El sustrato pedagógico en las políticas de recursos humanos : el caso de agilent technologies.

Resumen basado en el del autor

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.

Use of the Agilent 2100 bioanalyzer for rapid and reproducible molecular typing of Streptococcus pneumoniae

Restriction fragment length polymorphism (RFLP) analysis is an economic and fast technique for molecular typing but has the drawback of difficulties in accurately sizing DNA fragments and comparing banding patterns on agarose gels. We aimed to improve RFLP for typing of the important human pathogen Streptococcus pneumoniae and to compare the results with the commonly used typing techniques of pulsed-field gel electrophoresis and multilocus sequence typing. We designed primers to amplify a noncoding region adjacent to the pneumolysin gene. The PCR product was digested separately with six restriction endonucleases, and the DNA fragments were analyzed using an Agilent 2100 bioanalyzer for accurate sizing. The combined RFLP results for all enzymes allowed us to assign each of the 47 clinical isolates of S. pneumoniae tested to one of 33 RFLP types. RFLP analyzed using the bioanalyzer allowed discrimination between strains similar to that obtained by the more commonly used techniques of pulsed-field gel electrophoresis, which discriminated between 34 types, and multilocus sequence typing, which discriminated between 35 types, but more quickly and with less expense. RFLP of a noncoding region using the Agilent 2100 bioanalyzer could be a useful addition to the molecular typing techniques in current use for S. pneumoniae, especially as a first screen of a local population.

Determination of rare earth elements in geological samples using the agilent SVDV ICP-OES.

2016

Development and validation of a fast RP-HPLC method to determine the analogue of the thyroid hormone, 3,5,3 '-triiodothyroacetic acid (TRIAC), in polymeric nanoparticles

The objective of this work was to develop and validate a rapid Reversed-Phase High-Performance Liquid Chromatography method for the quantification of 3,5,3 '-triiodothyroacetic acid (TRIAC) in nanoparticles delivery system prepared in different polymeric matrices. Special attention was given to developing a reliable reproductive technique for the pretreatment of the samples. Chromatographic runs were performed on an Agilent 1200 Series HPLC with a RP Phenomenex (R) Gemini C18 (150 x 4, 6 mm i.d., 5 mu m) column using acetonitrile and triethylamine buffer 0.1% (TEA) (40 : 60 v/v) as a mobile phase in an isocratic elution, pH 5.6 at a flow rate of 1 ml min(-1). TRIAC was detected at a wavelength of 220 nm. The injection volume was 20 mu l and the column temperature was maintained at 35 degrees C. The validation characteristics included accuracy, precision, specificity, linearity, recovery, and robustness. The standard curve was found to have a linear relationship (r(2) - 0.9996) over the analytical range of 5-100 mu g ml(-1) . The detection and quantitation limits were 1.3 and 3.8 mu g ml(-1), respectively. The recovery and loaded TRIAC in colloidal system delivery was nearly 100% and 98%, respectively. The method was successfully applied in polycaprolactone, polyhydroxybutyrate, and polymethylmethacrylate nanoparticles.

LATENT RANK CHANGE DETECTION FOR ANALYSIS OF SPLICE-JUNCTION MICROARRAYS WITH NONLINEAR EFFECTS

Alternative splicing of gene transcripts greatly expands the functional capacity of the genome, and certain splice isoforms may indicate specific disease states such as cancer. Splice junction microarrays interrogate thousands of splice junctions, but data analysis is difficult and error prone because of the increased complexity compared to differential gene expression analysis. We present Rank Change Detection (RCD) as a method to identify differential splicing events based upon a straightforward probabilistic model comparing the over-or underrepresentation of two or more competing isoforms. RCD has advantages over commonly used methods because it is robust to false positive errors due to nonlinear trends in microarray measurements. Further, RCD does not depend on prior knowledge of splice isoforms, yet it takes advantage of the inherent structure of mutually exclusive junctions, and it is conceptually generalizable to other types of splicing arrays or RNA-Seq. RCD specifically identifies the biologically important cases when a splice junction becomes more or less prevalent compared to other mutually exclusive junctions. The example data is from different cell lines of glioblastoma tumors assayed with Agilent microarrays.

Time course proteomic profiling of human myocardial infarction plasma samples: An approach to new biomarker discovery

Background: The aim of this study was to identify novel candidate biomarker proteins differentially expressed in the plasma of patients with early stage acute myocardial infarction (AMI) using SELDI-TOF-MS as a high throughput screening technology. Methods: Ten individuals with recent acute ischemic-type chest pain (< 12 h duration) and ST-segment elevation AMI (1STEMI) and after a second AMI (2STEMI) were selected. Blood samples were drawn at six times after STEMI diagnosis. The first stage (T(0)) was in Emergency Unit before receiving any medication, the second was just after primary angioplasty (T(2)), and the next four stages occurred at 12 h intervals after T(0). Individuals (n = 7) with similar risk factors for cardiovascular disease and normal ergometric test were selected as a control group (CG). Plasma proteomic profiling analysis was performed using the top-down (i.e. intact proteins) SELDI-TOF-MS, after processing in a Multiple Affinity Removal Spin Cartridge System (Agilent). Results: Compared with the CG, the 1STEMI group exhibited 510 differentially expressed protein peaks in the first 48 h after the AMI (p < 0.05). The 2STEMI group, had similar to 85% fewer differently expressed protein peaks than those without previous history of AMI (76, p < 0.05). Among the 16 differentially-regulated protein peaks common to both STEMI cohorts (compared with the CG at T(0)), 6 peaks were persistently down-regulated at more than one time-stage, and also were inversed correlated with serum protein markers (cTnI, CK and CKMB) during 48 h-period after IAM. Conclusions: Proteomic analysis by SELDI-TOF-MS technology combined with bioinformatics tools demonstrated differential expression during a 48 h time course suggests a potential role of some of these proteins as biomarkers for the very early stages of AMI, as well as for monitoring early cardiac ischemic recovery. (C) 2011 Elsevier B.V. All rights reserved.

A unit cell waveguide model of a reflectarray formed by microstrip patches and slots

An equivalent unit cell waveguide approach (WGA) is described to obtain reflection coefficient phase curves for designing a microstrip patch reflectarray supported by a ground plane with periodic apertures or slots. Based on the presented theory, a computer algorithm for determining the reflection coefficient of a plane wave normally incident on a multi-layer structure of patches and apertures is developed. The validity of the developed algorithm is verified by comparing the obtained results with those published in the literature and the ones generated by Agilent High Frequency Structure Simulator (HFSS). A good agreement in all the presented examples is obtained, proving that the developed theory and computer algorithm can be an effective tool for designing multi-layer microstrip reflectarrays with a periodically perforated ground plane. (C) 2003 Wiley Periodicals, Inc.

Designing a 161-element Ku-band microstrip reflectarray of variable size patches using an equivalent unit cell waveguide approach

An equivalent unit cell waveguide approach (WGA) to designing 4 multilayer microstrip reflectarray of variable size patches is presented. In this approach, a normal incidence of a plane wave on an infinite periodic array of radiating elements is considered to obtain reflection coefficient phase curves for the reflectarray's elements. It is shown that this problem is equivalent to the problem of reflection of the dominant TEM mode in a waveguide with patches interleaved by layers of dielectric. This waveguide problem is solved using a field matching technique and a method of moments (MoM). Based on this solution, a fast computer algorithm is developed to generate reflection coefficient phase curves for a multilayer microstrip patch reflectarray. The validity of the developed algorithm is tested against alternative approaches and Agilent High Frequency Structure Simulator (HFSS). Having confirmed the validity of the WGA approach, a small offset feed two-layer microstrip patch array is designed and developed. This reflectarray is tested experimentally and shows good performance.

Monitorização e caracterização de uma UTA com tecnologia exsicante-evaporativa assistida por energia solar de acordo com a metodologia definida no âmbito da AIE SHC task 38

A presente dissertação fundamenta-se na monitorização e análise de uma “Unidade de Tratamento de Ar” baseada em tecnologia exsicante evaporativa assistida por energia solar. Primeiramente é apresentado um conjunto de conceitos associados ao tema abordado, de modo a facilitar a compreensão dos fenómenos termodinâmicos envolvidos. Após a abordagem inicial que serve de consolidação, é feito o ponto da situação actual, quer em termos tecnológicos, quer em termos de instalações existentes. A etapa seguinte da dissertação descreve pormenorizadamente a instalação do LNEG e seus princípios de funcionamento, nesta fase também é contemplada a descrição sumária dos equipamentos, dos componentes e dos elementos de medição e controlo presentes no sistema. A metodologia seguida assenta fortemente em dois pontos; primeiro, a monitorização do sistema através do software “Agilent VEE Pro” e pela análise dos dados recolhidos com auxílio da folha de cálculo do LNEG, desenvolvida especialmente para este sistema. Em segundo lugar, a metodologia seguida será a imposta pela “Tarefa 38” de acordo com a Agência Internacional de Energia, no âmbito do programa de Aquecimento e Arrefecimento Solar o que permite a comparação de sistemas a nível internacional. Alias a “Tarefa 38” pretende desenvolver esta tecnologia, ao nível da concepção, estandardização, optimização das instalações, conceder o fácil acesso à informação e promover a comparabilidade de resultados. O desempenho global do sistema é bastante positivo, o bom comportamento do sistema é ilustrado na análise gráfica feita nos modos de aquecimento e arrefecimento. O grau de satisfação dos utilizadores é bom e o sistema demonstra capacidade para manter o conforto térmico dos espaços a climatizar de acordo com as normas e regulamentos em vigor. A utilização das energias renováveis nos dias de hoje, como por exemplo a energia solar é mais do que uma obrigação, é um dever.

Caracterização da fase activa de catalisadores de Níquel suportados em α-Alumina, utilizando as reacções de desidrogenação e Hidrogenólise do Ciclohexano

A constante melhoria da eficiência energética dos processos industriais actuais é crucial para o contínuo desenvolvimento sustentável da espécie humana. O estudo das reacções de desidrogenação e hidrogenólise do ciclohexano, sobre catalisadores suportados, pode contribuir para um melhor entendimento acerca dos processos de formação e armazenamento de H2, uma das mais promissoras fontes de energia do futuro próximo, assim como para processos actuais tão importantes como a refinação ou o reforming catalítico do petróleo. Escolheu-se estudar as referidas reacções sobre catalisadores de Ni/α-Al2O3, preparados por três métodos distintos e submetidos a diferentes pré-tratamentos, de modo a realçar a dependência das reacções no que se refere às propriedades catalíticas. A maioria dos estudos anteriores sobre estas mesmas reacções recai sobre catalisadores com metais nobres, como a platina ou o paládio, bastante mais dispendiosos que o níquel para aplicações em larga escala. Os precursores e catalisadores previamente preparados foram submetidos à caracterização por diferentes técnicas: Termogravimetria (sob fluxo oxidativo e não oxidativo), Difracção de Raios-X e Quimissorção de H2. O estudo das reacções de desidrogenação e hidrogenólise do ciclohexano realizou-se recorrendo à análise por Cromatografia Gasosa, utilizando dois cromatógrafos distintos (HEWLETT PACKARD 5890 SERIES II, para GC, e 490 Micro GC Agilent, para Micro GC). Pôde concluir-se que o método de preparação dos catalisadores influenciou a actividade para ambas as reacções, assim como os diferentes pré-tratamentos aplicados. No geral, e na gama de temperaturas estudadas (entre 250 e 310º C), os catalisadores preparados pelo método com etilenodiamina evidenciaram maior actividade para a reacção de desidrogenação, sendo que os catalisadores preparados pelo método com etilenoglicol foram os mais activos para a reacção de hidrogenólise.

Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research

The MAP-i Doctoral Program of the Universities of Minho, Aveiro and Porto

Integrating data from heterogeneous DNA microarray platforms

DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination. In this work, a complete methodology for gene expression data integration and application is proposed, which comprehends a transcript-based re-annotation process and several methods for batch effect attenuation. The integrated data will be used to select the best feature set and learning algorithm for a brain tumor classification case study. The integration will consider data from heterogeneous Agilent and Affymetrix platforms, collected from public gene expression databases, such as The Cancer Genome Atlas and Gene Expression Omnibus.