and preclude the feasibility of its use in time-critical applications whereas, predictably, projecting the issue to a one-dimensional index allows constant updates using z-values to be implemented more efficiently.

AVALIAÇÃO DENTOESQUELÉTICA E TEGUMENTAR DA RETRAÇÃO ANTERIOR EM DUAS FASES

O objetivo do presente estudo consistiu em avaliar as alterações dentoesqueléticas e tegumentares promovidas pelo tratamento ortodôntico fixo com a retração anterior em duas fases, por meio de telerradiografias em norma lateral. Foram selecionados 14 pacientes com idade média de 14,6 anos que necessitavam de extrações dos quatro primeiros pré-molares, todos apresentando má oclusão de Classe I. A retração anterior foi realizada inicialmente pela retração dos caninos (previamente à colagem dos incisivos) e subsequentemente, pelos incisivos. Doze pacientes não utilizaram qualquer dispositivo para ancoragem e dois pacientes utilizaram como ancoragem o Arco Extra-Bucal (AEB) de uso noturno. Foram avaliadas as telerradiografias em norma lateral ao início, final da retração dos caninos e final de tratamento ortodôntico fixo. As telerradiografias foram escaneadas e mensuradas por meio do programa Radiocef® (RadiomemoryR- Belo Horizonte, Brasil). Os dados foram submetidos à Análise de Variância e teste de Tukey (p<0,05). Os resultados demonstraram poucas alterações esqueléticas, exceto por uma retrusão suave do ponto A e aumento do comprimento mandibular, da altura facial ântero-inferior e total e rotação suave anti-horária mandibular devido ao crescimento craniofacial. Após a retração dos caninos, houve uma inclinação para lingual e retrusão dos incisivos superiores e inferiores, que permaneceram estáveis para os incisivos superiores no período final de tratamento. Já os incisivos inferiores neste mesmo período, retruíram mais com uma inclinação semelhante àquela inicial. Além disso, não houve perda de ancoragem de forma estatisticamente significante. Estas alterações dentárias refletiram em retrusão dos lábios superior e inferior após a retração dos caninos, sendo que o lábio inferior continuou a retrair no período final de tratamento. Conclui-se que o tratamento com a retração em duas fases não representou perda de ancoragem estatisticamente significante, além de diminuir a convexidade facial.

ESTUDO COMPARATIVO DA POSIÇÃO ÂNTERO POSTERIOR DOS PRIMEIROS MOLARES INFERIORES NO TRATAMENTO ORTODÔNTICO, UTILIZANDO AS TÉCNICAS STRAIGHT-WIRE E EDGEWISE, EM CASOS DE MÁ OCLUSÃO DE CLASSE I DE ANGLE, COM EXTRAÇÃO DE PRIMEIROS PRÉ-MOLARES

Este estudo avaliou o posicionamento ântero posterior dos primeiros molares inferiores, durante o tratamento ortodôntico, utilizando o arco lingual inferior como acessório de ancoragem na técnica Straight-Wire, em comparação aos casos tratados pela técnica Edgewise, sem a utilização do arco lingual. Dois grupos foram selecionados, ambos apresentando má oclusão de Classe I de Angle7, tratados com extração dos primeiros pré-molares superiores e inferiores. Foi utilizada uma amostra de 255 telerradiografias em norma lateral, obtidas de pacientes brasileiros, de ambos os sexos, com média de idade de 13 anos e 6 meses e com diferentes padrões de crescimento facial. Embasado na análise e discussão dos resultados, concluiu-se que: 1) do início do tratamento ao fim da fase de nivelamento, a perda de ancoragem coronária do primeiro molar inferior foi maior nos casos tratados com a técnica Straight-Wire; 2) do fim da fase de nivelamento ao fim do tratamento, a perda de ancoragem coronária e radicular do primeiro molar inferior foi maior na técnica Edgewise; 3) do início ao fim tratamento a perda de ancoragem radicular foi maior nos pacientes tratados com a técnica Edgewise; e 4) o deslocamento ântero-posterior dos incisivos inferiores não apresentou diferença estatisticamente significante para ambas as técnicas, em todas as etapas observadas.(AU)

A UTILIZAÇÃO DO LASER DE BAIXA INTENSIDADE NA MOVIMENTAÇÃO DENTÁRIA E NA SENSIBILIDADE DOLOROSA APÓS APLICAÇÃO DE FORÇA ORTODÔNTICA

O presente estudo objetivou avaliar a eficácia do Laser de Baixa Intensidade (LBI) na aceleração da movimentação dentária e na diminuição da dor frente à aplicação de força ortodôntica. A amostra foi composta por 19 pacientes, sendo doze do sexo feminino e sete do sexo masculino, com idade inicial média de 14,69 anos, todos com indicação para extrações de primeiros pré-molares. Destes, 66 caninos foram submetidos à retração inicial, sendo que 33 receberam aplicação de laser e 33 foram considerados controle. Utilizou-se o Laser de Baixa Intensidade de arseneto de gálio e alumínio, com comprimento de onda de 780nm, na dosimetria de 40mW;10J/cm2;10s/ponto, aplicado apenas uma vez ao mês em dez pontos, sendo cinco por vestibular e cinco por lingual/palatino. Modelos de gesso foram confeccionados durante todos os meses de retração dos caninos, que teve duração de quatro meses, sendo, posteriormente, digitalizados para se mensurar a quantidade de movimentação de um lado em relação ao outro, utilizando-se como referência as papilas incisivas. Para a avaliação da dor experimentada pelos pacientes, os mesmos foram orientados a preencher uma escala analógica visual (VAS) que variava de 0 a 10 , em que zero significava nenhuma dor e dez significava dor insuportável, nos intervalos de 12, 24, 48 e 72 horas após a aplicação da força ortodôntica. Foi mensurado o apinhamento de todas as hemiarcadas dos pacientes na fase inicial, medindo-se a distância entre os pontos de contato de cada dente. Para a verificação do padrão de normalidade, empregou-se o teste de Kolmogorov-Smirnov, sendo que para comparar o lado irradiado com o lado não irradiado foi utilizado o teste t pareado, exceto para a variável razão caninos/molares , analisada pelo teste não paramétrico de Wilcoxon (p<0,05). Os resultados mostraram que em relação ao apinhamento dentário, os lados irradiado e não irradiado apresentaram-se compatíveis. Além disso, não houve diferença estatisticamente significante entre a quantidade de retração dos caninos irradiados comparados aos não irradiados, o mesmo acontecendo com a sensibilidade dolorosa experimentada pelos pacientes. Concluiu-se assim que o LBI na dosimetria e forma como foi utilizado não foi eficiente na aceleração da movimentação dentária nem na redução da dor experimentada pelos pacientes frente às forças ortodônticas.

Spatially orthogonal chemical functionalization of a hierarchical pore network for catalytic cascade reactions

The chemical functionality within porous architectures dictates their performance as heterogeneous catalysts; however, synthetic routes to control the spatial distribution of individual functions within porous solids are limited. Here we report the fabrication of spatially orthogonal bifunctional porous catalysts, through the stepwise template removal and chemical functionalization of an interconnected silica framework. Selective removal of polystyrene nanosphere templates from a lyotropic liquid crystal-templated silica sol–gel matrix, followed by extraction of the liquid crystal template, affords a hierarchical macroporous–mesoporous architecture. Decoupling of the individual template extractions allows independent functionalization of macropore and mesopore networks on the basis of chemical and/or size specificity. Spatial compartmentalization of, and directed molecular transport between, chemical functionalities affords control over the reaction sequence in catalytic cascades; herein illustrated by the Pd/Pt-catalysed oxidation of cinnamyl alcohol to cinnamic acid. We anticipate that our methodology will prompt further design of multifunctional materials comprising spatially compartmentalized functions.

BTX extraction by sulfolane in a mixer-settler cascade

The literature relating to the extraction of the aromatics, benzene, toluene and xylene (BTX) using different commercial solvents, and to mixer-settler design and performance, has been reviewed. Liquid-liquid equilibria of the ternary systems: hexane-benzene-sulfolane, n-heptane-toluene-sulfolane, and octane-xylene-sulfolane were determined experimentally at temperatures of 30oC, 35oC, and 40oC. The work was then extended to a multicomponent system. The data were correlated by using Hand's method and were found to be in a good agreement with theoretical predictions using the UNIFAC method. A study was made of the performance of a 10-stage laboratory mixer-settler cascade for the extraction of BTX from a synthetic reformate utilizing sulfolane as a solvent. Murphree stage efficiency decreased with stage number but 99% extraction was achievable within 4 stages. The effects of temperature, phase ratio, and agitator speed were investigated. The efficiency increased with agitator speed but > 1050 rpm resulted in secondary haze formation. An optimum temperature of 30oC was selected from the phase equilibria; the optimum solvent: feed ratio was 3:1 for 4 stages. The experimental overall mass transfer coefficients were compared with those predicted from single drop correlations and were in all cases greater, by a factor of 1.5 to 3, due to the surface renewal associated with drop break-up and coalescence promoted by agitation. A similar investigation was performed using real reformate from the Kuwait Oil Company. The phase ratios were in the range 0.5 to 1 to 3.25 to 1, the agitator speed 1050 rpm, and the operating temperature 30oC. A maximum recovery of 99% aromatics was achieved in 4 stages at a phase ratio of 3.25 to 1. A backflow model was extended to simulate conditions in the mixer-settler cascade with this multicomponent system. Overall mass transfer coefficients were estimated by obtaining the best fit between experimental and predicted concentration profiles. They were up to 10% greater than those with the synthetic feed but close agreement was not possible because the distribution coefficient and phase ratio varied with stage number. Sulfolane was demonstrated to be an excellent solvent for BTX recovery and a mixer-settler cascade was concluded to be a technically viable alternative to agitated columns for this process.

Analytical techniques for the study of soft contact lens spoilation

Soft contact lens wear has become a common phenomenon in recent times. The contact lens when placed in the eye rapidly undergoes change. A film of biological material builds up on and in the lens matrix. The long term wear characteristics of the lens ultimately depend on this process. With time distinct structures made up of biological material have been found to build up on the lens. A fuller understanding of this process and how it relates to the lens chemistry could lead to contact lenses that are better tolerated by the eye. The tear film is a complex biological fluid, it is this fluid that bathes the lens during wear. It is reasonable to suppose that it is material derived from this source that accumulates on the lens. To understand this phenomenon it was decided to investigate the make up and conformation of the protein species that are found on and in the lens. As inter individual variations in tear fluid composition have been found it is important to be able to study the proteins on a single lens. Many of the analytical techniques used in bio research are not suitable for this study because of the lack of sensitivity. Work with poly acrylamide electrophoresis showed the possibility of analyzing the proteins extracted from a single lens. The development of a biotin avidin electro-blot and an enzyme linked aniibody electro-blot, lead to the high sensitivity detection and identification of the proteins present. The extraction of proteins from a lens is always incomplete. A method that analyses the proteins in situ would be a great advancement. Fourier transform infra red microscopy was developed to a point where a thin section of a contact lens could yield information about the proteins present and their conformation. The three dimensional structure of the gross macroscopic structures termed white spots was investigated using confocal laser microscopy.

Automatic refinement of constructive solid geometry models

Geometric information relating to most engineering products is available in the form of orthographic drawings or 2D data files. For many recent computer based applications, such as Computer Integrated Manufacturing (CIM), these data are required in the form of a sophisticated model based on Constructive Solid Geometry (CSG) concepts. A recent novel technique in this area transfers 2D engineering drawings directly into a 3D solid model called `the first approximation'. In many cases, however, this does not represent the real object. In this thesis, a new method is proposed and developed to enhance this model. This method uses the notion of expanding an object in terms of other solid objects, which are either primitive or first approximation models. To achieve this goal, in addition to the prepared subroutine to calculate the first approximation model of input data, two other wireframe models are found for extraction of sub-objects. One is the wireframe representation on input, and the other is the wireframe of the first approximation model. A new fast method is developed for the latter special case wireframe, which is named the `first approximation wireframe model'. This method avoids the use of a solid modeller. Detailed descriptions of algorithms and implementation procedures are given. In these techniques utilisation of dashed line information is also considered in improving the model. Different practical examples are given to illustrate the functioning of the program. Finally, a recursive method is employed to automatically modify the output model towards the real object. Some suggestions for further work are made to increase the domain of objects covered, and provide a commercially usable package. It is concluded that the current method promises the production of accurate models for a large class of objects.

Cell surface analysis of the basidiomycete yeast cryptococcus neoformans

Cell surface properties of the basidiomycete yeast Cryptococcus neoformans were investigated with a combination of novel and well proven approaches. Non-specific cell adhesion forces, as well as exposed carbohydrate and protein moieties potentially associated with specific cellular interaction, were analysed. Experimentation and analysis employed cryptococcal cells of different strains, capsular status and culture age. Investigation of cellular charge by particulate microelectrophoresis revealed encapsulated yeast forms of C. neoformans manifest a distinctive negative charge regardless of the age of cells involved; in turn, the neutral charge of acapsulate yeasts confirmed that the polysaccharide capsule, and not the cell wall, was responsible for this occurrence. Hydrophobicity was measured by MATH and HICH techniques, as well as by the attachment of polystyrene microspheres. All three techniques, where applicable, found C. neoformans yeast to be consistently hydrophilic; this state varied little regardless of strain and culture age. Cell surface carbohydrates and protein were investigated with novel fluorescent tagging protocols, flow cytometry and confocal microscopy. Cell surface carbohydrate was identified by controlled oxidation in association with biotin hydrazide and fluorescein-streptavidin tagging. Marked amounts of carbohydrate were measured and observed on the cell wall surface of cryptococcal yeasts. Furthermore, tagging of carbohydrates with selective fluorescent lectins supported the identification, measurement and observation of substantial amounts of mannose, glucose and N-acetyl-glucosamine. Cryptococcal cell surface protein was identified using sulfo-NHS-biotin with fluorescein-streptavidin, and then readily quantified by flow cytometry. Confocal imaging of surface exposed carbohydrate and protein revealed common localised areas of vivid fluorescence associated with buds, bud scars and nascent daughter cells. Carbohydrate and protein fluorescence often varied between strains, culture age and capsule status of cells examined. Finally, extension of protein tagging techniques resulted in the isolation and extraction of two biotinylated proteins from the yeast cell wall surface of an acapsulate strain of C.neoformans.

Some aspects of the analytical chemistry of malathion

A thorough investigation of the recommended colorimetric method for the determination of malathion (an organophosphorus pesticide) has led to the identification of the major cause of all the problems with which the method suffers. The method, which involves the extraction of the copper (II) complex or the hydrolysis product of malathion from aqueous solution into immiscible organic solvents, has many drawbacks. For example, the colour of the organic extract fades very quickly and a slight increase in the contact time of the hydrolysis product and the copper reagent within the aqueous solution, results in a decrease in the ab-solute absorbance. Also, the presence of any reducing agents can be a significant source of error. In the present work, it has been shown that the basic cause of all these problems is the ability of copper (II) ion to be reduced to copper (I) ion. It has further been shown that these problems can be resolved by re-placing copper (II) by bismuth (III). This has led to the development of a modified colorimetric method for the determination. of malathion, which has distinct advantages over all other existing methods in terms of reagents required, ease in application, avoidance of interferences and stability of colour for extended periods of time. The modified colorimetric method described above has been further improved by making use of a ligand exchange reaction involving dithizone. The resulting final organic extract in this case is bright orange in colour, the absorbance of which can be measured even with simple photometers. The usefulness of the modified colorimetric method has been demonstrated by determining malathion in technical products, and in aqueous solution containing the compound down to sub ppm levels. The scope and applicability of atomic absorption spectrophotometry has been extended by demonstrating for the first time that the technique can be used for the indirect determination of malathion. Almost all of the work described above has been accepted for publication by international journals and considerable interest in the work has been shown by chemists working in the field of pesticide analysis and research.

The application of remote sensing to the management of urban wildlife habitats

The project set out with two main aims. The first aim was to determine whether large scale multispectral aerial photography could be used to successfully survey and monitor urban wildlife habitats. The second objective was to investigate whether this data source could be used to predict population numbers of selected species expected to be found in a particular habitat type. Panchromatic, colour and colour infra-red, 1:2500 scale aerial photographs, taken in 1981 and 1984, were used. For the orderly extraction of information from the imagery, an urban wildlife habitat classification was devised. This was based on classifications already in use in urban environments by the Nature Conservancy Council. Pilot tests identified that the colour infra-red imagery provided the most accurate results about urban wildlife habitats in the study area of the Blackbrook Valley, Dudley. Both the 1981 and 1984 colour infra-red photographs were analysed and information was obtained about the type, extent and distribution of habitats. In order to investigate whether large scale aerial photographs could be used to predict likely animal population numbers in urban environments, it was decided to limit the investigation to the possible prediction of bird population numbers in Saltwells Local Nature Reserve. A good deal of research has already been completed into the development of models to predict breeding bird population numbers in woodland habitats. These models were analysed to determine whether they could be used successfully with data extracted from the aerial photographs. The projects concluded that 1:2500 scale colour infra-red photographs can provide very useful and very detailed information about the wildlife habitats in an urban area. Such imagery can also provide habitat area data to be used with population predictive models of woodland breeding birds. Using the aerial photographs, further investigations into the relationship between area of habitat and the breeding of individual bird species were inconclusive and need further research.

The beneficiation of steel making slags

The thesis examines the possibilities for the beneficiation of steel making slags by using mineral processing methods. Chemical and Mineralogical investigations have been carried out by SEM and EP}ffi to determine the most suitable separation methods in terms of crystal size, chemical composition and surface properties. Magnetic separation was applied in connection with size reductions for the extraction of the metallic iron prills and other iron containing phases and the results were related to the feed size and operating conditions. The behaviour of the slags in flotation tests was studied with respect to the recovery and grade. It was found that the free lime presence in the slags caused a high acid consumption of both weak and strong acids. It also reacted with acids and consequently produced a white precipitate, (CaS04 for H2 S04 ). The poor response of the phases to the flotation by different types of collector was found to be due to surface alteration caused by the free lime. The flocculation tests were carried out at the natural pH of the slags to prevent surface alterations. Settling tests were done to determine the suitable flocculants for the separation tests. The effect of the settling period, flocculant concentration, conditioning period and number of cleaning cycles were determined to optimize the separation tests. The discussion brings together this study with previous theoretically based work cited in the literature to elucidate the factor5governing the utilisation of steel making slags.

Biomedical events extraction using the hidden vector state model

Objective: Biomedical events extraction concerns about events describing changes on the state of bio-molecules from literature. Comparing to the protein-protein interactions (PPIs) extraction task which often only involves the extraction of binary relations between two proteins, biomedical events extraction is much harder since it needs to deal with complex events consisting of embedded or hierarchical relations among proteins, events, and their textual triggers. In this paper, we propose an information extraction system based on the hidden vector state (HVS) model, called HVS-BioEvent, for biomedical events extraction, and investigate its capability in extracting complex events. Methods and material: HVS has been previously employed for extracting PPIs. In HVS-BioEvent, we propose an automated way to generate abstract annotations for HVS training and further propose novel machine learning approaches for event trigger words identification, and for biomedical events extraction from the HVS parse results. Results: Our proposed system achieves an F-score of 49.57% on the corpus used in the BioNLP'09 shared task, which is only 2.38% lower than the best performing system by UTurku in the BioNLP'09 shared task. Nevertheless, HVS-BioEvent outperforms UTurku's system on complex events extraction with 36.57% vs. 30.52% being achieved for extracting regulation events, and 40.61% vs. 38.99% for negative regulation events. Conclusions: The results suggest that the HVS model with the hierarchical hidden state structure is indeed more suitable for complex event extraction since it could naturally model embedded structural context in sentences.

Intermediate pyrolysis studies of aquatic biomass and potential applications in the BtVB-process

Aquatic biomass is seen as one of the major feedstocks to overcome difficulties associated with 1st generation biofuels, such as competition with food production, change of land use and further environmental issues. Although, this finding is widely accepted only little work has been carried out to investigate thermo-chemical conversion of algal specimen to produce biofuels, power and heat. This work aims at contributing fundamental knowledge for thermo-chemical processing of aquatic biomass via intermediate pyrolysis. Therefore, it was necessary to install and commission an analytical pyrolysis apparatus which facilitates intermediate pyrolysis process conditions as well as subsequent separation and detection of pyrolysates (Py- GC/MS). In addition, a methodology was established to analyse aquatic biomass under intermediate conditions by Thermo-Gravimetric Analysis (TGA). Several microalgae (e.g. Chlamydomonas reinhardtii, Chlorella vulgaris) and macroalgae specimen (e.g. Fucus vesiculosus) from main algal divisions and various natural habitats (fresh and saline water, temperate and polar climates) were chosen and their thermal degradation under intermediate pyrolysis conditions was studied. In addition, it was of interest to examine the contribution of biochemical constituents of algal biomass onto the chemical compounds contained in pyrolysates. Therefore, lipid and protein fractions were extracted from microalgae biomass and analysed separately. Furthermore, investigations of residual algal materials obtained by extraction of high valuable compounds (e.g. lipids, proteins, enzymes) were included to evaluate their potential for intermediate pyrolysis processing. On basis of these thermal degradation studies, possible applications of algal biomass and from there derived materials in the Bio-thermal Valorisation of Biomass-process (BtVB-process) are presented. It was of interest to evaluate the combination of the production of high valuable products and bioenergy generation derived by micro- and macro algal biomass.