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‣ Production of DNA microarray and expression analysis of genes from Xylella fastidiosa in different culture media

TRAVENSOLO, Regiane de Fátima; COSTA, Maria Vitória Cecchette Gottardi; CARARETO-ALVES, Lucia Maria; CARRILHO, Emanuel; LEMOS, Eliana Gertrudes de Macedo
Fonte: Tecpar Publicador: Tecpar
Tipo: Artigo de Revista Científica
Português
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DNA Microarray was developed to monitor the expression of many genes from Xylella fastidiosa, allowing the side by-side comparison of two situations in a single experiment. The experiments were performed using X. fastidiosa cells grown in two culture media: BCYE and XDM2. The primers were synthesized, spotted onto glass slides and the array was hybridized against fluorescently labeled cDNAs. The emitted signals were quantified, normalized and the data were statistically analyzed to verify the differentially expressed genes. According to the data, 104 genes were differentially expressed in XDM2 and 30 genes in BCYE media. The present study showed that DNA microarray technique efficiently differentiate the expressed genes under different conditions.; DNA Microarray foi desenvolvida para monitorar a expressão de muitos genes de Xylella fastidiosa, permitindo a comparação de duas situações distintas em um único experimento. Os experimentos foram feitos utilizando células de X. fastidiosa cultivada em dois meios de cultura: BCYE e XDM2. Pares de oligonucleotídeos iniciadores foram sintetizados, depositados em lâminas de vidro e o arranjo foi hibridizado contra cDNAs marcados fluorescentemente. Os sinais emitidos foram quantificados...

‣ Planejamento, gerenciamento e análise de dados de microarranjos de DNA para identificação de biomarcadores de diagnóstico e prognóstico de cânceres humanos; Planning, management and analysis of DNA microarray data aiming at discovery of biomarkers for diagnosis and prognosis of human cancers.

Simões, Ana Carolina Quirino
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 12/05/2009 Português
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Nesta tese, apresentamos nossas estratégias para desenvolver um ambiente matemático e computacional para análises em larga-escala de dados de expressão gênica obtidos pela tecnologia de microarranjos de DNA. As análises realizadas visaram principalmente à identificação de marcadores moleculares de diagnóstico e prognóstico de cânceres humanos. Apresentamos o resultado de diversas análises implementadas através do ambiente desenvolvido, as quais conduziram a implementação de uma ferramenta computacional para a anotação automática de plataformas de microarranjos de DNA e de outra ferramenta destinada ao rastreamento da análise de dados realizada em ambiente R. Programação eXtrema (eXtreme Programming, XP) foi utilizada como técnica de planejamento e gerenciamento dos projetos de análise dados de expressão gênica. Todos os conjuntos de dados foram obtidos por nossos colaboradores, utilizando-se duas diferentes plataformas de microarranjos de DNA: a primeira enriquecida em regiões não-codificantes do genoma humano, em particular regiões intrônicas, e a segunda representando regiões exônicas de genes humanos. A primeira plataforma foi utilizada para avaliação do perfil de expressão gênica em tumores de próstata e rim humanos...

‣ Production of DNA microarray and expression analysis of genes from Xylella fastidiosa in different culture media

Travensolo, Regiane de Fátima; Costa, Maria Vitória Cecchette Gottardi; Carareto-Alves, Lucia Maria; Carrilho, Emanuel; Lemos, Eliana Gertrudes de Macedo
Fonte: Brazilian Archives of Biology and Technology Publicador: Brazilian Archives of Biology and Technology
Tipo: Artigo de Revista Científica Formato: 555-566
Português
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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); Processo FAPESP: 00/06289-2; DNA Microarray foi desenvolvida para monitorar a expressão de muitos genes de Xylella fastidiosa, permitindo a comparação de duas situações distintas em um único experimento. Os experimentos foram feitos utilizando células de X. fastidiosa cultivada em dois meios de cultura: BCYE e XDM2. Pares de oligonucleotídeos iniciadores foram sintetizados, depositados em lâminas de vidro e o arranjo foi hibridizado contra cDNAs marcados fluorescentemente. Os sinais emitidos foram quantificados, normalizados e os dados foram estatisticamente analisados para verificar os genes diferencialmente expressos. de acordo com nossos dados, 104 genes foram diferencialmente expressos para o meio de cultura XDM2 e 30 genes para o BCYE. No presente estudo, nós demonstramos que a técnica de DNA microarrays eficientemente diferencia genes expressos sob diferentes condições de cultivo.; DNA Microarray was developed to monitor the expression of many genes from Xylella fastidiosa, allowing the side by-side comparison of two situations in a single experiment. The experiments were performed using X. fastidiosa cells grown in two culture media: BCYE and XDM2. The primers were synthesized...

‣ Perfil transcricional de Bradyrhizobium elkanii SEMIA 587 in vitro e em simbiose com soja (Glycine max L. Merrill) através de microarranjo de DNA

Souza, Jackson Antônio Marcondes de
Fonte: Universidade Estadual Paulista (UNESP) Publicador: Universidade Estadual Paulista (UNESP)
Tipo: Tese de Doutorado Formato: xvii, 139 f. : il.
Português
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Pós-graduação em Microbiologia Agropecuária - FCAV; O nitrogênio é o nutriente requerido em maior quantidade para a cultura da soja. Avanços nas pesquisas de melhoramento genético vegetal e microbiologia do solo permitiram expandir o uso de inoculantes comerciais contendo estirpes de Bradyrhizobium japonicum e Bradyrhizobium elkanii. Estas bactérias infectam as raízes da planta e induzem a formação de nódulos, que abrigam a forma bacterióide, diferenciada da bactéria, responsável pela fixação simbiótica do nitrogênio. Informações sobre processos bioquímicos envolvidos no metabolismo da relação simbiótica podem ser adquiridas através de análises globais de expressão gênica. Para esta finalidade, destaca-se a tecnologia de microarranjo de DNA para detecção de genes diferencialmente expressos em larga escala. O objetivo geral deste trabalho foi identificar genes diferencialmente expressos, por meio de microarranjos de DNA, em Bradyrhizobium elkanii SEMIA 587 cultivada em diferentes meios de cultura, RDM (Rhizobia Defined Medium), TY (Triptone-Yeast Medium) e YMB (Yeast-Mannitol Medium), e em bacterióides isolados de nódulos de soja em diferentes períodos de desenvolvimento...

‣ A visual analytics framework for cluster analysis of DNA microarray data

Castellanos-Garzón, José A.; García, Carlos Armando; Novais, Paulo; Díaz, Fernando
Fonte: Elsevier Publicador: Elsevier
Tipo: Artigo de Revista Científica
Publicado em //2013 Português
Relevância na Pesquisa
57.487705%
Prova tipográfica; Cluster analysis of DNA microarray data is an important but difficult task in knowledge discovery processes. Many clustering methods are applied to analysis of data for gene expression, but none of them is able to deal with an absolute way with the challenges that this technology raises. Due to this, many applications have been developed for visually representing clustering algorithm results on DNA microarray data, usually providing dendrogram and heat map visualizations. Most of these applications focus only on the above visualizations, and do not offer further visualization components to the validate the clustering methods or to validate one another. This paper proposes using a visual analytics framework in cluster analysis of gene expression data. Additionally, it presents a new method for finding cluster boundaries based on properties of metric spaces. Our approach presents a set of visualization components able to interact with each other; namely, parallel coordinates, cluster boundary genes, 3D cluster surfaces and DNA microarray visualizations as heat maps. Experimental results have shown that our framework can be very useful in the process of more fully understanding DNA microarray data. The software has been implemented in Java...

‣ Development of a microarray for Enchytraeus Albidus (oligochaeta): preliminary tool with diverse applications

Amorim, MJB; Novais, SC; Van Der Ven, K; Vandenbrouck, T; Soares, AMVM; De Coen, W
Fonte: SETAC Press Publicador: SETAC Press
Tipo: Artigo de Revista Científica
Português
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Standard bioassays allow hazard assessment at the population level, but much remains to be learned about the molecular level response of organisms to stressors. The main aim of this study was the development of a DNA microarray for Enchytraeus albidus, a common soil worm species. Further, this microarray was tested using worms exposed to Cu, phenmedipham, and different soil types. Hybridization onto the developed microarray revealed several genes with homology to known sequences. Genes of interest were confirmed through real-time polymerase chain reaction. It was possible to discriminate between natural and chemical stressors and chemical concentrations. Gene responses were detected under conditions known to have effects in the reproduction of individuals. It was confirmed that the integration of different endpoints improves the assessment process and enhances the understanding of the modes of action of stressors. The chemical stress-induced genes were related to factors such as immune response, stress response, metabolic processes, and/or signal transduction. The present study represents the first step of a gene-level study in the ecologically relevant and standard test species E. albidus. It demonstrates the usefulness of cDNA normalization in the production of cDNA libraries of ecotoxicological standard organisms that are not genome models like E. albidus. Environ. Toxicol. Chem. 2011;30:1395-1402. (C) 2011 SETAC

‣ Production of DNA microarray and expression analysis of genes from Xylella fastidiosa in different culture media

Travensolo,Regiane de Fátima; Costa,Maria Vitória Cecchette Gottardi; Carareto-Alves,Lucia Maria; Carrilho,Emanuel; Lemos,Eliana Gertrudes de Macedo
Fonte: Instituto de Tecnologia do Paraná - Tecpar Publicador: Instituto de Tecnologia do Paraná - Tecpar
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/06/2009 Português
Relevância na Pesquisa
67.34328%
DNA Microarray was developed to monitor the expression of many genes from Xylella fastidiosa, allowing the side by-side comparison of two situations in a single experiment. The experiments were performed using X. fastidiosa cells grown in two culture media: BCYE and XDM2. The primers were synthesized, spotted onto glass slides and the array was hybridized against fluorescently labeled cDNAs. The emitted signals were quantified, normalized and the data were statistically analyzed to verify the differentially expressed genes. According to the data, 104 genes were differentially expressed in XDM2 and 30 genes in BCYE media. The present study showed that DNA microarray technique efficiently differentiate the expressed genes under different conditions.

‣ Development and Clinical Evaluation of a Highly Sensitive DNA Microarray for Detection and Genotyping of Human Papillomaviruses

Oh, TaeJeong; Kim, ChangJin; Woo, SukKyung; Kim, TaeSeung; Jeong, DongJun; Kim, MyungSoon; Lee, Sunwoo; Cho, HyunSill; An, Sungwhan
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /07/2004 Português
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Human papillomavirus (HPV) has been found in cervical cancer, tonsillar cancer, and certain types of head and neck cancers. We report on a DNA microarray-based method for the simultaneous detection and typing of HPVs. The genotype spectrum discriminated by this HPV DNA microarray includes 15 high-risk HPV genotypes and 12 low-risk HPV genotypes. The HPV DNA microarray showed high degrees of specificity and reproducibility. We evaluated the performance of the HPV DNA microarray by application to three HPV-positive cell lines (HeLa, Caski, and SiHa cells) and two HPV-negative cell lines (C33A and A549 cells). The HPV DNA microarray successfully identified the known types of HPV present in the cell lines. The detection limit of the HPV DNA microarray was at least 100-fold higher than that of PCR. To assess the clinical applicability of the HPV DNA microarray, we performed the HPV genotyping assay with 73 nonmalignant and malignant samples from 39 tonsillar cancer patients. Twenty-five of the 39 (64.1%) malignant samples were positive for HPV, whereas 3 of 34 (8.8%) nonmalignant samples were positive for HPV. This result shows a preferential association of HPV with tonsillar carcinomas. The correlations of the presence of HPV with the grade of differentiation and risk factors were not significant. Our data show that the HPV DNA microarray may be useful for the diagnosis and typing of HPV in large-scale epidemiological studies.

‣ DNA Microarray-Based Detection and Identification of Fungal Pathogens in Clinical Samples from Neutropenic Patients▿

Spiess, Birgit; Seifarth, Wolfgang; Hummel, Margit; Frank, Oliver; Fabarius, Alice; Zheng, Chun; Mörz, Handan; Hehlmann, Rüdiger; Buchheidt, Dieter
Fonte: American Society for Microbiology (ASM) Publicador: American Society for Microbiology (ASM)
Tipo: Artigo de Revista Científica
Português
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The increasing incidence of invasive fungal infections (IFI) in immunocompromised patients emphasizes the need to improve diagnostic tools. We established a DNA microarray to detect and identify DNA from 14 fungal pathogens (Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus, Candida albicans, Candida dubliniensis, Candida glabrata, Candida lusitaniae, Candida tropicalis, Fusarium oxysporum, Fusarium solani, Mucor racemosus, Rhizopus microsporus, Scedosporium prolificans, and Trichosporon asahii) in blood, bronchoalveolar lavage, and tissue samples from high-risk patients. The assay combines multiplex PCR and consecutive DNA microarray hybridization. PCR primers and capture probes were derived from unique sequences of the 18S, 5.8S, and internal transcribed spacer 1 regions of the fungal rRNA genes. Hybridization with genomic DNA of fungal species resulted in species-specific hybridization patterns. By testing clinical samples from 46 neutropenic patients with proven, probable, or possible IFI or without IFI, we detected A. flavus, A. fumigatus, C. albicans, C. dubliniensis, C. glabrata, F. oxysporum, F. solani, R. microsporus, S. prolificans, and T. asahii. For 22 of 22 patients (5 without IFI and 17 with possible IFI)...

‣ DNA microarray-based identification and typing of Actinobacillus pleuropneumoniae

Xiao, GuoSheng; Cao, SanJie; Huang, XiaoBo; Wen, XinTian
Fonte: Canadian Veterinary Medical Association Publicador: Canadian Veterinary Medical Association
Tipo: Artigo de Revista Científica
Publicado em /07/2009 Português
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A DNA microarray system was prepared and shown to facilitate identification and typing of Actinobacillus pleuropneumoniae. The DNA microarray, composed of 18 DNA polymerase chain reaction (PCR) amplicons printed on glass slides and arranged in 3 subarrays, was developed. These target DNA included 1 or multiple fragments of the outer membrane lipoprotein, apx toxin, capsular polysaccharide, and disulfide bound formation protein E (dsbE)-like genes of A. pleuropneumoniae. These arrayed target DNA retained their expceted hybridization properties. The hybridization signal intensities ranged from the least-intense to the most-intense, 4626 to 9789 arbitrary fluorescence units, respectively. Cy3-probes of A. pleuropneumoniae strains labeled with multiplex PCR were hybridized to the DNA microarray. A total of 51 different A. pleuropneumoniae strains representing serotype 1 to 12 reference strains and clinical isolates were detected and typed by the DNA microarray. Twelve reference serotypes produced 11 distinct target DNA hybridization patterns, and hybridization patterns of serotypes 1 (n = 7), 3 (n = 5), and 7 (n = 6) field isolates were identical to hybridization patterns of reference serotypes 1, 3, and 7, respectively. Non-serotyped isolates 4...

‣ Comprehensive Analysis of Prokaryotes in Environmental Water Using DNA Microarray Analysis and Whole Genome Amplification

Akama, Takeshi; Kawashima, Akira; Tanigawa, Kazunari; Hayashi, Moyuru; Ishido, Yuko; Luo, Yuqian; Hata, Akihisa; Fujitani, Noboru; Ishii, Norihisa; Suzuki, Koichi
Fonte: MDPI Publicador: MDPI
Tipo: Artigo de Revista Científica
Publicado em 30/10/2013 Português
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The microflora in environmental water consists of a high density and diversity of bacterial species that form the foundation of the water ecosystem. Because the majority of these species cannot be cultured in vitro, a different approach is needed to identify prokaryotes in environmental water. A novel DNA microarray was developed as a simplified detection protocol. Multiple DNA probes were designed against each of the 97,927 sequences in the DNA Data Bank of Japan and mounted on a glass chip in duplicate. Evaluation of the microarray was performed using the DNA extracted from one liter of environmental water samples collected from seven sites in Japan. The extracted DNA was uniformly amplified using whole genome amplification (WGA), labeled with Cy3-conjugated 16S rRNA specific primers and hybridized to the microarray. The microarray successfully identified soil bacteria and environment-specific bacteria clusters. The DNA microarray described herein can be a useful tool in evaluating the diversity of prokaryotes and assessing environmental changes such as global warming.

‣ Comparative Evaluation of Effectiveness of IAVchip DNA Microarray in Influenza A Diagnosis

Sultankulova, K. T.; Chervyakova, O. V.; Kozhabergenov, N. S.; Shorayeva, K. A.; Strochkov, V. M.; Orynbayev, M. B.; Sandybayev, N. T.; Sansyzbay, A. R.; Vasin, A. V.
Fonte: Hindawi Publishing Corporation Publicador: Hindawi Publishing Corporation
Tipo: Artigo de Revista Científica
Português
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The paper describes comparative evaluation of IAVchip DNA microarray, reverse transcription PCR (RT-PCR), and real-time RT-PCR versus virus isolation in chicken embryos and shows their diagnostic effectiveness in detection and subtyping of influenza A virus. The tests were evaluated with use of 185 specimens from humans, animals, and birds. IAVchip DNA microarray demonstrates higher diagnostic effectiveness (99.45%) in early influenza A diagnosis as compared to the real-time PCR (98.38%) and RT-PCR (96.22%), thus showing its clear superiority. Diagnostic sensitivity of IAVchip DNA microarray (100%) exceeds the same of RT-PCR (95.95%) and real-time RT-PCR (97.96%) in the range of estimated confidence intervals. IAVchip DNA microarray and real-time RT-PCR displayed equal diagnostic specificity (98.85%), while diagnostic specificity of RT-PCR was 96.40%. IAVchip DNA microarray has an advantage over the other tests for influenza A diagnosis and virus identification as a more rapid method that allows performing simultaneous detection and subtyping of about tens of specimens within one experiment during 8–10 hours. The developed IAVchip DNA microarray is a general test tool that enables identifying simultaneously 16 hemagglutinin (HA) and 9 neuraminidase (NA) subtypes of influenza A virus and also to screen the influenza A viruses from humans...

‣ Hierarchical Multi-Bottleneck Classification Method And Its Application to DNA Microarray Expression Data

Xiong, Xuejian; Wong, Weng Fai; Hsu, Wen Jing
Fonte: MIT - Massachusetts Institute of Technology Publicador: MIT - Massachusetts Institute of Technology
Tipo: Artigo de Revista Científica Formato: 118852 bytes; application/pdf
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The recent development of DNA microarray technology is creating a wealth of gene expression data. Typically these datasets have high dimensionality and a lot of varieties. Analysis of DNA microarray expression data is a fast growing research area that interfaces various disciplines such as biology, biochemistry, computer science and statistics. It is concluded that clustering and classification techniques can be successfully employed to group genes based on the similarity of their expression patterns. In this paper, a hierarchical multi-bottleneck classification method is proposed, and it is applied to classify a publicly available gene microarray expression data of budding yeast Saccharomyces cerevisiae.; Singapore-MIT Alliance (SMA)

‣ Weiterentwicklung und Evaluierung eines DNS-Microarrays zur Identifikation von humanpathogenen Pilzen; Further development and evaluation of a DNA microarray for the identification of human pathogenic fungi

Strandhagen, Ulrike
Fonte: Universidade de Tubinga Publicador: Universidade de Tubinga
Tipo: Dissertação
Português
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Invasive Mykosen stellen eine wachsende Gefahr, insbesondere für immunsupprimierte Patienten, dar. Dabei hängt die Prognose wesentlich von einer umgehend eingeleiteten spezifischen Therapie auf der Basis einer schnellen und präzisen Diagnose ab. Die bisherigen diagnostischen Methoden sind jedoch zeitaufwendig und die Ergebnisse oft zu unspezifisch. Der 2004 am ITB Stuttgart entwickelte Oligonukleotid-Microarray zur Detektion von humanpathogenen Pilzen (Leinberger, 2004) ist in der Lage, ausgewählte Candida- und Aspergillusspezies schnell und zuverlässig zu identifizieren. In der vorliegenden Arbeit wurde dieses System von 12 Spezies aus 2 Gruppen auf 40 Spezies aus 15 Gruppen erweitert. Ein besonderer Schwerpunkt lag dabei auf den klinisch immer bedeutsamer werdenden Zygomyceten, von denen folgende Vertreter aufgenommen wurden: Absidia corymbifera und Absidia glauca, Mucor hiemalis, Rhizomucor pusillus, und Rhizopus oryzae. Für die DNS Extraktion aus den Pilzzellen wurde ein neues Protokoll verwendet, dass die Arbeitszeit von vier auf eine Stunde verkürzte. Das Extraktionsergebnis wurde dadurch nicht beeinträchtigt: Aus allen Spezies konnte DNS in ausreichender Menge isoliert werden. Um den optimalen Versuchsaufbau zu finden...

‣ Identification of gene networks modulated by activin in LßT2 cells using DNA microarray analysis

Mazhawidza, W.; Winters, S.J.; Kaiser, U.B.; Kakar, S.S.
Fonte: Murcia : F. Hernández Publicador: Murcia : F. Hernández
Tipo: Artigo de Revista Científica Formato: application/pdf
Português
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Activins, members of the TGFß family of proteins, are widely expressed in a variety of tissues. First identified based on their ability to regulate biosynthesis and secretion of follicle-stimulating hormone (FSH), activins have also been shown to modulate development, cell growth, apoptosis, and inflammation. Despite their many known functions, the precise mechanisms and downstream signaling pathways by which activins mediate their diverse effects remain unknown. We have used a DNA microarray assay to identify genes that are regulated by activin, alone or in combination with gonadotropin-releasing hormone (GnRH), another major regulator of FSH, in a murine gonadotrope-derived cell line (LßT2). We used mRNA from these cells to screen Affymetrix Mu74av2 mouse Gene Chip oligonucleotide microarrays, representing approximately 12,400 mouse genes. Treatment of LßT2 cells with activin A, a gonadotropin-releasing hormone agonist (GnRHA) or activin A plus GnRHA resulted in alterations in levels of gene expression that ranged in magnitude from 15 to 67-fold. Data analysis identified 268 transcripts that were up- or down-regulated by twofold or more. Distinct sets of genes were affected by treatment with activin, GnRHA and activin plus GnRHA...

‣ DNA Microarray Image Compression

Hernández-Cabronero, Miguel
Fonte: [Barcelona] : Universitat Autònoma de Barcelona, Publicador: [Barcelona] : Universitat Autònoma de Barcelona,
Tipo: Tesis i dissertacions electròniques; info:eu-repo/semantics/doctoralThesis; info:eu-repo/semantics/publishedVersion Formato: application/pdf
Publicado em //2015 Português
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En los experimentos con DNA microarrays se genran dos imágenes monocromo, las cuales es conveniente almacenar para poder realizar análisis más precisos en un futuro. Por tanto, la compresión de imágenes surge como una herramienta particularmente útil para minimizar los costes asociados al almacenamiento y la transmisión de dichas imágenes. Esta tesis tiene por objetivo mejorar el estado del arte en la compresión de imágenes de DNA microarrays. Como parte de esta tesis, se ha realizado una detallada investigación de las características de las imágenes de DNA microarray. Los resultados experimentales indican que los algoritmos de compresión no adaptados a este tipo de imágenes producen resultados más bien pobres debido a las características de estas imágenes. Analizando las entropías de primer orden y condicionales, se ha podido determinar un límite aproximado a la compresibilidad sin pérdida de estas imágenes. Aunque la compresión basada en contexto y en segmentación proporcionan mejoras modestas frente a algoritmos de compresión genéricos, parece necesario realizar avances rompedores en el campo de compresión de datos para superar los ratios 2:1 en la mayor parte de las imágenes. Antes del comienzo de esta tesis se habían propuesto varios algoritmos de compresión sin pérdida con rendimientos cercanos al límite óptimo anteriormente mencionado. Sin embargo...

‣ Compressió d'imatges de DNA microarray basada en autosimilaridad

Ruibal Montoro, Manuel
Fonte: Universidade Autônoma de Barcelona Publicador: Universidade Autônoma de Barcelona
Tipo: info:eu-repo/semantics/bachelorThesis; Text Formato: application/pdf
Publicado em 01/07/2014 Português
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Els experiments DNA microarray generen milers de dades en forma d'imatges al voltant de tot món. Aquesta informació ha de ser eficientment emmagatzemada ja que cal guardar fins que les tècniques d'investigació estiguin cent per cent desenvolupades i estandarditzades. A partir de l'estudi de les característiques de les imatges DNA microarray, aquest article descriu un algorisme de compressió d'imatge sense pèrdua basat en la autosimilaridad de les mateixes imatges. S'han generat taules de dades a partir d'experimentar amb la codificació definida en aquest article. Dels resultats obtinguts s'observa que en determinats casos s'aconsegueix obtenir una millora de fins a gairebé 2 bpp a la compressió d'una imatge codificada respecte a una sense codificar pel algoritme basat en la autosimilaridad. En altres casos aquesta codificació significa fins a 3 bpp d'empitjorament en els resultats. En conclusió, amb una tècnica encara per millorar s'ha demostrat que utilitzant la autosimilaridad de les imatges DNA microarray per fer una codificació és possible obtenir millors resultats de compressió.; Los experimentos DNA microarray generan miles de datos en forma de imágenes alrededor de todo mundo. Esta información tiene que ser eficientemente almacenada ya que es necesario guardarla hasta que las técnicas de investigación estén cien por ciento desarrolladas y estandarizadas. A partir del estudio de las características de las imágenes DNA microarray...

‣ Analysis-driven lossy compression of DNA microarray images

Hernández Cabronero, Miguel; Blanes Garcia, Ian; Pinho, Armando J.; Marcellin, Michael W.; Serra Sagristà, Joan
Fonte: Universidade Autônoma de Barcelona Publicador: Universidade Autônoma de Barcelona
Tipo: info:eu-repo/semantics/article; info:eu-repo/semantics/acceptedVersion Formato: application/pdf
Publicado em //2015 Português
Relevância na Pesquisa
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DNA microarrays are one of the fastest-growing new technologies in the field of genetic research, and DNA microarray images continue to grow in number and size. Since analysis techniques are under active and ongoing development, storage, transmission and sharing of DNA microarray images need be addressed, with compression playing a significant role. However, existing lossless coding algorithms yield only limited compression performance (compression ratios below 2:1), whereas lossy coding methods may introduce unacceptable distortions in the analysis process. This work introduces a novel Relative Quantizer (RQ), which employs non-uniform quantization intervals designed for improved compression while bounding the impact on the DNA microarray analysis. This quantizer constrains the maximum relative error introduced into quantized imagery, devoting higher precision to pixels critical to the analysis process. For suitable parameter choices, the resulting variations in the DNA microarray analysis are less than half of those inherent to the experimental variability. Experimental results reveal that appropriate analysis can still be performed for average compression ratios exceeding 4.5:1.

‣ Compressió de microarrays d'ADN

Pueyo Navarro, Iván
Fonte: Universidade Autônoma de Barcelona Publicador: Universidade Autônoma de Barcelona
Tipo: info:eu-repo/semantics/bachelorThesis; Text Formato: application/pdf
Publicado em 30/06/2015 Português
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La tecnologia relacionada amb la creació d'imatges de microarray d'ADN és una eina de gran importància en el descobriment de l'estructura i funcionament de la nostra informació genètica. Dins d'aquest camp, la detecció del comportament de determinats gens sota condicions especifiques adquireix una gran rellevància. La grandària de les imatges de microarray sol ser de mitjana elevada, a causa de la gran quantitat de gens que s'analitzen i al fet que s'intenta mantenir en les imatges el major contingut d'informació possible. Aquestes són generades en grups de dues imatges i en escala de grisos. La finalitat d'aquest projecte és facilitar l'anàlisi de les imatges de microarray als especialistes a través de la combinació del parell d'imatges per formar una imatge en color en RGB, i alhora reduir la grandària d'aquestes imatges per no desaprofitar l'espai físic. En el camp dels microarrays d'ADN perdre informació en les imatges equival a perdre dades d'anàlisi, per aquesta raó la reducció de la mida de les imatges és realitza a través de la compressió sense pèrdua amb l'estàndard JPEG 2000, el que permet reduir la grandària d'aquestes alhora que manté la informació original continguda en elles.; The technology related to the DNA microarray image generation is a very important tool in the discovery of the structure and operation of our genetic information. Within this field...

‣ In situ synthesis of DNA microarray on functionalized cyclic olefin copolymer substrate.;

Saaem, I; Ma, KS; Marchi, AN; LaBean, TH; Tian, J
Fonte: Universidade Duke Publicador: Universidade Duke
Tipo: Artigo de Revista Científica Formato: 491 - 497
Publicado em /02/2010 Português
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Thermoplastic materials such as cyclic-olefin copolymers (COC) provide a versatile and cost-effective alternative to the traditional glass or silicon substrate for rapid prototyping and industrial scale fabrication of microdevices. To extend the utility of COC as an effective microarray substrate, we developed a new method that enabled for the first time in situ synthesis of DNA oligonucleotide microarrays on the COC substrate. To achieve high-quality DNA synthesis, a SiO(2) thin film array was prepatterned on the inert and hydrophobic COC surface using RF sputtering technique. The subsequent in situ DNA synthesis was confined to the surface of the prepatterned hydrophilic SiO(2) thin film features by precision delivery of the phosphoramidite chemistry using an inkjet DNA synthesizer. The in situ SiO(2)-COC DNA microarray demonstrated superior quality and stability in hybridization assays and thermal cycling reactions. Furthermore, we demonstrate that pools of high-quality mixed-oligos could be cleaved off the SiO(2)-COC microarrays and used directly for construction of DNA origami nanostructures. It is believed that this method will not only enable synthesis of high-quality and low-cost COC DNA microarrays but also provide a basis for further development of integrated microfluidics microarrays for a broad range of bioanalytical and biofabrication applications.