Unlocking hidden genomic sequence

Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs.

Metal-centred versus ligand-centred luminescence quenching of a macrocyclic copper(II) complex

The new macrocyclic ligand trans-6-(9-anthracenylmethylamino)-6,13-dimethyl-1,4,8,11-tetraazacyclotetradecan-13-amine has been synthesized and characterised as its copper(II) complex and the crystal structure of this complex has been determined. Fluorescence of the anthracenyl group of the macrocycle is quenched in its free base form and when complexed with Cu-II. Fluorescence returns when Lewis acids such as H+ and Zn-II are added to solutions of the ligand, indicating that photoinduced electron transfer from the amine lone pairs is responsible for fluorescence quenching in the free base form. By contrast, fluorescence of the complex is quenched by intramolecular electronic energy transfer.

Returns to farm-level soil conservation on tropical steep slopes: The case of the Eritrean highlands

This study conducts an economic analysis of investment in simple soil conservation technologies in the highlands of Eritrea. The data used in the analysis were obtained from a farm survey and supplemented with data from secondary sources. Risk analysis techniques are used to take account of the uncertainties regarding the relationship between soil erosion and crop yield. The financial analysis reveals negative net present values (NPVs) and internal rates of return (IRRs) below 12 per cent for various slope categories. On the other hand, the economic analysis returns positive NPVs and IRRs of over 20 per cent. The results clearly indicate that in-vestment in soil conservation technology may not be a viable short-term proposition from the farmer's point of view and yet the net social benefits are positive. There is a strong case for government to provide incentives for soil conservation in view of the economic benefits.

Osteoprotegerin/RANKL system imbalance in active polyarticularonset juvenile idiopathic arthritis: a bone damage biomarker?

Objective: To evaluate the importance of receptor activator of nuclear factor kappa B (RANK)/receptor activator of nuclear factor kappa B ligand (RANKL)/osteoprotegerin (OPG) modulation in active polyarticular juvenile idiopathic arthritis (pJIA) patients with and without bone erosions. Methods: Thirty female patients (mean age 11.07 +/- 3.77 years, range 4-17 years) with active pJIA and 30 healthy gender-and age-matched controls were consecutively selected for this study. All involved articulations were assessed by X-ray and examined for the presence of bone erosions. The serum levels of RANKL and OPG were measured using an enzyme-linked immunosorbent assay (ELISA). Results: Patients with active pJIA had higher levels of serum RANKL than controls [2.90 (0.1-37.4) vs. 0.25 (0.1-5.7) pg/mL, p=0.007] and a lower OPG/RANKL ratio [21.25 (1.8-897.6) vs. 347.5 (9-947.8), p=0.005]. However, levels of OPG were comparable in both groups [55.24 (28.34-89.76) vs. 64.42 (30.68-111.28) pg/mL, p=0.255]. Higher levels of serum RANKL and a lower OPG/RANKL ratio were also observed in active pJIA patients with bone erosions compared to controls [3.49 (0.1-37.4) vs. 0.25 (0.1-5.7) pg/mL, p=0.0115 and 14.3 (1.8-897.6) vs. 347.5 (9-947.8), p=0.016]. However, RANKL levels and OPG/RANKL ratio were similar in pJIA patients without bone erosion and controls [1.75 (0.1-10.9) vs. 0.25 (0.1-5.7) pg/mL, p=0.055 and 29.2 (3.3-756.8) vs. 347.5 (9-947.8), p=0.281]. Conclusion: These data suggest that active pJIA with bone erosions is associated with high serum levels of RANKL and a low OPG/RANKL ratio, indicating that these alterations may reflect bone damage in this disease.

Evolutive physicochemical characterization of diabetic ketoacidosis in adult patients admitted to the intensive care unit

Purpose: The aim of this study was to characterize the first 48-hour evolution of metabolic acidosis of adult patients with diabetic ketoacidosis admitted to the intensive care unit. Materials and Methods: We studied 9 patients retrieved from our prospective collected database, using the physicochemical approach to acid-base disturbances. Results: Mean (SD) age was 34 (13) years; mean (SD) Acute Physiology and Chronic Health Evaluation II score was 16 (10); mean (SD) blood glucose level on admission was 480 (144) mg/dL; mean (SD) pH was 7.17 (0.18); and mean (SD) standard base excess was -16.8 (7.7) mEq/L. On admission, a great part of metabolic acidosis was attributed to unmeasured anions (strong ion gap [SIG], 20 +/- 10 mEq/L), with a wide range of strong ion difference (41 +/- 10 mEq/L). During the first 48 hours of treatment, 297 +/- 180 IU of insulin and 9240 +/- 6505 mL of fluids were used. Metabolic improvement was marked by the normalization of pH, partial correction of standard base excess, and a reduction of hyperglycemia. There was a significant improvement of SIG (7.6 +/- 6.2 mEq/L) and a worsening of strong ion difference acidosis (36 +/- 5 mEq/L) in the first 24 hours, with a trend toward recuperation between 24 and 48 hours (38 +/- 6 mEq/L). Conclusion: Initial metabolic acidosis was due to SIG, and the treatment was associated with a significant decrease of SIG with an elevation of serum chloride above the normal range. (C) 2011 Elsevier Inc. All rights reserved.

Establishment of native ecosystems after mining - Australian experience across diverse biogeographic zones

The Australian minerals industry, which is dominated by coal, gold, bauxite, iron ore, base metals and mineral sand operations, is widely scattered across a continent which has a wide range of climatic zones ranging from moist temperate in the south through hot deserts in the centre to moist tropical in the north. There is an emphasis at most mines on establishing native ecosystems after mining, and technologies have had to be developed to ensure successful establishment and stability of these ecosystems under often adverse climatic conditions. This paper describes some of the innovative practices used to establish native ecosystenms in bauxite, mineral sand and coal operations across diverse biogeographic zones. Additionally, brief reference is made to an ecosystem function analysis, which has been developed to assess the success of establishment of these ecosystems. (C) 2001 Elsevier Science B.V. All rights reserved.

Advances in application of climate prediction in agriculture

Agricultural ecosystems and their associated business and government systems are diverse and varied. They range from farms, to input supply businesses, to marketing and government policy systems, among others. These systems are dynamic and responsive to fluctuations in climate. Skill in climate prediction offers considerable opportunities to managers via its potential to realise system improvements (i.e. increased food production and profit and/or reduced risks). Realising these opportunities, however, is not straightforward as the forecasting skill is imperfect and approaches to applying the existing skill to management issues have not been developed and tested extensively. While there has been much written about impacts of climate variability, there has been relatively little done in relation to applying knowledge of climate predictions to modify actions ahead of likely impacts. However, a considerable body of effort in various parts of the world is now being focused on this issue of applying climate predictions to improve agricultural systems. In this paper, we outline the basis for climate prediction, with emphasis on the El Nino-Southern Oscillation phenomenon, and catalogue experiences at field, national and global scales in applying climate predictions to agriculture. These diverse experiences are synthesised to derive general lessons about approaches to applying climate prediction in agriculture. The case studies have been selected to represent a diversity of agricultural systems and scales of operation. They also represent the on-going activities of some of the key research and development groups in this field around the world. The case studies include applications at field/farm scale to dryland cropping systems in Australia, Zimbabwe, and Argentina. This spectrum covers resource-rich and resource-poor farming with motivations ranging from profit to food security. At national and global scale we consider possible applications of climate prediction in commodity forecasting (wheat in Australia) and examine implications on global wheat trade and price associated with global consequences of climate prediction. In cataloguing these experiences we note some general lessons. Foremost is the value of an interdisciplinary systems approach in connecting disciplinary Knowledge in a manner most suited to decision-makers. This approach often includes scenario analysis based oil simulation with credible models as a key aspect of the learning process. Interaction among researchers, analysts and decision-makers is vital in the development of effective applications all of the players learn. Issues associated with balance between information demand and supply as well as appreciation of awareness limitations of decision-makers, analysts, and scientists are highlighted. It is argued that understanding and communicating decision risks is one of the keys to successful applications of climate prediction. We consider that advances of the future will be made by better connecting agricultural scientists and practitioners with the science of climate prediction. Professions involved in decision making must take a proactive role in the development of climate forecasts if the design and use of climate predictions are to reach their full potential. (C) 2001 Elsevier Science Ltd. All rights reserved.

Cloning of a differentially expressed tropomyosin isoform from cultured rabbit aortic smooth muscle cells

The four known tropomyosin genes have highly conserved DNA and amino acid sequences, and at least 18 isoforms are generated by alternative RNA splicing in muscle and non-muscle cells. No rabbit tropomyosin nucleotide sequences are known, although protein sequences for alpha- and beta-tropomyosin expressed by rabbit skeletal muscle have been described. Subtractive hybridisation was used to select for genes differentially expressed in rabbit aortic smooth muscle cells (SMC), during the change in cell phenotype in primary culture that is characterised by a loss of cytoskeletal filaments and contractile proteins. This led to the cloning of a tropomyosin gene predominantly expressed in rabbit SMC during this change. The full-length cDNA clone, designated rabbit TM-beta, contains an open reading frame of 284 amino acids, 5' untranslated region (UTR) of I 17 base pairs and 3' UTR of 79 base pairs. It is closely related to the beta-gene isoforms in other species, with the highest homology in DNA and protein sequences to the human fibroblast isoform TM-1 (91.7% identity in 1035 bp and 93.3% identity in the entire 284 amino acid sequence of the protein), It differs from rabbit skeletal muscle P-tropomyosin (81.7% homology at the protein level) mainly in two regions at amino acids 189-213 and 258-283 suggesting alternative splicing of exons 6a for 6b and 9d for 9a. Since this TM-P gene was the only gene strongly enough expressed in SMC changing phenotype to be observed by the subtractive hybridisation screen, it likely plays a significant role in this process. (C) 2002 Published by Elsevier Science Ltd.

Molecular confirmation of an adenovirus in brushtail possums (Trichosurus vulpecula)

Partial genome characterisation of a non-cultivable marsupial adenovirus is described. Adenovirus-like particles were found by electron microscopy (EM) in the intestinal contents of brushtail possums (Trichosurus vulpecula) in New Zealand. Using degenerate PCR primers complementary to the most conserved genome regions of adenoviruses, the complete nucleotide sequence of the penton base gene, and partial nucleotide sequences of the DNA polymerase, hexon, and pVII genes were obtained. Phylogenetic analysis of the penton base gene strongly suggested that the brushtail possum adenovirus (candidate PoAdV-1) belongs to the recently proposed genus Atadenovirus. Sequence analysis of the PCR products amplified from the intestinal contents of brushtail possums originating from different geographical regions of New Zealand identified a single genotype. This is the first report of molecular confirmation of an adenovirus in a marsupial.

An overview of APSIM, a model designed for farming systems simulation

The Agricultural Production Systems Simulator (APSIM) is a modular modelling framework that has been developed by the Agricultural Production Systems Research Unit in Australia. APSIM was developed to simulate biophysical process in farming systems, in particular where there is interest in the economic and ecological outcomes of management practice in the face of climatic risk. The paper outlines APSIM's structure and provides details of the concepts behind the different plant, soil and management modules. These modules include a diverse range of crops, pastures and trees, soil processes including water balance, N and P transformations, soil pH, erosion and a full range of management controls. Reports of APSIM testing in a diverse range of systems and environments are summarised. An example of model performance in a long-term cropping systems trial is provided. APSIM has been used in a broad range of applications, including support for on-farm decision making, farming systems design for production or resource management objectives, assessment of the value of seasonal climate forecasting, analysis of supply chain issues in agribusiness activities, development of waste management guidelines, risk assessment for government policy making and as a guide to research and education activity. An extensive citation list for these model testing and application studies is provided. Crown Copyright (C) 2002 Published by Elsevier Science B.V. All rights reserved.

Influence of LPG composition on straw applied one componente PU winter foam

O principal objectivo desta tese é obter uma relação directa entre a composição dos gases liquefeitos de petróleo (GLP), propano, n-butano e isobutano, usados como aerossóis propulsores numa lata de poliuretano de um componente, com as propriedades das espumas produzidas por spray. As espumas obtidas, terão de ter como requisito principal, um bom desempenho a temperaturas baixas, -10ºC, sendo por isso designadas por espumas de Inverno. Uma espuma é considerada como tendo um bom desempenho se não apresentar a -10/-10ºC (temperatura lata/ spray) glass bubbles, base holes e cell collapse. As espumas deverão ainda ter densidades do spray no molde a +23/+23ºC abaixo dos 30 g/L, um rendimento superior a 30 L, boa estabilidade dimensional e um caudal de espuma a +5/+5ºC superior a 5 g/s. Os ensaios experimentais foram realizados a +23/+23ºC, +5/+5ºC e a -10/-10ºC. A cada temperatura, as espumas desenvolvidas, foram submetidas a testes que permitiram determinar a sua qualidade. Testes esses que incluem os designados por Quick Tests (QT): o spray no papel e no molde das espumas nas referidas temperaturas. As amostras do papel e no molde são especialmente analisadas, quanto, às glass bubbles, cell collapse, base holes, cell structur e, cutting shrinkage, para além de outras propriedades. Os QT também incluem a análise da densidade no molde (ODM) e o estudo do caudal de espumas. Além dos QT foram realizados os testes da estabilidade dimensional das espumas, testes físicos de compressão e adesão, testes de expansão das espumas após spray e do rendimento por lata de espuma. Em todos os ensaios foi utilizado um tubo adaptador colocado na válvula da lata como método de spray e ainda mantida constante a proporção das matérias-primas (excepto os gases, em estudo). As experiências iniciaram-se com o estudo de GLPs presentes no mercado de aerossóis. Estes resultaram que o GLP: propano/ n-butano/ isobutano: (30/ 0/ 70 w/w%), produz as melhores espumas de inverno a -10/-10ºC, reduzindo desta forma as glass bubbles, base holes e o cell collapse produzido pelos restantes GLP usados como aerossóis nas latas de poliuretano. Testes posteriores tiveram como objectivo estudar a influência directa de cada gás, propano, n-butano e isobutano nas espumas. Para tal, foram usadas duas referências do estudo com GLP comercializáveis, 7396 (30 /0 /70 w/w %) e 7442 (0/ 0/ 100 w/w %). Com estes resultados concluí-se que o n-butano produz más propriedades nas espumas a -10/- 10ºC, formando grandes quantidades de glass bubbles, base holes e cell collapse. Contudo, o uso de propano reduz essas glass bubbles, mas em contrapartida, forma cell collapse.Isobutano, porém diminui o cell collapse mas não as glass bubbles. Dos resultados experimentais podemos constatar que o caudal a +5/+5ºC e densidade das espumas a +23/+23ºC, são influenciados pela composição do GLP. O propano e n-butano aumentam o caudal de espuma das latas e a sua densidade, ao contrário com o que acontece com o isobutano. Todavia, pelos resultados obtidos, o isobutano proporciona os melhores rendimentos de espumas por lata. Podemos concluir que os GLPs que contivessem cerca de 30 w/w % de propano (bons caudais a +5/+5ºC e menos glass bubbles a -10/-10ºC), e cerca 70 w/w % de isobutano (bons rendimentos de espumas, bem como menos cell collapse a -10/-10ºC) produziam as melhores espumas. Também foram desenvolvidos testes sobre a influência da quantidade de gás GLP presente numa lata. A análise do volume de GLP usado, foi realizada com base na melhor espuma obtida nos estudos anteriores, 7396, com um GLP (30 / 0/ 70 w/w%), e foram feitas alterações ao seu volume gás GLP presente no pré-polímero. O estudo concluiu, que o aumento do volume pode diminuir a densidade das espumas, e o seu decréscimo, um aumento da densidade. Também indico u que um mau ajuste do volume poderá causar más propriedades nas espumas. A análise económica, concluiu que o custo das espumas com mais GLP nas suas formulações, reduz-se em cerca de 3%, a quando de um aumento do volume de GLP no pré-polímero de cerca de 8 %. Esta diminuição de custos deveu-se ao facto, de um aumento de volume de gás, implicar uma diminuição na quantidade das restantes matérias-primas, com custos superiores, já que o volume útil total da lata terá de ser sempre mantido nos 750 mL. Com o objectivo de melhorar a qualidade da espuma 7396 (30/0/70 w/w %) obtida nos ensaios anteriores adicionou-se à formulação 7396 o HFC-152a (1,1-di fluoroetano). Os resultados demonstram que se formam espumas com más propriedades, especialmente a -10/-10ºC, contudo proporcionou excelentes shaking rate da lata. Através de uma pequena análise de custos não é aconselhável o seu uso pelos resultados obtidos, não proporcionando um balanço custo/benefício favorável. As três melhores espumas obtidas de todos os estudos foram comparadas com uma espuma de inverno presente no mercado. 7396 e 7638 com um volume de 27 % no prépolímero e uma composição de GLP (30/ 0 / 70 w/w%) e (13,7/ 0/ 86,3 w/w%), respectivamente, e 7690, com 37 % de volume no pré-polímero e GLP (30/ 0 / 70 w/w%), apresentaram em geral melhores resultados, comparando com a espuma benchmark . Contudo, os seus shaking rate a -10/-10ºC, de cada espuma, apresentaram valores bastante inferiores à composição benchmarking.

Controlador dedicado de Ecrãs LCD/TFT

Para dar resposta aos grandes avanços tecnológicos e, consequentemente, à postura mais exigente dos clientes, a empresa Francisco Parracho – Electrónica Industrial, Lda., que tem actividade no ramo dos elevadores, decidiu introduzir no mercado um controlador dedicado de ecrãs Liquid Crystal Display / Thin Film Transistor (LCD / TFT). O objectivo é substituir um sistema suportado por um computador, caracterizado pelas suas elevadas dimensões e custos, mas incontornável até à data, nomeadamente para resoluções de ecrã elevadas. E assim nasceu este trabalho. Com uma selecção criteriosa de todos os componentes e, principalmente, sem funcionalidades inúteis, obteve-se um sistema embebido com dimensões e custos bem mais reduzidos face ao seu opositor. O ecrã apontado para este projecto é um Thin Film Transistor – Liquid Crystal Display (TFT-LCD) da Sharp de 10.4” de qualidade industrial, com uma resolução de 800 x 600 píxeis a 18 bits por píxel. Para tal, foi escolhido um micro-controlador da ATMEL, um AVR de 32 bits que, entre outras características, possui um controlador LCD que suporta resoluções até 2048 x 2048 píxeis, de 1 a 24 bits por píxel. Atendendo ao facto deste produto ser inserido na área dos elevadores, as funcionalidades, quer a nível do hardware quer a nível do software, foram projectadas para este âmbito. Contudo, o conceito aqui exposto é adjacente a quaisquer outras áreas onde este produto se possa aplicar, até porque o software está feito para se tornar bem flexível. Com a ajuda de um kit de desenvolvimento, foram validados os drivers dos controladores e periféricos base deste projecto. De seguida, aplicou-se esse software numa placa de circuito impresso, elaborada no âmbito deste trabalho, para que fossem cumpridos todos os requisitos requeridos pela empresa patrocinadora: - Apresentação de imagens no ecrã consoante o piso; - Possibilidade de ter um texto horizontalmente deslizante;Indicação animada do sentido do elevador; - Representação do piso com deslizamento vertical; - Descrição sumária do directório de pisos também com deslizamento vertical; - Relógio digital; - Leitura dos conteúdos pretendidos através de um cartão SD/MMC; - Possibilidade de actualização dos conteúdos via USB flash drive.

Alterações de geometria e sinalização rodoviária em zonas consolidadas no contexto da gestão da mobilidade urbana

Relatório de Estágio para obtenção do grau de Mestre em Engenharia Civil na Área de Especialização de Vias de Comunicação e Transportes

Implementação em hardware reconfigurável de método de separação de dados hiperespetrais

Relatório do Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia de Electrónica e Telecomunicações

Planeamento de rede LTE de baixo custo com uso de repetidor

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia de Electrónica e Telecomunicações