Detection of mitochondrial single nucleotide polymorphisms using a primer elongation reaction on oligonucleotide microarrays

We have developed a novel allele-specific primer elongation protocol using a DNA polymerase on oligonucleotide chips. Oligonucleotide primers carrying polymorphic sites at their free 3́end were covalently bound to glass slides. The generation of single-stranded targets of genomic DNA containing single nuclotide polymorphisms (SNPs) to be typed was achieved by an asymmetric PCR reaction or exonuclease treatment of phosphothioate (PTO)-modified PCR products. In the presence of DNA polymerase and all four dNTPs, with Cy3-dUTP replacing dTTP, allele-specific extension of the immobilized primers took place along a stretch of target DNA sequence. The yield of elongated products was increased by repeated reaction cycles. We performed multiplexed assays with many small DNA targets, or used single targets of up to 4.4 kb mitochondrial DNA (mtDNA) sequence to detect multiple SNPs in one reaction. The latter approach greatly simplifies preamplification of SNP-containing regions, thereby providing a framework for typing hundreds of mtDNA polymorphisms.

Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.

Microarrays containing 1046 human cDNAs of unknown sequence were printed on glass with high-speed robotics. These 1.0-cm2 DNA "chips" were used to quantitatively monitor differential expression of the cognate human genes using a highly sensitive two-color hybridization assay. Array elements that displayed differential expression patterns under given experimental conditions were characterized by sequencing. The identification of known and novel heat shock and phorbol ester-regulated genes in human T cells demonstrates the sensitivity of the assay. Parallel gene analysis with microarrays provides a rapid and efficient method for large-scale human gene discovery.

Resistência à abrasão de aço Hadfield para britadores: efeito do tamanho do abrasivo e do pH do meio.

Neste trabalho, foi investigado o efeito do tamanho do abrasivo e do pH do meio na resistência ao desgaste abrasivo do aço H-13 com matriz martensítica e do aço Hadfield com matriz austenítica. Ensaios de abrasão foram realizados utilizando o equipamento roda de borracha a úmido, variando o tamanho do abrasivo entre 0,15 e 2,40 mm e o pH do meio entre 5,5 e 12,8. As microestruturas dos materiais estudados foram analisadas utilizando microscopia óptica, as superfícies de desgaste e as partículas de desgaste foram analisadas em microscópio eletrônico de varredura. A macrodureza e a microdureza, antes e após os ensaios, foram obtidas utilizando durômetro Vickers. A topografia da região central da superfície de desgaste foi obtida utilizando Perfilometria 3D, visando obter valores de profundidade de penetração do abrasivo. Os resultados mostraram que o aço Hadfield é mais resistente do que o aço H-13 em todos os valores de pH e tamanhos de abrasivo utilizados. Para os dois materiais, a perda de massa aumenta linearmente até um tamanho crítico de abrasivo (TCA) e, após este, a mesma continua a aumentar, mas com uma intensidade menor. Para os dois materiais e para todos os tamanhos de abrasivo, o aumento do pH do meio resultou em menores perdas de massa, sendo este efeito maior para os dois menores tamanhos de abrasivo. Para maiores valores de pH, foram observadas menores profundidades de penetração do abrasivo. A microdureza da superfície de desgaste do aço H-13 sofreu um pequeno aumento com o aumento do tamanho do abrasivo enquanto que para o aço Hadfield esse aumento foi mais intenso. A análise das partículas de desgaste mostraram que, para todas as condições ensaiadas, os debris do aço H-13 tinham duas morfologias, contínuas e descontínuas enquanto que os cavacos do aço Hadfield foram sempre descontínuos. Para os dois materiais, foram observados dois micromecanismos de desgaste, sendo eles microcorte e microsulcamento. Por fim, os resultados apresentados neste trabalho sugerem que a análise de desempenho do aço Hadfield em serviço deve considerar o pH do meio bem como a granulometria do abrasivo em contato.

Synthèse systématique des écrits : les instruments d’évaluation de la comorbidité psychiatrique présentée par les adolescent(e)s

Ce mémoire présente les résultats d’une synthèse systématique (SS) des écrits traitant des instruments d’évaluation multidimensionnelle des troubles concomitants qui peuvent être présentés par les adolescent(e)s. La SS a permis d’identifier 11 instruments en mesure d’évaluer les troubles comorbides de l’Axe I du DSM-IV, incluant chaque fois les troubles liés à l’utilisation de substances psychoactives (TUS). Une fois les instruments répertoriés, une seconde recherche fut effectuée afin identifier les études les ayant mis à l’épreuve du point de vue de leur validité et de leur fidélité diagnostique : 57 études furent identifiées. La robustesse méthodologique de ces études fut analysée à l’aide de la grille du QUADAS-2 et 47 études furent retenues pour l’échantillon final. Les résultats sont présentés par diagnostics (troubles liés à l’utilisation des substances (TUS) (obligatoire), trouble d’anxiété généralisée (TAG), épisode dépressif majeur (ÉDM), troubles des conduites (TC), trouble du déficit de l’attention /hyperactivité (TDA/H), état de stress post-traumatique (ÉSPT) et par instrument retenu. Suite à l’analyse des données recueillies, il s’avère difficile de comparer les instruments les uns aux autres, étant donnée la très grande diversité des échelles qu’ils contiennent, ainsi que les devis fort différents des études qui les ont mis à l’épreuve. Par contre, deux instruments se distinguent par la robustesse méthodologique des études à leur sujet, ainsi que leur excellente performance globale. Il s’agit du ChIPS et du K-SADS.

Synthèse systématique des écrits : les instruments d’évaluation de la comorbidité psychiatrique présentée par les adolescent(e)s.

Ce mémoire présente les résultats d’une synthèse systématique (SS) des écrits traitant des instruments d’évaluation multidimensionnelle des troubles concomitants qui peuvent être présentés par les adolescent(e)s. La SS a permis d’identifier 11 instruments en mesure d’évaluer les troubles comorbides de l’Axe I du DSM-IV, incluant chaque fois les troubles liés à l’utilisation de substances psychoactives (TUS). Une fois les instruments répertoriés, une seconde recherche fut effectuée afin identifier les études les ayant mis à l’épreuve du point de vue de leur validité et de leur fidélité diagnostique : 57 études furent identifiées. La robustesse méthodologique de ces études fut analysée à l’aide de la grille du QUADAS-2 et 47 études furent retenues pour l’échantillon final. Les résultats sont présentés par diagnostics (troubles liés à l’utilisation des substances (TUS) (obligatoire), trouble d’anxiété généralisée (TAG), épisode dépressif majeur (ÉDM), troubles des conduites (TC), trouble du déficit de l’attention /hyperactivité (TDA/H), état de stress post-traumatique (ÉSPT) et par instrument retenu. Suite à l’analyse des données recueillies, il s’avère difficile de comparer les instruments les uns aux autres, étant donnée la très grande diversité des échelles qu’ils contiennent, ainsi que les devis fort différents des études qui les ont mis à l’épreuve. Par contre, deux instruments se distinguent par la robustesse méthodologique des études à leur sujet, ainsi que leur excellente performance globale. Il s’agit du ChIPS et du K-SADS.

Quantitative composition and distribution of the silt fraction in surface sediments of the North-West African continental margin

Surface sediments from the continental slope and rise of North-West Africa between the Canary lslands and the Cape Verde Islands are mainly composed of silt-sized material (2-63 µm). A number of sampling profiles were run normal to the coast and the composition of the silt fraction was determined quantitatively by scanning electron microscope analysis. The carbonate portion of the sediment was found to be nearly exclusively of biogenic origin. The most important contributors are planktonic foraminifers and coccoliths with minor contributions derived from pteropods. Plankton-produced biogenic opal such as diatoms and radiolarians play a very minor role. The high production rates of opal-silica plankton which exists in the surface waters of the NW-African upwelling system does not give rise to corresponding increases of opal accumulation in the bottom sediment. Benthic producers consist mainly of foraminifers and molluscs but the entire input from benthic producers is extremely small. An exception to this occurs in the prodelta sediments of the Senegal river. Downslope particle transport is indicated by the occurrence of shallow-water coralline algae, ascidian sclerites and cliona boring chips and can be traced as far down as the continental rise. The non-carbonate silt fraction mostly consists of quartz which is derived as eolian dust from the Sahara desert by the Harmattan and the NE-Trade-wind system. The percentage of carbonate in the surface sediments directly indicates the relative proportions of autochthonous biogenic components and terrigenous allochthonous quartz particles.

The principles of beauty in colouring systematized /

Illustrations consist of color chips.

Utilizing urban tree debris : an analysis of alternatives for Chicago, Illinois /

Prepared in cooperation with Chicago Bureau of Forestry, Parkways, and Beautification.

Ablative Pyrolysis of Beetle-killed Trees

Thesis (Ph.D.)--University of Washington, 2016-06

Analysis of the effect of transverse modes on free-space optical interconnect performance

Vertical-cavity surface-emitting lasers (VCSELs) and microlenses can be used to implement free space optical interconnects (FSOIs) which do not suffer from the bandwidth limitations inherent in metallic interconnects. A comprehensive link equation describing the effects of both optical and electrical noise is introduced. We have evaluated FSOI performance by examining the following metrics: the space-bandwidth product (SBP), describing the density of channels and aggregate bandwidth that can be achieved, and the carrier-to-noise ratio (CNR), which represents the relative strength of the carrier signal. The mode expansion method (MEM) was used to account for the primary cause of optical noise: laser beam diffraction. While the literature commonly assumes an ideal single-mode laser beam, we consider the experimentally determined multimodal structure of a VCSEL beam in our calculations. It was found that maximum achievable interconnect length and density for a given CNR was significantly reduced when the higher order transverse modes were present in Simulations. However, the Simulations demonstrate that free-space optical interconnects are still a suitable solution for the communications bottleneck, despite the adverse effects introduced by transverse modes.

Heat and mass transfer during fry-drying of sewage sludge

Deep-frying, which consists of immersing a wet material in a large volume of hot oil, presents a process easily adaptable to dry rather than cook materials. A suitable material for drying is sewage sludge, which may be dried using recycled cooking oils (RCO) as frying oil. One advantage is that this prepares both materials for convenient disposal by incineration. This study examines fry-drying of municipal sewage sludge using recycled cooking oil. The transport processes occurring during fry-drying were monitored through sample weight, temperature, and image analysis. Due to the thicker and wetter samples than the common fried foods, high residual moisture is observed in the sludge when the boiling front has reached the geometric center of the sample, suggesting that the operation is heat transfer controlled only during the first half of the process followed by the addition of other mechanisms that allow complete drying of the sample. A series of mechanisms comprising four stages (i.e., initial heating accompanied by a surface boiling onset, film vapor regime, transitional nucleate boiling, and bound water removal) is proposed. In order to study the effect of the operating conditions on the fry-drying kinetics, different oil temperatures (from 120 to 180 degrees C), diameter (D = 15 to 25 mm), and initial moisture content of the sample (4.8 and 5.6 kg water(.)kg(-1) total dry solids) were investigated.

The properties of the International Classification of the External Cause of Injury when used as an instrument for injury prevention research

Objective: To demonstrate properties of the International Classification of the External Cause of Injury (ICECI) as a tool for use in injury prevention research. Methods: The Childhood Injury Prevention Study (CHIPS) is a prospective longitudinal follow up study of a cohort of 871 children 5 - 12 years of age, with a nested case crossover component. The ICECI is the latest tool in the International Classification of Diseases (ICD) family and has been designed to improve the precision of coding injury events. The details of all injury events recorded in the study, as well as all measured injury related exposures, were coded using the ICECI. This paper reports a substudy on the utility and practicability of using the ICECI in the CHIPS to record exposures. Interrater reliability was quantified for a sample of injured participants using the Kappa statistic to measure concordance between codes independently coded by two research staff. Results: There were 767 diaries collected at baseline and event details from 563 injuries and exposure details from injury crossover periods. There were no event, location, or activity details which could not be coded using the ICECI. Kappa statistics for concordance between raters within each of the dimensions ranged from 0.31 to 0.93 for the injury events and 0.94 and 0.97 for activity and location in the control periods. Discussion: This study represents the first detailed account of the properties of the ICECI revealed by its use in a primary analytic epidemiological study of injury prevention. The results of this study provide considerable support for the ICECI and its further use.

Experiments with Bose-Einstein condensates on an atom chip

We describe the production of BECs on a new type of atom chip based on silver foil. Our atom chip is fabricated with thick wires capable of carrying currents of several amperes without overheating. The silver surface is highly reflective to light resonant with optical transitions used for Rb. The pattern on the chip consists of two parallel Z-trap wires, capable of producing two-wire guide, and two additional endcap wires for varying the axial confinement. Condensates are produced in magnetic microtraps formed within 1 mm of surface of the chip. We have observed the fragmentation of cold atom clouds when brought close to the chip surface. This results from a perturbed trapping potential caused by nanometer deviations of the current path through the wires on the chip. We present results of fragmentation of cold clouds at distances below 100 µm from the wires and investigate the origin of the deviating current. The fragmentation has different characteristics to those seen with copper conductors. The dynamics of atoms in these microtraps is also investigated. ©2005 COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

A comparison of integrated biomass to electricity systems

This thesis presents a comparison of integrated biomass to electricity systems on the basis of their efficiency, capital cost and electricity production cost. Four systems are evaluated: combustion to raise steam for a steam cycle; atmospheric gasification to produce fuel gas for a dual fuel diesel engine; pressurised gasification to produce fuel gas for a gas turbine combined cycle; and fast pyrolysis to produce pyrolysis liquid for a dual fuel diesel engine. The feedstock in all cases is wood in chipped form. This is the first time that all three thermochemical conversion technologies have been compared in a single, consistent evaluation.The systems have been modelled from the transportation of the wood chips through pretreatment, thermochemical conversion and electricity generation. Equipment requirements during pretreatment are comprehensively modelled and include reception, storage, drying and communication. The de-coupling of the fast pyrolysis system is examined, where the fast pyrolysis and engine stages are carried out at separate locations. Relationships are also included to allow learning effects to be studied. The modelling is achieved through the use of multiple spreadsheets where each spreadsheet models part of the system in isolation and the spreadsheets are combined to give the cost and performance of a whole system.The use of the models has shown that on current costs the combustion system remains the most cost-effective generating route, despite its low efficiency. The novel systems only produce lower cost electricity if learning effects are included, implying that some sort of subsidy will be required during the early development of the gasification and fast pyrolysis systems to make them competitive with the established combustion approach. The use of decoupling in fast pyrolysis systems is a useful way of reducing system costs if electricity is required at several sites because• a single pyrolysis site can be used to supply all the generators, offering economies of scale at the conversion step. Overall, costs are much higher than conventional electricity generating costs for fossil fuels, due mainly to the small scales used. Biomass to electricity opportunities remain restricted to niche markets where electricity prices are high or feed costs are very low. It is highly recommended that further work examines possibilities for combined beat and power which is suitable for small scale systems and could increase revenues that could reduce electricity prices.

The influence of cutting tool geometry upon aspects of chip flow and tool wear:a theoretical, three dimensional examination of the cutting geometry and the shape of the twist drill

This work is undertaken in the attempt to understand the processes at work at the cutting edge of the twist drill. Extensive drill life testing performed by the University has reinforced a survey of previously published information. This work demonstrated that there are two specific aspects of drilling which have not previously been explained comprehensively. The first concerns the interrelating of process data between differing drilling situations, There is no method currently available which allows the cutting geometry of drilling to be defined numerically so that such comparisons, where made, are purely subjective. Section one examines this problem by taking as an example a 4.5mm drill suitable for use with aluminium. This drill is examined using a prototype solid modelling program to explore how the required numerical information may be generated. The second aspect is the analysis of drill stiffness. What aspects of drill stiffness provide the very great difference in performance between short flute length, medium flute length and long flute length drills? These differences exist between drills of identical point geometry and the practical superiority of short drills has been known to shop floor drilling operatives since drilling was first introduced. This problem has been dismissed repeatedly as over complicated but section two provides a first approximation and shows that at least for smaller drills of 4. 5mm the effects are highly significant. Once the cutting action of the twist drill is defined geometrically there is a huge body of machinability data that becomes applicable to the drilling process. Work remains to interpret the very high inclination angles of the drill cutting process in terms of cutting forces and tool wear but aspects of drill design may already be looked at in new ways with the prospect of a more analytical approach rather than the present mix of experience and trial and error. Other problems are specific to the twist drill, such as the behaviour of the chips in the flute. It is now possible to predict the initial direction of chip flow leaving the drill cutting edge. For the future the parameters of further chip behaviour may also be explored within this geometric model.