One-pot synthesis of multivalent arrays of mannose mono- and disaccharides

The synthesis of a selection of multivalent arrays of mannose mono- and disaccharides, that are of potential use as anti-infective agents against enterobacteria infections, is described. (C) 2003 Elsevier Ltd. All rights reserved.

Compositional technique for synthesising multi-phase regular arrays

We describe a high-level design method to synthesize multi-phase regular arrays. The method is based on deriving component designs using classical regular (or systolic) array synthesis techniques and composing these separately evolved component design into a unified global design. Similarity transformations ar e applied to component designs in the composition stage in order to align data ow between the phases of the computations. Three transformations are considered: rotation, re ection and translation. The technique is aimed at the design of hardware components for high-throughput embedded systems applications and we demonstrate this by deriving a multi-phase regular array for the 2-D DCT algorithm which is widely used in many vide ocommunications applications.

Use of miniaturized protein arrays for Escherichia coli O serotyping

Serological typing of Escherichia coli O antigens is a well-established method used for differentiation and identification of O serotypes commonly associated with disease. In this feasibility study, we have developed a novel somatic antibody-based miniaturized microarray chip, using 17 antisera, which can be used to detect bound whole-cell E. coli antigen with its corresponding immobilized antibody, to assess the feasibility of this approach. The chip was tested using the related 17 control strains, and the O types found by the microarray chip showed 100% correlation with the O types found by conventional typing. A blind trial was performed in which 100 E. coli isolates that had been O serotyped previously by the conventional assay were tested by the array approach. Overall, the O serotypes of 88% of isolates were correctly identified by the microarray method. For several isolates, ambiguity of O-type designation by microarray arose due to increased sensitivity of this method, allowing signal intensities of cross-reactions to be quantified. Investigation of discrepancies between conventional and microarray O serotyping indicated that some isolates upon storage had become untypeable and, therefore, gave poor signal intensity when tested by the microarray or retested by conventional means. For all 20 serotype O26 and O157 isolates, the apparent discrepancy in O serotyping was analyzed further by a third independent test, which confirmed the microarray results. Therefore, the use of miniaturized protein arrays increases the speed and efficiency of O serotyping in a cost-effective manner, and these preliminary findings suggest the microarray approach may have a higher accuracy than those of traditional O-serotyping methods.

Endogenous cholinergic tone modulates spontaneous network level neuronal activity in primary cortical cultures grown on multi-electrode arrays

Background Cortical cultures grown long-term on multi-electrode arrays (MEAs) are frequently and extensively used as models of cortical networks in studies of neuronal firing activity, neuropharmacology, toxicology and mechanisms underlying synaptic plasticity. However, in contrast to the predominantly asynchronous neuronal firing activity exhibited by intact cortex, electrophysiological activity of mature cortical cultures is dominated by spontaneous epileptiform-like global burst events which hinders their effective use in network-level studies, particularly for neurally-controlled animat (‘artificial animal’) applications. Thus, the identification of culture features that can be exploited to produce neuronal activity more representative of that seen in vivo could increase the utility and relevance of studies that employ these preparations. Acetylcholine has a recognised neuromodulatory role affecting excitability, rhythmicity, plasticity and information flow in vivo although its endogenous production by cortical cultures and subsequent functional influence upon neuronal excitability remains unknown. Results Consequently, using MEA electrophysiological recording supported by immunohistochemical and RT-qPCR methods, we demonstrate for the first time, the presence of intrinsic cholinergic neurons and significant, endogenous cholinergic tone in cortical cultures with a characterisation of the muscarinic and nicotinic components that underlie modulation of spontaneous neuronal activity. We found that tonic muscarinic ACh receptor (mAChR) activation affects global excitability and burst event regularity in a culture age-dependent manner whilst, in contrast, tonic nicotinic ACh receptor (nAChR) activation can modulate burst duration and the proportion of spikes occurring within bursts in a spatio-temporal fashion. Conclusions We suggest that the presence of significant endogenous cholinergic tone in cortical cultures and the comparability of its modulatory effects to those seen in intact brain tissues support emerging, exploitable commonalities between in vivo and in vitro preparations. We conclude that experimental manipulation of endogenous cholinergic tone could offer a novel opportunity to improve the use of cortical cultures for studies of network-level mechanisms in a manner that remains largely consistent with its functional role.

Measuring motion with kinematically redundant accelerometer arrays: theory, simulation and implementation

This work presents two schemes of measuring the linear and angular kinematics of a rigid body using a kinematically redundant array of triple-axis accelerometers with potential applications in biomechanics. A novel angular velocity estimation algorithm is proposed and evaluated that can compensate for angular velocity errors using measurements of the direction of gravity. Analysis and discussion of optimal sensor array characteristics are provided. A damped 2 axis pendulum was used to excite all 6 DoF of the a suspended accelerometer array through determined complex motion and is the basis of both simulation and experimental studies. The relationship between accuracy and sensor redundancy is investigated for arrays of up to 100 triple axis (300 accelerometer axes) accelerometers in simulation and 10 equivalent sensors (30 accelerometer axes) in the laboratory test rig. The paper also reports on the sensor calibration techniques and hardware implementation.

Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays

Background: Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples. Results: We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2 of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log(2) units (6 of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators. Conclusions: This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells.

Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection

Background: Affymetrix GeneChip arrays are widely used for transcriptomic studies in a diverse range of species. Each gene is represented on a GeneChip array by a probe- set, consisting of up to 16 probe-pairs. Signal intensities across probe- pairs within a probe-set vary in part due to different physical hybridisation characteristics of individual probes with their target labelled transcripts. We have previously developed a technique to study the transcriptomes of heterologous species based on hybridising genomic DNA (gDNA) to a GeneChip array designed for a different species, and subsequently using only those probes with good homology. Results: Here we have investigated the effects of hybridising homologous species gDNA to study the transcriptomes of species for which the arrays have been designed. Genomic DNA from Arabidopsis thaliana and rice (Oryza sativa) were hybridised to the Affymetrix Arabidopsis ATH1 and Rice Genome GeneChip arrays respectively. Probe selection based on gDNA hybridisation intensity increased the number of genes identified as significantly differentially expressed in two published studies of Arabidopsis development, and optimised the analysis of technical replicates obtained from pooled samples of RNA from rice. Conclusion: This mixed physical and bioinformatics approach can be used to optimise estimates of gene expression when using GeneChip arrays.

Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

High-density oligonucleotide (oligo) arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip® array is available, using a GeneChip® array designed for Arabidopsis thaliana (L.) Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM) probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P) stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ webcite and may be used to facilitate transcriptomic analyses of a wide range of plant and animal species in the absence of custom arrays.

Arrays of chiral nanotubes and a layered coordination polymer containing gallium-sulfide supertetrahedral clusters

We report here a unique chiral hybrid gallium sulfide, [NC2H8]2[Ga10S16(N2C12H12)(NC2H7)2] 1, consisting of helical chains of organically-functionalised supertetrahedral clusters which form quadruple-stranded helical nanotubes of ca. 3 nm diameter. This material therefore consists of discrete metal-organic nanotubes which, to the best of our knowledge, are extremely rare. Whilst solvothermal reactions involving 1,2-di(4-pyridyl)ethylene (DPE) resulted in the formation of such single-walled chiral nanotubes, the use of longer 4,4’-trimethylenedipyridine (TMP) ligands resulted in the synthesis of a two-dimensional hybrid gallium sulfide, [C5H6N]3[Ga10S16(OH)(N2C13H14)] 2 in which, for the first time, inorganic and organic linkages between supertetrahedral clusters coexist.

Flow structure and near-field dispersion in arrays of building-like obstacles

Dispersion in the near-field region of localised releases in urban areas is difficult to predict because of the strong influence of individual buildings. Effects include upstream dispersion, trapping of material into building wakes and enhanced concentration fluctuations. As a result, concentration patterns are highly variable in time and mean profiles in the near field are strongly non-Gaussian. These aspects of near-field dispersion are documented by analysing data from direct numerical simulations in arrays of building-like obstacles and are related to the underlying flow structure. The mean flow structure around the buildings is found to exert a strong influence over the dispersion of material in the near field. Diverging streamlines around buildings enhance lateral dispersion. Entrainment of material into building wakes in the very near field gives rise to secondary sources, which then affect the subsequent dispersion pattern. High levels of concentration fluctuations are also found in this very near field; the fluctuation intensity is of order 2 to 5.

Teste da rede de interconexões de field programmable analog arrays

Os dispositivos analógicos programáveis (FPAAs, do inglês, Field Programmable Analog Arrays), apesar de ainda não terem a mesma popularidade de seus pares digitais (FPGAs, do inglês, Field Programmable Gate Arrays), possuem uma gama de aplicações bastante ampla, que vai desde o condicionamento de sinais em sistemas de instrumentação, até o processamento de sinais de radiofreqüência (RF) em telecomunicações. Porém, ao mesmo tempo em que os FPAAs trouxeram um impressionante ganho na agilidade de concepção de circuitos analógicos, também trouxeram um conjunto de novos problemas relativos ao teste deste tipo de dispositivo. Os FPAAs podem ser divididos em duas partes fundamentais: seus blocos programáveis básicos (CABs, do inglês, Configurable Analog Blocks) e sua rede de interconexões. A rede de interconexões, por sua vez, pode ser dividida em duas partes: interconexões internas (locais e globais entre CABs) e interconexões externas (envolvendo células de I/O). Todas estas partes apresentam características estruturais e funcionais distintas, de forma que devem ser testadas separadamente, pois necessitam que se considerem modelos de falhas, configurações e estímulos de teste específicos para assegurar uma boa taxa de detecção de defeitos. Como trabalhos anteriores já estudaram o teste dos CABs, o foco desta dissertação está direcionado ao desenvolvimento de metodologias que se propõem a testar a rede de interconexões de FPAAs. Apesar das várias diferenças entre as redes de interconexões de FPGAs e FPAAs, muitas também são as semelhanças entre elas, sendo, portanto, indiscutível que o ponto de partida deste trabalho tenha que ser o estudo das muitas técnicas propostas para o teste de interconexões em FPGAs, para posterior adaptação ao caso dos FPAAs. Além disto, embora o seu foco não recaia sobre o teste de CABs, pretende-se utilizá-los como recursos internos do dispositivo passíveis de gerar sinais e analisar respostas de teste, propondo uma abordagem de auto-teste integrado de interconexões que reduza o custo relativo ao equipamento externo de teste. Eventualmente, estes mesmos recursos poderão também ser utilizados para diagnóstico das partes defeituosas. Neste trabalho, utiliza-se como veículo de experimentação um dispositivo específico (Anadigm AN10E40), mas pretende-se que as metodologias de teste propostas sejam abrangentes e possam ser facilmente adaptadas a outros FPAAs comerciais que apresentem redes de interconexão semelhantes.

Aplicações de arranjos de antenas de microfita com patch supercondutor

This work has as main objective the study of arrays of microstrip antennas with superconductor rectangular patch. The phases and the radiation patterns are analyzed. A study of the main theories is presented that explain the microscopic and macroscopic phenomena of superconductivity. The BCS, London equations and the Two Fluid Model, are theories used in the applications of superconductors, at the microstrip antennas and antennas arrays. Phase Arrangements will be analyzed in linear and planar configurations. The arrangement factors of these configurations are obtained, and the phase criteria and the spacing between the elements, are examined in order to minimize losses in the superconductor, compared with normal conductors. The new rectangular patch antenna, consist of a superconducting material, with the critical temperature of 233 K, whose formula is Tl5Ba4Ca2Cu9Oy, is analyzed by the method of the Transverse nTransmission Line (TTL), developed by H. C. C. Fernandes, applied in the Fourier Transform Domain (FTD). The TTL is a full-wave method, which has committed to obtaining the electromagnetic fields in terms of the transverse components of the structure. The inclusion of superconducting patch is made using the complex resistive boundary condition, using the impedance of the superconductor in the Dyadic Green function, in the structure. Results are obtained from the resonance frequency depending on the parameters of the antenna using superconducting material, radiation patterns in E-Plane and H -Plane, the phased antennas array in linear and planar configurations, for different values of phase angles and different spacing between the elements

Digital radiography using digital detector arrays fulfills critical applications for offshore pipelines

Digital radiography in the inspection of welded pipes to be installed under deep water offshore gas and oil pipelines, like a presalt in Brazil, in the paper has been investigated. The aim is to use digital radiography for nondestructive testing of welds as it is already in use in the medical, aerospace, security, automotive, and petrochemical sectors. Among the current options, the DDA (Digital Detector Array) is considered as one of the best solutions to replace industrial films, as well as to increase the sensitivity to reduce the inspection cycle time. This paper shows the results of this new technique, comparing it to radiography with industrial films systems. In this paper, 20 test specimens of longitudinal welded pipe joints, specially prepared with artificial defects like cracks, lack of fusion, lack of penetration, and porosities and slag inclusions with varying dimensions and in 06 different base metal wall thicknesses, were tested and a comparison of the techniques was made. These experiments verified the purposed rules for parameter definitions and selections to control the required digital radiographic image quality as described in the draft international standard ISO/DIS 10893-7. This draft is first standard establishing the parameters for digital radiography on weld seam of welded steel pipes for pressure purposes to be used on gas and oil pipelines.