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Sample records for temporal microarray study

  1. The global response of Nostoc punctiforme ATCC 29133 to UVA stress, assessed in a temporal DNA microarray study.

    Science.gov (United States)

    Soule, Tanya; Gao, Qunjie; Stout, Valerie; Garcia-Pichel, Ferran

    2013-01-01

    Cyanobacteria in nature are exposed not only to the visible spectrum of sunlight but also to its harmful ultraviolet components (UVA and UVB). We used Nostoc punctiforme ATCC 29133 as a model to study the UVA response by analyzing global gene expression patterns using genomic microarrays. UVA exposure resulted in the statistically detectable differential expression of 573 genes of the 6903 that were probed, compared with that of the control cultures. Of those genes, 473 were up-regulated, while only 100 were down-regulated. Many of the down-regulated genes were involved in photosynthetic pigment biosynthesis, indicating a significant shift in this metabolism. As expected, we detected the up-regulation of genes encoding antioxidant enzymes and the sunscreen, scytonemin. However, a majority of the up-regulated genes, 47%, were unassignable bioinformatically to known functional categories, suggesting that the UVA stress response is not well understood. Interestingly, the most dramatic up-regulation involved several contiguous genes of unassigned metabolism on plasmid A. This is the first global UVA stress response analysis of any phototrophic microorganism and the differential expression of 8% of the genes of the Nostoc genome indicates that adaptation to UVA in Nostoc has been an evolutionary force of significance. © 2012 Wiley Periodicals, Inc. Photochemistry and Photobiology © 2012 The American Society of Photobiology.

  2. Reconstructing the temporal ordering of biological samples using microarray data.

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    Magwene, Paul M; Lizardi, Paul; Kim, Junhyong

    2003-05-01

    Accurate time series for biological processes are difficult to estimate due to problems of synchronization, temporal sampling and rate heterogeneity. Methods are needed that can utilize multi-dimensional data, such as those resulting from DNA microarray experiments, in order to reconstruct time series from unordered or poorly ordered sets of observations. We present a set of algorithms for estimating temporal orderings from unordered sets of sample elements. The techniques we describe are based on modifications of a minimum-spanning tree calculated from a weighted, undirected graph. We demonstrate the efficacy of our approach by applying these techniques to an artificial data set as well as several gene expression data sets derived from DNA microarray experiments. In addition to estimating orderings, the techniques we describe also provide useful heuristics for assessing relevant properties of sample datasets such as noise and sampling intensity, and we show how a data structure called a PQ-tree can be used to represent uncertainty in a reconstructed ordering. Academic implementations of the ordering algorithms are available as source code (in the programming language Python) on our web site, along with documentation on their use. The artificial 'jelly roll' data set upon which the algorithm was tested is also available from this web site. The publicly available gene expression data may be found at http://genome-www.stanford.edu/cellcycle/ and http://caulobacter.stanford.edu/CellCycle/.

  3. Classification across gene expression microarray studies

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    Kuner Ruprecht

    2009-12-01

    Full Text Available Abstract Background The increasing number of gene expression microarray studies represents an important resource in biomedical research. As a result, gene expression based diagnosis has entered clinical practice for patient stratification in breast cancer. However, the integration and combined analysis of microarray studies remains still a challenge. We assessed the potential benefit of data integration on the classification accuracy and systematically evaluated the generalization performance of selected methods on four breast cancer studies comprising almost 1000 independent samples. To this end, we introduced an evaluation framework which aims to establish good statistical practice and a graphical way to monitor differences. The classification goal was to correctly predict estrogen receptor status (negative/positive and histological grade (low/high of each tumor sample in an independent study which was not used for the training. For the classification we chose support vector machines (SVM, predictive analysis of microarrays (PAM, random forest (RF and k-top scoring pairs (kTSP. Guided by considerations relevant for classification across studies we developed a generalization of kTSP which we evaluated in addition. Our derived version (DV aims to improve the robustness of the intrinsic invariance of kTSP with respect to technologies and preprocessing. Results For each individual study the generalization error was benchmarked via complete cross-validation and was found to be similar for all classification methods. The misclassification rates were substantially higher in classification across studies, when each single study was used as an independent test set while all remaining studies were combined for the training of the classifier. However, with increasing number of independent microarray studies used in the training, the overall classification performance improved. DV performed better than the average and showed slightly less variance. In

  4. Identifying significant temporal variation in time course microarray data without replicates

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    Porter Weston

    2009-03-01

    Full Text Available Abstract Background An important component of time course microarray studies is the identification of genes that demonstrate significant time-dependent variation in their expression levels. Until recently, available methods for performing such significance tests required replicates of individual time points. This paper describes a replicate-free method that was developed as part of a study of the estrous cycle in the rat mammary gland in which no replicate data was collected. Results A temporal test statistic is proposed that is based on the degree to which data are smoothed when fit by a spline function. An algorithm is presented that uses this test statistic together with a false discovery rate method to identify genes whose expression profiles exhibit significant temporal variation. The algorithm is tested on simulated data, and is compared with another recently published replicate-free method. The simulated data consists both of genes with known temporal dependencies, and genes from a null distribution. The proposed algorithm identifies a larger percentage of the time-dependent genes for a given false discovery rate. Use of the algorithm in a study of the estrous cycle in the rat mammary gland resulted in the identification of genes exhibiting distinct circadian variation. These results were confirmed in follow-up laboratory experiments. Conclusion The proposed algorithm provides a new approach for identifying expression profiles with significant temporal variation without relying on replicates. When compared with a recently published algorithm on simulated data, the proposed algorithm appears to identify a larger percentage of time-dependent genes for a given false discovery rate. The development of the algorithm was instrumental in revealing the presence of circadian variation in the virgin rat mammary gland during the estrous cycle.

  5. Analysis of Temporal-spatial Co-variation within Gene Expression Microarray Data in an Organogenesis Model

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    Ehler, Martin; Rajapakse, Vinodh; Zeeberg, Barry; Brooks, Brian; Brown, Jacob; Czaja, Wojciech; Bonner, Robert F.

    The gene networks underlying closure of the optic fissure during vertebrate eye development are poorly understood. We used a novel clustering method based on Laplacian Eigenmaps, a nonlinear dimension reduction method, to analyze microarray data from laser capture microdissected (LCM) cells at the site and developmental stages (days 10.5 to 12.5) of optic fissure closure. Our new method provided greater biological specificity than classical clustering algorithms in terms of identifying more biological processes and functions related to eye development as defined by Gene Ontology at lower false discovery rates. This new methodology builds on the advantages of LCM to isolate pure phenotypic populations within complex tissues and allows improved ability to identify critical gene products expressed at lower copy number. The combination of LCM of embryonic organs, gene expression microarrays, and extracting spatial and temporal co-variations appear to be a powerful approach to understanding the gene regulatory networks that specify mammalian organogenesis.

  6. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

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    Brahmbhatt Sonal

    2008-11-01

    Full Text Available Abstract Background Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish. Results 298,304 expressed sequence tags (ESTs from Atlantic salmon (69% of the total, 11,664 chinook, 10,813 sockeye, 10,051 brook trout, 10,975 grayling, 8,630 lake whitefish, and 3,624 northern pike ESTs were obtained in this study and have been deposited into the public databases. Contigs were built and putative full-length Atlantic salmon clones have been identified. A database containing ESTs, assemblies, consensus sequences, open reading frames, gene predictions and putative annotation is available. The overall similarity between Atlantic salmon ESTs and those of rainbow trout, chinook, sockeye, brook trout, grayling, lake whitefish, northern pike and rainbow smelt is 93.4, 94.2, 94.6, 94.4, 92.5, 91.7, 89.6, and 86.2% respectively. An analysis of 78 transcript sets show Salmo as a sister group to Oncorhynchus and Salvelinus within Salmoninae, and Thymallinae as a sister group to Salmoninae and Coregoninae within Salmonidae. Extensive gene duplication is consistent with a genome duplication in the common ancestor of salmonids. Using all of the available EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-species hybridizations to this cDNA microarray indicate that this resource will be useful for studies of all 68 salmonid species. Conclusion An extensive collection and analysis of salmonid RNA putative transcripts indicate that Pacific salmon, Atlantic salmon and charr are 94–96% similar while the more distant whitefish, grayling, pike and smelt are 93, 92, 89 and 86% similar to salmon. The salmonid transcriptome reveals a complex history of gene duplication that is

  7. Microarrays in ecological research: A case study of a cDNA microarray for plant-herbivore interactions

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    Gase Klaus

    2004-09-01

    Full Text Available Abstract Background Microarray technology allows researchers to simultaneously monitor changes in the expression ratios (ERs of hundreds of genes and has thereby revolutionized most of biology. Although this technique has the potential of elucidating early stages in an organism's phenotypic response to complex ecological interactions, to date, it has not been fully incorporated into ecological research. This is partially due to a lack of simple procedures of handling and analyzing the expression ratio (ER data produced from microarrays. Results We describe an analysis of the sources of variation in ERs from 73 hybridized cDNA microarrays, each with 234 herbivory-elicited genes from the model ecological expression system, Nicotiana attenuata, using procedures that are commonly used in ecologic research. Each gene is represented by two independently labeled PCR products and each product was arrayed in quadruplicate. We present a robust method of normalizing and analyzing ERs based on arbitrary thresholds and statistical criteria, and characterize a "norm of reaction" of ERs for 6 genes (4 of known function, 2 of unknown with different ERs as determined across all analyzed arrays to provide a biologically-informed alternative to the use of arbitrary expression ratios in determining significance of expression. These gene-specific ERs and their variance (gene CV were used to calculate array-based variances (array CV, which, in turn, were used to study the effects of array age, probe cDNA quantity and quality, and quality of spotted PCR products as estimates of technical variation. Cluster analysis and a Principal Component Analysis (PCA were used to reveal associations among the transcriptional "imprints" of arrays hybridized with cDNA probes derived from mRNA from N. attenuata plants variously elicited and attacked by different herbivore species and from three congeners: N. quadrivalis, N. longiflora and N. clevelandii. Additionally, the PCA

  8. Carbohydrate microarrays

    DEFF Research Database (Denmark)

    Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Klas Ola

    2012-01-01

    In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray...... of substrate specificities of glycosyltransferases. This review covers the construction of carbohydrate microarrays, detection methods of carbohydrate microarrays and their applications in biological and biomedical research....

  9. Generation of EST and Microarray Resources for Functional Genomic Studies on Chicken Intestinal Health

    NARCIS (Netherlands)

    Hemert, van S.; Ebbelaar, B.H.; Smits, M.A.; Rebel, J.M.J.

    2003-01-01

    Expressed sequenced tags (ESTs) and microarray resources have a great impact on the ability to study host response in mice and humans. Unfortunately, these resources are not yet available for domestic farm animals. The aim of this study was to provide genomic resources to study chicken intestinal

  10. A study of metaheuristic algorithms for high dimensional feature selection on microarray data

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    Dankolo, Muhammad Nasiru; Radzi, Nor Haizan Mohamed; Sallehuddin, Roselina; Mustaffa, Noorfa Haszlinna

    2017-11-01

    Microarray systems enable experts to examine gene profile at molecular level using machine learning algorithms. It increases the potentials of classification and diagnosis of many diseases at gene expression level. Though, numerous difficulties may affect the efficiency of machine learning algorithms which includes vast number of genes features comprised in the original data. Many of these features may be unrelated to the intended analysis. Therefore, feature selection is necessary to be performed in the data pre-processing. Many feature selection algorithms are developed and applied on microarray which including the metaheuristic optimization algorithms. This paper discusses the application of the metaheuristics algorithms for feature selection in microarray dataset. This study reveals that, the algorithms have yield an interesting result with limited resources thereby saving computational expenses of machine learning algorithms.

  11. APPLICATION OF CDNA MICROARRAY TO THE STUDY OF ARSENIC TOXICOLOGY AND CARCINOGENESIS

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    Arsenic (As) is a common environmental toxicant and known human carcinogen. Epidemiological studies link As exposure to various disorders and cancers. However, the molecular mechanisms for As toxicity and carcinogenicity are not completely known. The cDNA microarray, a high-th...

  12. Identification of listeria species isolated in Tunisia by Microarray based assay : results of a preliminary study

    International Nuclear Information System (INIS)

    Hmaied, Fatma; Helel, Salma; Barkallah, Insaf; Leberre, V.; Francois, J.M.; Kechrid, A.

    2008-01-01

    Microarray-based assay is a new molecular approach for genetic screening and identification of microorganisms. We have developed a rapid microarray-based assay for the reliable detection and discrimination of Listeria spp. in food and clinical isolates from Tunisia. The method used in the present study is based on the PCR amplification of a virulence factor gene (iap gene). the PCR mixture contained cyanine Cy5labeled dCTP. Therefore, The PCR products were fluorescently labeled. The presence of multiple species-specific sequences within the iap gene enabled us to design different oligoprobes per species. The species-specific sequences of the iap gene used in this study were obtained from genBank and then aligned for phylogenetic analysis in order to identify and retrieve the sequences of homologues of the amplified iap gene analysed. 20 probes were used for detection and identification of 22 food isolates and clinical isolates of Listeria spp (L. monocytogenes, L. ivanovi), L. welshimeri, L. seeligeri, and L. grayi). Each bacterial gene was identified by hybridization to oligoprobes specific for each Listeria species and immobilized on a glass surface. The microarray analysis showed that 5 clinical isolates and 2 food isolates were identified listeria monocytogenes. Concerning the remaining 15 food isolates; 13 were identified listeria innocua and 2 isolates could not be identified by microarray based assay. Further phylogenetic and molecular analysis are required to design more species-specific probes for the identification of Listeria spp. Microarray-based assay is a simple and rapid method used for Listeria species discrimination

  13. Temporal Gene Expression Profiling of the Wheat Leaf Rust Pathosystem Using cDNA Microarray Reveals Differences in Compatible and Incompatible Defence Pathways

    OpenAIRE

    Fofana, Bourlaye; Banks, Travis W.; McCallum, Brent; Strelkov, Stephen E.; Cloutier, Sylvie

    2007-01-01

    In this study, we detail the construction of a custom cDNA spotted microarray containing 7728 wheat ESTs and the use of the array to identify host genes that are differentially expressed upon challenges with leaf rust fungal pathogens. Wheat cultivar RL6003 (Thatcher Lr1) was inoculated with Puccinia triticina virulence phenotypes BBB (incompatible) or TJB (7-2) (compatible) and sampled at four different time points (3, 6, 12, and 24 hours) after inoculation. Transcript expression levels rela...

  14. Bayesian meta-analysis models for microarray data: a comparative study

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    Song Joon J

    2007-03-01

    Full Text Available Abstract Background With the growing abundance of microarray data, statistical methods are increasingly needed to integrate results across studies. Two common approaches for meta-analysis of microarrays include either combining gene expression measures across studies or combining summaries such as p-values, probabilities or ranks. Here, we compare two Bayesian meta-analysis models that are analogous to these methods. Results Two Bayesian meta-analysis models for microarray data have recently been introduced. The first model combines standardized gene expression measures across studies into an overall mean, accounting for inter-study variability, while the second combines probabilities of differential expression without combining expression values. Both models produce the gene-specific posterior probability of differential expression, which is the basis for inference. Since the standardized expression integration model includes inter-study variability, it may improve accuracy of results versus the probability integration model. However, due to the small number of studies typical in microarray meta-analyses, the variability between studies is challenging to estimate. The probability integration model eliminates the need to model variability between studies, and thus its implementation is more straightforward. We found in simulations of two and five studies that combining probabilities outperformed combining standardized gene expression measures for three comparison values: the percent of true discovered genes in meta-analysis versus individual studies; the percent of true genes omitted in meta-analysis versus separate studies, and the number of true discovered genes for fixed levels of Bayesian false discovery. We identified similar results when pooling two independent studies of Bacillus subtilis. We assumed that each study was produced from the same microarray platform with only two conditions: a treatment and control, and that the data sets

  15. A Combinatory Approach for Selecting Prognostic Genes in Microarray Studies of Tumour Survivals

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    Qihua Tan

    2009-01-01

    Full Text Available Different from significant gene expression analysis which looks for genes that are differentially regulated, feature selection in the microarray-based prognostic gene expression analysis aims at finding a subset of marker genes that are not only differentially expressed but also informative for prediction. Unfortunately feature selection in literature of microarray study is predominated by the simple heuristic univariate gene filter paradigm that selects differentially expressed genes according to their statistical significances. We introduce a combinatory feature selection strategy that integrates differential gene expression analysis with the Gram-Schmidt process to identify prognostic genes that are both statistically significant and highly informative for predicting tumour survival outcomes. Empirical application to leukemia and ovarian cancer survival data through-within- and cross-study validations shows that the feature space can be largely reduced while achieving improved testing performances.

  16. permGPU: Using graphics processing units in RNA microarray association studies

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    George Stephen L

    2010-06-01

    Full Text Available Abstract Background Many analyses of microarray association studies involve permutation, bootstrap resampling and cross-validation, that are ideally formulated as embarrassingly parallel computing problems. Given that these analyses are computationally intensive, scalable approaches that can take advantage of multi-core processor systems need to be developed. Results We have developed a CUDA based implementation, permGPU, that employs graphics processing units in microarray association studies. We illustrate the performance and applicability of permGPU within the context of permutation resampling for a number of test statistics. An extensive simulation study demonstrates a dramatic increase in performance when using permGPU on an NVIDIA GTX 280 card compared to an optimized C/C++ solution running on a conventional Linux server. Conclusions permGPU is available as an open-source stand-alone application and as an extension package for the R statistical environment. It provides a dramatic increase in performance for permutation resampling analysis in the context of microarray association studies. The current version offers six test statistics for carrying out permutation resampling analyses for binary, quantitative and censored time-to-event traits.

  17. Empirical Bayes ranking and selection methods via semiparametric hierarchical mixture models in microarray studies.

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    Noma, Hisashi; Matsui, Shigeyuki

    2013-05-20

    The main purpose of microarray studies is screening of differentially expressed genes as candidates for further investigation. Because of limited resources in this stage, prioritizing genes are relevant statistical tasks in microarray studies. For effective gene selections, parametric empirical Bayes methods for ranking and selection of genes with largest effect sizes have been proposed (Noma et al., 2010; Biostatistics 11: 281-289). The hierarchical mixture model incorporates the differential and non-differential components and allows information borrowing across differential genes with separation from nuisance, non-differential genes. In this article, we develop empirical Bayes ranking methods via a semiparametric hierarchical mixture model. A nonparametric prior distribution, rather than parametric prior distributions, for effect sizes is specified and estimated using the "smoothing by roughening" approach of Laird and Louis (1991; Computational statistics and data analysis 12: 27-37). We present applications to childhood and infant leukemia clinical studies with microarrays for exploring genes related to prognosis or disease progression. Copyright © 2012 John Wiley & Sons, Ltd.

  18. Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks

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    Ji Wei

    2010-10-01

    Full Text Available Abstract Background Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selection of the discretization method is often arbitrary and no systematic comparison of different discretization has been conducted, in the context of gene regulatory network inference from time series gene expression data. Results In this study, we propose a new discretization method "bikmeans", and compare its performance with four other widely-used discretization methods using different datasets, modeling algorithms and number of intervals. Sensitivities, specificities and total accuracies were calculated and statistical analysis was carried out. Bikmeans method always gave high total accuracies. Conclusions Our results indicate that proper discretization methods can consistently improve gene regulatory network inference independent of network modeling algorithms and datasets. Our new method, bikmeans, resulted in significant better total accuracies than other methods.

  19. A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray

    DEFF Research Database (Denmark)

    Stolc, Viktor; Li, Lei; Wang, Xiangfeng

    2005-01-01

    As the international efforts to sequence the rice genome are completed, an immediate challenge and opportunity is to comprehensively and accurately define all transcription units in the rice genome. Here we describe a strategy of using high-density oligonucleotide tiling-path microarrays to map...... transcription of the japonica rice genome. In a pilot experiment to test this approach, one array representing the reverse strand of the last 11.2 Mb sequence of chromosome 10 was analyzed in detail based on a mathematical model developed in this study. Analysis of the array data detected 77% of the reference...... gene models in a mixture of four RNA populations. Moreover, significant transcriptional activities were found in many of the previously annotated intergenic regions. These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models...

  20. PERBANDINGAN ANALISIS LEAST ABSOLUTE SHRINKAGE AND SELECTION OPERATOR DAN PARTIAL LEAST SQUARES (Studi Kasus: Data Microarray

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    KADEK DWI FARMANI

    2012-09-01

    Full Text Available Linear regression analysis is one of the parametric statistical methods which utilize the relationship between two or more quantitative variables. In linear regression analysis, there are several assumptions that must be met that is normal distribution of errors, there is no correlation between the error and error variance is constant and homogent. There are some constraints that caused the assumption can not be met, for example, the correlation between independent variables (multicollinearity, constraints on the number of data and independent variables are obtained. When the number of samples obtained less than the number of independent variables, then the data is called the microarray data. Least Absolute shrinkage and Selection Operator (LASSO and Partial Least Squares (PLS is a statistical method that can be used to overcome the microarray, overfitting, and multicollinearity. From the above description, it is necessary to study with the intention of comparing LASSO and PLS method. This study uses coronary heart and stroke patients data which is a microarray data and contain multicollinearity. With these two characteristics of the data that most have a weak correlation between independent variables, LASSO method produces a better model than PLS seen from the large RMSEP.

  1. Microarray-based DNA methylation study of Ewing's sarcoma of the bone.

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    Park, Hye-Rim; Jung, Woon-Won; Kim, Hyun-Sook; Park, Yong-Koo

    2014-10-01

    Alterations in DNA methylation patterns are a hallmark of malignancy. However, the majority of epigenetic studies of Ewing's sarcoma have focused on the analysis of only a few candidate genes. Comprehensive studies are thus lacking and are required. The aim of the present study was to identify novel methylation markers in Ewing's sarcoma using microarray analysis. The current study reports the microarray-based DNA methylation study of 1,505 CpG sites of 807 cancer-related genes from 69 Ewing's sarcoma samples. The Illumina GoldenGate Methylation Cancer Panel I microarray was used, and with the appropriate controls (n=14), a total of 92 hypermethylated genes were identified in the Ewing's sarcoma samples. The majority of the hypermethylated genes were associated with cell adhesion, cell regulation, development and signal transduction. The overall methylation mean values were compared between patients who survived and those that did not. The overall methylation mean was significantly higher in the patients who did not survive (0.25±0.03) than in those who did (0.22±0.05) (P=0.0322). However, the overall methylation mean was not found to significantly correlate with age, gender or tumor location. GDF10 , OSM , APC and HOXA11 were the most significant differentially-methylated genes, however, their methylation levels were not found to significantly correlate with the survival rate. The DNA methylation profile of Ewing's sarcoma was characterized and 92 genes that were significantly hypermethylated were detected. A trend towards a more aggressive behavior was identified in the methylated group. The results of this study indicated that methylation may be significant in the development of Ewing's sarcoma.

  2. Graph Based Study of Allergen Cross-Reactivity of Plant Lipid Transfer Proteins (LTPs) Using Microarray in a Multicenter Study

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    Palacín, Arantxa; Gómez-Casado, Cristina; Rivas, Luis A.; Aguirre, Jacobo; Tordesillas, Leticia; Bartra, Joan; Blanco, Carlos; Carrillo, Teresa; Cuesta-Herranz, Javier; de Frutos, Consolación; Álvarez-Eire, Genoveva García; Fernández, Francisco J.; Gamboa, Pedro; Muñoz, Rosa; Sánchez-Monge, Rosa; Sirvent, Sofía; Torres, María J.; Varela-Losada, Susana; Rodríguez, Rosalía; Parro, Victor; Blanca, Miguel; Salcedo, Gabriel; Díaz-Perales, Araceli

    2012-01-01

    The study of cross-reactivity in allergy is key to both understanding. the allergic response of many patients and providing them with a rational treatment In the present study, protein microarrays and a co-sensitization graph approach were used in conjunction with an allergen microarray immunoassay. This enabled us to include a wide number of proteins and a large number of patients, and to study sensitization profiles among members of the LTP family. Fourteen LTPs from the most frequent plant food-induced allergies in the geographical area studied were printed into a microarray specifically designed for this research. 212 patients with fruit allergy and 117 food-tolerant pollen allergic subjects were recruited from seven regions of Spain with different pollen profiles, and their sera were tested with allergen microarray. This approach has proven itself to be a good tool to study cross-reactivity between members of LTP family, and could become a useful strategy to analyze other families of allergens. PMID:23272072

  3. Graph based study of allergen cross-reactivity of plant lipid transfer proteins (LTPs using microarray in a multicenter study.

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    Arantxa Palacín

    Full Text Available The study of cross-reactivity in allergy is key to both understanding. the allergic response of many patients and providing them with a rational treatment In the present study, protein microarrays and a co-sensitization graph approach were used in conjunction with an allergen microarray immunoassay. This enabled us to include a wide number of proteins and a large number of patients, and to study sensitization profiles among members of the LTP family. Fourteen LTPs from the most frequent plant food-induced allergies in the geographical area studied were printed into a microarray specifically designed for this research. 212 patients with fruit allergy and 117 food-tolerant pollen allergic subjects were recruited from seven regions of Spain with different pollen profiles, and their sera were tested with allergen microarray. This approach has proven itself to be a good tool to study cross-reactivity between members of LTP family, and could become a useful strategy to analyze other families of allergens.

  4. Association Study between BDNF Gene Polymorphisms and Autism by Three-Dimensional Gel-Based Microarray

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    Zuhong Lu

    2009-06-01

    Full Text Available Single nucleotide polymorphisms (SNPs are important markers which can be used in association studies searching for susceptible genes of complex diseases. High-throughput methods are needed for SNP genotyping in a large number of samples. In this study, we applied polyacrylamide gel-based microarray combined with dual-color hybridization for association study of four BDNF polymorphisms with autism. All the SNPs in both patients and controls could be analyzed quickly and correctly. Among four SNPs, only C270T polymorphism showed significant differences in the frequency of the allele (χ2 = 7.809, p = 0.005 and genotype (χ2 = 7.800, p = 0.020. In the haplotype association analysis, there was significant difference in global haplotype distribution between the groups (χ2 = 28.19,p = 3.44e-005. We suggest that BDNF has a possible role in the pathogenesis of autism. The study also show that the polyacrylamide gel-based microarray combined with dual-color hybridization is a rapid, simple and high-throughput method for SNPs genotyping, and can be used for association study of susceptible gene with disorders in large samples.

  5. Altered metabolism of growth hormone receptor mutant mice: a combined NMR metabonomics and microarray study.

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    Horst Joachim Schirra

    Full Text Available BACKGROUND: Growth hormone is an important regulator of post-natal growth and metabolism. We have investigated the metabolic consequences of altered growth hormone signalling in mutant mice that have truncations at position 569 and 391 of the intracellular domain of the growth hormone receptor, and thus exhibit either low (around 30% maximum or no growth hormone-dependent STAT5 signalling respectively. These mutations result in altered liver metabolism, obesity and insulin resistance. METHODOLOGY/PRINCIPAL FINDINGS: The analysis of metabolic changes was performed using microarray analysis of liver tissue and NMR metabonomics of urine and liver tissue. Data were analyzed using multivariate statistics and Gene Ontology tools. The metabolic profiles characteristic for each of the two mutant groups and wild-type mice were identified with NMR metabonomics. We found decreased urinary levels of taurine, citrate and 2-oxoglutarate, and increased levels of trimethylamine, creatine and creatinine when compared to wild-type mice. These results indicate significant changes in lipid and choline metabolism, and were coupled with increased fat deposition, leading to obesity. The microarray analysis identified changes in expression of metabolic enzymes correlating with alterations in metabolite concentration both in urine and liver. Similarity of mutant 569 to the wild-type was seen in young mice, but the pattern of metabolites shifted to that of the 391 mutant as the 569 mice became obese after six months age. CONCLUSIONS/SIGNIFICANCE: The metabonomic observations were consistent with the parallel analysis of gene expression and pathway mapping using microarray data, identifying metabolites and gene transcripts involved in hepatic metabolism, especially for taurine, choline and creatinine metabolism. The systems biology approach applied in this study provides a coherent picture of metabolic changes resulting from impaired STAT5 signalling by the growth hormone

  6. Prenatal chromosomal microarray analysis in fetuses with congenital heart disease: a prospective cohort study.

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    Wang, Yan; Cao, Li; Liang, Dong; Meng, Lulu; Wu, Yun; Qiao, Fengchang; Ji, Xiuqing; Luo, Chunyu; Zhang, Jingjing; Xu, Tianhui; Yu, Bin; Wang, Leilei; Wang, Ting; Pan, Qiong; Ma, Dingyuan; Hu, Ping; Xu, Zhengfeng

    2018-02-01

    Currently, chromosomal microarray analysis is considered the first-tier test in pediatric care and prenatal diagnosis. However, the diagnostic yield of chromosomal microarray analysis for prenatal diagnosis of congenital heart disease has not been evaluated based on a large cohort. Our aim was to evaluate the clinical utility of chromosomal microarray as the first-tier test for chromosomal abnormalities in fetuses with congenital heart disease. In this prospective study, 602 prenatal cases of congenital heart disease were investigated using single nucleotide polymorphism array over a 5-year period. Overall, pathogenic chromosomal abnormalities were identified in 125 (20.8%) of 602 prenatal cases of congenital heart disease, with 52.0% of them being numerical chromosomal abnormalities. The detection rates of likely pathogenic copy number variations and variants of uncertain significance were 1.3% and 6.0%, respectively. The detection rate of pathogenic chromosomal abnormalities in congenital heart disease plus additional structural anomalies (48.9% vs 14.3%, P congenital heart disease group. Additionally, the detection rate in congenital heart disease with additional structural anomalies group was significantly higher than that in congenital heart disease with soft markers group (48.9% vs 19.8%, P congenital heart disease with additional structural anomalies and congenital heart disease with intrauterine growth retardation groups (48.9% vs 50.0%), congenital heart disease with soft markers and congenital heart disease with intrauterine growth retardation groups (19.8% vs 50.0%), or congenital heart disease with soft markers and isolated congenital heart disease groups (19.8% vs 14.3%). The detection rate in fetuses with congenital heart disease plus mild ventriculomegaly was significantly higher than in those with other types of soft markers (50.0% vs 15.6%, P congenital heart disease in clinical practice. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Fibre optic microarrays.

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    Walt, David R

    2010-01-01

    This tutorial review describes how fibre optic microarrays can be used to create a variety of sensing and measurement systems. This review covers the basics of optical fibres and arrays, the different microarray architectures, and describes a multitude of applications. Such arrays enable multiplexed sensing for a variety of analytes including nucleic acids, vapours, and biomolecules. Polymer-coated fibre arrays can be used for measuring microscopic chemical phenomena, such as corrosion and localized release of biochemicals from cells. In addition, these microarrays can serve as a substrate for fundamental studies of single molecules and single cells. The review covers topics of interest to chemists, biologists, materials scientists, and engineers.

  8. Statistical Analysis of Microarray Data with Replicated Spots: A Case Study with Synechococcus WH8102

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    E. V. Thomas

    2009-01-01

    Full Text Available Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in part to the replication within an array, it was possible to detect very small changes in the levels of expression between the wild type and mutant strains. One interesting biological outcome of this experiment is the indication of the extent to which the phosphorus regulatory system of this cyanobacterium affects the expression of multiple genes beyond those strictly involved in phosphorus acquisition.

  9. A Microarray Study of Middle Cerebral Occlusion Rat Brain with Acupuncture Intervention

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    Chao Zhang

    2015-01-01

    Full Text Available Microarray analysis was used to investigate the changes of gene expression of ischemic stroke and acupuncture intervention in middle cerebral artery occlusion (MCAo rat brain. Results showed that acupuncture intervention had a remarkable improvement in neural deficit score, cerebral blood flow, and cerebral infarction volume of MCAo rats. Microarray analysis showed that a total of 627 different expression genes were regulated in ischemic stroke. 417 genes were upregulated and 210 genes were downregulated. A total of 361 different expression genes were regulated after acupuncture intervention. Three genes were upregulated and 358 genes were downregulated. The expression of novel genes after acupuncture intervention, including Tph1 and Olr883, was further analyzed by Real-Time Quantitative Polymerase Chain Reaction (RT-PCR. Upregulation of Tph1 and downregulation of Olr883 indicated that the therapeutic effect of acupuncture for ischemic stroke may be closely related to the suppression of poststroke depression and regulation of olfactory transduction. In conclusion, the present study may enrich our understanding of the multiple pathological process of ischemic brain injury and indicate possible mechanisms of acupuncture on ischemic stroke.

  10. Comparing independent microarray studies: the case of human embryonic stem cells

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    Hemmati-Brivanlou Ali

    2005-07-01

    Full Text Available Abstract Background Microarray studies of the same phenomenon in different labs often appear at variance because the published lists of regulated transcripts have disproportionately small intersections. We demonstrate that comparing studies by intersecting lists in this manner is methodologically flawed by reanalyzing three studies of the molecular signature of "stemness" in human embryonic stem cells. There are only 7 genes common to all three published lists, suggesting disagreement. Results Carefully reanalyzing all three together from the raw data we detect 111 genes upregulated and 95 downregulated in all three studies. The upregulated list was subject to rtRTPCR analysis and 75% of the genes were confirmed. Conclusion Our findings show that the three studies have a substantial core of common genes, which is missed if only the published lists are examined. Combined analysis of multiple experiments can be a powerful way to distil coherent conclusions.

  11. DNA Microarray Technology; TOPICAL

    International Nuclear Information System (INIS)

    WERNER-WASHBURNE, MARGARET; DAVIDSON, GEORGE S.

    2002-01-01

    Collaboration between Sandia National Laboratories and the University of New Mexico Biology Department resulted in the capability to train students in microarray techniques and the interpretation of data from microarray experiments. These studies provide for a better understanding of the role of stationary phase and the gene regulation involved in exit from stationary phase, which may eventually have important clinical implications. Importantly, this research trained numerous students and is the basis for three new Ph.D. projects

  12. Performance analysis of clustering techniques over microarray data: A case study

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    Dash, Rasmita; Misra, Bijan Bihari

    2018-03-01

    Handling big data is one of the major issues in the field of statistical data analysis. In such investigation cluster analysis plays a vital role to deal with the large scale data. There are many clustering techniques with different cluster analysis approach. But which approach suits a particular dataset is difficult to predict. To deal with this problem a grading approach is introduced over many clustering techniques to identify a stable technique. But the grading approach depends on the characteristic of dataset as well as on the validity indices. So a two stage grading approach is implemented. In this study the grading approach is implemented over five clustering techniques like hybrid swarm based clustering (HSC), k-means, partitioning around medoids (PAM), vector quantization (VQ) and agglomerative nesting (AGNES). The experimentation is conducted over five microarray datasets with seven validity indices. The finding of grading approach that a cluster technique is significant is also established by Nemenyi post-hoc hypothetical test.

  13. Adaptation of a Bioinformatics Microarray Analysis Workflow for a Toxicogenomic Study in Rainbow Trout.

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    Sophie Depiereux

    Full Text Available Sex steroids play a key role in triggering sex differentiation in fish, the use of exogenous hormone treatment leading to partial or complete sex reversal. This phenomenon has attracted attention since the discovery that even low environmental doses of exogenous steroids can adversely affect gonad morphology (ovotestis development and induce reproductive failure. Modern genomic-based technologies have enhanced opportunities to find out mechanisms of actions (MOA and identify biomarkers related to the toxic action of a compound. However, high throughput data interpretation relies on statistical analysis, species genomic resources, and bioinformatics tools. The goals of this study are to improve the knowledge of feminisation in fish, by the analysis of molecular responses in the gonads of rainbow trout fry after chronic exposure to several doses (0.01, 0.1, 1 and 10 μg/L of ethynylestradiol (EE2 and to offer target genes as potential biomarkers of ovotestis development. We successfully adapted a bioinformatics microarray analysis workflow elaborated on human data to a toxicogenomic study using rainbow trout, a fish species lacking accurate functional annotation and genomic resources. The workflow allowed to obtain lists of genes supposed to be enriched in true positive differentially expressed genes (DEGs, which were subjected to over-representation analysis methods (ORA. Several pathways and ontologies, mostly related to cell division and metabolism, sexual reproduction and steroid production, were found significantly enriched in our analyses. Moreover, two sets of potential ovotestis biomarkers were selected using several criteria. The first group displayed specific potential biomarkers belonging to pathways/ontologies highlighted in the experiment. Among them, the early ovarian differentiation gene foxl2a was overexpressed. The second group, which was highly sensitive but not specific, included the DEGs presenting the highest fold change and

  14. Microarray studies on lager brewer's yeasts reveal cell status in the process of autolysis.

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    Xu, Weina; Wang, Jinjing; Li, Qi

    2014-08-01

    In this work, we performed DNA microarray studies on lager brewer's yeast Saccharomyces pastorianus to investigate changes in gene expression in the process of autolysis. The two strains we used were Qing2 and 5-2. Strain 5-2 is a mutant of Qing2 and autolyzes much more slowly than its parent strain. Four samples of these two strains during different autolysis stages (0% and 15%) were tested using DNA microarray containing > 10,000 yeast's genes. Analysis of genes with the same transcription pattern (up- or down-regulated in both strains) showed that the same 99 genes were up-regulated (transcription levels were increased), and the same 97 genes were down-regulated (transcription levels were decreased) by fivefold or more during autolysis. Genes involved in energy production/utilization, protein anabolism, and stress response were down-regulated. Genes related to cell wall organization and biogenesis, starvation response and DNA damage response were up-regulated. Analysis of genes with opposite transcription patterns (up-regulated in one strain and down-regulated in the other one) showed that 246 genes were up-regulated in 5-2 (autolyzes slowly) and down-regulated in Qing2 (autolyzes rapidly). Another 18 genes had opposite transcription levels, indicating that the strain which autolyzes slowly had better cell vitality despite the same autolysis stage. These findings might further promote the global understanding of autolysis in yeast. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  15. Cross-platform comparison of SYBR® Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC study

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    Dial Stacey L

    2008-07-01

    Full Text Available Abstract Background The MicroArray Quality Control (MAQC project evaluated the inter- and intra-platform reproducibility of seven microarray platforms and three quantitative gene expression assays in profiling the expression of two commercially available Reference RNA samples (Nat Biotechnol 24:1115-22, 2006. The tested microarrays were the platforms from Affymetrix, Agilent Technologies, Applied Biosystems, GE Healthcare, Illumina, Eppendorf and the National Cancer Institute, and quantitative gene expression assays included TaqMan® Gene Expression PCR Assay, Standardized (Sta RT-PCR™ and QuantiGene®. The data showed great consistency in gene expression measurements across different microarray platforms, different technologies and test sites. However, SYBR® Green real-time PCR, another common technique utilized by half of all real-time PCR users for gene expression measurement, was not addressed in the MAQC study. In the present study, we compared the performance of SYBR Green PCR with TaqMan PCR, microarrays and other quantitative technologies using the same two Reference RNA samples as the MAQC project. We assessed SYBR Green real-time PCR using commercially available RT2 Profiler™ PCR Arrays from SuperArray, containing primer pairs that have been experimentally validated to ensure gene-specificity and high amplification efficiency. Results The SYBR Green PCR Arrays exhibit good reproducibility among different users, PCR instruments and test sites. In addition, the SYBR Green PCR Arrays have the highest concordance with TaqMan PCR, and a high level of concordance with other quantitative methods and microarrays that were evaluated in this study in terms of fold-change correlation and overlap of lists of differentially expressed genes. Conclusion These data demonstrate that SYBR Green real-time PCR delivers highly comparable results in gene expression measurement with TaqMan PCR and other high-density microarrays.

  16. Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: Implications for transcriptomics studies

    NARCIS (Netherlands)

    Ballerstedt, H.; Volkers, R.J.M.; Mars, A.E.; Hallsworth, J.E.; Santos, V.A.M.D.; Puchalka, J.; Duuren, J. van; Eggink, G.; Timmis, K.N.; Bont, J.A.M. de; Wery, J.

    2007-01-01

    Pseudomonas putida KT2440 is the only fully sequenced P. putida strain. Thus, for transcriptomics and proteomics studies with other P. putida strains, the P. putida KT2440 genomic database serves as standard reference. The utility of KT2440 whole-genome, high-density oligonucleotide microarrays for

  17. Immunohistochemical localization of steroid receptor coactivators in chondrosarcoma: an in vivo tissue microarray study.

    Science.gov (United States)

    Li, Wei; Fu, Jingshu; Bian, Chen; Zhang, Jiqiang; Xie, Zhao

    2014-12-01

    Chondrosarcoma is the second most common type of primary bone malignancy following up osteosarcoma, characterized by resistance to conventional chemotherapeutic agents and radiation regimens. The p160 family members steroid receptor coactivator-1 and -3 (SRC-1 and SRC-3) have been implied in the regulation of cancer growth, migration, invasion, metastasis and chemotherapeutic resistance; but we still lack detailed information about the levels of SRCs in chondrosarcoma. In this study, expression of SRC-1 and SRC-3 in chondrosarcoma was examined by immunohistochemistry with tissue microarrays; the four score system (0, 1, 2 and 3) was used to evaluate the staining. The results showed that there were no gender-, site- or age-differences regarding the expression of SRC-1 or SRC-3 (p>0.05); organ (bone or cartilage) -differences were only detected for SRC-1 but not SRC-3 (pchondrosarcoma, may be novel targets for the prognosis and/or treatment of chondrosarcoma, would have opened a new avenue and established foundation for studying chondrosarcoma. Copyright © 2014 Elsevier GmbH. All rights reserved.

  18. Study of hepatitis B virus gene mutations with enzymatic colorimetry-based DNA microarray.

    Science.gov (United States)

    Mao, Hailei; Wang, Huimin; Zhang, Donglei; Mao, Hongju; Zhao, Jianlong; Shi, Jian; Cui, Zhichu

    2006-01-01

    To establish a modified microarray method for detecting HBV gene mutations in the clinic. Site-specific oligonucleotide probes were immobilized to microarray slides and hybridized to biotin-labeled HBV gene fragments amplified from two-step PCR. Hybridized targets were transferred to nitrocellulose membranes, followed by intensity measurement using BCIP/NBT colorimetry. HBV genes from 99 Hepatitis B patients and 40 healthy blood donors were analyzed. Mutation frequencies of HBV pre-core/core and basic core promoter (BCP) regions were found to be significantly higher in the patient group (42%, 40% versus 2.5%, 5%, P colorimetry method exhibited the same level of sensitivity and reproducibility. An enzymatic colorimetry-based DNA microarray assay was successfully established to monitor HBV mutations. Pre-core/core and BCP mutations of HBV genes could be major causes of HBV infection in HBeAg-negative patients and could also be relevant to chronicity and aggravation of hepatitis B.

  19. Genetic response in masseter muscle after orthognathic surgery in comparison with healthy controls - A Microarray study.

    Science.gov (United States)

    Marewski, Maya; Petto, Carola; Schneider, Matthias; Harzer, Winfried

    2017-04-01

    One third of adult patients with orthognathic surgery of a prognathic or retrognathic mandible show relapse. The sagittal split osteotomy of the mandible leads to a displacement of both parts up to 10 mm without any changes of muscle attachment. Changed mandible length needs adaptation of muscle capacity because of changed force to moment ratio. The aim of this Microarray study was to analyze the general genetic response of masseter muscle in patients with retrognathism or prognathism of the mandible six months after surgery in comparison with healthy untreated controls. We found in tissue samples from masseter muscle a reduction of different entities between patients and controls but less in retrognathic than in prognathic patients (274/429). The different entities to controls in prognathia were reduced from 1862 to 1749 but increased in retrognathia from 1070 to 1563. We have to consider that the total amount of different entities to the controls is higher in patients with prognathic mandible (7364) because of their strong genetic controlled development compared with that in patients with retrognathic mandible (4126), which is more environmentally influenced. It can be concluded that function follows form after surgical change with high inheritance. In retrognathic patients the adaptation could be delayed or the capacity of regeneration potential is not sufficient. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

  20. Fascin and EMMPRIN expression in primary mucinous tumors of ovary: a tissue microarray study.

    Science.gov (United States)

    Alici, Omer; Kefeli, Mehmet; Yildiz, Levent; Baris, Sancar; Karagoz, Filiz; Kandemir, Bedri

    2014-12-01

    The aim of this study was to compare the expressions of fascin and EMMPRIN in primary malignant, borderline and benign mucinous ovarian tumors, and to investigate the relationship of these markers with tumor progression and their applicability to differential diagnosis. An immunohistochemical study was performed for fascin and EMMPRIN using the tissue microarray technique. Eighty-one cases were included in the study; there were 37 benign, 25 borderline and 19 malignant primary mucinous ovarian tumors. For each case, a total staining score was determined, consisting of scores for extent of staining and intensity of staining. The cases were allocated to negative, weakly positive and strongly positive staining categories, according to the total staining score. Both of the markers were significantly negative in benign tumors as compared with borderline and malignant tumors. There was no significant difference between borderline and malignant groups for both markers. Sixty-eight percent of malignant tumors were stained positive by fascin, while this rate was 40% for borderline mucinous tumors. All malignant tumors were strongly stained positive for EMMPRIN, while this rate was 92% for borderline mucinous tumors. The rest of the cases stained weakly positive. No significant difference in staining score was found between fascin and EMMPRIN expression. In ovarian primary mucinous tumors, fascin and EMMPRIN may play an important role in tumor progression from benign tumor to carcinoma. In that context, EMMPRIN and fascin expression may have potential application in the differential diagnosis of some diagnostically problematic mucinous ovarian tumors. However, the differential diagnostic applicability of EMMPRIN appears to be more limited than that of fascin due to its wide spectrum of staining in mucinous ovarian tumors. Copyright © 2014 Elsevier GmbH. All rights reserved.

  1. Increased Inhibitor of Differentiation 4 (Id4 Expression in Glioblastoma: A Tissue Microarray Study

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    Weifin Zeng, Elisabeth J. Rushing, Daniel P. Hartmann, Norio Azumi

    2010-01-01

    Full Text Available Background: The inhibitor of differentiation/DNA binding protein family (Id1-4 is involved in cell cycle control, tumorigenesis and angiogenesis through the negative regulation of helix-loop-helix transcription factors. Of these proteins, Id4 is known to play an important role in neural stem cell differentiation, and deregulation has been implicated in glial neoplasia. However, the expression and significance of Id4 in astrocytomas has not been fully addressed. Herein we report the differential expression of Id4 in astrocytomas of various grades using tissue microarrays (TMA and immunohistochemistry (IHC. Design: The GBM TMA was constructed from 53 archival cases at Georgetown University Hospital and a TMA with normal brain controls and grades II-III astrocytoma was obtained from Cybrdi (Rockville, MD. TMA sections were stained with Id4 antibody and the slides were scored according to the percentage of staining astrocytic nuclei (<9% -, 10-50% +, >51% ++. The Fisher Exact test was used to test for statistical significance. Results: Nuclear staining for Id4 was seen in 73.58% GBMs, 25% grade III, and 12.5% grade II astrocytomas; staining was absent in normal brain tissue. There was a statistically significant difference between GBM and grades II, III astrocytoma (p <0.01. Significant Id4 expression was not detected in normal brain. Conclusions: Our study confirms the frequent upregulation of Id4 expression in GBM, which lends support to its role in tumorigenesis, possibly in the transformation of low to high-grade astrocytoma (i.e. GBM. Further studies are warranted to determine the precise role of Id4 in glial neoplasia and its potential use in targeted therapy for GBM.

  2. Meta-analysis of Drosophila circadian microarray studies identifies a novel set of rhythmically expressed genes.

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    Kevin P Keegan

    2007-11-01

    Full Text Available Five independent groups have reported microarray studies that identify dozens of rhythmically expressed genes in the fruit fly Drosophila melanogaster. Limited overlap among the lists of discovered genes makes it difficult to determine which, if any, exhibit truly rhythmic patterns of expression. We reanalyzed data from all five reports and found two sources for the observed discrepancies, the use of different expression pattern detection algorithms and underlying variation among the datasets. To improve upon the methods originally employed, we developed a new analysis that involves compilation of all existing data, application of identical transformation and standardization procedures followed by ANOVA-based statistical prescreening, and three separate classes of post hoc analysis: cross-correlation to various cycling waveforms, autocorrelation, and a previously described fast Fourier transform-based technique. Permutation-based statistical tests were used to derive significance measures for all post hoc tests. We find application of our method, most significantly the ANOVA prescreening procedure, significantly reduces the false discovery rate relative to that observed among the results of the original five reports while maintaining desirable statistical power. We identify a set of 81 cycling transcripts previously found in one or more of the original reports as well as a novel set of 133 transcripts not found in any of the original studies. We introduce a novel analysis method that compensates for variability observed among the original five Drosophila circadian array reports. Based on the statistical fidelity of our meta-analysis results, and the results of our initial validation experiments (quantitative RT-PCR, we predict many of our newly found genes to be bona fide cyclers, and suggest that they may lead to new insights into the pathways through which clock mechanisms regulate behavioral rhythms.

  3. A regression-based differential expression detection algorithm for microarray studies with ultra-low sample size.

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    Daniel Vasiliu

    Full Text Available Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sample size, high dimensionality, and high variance remains challenging, limiting the usability of these tens of thousands of publicly available, and possibly many more unpublished, gene expression datasets. We propose a novel variable selection algorithm for ultra-low-n microarray studies using generalized linear model-based variable selection with a penalized binomial regression algorithm called penalized Euclidean distance (PED. Our method uses PED to build a classifier on the experimental data to rank genes by importance. In place of cross-validation, which is required by most similar methods but not reliable for experiments with small sample size, we use a simulation-based approach to additively build a list of differentially expressed genes from the rank-ordered list. Our simulation-based approach maintains a low false discovery rate while maximizing the number of differentially expressed genes identified, a feature critical for downstream pathway analysis. We apply our method to microarray data from an experiment perturbing the Notch signaling pathway in Xenopus laevis embryos. This dataset was chosen because it showed very little differential expression according to limma, a powerful and widely-used method for microarray analysis. Our method was able to detect a significant number of differentially expressed genes in this dataset and suggest future directions for investigation. Our method is easily adaptable for analysis of data from RNA-seq and other global expression experiments with low sample size and high dimensionality.

  4. Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton

    Science.gov (United States)

    Muller, Jean; Mehlen, André; Vetter, Guillaume; Yatskou, Mikalai; Muller, Arnaud; Chalmel, Frédéric; Poch, Olivier; Friederich, Evelyne; Vallar, Laurent

    2007-01-01

    Background The actin cytoskeleton plays a crucial role in supporting and regulating numerous cellular processes. Mutations or alterations in the expression levels affecting the actin cytoskeleton system or related regulatory mechanisms are often associated with complex diseases such as cancer. Understanding how qualitative or quantitative changes in expression of the set of actin cytoskeleton genes are integrated to control actin dynamics and organisation is currently a challenge and should provide insights in identifying potential targets for drug discovery. Here we report the development of a dedicated microarray, the Actichip, containing 60-mer oligonucleotide probes for 327 genes selected for transcriptome analysis of the human actin cytoskeleton. Results Genomic data and sequence analysis features were retrieved from GenBank and stored in an integrative database called Actinome. From these data, probes were designed using a home-made program (CADO4MI) allowing sequence refinement and improved probe specificity by combining the complementary information recovered from the UniGene and RefSeq databases. Actichip performance was analysed by hybridisation with RNAs extracted from epithelial MCF-7 cells and human skeletal muscle. Using thoroughly standardised procedures, we obtained microarray images with excellent quality resulting in high data reproducibility. Actichip displayed a large dynamic range extending over three logs with a limit of sensitivity between one and ten copies of transcript per cell. The array allowed accurate detection of small changes in gene expression and reliable classification of samples based on the expression profiles of tissue-specific genes. When compared to two other oligonucleotide microarray platforms, Actichip showed similar sensitivity and concordant expression ratios. Moreover, Actichip was able to discriminate the highly similar actin isoforms whereas the two other platforms did not. Conclusion Our data demonstrate that

  5. Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease

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    van Ommen Gert-Jan B

    2008-06-01

    Full Text Available Abstract Background Comparative analysis of expression microarray studies is difficult due to the large influence of technical factors on experimental outcome. Still, the identified differentially expressed genes may hint at the same biological processes. However, manually curated assignment of genes to biological processes, such as pursued by the Gene Ontology (GO consortium, is incomplete and limited. We hypothesised that automatic association of genes with biological processes through thesaurus-controlled mining of Medline abstracts would be more effective. Therefore, we developed a novel algorithm (LAMA: Literature-Aided Meta-Analysis to quantify the similarity between transcriptomics studies. We evaluated our algorithm on a large compendium of 102 microarray studies published in the field of muscle development and disease, and compared it to similarity measures based on gene overlap and over-representation of biological processes assigned by GO. Results While the overlap in both genes and overrepresented GO-terms was poor, LAMA retrieved many more biologically meaningful links between studies, with substantially lower influence of technical factors. LAMA correctly grouped muscular dystrophy, regeneration and myositis studies, and linked patient and corresponding mouse model studies. LAMA also retrieves the connecting biological concepts. Among other new discoveries, we associated cullin proteins, a class of ubiquitinylation proteins, with genes down-regulated during muscle regeneration, whereas ubiquitinylation was previously reported to be activated during the inverse process: muscle atrophy. Conclusion Our literature-based association analysis is capable of finding hidden common biological denominators in microarray studies, and circumvents the need for raw data analysis or curated gene annotation databases.

  6. [Study of generational risk in deafness inflicted couples using deafness gene microarray technique].

    Science.gov (United States)

    Wang, Ping; Zhao, Jia; Yu, Shu-yuan; Jin, Peng; Zhu, Wei; DU, Bo

    2011-06-01

    To explored the significance of screening the gene mutations of deafness related in deaf-mute (deaf & dumb) family using DNA microarray. Total of 52 couples of deaf-mute were recruited from Changchun deaf-mute community. With an average age of (58.3 ± 6.7) years old (x(-) ± s). Blood samples were obtained with informed consent. Their genomic DNA was extracted from peripheral blood and PCR was performed. Nine of hot spot mutations in four most common deafness pathologic gene were examined with the DNA microarray, including GJB2, GJB3, PDS and mtDNA 12S rRNA genes. At the same time, the results were verified with the traditional methods of sequencing. Fifty of normal people served as a control group. All patients were diagnosed non-syndromic sensorineural hearing loss by subjective pure tone audiometry. Thirty-two of 104 cases appeared GJB2 gene mutation (30.7%), the mutation sites included 35delG, 176del16, 235delC and 299delAT. Eighteen of 32 cases of GJB2 mutations were 235delC (59.1%). Seven of 104 cases appeared SLC26A4 gene IVS7-2 A > G mutation. Questionnaire survey and gene diagnosis revealed that four of 52 families have deaf offspring (7.6%). When a couple carries the same gene mutation, the risk of their children deafness was 100%. The results were confirmed with the traditional methods of sequencing. There is a high risk of deafness if a deaf-mute family is planning to have a new baby. It is very important and helpful to avoid deaf newborns again in deaf-mute family by DNA microarray.

  7. Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs.

    Science.gov (United States)

    Jouffe, Vincent; Rowe, Suzanne; Liaubet, Laurence; Buitenhuis, Bart; Hornshøj, Henrik; SanCristobal, Magali; Mormède, Pierre; de Koning, D J

    2009-07-16

    Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH). Different approaches to localize the differentially expressed (DE) genes to the pig genome showed different levels of success and a clear lack of concordance for some genes between the various approaches. For a focused analysis on 12 genes, overlapping QTL from the public domain were presented. Also, differentially expressed genes underlying QTL for ACTH response were described. Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. This enabled co-location of DE genes and previously studied QTL regions, but the draft genome sequence is still incomplete and will contain many errors. A further step to explore links between DE genes and QTL at the pathway level was largely unsuccessful due to the lack of annotation of the pig genome. This could be improved by further comparative mapping analyses but this would be time consuming. This paper provides a case study for the integration of QTL data and microarray data for a species with limited genome sequence information and annotation. The results illustrate the challenges that must be addressed but also provide a roadmap for future work that is applicable to other non-model species.

  8. Radiation-induced adaptive response in fetal mice: a micro-array study

    International Nuclear Information System (INIS)

    Vares, G.; Bing, Wang; Mitsuru, Nenoi; Tetsuo, Nakajima; Kaoru, Tanaka; Isamu, Hayata

    2006-01-01

    Exposure of sublethal doses of ionizing radiation can induce protective mechanisms against a subsequent higher dose irradiation. This phenomenon called radio-adaptation (or adaptive response - AR), has been described in a wide range of biological models. In a series of studies, we demonstrated the existence of a radiation-induced AR in mice during late organogenesis. For better understanding of molecular mechanisms underlying AR in our model, we performed a global analysis of transcriptome regulations in cells collected from whole mouse fetuses. Using cDNA micro-arrays, we studied gene expression in these cells after in utero priming exposure to irradiation. Several combinations of radiation dose and dose-rate were applied to induce or not an AR in our system. Gene regulation was observed after exposure to priming radiation in each condition. Student's t-test was performed in order to identify genes whose expression modulation was specifically different in AR-inducing an( non-AR-inducing conditions. Genes were ranked according to their ability in discriminating AR-specific modulations. Since AR genes were implicated in variety of functions and cellular processes, we applied a functional classification algorithm, which clustered genes in a limited number of functionally related group: We established that AR genes are significantly enriched for specific keywords. Our results show a significant modulation of genes implicated in signal transduction pathways. No AR-specific alteration of DNA repair could be observed. Nevertheless, it is likely that modulation of DNA repair activity results, at least partly, from post-transcriptional regulation. One major hypothesis is that de-regulations of signal transduction pathways and apoptosis may be responsible for AR phenotype. In previous work, we demonstrated that radiation-induced AR in mice during organogenesis is related to Trp53 gene status and to the occurrence of radiation-induced apoptosis. Other work proposed that p53

  9. Expression of the G protein-coupled estrogen receptor (GPER in endometriosis: a tissue microarray study

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    Samartzis Nicolas

    2012-04-01

    Full Text Available Abstract Background The G protein-coupled estrogen receptor (GPER is thought to be involved in non-genomic estrogen responses as well as processes such as cell proliferation and migration. In this study, we analyzed GPER expression patterns from endometriosis samples and normal endometrial tissue samples and compared these expression profiles to those of the classical sex hormone receptors. Methods A tissue microarray, which included 74 samples from different types of endometriosis (27 ovarian, 19 peritoneal and 28 deep-infiltrating and 30 samples from normal endometrial tissue, was used to compare the expression levels of the GPER, estrogen receptor (ER-alpha, ER-beta and progesterone receptor (PR. The immunoreactive score (IRS was calculated separately for epithelium and stroma as the product of the staining intensity and the percentage of positive cells. The expression levels of the hormonal receptors were dichotomized into low (IRS  =6 expression groups. Results The mean epithelial IRS (+/−standard deviation, range of cytoplasmic GPER expression was 1.2 (+/−1.7, 0–4 in normal endometrium and 5.1 (+/−3.5, 0–12 in endometriosis (p p = 0.71, of ER-alpha 10.6 (+/−2.4, 3–12 and 9.8 (+/−3.0, 2–12; p = 0.26, of ER-beta 2.4 (+/−2.2; 0–8 and 5.6 (+/−2.6; 0–10; p p p p = 0.001, of ER-beta 1.8 (+/−2.0; 0–8 and 5.4 (+/−2.5; 0–10; p p���= 0.044, respectively. Cytoplasmic GPER expression was not detectable in the stroma of endometrium and endometriosis. The observed frequency of high epithelial cytoplasmic GPER expression levels was 50% (n = 30/60 in the endometriosis and none (0/30 in the normal endometrium samples (p p = 0.01, as compared to peritoneal (9/18, 50% or deep-infiltrating endometriotic lesions (7/22, 31.8%. The frequency of high stromal nuclear GPER expression levels was 100% (n = 74/74 in endometriosis and 76.7% (n = 23/30 in normal endometrium (p

  10. Effects of ingested turmeric oleoresin on glucose and lipid metabolisms in obese diabetic mice: a DNA microarray study.

    Science.gov (United States)

    Honda, Shinichi; Aoki, Fumiki; Tanaka, Hozumi; Kishida, Hideyuki; Nishiyama, Tozo; Okada, Shinji; Matsumoto, Ichiro; Abe, Keiko; Mae, Tatsumasa

    2006-11-29

    Turmeric, the rhizome of Curcuma longa L., has a wide range of effects on human health. Turmeric oleoresin, an extract of turmeric, is often used for flavoring and coloring. Curcuminoids and turmeric essential oil are both contained in turmeric oleoresin, and both of these fractions have hypoglycemic effects. In the present study, we comprehensively assessed the effect of turmeric oleoresin on hepatic gene expression in obese diabetic KK-Ay mice using DNA microarray analysis and quantitative real-time polymerase chain reaction (PCR). Female KK-Ay mice aged 6 weeks (n = 6/group) were fed a high-fat diet containing turmeric oleoresin, curcuminoids, and essential oil for 5 weeks. The same diet without any of these fractions was used as a control diet. Ingestion of turmeric oleoresin and essential oil inhibited the development of increased blood glucose and abdominal fat mass, while curcuminoids only inhibited the increase in blood glucose. DNA microarray analysis indicated that turmeric oleoresin ingestion up-regulated the expression of genes related to glycolysis, beta-oxidation, and cholesterol metabolism in the liver of KK-Ay mice, while expression of gluconeogenesis-related genes was down-regulated. Real-time PCR analysis was conducted to assess the contribution of the curcuminoids and essential oil in turmeric oleoresin to the changes in expression of representative genes selected by DNA microarray analysis. This analysis suggested that curcuminoids regulated turmeric oleoresin ingestion-induced expression of glycolysis-related genes and also that curcuminoids and turmeric essential oil acted synergistically to regulate the peroxisomal beta-oxidation-related gene expression induced by turmeric oleoresin ingestion. These changes in gene expression were considered to be the mechanism by which the turmeric oleoresin affected the control of both blood glucose levels and abdominal adipose tissue masses. All of these results suggest that the use of whole turmeric

  11. cDNA microarray analysis of human keratinocytes cells of patients submitted to chemoradiotherapy and oral photobiomodulation therapy: pilot study.

    Science.gov (United States)

    Antunes, Heliton S; Wajnberg, Gabriel; Pinho, Marcos B; Jorge, Natasha Andressa Nogueira; de Moraes, Joyce Luana Melo; Stefanoff, Claudio Gustavo; Herchenhorn, Daniel; Araújo, Carlos M M; Viégas, Celia Maria Pais; Rampini, Mariana P; Dias, Fernando L; de Araujo-Souza, Patricia Savio; Passetti, Fabio; Ferreira, Carlos G

    2018-01-01

    Oral mucositis is an acute toxicity that occurs in patients submitted to chemoradiotherapy to treat head and neck squamous cell carcinoma. In this study, we evaluated differences in gene expression in the keratinocytes of the oral mucosa of patients treated with photobiomodulation therapy and tried to associate the molecular mechanisms with clinical findings. From June 2009 to December 2010, 27 patients were included in a randomized double-blind pilot study. Buccal smears from 13 patients were obtained at days 1 and 10 of chemoradiotherapy, and overall gene expression of samples from both dates were analyzed by complementary DNA (cDNA) microarray. In addition, samples from other 14 patients were also collected at D1 and D10 of chemoradiotherapy for subsequent validation of cDNA microarray findings by qPCR. The expression array analysis identified 105 upregulated and 60 downregulated genes in our post-treatment samples when compared with controls. Among the upregulated genes with the highest fold change, it was interesting to observe the presence of genes related to keratinocyte differentiation. Among downregulated genes were observed genes related to cytotoxicity and immune response. The results indicate that genes known to be induced during differentiation of human epidermal keratinocytes were upregulated while genes associated with cytotoxicity and immune response were downregulated in the laser group. These results support previous clinical findings indicating that the lower incidence of oral mucositis associated with photobiomodulation therapy might be correlated to the activation of genes involved in keratinocyte differentiation.

  12. High-Dimensional Additive Hazards Regression for Oral Squamous Cell Carcinoma Using Microarray Data: A Comparative Study

    Directory of Open Access Journals (Sweden)

    Omid Hamidi

    2014-01-01

    Full Text Available Microarray technology results in high-dimensional and low-sample size data sets. Therefore, fitting sparse models is substantial because only a small number of influential genes can reliably be identified. A number of variable selection approaches have been proposed for high-dimensional time-to-event data based on Cox proportional hazards where censoring is present. The present study applied three sparse variable selection techniques of Lasso, smoothly clipped absolute deviation and the smooth integration of counting, and absolute deviation for gene expression survival time data using the additive risk model which is adopted when the absolute effects of multiple predictors on the hazard function are of interest. The performances of used techniques were evaluated by time dependent ROC curve and bootstrap .632+ prediction error curves. The selected genes by all methods were highly significant (P<0.001. The Lasso showed maximum median of area under ROC curve over time (0.95 and smoothly clipped absolute deviation showed the lowest prediction error (0.105. It was observed that the selected genes by all methods improved the prediction of purely clinical model indicating the valuable information containing in the microarray features. So it was concluded that used approaches can satisfactorily predict survival based on selected gene expression measurements.

  13. ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

    Directory of Open Access Journals (Sweden)

    Krasnogor Natalio

    2009-10-01

    Full Text Available Abstract Background Statistical analysis of DNA microarray data provides a valuable diagnostic tool for the investigation of genetic components of diseases. To take advantage of the multitude of available data sets and analysis methods, it is desirable to combine both different algorithms and data from different studies. Applying ensemble learning, consensus clustering and cross-study normalization methods for this purpose in an almost fully automated process and linking different analysis modules together under a single interface would simplify many microarray analysis tasks. Results We present ArrayMining.net, a web-application for microarray analysis that provides easy access to a wide choice of feature selection, clustering, prediction, gene set analysis and cross-study normalization methods. In contrast to other microarray-related web-tools, multiple algorithms and data sets for an analysis task can be combined using ensemble feature selection, ensemble prediction, consensus clustering and cross-platform data integration. By interlinking different analysis tools in a modular fashion, new exploratory routes become available, e.g. ensemble sample classification using features obtained from a gene set analysis and data from multiple studies. The analysis is further simplified by automatic parameter selection mechanisms and linkage to web tools and databases for functional annotation and literature mining. Conclusion ArrayMining.net is a free web-application for microarray analysis combining a broad choice of algorithms based on ensemble and consensus methods, using automatic parameter selection and integration with annotation databases.

  14. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

    KAUST Repository

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Wong, Hau-San

    2015-01-01

    Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  15. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

    KAUST Repository

    Wong, Ka-Chun

    2015-06-11

    Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  16. Bone health nutraceuticals alter microarray mRNA gene expression: A randomized, parallel, open-label clinical study.

    Science.gov (United States)

    Lin, Yumei; Kazlova, Valentina; Ramakrishnan, Shyam; Murray, Mary A; Fast, David; Chandra, Amitabh; Gellenbeck, Kevin W

    2016-01-15

    Dietary intake of fruits and vegetables has been suggested to have a role in promoting bone health. More specifically, the polyphenols they contain have been linked to physiological effects related to bone mineral density and bone metabolism. In this research, we use standard microarray analyses of peripheral whole blood from post-menopausal women treated with two fixed combinations of plant extracts standardized to polyphenol content to identify differentially expressed genes relevant to bone health. In this 28-day open-label study, healthy post-menopausal women were randomized into three groups, each receiving one of three investigational fixed combinations of plant extracts: an anti-resorptive (AR) combination of pomegranate fruit (Punica granatum L.) and grape seed (Vitis vinifera L.) extracts; a bone formation (BF) combination of quercetin (Dimorphandra mollis Benth) and licorice (Glycyrrhiza glabra L.) extracts; and a fixed combination of all four plant extracts (AR plus BF). Standard microarray analysis was performed on peripheral whole blood samples taken before and after each treatment. Annotated genes were analyzed for their association to bone health by comparison to a gene library. The AR combination down-regulated a number of genes involved in reduction of bone resorption including cathepsin G (CTSG) and tachykinin receptor 1 (TACR1). The AR combination also up-regulated genes associated with formation of extracellular matrix including heparan sulfate proteoglycan 2 (HSPG2) and hyaluronoglucosaminidase 1 (HYAL1). In contrast, treatment with the BF combination resulted in up-regulation of bone morphogenetic protein 2 (BMP-2) and COL1A1 (collagen type I α1) genes which are linked to bone and collagen formation while down-regulating genes linked to osteoclastogenesis. Treatment with a combination of all four plant extracts had a distinctly different effect on gene expression than the results of the AR and BF combinations individually. These results could

  17. miRNAs in lung cancer - Studying complex fingerprints in patient's blood cells by microarray experiments

    Directory of Open Access Journals (Sweden)

    Huwer Hanno

    2009-10-01

    Full Text Available Abstract Background Deregulated miRNAs are found in cancer cells and recently in blood cells of cancer patients. Due to their inherent stability miRNAs may offer themselves for blood based tumor diagnosis. Here we addressed the question whether there is a sufficient number of miRNAs deregulated in blood cells of cancer patients to be able to distinguish between cancer patients and controls. Methods We synthesized 866 human miRNAs and miRNA star sequences as annotated in the Sanger miRBase onto a microarray designed by febit biomed gmbh. Using the fully automated Geniom Real Time Analyzer platform, we analyzed the miRNA expression in 17 blood cell samples of patients with non-small cell lung carcinomas (NSCLC and in 19 blood samples of healthy controls. Results Using t-test, we detected 27 miRNAs significantly deregulated in blood cells of lung cancer patients as compared to the controls. Some of these miRNAs were validated using qRT-PCR. To estimate the value of each deregulated miRNA, we grouped all miRNAs according to their diagnostic information that was measured by Mutual Information. Using a subset of 24 miRNAs, a radial basis function Support Vector Machine allowed for discriminating between blood cellsamples of tumor patients and controls with an accuracy of 95.4% [94.9%-95.9%], a specificity of 98.1% [97.3%-98.8%], and a sensitivity of 92.5% [91.8%-92.5%]. Conclusion Our findings support the idea that neoplasia may lead to a deregulation of miRNA expression in blood cells of cancer patients compared to blood cells of healthy individuals. Furthermore, we provide evidence that miRNA patterns can be used to detect human cancers from blood cells.

  18. The clinicopathologic association of c-MET overexpression in Iranian gastric carcinomas; an immunohistochemical study of tissue microarrays.

    Science.gov (United States)

    Sotoudeh, Kambiz; Hashemi, Forough; Madjd, Zahra; Sadeghipour, Alireza; Molanaei, Saadat; Kalantary, Elham

    2012-05-28

    c-MET is an oncogene protein that plays important role in gastric carcinogenesis and has been introduced as a prognostic marker and potential therapeutic target. The aim of this study was to evaluate the frequency of c-MET overexpression and its relationship with clinicopathological variables in gastric cancer of Iranian population using tissue microarray. In a cross sectional study, representative paraffin blocks of 130 patients with gastric carcinoma treated by curative gastrectomy during a 2 years period of 2008-2009 in two university hospitals in Tehran-Iran were collected in tissue microarray and c-MET expression was studied by immunohistochemical staining. Finally 124 cases were evaluated, constituted of 99 male and 25 female with the average age of 61.5 years. In 71% (88/124) of tumors, c-MET high expression was found. c-MET high expression was more associated with intestinal than diffuse tumor type (P = 0.04), deeper tumor invasion, pT3 and pT4 versus pT1 and pT2 (P = 0.014), neural invasion (P = 0.002) and advanced TNM staging, stage 3 and 4 versus stage 1 and2 (P = 0.044). The c-MET high expression was not associated with age, sex, tumor location, differentiation grade and distant metastasis, but relative associations with lymph node metastasis (P = 0.065) and vascular invasion (P = 0.078) were observed. c-MET oncogene protein was frequently overexpressed in Iranian gastric carcinomas and it was related to clinicopathological characteristics such as tumor type, depth of invasion, neural invasion and TNM staging. It can also support the idea that c-MET is a potential marker for target therapy in Iranian gastric cancer. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/9744598757151429.

  19. p16 as a diagnostic marker of cervical neoplasia: a tissue microarray study of 796 archival specimens

    DEFF Research Database (Denmark)

    Lesnikova, Iana; Lidang, Marianne; Hamilton-Dutoit, Stephen

    2009-01-01

    from archival formalin fixed, paraffin-embedded donor tissues from 796 patients, and included cases of cervical intraepithelial neoplasia (CIN)1 (n = 249), CIN2 (n = 233), CIN3 (n = 181), and invasive cervical carcinoma (n = 133). p16INK4a expression was scored using two different protocols: 1......BACKGROUND: To evaluate the usefulness of this biomarker in the diagnosis of cases of cervical neoplasia we studied the immunohistochemical expression of p16INK4a in a large series of archival cervical biopsies arranged into tissue microarray format. METHODS: TMAs were constructed with tissue cores...... dysplasia or the presence of invasive carcinoma. CONCLUSION: Immunohistochemical analysis of p16INK4a expression is a useful diagnostic tool. Expression is related to the degree of histological dysplasia, suggesting that it may have prognostic and predicative value in the management of cervical neoplasia....

  20. Mining Temporal Patterns to Improve Agents Behavior: Two Case Studies

    Science.gov (United States)

    Fournier-Viger, Philippe; Nkambou, Roger; Faghihi, Usef; Nguifo, Engelbert Mephu

    We propose two mechanisms for agent learning based on the idea of mining temporal patterns from agent behavior. The first one consists of extracting temporal patterns from the perceived behavior of other agents accomplishing a task, to learn the task. The second learning mechanism consists in extracting temporal patterns from an agent's own behavior. In this case, the agent then reuses patterns that brought self-satisfaction. In both cases, no assumption is made on how the observed agents' behavior is internally generated. A case study with a real application is presented to illustrate each learning mechanism.

  1. A newly designed 45 to 60 mer oligonucleotide Agilent platform microarray for global gene expression studies of Synechocystis PCC6803: example salt stress experiment

    NARCIS (Netherlands)

    Aguirre von Wobeser, E.; Huisman, J.; Ibelings, B.; Matthijs, H.C.P.; Matthijs, H.C.P.

    2005-01-01

    A newly designed 45 to 60 mer oligonucleotide Agilent platform microarray for global gene expression studies of Synechocystis PCC6803: example salt stress experiment Eneas Aguirre-von-Wobeser 1, Jef Huisman1, Bas Ibelings2 and Hans C.P. Matthijs1 1 Universiteit van Amsterdam, Amsterdam, The

  2. Layered signaling regulatory networks analysis of gene expression involved in malignant tumorigenesis of non-resolving ulcerative colitis via integration of cross-study microarray profiles.

    Science.gov (United States)

    Fan, Shengjun; Pan, Zhenyu; Geng, Qiang; Li, Xin; Wang, Yefan; An, Yu; Xu, Yan; Tie, Lu; Pan, Yan; Li, Xuejun

    2013-01-01

    Ulcerative colitis (UC) was the most frequently diagnosed inflammatory bowel disease (IBD) and closely linked to colorectal carcinogenesis. By far, the underlying mechanisms associated with the disease are still unclear. With the increasing accumulation of microarray gene expression profiles, it is profitable to gain a systematic perspective based on gene regulatory networks to better elucidate the roles of genes associated with disorders. However, a major challenge for microarray data analysis is the integration of multiple-studies generated by different groups. In this study, firstly, we modeled a signaling regulatory network associated with colorectal cancer (CRC) initiation via integration of cross-study microarray expression data sets using Empirical Bayes (EB) algorithm. Secondly, a manually curated human cancer signaling map was established via comprehensive retrieval of the publicly available repositories. Finally, the co-differently-expressed genes were manually curated to portray the layered signaling regulatory networks. Overall, the remodeled signaling regulatory networks were separated into four major layers including extracellular, membrane, cytoplasm and nucleus, which led to the identification of five core biological processes and four signaling pathways associated with colorectal carcinogenesis. As a result, our biological interpretation highlighted the importance of EGF/EGFR signaling pathway, EPO signaling pathway, T cell signal transduction and members of the BCR signaling pathway, which were responsible for the malignant transition of CRC from the benign UC to the aggressive one. The present study illustrated a standardized normalization approach for cross-study microarray expression data sets. Our model for signaling networks construction was based on the experimentally-supported interaction and microarray co-expression modeling. Pathway-based signaling regulatory networks analysis sketched a directive insight into colorectal carcinogenesis

  3. Pathway modeling of microarray data: A case study of pathway activity changes in the testis following in utero exposure to dibutyl phthalate (DBP)

    International Nuclear Information System (INIS)

    Ovacik, Meric A.; Sen, Banalata; Euling, Susan Y.; Gaido, Kevin W.; Ierapetritou, Marianthi G.; Androulakis, Ioannis P.

    2013-01-01

    Pathway activity level analysis, the approach pursued in this study, focuses on all genes that are known to be members of metabolic and signaling pathways as defined by the KEGG database. The pathway activity level analysis entails singular value decomposition (SVD) of the expression data of the genes constituting a given pathway. We explore an extension of the pathway activity methodology for application to time-course microarray data. We show that pathway analysis enhances our ability to detect biologically relevant changes in pathway activity using synthetic data. As a case study, we apply the pathway activity level formulation coupled with significance analysis to microarray data from two different rat testes exposed in utero to Dibutyl Phthalate (DBP). In utero DBP exposure in the rat results in developmental toxicity of a number of male reproductive organs, including the testes. One well-characterized mode of action for DBP and the male reproductive developmental effects is the repression of expression of genes involved in cholesterol transport, steroid biosynthesis and testosterone synthesis that lead to a decreased fetal testicular testosterone. Previous analyses of DBP testes microarray data focused on either individual gene expression changes or changes in the expression of specific genes that are hypothesized, or known, to be important in testicular development and testosterone synthesis. However, a pathway analysis may inform whether there are additional affected pathways that could inform additional modes of action linked to DBP developmental toxicity. We show that Pathway activity analysis may be considered for a more comprehensive analysis of microarray data

  4. Pathway modeling of microarray data: A case study of pathway activity changes in the testis following in utero exposure to dibutyl phthalate (DBP)

    Energy Technology Data Exchange (ETDEWEB)

    Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Sen, Banalata [National Center for Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC 27709 (United States); Euling, Susan Y. [National Center for Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Washington, DC 20460 (United States); Gaido, Kevin W. [U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of New Animal Drug Evaluation, Division of Human Food Safety, Rockville, MD 20855 (United States); Ierapetritou, Marianthi G. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, NJ 08854 (United States)

    2013-09-15

    Pathway activity level analysis, the approach pursued in this study, focuses on all genes that are known to be members of metabolic and signaling pathways as defined by the KEGG database. The pathway activity level analysis entails singular value decomposition (SVD) of the expression data of the genes constituting a given pathway. We explore an extension of the pathway activity methodology for application to time-course microarray data. We show that pathway analysis enhances our ability to detect biologically relevant changes in pathway activity using synthetic data. As a case study, we apply the pathway activity level formulation coupled with significance analysis to microarray data from two different rat testes exposed in utero to Dibutyl Phthalate (DBP). In utero DBP exposure in the rat results in developmental toxicity of a number of male reproductive organs, including the testes. One well-characterized mode of action for DBP and the male reproductive developmental effects is the repression of expression of genes involved in cholesterol transport, steroid biosynthesis and testosterone synthesis that lead to a decreased fetal testicular testosterone. Previous analyses of DBP testes microarray data focused on either individual gene expression changes or changes in the expression of specific genes that are hypothesized, or known, to be important in testicular development and testosterone synthesis. However, a pathway analysis may inform whether there are additional affected pathways that could inform additional modes of action linked to DBP developmental toxicity. We show that Pathway activity analysis may be considered for a more comprehensive analysis of microarray data.

  5. The clinicopathologic association of c-MET overexpression in Iranian gastric carcinomas; an immunohistochemical study of tissue microarrays

    Directory of Open Access Journals (Sweden)

    Sotoudeh Kambiz

    2012-05-01

    Full Text Available Abstract Background c-MET is an oncogene protein that plays important role in gastric carcinogenesis and has been introduced as a prognostic marker and potential therapeutic target. The aim of this study was to evaluate the frequency of c-MET overexpression and its relationship with clinicopathological variables in gastric cancer of Iranian population using tissue microarray. Methods In a cross sectional study, representative paraffin blocks of 130 patients with gastric carcinoma treated by curative gastrectomy during a 2 years period of 2008–2009 in two university hospitals in Tehran-Iran were collected in tissue microarray and c-MET expression was studied by immunohistochemical staining. Results Finally 124 cases were evaluated, constituted of 99 male and 25 female with the average age of 61.5 years. In 71% (88/124 of tumors, c-MET high expression was found. c-MET high expression was more associated with intestinal than diffuse tumor type (P = 0.04, deeper tumor invasion, pT3 and pT4 versus pT1 and pT2 (P = 0.014, neural invasion (P = 0.002 and advanced TNM staging, stage 3 and 4 versus stage 1 and2 (P = 0.044. The c-MET high expression was not associated with age, sex, tumor location, differentiation grade and distant metastasis, but relative associations with lymph node metastasis (P = 0.065 and vascular invasion (P = 0.078 were observed. Conclusions c-MET oncogene protein was frequently overexpressed in Iranian gastric carcinomas and it was related to clinicopathological characteristics such as tumor type, depth of invasion, neural invasion and TNM staging. It can also support the idea that c-MET is a potential marker for target therapy in Iranian gastric cancer. Virtual slides The virtual slide(s for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/9744598757151429

  6. Extensive innate immune gene activation accompanies brain aging, increasing vulnerability to cognitive decline and neurodegeneration: a microarray study

    Science.gov (United States)

    2012-01-01

    Background This study undertakes a systematic and comprehensive analysis of brain gene expression profiles of immune/inflammation-related genes in aging and Alzheimer’s disease (AD). Methods In a well-powered microarray study of young (20 to 59 years), aged (60 to 99 years), and AD (74 to 95 years) cases, gene responses were assessed in the hippocampus, entorhinal cortex, superior frontal gyrus, and post-central gyrus. Results Several novel concepts emerge. First, immune/inflammation-related genes showed major changes in gene expression over the course of cognitively normal aging, with the extent of gene response far greater in aging than in AD. Of the 759 immune-related probesets interrogated on the microarray, approximately 40% were significantly altered in the SFG, PCG and HC with increasing age, with the majority upregulated (64 to 86%). In contrast, far fewer immune/inflammation genes were significantly changed in the transition to AD (approximately 6% of immune-related probesets), with gene responses primarily restricted to the SFG and HC. Second, relatively few significant changes in immune/inflammation genes were detected in the EC either in aging or AD, although many genes in the EC showed similar trends in responses as in the other brain regions. Third, immune/inflammation genes undergo gender-specific patterns of response in aging and AD, with the most pronounced differences emerging in aging. Finally, there was widespread upregulation of genes reflecting activation of microglia and perivascular macrophages in the aging brain, coupled with a downregulation of select factors (TOLLIP, fractalkine) that when present curtail microglial/macrophage activation. Notably, essentially all pathways of the innate immune system were upregulated in aging, including numerous complement components, genes involved in toll-like receptor signaling and inflammasome signaling, as well as genes coding for immunoglobulin (Fc) receptors and human leukocyte antigens I

  7. Extensive innate immune gene activation accompanies brain aging, increasing vulnerability to cognitive decline and neurodegeneration: a microarray study

    Directory of Open Access Journals (Sweden)

    Cribbs David H

    2012-07-01

    Full Text Available Abstract Background This study undertakes a systematic and comprehensive analysis of brain gene expression profiles of immune/inflammation-related genes in aging and Alzheimer’s disease (AD. Methods In a well-powered microarray study of young (20 to 59 years, aged (60 to 99 years, and AD (74 to 95 years cases, gene responses were assessed in the hippocampus, entorhinal cortex, superior frontal gyrus, and post-central gyrus. Results Several novel concepts emerge. First, immune/inflammation-related genes showed major changes in gene expression over the course of cognitively normal aging, with the extent of gene response far greater in aging than in AD. Of the 759 immune-related probesets interrogated on the microarray, approximately 40% were significantly altered in the SFG, PCG and HC with increasing age, with the majority upregulated (64 to 86%. In contrast, far fewer immune/inflammation genes were significantly changed in the transition to AD (approximately 6% of immune-related probesets, with gene responses primarily restricted to the SFG and HC. Second, relatively few significant changes in immune/inflammation genes were detected in the EC either in aging or AD, although many genes in the EC showed similar trends in responses as in the other brain regions. Third, immune/inflammation genes undergo gender-specific patterns of response in aging and AD, with the most pronounced differences emerging in aging. Finally, there was widespread upregulation of genes reflecting activation of microglia and perivascular macrophages in the aging brain, coupled with a downregulation of select factors (TOLLIP, fractalkine that when present curtail microglial/macrophage activation. Notably, essentially all pathways of the innate immune system were upregulated in aging, including numerous complement components, genes involved in toll-like receptor signaling and inflammasome signaling, as well as genes coding for immunoglobulin (Fc receptors and human

  8. Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation

    Directory of Open Access Journals (Sweden)

    Lundberg Cathryn

    2008-01-01

    Full Text Available Abstract Background Gene expression measurements from breast cancer (BrCa tumors are established clinical predictive tools to identify tumor subtypes, identify patients showing poor/good prognosis, and identify patients likely to have disease recurrence. However, diverse breast cancer datasets in conjunction with diagnostic clinical arrays show little overlap in the sets of genes identified. One approach to identify a set of consistently dysregulated candidate genes in these tumors is to employ meta-analysis of multiple independent microarray datasets. This allows one to compare expression data from a diverse collection of breast tumor array datasets generated on either cDNA or oligonucleotide arrays. Results We gathered expression data from 9 published microarray studies examining estrogen receptor positive (ER+ and estrogen receptor negative (ER- BrCa tumor cases from the Oncomine database. We performed a meta-analysis and identified genes that were universally up or down regulated with respect to ER+ versus ER- tumor status. We surveyed both the proximal promoter and 3' untranslated regions (3'UTR of our top-ranking genes in each expression group to test whether common sequence elements may contribute to the observed expression patterns. Utilizing a combination of known transcription factor binding sites (TFBS, evolutionarily conserved mammalian promoter and 3'UTR motifs, and microRNA (miRNA seed sequences, we identified numerous motifs that were disproportionately represented between the two gene classes suggesting a common regulatory network for the observed gene expression patterns. Conclusion Some of the genes we identified distinguish key transcripts previously seen in array studies, while others are newly defined. Many of the genes identified as overexpressed in ER- tumors were previously identified as expression markers for neoplastic transformation in multiple human cancers. Moreover, our motif analysis identified a collection of

  9. THE VALIDATION OF THE RESULTS OF MICROARRAY STUDIES OF ASSOCIATION BETWEEN GENE POLYMORPHISMS AND THE FREQUENCY OF RADIATION EXPOSURE MARKERS

    Directory of Open Access Journals (Sweden)

    M. V. Khalyuzova

    2014-01-01

    Full Text Available The results from the selective validation research into the association between genetic polymorphisms and the frequency of cytogenetic abnormalities on a large independent sample are analyzed. These polymorphisms have been identified previously during own microarray studies. It has been shown an association with the frequency of dicentric and ring chromosomes induced by radiation exposure. The study was conducted among Siberian Group of Chemical Enterprises healthy employees (n = 573 exposed to professional irradiation in a dose range of 40–400 mSv. We have found that 5 SNP are confirmed to be associated with the frequency of dicentric and ring: INSR rs1051690 – insulin receptor gene; WRNrs2725349 – Werner syndrome gene, RecQ helicase-like; VCAM1 rs1041163 – vascular cell adhesion molecule 1 gene; PCTP rs2114443 – phosphatidylcholine transfer protein gene; TNKS rs7462102 – tankyrase gene; TRF1-interacting ankyrin-related ADP-ribose polymerase. IGF1 rs2373721 – insulin-like growth factor 1 gene has not confirmed to be associated with the frequency of dicentric and ring chromosomes.

  10. Gene expression profiling to characterize sediment toxicity – a pilot study using Caenorhabditis elegans whole genome microarrays

    Directory of Open Access Journals (Sweden)

    Reifferscheid Georg

    2009-04-01

    Full Text Available Abstract Background Traditionally, toxicity of river sediments is assessed using whole sediment tests with benthic organisms. The challenge, however, is the differentiation between multiple effects caused by complex contaminant mixtures and the unspecific toxicity endpoints such as survival, growth or reproduction. The use of gene expression profiling facilitates the identification of transcriptional changes at the molecular level that are specific to the bio-available fraction of pollutants. Results In this pilot study, we exposed the nematode Caenorhabditis elegans to three sediments of German rivers with varying (low, medium and high levels of heavy metal and organic contamination. Beside chemical analysis, three standard bioassays were performed: reproduction of C. elegans, genotoxicity (Comet assay and endocrine disruption (YES test. Gene expression was profiled using a whole genome DNA-microarray approach to identify overrepresented functional gene categories and derived cellular processes. Disaccharide and glycogen metabolism were found to be affected, whereas further functional pathways, such as oxidative phosphorylation, ribosome biogenesis, metabolism of xenobiotics, aging and several developmental processes were found to be differentially regulated only in response to the most contaminated sediment. Conclusion This study demonstrates how ecotoxicogenomics can identify transcriptional responses in complex mixture scenarios to distinguish different samples of river sediments.

  11. A microarray study of gene and protein regulation in human and rat brain following middle cerebral artery occlusion

    Science.gov (United States)

    Mitsios, Nick; Saka, Mohamad; Krupinski, Jerzy; Pennucci, Roberta; Sanfeliu, Coral; Wang, Qiuyu; Rubio, Francisco; Gaffney, John; Kumar, Pat; Kumar, Shant; Sullivan, Matthew; Slevin, Mark

    2007-01-01

    Background Altered gene expression is an important feature of ischemic cerebral injury and affects proteins of many functional classes. We have used microarrays to investigate the changes in gene expression at various times after middle cerebral artery occlusion in human and rat brain. Results Our results demonstrated a significant difference in the number of genes affected and the time-course of expression between the two cases. The total number of deregulated genes in the rat was 335 versus 126 in the human, while, of 393 overlapping genes between the two array sets, 184 were changed only in the rat and 36 in the human with a total of 41 genes deregulated in both cases. Interestingly, the mean fold changes were much higher in the human. The expression of novel genes, including p21-activated kinase 1 (PAK1), matrix metalloproteinase 11 (MMP11) and integrase interactor 1, was further analyzed by RT-PCR, Western blotting and immunohistochemistry. Strong neuronal staining was seen for PAK1 and MMP11. Conclusion Our findings confirmed previous studies reporting that gene expression screening can detect known and unknown transcriptional features of stroke and highlight the importance of research using human brain tissue in the search for novel therapeutic agents. PMID:17997827

  12. Micro-array versus nano-array platforms: a comparative study for ODN detection based on SPR enhanced ellipsometry

    International Nuclear Information System (INIS)

    Celen, Burcu; Piskin, Erhan; Demirel, Goekhan

    2011-01-01

    The rapid and sensitive detection of DNA has recently attracted worldwide attention for a variety of disease diagnoses and detection of harmful bacteria in food and drink. In this paper, we carried out a comparative study based on surface plasmon resonance enhanced ellipsometry (SPREE) for the detection of oligodeoxynucleotides (ODNs) using micro- and nano-array platforms. The micro-arrayed surfaces were fabricated by a photolithography approach using different types of mask having varying size and shape. Well-ordered arrays of high aspect ratio polymeric nanotubes were also obtained using high molecular weight polystyrene (PS) and anodic aluminum oxide (AAO) membranes having 200 nm pore diameters. The SPREE sensors were then prepared by direct coupling of thiolated probe-ODNs, which contain suitable spacer arms, on gold-coated micro- and nano-arrayed surfaces. We experimentally demonstrated that, for the first time, gold-coated free standing polymeric nano-arrayed platforms can easily be produced and lead to a significant sensor sensitivity gain compared to that of the conventional SPREE surfaces of about four times. We believe that such an enhancement in sensor response could be useful for next generation sensor systems.

  13. Micro-array versus nano-array platforms: a comparative study for ODN detection based on SPR enhanced ellipsometry

    Science.gov (United States)

    Celen, Burcu; Demirel, Gökhan; Piskin, Erhan

    2011-04-01

    The rapid and sensitive detection of DNA has recently attracted worldwide attention for a variety of disease diagnoses and detection of harmful bacteria in food and drink. In this paper, we carried out a comparative study based on surface plasmon resonance enhanced ellipsometry (SPREE) for the detection of oligodeoxynucleotides (ODNs) using micro- and nano-array platforms. The micro-arrayed surfaces were fabricated by a photolithography approach using different types of mask having varying size and shape. Well-ordered arrays of high aspect ratio polymeric nanotubes were also obtained using high molecular weight polystyrene (PS) and anodic aluminum oxide (AAO) membranes having 200 nm pore diameters. The SPREE sensors were then prepared by direct coupling of thiolated probe-ODNs, which contain suitable spacer arms, on gold-coated micro- and nano-arrayed surfaces. We experimentally demonstrated that, for the first time, gold-coated free standing polymeric nano-arrayed platforms can easily be produced and lead to a significant sensor sensitivity gain compared to that of the conventional SPREE surfaces of about four times. We believe that such an enhancement in sensor response could be useful for next generation sensor systems.

  14. Clinical study on temporal lobe epilepsy in childhood caused by temporal lobe space occupying lesions

    International Nuclear Information System (INIS)

    Matsuura, Mariko; Oguni, Hirokazu; Funatsuka, Makoto; Osawa, Makiko; Yamane, Fumitaka; Hori, Tomokatsu; Shimizu, Hiroyuki

    2008-01-01

    We studied the clinicoelectrical and neuroimaging features of 11 patients with symptomatic temporal lobe epilepsy (TLE) caused by temporal lobe space occupying lesions (SOLs), and compared its characteristics with those of 19 mesial TLE (MTLE) patients. Brain MRI demonstrated SOLs in the mesiotemporal lobe in 9, and laterotemporal lobe in the remaining 2 patients. Ten of the 11 patients successfully underwent surgery, which revealed tumors in 7 and focal cortical dysplasia in 3 patients. Comparisons of the clinical features between those with space occupying TLE (SOTLE) and MTLE showed that both conditions shared the same clinical seizure manifestations such as gastric uprising sensation or ictal fear and a favorable response to surgery. However, the patients with SOTLE had fewer febrile convulsion, and more frequent seizure recurrences as well as TLE EEG discharges and associations of the monophasic clinical course than those with MTLE. In addition, the MRI findings were characterized by unilateral hippocampal atrophy in MTLE and expanding or SOLs in the SOTLE group. Children with complex partial seizures of suspected temporal lobe origin should undergo extensive neuroimaging evaluation. (author)

  15. A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Nookaew, Intawat; Papini, Marta; Pornputtapong, Natapol

    2012-01-01

    RNA-seq, has recently become an attractive method of choice in the studies of transcriptomes, promising several advantages compared with microarrays. In this study, we sought to assess the contribution of the different analytical steps involved in the analysis of RNA-seq data generated with the I......RNA-seq, has recently become an attractive method of choice in the studies of transcriptomes, promising several advantages compared with microarrays. In this study, we sought to assess the contribution of the different analytical steps involved in the analysis of RNA-seq data generated...... gene expression identification derived from the different statistical methods, as well as their integrated analysis results based on gene ontology annotation are in good agreement. Overall, our study provides a useful and comprehensive comparison between the two platforms (RNA-seq and microrrays...

  16. Temporal lobe dysfunction in childhood autism: a PET study

    International Nuclear Information System (INIS)

    Boddaert, N.; Poline, J.B.; Brunelle, F.; Zilbovicius, M.; Boddaert, N.; Brunelle, F.; Chabane, N.; Barthelemy, C.; Zilbovicius, M.; Bourgeois, M.; Samson, Y.

    2002-01-01

    Childhood autism is a severe developmental disorder that impairs the acquisition of some of the most important skills in human life. Progress in understanding the neural basis of childhood autism requires clear and reliable data indicating specific neuro-anatomical or neuro-physiological abnormalities. The purpose of the present study was to research localized brain dysfunction in autistic children using functional brain imaging. Regional cerebral blood flow (rCBF) was measured with positron emission tomography (PET) in 21 primary autistic children and 10 age-matched non autistic children. A statistical parametric analysis of rCBF images revealed significant bilateral temporal hypoperfusion in the associative auditory cortex (superior temporal gyrus) and in the multimodal cortex (superior temporal sulcus) in the autistic group (p<0.001). In addition, temporal hypoperfusion was detected individually in 77% of autistic children. These findings provide robust evidence of well localized functional abnormalities in autistic children located in the superior temporal lobe. Such localized abnormalities were not detected with the low resolution PET camera (14-22). This study suggests that high resolution PET camera combined with statistical parametric mapping is useful to understand developmental disorders. (authors)

  17. Transcriptome analysis of zebrafish embryogenesis using microarrays.

    Directory of Open Access Journals (Sweden)

    Sinnakaruppan Mathavan

    2005-08-01

    Full Text Available Zebrafish (Danio rerio is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html.

  18. Anatomical study of the pigs temporal bone by microdissection.

    Science.gov (United States)

    Garcia, Leandro de Borborema; Andrade, José Santos Cruz de; Testa, José Ricardo Gurgel

    2014-01-01

    Initial study of the pig`s temporal bone anatomy in order to enable a new experimental model in ear surgery. Dissection of five temporal bones of Sus scrofa pigs obtained from UNIFESP - Surgical Skills Laboratory, removed with hole saw to avoid any injury and stored in formaldehyde 10% for better conservation. The microdissection in all five temporal bone had the following steps: inspection of the outer part, external canal and tympanic membrane microscopy, mastoidectomy, removal of external ear canal and tympanic membrane, inspection of ossicular chain and middle ear. Anatomically it is located at the same position than in humans. Some landmarks usually found in humans are missing. The tympanic membrane of the pig showed to be very similar to the human, separating the external and the middle ear. The middle ear`s appearance is very similar than in humans. The ossicular chain is almost exactly the same, as well as the facial nerve, showing the same relationship with the lateral semicircular canal. The temporal bone of the pigs can be used as an alternative for training in ear surgery, especially due the facility to find it and its similarity with temporal bone of the humans.

  19. DNA Microarray Technology

    Science.gov (United States)

    Skip to main content DNA Microarray Technology Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News Features Funding Divisions Funding ...

  20. A study on temporal accuracy of OpenFOAM

    Directory of Open Access Journals (Sweden)

    Sang Bong Lee

    2017-07-01

    Full Text Available Crank–Nicolson scheme in native OpenFOAM source libraries was not able to provide 2nd order temporal accuracy of velocity and pressure since the volume flux of convective nonlinear terms was 1st accurate in time. In the present study the simplest way of getting the volume flux with 2nd order accuracy was proposed by using old fluxes. A possible numerical instability originated from an explicit estimation of volume fluxes could be handled by introducing a weighting factor which was determined by observing the ratio of the finally corrected volume flux to the intermediate volume flux at the previous step. The new calculation of volume fluxes was able to provide temporally accurate velocity and pressure with 2nd order. The improvement of temporal accuracy was validated by performing numerical simulations of 2D Taylor–Green vortex of which an exact solution was known and 2D vortex shedding from a circular cylinder.

  1. Microarray study of temperature-dependent sensitivity and selectivity of metal/oxide sensing interfaces

    Science.gov (United States)

    Tiffany, Jason; Cavicchi, Richard E.; Semancik, Stephen

    2001-02-01

    Conductometric gas microsensors offer the benefits of ppm-level sensitivity, real-time data, simple interfacing to electronics hardware, and low power consumption. The type of device we have been exploring consists of a sensor film deposited on a "microhotplate"- a 100 micron platform with built-in heating (to activate reactions on the sensing surface) and thermometry. We have been using combinatorial studies of 36-element arrays to characterize the relationship between sensor film composition, operating temperature, and response, as measured by the device's sensitivity and selectivity. Gases that have been tested on these arrays include methanol, ethanol, dichloromethane, propane, methane, acetone, benzene, hydrogen, and carbon monoxide, and are of interest in the management of environmental waste sites. These experiments compare tin oxide films modified by catalyst overlayers, and ultrathin metal seed layers. The seed layers are used as part of a chemical vapor deposition process that uses each array element's microheater to activate the deposition of SnO2, and control its microstructure. Low coverage (20 Ê) catalytic metals (Pd, Cu, Cr, In, Au) are deposited on the oxides by masked evaporation or sputtering. This presentation demonstrates the value of an array-based approach for developing film processing methods, measuring performance characteristics, and establishing reproducibility. It also illustrates how temperature-dependent response data for varied metal/oxide compositions can be used to tailor a microsensor array for a given application.

  2. Growth hormone regulation of metabolic gene expression in muscle: a microarray study in hypopituitary men.

    Science.gov (United States)

    Sjögren, Klara; Leung, Kin-Chuen; Kaplan, Warren; Gardiner-Garden, Margaret; Gibney, James; Ho, Ken K Y

    2007-07-01

    Muscle is a target of growth hormone (GH) action and a major contributor to whole body metabolism. Little is known about how GH regulates metabolic processes in muscle or the extent to which muscle contributes to changes in whole body substrate metabolism during GH treatment. To identify GH-responsive genes that regulate substrate metabolism in muscle, we studied six hypopituitary men who underwent whole body metabolic measurement and skeletal muscle biopsies before and after 2 wk of GH treatment (0.5 mg/day). Transcript profiles of four subjects were analyzed using Affymetrix GeneChips. Serum insulin-like growth factor I (IGF-I) and procollagens I and III were measured by RIA. GH increased serum IGF-I and procollagens I and III, enhanced whole body lipid oxidation, reduced carbohydrate oxidation, and stimulated protein synthesis. It induced gene expression of IGF-I and collagens in muscle. GH reduced expression of several enzymes regulating lipid oxidation and energy production. It reduced calpain 3, increased ribosomal protein L38 expression, and displayed mixed effects on genes encoding myofibrillar proteins. It increased expression of circadian gene CLOCK, and reduced that of PERIOD. In summary, GH exerted concordant effects on muscle expression and blood levels of IGF-I and collagens. It induced changes in genes regulating protein metabolism in parallel with a whole body anabolic effect. The discordance between muscle gene expression profiles and metabolic responses suggests that muscle is unlikely to contribute to GH-induced stimulation of whole body energy and lipid metabolism. GH may regulate circadian function in skeletal muscle by modulating circadian gene expression with possible metabolic consequences.

  3. Characterisation of peptide microarrays for studying antibody-antigen binding using surface plasmon resonance imagery.

    Directory of Open Access Journals (Sweden)

    Claude Nogues

    Full Text Available BACKGROUND: Non-specific binding to biosensor surfaces is a major obstacle to quantitative analysis of selective retention of analytes at immobilized target molecules. Although a range of chemical antifouling monolayers has been developed to address this problem, many macromolecular interactions still remain refractory to analysis due to the prevalent high degree of non-specific binding. We describe how we use the dynamic process of the formation of self assembling monolayers and optimise physical and chemical properties thus reducing considerably non-specific binding and allowing analysis of specific binding of analytes to immobilized target molecules. METHODOLOGY/PRINCIPAL FINDINGS: We illustrate this approach by the production of specific protein arrays for the analysis of interactions between the 65kDa isoform of human glutamate decarboxylase (GAD65 and a human monoclonal antibody. Our data illustrate that we have effectively eliminated non-specific interactions with the surface containing the immobilised GAD65 molecules. The findings have several implications. First, this approach obviates the dubious process of background subtraction and gives access to more accurate kinetic and equilibrium values that are no longer contaminated by multiphase non-specific binding. Second, an enhanced signal to noise ratio increases not only the sensitivity but also confidence in the use of SPR to generate kinetic constants that may then be inserted into van't Hoff type analyses to provide comparative DeltaG, DeltaS and DeltaH values, making this an efficient, rapid and competitive alternative to ITC measurements used in drug and macromolecular-interaction mechanistic studies. Third, the accuracy of the measurements allows the application of more intricate interaction models than simple Langmuir monophasic binding. CONCLUSIONS: The detection and measurement of antibody binding by the type 1 diabetes autoantigen GAD65 represents an example of an antibody

  4. Metric learning for DNA microarray data analysis

    International Nuclear Information System (INIS)

    Takeuchi, Ichiro; Nakagawa, Masao; Seto, Masao

    2009-01-01

    In many microarray studies, gene set selection is an important preliminary step for subsequent main task such as tumor classification, cancer subtype identification, etc. In this paper, we investigate the possibility of using metric learning as an alternative to gene set selection. We develop a simple metric learning algorithm aiming to use it for microarray data analysis. Exploiting a property of the algorithm, we introduce a novel approach for extending the metric learning to be adaptive. We apply the algorithm to previously studied microarray data on malignant lymphoma subtype identification.

  5. MARS: Microarray analysis, retrieval, and storage system

    Directory of Open Access Journals (Sweden)

    Scheideler Marcel

    2005-04-01

    Full Text Available Abstract Background Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. Results MARS (Microarray Analysis and Retrieval System provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS, a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. Conclusion We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at http://genome.tugraz.at.

  6. Microarray based study on virulence-associated genes and resistance determinants of Staphylococcus aureus isolates from cattle.

    Science.gov (United States)

    Monecke, Stefan; Kuhnert, Peter; Hotzel, Helmut; Slickers, Peter; Ehricht, Ralf

    2007-11-15

    Staphylococcus aureus is a common pathogen which can colonise and infect not only man, but also domestic animals. Especially, infection of cattle is of high economic relevance as S. aureus is an important causal agent of bovine mastitis. In the present contribution, a DNA microarray was applied for the study of 144 different gene targets, including resistance genes and genes encoding exotoxins, in S. aureus isolated from cows. One hundred and twenty-eight isolates from Germany and Switzerland were tested. These isolates were assigned to 20 different strains and nine clonal complexes. The majority of isolates belonged either to apparently closely related clonal complexes 8, 25, and 97 (together 34.4%) or were related to the sequenced bovine strain RF122 (48.4%). Notable characteristics of S. aureus of bovine origin are the carriage of intact haemolysin beta (in 82% of isolates tested), the absence of staphylokinase (in 89.1%), the presence of allelic variants of several exotoxins such as toxic shock syndrome toxin and enterotoxin N, and the occurrence of the leukocidin lukF-P83/lukM (in 53.1%). Two isolates were methicillin-resistant S. aureus (MRSA). One of them was a clonal complex 8 MRSA related to the epidemic MRSA strain Irish 01. The other one belonged to ST398/spa-type 34 resembling a newly emerging MRSA strain which has been described to occur in humans as well as in domestic animals. The presence of these two strains highlights the possibility of transfers of S. aureus strains between different host species.

  7. Spatial Temporal Modelling of Particulate Matter for Health Effects Studies

    Science.gov (United States)

    Hamm, N. A. S.

    2016-10-01

    Epidemiological studies of the health effects of air pollution require estimation of individual exposure. It is not possible to obtain measurements at all relevant locations so it is necessary to predict at these space-time locations, either on the basis of dispersion from emission sources or by interpolating observations. This study used data obtained from a low-cost sensor network of 32 air quality monitoring stations in the Dutch city of Eindhoven, which make up the ILM (innovative air (quality) measurement system). These stations currently provide PM10 and PM2.5 (particulate matter less than 10 and 2.5 m in diameter), aggregated to hourly means. The data provide an unprecedented level of spatial and temporal detail for a city of this size. Despite these benefits the time series of measurements is characterized by missing values and noisy values. In this paper a space-time analysis is presented that is based on a dynamic model for the temporal component and a Gaussian process geostatistical for the spatial component. Spatial-temporal variability was dominated by the temporal component, although the spatial variability was also substantial. The model delivered accurate predictions for both isolated missing values and 24-hour periods of missing values (RMSE = 1.4 μg m-3 and 1.8 μg m-3 respectively). Outliers could be detected by comparison to the 95% prediction interval. The model shows promise for predicting missing values, outlier detection and for mapping to support health impact studies.

  8. Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution

    DEFF Research Database (Denmark)

    Novak, Jaroslav P; Kim, Seon-Young; Xu, Jun

    2006-01-01

    BACKGROUND: DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inherent variability of DNA microarray data, many new statistical methods have...

  9. Middle and Inferior Temporal Gyrus Gray Matter Volume Abnormalities in Chronic Schizophrenia: An MRI Study

    OpenAIRE

    Onitsuka, Toshiaki; Shenton, Martha E.; Salisbury, Dean F.; Dickey, Chandlee C.; Kasai, Kiyoto; Toner, Sarah K.; Frumin, Melissa; Kikinis, Ron; Jolesz, Ferenc A.; McCarley, Robert W.

    2004-01-01

    Objective: The middle temporal gyrus and inferior temporal gyrus subserve language and semantic memory processing, visual perception, and multimodal sensory integration. Functional deficits in these cognitive processes have been well documented in patients with schizophrenia. However, there have been few in vivo structural magnetic resonance imaging (MRI) studies of the middle temporal gyrus and inferior temporal gyrus in schizophrenia. Method: Middle temporal gyrus and inferior temporal gyru...

  10. Directional selection in temporally replicated studies is remarkably consistent.

    Science.gov (United States)

    Morrissey, Michael B; Hadfield, Jarrod D

    2012-02-01

    Temporal variation in selection is a fundamental determinant of evolutionary outcomes. A recent paper presented a synthetic analysis of temporal variation in selection in natural populations. The authors concluded that there is substantial variation in the strength and direction of selection over time, but acknowledged that sampling error would result in estimates of selection that were more variable than the true values. We reanalyze their dataset using techniques that account for the necessary effect of sampling error to inflate apparent levels of variation and show that directional selection is remarkably constant over time, both in magnitude and direction. Thus we cannot claim that the available data support the existence of substantial temporal heterogeneity in selection. Nonetheless, we conject that temporal variation in selection could be important, but that there are good reasons why it may not appear in the available data. These new analyses highlight the importance of applying techniques that estimate parameters of the distribution of selection, rather than parameters of the distribution of estimated selection (which will reflect both sampling error and "real" variation in selection); indeed, despite availability of methods for the former, focus on the latter has been common in synthetic reviews of the aspects of selection in nature, and can lead to serious misinterpretations. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  11. Radioactive cDNA microarray in neurospsychiatry

    International Nuclear Information System (INIS)

    Choe, Jae Gol; Shin, Kyung Ho; Lee, Min Soo; Kim, Meyoung Kon

    2003-01-01

    Microarray technology allows the simultaneous analysis of gene expression patterns of thousands of genes, in a systematic fashion, under a similar set of experimental conditions, thus making the data highly comparable. In some cases arrays are used simply as a primary screen leading to downstream molecular characterization of individual gene candidates. In other cases, the goal of expression profiling is to begin to identify complex regulatory networks underlying developmental processes and disease states. Microarrays were originally used with cell lines or other simple model systems. More recently, microarrays have been used in the analysis of more complex biological tissues including neural systems and the brain. The application of cDNA arrays in neuropsychiatry has lagged behind other fields for a number of reasons. These include a requirement for a large amount of input probe RNA in fluorescent-glass based array systems and the cellular complexity introduced by multicellular brain and neural tissues. An additional factor that impacts the general use of microarrays in neuropsychiatry is the lack of availability of sequenced clone sets from model systems. While human cDNA clones have been widely available, high quality rat, mouse, and drosophilae, among others are just becoming widely available. A final factor in the application of cDNA microarrays in neuropsychiatry is cost of commercial arrays. As academic microarray facilitates become more commonplace custom made arrays will become more widely available at a lower cost allowing more widespread applications. In summary, microarray technology is rapidly having an impact on many areas of biomedical research. Radioisotope-nylon based microarrays offer alternatives that may in some cases be more sensitive, flexible, inexpensive, and universal as compared to other array formats, such as fluorescent-glass arrays. In some situations of limited RNA or exotic species, radioactive membrane microarrays may be the most

  12. Radioactive cDNA microarray in neurospsychiatry

    Energy Technology Data Exchange (ETDEWEB)

    Choe, Jae Gol; Shin, Kyung Ho; Lee, Min Soo; Kim, Meyoung Kon [Korea University Medical School, Seoul (Korea, Republic of)

    2003-02-01

    Microarray technology allows the simultaneous analysis of gene expression patterns of thousands of genes, in a systematic fashion, under a similar set of experimental conditions, thus making the data highly comparable. In some cases arrays are used simply as a primary screen leading to downstream molecular characterization of individual gene candidates. In other cases, the goal of expression profiling is to begin to identify complex regulatory networks underlying developmental processes and disease states. Microarrays were originally used with cell lines or other simple model systems. More recently, microarrays have been used in the analysis of more complex biological tissues including neural systems and the brain. The application of cDNA arrays in neuropsychiatry has lagged behind other fields for a number of reasons. These include a requirement for a large amount of input probe RNA in fluorescent-glass based array systems and the cellular complexity introduced by multicellular brain and neural tissues. An additional factor that impacts the general use of microarrays in neuropsychiatry is the lack of availability of sequenced clone sets from model systems. While human cDNA clones have been widely available, high quality rat, mouse, and drosophilae, among others are just becoming widely available. A final factor in the application of cDNA microarrays in neuropsychiatry is cost of commercial arrays. As academic microarray facilitates become more commonplace custom made arrays will become more widely available at a lower cost allowing more widespread applications. In summary, microarray technology is rapidly having an impact on many areas of biomedical research. Radioisotope-nylon based microarrays offer alternatives that may in some cases be more sensitive, flexible, inexpensive, and universal as compared to other array formats, such as fluorescent-glass arrays. In some situations of limited RNA or exotic species, radioactive membrane microarrays may be the most

  13. A Comparative Genomic Study in Schizophrenic and in Bipolar Disorder Patients, Based on Microarray Expression Profiling Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Marianthi Logotheti

    2013-01-01

    Full Text Available Schizophrenia affecting almost 1% and bipolar disorder affecting almost 3%–5% of the global population constitute two severe mental disorders. The catecholaminergic and the serotonergic pathways have been proved to play an important role in the development of schizophrenia, bipolar disorder, and other related psychiatric disorders. The aim of the study was to perform and interpret the results of a comparative genomic profiling study in schizophrenic patients as well as in healthy controls and in patients with bipolar disorder and try to relate and integrate our results with an aberrant amino acid transport through cell membranes. In particular we have focused on genes and mechanisms involved in amino acid transport through cell membranes from whole genome expression profiling data. We performed bioinformatic analysis on raw data derived from four different published studies. In two studies postmortem samples from prefrontal cortices, derived from patients with bipolar disorder, schizophrenia, and control subjects, have been used. In another study we used samples from postmortem orbitofrontal cortex of bipolar subjects while the final study was performed based on raw data from a gene expression profiling dataset in the postmortem superior temporal cortex of schizophrenics. The data were downloaded from NCBI's GEO datasets.

  14. PATMA: parser of archival tissue microarray

    Directory of Open Access Journals (Sweden)

    Lukasz Roszkowiak

    2016-12-01

    Full Text Available Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images.

  15. Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata, by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs

    Directory of Open Access Journals (Sweden)

    Sebastian Boltaña

    2017-02-01

    Full Text Available This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge. The developed microarray was further validated by analysing monocyte/macrophage activation profiles after challenge with two Gram-negative bacterial pathogen-associated molecular patterns (PAMPs; lipopolysaccharide (LPS and peptidoglycan (PGN. Of the approximately 10,000 EST sequenced, we obtained a total of 6837 EST longer than 100 nt, with 3778 and 3059 EST obtained from the bacterial-primed and from the viral-primed cDNA libraries, respectively. Functional classification of contigs from the bacterial- and viral-primed cDNA libraries by Gene Ontology (GO showed that the top five represented categories were equally represented in the two libraries: metabolism (approximately 24% of the total number of contigs, carrier proteins/membrane transport (approximately 15%, effectors/modulators and cell communication (approximately 11%, nucleoside, nucleotide and nucleic acid metabolism (approximately 7.5% and intracellular transducers/signal transduction (approximately 5%. Transcriptome analyses using this enriched oligonucleotide platform identified differential shifts in the response to PGN and LPS in macrophage-like cells, highlighting responsive gene-cassettes tightly related to PAMP host recognition. As observed in other fish species, PGN is a powerful activator of the inflammatory response in S. aurata macrophage-like cells. We have developed and validated an oligonucleotide microarray (SAQ that provides a platform enriched for the study

  16. Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata, by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs.

    Science.gov (United States)

    Boltaña, Sebastian; Castellana, Barbara; Goetz, Giles; Tort, Lluis; Teles, Mariana; Mulero, Victor; Novoa, Beatriz; Figueras, Antonio; Goetz, Frederick W; Gallardo-Escarate, Cristian; Planas, Josep V; Mackenzie, Simon

    2017-02-03

    This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ) to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST) from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge. The developed microarray was further validated by analysing monocyte/macrophage activation profiles after challenge with two Gram-negative bacterial pathogen-associated molecular patterns (PAMPs; lipopolysaccharide (LPS) and peptidoglycan (PGN)). Of the approximately 10,000 EST sequenced, we obtained a total of 6837 EST longer than 100 nt, with 3778 and 3059 EST obtained from the bacterial-primed and from the viral-primed cDNA libraries, respectively. Functional classification of contigs from the bacterial- and viral-primed cDNA libraries by Gene Ontology (GO) showed that the top five represented categories were equally represented in the two libraries: metabolism (approximately 24% of the total number of contigs), carrier proteins/membrane transport (approximately 15%), effectors/modulators and cell communication (approximately 11%), nucleoside, nucleotide and nucleic acid metabolism (approximately 7.5%) and intracellular transducers/signal transduction (approximately 5%). Transcriptome analyses using this enriched oligonucleotide platform identified differential shifts in the response to PGN and LPS in macrophage-like cells, highlighting responsive gene-cassettes tightly related to PAMP host recognition. As observed in other fish species, PGN is a powerful activator of the inflammatory response in S. aurata macrophage-like cells. We have developed and validated an oligonucleotide microarray (SAQ) that provides a platform enriched for the study of gene

  17. Efficacy of functional microarray of microneedles combined with topical tranexamic acid for melasma: A randomized, self-controlled, split-face study.

    Science.gov (United States)

    Xu, Yang; Ma, Renyan; Juliandri, Juliandri; Wang, Xiaoyan; Xu, Bai; Wang, Daguang; Lu, Yan; Zhou, Bingrong; Luo, Dan

    2017-05-01

    To evaluate the efficacy of a functional microarray of microneedles (MNs) plus topical tranexamic acid (TA) for melasma in middle-aged women in China.Thirty female subjects with melasma were enrolled in this study. The left or right side of the face was chosen randomly to be pretreated with a functional microarray of MNs, followed by topical 0.5% TA solution once per week for 12 weeks. The other half-face was the control, treated with a sham device plus topical 0.5% TA solution. At baseline and at weeks 4, 8, and 12 of treatment, clinical (photographic) evaluations and parameters determined by Visia were recorded. At baseline and week 12, patient satisfaction scores and the biophysical parameters measured by Mexameter were also recorded. Side effects were evaluated at baseline and at the end of the 12 weeks.In total, 28 women (93.3%) completed the study. The brown spots' scores measured by Visia were significantly lower on the combined therapy side than on the control side at 12 weeks after starting treatment; there was no significant difference between sides at 4 or 8 weeks. After 12 weeks, melanin index (MI) decreased significantly in both 2 groups, and the MI was significantly less on the combined side at week 12. Transepidermal water loss, roughness, skin hydration, skin elasticity, and erythema index showed no significant differences between 2 sides at baseline, 4, 8, and 12 weeks after treatment. Physicians' evaluations of photographs showed better results at week 12 with combined therapy: >25% improvement was observed in the MNs plus TA side in 25 patients, and in the TA side in only 10 patients. Subjective satisfaction scores on both sides increased significantly. The participants were more satisfied with the results of the combined therapy side than the control side. No obvious adverse reactions were observed throughout the study.Combined therapy with a functional microarray of MNs and topical TA solution is a promising treatment for melasma.

  18. Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study

    Directory of Open Access Journals (Sweden)

    Beltrame Francesco

    2010-11-01

    Full Text Available Abstract Background Tissue MicroArray technology aims to perform immunohistochemical staining on hundreds of different tissue samples simultaneously. It allows faster analysis, considerably reducing costs incurred in staining. A time consuming phase of the methodology is the selection of tissue areas within paraffin blocks: no utilities have been developed for the identification of areas to be punched from the donor block and assembled in the recipient block. Results The presented work supports, in the specific case of a primary subtype of breast cancer (tubular breast cancer, the semi-automatic discrimination and localization between normal and pathological regions within the tissues. The diagnosis is performed by analysing specific morphological features of the sample such as the absence of a double layer of cells around the lumen and the decay of a regular glands-and-lobules structure. These features are analysed using an algorithm which performs the extraction of morphological parameters from images and compares them to experimentally validated threshold values. Results are satisfactory since in most of the cases the automatic diagnosis matches the response of the pathologists. In particular, on a total of 1296 sub-images showing normal and pathological areas of breast specimens, algorithm accuracy, sensitivity and specificity are respectively 89%, 84% and 94%. Conclusions The proposed work is a first attempt to demonstrate that automation in the Tissue MicroArray field is feasible and it can represent an important tool for scientists to cope with this high-throughput technique.

  19. Microarray Study of Pathway Analysis Expression Profile Associated with MicroRNA-29a with Regard to Murine Cholestatic Liver Injuries

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    Sung-Chou Li

    2016-03-01

    Full Text Available Accumulating evidence demonstrates that microRNA-29 (miR-29 expression is prominently decreased in patients with hepatic fibrosis, which consequently stimulates hepatic stellate cells’ (HSCs activation. We used a cDNA microarray study to gain a more comprehensive understanding of genome-wide gene expressions by adjusting miR-29a expression in a bile duct-ligation (BDL animal model. Methods: Using miR-29a transgenic mice and wild-type littermates and applying the BDL mouse model, we characterized the function of miR-29a with regard to cholestatic liver fibrosis. Pathway enrichment analysis and/or specific validation were performed for differentially expressed genes found within the comparisons. Results: Analysis of the microarray data identified a number of differentially expressed genes due to the miR-29a transgene, BDL, or both. Additional pathway enrichment analysis revealed that TGF-β signaling had a significantly differential activated pathway depending on the occurrence of miR-29a overexpression or the lack thereof. Furthermore, overexpression was found to elicit changes in Wnt/β-catenin after BDL. Conclusion: This study verified that an elevated miR-29a level could alleviate liver fibrosis caused by cholestasis. Furthermore, the protective effects of miR-29a correlate with the downregulation of TGF-β and associated with Wnt/β-catenin signal pathway following BDL.

  20. Extended -Regular Sequence for Automated Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jin Hee-Jeong

    2006-01-01

    Full Text Available Microarray study enables us to obtain hundreds of thousands of expressions of genes or genotypes at once, and it is an indispensable technology for genome research. The first step is the analysis of scanned microarray images. This is the most important procedure for obtaining biologically reliable data. Currently most microarray image processing systems require burdensome manual block/spot indexing work. Since the amount of experimental data is increasing very quickly, automated microarray image analysis software becomes important. In this paper, we propose two automated methods for analyzing microarray images. First, we propose the extended -regular sequence to index blocks and spots, which enables a novel automatic gridding procedure. Second, we provide a methodology, hierarchical metagrid alignment, to allow reliable and efficient batch processing for a set of microarray images. Experimental results show that the proposed methods are more reliable and convenient than the commercial tools.

  1. Activations in temporal areas using visual and auditory naming stimuli: A language fMRI study in temporal lobe epilepsy.

    Science.gov (United States)

    Gonzálvez, Gloria G; Trimmel, Karin; Haag, Anja; van Graan, Louis A; Koepp, Matthias J; Thompson, Pamela J; Duncan, John S

    2016-12-01

    Verbal fluency functional MRI (fMRI) is used for predicting language deficits after anterior temporal lobe resection (ATLR) for temporal lobe epilepsy (TLE), but primarily engages frontal lobe areas. In this observational study we investigated fMRI paradigms using visual and auditory stimuli, which predominately involve language areas resected during ATLR. Twenty-three controls and 33 patients (20 left (LTLE), 13 right (RTLE)) were assessed using three fMRI paradigms: verbal fluency, auditory naming with a contrast of auditory reversed speech; picture naming with a contrast of scrambled pictures and blurred faces. Group analysis showed bilateral temporal activations for auditory naming and picture naming. Correcting for auditory and visual input (by subtracting activations resulting from auditory reversed speech and blurred pictures/scrambled faces respectively) resulted in left-lateralised activations for patients and controls, which was more pronounced for LTLE compared to RTLE patients. Individual subject activations at a threshold of T>2.5, extent >10 voxels, showed that verbal fluency activated predominantly the left inferior frontal gyrus (IFG) in 90% of LTLE, 92% of RTLE, and 65% of controls, compared to right IFG activations in only 15% of LTLE and RTLE and 26% of controls. Middle temporal (MTG) or superior temporal gyrus (STG) activations were seen on the left in 30% of LTLE, 23% of RTLE, and 52% of controls, and on the right in 15% of LTLE, 15% of RTLE, and 35% of controls. Auditory naming activated temporal areas more frequently than did verbal fluency (LTLE: 93%/73%; RTLE: 92%/58%; controls: 82%/70% (left/right)). Controlling for auditory input resulted in predominantly left-sided temporal activations. Picture naming resulted in temporal lobe activations less frequently than did auditory naming (LTLE 65%/55%; RTLE 53%/46%; controls 52%/35% (left/right)). Controlling for visual input had left-lateralising effects. Auditory and picture naming activated

  2. Carbon ion irradiation of the human prostate cancer cell line PC3: A whole genome microarray study

    Science.gov (United States)

    SUETENS, ANNELIES; MOREELS, MARJAN; QUINTENS, ROEL; CHIRIOTTI, SABINA; TABURY, KEVIN; MICHAUX, ARLETTE; GRÉGOIRE, VINCENT; BAATOUT, SARAH

    2014-01-01

    Hadrontherapy is a form of external radiation therapy, which uses beams of charged particles such as carbon ions. Compared to conventional radiotherapy with photons, the main advantage of carbon ion therapy is the precise dose localization along with an increased biological effectiveness. The first results obtained from prostate cancer patients treated with carbon ion therapy showed good local tumor control and survival rates. In view of this advanced treatment modality we investigated the effects of irradiation with different beam qualities on gene expression changes in the PC3 prostate adenocarcinoma cell line. For this purpose, PC3 cells were irradiated with various doses (0.0, 0.5 and 2.0 Gy) of carbon ions (LET=33.7 keV/μm) at the beam of the Grand Accélérateur National d’Ions Lourds (Caen, France). Comparative experiments with X-rays were performed at the Belgian Nuclear Research Centre. Genome-wide gene expression was analyzed using microarrays. Our results show a downregulation in many genes involved in cell cycle and cell organization processes after 2.0 Gy irradiation. This effect was more pronounced after carbon ion irradiation compared with X-rays. Furthermore, we found a significant downregulation of many genes related to cell motility. Several of these changes were confirmed using qPCR. In addition, recurrence-free survival analysis of prostate cancer patients based on one of these motility genes (FN1) revealed that patients with low expression levels had a prolonged recurrence-free survival time, indicating that this gene may be a potential prognostic biomarker for prostate cancer. Understanding how different radiation qualities affect the cellular behavior of prostate cancer cells is important to improve the clinical outcome of cancer radiation therapy. PMID:24504141

  3. miRNAs in lung cancer - Studying complex fingerprints in patient's blood cells by microarray experiments

    International Nuclear Information System (INIS)

    Keller, Andreas; Leidinger, Petra; Borries, Anne; Wendschlag, Anke; Wucherpfennig, Frank; Scheffler, Matthias; Huwer, Hanno; Lenhof, Hans-Peter; Meese, Eckart

    2009-01-01

    Deregulated miRNAs are found in cancer cells and recently in blood cells of cancer patients. Due to their inherent stability miRNAs may offer themselves for blood based tumor diagnosis. Here we addressed the question whether there is a sufficient number of miRNAs deregulated in blood cells of cancer patients to be able to distinguish between cancer patients and controls. We synthesized 866 human miRNAs and miRNA star sequences as annotated in the Sanger miRBase onto a microarray designed by febit biomed gmbh. Using the fully automated Geniom Real Time Analyzer platform, we analyzed the miRNA expression in 17 blood cell samples of patients with non-small cell lung carcinomas (NSCLC) and in 19 blood samples of healthy controls. Using t-test, we detected 27 miRNAs significantly deregulated in blood cells of lung cancer patients as compared to the controls. Some of these miRNAs were validated using qRT-PCR. To estimate the value of each deregulated miRNA, we grouped all miRNAs according to their diagnostic information that was measured by Mutual Information. Using a subset of 24 miRNAs, a radial basis function Support Vector Machine allowed for discriminating between blood cellsamples of tumor patients and controls with an accuracy of 95.4% [94.9%-95.9%], a specificity of 98.1% [97.3%-98.8%], and a sensitivity of 92.5% [91.8%-92.5%]. Our findings support the idea that neoplasia may lead to a deregulation of miRNA expression in blood cells of cancer patients compared to blood cells of healthy individuals. Furthermore, we provide evidence that miRNA patterns can be used to detect human cancers from blood cells

  4. Temporal focus, temporal distance, and mind-wandering valence: Results from an experience sampling and an experimental study.

    Science.gov (United States)

    Spronken, Maitta; Holland, Rob W; Figner, Bernd; Dijksterhuis, Ap

    2016-04-01

    When mind-wandering, people may think about events that happened in the past, or events that may happen in the future. Using experience sampling, we first aimed to replicate the finding that future-oriented thoughts show a greater positivity bias than past-oriented thoughts. Furthermore, we investigated whether there is a relation between the temporal distance of past- and future-oriented thoughts and the frequency of positive thoughts, a factor that has received little attention in previous work. Second, we experimentally investigated the relation between temporal focus, temporal distance, and thought valence. Both studies showed that future-oriented thoughts were more positive compared to past-oriented thoughts. Regarding temporal distance, thoughts about the distant past and future were more positive than thoughts about the near past and future in the experiment. However, the experience sampling study did not provide clear insight into this relation. Potential theoretical and methodological explanations for these findings are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Study of a temporal bone of Homo heildelbergensis.

    Science.gov (United States)

    Urquiza, Rafael; Botella, Miguel; Ciges, Miguel

    2005-05-01

    The characteristic features of the Hh specimen conformed to those of other Pleistocene human fossils, indicating strong cranial structures and a heavy mandible. The mastoid was large and suggested a powerful sternocleidomastoid muscle. The inner ear and tympanic cavities were similar in size and orientation, suggesting that their functions were probably similar. Our observations suggest that the left ear of this Hh specimen was healthy. The large canaliculo-fenestral angle confirms that this ancestor was bipedal. It also strongly suggests that Hh individuals were predisposed to develop certain pathologies of the labyrinth capsule associated with bipedalism, in particular otosclerosis. We studied a temporal bone of Homo heidelbergensis (Hh) in order to investigate the clinical and physiological implications of certain morphological features, especially those associated with the evolutionary reorganization of the inner ear. The bone, found in a breach of a cave near MAáaga in southern Spain, together with Middle Upper Pleistocene faunal remains, is >300000 years old. Four analytical methods were employed. A 3D high-resolution surface laser scan was used for anatomical measurements. For the sectional analysis of the middle and inner ears of Hh we used high-resolution CT, simultaneously studying a normal temporal bone from Homo sapiens sapiens (Hss). To study the middle and inner ear spaces we used 3D reconstruction CT preceded by an intra-bone air shielding technique. To examine the tympanic cavities and measure the canaliculo fenestral angle, we used a special minimally invasive endoscopic procedure. The surface, sectional and 3D CT examinations showed that the Hh specimen was generally more robust and larger than the Hss specimen. It had a large glenoid fossa. The external meatus was wide and deep. The middle ear, and especially the mastoid, was large and widely pneumatized. There were no appreciable differences in the position and size of the labyrinthine spaces

  6. The Involvement of Thaumatin-Like Proteins in Plant Food Cross-Reactivity: A Multicenter Study Using a Specific Protein Microarray

    Science.gov (United States)

    Palacín, Arantxa; Rivas, Luis A.; Gómez-Casado, Cristina; Aguirre, Jacobo; Tordesillas, Leticia; Bartra, Joan; Blanco, Carlos; Carrillo, Teresa; Cuesta-Herranz, Javier; Bonny, José A. Cumplido; Flores, Enrique; García-Alvarez-Eire, Mar G.; García-Nuñez, Ignacio; Fernández, Francisco J.; Gamboa, Pedro; Muñoz, Rosa; Sánchez-Monge, Rosa; Torres, Maria; Losada, Susana Varela; Villalba, Mayte; Vega, Francisco; Parro, Victor; Blanca, Miguel; Salcedo, Gabriel; Díaz-Perales, Araceli

    2012-01-01

    Cross-reactivity of plant foods is an important phenomenon in allergy, with geographical variations with respect to the number and prevalence of the allergens involved in this process, whose complexity requires detailed studies. We have addressed the role of thaumatin-like proteins (TLPs) in cross-reactivity between fruit and pollen allergies. A representative panel of 16 purified TLPs was printed onto an allergen microarray. The proteins selected belonged to the sources most frequently associated with peach allergy in representative regions of Spain. Sera from two groups of well characterized patients, one with allergy to Rosaceae fruit (FAG) and another against pollens but tolerant to food-plant allergens (PAG), were obtained from seven geographical areas with different environmental pollen profiles. Cross-reactivity between members of this family was demonstrated by inhibition assays. Only 6 out of 16 purified TLPs showed noticeable allergenic activity in the studied populations. Pru p 2.0201, the peach TLP (41%), chestnut TLP (24%) and plane pollen TLP (22%) proved to be allergens of probable relevance to fruit allergy, being mainly associated with pollen sensitization, and strongly linked to specific geographical areas such as Barcelona, Bilbao, the Canary Islands and Madrid. The patients exhibited >50% positive response to Pru p 2.0201 and to chestnut TLP in these specific areas. Therefore, their recognition patterns were associated with the geographical area, suggesting a role for pollen in the sensitization of these allergens. Finally, the co-sensitizations of patients considering pairs of TLP allergens were analyzed by using the co-sensitization graph associated with an allergen microarray immunoassay. Our data indicate that TLPs are significant allergens in plant food allergy and should be considered when diagnosing and treating pollen-food allergy. PMID:22970164

  7. The involvement of thaumatin-like proteins in plant food cross-reactivity: a multicenter study using a specific protein microarray.

    Directory of Open Access Journals (Sweden)

    Arantxa Palacín

    Full Text Available Cross-reactivity of plant foods is an important phenomenon in allergy, with geographical variations with respect to the number and prevalence of the allergens involved in this process, whose complexity requires detailed studies. We have addressed the role of thaumatin-like proteins (TLPs in cross-reactivity between fruit and pollen allergies. A representative panel of 16 purified TLPs was printed onto an allergen microarray. The proteins selected belonged to the sources most frequently associated with peach allergy in representative regions of Spain. Sera from two groups of well characterized patients, one with allergy to Rosaceae fruit (FAG and another against pollens but tolerant to food-plant allergens (PAG, were obtained from seven geographical areas with different environmental pollen profiles. Cross-reactivity between members of this family was demonstrated by inhibition assays. Only 6 out of 16 purified TLPs showed noticeable allergenic activity in the studied populations. Pru p 2.0201, the peach TLP (41%, chestnut TLP (24% and plane pollen TLP (22% proved to be allergens of probable relevance to fruit allergy, being mainly associated with pollen sensitization, and strongly linked to specific geographical areas such as Barcelona, Bilbao, the Canary Islands and Madrid. The patients exhibited >50% positive response to Pru p 2.0201 and to chestnut TLP in these specific areas. Therefore, their recognition patterns were associated with the geographical area, suggesting a role for pollen in the sensitization of these allergens. Finally, the co-sensitizations of patients considering pairs of TLP allergens were analyzed by using the co-sensitization graph associated with an allergen microarray immunoassay. Our data indicate that TLPs are significant allergens in plant food allergy and should be considered when diagnosing and treating pollen-food allergy.

  8. Applications of temporal kernel canonical correlation analysis in adherence studies.

    Science.gov (United States)

    John, Majnu; Lencz, Todd; Ferbinteanu, Janina; Gallego, Juan A; Robinson, Delbert G

    2017-10-01

    Adherence to medication is often measured as a continuous outcome but analyzed as a dichotomous outcome due to lack of appropriate tools. In this paper, we illustrate the use of the temporal kernel canonical correlation analysis (tkCCA) as a method to analyze adherence measurements and symptom levels on a continuous scale. The tkCCA is a novel method developed for studying the relationship between neural signals and hemodynamic response detected by functional MRI during spontaneous activity. Although the tkCCA is a powerful tool, it has not been utilized outside the application that it was originally developed for. In this paper, we simulate time series of symptoms and adherence levels for patients with a hypothetical brain disorder and show how the tkCCA can be used to understand the relationship between them. We also examine, via simulations, the behavior of the tkCCA under various missing value mechanisms and imputation methods. Finally, we apply the tkCCA to a real data example of psychotic symptoms and adherence levels obtained from a study based on subjects with a first episode of schizophrenia, schizophreniform or schizoaffective disorder.

  9. The Importance of Normalization on Large and Heterogeneous Microarray Datasets

    Science.gov (United States)

    DNA microarray technology is a powerful functional genomics tool increasingly used for investigating global gene expression in environmental studies. Microarrays can also be used in identifying biological networks, as they give insight on the complex gene-to-gene interactions, ne...

  10. The application of DNA microarrays in gene expression analysis

    NARCIS (Netherlands)

    Hal, van N.L.W.; Vorst, O.; Houwelingen, van A.M.M.L.; Kok, E.J.; Peijnenburg, A.A.C.M.; Aharoni, A.; Tunen, van A.J.; Keijer, J.

    2000-01-01

    DNA microarray technology is a new and powerful technology that will substantially increase the speed of molecular biological research. This paper gives a survey of DNA microarray technology and its use in gene expression studies. The technical aspects and their potential improvements are discussed.

  11. A Microarray Study of Carpet-Shell Clam (Ruditapes decussatus Shows Common and Organ-Specific Growth-Related Gene Expression Differences in Gills and Digestive Gland

    Directory of Open Access Journals (Sweden)

    Carlos Saavedra

    2017-11-01

    Full Text Available Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes. A total of 356 differentially expressed genes (DEG were found. We tested the hypothesis that differential expression might be concentrated at the growth control gene core (GCGC, i.e., the set of genes that underlie the molecular mechanisms of genetic control of tissue and organ growth and body size, as demonstrated in model organisms. The GCGC includes the genes coding for enzymes of the insulin/insulin-like growth factor signaling pathway (IIS, enzymes of four additional signaling pathways (Raf/Ras/Mapk, Jnk, TOR, and Hippo, and transcription factors acting at the end of those pathways. Only two out of 97 GCGC genes present in the microarray showed differential expression, indicating a very little contribution of GCGC genes to growth-related differential gene expression. Forty eight DEGs were shared by both organs, with gene ontology (GO annotations corresponding to transcription regulation, RNA splicing, sugar metabolism, protein catabolism, immunity, defense against pathogens, and fatty acid biosynthesis. GO term enrichment tests indicated that genes related to growth regulation, development and morphogenesis, extracellular matrix proteins, and proteolysis were overrepresented in the gills. In the digestive gland overrepresented GO terms referred to gene expression control through chromatin rearrangement, RAS-related small GTPases, glucolysis, and energy metabolism. These analyses suggest a relevant role of, among others

  12. Toxicity of Doxorubicin on Pig Liver After Chemoembolization with Doxorubicin-loaded Microspheres: A Pilot DNA-microarrays and Histology Study

    Energy Technology Data Exchange (ETDEWEB)

    Verret, Valentin, E-mail: valentin.verret@archimmed.com; Namur, Julien; Ghegediban, Saieda Homayra [ArchimMed (France); Wassef, Michel [University of Paris 7-Denis Diderot, Department of Pathology, Faculty of Medicine, AP-HP Hopital Lariboisiere (France); Moine, Laurence [Universite Paris Sud, Faculte de Pharmacie, UMR CNRS 8612, IFR 141-ITFM (France); Bonneau, Michel [AP-HP/INRA, Centre de Recherche En Imagerie Interventionnelle (France); Pelage, Jean-Pierre [AP-HP Hopital Ambroise Pare, Department of Interventional Radiology (France); Laurent, Alexandre [AP-HP/INRA, Centre de Recherche En Imagerie Interventionnelle (France)

    2013-02-15

    The potential mechanisms accounting for the hepatotoxicity of doxorubicin-loaded microspheres in chemoembolization were examined by combining histology and DNA-microarray techniques.The left hepatic arteries of two pigs were embolized with 1 mL of doxorubicin-loaded (25 mg; (DoxMS)) or non-loaded (BlandMS) microspheres. The histopathological effects of the embolization were analyzed at 1 week. RNAs extracted from both the embolized and control liver areas were hybridized onto Agilent porcine microarrays. Genes showing significantly different expression (p < 0.01; fold-change > 2) between two groups were classified by biological process. At 1 week after embolization, DoxMS caused arterial and parenchymal necrosis in 51 and 38 % of embolized vessels, respectively. By contrast, BlandMS did not cause any tissue damage. Up-regulated genes following embolization with DoxMS (vs. BlandMS, n = 353) were mainly involved in cell death, apoptosis, and metabolism of doxorubicin. Down-regulated genes (n = 120) were mainly related to hepatic functions, including enzymes of lipid and carbohydrate metabolisms. Up-regulated genes included genes related to cell proliferation (growth factors and transcription factors), tissue remodeling (MMPs and several collagen types), inflammatory reaction (interleukins and chemokines), and angiogenesis (angiogenic factors and HIF1a pathway), all of which play an important role in liver healing and regeneration. DoxMS caused lesions to the liver, provoked cell death, and disturbed liver metabolism. An inflammatory repair process with cell proliferation, tissue remodeling, and angiogenesis was rapidly initiated during the first week after chemoembolization. This pilot study provides a comprehensive method to compare different types of DoxMS in healthy animals or tumor models.

  13. Comparing transformation methods for DNA microarray data

    NARCIS (Netherlands)

    Thygesen, Helene H.; Zwinderman, Aeilko H.

    2004-01-01

    Background: When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order to improve comparability and signal/noise ratio. These steps may include

  14. DNA microarrays : a molecular cloning manual

    National Research Council Canada - National Science Library

    Sambrook, Joseph; Bowtell, David

    2002-01-01

    .... DNA Microarrays provides authoritative, detailed instruction on the design, construction, and applications of microarrays, as well as comprehensive descriptions of the software tools and strategies...

  15. Facilitating functional annotation of chicken microarray data

    Directory of Open Access Journals (Sweden)

    Gresham Cathy R

    2009-10-01

    Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

  16. Computational biology of genome expression and regulation--a review of microarray bioinformatics.

    Science.gov (United States)

    Wang, Junbai

    2008-01-01

    Microarray technology is being used widely in various biomedical research areas; the corresponding microarray data analysis is an essential step toward the best utilizing of array technologies. Here we review two components of the microarray data analysis: a low level of microarray data analysis that emphasizes the designing, the quality control, and the preprocessing of microarray experiments, then a high level of microarray data analysis that focuses on the domain-specific microarray applications such as tumor classification, biomarker prediction, analyzing array CGH experiments, and reverse engineering of gene expression networks. Additionally, we will review the recent development of building a predictive model in genome expression and regulation studies. This review may help biologists grasp a basic knowledge of microarray bioinformatics as well as its potential impact on the future evolvement of biomedical research fields.

  17. An MRI Study of Superior Temporal Gyrus Volume in Women With Schizotypal Personality Disorder

    OpenAIRE

    Dickey, Chandlee C.; McCarley, Robert William; Voglmaier, Martina M.; Niznikiewicz, Margaret A.; Seidman, Larry Joel; Demeo, Susan; Frumin, Melissa; Shenton, Martha Elizabeth

    2003-01-01

    Objective: An abnormal superior temporal gyrus has figured prominently in schizophrenia research, and left superior temporal gyrus volume has been shown to be smaller in male subjects with schizotypal personality disorder. This is the first structural magnetic resonance imaging study to examine a group of female subjects with schizotypal personality disorder. Method: The superior temporal gyrus was drawn on coronal images acquired from female subjects recruited from the community (schizotypal...

  18. Synthesizing genome-wide association studies and expression microarray reveals novel genes that act in the human growth plate to modulate height.

    Science.gov (United States)

    Lui, Julian C; Nilsson, Ola; Chan, Yingleong; Palmer, Cameron D; Andrade, Anenisia C; Hirschhorn, Joel N; Baron, Jeffrey

    2012-12-01

    Previous meta-analysis of genome-wide association (GWA) studies has identified 180 loci that influence adult height. However, each GWA locus typically comprises a set of contiguous genes, only one of which presumably modulates height. We reasoned that many of the causative genes within these loci influence height because they are expressed in and function in the growth plate, a cartilaginous structure that causes bone elongation and thus determines stature. Therefore, we used expression microarray studies of mouse and rat growth plate, human disease databases and a mouse knockout phenotype database to identify genes within the GWAS loci that are likely required for normal growth plate function. Each of these approaches identified significantly more genes within the GWA height loci than at random genomic locations (P analysis strongly implicates 78 genes in growth plate function, including multiple genes that participate in PTHrP-IHH, BMP and CNP signaling, and many genes that have not previously been implicated in the growth plate. Thus, this analysis reveals a large number of novel genes that regulate human growth plate chondrogenesis and thereby contribute to the normal variations in human adult height. The analytic approach developed for this study may be applied to GWA studies for other common polygenic traits and diseases, thus providing a new general strategy to identify causative genes within GWA loci and to translate genetic associations into mechanistic biological insights.

  19. Identifying Fishes through DNA Barcodes and Microarrays.

    Directory of Open Access Journals (Sweden)

    Marc Kochzius

    2010-09-01

    Full Text Available International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S, cytochrome b (cyt b, and cytochrome oxidase subunit I (COI for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90% renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

  20. Meta-analysis of studies using suppression subtractive hybridization and microarrays to investigate the effects of environmental stress on gene transcription in oysters.

    Science.gov (United States)

    Anderson, Kelli; Taylor, Daisy A; Thompson, Emma L; Melwani, Aroon R; Nair, Sham V; Raftos, David A

    2015-01-01

    Many microarray and suppression subtractive hybridization (SSH) studies have analyzed the effects of environmental stress on gene transcription in marine species. However, there have been no unifying analyses of these data to identify common stress response pathways. To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters. The stressors tested included chemical contamination, hypoxia and infection, as well as extremes of temperature, pH and turbidity. We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress. A repeating pattern was evident in these transcriptional responses, regardless of the type of stress applied. Many of the genes that responded to environmental stress encoded proteins involved in translation and protein processing (including molecular chaperones), the mitochondrial electron transport chain, anti-oxidant activity and the cytoskeleton. In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters.

  1. A functional magnetic resonance imaging study mapping the episodic memory encoding network in temporal lobe epilepsy

    Science.gov (United States)

    Sidhu, Meneka K.; Stretton, Jason; Winston, Gavin P.; Bonelli, Silvia; Centeno, Maria; Vollmar, Christian; Symms, Mark; Thompson, Pamela J.; Koepp, Matthias J.

    2013-01-01

    Functional magnetic resonance imaging has demonstrated reorganization of memory encoding networks within the temporal lobe in temporal lobe epilepsy, but little is known of the extra-temporal networks in these patients. We investigated the temporal and extra-temporal reorganization of memory encoding networks in refractory temporal lobe epilepsy and the neural correlates of successful subsequent memory formation. We studied 44 patients with unilateral temporal lobe epilepsy and hippocampal sclerosis (24 left) and 26 healthy control subjects. All participants performed a functional magnetic resonance imaging memory encoding paradigm of faces and words with subsequent out-of-scanner recognition assessments. A blocked analysis was used to investigate activations during encoding and neural correlates of subsequent memory were investigated using an event-related analysis. Event-related activations were then correlated with out-of-scanner verbal and visual memory scores. During word encoding, control subjects activated the left prefrontal cortex and left hippocampus whereas patients with left hippocampal sclerosis showed significant additional right temporal and extra-temporal activations. Control subjects displayed subsequent verbal memory effects within left parahippocampal gyrus, left orbitofrontal cortex and fusiform gyrus whereas patients with left hippocampal sclerosis activated only right posterior hippocampus, parahippocampus and fusiform gyrus. Correlational analysis showed that patients with left hippocampal sclerosis with better verbal memory additionally activated left orbitofrontal cortex, anterior cingulate cortex and left posterior hippocampus. During face encoding, control subjects showed right lateralized prefrontal cortex and bilateral hippocampal activations. Patients with right hippocampal sclerosis showed increased temporal activations within the superior temporal gyri bilaterally and no increased extra-temporal areas of activation compared with

  2. Transcortical selective amygdalohippocampectomy technique through the middle temporal gyrus revisited: An anatomical study laboratory investigation.

    Science.gov (United States)

    Bozkurt, Baran; da Silva Centeno, Ricardo; Chaddad-Neto, Feres; da Costa, Marcos Devanir Silva; Goiri, Marcelo Augusto Acosta; Karadag, Ali; Tugcu, Bekir; Ovalioglu, Talat Cem; Tanriover, Necmettin; Kaya, Serdar; Yagmurlu, Kaan; Grande, Andrew

    2016-12-01

    The anterior temporal lobectomy (ATL) and selective amygdalohippocampectomy (SelAH) have been used for surgical treatment of mesial temporal lobe epilepsy. We examined the comprehensive white matter tract anatomy of the temporal lobe to gain an insight into the trans-middle temporal gyrus, a lateral approach which has been commonly used. The transmiddle temporal gyrus approach was performed in a stepwise manner on cadaveric human heads to examine the traversing white matter pathways through it and the structures located in the temporal horn. We reviewed the literature to compare the trans-middle temporal gyrus approach with other SelAH techniques based on surgical outcomes. There does not appear to be a significant difference in seizure outcome between SelAH and ATL. However, the SelAH provides a better neuropsychological outcomes than the ATL in selected patients. Each SelAH approach has individual advantages and disadvantages. Based on our anatomical study, in the transcortical amygdalohippocampectomy technique through the middle temporal gyrus the white matter pathways to be encountered. In the temporal horn, the collateral eminence, hippocampus, lateral ventricular sulcus, choroidal fissure, inferior choroidal point, choroid plexus, fimbria of the fornix, and amygdala are exposed. The subpial dissection is performed along the lateral ventricular sulcus from the collateral eminence on lateral side and from the choroidal fissure on medial side by microdissector for en bloc resection of the hippocampus proper. The trans-middle temporal gyrus approach is commonly used in treatment of mesial temporal lobe epilepsy patients. A better anatomical and functional understanding of the structures of the temporal lobe is crucial for safer and more accurate surgery. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. A novel supra-temporal approach to retrobulbar anaesthesia in dogs: Preliminary study in cadavers.

    Science.gov (United States)

    Chiavaccini, Ludovica; Micieli, Fabiana; Meomartino, Leonardo; Duffee, Lauren R; Vesce, Giancarlo

    2017-05-01

    A novel supra-temporal technique for retrobulbar anaesthesia in dogs is described and compared to the inferior temporal palpebral approach. Supra-temporal and inferior temporal palpebral retrobulbar injections were performed in 20 orbits of canine cadavers. Distribution of injected contrast medium within the intraconal space and around the optic nerve was analysed using computed tomography. There was adequate distribution of contrast medium within the intraconal space with both techniques. Concurrent intraconal and extraconal distribution was observed using the inferior temporal palpebral approach in 3/10 orbits and using the supra-temporal approach in 5/10 orbits. In 3/10 supra-temporal injections, the injected vehicle was distributed preferentially in the caudal aspect of the retrobulbar cone, closer to the orbital fissure. Accidental intraocular injection was never observed. The supra-temporal approach appears to be a valid alternative to the inferior temporal palpebral approach for retrobulbar anaesthesia in dogs, being less technically challenging. Further studies are required to confirm the clinical efficacy of this approach in dogs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Feasibility of using tissue microarray cores of paraffin-embedded breast cancer tissue for measurement of gene expression: a proof-of-concept study.

    Science.gov (United States)

    Drury, Suzanne; Salter, Janine; Baehner, Frederick L; Shak, Steven; Dowsett, Mitch

    2010-06-01

    To determine whether 0.6 mm cores of formalin-fixed paraffin-embedded (FFPE) tissue, as commonly used to construct immunohistochemical tissue microarrays, may be a valid alternative to tissue sections as source material for quantitative real-time PCR-based transcriptional profiling of breast cancer. Four matched 0.6 mm cores of invasive breast tumour and two 10 microm whole sections were taken from eight FFPE blocks. RNA was extracted and reverse transcribed, and TaqMan assays were performed on the 21 genes of the Oncotype DX Breast Cancer assay. Expression of the 16 recurrence-related genes was normalised to the set of five reference genes, and the recurrence score (RS) was calculated. RNA yield was lower from 0.6 mm cores than from 10 microm whole sections, but was still more than sufficient to perform the assay. RS and single gene data from cores were highly comparable with those from whole sections (RS p=0.005). Greater variability was seen between cores than between sections. FFPE sections are preferable to 0.6 mm cores for RNA profiling in order to maximise RNA yield and to allow for standard histopathological assessment. However, 0.6 mm cores are sufficient and would be appropriate to use for large cohort studies.

  5. Microarray Analysis Reveals Higher Gestational Folic Acid Alters Expression of Genes in the Cerebellum of Mice Offspring—A Pilot Study

    Directory of Open Access Journals (Sweden)

    Subit Barua

    2015-01-01

    Full Text Available Folate is a water-soluble vitamin that is critical for nucleotide synthesis and can modulate methylation of DNA by altering one-carbon metabolism. Previous studies have shown that folate status during pregnancy is associated with various congenital defects including the risk of aberrant neural tube closure. Maternal exposure to a methyl supplemented diet also can alter DNA methylation and gene expression, which may influence the phenotype of offspring. We investigated if higher gestational folic acid (FA in the diet dysregulates the expression of genes in the cerebellum of offspring in C57BL/6 J mice. One week before gestation and throughout the pregnancy, groups of dams were supplemented with FA either at 2 mg/kg or 20 mg/kg of diet. Microarray analysis was used to investigate the genome wide gene expression profile in the cerebellum from day old pups. Our results revealed that exposure to the higher dose FA diet during gestation dysregulated expression of several genes in the cerebellum of both male and female pups. Several transcription factors, imprinted genes, neuro-developmental genes and genes associated with autism spectrum disorder exhibited altered expression levels. These findings suggest that higher gestational FA potentially dysregulates gene expression in the offspring brain and such changes may adversely alter fetal programming and overall brain development.

  6. Evaluation of toxicity of the mycotoxin citrinin using yeast ORF DNA microarray and Oligo DNA microarray

    Directory of Open Access Journals (Sweden)

    Nobumasa Hitoshi

    2007-04-01

    Full Text Available Abstract Background Mycotoxins are fungal secondary metabolites commonly present in feed and food, and are widely regarded as hazardous contaminants. Citrinin, one of the very well known mycotoxins that was first isolated from Penicillium citrinum, is produced by more than 10 kinds of fungi, and is possibly spread all over the world. However, the information on the action mechanism of the toxin is limited. Thus, we investigated the citrinin-induced genomic response for evaluating its toxicity. Results Citrinin inhibited growth of yeast cells at a concentration higher than 100 ppm. We monitored the citrinin-induced mRNA expression profiles in yeast using the ORF DNA microarray and Oligo DNA microarray, and the expression profiles were compared with those of the other stress-inducing agents. Results obtained from both microarray experiments clustered together, but were different from those of the mycotoxin patulin. The oxidative stress response genes – AADs, FLR1, OYE3, GRE2, and MET17 – were significantly induced. In the functional category, expression of genes involved in "metabolism", "cell rescue, defense and virulence", and "energy" were significantly activated. In the category of "metabolism", genes involved in the glutathione synthesis pathway were activated, and in the category of "cell rescue, defense and virulence", the ABC transporter genes were induced. To alleviate the induced stress, these cells might pump out the citrinin after modification with glutathione. While, the citrinin treatment did not induce the genes involved in the DNA repair. Conclusion Results from both microarray studies suggest that citrinin treatment induced oxidative stress in yeast cells. The genotoxicity was less severe than the patulin, suggesting that citrinin is less toxic than patulin. The reproducibility of the expression profiles was much better with the Oligo DNA microarray. However, the Oligo DNA microarray did not completely overcome cross

  7. Temporal lobe epilepsy in patients with nonlesional MRI and normal memory: an SEEG study.

    Science.gov (United States)

    Suresh, Suraj; Sweet, Jennifer; Fastenau, Philip S; Lüders, Hans; Landazuri, Patrick; Miller, Jonathan

    2015-12-01

    Temporal lobe epilepsy (TLE) in the absence of MRI abnormalities and memory deficits is often presumed to have an extramesial or even extratemporal source. In this paper the authors report the results of a comprehensive stereoelectroencephalography (SEEG) analysis in patients with TLE with normal MRI images and memory scores. Eighteen patients with medically refractory epilepsy who also had unremarkable MR images and normal verbal and visual memory scores on neuropsychological testing were included in the study. All patients had seizure semiology and video electroencephalography (EEG) findings suggestive of TLE. A standardized SEEG investigation was performed for each patient with electrodes implanted into the mesial and lateral temporal lobe, temporal tip, posterior temporal neocortex, orbitomesiobasal frontal lobe, posterior cingulate gyrus, and insula. This information was used to plan subsequent surgical management. Interictal SEEG abnormalities were observed in the mesial temporal structures in 17 patients (94%) and in the temporal tip in 6 (33%). Seizure onset was exclusively from mesial structures in 13 (72%), exclusively from lateral temporal cortex and/or temporal tip structures in 2 (11%), and independently from mesial and neocortical foci in 3 (17%). No seizure activity was observed arising from any extratemporal location. All patients underwent surgical intervention targeting the temporal lobe and tailored to the SEEG findings, and all experienced significant improvement in seizure frequency with a postoperative follow-up observation period of at least 1 year. This study demonstrates 3 important findings: 1) normal memory does not preclude mesial temporal seizure onset; 2) onset of seizures exclusively from mesial temporal structures without early neocortical involvement is common, even in the absence of memory deficits; and 3) extratemporal seizure onset is rare when video EEG and semiology are consistent with focal TLE.

  8. The application of DNA microarrays in gene expression analysis.

    Science.gov (United States)

    van Hal, N L; Vorst, O; van Houwelingen, A M; Kok, E J; Peijnenburg, A; Aharoni, A; van Tunen, A J; Keijer, J

    2000-03-31

    DNA microarray technology is a new and powerful technology that will substantially increase the speed of molecular biological research. This paper gives a survey of DNA microarray technology and its use in gene expression studies. The technical aspects and their potential improvements are discussed. These comprise array manufacturing and design, array hybridisation, scanning, and data handling. Furthermore, it is discussed how DNA microarrays can be applied in the working fields of: safety, functionality and health of food and gene discovery and pathway engineering in plants.

  9. High throughput screening of starch structures using carbohydrate microarrays

    DEFF Research Database (Denmark)

    Tanackovic, Vanja; Rydahl, Maja Gro; Pedersen, Henriette Lodberg

    2016-01-01

    In this study we introduce the starch-recognising carbohydrate binding module family 20 (CBM20) from Aspergillus niger for screening biological variations in starch molecular structure using high throughput carbohydrate microarray technology. Defined linear, branched and phosphorylated...

  10. A study using computerized tomography in the clinical practice of temporal lobe epilepsy

    International Nuclear Information System (INIS)

    Yamamoto, Kunimitsu

    1982-01-01

    The author has studied about analysis of clinical data and CT findings examined conventional method for 50 cases of temporal lobe epilepsy and how to assess the foci of temporal lobe by CT. According to the examination of conventional neuroradiologic technique and routine work of CT for temporal lobe epilepsy, an extreme space occuping lesions were detected and marked cerebral atrophy, low density area in temporal lobe were found out, but, most of them were not able to detect foci of the temporal lobe and yet, the study of CT number based on the print out data did not give any precise informations about epileptogenic lesions of temporal lobe epilepsy. The method of reversed axial section CT was designed to photograph inferior horn of lateral ventricles with the purpose to delineate the hippocampus and amygdata, and precise pictures from autopsy brain and clinical cases were obtained by that method about scanning angle of reversed axial section CT, various angles are made an experiment on scanning, such as reversed 15 0 , 20 0 , 25 0 , 30 0 , 35 0 . Among them, it is proved that the reversed angle of almost 25 0 is most suitable to delineate mesial temporal structure, so as to say, foci of the temporal lobe. (J.P.N.)

  11. Clinical study of acute and chronic pain after temporal craniotomy

    Directory of Open Access Journals (Sweden)

    WANG Cheng-wei

    2013-10-01

    Full Text Available Objective To investigate the correlation of chronic pain after surgery and acute pain within 48 h after temporal craniotomy. Methods One hundred and seventy-six patients who underwent surgery through temporal approach were divided into 3 groups and treated with morphine 30 mg (Group M, N = 57, tramadol 1000 mg (Group T, N = 60 and morphine 20 mg + flurbiprofen 200 mg (Group F, N = 59 by patient-controlled intravenous analgesia (PCIA. Postoperative acute pain (resting and movement was evaluated by Visual Analogue Scale (VAS at 4, 16, 24 and 48 h respectively. Chronic pain was measured by Short-Form McGill Pain Questionnaire (SF-MPQ 3 months after surgery. The characteristics of acute and chronic pain, the relationship between them and analgesic effect of 3 kinds of analgesic drugs were analyzed. Results The differences of observed indicators including gender, age, weight and operating time, which might affect the degree of postoperative pain between before and after surgery were not statistically significant (P > 0.05. VAS scores at different time points within 48 h after surgery in each group decreased gradually. The VAS scores in group T (2.91 ± 1.64 was significantly higher than group M (2.19 ± 1.68 and group F (1.71 ± 1.17, P 0.05. The overall incidence rate of chronic pain was 71.02% (125/176, with moderate and severe pain in 15.91% (28/176. Chronic pain and acute postoperative pain severity were positively correlated (resting: rs = 0.171, P = 0.012; movement: rs = 0.190, P = 0.006. The difference of the acute pain (VAS corresponding to SF-MPQ Ⅱ score > 0 and SF-MPQ Ⅱ score = 0 was statistically significant (P < 0.05. Conclusion The postoperative chronic pain following temporal craniotomy is related to acute pain within 48 h after operation. Effective treatment of early postoperative acute pain may reduce the incidence of chronic pain.

  12. Immunohistochemical study of Metallothionein in patients with temporal lobe epilepsy.

    Science.gov (United States)

    Juárez-Rebollar, Daniel; Alonso-Vanegas, Mario; Nava-Ruíz, Concepción; Buentello-García, Masao; Yescas-Gómez, Petra; Díaz-Ruíz, Araceli; Rios, Camilo; Méndez-Armenta, Marisela

    2017-05-01

    Epilepsy is characterized by spontaneous recurrent seizures and temporal lobe epilepsy (TLE) is the most common serious neurological example of acquired and frequent epilepsy. Oxidative stress is recognized as playing a contributing role in several neurological disorders, and most recently have been implicated in acquired epilepsies. The MTs occur in several brain regions and may serve as neuroprotective proteins against reactive oxygen species causing oxidative damage and stress. The main aim of this work was to describe the immunohistochemical localization of MT in the specimens derived from the patients affected by TLE. Histopathological examination showed NeuN, GFAP and MT immunopositive cells that were analyzed for determinate in hippocampal and parietal cortex samples. An increase in the reactive gliosis associated with increased MT expression was observed in patients with TLE. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Tissue Microarray Analysis Applied to Bone Diagenesis

    OpenAIRE

    Barrios Mello, Rafael; Regis Silva, Maria Regina; Seixas Alves, Maria Teresa; Evison, Martin; Guimarães, Marco Aurélio; Francisco, Rafaella Arrabaça; Dias Astolphi, Rafael; Miazato Iwamura, Edna Sadayo

    2017-01-01

    Taphonomic processes affecting bone post mortem are important in forensic, archaeological and palaeontological investigations. In this study, the application of tissue microarray (TMA) analysis to a sample of femoral bone specimens from 20 exhumed individuals of known period of burial and age at death is described. TMA allows multiplexing of subsamples, permitting standardized comparative analysis of adjacent sections in 3-D and of representative cross-sections of a large number of specimens....

  14. Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms

    DEFF Research Database (Denmark)

    Gunnarsson, R.; Staaf, J.; Jansson, M.

    2008-01-01

    Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K)...

  15. Influence of memory, attention, IQ and age on auditory temporal processing tests: preliminary study.

    Science.gov (United States)

    Murphy, Cristina Ferraz Borges; Zachi, Elaine Cristina; Roque, Daniela Tsubota; Ventura, Dora Selma Fix; Schochat, Eliane

    2014-01-01

    To investigate the existence of correlations between the performance of children in auditory temporal tests (Frequency Pattern and Gaps in Noise--GIN) and IQ, attention, memory and age measurements. Fifteen typically developing individuals between the ages of 7 to 12 years and normal hearing participated in the study. Auditory temporal processing tests (GIN and Frequency Pattern), as well as a Memory test (Digit Span), Attention tests (auditory and visual modality) and intelligence tests (RAVEN test of Progressive Matrices) were applied. Significant and positive correlation between the Frequency Pattern test and age variable were found, which was considered good (p<0.01, 75.6%). There were no significant correlations between the GIN test and the variables tested. Auditory temporal skills seem to be influenced by different factors: while the performance in temporal ordering skill seems to be influenced by maturational processes, the performance in temporal resolution was not influenced by any of the aspects investigated.

  16. Mining meiosis and gametogenesis with DNA microarrays.

    Science.gov (United States)

    Schlecht, Ulrich; Primig, Michael

    2003-04-01

    Gametogenesis is a key developmental process that involves complex transcriptional regulation of numerous genes including many that are conserved between unicellular eukaryotes and mammals. Recent expression-profiling experiments using microarrays have provided insight into the co-ordinated transcription of several hundred genes during mitotic growth and meiotic development in budding and fission yeast. Furthermore, microarray-based studies have identified numerous loci that are regulated during the cell cycle or expressed in a germ-cell specific manner in eukaryotic model systems like Caenorhabditis elegans, Mus musculus as well as Homo sapiens. The unprecedented amount of information produced by post-genome biology has spawned novel approaches to organizing biological knowledge using currently available information technology. This review outlines experiments that contribute to an emerging comprehensive picture of the molecular machinery governing sexual reproduction in eukaryotes.

  17. Time-course investigation of the gene expression profile during Fasciola hepatica infection: A microarray-based study

    Directory of Open Access Journals (Sweden)

    Jose Rojas-Caraballo

    2015-12-01

    Full Text Available Fasciolosis is listed as one of the most important neglected tropical diseases according with the World Health Organization and is also considered as a reemerging disease in the human beings. Despite there are several studies describing the immune response induced by Fasciola hepatica in the mammalian host, investigations aimed at identifying the expression profile of genes involved in inducing hepatic injury are currently scarce. Data presented here belong to a time-course investigation of the gene expression profile in the liver of BALB/c mice infected with F. hepatica metacercariae at 7 and 21 days after experimental infection. The data published here have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE69588, previously published by Rojas-Caraballo et al. (2015 in PLoS One [1].

  18. Polyadenylation state microarray (PASTA) analysis.

    Science.gov (United States)

    Beilharz, Traude H; Preiss, Thomas

    2011-01-01

    Nearly all eukaryotic mRNAs terminate in a poly(A) tail that serves important roles in mRNA utilization. In the cytoplasm, the poly(A) tail promotes both mRNA stability and translation, and these functions are frequently regulated through changes in tail length. To identify the scope of poly(A) tail length control in a transcriptome, we developed the polyadenylation state microarray (PASTA) method. It involves the purification of mRNA based on poly(A) tail length using thermal elution from poly(U) sepharose, followed by microarray analysis of the resulting fractions. In this chapter we detail our PASTA approach and describe some methods for bulk and mRNA-specific poly(A) tail length measurements of use to monitor the procedure and independently verify the microarray data.

  19. A DNA methylation microarray-based study identifies ERG as a gene commonly methylated in prostate cancer.

    Science.gov (United States)

    Schwartzman, Jacob; Mongoue-Tchokote, Solange; Gibbs, Angela; Gao, Lina; Corless, Christopher L; Jin, Jennifer; Zarour, Luai; Higano, Celestia; True, Lawrence D; Vessella, Robert L; Wilmot, Beth; Bottomly, Daniel; McWeeney, Shannon K; Bova, G Steven; Partin, Alan W; Mori, Motomi; Alumkal, Joshi

    2011-10-01

    DNA methylation of promoter regions is a common event in prostate cancer, one of the most common cancers in men worldwide. Because prior reports demonstrating that DNA methylation is important in prostate cancer studied a limited number of genes, we systematically quantified the DNA methylation status of 1505 CpG dinucleotides for 807 genes in 78 paraffin-embedded prostate cancer samples and three normal prostate samples. The ERG gene, commonly repressed in prostate cells in the absence of an oncogenic fusion to the TMPRSS2 gene, was one of the most commonly methylated genes, occurring in 74% of prostate cancer specimens. In an independent group of patient samples, we confirmed that ERG DNA methylation was common, occurring in 57% of specimens, and cancer-specific. The ERG promoter is marked by repressive chromatin marks mediated by polycomb proteins in both normal prostate cells and prostate cancer cells, which may explain ERG's predisposition to DNA methylation and the fact that tumors with ERG DNA methylation were more methylated, in general. These results demonstrate that bead arrays offer a high-throughput method to discover novel genes with promoter DNA methylation such as ERG, whose measurement may improve our ability to more accurately detect prostate cancer.

  20. A molecular smart surface for spatio-temporal studies of cell mobility.

    Science.gov (United States)

    Lee, Eun-ju; Luo, Wei; Chan, Eugene W L; Yousaf, Muhammad N

    2015-01-01

    Active migration in both healthy and malignant cells requires the integration of information derived from soluble signaling molecules with positional information gained from interactions with the extracellular matrix and with other cells. How a cell responds and moves involves complex signaling cascades that guide the directional functions of the cytoskeleton as well as the synthesis and release of proteases that facilitate movement through tissues. The biochemical events of the signaling cascades occur in a spatially and temporally coordinated manner then dynamically shape the cytoskeleton in specific subcellular regions. Therefore, cell migration and invasion involve a precise but constantly changing subcellular nano-architecture. A multidisciplinary effort that combines new surface chemistry and cell biological tools is required to understand the reorganization of cytoskeleton triggered by complex signaling during migration. Here we generate a class of model substrates that modulate the dynamic environment for a variety of cell adhesion and migration experiments. In particular, we use these dynamic substrates to probe in real-time how the interplay between the population of cells, the initial pattern geometry, ligand density, ligand affinity and integrin composition affects cell migration and growth. Whole genome microarray analysis indicates that several classes of genes ranging from signal transduction to cytoskeletal reorganization are differentially regulated depending on the nature of the surface conditions.

  1. Microarray of DNA probes on carboxylate functional beads surface

    Institute of Scientific and Technical Information of China (English)

    黄承志; 李原芳; 黄新华; 范美坤

    2000-01-01

    The microarray of DNA probes with 5’ -NH2 and 5’ -Tex/3’ -NH2 modified terminus on 10 um carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) is characterized in the preseni paper. it was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentra-tion of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.

  2. Microarray of DNA probes on carboxylate functional beads surface

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The microarray of DNA probes with 5′-NH2 and 5′-Tex/3′-NH2 modified terminus on 10 m m carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)- carbodiimide (EDC) is characterized in the present paper. It was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentration of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.

  3. Spatial and temporal variability of precipitation and chemistry: Case studies from the Frontal Boundary Study

    International Nuclear Information System (INIS)

    Dana, M.T.

    1993-01-01

    Regional and larger-scale models of pollutant transport and deposition generally, by practical necessity, must be limited in output of precipitation rate and chemical composition to values for selected time intervals representing areas on the order of 10 4 km 2 . Naturally, it is of some concern that these values be reasonably representative of natural variations both in time and space. This question may be approached through field studies involving detailed spatial (using a network of samplers on the model grid scale) and temporal (using sequential sampling) measurements. This paper presents an initial analysis, using simple statistical concepts, of data bases from such a field study, the Frontal Boundary Study (FBS)

  4. Uso de microarrays na busca de perfis de expressão gênica: aplicação no estudo de fenótipos complexos Use of microarrays in the search of gene expression patterns: application to the study of complex phenotypes

    Directory of Open Access Journals (Sweden)

    Camila Guindalini

    2007-12-01

    . By the simultaneous determination of the expression levels of thousands of genes, microarrays allow researchers to compare the molecular behaviour of different types of cells lines or specific tissues that have been exposed to pathological or experimental conditions. The method may provide insights into physiological processes and facilitate the identification of novel biological markers for diagnostic, prognostic and pharmacological treatments for a number of diseases. In this article, we present theoretical and methodological concepts underlying the microarray technology, as well as an overview of its advantages, perspectives and future scientific directions. In an attempt to demonstrate the applicability and efficiency of the method in the study of complex phenotypes, initial results on gene expression studies in post mortem brain samples of psychiatric patients and on the molecular and functional consequences of sleep disturbances, which is strongly associated with psychiatric illness, will be described and discussed.

  5. A comparative analysis of DNA barcode microarray feature size

    Directory of Open Access Journals (Sweden)

    Smith Andrew M

    2009-10-01

    Full Text Available Abstract Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density, but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO collection used for screens of pooled yeast (Saccharomyces cerevisiae deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be ALG7. Conclusion We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.

  6. A panel of prognostic protein markers for progression in non-muscle invasive bladder cancer - a multicenter tissue microarray validation study

    DEFF Research Database (Denmark)

    Fristrup, Niels; Birkenkamp-Demtröder, Karin; Ulhøi, Benedicte Parm

    2012-01-01

    cohort of 283 patients with long-term follow-up. For validation of the results we used three independent patient cohorts with long-term follow-up from Sweden, Spain, and Taiwan. In total 649 primary NMIBC tissue-microarray specimens from patients with long-term follow-up were used. Protein expression......Bladder cancer is the fifth most common cancer in the Western world. The histopathological parameters used in the clinic cannot precisely predict the individual disease course. Bladder cancer patients are therefore monitored thoroughly for disease recurrence and progression by urine and cystoscopy...... Ta and T1 urothelial carcinomas. Transcripts from the five genes encoding these proteins were previously included in gene expression signatures for outcome prediction for non-muscle invasive bladder cancer (NMIBC). As a training-set, we used primary NMIBC tissue-microarray specimens from a Danish...

  7. Universal Reference RNA as a standard for microarray experiments

    Directory of Open Access Journals (Sweden)

    Fero Michael

    2004-03-01

    Full Text Available Abstract Background Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation and labeling, hybridization conditions and data acquisition and analysis are variables difficult to simultaneously control. A useful tool for monitoring and controlling intra- and inter-experimental variation is Universal Reference RNA (URR, developed with the goal of providing hybridization signal at each microarray probe location (spot. Measuring signal at each spot as the ratio of experimental RNA to reference RNA targets, rather than relying on absolute signal intensity, decreases variability by normalizing signal output in any two-color hybridization experiment. Results Human, mouse and rat URR (UHRR, UMRR and URRR, respectively were prepared from pools of RNA derived from individual cell lines representing different tissues. A variety of microarrays were used to determine percentage of spots hybridizing with URR and producing signal above a user defined threshold (microarray coverage. Microarray coverage was consistently greater than 80% for all arrays tested. We confirmed that individual cell lines contribute their own unique set of genes to URR, arguing for a pool of RNA from several cell lines as a better configuration for URR as opposed to a single cell line source for URR. Microarray coverage comparing two separately prepared batches each of UHRR, UMRR and URRR were highly correlated (Pearson's correlation coefficients of 0.97. Conclusion Results of this study demonstrate that large quantities of pooled RNA from individual cell lines are reproducibly prepared and possess diverse gene representation. This type of reference provides a standard for reducing variation in microarray experiments and allows more reliable comparison of gene expression data within and between experiments and

  8. Emerging use of gene expression microarrays in plant physiology.

    Science.gov (United States)

    Wullschleger, Stan D; Difazio, Stephen P

    2003-01-01

    Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.

  9. Emerging Use of Gene Expression Microarrays in Plant Physiology

    Directory of Open Access Journals (Sweden)

    Stephen P. Difazio

    2006-04-01

    Full Text Available Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.

  10. Influence of memory, attention, IQ and age on auditory temporal processing tests: preliminary study

    OpenAIRE

    Murphy, Cristina Ferraz Borges; Zachi, Elaine Cristina; Roque, Daniela Tsubota; Ventura, Dora Selma Fix; Schochat, Eliane

    2014-01-01

    PURPOSE: To investigate the existence of correlations between the performance of children in auditory temporal tests (Frequency Pattern and Gaps in Noise - GIN) and IQ, attention, memory and age measurements. METHOD: Fifteen typically developing individuals between the ages of 7 to 12 years and normal hearing participated in the study. Auditory temporal processing tests (GIN and Frequency Pattern), as well as a Memory test (Digit Span), Attention tests (auditory and visual modality) and ...

  11. Study on memories of temporal lobes and the principles of lateralization using near infrared spectroscopy

    Science.gov (United States)

    Kamakura, Katsutoshi

    2007-01-01

    In this study we measured the variation of brain blood quantity (Oxy-Hb, Deoxy-Hb and Total-Hb) in the temporal lobes using near infrared spectroscopy (NIRS) when the tasks of the memories were presented to the subjects. The memories are classified into the short-term memory (STM) and the long-term memory (LTM) including the episodic and semantic memories. The subjects joined in this study are 11 persons who are university students including graduate students. We used the language task of letter-number sequencing, also reverse sequencing to measure STM and the task of the episodic memory to measure LTM. As a result of analysis, concerning the episodic memory, the variation of Oxy-Hb in the left temporal lobe was larger than that of Oxy-Hb in the right temporal lobe. The result might suggest that the episodic memory has a relationship with cerebral dominance concerning language area in the left temporal lobe. It seems that the episodic memory meditated with the function of language used in this study is much stored in the left temporal lobe than in the right temporal lobe. This result coincides with the principles of lateralization. The variation of Oxy-Hb in the language task of letter-number sequencing was smaller than that of Oxy-Hb in the language task of the episodic memory.

  12. Anterior & lateral extension of optic radiation & safety of amygdalohippocampectomy through middle temporal gyrus: a cadaveric study of 11 cerebral hemispheres.

    Science.gov (United States)

    Chowdhury, F H; Khan, A H

    2010-01-01

    This is a cadaveric anatomical study on the localization of the optic radiation within the temporal lobe and to find whether surgical intervention to the temporal lobe, especially amygdalohippocampectomy, can damage the optic radiation or not. 11 cadaveric cerebral hemispheres were used for the study. A 2 cm long antero-posterior incision was done with a sharp knife, on middle temporal gyrus, starting 3 cm posterior to temporal pole. The incision was deepened perpendicular to surface of the gyrus to reach the temporal horn. The optic radiation was dissected under operating microscope using Klinger's fiber dissection technique and measurements were taken to define the anterior and lateral extension of optic radiation. The optic radiation in each hemispehere was inspected for any incision related damage. No damage to the optic radiation was found, caused by the 2 cm long anterior-posterior incision on middle temporal gyrus 3 cm posterior to temporal pole. Most anterior 9mm (8-10mm) of the Meyer loop was completely on the roof and there was no extension over lateral wall of the temporal horn. In next posterior 17.5mm (16-20 mm) it extended over lateral wall of temporal horn with gradual progression. The most anterior extension of optic radiation was 26mm (23-31mm) posterior to temporal pole. Amygdalohippocampectomy through a 2 cm long horizontal incision on the middle temporal gyrus, starting 3 cm posterior to the temporal pole, to enter into the temporal horn through the lower aspect of the lateral wall is unlikely to cause damage to the Meyer's loop. Any entry from the superior aspect of the temporal horn and any temporal lobectomy inclusive of the superior temporal gyrus to enter the temporal horn is likely to cause Meyer's loop injury. The findings support the fact that the more inferior the surgical trajectory to the temporal horn of the lateral ventricle, the lover is the risk of visual field damage.

  13. Direct calibration of PICKY-designed microarrays

    Directory of Open Access Journals (Sweden)

    Ronald Pamela C

    2009-10-01

    Full Text Available Abstract Background Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples. Results Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu under the PICKY Download area. Conclusion PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration.

  14. Current Knowledge on Microarray Technology - An Overview

    African Journals Online (AJOL)

    Erah

    This paper reviews basics and updates of each microarray technology and serves to .... through protein microarrays. Protein microarrays also known as protein chips are nothing but grids that ... conditioned media, patient sera, plasma and urine. Clontech ... based antibody arrays) is similar to membrane-based antibody ...

  15. Diagnostic and analytical applications of protein microarrays

    DEFF Research Database (Denmark)

    Dufva, Hans Martin; Christensen, C.B.V.

    2005-01-01

    DNA microarrays have changed the field of biomedical sciences over the past 10 years. For several reasons, antibody and other protein microarrays have not developed at the same rate. However, protein and antibody arrays have emerged as a powerful tool to complement DNA microarrays during the post...

  16. Temporal and spectral studies of high-order harmonics generated by polarization-modulated infrared fields

    International Nuclear Information System (INIS)

    Sola, I. J.; Zaier, A.; Cormier, E.; Mevel, E.; Constant, E.; Lopez-Martens, R.; Johnsson, P.; Varju, K.; Mauritsson, J.; L'Huillier, A.; Strelkov, V.

    2006-01-01

    The temporal confinement of high harmonic generation (HHG) via modulation of the polarization of the fundamental pulse is studied in both temporal and spectral domains. In the temporal domain, a collinear cross-correlation setup using a 40 fs IR pump for the HHG and a 9 fs IR pulse to probe the generated emission is used to measure the XUV pulse duration. The observed temporal confinement is found to be consistent with theoretical predictions. An increased confinement is observed when a 9 fs pulse is used to generate the harmonics. An important spectral broadening, including a continuum background, is also measured. Theoretical calculations show that with 10 fs driving pulses, either one or two main attosecond pulses are created depending on the value of the carrier envelope phase

  17. Declarative long-term memory and the mesial temporal lobe: Insights from a 5-year postsurgery follow-up study on refractory temporal lobe epilepsy.

    Science.gov (United States)

    Salvato, Gerardo; Scarpa, Pina; Francione, Stefano; Mai, Roberto; Tassi, Laura; Scarano, Elisa; Lo Russo, Giorgio; Bottini, Gabriella

    2016-11-01

    It is largely recognized that the mesial temporal lobe and its substructure support declarative long-term memory (LTM). So far, different theories have been suggested, and the organization of declarative verbal LTM in the brain is still a matter of debate. In the current study, we retrospectively selected 151 right-handed patients with temporal lobe epilepsy with and without hippocampal sclerosis, with a homogeneous (seizure-free) clinical outcome. We analyzed verbal memory performance within a normalized scores context, by means of prose recall and word paired-associate learning tasks. Patients were tested at presurgical baseline, 6months, 2 and 5years after anteromesial temporal lobe surgery, using parallel versions of the neuropsychological tests. Our main finding revealed a key involvement of the left temporal lobe and, in particular, of the left hippocampus in prose recall rather than word paired-associate task. We also confirmed that shorter duration of epilepsy, younger age, and withdrawal of antiepileptic drugs would predict a better memory outcome. When individual memory performance was taken into account, data showed that females affected by left temporal lobe epilepsy for longer duration were more at risk of presenting a clinically pathologic LTM at 5years after surgery. Taken together, these findings shed new light on verbal declarative memory in the mesial temporal lobe and on the behavioral signature of the functional reorganization after the surgical treatment of temporal lobe epilepsy. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. [Application of single nucleotide polymorphism-microarray and target gene sequencing in the study of genetic etiology of children with unexplained intellectual disability or developmental delay].

    Science.gov (United States)

    Gao, Z J; Jiang, Q; Cheng, D Z; Yan, X X; Chen, Q; Xu, K M

    2016-10-02

    Objective: To evaluate the application of single nucleotide polymorphism (SNP)-microarray and target gene sequencing technology in the clinical molecular genetic diagnosis of unexplained intellectual disability(ID) or developmental delay (DD). Method: Patients with ID or DD were recruited in the Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics between September 2015 and February 2016. The intellectual assessment of the patients was performed using 0-6-year-old pediatric examination table of neuropsychological development or Wechsler intelligence scale (>6 years). Patients with a DQ less than 49 or IQ less than 51 were included in this study. The patients were scanned by SNP-array for detection of genomic copy number variations (CNV), and the revealed genomic imbalance was confirmed by quantitative real time-PCR. Candidate gene mutation screening was carried out by target gene sequencing technology.Causal mutations or likely pathogenic variants were verified by polymerase chain reaction and direct sequencing. Result: There were 15 children with ID or DD enrolled, 9 males and 6 females. The age of these patients was 7 months-16 years and 9 months. SNP-array revealed that two of the 15 patients had genomic CNV. Both CNV were de novo micro deletions, one involved 11q24.1q25 and the other micro deletion located on 21q22.2q22.3. Both micro deletions were proved to have a clinical significance due to their association with ID, brain DD, unusual faces etc. by querying Decipher database. Thirteen patients with negative findings in SNP-array were consequently examined with target gene sequencing technology, genotype-phenotype correlation analysis and genetic analysis. Five patients were diagnosed with monogenic disorder, two were diagnosed with suspected genetic disorder and six were still negative. Conclusion: Sequential use of SNP-array and target gene sequencing technology can significantly increase the molecular genetic etiologic

  19. Middle and Inferior Temporal Gyrus Gray Matter Volume Abnormalities in First-Episode Schizophrenia: An MRI Study

    OpenAIRE

    Kuroki, Noriomi; Shenton, Martha Elizabeth; Salisbury, Dean; Hirayasu, Yoshio; Onitsuka, Toshiaki; Ersner-Hershfield, Hal; Yurgelun-Todd, Deborah; Kikinis, Ron; Jolesz, Ferenc A.; McCarley, Robert William

    2006-01-01

    Objective: Magnetic resonance imaging (MRI) studies of schizophrenia reveal temporal lobe structural brain abnormalities in the superior temporal gyrus and the amygdala-hippocampal complex. However, the middle and inferior temporal gyri have received little investigation, especially in first-episode schizophrenia. Method: High-spatial-resolution MRI was used to measure gray matter volume in the inferior, middle, and superior temporal gyri in 20 patients with first-episode schizophrenia, 20 pa...

  20. Temporal networks

    CERN Document Server

    Saramäki, Jari

    2013-01-01

    The concept of temporal networks is an extension of complex networks as a modeling framework to include information on when interactions between nodes happen. Many studies of the last decade examine how the static network structure affect dynamic systems on the network. In this traditional approach  the temporal aspects are pre-encoded in the dynamic system model. Temporal-network methods, on the other hand, lift the temporal information from the level of system dynamics to the mathematical representation of the contact network itself. This framework becomes particularly useful for cases where there is a lot of structure and heterogeneity both in the timings of interaction events and the network topology. The advantage compared to common static network approaches is the ability to design more accurate models in order to explain and predict large-scale dynamic phenomena (such as, e.g., epidemic outbreaks and other spreading phenomena). On the other hand, temporal network methods are mathematically and concept...

  1. Global pathway analysis using DNA microarrays in skeletal muscle of women with polycystic ovary syndrome

    DEFF Research Database (Denmark)

    Skov, Vibe

    2007-01-01

    (study 1), to investigate whether pioglitazone therapy could reverse abnormalities in the transcriptional profile of muscle associated with insulin resistance in skeletal muscle of obese PCOS patients (study 2), and to develop a microarray platform for global gene expression profiling (study 3). In study...... comparable to other commercial and custom made microarrays and is a cost-effective alternative especially in larger epidemiological studies....

  2. Spatio-temporal evolution of volcano seismicity: A laboratory study

    Science.gov (United States)

    Benson, Philip M.; Vinciguerra, Sergio; Meredith, Philip G.; Young, R. Paul

    2010-08-01

    We report a laboratory and microstructural study of a suite of deformation experiments in which basalt from Mount Etna volcano is deformed and fractured at an effective confining pressure representative of conditions under a volcanic edifice (40 MPa). Particular attention was paid to the formation of a fracture and damage zone with which to stimulate coupled hydro-mechanical interactions that create the various types of seismicity recorded on volcanic edifices, and which usually precede eruption. Location of AE events through time shows the formation of a fault plane during which waveforms exhibit the typical high frequency characteristics of volcano-tectonic (VT) earthquakes. We found that these VT earthquakes were particularly pronounced when generated using dry samples, compared to samples saturated with a pore fluid (water). VT events generated during deformation of water saturated sample are characterised by a distinctive high frequency onset and a longer, low frequency coda exhibiting properties often seen in the field as hybrid events. We present evidence that hybrid events are, in fact, the common type of volcanic seismic event with either VT or low frequency (LF) events representing end members, and whose proportion depend on pore fluid being present in the rock type being deformed, as well as how close the rock is to failure. We find a notable trend of reducing instances of hybrid events leading up to the failure stage in our experiments, suggesting that during this stage, the pore fluid present in the rock moves sufficiently quickly to provide a resonance, seen as a LF coda. Our data supports recent modeling and field studies that postulate that hybrid events generated in volcanic areas are likely to be generated through the interaction of hydrothermal fluids moving through a combination of pre-existing microcrack networks and larger faults, such as those we observe in forensic (post-test) examination.

  3. Temporal and Spatial Melanoma Trends in Austria: An Ecological Study

    Directory of Open Access Journals (Sweden)

    Daniela Haluza

    2014-01-01

    Full Text Available Annual solar ultraviolet radiation (UVR is mostly determined by latitude and altitude. Over the last decades, increasing UVR ground levels have been observed. Exposure to UVR is associated with a life-time risk to develop melanoma, a malign skin cancer. Thus, we hypothesized that melanoma incidence in Austria is associated with altitude of place of living and time of diagnosis. We investigated this hypothesis in an ecological study by district and year for Austrian melanoma incidence (1990–2010 and mortality (1970–2011 data. As expected, incidence rates increased with altitude (about 2% per 10 m and year (about 2%. Additionally, melanoma incidence rates were about 50% higher in urban than in rural districts. In contrast, mortality rates decreased with altitude (for males: 0.4% per 10 m, for women: 0.7% per 10 m, respectively. The observed discrepancy between incidence and mortality data could partly be explained by melanoma diagnosis at earlier tumor stage in districts with higher altitude. Possible reasons for this finding include higher awareness of patients, better diagnostic performance of medical professionals working at higher altitudes, or slower tumor growth due to protective effects of sun light-associated vitamin D synthesis.

  4. Temporal and Spatial Melanoma Trends in Austria: An Ecological Study

    Science.gov (United States)

    Haluza, Daniela; Simic, Stana; Moshammer, Hanns

    2014-01-01

    Annual solar ultraviolet radiation (UVR) is mostly determined by latitude and altitude. Over the last decades, increasing UVR ground levels have been observed. Exposure to UVR is associated with a life-time risk to develop melanoma, a malign skin cancer. Thus, we hypothesized that melanoma incidence in Austria is associated with altitude of place of living and time of diagnosis. We investigated this hypothesis in an ecological study by district and year for Austrian melanoma incidence (1990–2010) and mortality (1970–2011) data. As expected, incidence rates increased with altitude (about 2% per 10 m) and year (about 2%). Additionally, melanoma incidence rates were about 50% higher in urban than in rural districts. In contrast, mortality rates decreased with altitude (for males: 0.4% per 10 m, for women: 0.7% per 10 m, respectively). The observed discrepancy between incidence and mortality data could partly be explained by melanoma diagnosis at earlier tumor stage in districts with higher altitude. Possible reasons for this finding include higher awareness of patients, better diagnostic performance of medical professionals working at higher altitudes, or slower tumor growth due to protective effects of sun light-associated vitamin D synthesis. PMID:24398911

  5. The diachronic temporality as a category in the study of contemporary cultures

    Directory of Open Access Journals (Sweden)

    Rodrigo Manoel Dias da Silva

    2011-12-01

    Full Text Available This article examines the possible interpretations of diachrony, as a category of social analysis, in the study of contemporary cultural differences. The author reviews some studies and surveys that show the temporalities experienced in cultural practices, interested in observing different understandings of the category, in the investigative plan. It concludes that the temporality of events present in cultures have been a privileged locus for questioning about the personal trajectories and biographies of various actors, and the same wording that several areas of social practices are expected when individuals tense or move their strategies of appropriation of cultures in their times and spaces.

  6. The Temporal Relation Between Pain and Depression : Results From the Longitudinal Aging Study Amsterdam

    NARCIS (Netherlands)

    Hilderink, Peter H.; Burger, Huibert; Deeg, Dorly J.; Beekman, Aartjan T.; Voshaar, Richard C. Oude

    2012-01-01

    Objective: Pain and depression are both common in old age, but their (long-term) temporal relationship remains unknown. This study is designed to determine whether pain predicts the onset of depression and vice versa. Methods: This is a prospective, population-based cohort study with 12-year

  7. Insomnia and Its Temporal Association with Academic Performance among University Students : A Cross-Sectional Study

    NARCIS (Netherlands)

    Haile, Yohannes Gebreegziabhere; Alemu, Sisay Mulugeta; Habtewold, Tesfa Dejenie

    2017-01-01

    INTRODUCTION: Studies show that 9.4% to 38.2% of university students are suffering from insomnia. However, research data in developing countries is limited. Thus, the aim of the study was to assess insomnia and its temporal association with academic performance. METHODS AND MATERIALS: Institution

  8. Normalization for triple-target microarray experiments

    Directory of Open Access Journals (Sweden)

    Magniette Frederic

    2008-04-01

    Full Text Available Abstract Background Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are Cy3 and Cy5. Recent improvements in the technology (dye-labelling, scanner and, image analysis allow hybridization up to four samples simultaneously. The two additional dyes are Alexa488 and Alexa494. The triple-target or four-target technology is very promising, since it allows more flexibility in the design of experiments, an increase in the statistical power when comparing gene expressions induced by different conditions and a scaled down number of slides. However, there have been few methods proposed for statistical analysis of such data. Moreover the lowess correction of the global dye effect is available for only two-color experiments, and even if its application can be derived, it does not allow simultaneous correction of the raw data. Results We propose a two-step normalization procedure for triple-target experiments. First the dye bleeding is evaluated and corrected if necessary. Then the signal in each channel is normalized using a generalized lowess procedure to correct a global dye bias. The normalization procedure is validated using triple-self experiments and by comparing the results of triple-target and two-color experiments. Although the focus is on triple-target microarrays, the proposed method can be used to normalize p differently labelled targets co-hybridized on a same array, for any value of p greater than 2. Conclusion The proposed normalization procedure is effective: the technical biases are reduced, the number of false positives is under control in the analysis of differentially expressed genes, and the triple-target experiments are more powerful than the corresponding two-color experiments. There is room for improving the microarray experiments by simultaneously hybridizing more than two samples.

  9. Project Temporalities

    DEFF Research Database (Denmark)

    Tryggestad, Kjell; Justesen, Lise; Mouritsen, Jan

    2013-01-01

    Purpose – The purpose of this paper is to explore how animals can become stakeholders in interaction with project management technologies and what happens with project temporalities when new and surprising stakeholders become part of a project and a recognized matter of concern to be taken...... into account. Design/methodology/approach – The paper is based on a qualitative case study of a project in the building industry. The authors use actor-network theory (ANT) to analyze the emergence of animal stakeholders, stakes and temporalities. Findings – The study shows how project temporalities can...... multiply in interaction with project management technologies and how conventional linear conceptions of project time may be contested with the emergence of new non-human stakeholders and temporalities. Research limitations/implications – The study draws on ANT to show how animals can become stakeholders...

  10. The right hemisphere's contribution to discourse processing: A study in temporal lobe epilepsy.

    Science.gov (United States)

    Lomlomdjian, Carolina; Múnera, Claudia P; Low, Daniel M; Terpiluk, Verónica; Solís, Patricia; Abusamra, Valeria; Kochen, Silvia

    2017-08-01

    Discourse skills - in which the right hemisphere has an important role - enables verbal communication by selecting contextually relevant information and integrating it coherently to infer the correct meaning. However, language research in epilepsy has focused on single word analysis related mainly to left hemisphere processing. The purpose of this study was to investigate discourse abilities in patients with right lateralized medial temporal lobe epilepsy (RTLE) by comparing their performance to that of patients with left temporal lobe epilepsy (LTLE). 74 pharmacoresistant temporal lobe epilepsy (TLE) patients were evaluated: 34 with RTLE and 40 with LTLE. Subjects underwent a battery of tests that measure comprehension and production of conversational and narrative discourse. Disease related variables and general neuropsychological data were evaluated. The RTLE group presented deficits in interictal conversational and narrative discourse, with a disintegrated speech, lack of categorization and misinterpretation of social meaning. LTLE group, on the other hand, showed a tendency to lower performance in logical-temporal sequencing. RTLE patients showed discourse deficits which have been described in right hemisphere damaged patients due to other etiologies. Medial and anterior temporal lobe structures appear to link semantic, world knowledge, and social cognition associated areas to construct a contextually related coherent meaning. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. A permutation-based multiple testing method for time-course microarray experiments

    Directory of Open Access Journals (Sweden)

    George Stephen L

    2009-10-01

    Full Text Available Abstract Background Time-course microarray experiments are widely used to study the temporal profiles of gene expression. Storey et al. (2005 developed a method for analyzing time-course microarray studies that can be applied to discovering genes whose expression trajectories change over time within a single biological group, or those that follow different time trajectories among multiple groups. They estimated the expression trajectories of each gene using natural cubic splines under the null (no time-course and alternative (time-course hypotheses, and used a goodness of fit test statistic to quantify the discrepancy. The null distribution of the statistic was approximated through a bootstrap method. Gene expression levels in microarray data are often complicatedly correlated. An accurate type I error control adjusting for multiple testing requires the joint null distribution of test statistics for a large number of genes. For this purpose, permutation methods have been widely used because of computational ease and their intuitive interpretation. Results In this paper, we propose a permutation-based multiple testing procedure based on the test statistic used by Storey et al. (2005. We also propose an efficient computation algorithm. Extensive simulations are conducted to investigate the performance of the permutation-based multiple testing procedure. The application of the proposed method is illustrated using the Caenorhabditis elegans dauer developmental data. Conclusion Our method is computationally efficient and applicable for identifying genes whose expression levels are time-dependent in a single biological group and for identifying the genes for which the time-profile depends on the group in a multi-group setting.

  12. The prognostic implication of the expression of EGFR, p53, cyclin D1, Bcl-2 and p16 in primary locally advanced oral squamous cell carcinoma cases: a tissue microarray study.

    Science.gov (United States)

    Solomon, Monica Charlotte; Vidyasagar, M S; Fernandes, Donald; Guddattu, Vasudev; Mathew, Mary; Shergill, Ankur Kaur; Carnelio, Sunitha; Chandrashekar, Chetana

    2016-12-01

    Oral squamous cell carcinomas comprise a heterogeneous tumor cell population with varied molecular characteristics, which makes prognostication of these tumors a complex and challenging issue. Thus, molecular profiling of these tumors is advantageous for an accurate prognostication and treatment planning. This is a retrospective study on a cohort of primary locally advanced oral squamous cell carcinomas (n = 178) of an Indian rural population. The expression of EGFR, p53, cyclin D1, Bcl-2 and p16 in a cohort of primary locally advanced oral squamous cell carcinomas was evaluated. A potential biomarker that can predict the tumor response to treatment was identified. Formalin-fixed paraffin-embedded tumor blocks of (n = 178) of histopathologically diagnosed cases of locally advanced oral squamous cell carcinomas were selected. Tissue microarray blocks were constructed with 2 cores of 2 mm diameter from each tumor block. Four-micron-thick sections were cut from these tissue microarray blocks. These tissue microarray sections were immunohistochemically stained for EGFR, p53, Bcl-2, cyclin D1 and p16. In this cohort, EGFR was the most frequently expressed 150/178 (84%) biomarker of the cases. Kaplan-Meier analysis showed a significant association (p = 0.038) between expression of p53 and a poor prognosis. A Poisson regression analysis showed that tumors that expressed p53 had a two times greater chance of recurrence (unadjusted IRR-95% CI 2.08 (1.03, 4.5), adjusted IRR-2.29 (1.08, 4.8) compared with the tumors that did not express this biomarker. Molecular profiling of oral squamous cell carcinomas will enable us to categorize our patients into more realistic risk groups. With biologically guided tumor characterization, personalized treatment protocols can be designed for individual patients, which will improve the quality of life of these patients.

  13. Advanced Data Mining of Leukemia Cells Micro-Arrays

    Directory of Open Access Journals (Sweden)

    Richard S. Segall

    2009-12-01

    Full Text Available This paper provides continuation and extensions of previous research by Segall and Pierce (2009a that discussed data mining for micro-array databases of Leukemia cells for primarily self-organized maps (SOM. As Segall and Pierce (2009a and Segall and Pierce (2009b the results of applying data mining are shown and discussed for the data categories of microarray databases of HL60, Jurkat, NB4 and U937 Leukemia cells that are also described in this article. First, a background section is provided on the work of others pertaining to the applications of data mining to micro-array databases of Leukemia cells and micro-array databases in general. As noted in predecessor article by Segall and Pierce (2009a, micro-array databases are one of the most popular functional genomics tools in use today. This research in this paper is intended to use advanced data mining technologies for better interpretations and knowledge discovery as generated by the patterns of gene expressions of HL60, Jurkat, NB4 and U937 Leukemia cells. The advanced data mining performed entailed using other data mining tools such as cubic clustering criterion, variable importance rankings, decision trees, and more detailed examinations of data mining statistics and study of other self-organized maps (SOM clustering regions of workspace as generated by SAS Enterprise Miner version 4. Conclusions and future directions of the research are also presented.

  14. Senescent vs. non-senescent cells in the human annulus in vivo: Cell harvest with laser capture microdissection and gene expression studies with microarray analysis

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    Ingram Jane A

    2010-01-01

    Full Text Available Abstract Background Senescent cells are well-recognized in the aging/degenerating human disc. Senescent cells are viable, cannot divide, remain metabolically active and accumulate within the disc over time. Molecular analysis of senescent cells in tissue offers a special challenge since there are no cell surface markers for senescence which would let one use fluorescence-activated cell sorting as a method for separating out senescent cells. Methods We employed a novel laser capture microdissection (LCM design to selectively harvest senescent and non-senescent annulus cells in paraffin-embedded tissue, and compared their gene expression with microarray analysis. LCM was used to separately harvest senescent and non-senescent cells from 11 human annulus specimens. Results Microarray analysis revealed significant differences in expression levels in senescent cells vs non-senescent cells: 292 genes were upregulated, and 321 downregulated. Genes with established relationships to senescence were found to be significantly upregulated in senescent cells vs. non-senescent cells: p38 (MPAK14, RB-Associated KRAB zinc finger, Discoidin, CUB and LCCL domain, growth arrest and DNA-damage inducible beta, p28ING5, sphingosine-1-phosphate receptor 2 and somatostatin receptor 3; cyclin-dependent kinase 8 showed significant downregulation in senescent cells. Nitric oxidase synthase 1, and heat shock 70 kDa protein 6, both of which were significantly down-regulated in senescent cells, also showed significant changes. Additional genes related to cytokines, cell proliferation, and other processes were also identified. Conclusions Our LCM-microarray analyses identified a set of genes associated with senescence which were significantly upregulated in senescent vs non-senescent cells in the human annulus. These genes include p38 MAP kinase, discoidin, inhibitor of growth family member 5, and growth arrest and DNA-damage-inducible beta. Other genes, including genes

  15. A Case Study of a Child with Dyslexia and Spatial-Temporal Gifts

    Science.gov (United States)

    Cooper, Eileen E.; Ness, Maryann; Smith, Mary

    2004-01-01

    This case study details the history and K-5 school experience of a boy with dyslexia and spatial-temporal gifts. It describes assessment, evaluation, and identification procedures; the learning specialist's interventions and program; the critical role of the parent; and the services provided by the gifted program. Specific interventions are…

  16. Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes

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    Eils Roland

    2005-11-01

    Full Text Available Abstract Background The extensive use of DNA microarray technology in the characterization of the cell transcriptome is leading to an ever increasing amount of microarray data from cancer studies. Although similar questions for the same type of cancer are addressed in these different studies, a comparative analysis of their results is hampered by the use of heterogeneous microarray platforms and analysis methods. Results In contrast to a meta-analysis approach where results of different studies are combined on an interpretative level, we investigate here how to directly integrate raw microarray data from different studies for the purpose of supervised classification analysis. We use median rank scores and quantile discretization to derive numerically comparable measures of gene expression from different platforms. These transformed data are then used for training of classifiers based on support vector machines. We apply this approach to six publicly available cancer microarray gene expression data sets, which consist of three pairs of studies, each examining the same type of cancer, i.e. breast cancer, prostate cancer or acute myeloid leukemia. For each pair, one study was performed by means of cDNA microarrays and the other by means of oligonucleotide microarrays. In each pair, high classification accuracies (> 85% were achieved with training and testing on data instances randomly chosen from both data sets in a cross-validation analysis. To exemplify the potential of this cross-platform classification analysis, we use two leukemia microarray data sets to show that important genes with regard to the biology of leukemia are selected in an integrated analysis, which are missed in either single-set analysis. Conclusion Cross-platform classification of multiple cancer microarray data sets yields discriminative gene expression signatures that are found and validated on a large number of microarray samples, generated by different laboratories and

  17. Gene Expression Profile in the Early Stage of Angiotensin II-induced Cardiac Remodeling: a Time Series Microarray Study in a Mouse Model

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    Meng-Qiu Dang

    2015-01-01

    Full Text Available Background/Aims: Angiotensin II (Ang II plays a critical role in the cardiac remodeling contributing to heart failure. However, the gene expression profiles induced by Ang II in the early stage of cardiac remodeling remain unknown. Methods: Wild-type male mice (C57BL/6 background, 10-weeek-old were infused with Ang II (1500 ng/kg/min for 7 days. Blood pressure was measured. Cardiac function and remodeling were examined by echocardiography, H&E and Masson staining. The time series microarrays were then conducted to detected gene expression profiles. Results: Microarray results identified that 1,489 genes were differentially expressed in the hearts at day 1, 3 and 7 of Ang II injection. These genes were further classified into 26 profiles by hierarchical cluster analysis. Of them, 4 profiles were significant (No. 19, 8, 21 and 22 and contained 904 genes. Gene Ontology showed that these genes mainly participate in metabolic process, oxidation-reduction process, extracellular matrix organization, apoptotic process, immune response, and others. Significant pathways included focal adhesion, ECM-receptor interaction, cytokine-cytokine receptor interaction, MAPK and insulin signaling pathways, which were known to play important roles in Ang II-induced cardiac remodeling. Moreover, gene co-expression networks analysis suggested that serine/cysteine peptidase inhibitor, member 1 (Serpine1, also known as PAI-1 localized in the core of the network. Conclusions: Our results indicate that many genes are mainly involved in metabolism, inflammation, cardiac fibrosis and hypertrophy. Serpine1 may play a central role in the development of Ang II-induced cardiac remodeling at the early stage.

  18. Surgical and postmortem pathology studies: contribution for the investigation of temporal lobe epilepsy.

    Science.gov (United States)

    Caboclo, Luís Otávio Sales Ferreira; Neves, Rafael Scarpa; Jardim, Anaclara Prada; Hamad, Ana Paula Andrade; Centeno, Ricardo Silva; Lancellotti, Carmen Lucia Penteado; Scorza, Carla Alessandra; Cavalheiro, Esper Abrão; Yacubian, Elza Márcia Targas; Sakamoto, Américo Ceiki

    2012-12-01

    Pathology studies in epilepsy patients bring useful information for comprehending the physiopathology of various forms of epilepsy, as well as aspects related to response to treatment and long-term prognosis. These studies are usually restricted to surgical specimens obtained from patients with refractory focal epilepsies. Therefore, most of them pertain to temporal lobe epilepsy (TLE) with mesial temporal sclerosis (MTS) and malformations of cortical development (MCD), thus providing information of a selected group of patients and restricted regions of the brain. Postmortem whole brain studies are rarely performed in epilepsy patients, however they may provide extensive information on brain pathology, allowing the analysis of areas beyond the putative epileptogenic zone. In this article, we reviewed pathology studies performed in epilepsy patients with emphasis on neuropathological findings in TLE with MTS and MCD. Furthermore, we reviewed data from postmortem studies and discussed the importance of performing these studies in epilepsy populations.

  19. Surgical and postmortem pathology studies: contribution for the investigation of temporal lobe epilepsy

    Directory of Open Access Journals (Sweden)

    Luís Otávio Sales Ferreira Caboclo

    2012-12-01

    Full Text Available Pathology studies in epilepsy patients bring useful information for comprehending the physiopathology of various forms of epilepsy, as well as aspects related to response to treatment and long-term prognosis. These studies are usually restricted to surgical specimens obtained from patients with refractory focal epilepsies. Therefore, most of them pertain to temporal lobe epilepsy (TLE with mesial temporal sclerosis (MTS and malformations of cortical development (MCD, thus providing information of a selected group of patients and restricted regions of the brain. Postmortem whole brain studies are rarely performed in epilepsy patients, however they may provide extensive information on brain pathology, allowing the analysis of areas beyond the putative epileptogenic zone. In this article, we reviewed pathology studies performed in epilepsy patients with emphasis on neuropathological findings in TLE with MTS and MCD. Furthermore, we reviewed data from postmortem studies and discussed the importance of performing these studies in epilepsy populations.

  20. Comparing transformation methods for DNA microarray data

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    Zwinderman Aeilko H

    2004-06-01

    Full Text Available Abstract Background When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order to improve comparability and signal/noise ratio. These steps may include subtraction of an estimated background signal, subtracting the reference signal, smoothing (to account for nonlinear measurement effects, and more. Different authors use different approaches, and it is generally not clear to users which method they should prefer. Results We used the ratio between biological variance and measurement variance (which is an F-like statistic as a quality measure for transformation methods, and we demonstrate a method for maximizing that variance ratio on real data. We explore a number of transformations issues, including Box-Cox transformation, baseline shift, partial subtraction of the log-reference signal and smoothing. It appears that the optimal choice of parameters for the transformation methods depends on the data. Further, the behavior of the variance ratio, under the null hypothesis of zero biological variance, appears to depend on the choice of parameters. Conclusions The use of replicates in microarray experiments is important. Adjustment for the null-hypothesis behavior of the variance ratio is critical to the selection of transformation method.

  1. DNA microarray data and contextual analysis of correlation graphs

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    Hingamp Pascal

    2003-04-01

    Full Text Available Abstract Background DNA microarrays are used to produce large sets of expression measurements from which specific biological information is sought. Their analysis requires efficient and reliable algorithms for dimensional reduction, classification and annotation. Results We study networks of co-expressed genes obtained from DNA microarray experiments. The mathematical concept of curvature on graphs is used to group genes or samples into clusters to which relevant gene or sample annotations are automatically assigned. Application to publicly available yeast and human lymphoma data demonstrates the reliability of the method in spite of its simplicity, especially with respect to the small number of parameters involved. Conclusions We provide a method for automatically determining relevant gene clusters among the many genes monitored with microarrays. The automatic annotations and the graphical interface improve the readability of the data. A C++ implementation, called Trixy, is available from http://tagc.univ-mrs.fr/bioinformatics/trixy.html.

  2. "Harshlighting" small blemishes on microarrays

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    Wittkowski Knut M

    2005-03-01

    Full Text Available Abstract Background Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans show similar artefacts, which affect the analysis, particularly when one tries to detect subtle changes. However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs. Results We present a method that harnesses the statistical power provided by having several HDONAs available, which are obtained under similar conditions except for the experimental factor. This method "harshlights" blemishes and renders them evident. We find empirically that about 25% of our chips are blemished, and we analyze the impact of masking them on screening for differentially expressed genes. Conclusion Experiments attempting to assess subtle expression changes should be carefully screened for blemishes on the chips. The proposed method provides investigators with a novel robust approach to improve the sensitivity of microarray analyses. By utilizing topological information to identify and mask blemishes prior to model based analyses, the method prevents artefacts from confounding the process of background correction, normalization, and summarization.

  3. Insomnia and Its Temporal Association with Academic Performance among University Students: A Cross-Sectional Study

    OpenAIRE

    Haile, Yohannes Gebreegziabhere; Alemu, Sisay Mulugeta; Habtewold, Tesfa Dejenie

    2017-01-01

    INTRODUCTION: Studies show that 9.4% to 38.2% of university students are suffering from insomnia. However, research data in developing countries is limited. Thus, the aim of the study was to assess insomnia and its temporal association with academic performance. METHODS AND MATERIALS: Institution based cross-sectional study was conducted with 388 students at Debre Berhan University. Data were collected at the nine colleges. Logistic and linear regression analysis was performed for modeling in...

  4. Gender and hemispheric differences in temporal lobe epilepsy: a VBM study.

    Science.gov (United States)

    Santana, Maria Teresa Castilho Garcia; Jackowski, Andrea Parolin; Britto, Fernanda Dos Santos; Sandim, Gabriel Barbosa; Caboclo, Luís Otávio Sales Ferreira; Centeno, Ricardo Silva; Carrete, Henrique; Yacubian, Elza Márcia Targas

    2014-04-01

    Gender differences are recognized in the functional and anatomical organization of the human brain. Differences between genders are probably expressed early in life, when differential rates of cerebral maturation occur. Sexual dimorphism has been described in temporal lobe epilepsy with mesial temporal sclerosis (TLE-MTS). Several voxel-based morphometry (VBM) studies have shown that TLE-MTS extends beyond mesial temporal structures, and that there are differences in the extent of anatomical damage between hemispheres, although none have approached gender differences. Our aim was to investigate gender differences and anatomical abnormalities in TLE-MTS. VBM5 was employed to analyze gender and hemispheric differences in 120 patients with TLE-MTS and 50 controls. VBM abnormalities were more widespread in left-TLE; while in women changes were mostly seen in temporal areas, frontal regions were more affected in men. Our study confirmed that gender and laterality are important factors determining the nature and severity of brain damage in TLE-MTS. Differential rates of maturation between gender and hemispheres may explain the distinct areas of anatomical damage in men and women. Copyright © 2013 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

  5. Carbamazepine reduces memory induced activation of mesial temporal lobe structures: a pharmacological fMRI-study

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    Okujava Michael

    2001-11-01

    Full Text Available Abstract Background and Purpose It is not known whether carbamazepine (CBZ; a drug widely used in neurology and psychiatry influences the blood oxygenation level dependent (BOLD contrast changes induced by neuronal activation and measured by functional MRI (fMRI. We aimed to investigate the influence of CBZ on memory induced activation of the mesial temporal lobes in patients with symptomatic temporal lobe epilepsy (TLE. Material and Methods Twenty-one individual patients with refractory symptomatic TLE with different CBZ serum levels and 20 healthy controls were studied using BOLD fMRI. Mesial temporal lobe (MTL activation was induced by a task that is based on the retrieval of individually familiar visuo-spatial knowledge. The extent of significant MTL fMRI activation was measured and correlated with the CBZ serum level. Results In TLE patients, the extent of significant fMRI activation over both MTL was negatively correlated to the CBZ serum level (Spearman r = -0.654, P Conclusions In TLE patients, carbamazepine reduces the fMRI-detectable changes within the mesial temporal lobes as induced by effortful memory retrieval. FMRI appears to be suitable to study the effects of chronic drug treatment in patients with epilepsy.

  6. Temporal Bone Fractures and its Classification: Retrospective Study of Incidence, Causes, Clinical Features, Complications and Outcome

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    Umamaheshwari Basavaraju

    2017-10-01

    Full Text Available Introduction: Temporal bone fracture is usually associated with high energy head injury and can cause potentially severe complications. Immediate detection of temporal bone fracture and its complications helps in providing early and effective treatment, which if left untreated can have drastic consequences. Aim: The main objective of the study is to document the frequency and most prevalent type of temporal bone fracture, co-existing complications and to establish association between them. Materials and Methods: One year (2015-2016 retrospective study of head injured patients presented to the Emergency Department, Mysore Medical College And Research Institute was conducted. Age and gender distribution, cause of injury, radiological findings, otorhinolaryngological clinical presentations and treatment given were analyzed. The results were tabulated and were evaluated by Microsoft Excel 2013. Results: Out of 1450 patients evaluated for head injury 154 patients were positive for temporal bone fracture. Incidence of the study was 10.6%. Majority of the patients were male (66.2% and were between 30 to 40 years (50.1%. The major cause of injury was motor vehicle accidents (84.48%. Right side was involved (58.4% more than the left side (41.5%. Most common clinical presentation was otorrhea 68.8%, followed by otalgia (35.04% and otorhinorrhea (24.67%. Longitudinal type fracture was most frequent 56.25%. Otic capsule involvement was present in 35.93%. Most of the fractures were managed conservatively whereas surgery was required in 12 patients (7.7%. Conclusion: Temporal bone fractures were frequently associated with severe traumatic brain injury leading to serious long term morbidity and sequelae. CT-scan is of utmost importance in detection of fractures and its complications.

  7. Quantitative Evaluation of Medial Temporal Lobe Morphology in Children with Febrile Status Epilepticus: Results of the FEBSTAT Study.

    Science.gov (United States)

    McClelland, A C; Gomes, W A; Shinnar, S; Hesdorffer, D C; Bagiella, E; Lewis, D V; Bello, J A; Chan, S; MacFall, J; Chen, M; Pellock, J M; Nordli, D R; Frank, L M; Moshé, S L; Shinnar, R C; Sun, S

    2016-12-01

    The pathogenesis of febrile status epilepticus is poorly understood, but prior studies have suggested an association with temporal lobe abnormalities, including hippocampal malrotation. We used a quantitative morphometric method to assess the association between temporal lobe morphology and febrile status epilepticus. Brain MR imaging was performed in children presenting with febrile status epilepticus and control subjects as part of the Consequences of Prolonged Febrile Seizures in Childhood study. Medial temporal lobe morphologic parameters were measured manually, including the distance of the hippocampus from the midline, hippocampal height:width ratio, hippocampal angle, collateral sulcus angle, and width of the temporal horn. Temporal lobe morphologic parameters were correlated with the presence of visual hippocampal malrotation; the strongest association was with left temporal horn width (P status epilepticus, encompassing both the right and left sides. This association was statistically strongest in the right temporal lobe, whereas hippocampal malrotation was almost exclusively left-sided in this cohort. The association between temporal lobe measurements and febrile status epilepticus persisted when the analysis was restricted to cases with visually normal imaging findings without hippocampal malrotation or other visually apparent abnormalities. Several component morphologic features of hippocampal malrotation are independently associated with febrile status epilepticus, even when complete hippocampal malrotation is absent. Unexpectedly, this association predominantly involves the right temporal lobe. These findings suggest that a spectrum of bilateral temporal lobe anomalies are associated with febrile status epilepticus in children. Hippocampal malrotation may represent a visually apparent subset of this spectrum. © 2016 by American Journal of Neuroradiology.

  8. Atrophy progression in semantic dementia with asymmetric temporal involvement: a tensor-based morphometry study.

    Science.gov (United States)

    Brambati, S M; Rankin, K P; Narvid, J; Seeley, W W; Dean, D; Rosen, H J; Miller, B L; Ashburner, J; Gorno-Tempini, M L

    2009-01-01

    We performed a longitudinal anatomical study to map the progression of gray matter atrophy in anatomically defined predominantly left (LTLV) and right (RTLV) temporal lobe variants of semantic dementia (SD). T1-weighted MRI scans were obtained at presentation and one-year follow-up from 13 LTLV, 6 RTLV, and 25 control subjects. Tensor-based morphometry (TBM) in SPM2 was applied to derive a voxel-wise estimation of regional tissue loss over time from the deformation field required to warp the follow-up scan to the presentation scan in each subject. When compared to controls, both LTLV and RTLV showed significant progression of gray matter atrophy not only within the temporal lobe most affected at presentation, but also in the controlateral temporal regions (p<0.05 FWE corrected). In LTLV, significant progression of volume loss also involved the ventromedial frontal and the left anterior insular regions. These results identified the anatomic substrates of the previously reported clinical evolution of LTLV and RTLV into a unique 'merged' clinical syndrome characterized by semantic and behavioral deficits and bilateral temporal atrophy.

  9. Distorted temporal consciousness and preserved knowing consciousness in confabulation: a case study.

    Science.gov (United States)

    La Corte, Valentina; George, Nathalie; Pradat-Diehl, Pascale; Barba, Gianfranco Dalla

    2011-01-01

    In this study we describe a patient, TA, who developed a chronic amnesic-confabulatory syndrome, following rupture of a right internal carotid siphon aneurysm. Our aim was to elucidate as fully as possible the nature of TA's impairment and to test the hypothesis of confabulation as reflecting a dysfunction of Temporal Consciousness, i.e., to become aware of something as part of a personal past, present or future. TA's confabulations were present in answers to questions tapping Temporal Consciousness, i.e., autobiographical episodic memory, orientation in time and place, and foresight of personal future. In contrast, confabulations were not observed in answers to questions tapping Knowing Consciousness, i.e., to become aware of something as a meaning or as an element of impersonal knowledge. In fact, he had normal access to semantic knowledge, including foresight of impersonal future. TA's brain MRI showed lesions involving the right hippocampus, parahippocampal gyrus, fornix, mammillary bodies, and thalamus. Moreover TA showed sub-cortical lesions involving the caudate and putamen nuclei bilaterally, a lesion site not commonly described in amnesic-confabulatory syndrome. We suggest that this pattern of results is better accounted for within the framework of the Memory, Consciousness and Temporality Theory and reflects a specific distortion of Temporal Consciousness.

  10. Oscar Wilde as a Temporal Designer: A Case Study of The Picture of Dorian Gray

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    Bahram Behin

    2015-03-01

    Full Text Available Since the publication of Oscar Wilde’s The Picture of Dorian Gray, there have been great amounts of ideological criticism both for and against the author and the work. Critics have variously evaluated the work from different perspectives; however, these studies have largely targeted the thematic aspects of the novel, while little serious attempt has been made to examine the narrativity of this great work. As a result, the narrative structure of this novel still remains quite untouched. As a partial fulfillment, the present paper has examined the temporal structure of the novel. The analysis indicated that temporality is one of the very functional elements of the work. In fact, much of the meaning or the effect the author intends to converse through each action, character, or dialogue is firstly embedded in a proper and effective temporal setting. Moreover, the analysis ascertained that the well-set temporal structure of the work has resulted in (1 Ekphrasis, (2 Characterization, and (3 Reader manipulation. According to the paper, these three elements dramatically carry out the influentiality of this great novel.

  11. Large cross-sectional study of presbycusis reveals rapid progressive decline in auditory temporal acuity.

    Science.gov (United States)

    Ozmeral, Erol J; Eddins, Ann C; Frisina, D Robert; Eddins, David A

    2016-07-01

    The auditory system relies on extraordinarily precise timing cues for the accurate perception of speech, music, and object identification. Epidemiological research has documented the age-related progressive decline in hearing sensitivity that is known to be a major health concern for the elderly. Although smaller investigations indicate that auditory temporal processing also declines with age, such measures have not been included in larger studies. Temporal gap detection thresholds (TGDTs; an index of auditory temporal resolution) measured in 1071 listeners (aged 18-98 years) were shown to decline at a minimum rate of 1.05 ms (15%) per decade. Age was a significant predictor of TGDT when controlling for audibility (partial correlation) and when restricting analyses to persons with normal-hearing sensitivity (n = 434). The TGDTs were significantly better for males (3.5 ms; 51%) than females when averaged across the life span. These results highlight the need for indices of temporal processing in diagnostics, as treatment targets, and as factors in models of aging. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Microscopic mild focal cortical dysplasia in temporal lobe dual pathology: an electrocorticography study.

    Science.gov (United States)

    Morales Chacón, L; Estupiñán, B; Lorigados Pedre, L; Trápaga Quincoses, O; García Maeso, I; Sanchez, A; Bender del Busto, J; Garcia, M E; Baez Martin, M; Zaldivar, M; Gómez, A; Orozco, S; Rocha Arrieta, L

    2009-10-01

    Associations between electrophysiological and histological findings might provide an insight into the epileptogenicity of mild focal cortical dysplasia (FCD) in patients with temporal lobe epilepsy (TLE) and a dual pathology. A total of 22 patients with pharmacoresistant TLE were included in the study, 16 of them with histologically confirmed hippocampal sclerosis (HS) associated with neocortical temporal mild Palmini Type-I FCD subtypes and 6 with HS. Intraoperative electrocorticography (ECoG) recordings were analysed for epileptiform discharge frequency and morphology. Associations between histological, and electrocorticography pattern findings in these patients were analysed. Electroclinical outcomes in these patients were also evaluated. Neocortical areas with mild Palmini Type-I FCD showed a significantly higher spike frequency (SF) recorded in the inferior temporal gyrus than those neocortical areas in patients with HS. There was a tendency to higher spike frequency and lower amplitude in neocortical areas with histopathologic subtype IB FCD in relation with IA during intraoperative ECoG. Post-SF excision and amplitude were significantly lower during neocortical post-excision intraoperative ECoG than during neocortical pre-excision recording. There was no difference found in the clinical outcome between patients with and without FCD. Intraoperative electrocorticographic interictal spike frequency recorded in the neocortical inferior temporal gyrus may help to characterize the histopathologic subtypes of mild Palmini Type-I FCD in patients with temporal lobe epilepsy (TLE) and a dual pathology. Our data support the epileptogenicity of neocortical mild FCD in TLE and assessments of ECoG patterns are relevant to determine the extent of the resection in these patients which can influence the electroclinical outcome.

  13. Advanced microarray technologies for clinical diagnostics

    NARCIS (Netherlands)

    Pierik, Anke

    2011-01-01

    DNA microarrays become increasingly important in the field of clinical diagnostics. These microarrays, also called DNA chips, are small solid substrates, typically having a maximum surface area of a few cm2, onto which many spots are arrayed in a pre-determined pattern. Each of these spots contains

  14. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.

    Science.gov (United States)

    Fernandez, Paula; Soria, Marcelo; Blesa, David; DiRienzo, Julio; Moschen, Sebastian; Rivarola, Maximo; Clavijo, Bernardo Jose; Gonzalez, Sergio; Peluffo, Lucila; Príncipi, Dario; Dosio, Guillermo; Aguirrezabal, Luis; García-García, Francisco; Conesa, Ana; Hopp, Esteban; Dopazo, Joaquín; Heinz, Ruth Amelia; Paniego, Norma

    2012-01-01

    Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (psunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  15. Carbohydrate Microarrays in Plant Science

    DEFF Research Database (Denmark)

    Fangel, Jonatan Ulrik; Pedersen, H.L.; Vidal-Melgosa, S.

    2012-01-01

    Almost all plant cells are surrounded by glycan-rich cell walls, which form much of the plant body and collectively are the largest source of biomass on earth. Plants use polysaccharides for support, defense, signaling, cell adhesion, and as energy storage, and many plant glycans are also important...... industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high...... for plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities....

  16. The EADGENE Microarray Data Analysis Workshop

    DEFF Research Database (Denmark)

    de Koning, Dirk-Jan; Jaffrézic, Florence; Lund, Mogens Sandø

    2007-01-01

    Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from...... 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays...... statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful...

  17. Examining Procrastination Across Multiple Goal Stages: A Longitudinal Study of Temporal Motivation Theory

    Directory of Open Access Journals (Sweden)

    Piers Steel

    2018-04-01

    Full Text Available Procrastination is among the most common of motivational failures, putting off despite expecting to be worse off. We examine this dynamic phenomenon in a detailed and realistic longitudinal design (Study 1 as well as in a large correlational data set (N = 7400; Study 2. The results are largely consistent with temporal motivation theory. People’s pacing style reflects a hyperbolic curve, with the steepness of the curve predicted by self-reported procrastination. Procrastination is related to intention-action gaps, but not intentions. Procrastinators are susceptible to proximity of temptation and to the temporal separation between their intention and the planned act; the more distal, the greater the gap. Critical self-regulatory skills in explaining procrastination are attention control, energy regulation and automaticity, accounting for 74% of the variance. Future research using this design is recommended, as it provides an almost ideal blend of realism and detailed longitudinal assessment.

  18. Examining Procrastination Across Multiple Goal Stages: A Longitudinal Study of Temporal Motivation Theory.

    Science.gov (United States)

    Steel, Piers; Svartdal, Frode; Thundiyil, Tomas; Brothen, Thomas

    2018-01-01

    Procrastination is among the most common of motivational failures, putting off despite expecting to be worse off. We examine this dynamic phenomenon in a detailed and realistic longitudinal design (Study 1) as well as in a large correlational data set ( N = 7400; Study 2). The results are largely consistent with temporal motivation theory. People's pacing style reflects a hyperbolic curve, with the steepness of the curve predicted by self-reported procrastination. Procrastination is related to intention-action gaps, but not intentions. Procrastinators are susceptible to proximity of temptation and to the temporal separation between their intention and the planned act; the more distal, the greater the gap. Critical self-regulatory skills in explaining procrastination are attention control, energy regulation and automaticity, accounting for 74% of the variance. Future research using this design is recommended, as it provides an almost ideal blend of realism and detailed longitudinal assessment.

  19. Studies of the expression of human poly(ADP-ribose) polymerase-1 in Saccharomyces cerevisiae and identification of PARP-1 substrates by yeast proteome microarray screening.

    Science.gov (United States)

    Tao, Zhihua; Gao, Peng; Liu, Hung-Wen

    2009-12-15

    Poly(ADP-ribosyl)ation of various nuclear proteins catalyzed by a family of NAD(+)-dependent enzymes, poly(ADP-ribose) polymerases (PARPs), is an important posttranslational modification reaction. PARP activity has been demonstrated in all types of eukaryotic cells with the exception of yeast, in which the expression of human PARP-1 was shown to lead to retarded cell growth. We investigated the yeast growth inhibition caused by human PARP-1 expression in Saccharomyces cerevisiae. Flow cytometry analysis reveals that PARP-1-expressing yeast cells accumulate in the G(2)/M stage of the cell cycle. Confocal microscopy analysis shows that human PARP-1 is distributed throughout the nucleus of yeast cells but is enriched in the nucleolus. Utilizing yeast proteome microarray screening, we identified 33 putative PARP-1 substrates, six of which are known to be involved in ribosome biogenesis. The poly(ADP-ribosyl)ation of three of these yeast proteins, together with two human homologues, was confirmed by an in vitro PARP-1 assay. Finally, a polysome profile analysis using sucrose gradient ultracentrifugation demonstrated that the ribosome levels in yeast cells expressing PARP-1 are lower than those in control yeast cells. Overall, our data suggest that human PARP-1 may affect ribosome biogenesis by modifying certain nucleolar proteins in yeast. The artificial PARP-1 pathway in yeast may be used as a simple platform to identify substrates and verify function of this important enzyme.

  20. Temporal pole signal abnormality on MR imaging in temporal lobe epilepsy with hippocampal sclerosis: a fluid-attenuated inversion-recovery study.

    Science.gov (United States)

    Carrete, Henrique; Abdala, Nitamar; Lin, Kátia; Caboclo, Luís Otávio; Centeno, Ricardo Silva; Sakamoto, Américo Ceiki; Szjenfeld, Jacob; Nogueira, Roberto Gomes; Yacubian, Elza Márcia Targas

    2007-09-01

    To determine the frequency and regional involvement of temporal pole signal abnormality (TPA) in patients with hippocampal sclerosis (HS) using fluid-attenuated inversion-recovery (FLAIR) MR imaging, and to correlate this feature with history. Coronal FLAIR images of the temporal pole were assessed in 120 patients with HS and in 30 normal subjects, to evaluate gray-white matter demarcation. Ninety (75%) of 120 patients had associated TPA. The HS side made difference regarding the presence of TPA, with a left side prevalence (p=0.04, chi2 test). The anteromedial zone of temporal pole was affected in 27 (30%) out of 90 patients. In 63 (70%) patients the lateral zone were also affected. Patients with TPA were younger at seizure onset (p=0.018), but without association with duration of epilepsy. Our FLAIR study show temporal pole signal abnormality in 3/4 of patients with HS, mainly seen on the anteromedial region, with a larger prevalence when the left hippocampus was involved.

  1. Temporal pole signal abnormality on MR imaging in temporal lobe epilepsy with hippocampal sclerosis: a fluid-attenuated inversion-recovery study

    International Nuclear Information System (INIS)

    Carrete Junior, Henrique; Abdala, Nitamar; Szjenfeld, Jacob; Nogueira, Roberto Gomes; Lin, Katia; Caboclo, Luis Otavio; Centeno, Ricardo Silva; Sakamoto, Americo Ceiki; Yacubian, Elza Marcia Targas

    2007-01-01

    Objective: To determine the frequency and regional involvement of temporal pole signal abnormality (TPA) in patients with hippocampal sclerosis (HS) using fluid-attenuated inversion-recovery (FLAIR) MR imaging, and to correlate this feature with history. Method: Coronal FLAIR images of the temporal pole were assessed in 120 patients with HS and in 30 normal subjects, to evaluate gray-white matter demarcation. Results: Ninety (75%) of 120 patients had associated TPA. The HS side made difference regarding the presence of TPA, with a left side prevalence (p=0.04, χ 2 test). The anteromedial zone of temporal pole was affected in 27 (30%) out of 90 patients. In 63 (70%) patients the lateral zone were also affected. Patients with TPA were younger at seizure onset (p=0.018), but without association with duration of epilepsy. Conclusion: Our FLAIR study show temporal pole signal abnormality in 3/4 of patients with HS, mainly seen on the anteromedial region, with a larger prevalence when the left hippocampus was involved. (author)

  2. CONFIRMING MICROARRAY DATA--IS IT REALLY NECESSARY?

    Science.gov (United States)

    The generation of corroborative data has become a commonly used approach for ensuring the veracity of microarray data. Indeed, the need to conduct corroborative studies has now become official editorial policy for at least two journals, and several more are considering introducin...

  3. Development of DNA Microarrays for Metabolic Pathway and Bioprocess Monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Gregory Stephanopoulos

    2004-07-31

    Transcriptional profiling experiments utilizing DNA microarrays to study the intracellular accumulation of PHB in Synechocystis has proved difficult in large part because strains that show significant differences in PHB which would justify global analysis of gene expression have not been isolated.

  4. Effect of emotional arousal on inter-temporal decision-making: an fMRI study

    OpenAIRE

    Sohn, Jin-Hun; Kim, Hyo-Eun; Sohn, Sunju; Seok, Ji-Woo; Choi, Damee; Watanuki, Shigeki

    2015-01-01

    Background Previous research has shown that emotion can significantly impact decision-making in humans. The current study examined whether or not and how situationally induced emotion influences people to make inter-temporal choices. Methods Affective pictures were used as experiment stimuli to provoke emotion, immediately followed by subjects? performance of a delay-discounting task to measure impulsivity during functional magnetic resonance imaging. Results Results demonstrate a subsequent ...

  5. Diabetes mellitus, hypertension and medial temporal lobe atrophy: the LADIS study

    DEFF Research Database (Denmark)

    Korf, E S C; van Straaten, E C W; de Leeuw, F-E

    2007-01-01

    HYPOTHESIS: Based on recent findings on the association between vascular risk factors and hippocampal atrophy, we hypothesized that hypertension and diabetes mellitus (DM) are associated with medial temporal lobe atrophy (MTA) in subjects without disability, independent of the severity of white...... matter hyperintensities. METHODS: In the Leukoaraiosis And DISability in the elderly (LADIS) study, we investigated the relationships between DM, hypertension, blood pressure and MTA in 582 subjects, stratified by white matter hyperintensity severity, using multinomial logistic regression. MTA...... was visually scored for the left and right medial temporal lobe (score 0-4), and meaned. RESULTS: Mean age was 73.5 years (sd 5.1), 54% was female. Of the subjects, 15% had DM, and 70% had a history of hypertension. The likelihood of having MTA score 3 was significantly higher in subjects with DM (OR 2.9; 95...

  6. Clinical studies of /sup 131/I labeled fat absorption test by the temporal counting

    Energy Technology Data Exchange (ETDEWEB)

    Kaneko, T [Kumamoto Univ. (Japan). School of Medicine

    1974-09-01

    After administration of the /sup 131/I-triolein capsule test meal, a temporal count curve was obtained. In all, 87 cases were studied of which twenty were normal and 67 were pathological. The time required to reach the highest value (TRHV) of the temporal count curve, 60% in chronic pancreatitis was more than 6 hours, while it took less than 5 hours in normal cases. In cases of intrathoracic esophagogastrostomy and hypothyroidism, TRHV was longer than the normal value. In cases of radiation therapy, TRHV was prolongated with the increase of the radiation dose. Correlation coefficient between TRHV and fecal radioactivity levels (% of dose) was investigated for each patient and was found to be significant.

  7. Diffusion tensor imaging study of the temporal stem in Alzheimer's disease

    Directory of Open Access Journals (Sweden)

    Yue WANG

    2014-03-01

    Full Text Available Objective To study the changes of fractional anisotropy (FA value of white matter of brain and temporal stem in Alzheimer's disease (AD and amnestic mild cognitive impairment (aMCI patients as well as normal cognitive (NC aged people with diffusion tensor imaging (DTI, and explore the damage mechanism of temporal stem and its diagnostic value on AD and aMCI. Methods Ten patients with AD, 10 patients with aMCI and 10 NC volunteers as control group were scanned by routine MRI and DTI. FA values were calculated by post-processing software (DTIstudio in temporal stem (including anterior commissure, uncinate fasciculus and inferior occipitofrontal fasciculus, and white matter in anterior frontal, temperal, parietal and occipital lobes. The data were analyzed by SPSS 13.0. If bilateral differences of FA values were not statistically significant (P > 0.05, the average values of bilateral FA were selected and compared among 3 groups. If bilateral differences of FA values were statistically significant (P < 0.05, the measurement values were directly compared. Results 1 There was no significantdifference of FA values in bilateral symmetric white matter and temporal stem among AD, aMCI and NC groups (P > 0.05, for all. 2 There was significant difference of FA values in anterior commissure, uncinate fasciculus and inferior occipitofrontal fasciculus between AD and aMCI groups (P < 0.05, for all. 3 There was significant difference of FA values in anterior commissure, uncinate fasciculus, inferior occipitofrontal fasciculus, anterior frontal and parietal lobes between AD and NC groups (P < 0.05, for all. 4 There was no significant difference of FA values in anterior commissure, uncinate fasciculus, inferior occipitofrontal fasciculus, anterior frontal lobe between aMCI and NC groups (P > 0.05, for all. Conclusions The significant difference of FA values in temporal stem among AD, aMCI and NC groups suggests that temporal stem fiber bundles are of great

  8. Spatial and temporal characteristics of poloidal waves in the terrestrial plasmasphere: a CLUSTER case study

    Directory of Open Access Journals (Sweden)

    S. Schäfer

    2007-05-01

    Full Text Available Oscillating magnetic field lines are frequently observed by spacecraft in the terrestrial and other planetary magnetospheres. The CLUSTER mission is a very suitable tool to further study these Alfvén waves as the four CLUSTER spacecraft provide for an opportunity to separate spatial and temporal structures in the terrestrial magnetosphere. Using a large scaled configuration formed by the four spacecraft we are able to detect a poloidal Ultra-Low-Frequency (ULF pulsation of the magnetic and electric field in order to analyze its temporal and spatial structures. For this purpose the measurements are transformed into a specific field line related coordinate system to investigate their specific amplitude pattern depending on the path of the CLUSTER spacecraft across oscillating field lines. These measurements are then compared with modeled spacecraft observations across a localized poloidal wave resonator in the dayside plasmasphere. A detailed investigation of theoretically expected poloidal eigenfrequencies allows us to specify the observed 16 mHz pulsation as a third harmonic oscillation. Based on this we perform a case study providing a clear identification of wave properties such as an spatial scale structure of about 0.67 RE, the azimuthal wave number m≈30, temporal evolution, and energy transport in the detected ULF pulsations.

  9. Spatial and temporal air quality pattern recognition using environmetric techniques: a case study in Malaysia.

    Science.gov (United States)

    Syed Abdul Mutalib, Sharifah Norsukhairin; Juahir, Hafizan; Azid, Azman; Mohd Sharif, Sharifah; Latif, Mohd Talib; Aris, Ahmad Zaharin; Zain, Sharifuddin M; Dominick, Doreena

    2013-09-01

    The objective of this study is to identify spatial and temporal patterns in the air quality at three selected Malaysian air monitoring stations based on an eleven-year database (January 2000-December 2010). Four statistical methods, Discriminant Analysis (DA), Hierarchical Agglomerative Cluster Analysis (HACA), Principal Component Analysis (PCA) and Artificial Neural Networks (ANNs), were selected to analyze the datasets of five air quality parameters, namely: SO2, NO2, O3, CO and particulate matter with a diameter size of below 10 μm (PM10). The three selected air monitoring stations share the characteristic of being located in highly urbanized areas and are surrounded by a number of industries. The DA results show that spatial characterizations allow successful discrimination between the three stations, while HACA shows the temporal pattern from the monthly and yearly factor analysis which correlates with severe haze episodes that have happened in this country at certain periods of time. The PCA results show that the major source of air pollution is mostly due to the combustion of fossil fuel in motor vehicles and industrial activities. The spatial pattern recognition (S-ANN) results show a better prediction performance in discriminating between the regions, with an excellent percentage of correct classification compared to DA. This study presents the necessity and usefulness of environmetric techniques for the interpretation of large datasets aiming to obtain better information about air quality patterns based on spatial and temporal characterizations at the selected air monitoring stations.

  10. Ex vivo study of dentate gyrus neurogenesis in human pharmacoresistant temporal lobe epilepsy.

    Science.gov (United States)

    Paradisi, M; Fernández, M; Del Vecchio, G; Lizzo, G; Marucci, G; Giulioni, M; Pozzati, E; Antonelli, T; Lanzoni, G; Bagnara, G P; Giardino, L; Calzà, L

    2010-10-01

    Neurogenesis in adult humans occurs in at least two areas of the brain, the subventricular zone of the telencephalon and the subgranular layer of the dentate gyrus in the hippocampal formation. We studied dentate gyrus subgranular layer neurogenesis in patients subjected to tailored antero-mesial temporal resection including amygdalohippocampectomy due to pharmacoresistant temporal lobe epilepsy (TLE) using the in vitro neurosphere assay. Sixteen patients were enrolled in the study; mesial temporal sclerosis (MTS) was present in eight patients. Neurogenesis was investigated by ex vivo neurosphere expansion in the presence of mitogens (epidermal growth factor + basic fibroblast growth factor) and spontaneous differentiation after mitogen withdrawal. Growth factor synthesis was investigated by qRT-PCR in neurospheres. We demonstrate that in vitro proliferation of cells derived from dentate gyrus of TLE patients is dependent on disease duration. Moreover, the presence of MTS impairs proliferation. As long as in vitro proliferation occurs, neurogenesis is maintained, and cells expressing a mature neurone phenotype (TuJ1, MAP2, GAD) are spontaneously formed after mitogen withdrawal. Finally, formed neurospheres express mRNAs encoding for growth (vascular endothelial growth factor) as well as neurotrophic factors (brain-derived neurotrophic factor, ciliary neurotrophic factor, glial-derived neurotrophic factor, nerve growth factor). We demonstrated that residual neurogenesis in the subgranular layer of the dentate gyrus in TLE is dependent on diseases duration and absent in MTS. © 2010 The Authors. Neuropathology and Applied Neurobiology © 2010 British Neuropathological Society.

  11. Gray and white matter distribution in dyslexia: a VBM study of superior temporal gyrus asymmetry.

    Directory of Open Access Journals (Sweden)

    Marjorie Dole

    Full Text Available In the present study, we investigated brain morphological signatures of dyslexia by using a voxel-based asymmetry analysis. Dyslexia is a developmental disorder that affects the acquisition of reading and spelling abilities and is associated with a phonological deficit. Speech perception disabilities have been associated with this deficit, particularly when listening conditions are challenging, such as in noisy environments. These deficits are associated with known neurophysiological correlates, such as a reduction in the functional activation or a modification of functional asymmetry in the cortical regions involved in speech processing, such as the bilateral superior temporal areas. These functional deficits have been associated with macroscopic morphological abnormalities, which potentially include a reduction in gray and white matter volumes, combined with modifications of the leftward asymmetry along the perisylvian areas. The purpose of this study was to investigate gray/white matter distribution asymmetries in dyslexic adults using automated image processing derived from the voxel-based morphometry technique. Correlations with speech-in-noise perception abilities were also investigated. The results confirmed the presence of gray matter distribution abnormalities in the superior temporal gyrus (STG and the superior temporal Sulcus (STS in individuals with dyslexia. Specifically, the gray matter of adults with dyslexia was symmetrically distributed over one particular region of the STS, the temporal voice area, whereas normal readers showed a clear rightward gray matter asymmetry in this area. We also identified a region in the left posterior STG in which the white matter distribution asymmetry was correlated to speech-in-noise comprehension abilities in dyslexic adults. These results provide further information concerning the morphological alterations observed in dyslexia, revealing the presence of both gray and white matter distribution

  12. Childhood temporal lobe epilepsy: correlation between electroencephalography and magnetic resonance spectroscopy: a case-control study.

    Science.gov (United States)

    Azab, Seham Fa; Sherief, Laila M; Saleh, Safaa H; Elshafeiy, Mona M; Siam, Ahmed G; Elsaeed, Wafaa F; Arafa, Mohamed A; Bendary, Eman A; Sherbiny, Hanan S; Elbehedy, Rabab M; Aziz, Khalid A

    2015-04-18

    The diagnosis of epilepsy should be made as early as possible to give a child the best chance for treatment success and also to decrease complications such as learning difficulties and social and behavioral problems. In this study, we aimed to assess the ability of magnetic resonance spectroscopy (MRS) in detecting the lateralization side in patients with Temporal lobe epilepsy (TLE) in correlation with EEG and MRI findings. This was a case-control study including 40 patients diagnosed (clinically and by EEG) as having temporal lobe epilepsy aged 8 to 14 years (mean, 10.4 years) and 20 healthy children with comparable age and gender as the control group. All patients were subjected to clinical examination, interictal electroencephalography and magnetic resonance imaging (MRI). Proton magnetic resonance spectroscopic examination (MRS) was performed to the patients and the controls. According to the findings of electroencephalography, our patients were classified to three groups: Group 1 included 20 patients with unitemporal (lateralized) epileptic focus, group 2 included 12 patients with bitemporal (non-lateralized) epileptic focus and group 3 included 8 patients with normal electroencephalography. Magnetic resonance spectroscopy could lateralize the epileptic focus in 19 patients in group 1, nine patients in group2 and five patients in group 3 with overall lateralization of (82.5%), while electroencephalography was able to lateralize the focus in (50%) of patients and magnetic resonance imaging detected lateralization of mesial temporal sclerosis in (57.5%) of patients. Magnetic resonance spectroscopy is a promising tool in evaluating patients with epilepsy and offers increased sensitivity to detect temporal pathology that is not obvious on structural MRI imaging.

  13. Gray and white matter distribution in dyslexia: a VBM study of superior temporal gyrus asymmetry.

    Science.gov (United States)

    Dole, Marjorie; Meunier, Fanny; Hoen, Michel

    2013-01-01

    In the present study, we investigated brain morphological signatures of dyslexia by using a voxel-based asymmetry analysis. Dyslexia is a developmental disorder that affects the acquisition of reading and spelling abilities and is associated with a phonological deficit. Speech perception disabilities have been associated with this deficit, particularly when listening conditions are challenging, such as in noisy environments. These deficits are associated with known neurophysiological correlates, such as a reduction in the functional activation or a modification of functional asymmetry in the cortical regions involved in speech processing, such as the bilateral superior temporal areas. These functional deficits have been associated with macroscopic morphological abnormalities, which potentially include a reduction in gray and white matter volumes, combined with modifications of the leftward asymmetry along the perisylvian areas. The purpose of this study was to investigate gray/white matter distribution asymmetries in dyslexic adults using automated image processing derived from the voxel-based morphometry technique. Correlations with speech-in-noise perception abilities were also investigated. The results confirmed the presence of gray matter distribution abnormalities in the superior temporal gyrus (STG) and the superior temporal Sulcus (STS) in individuals with dyslexia. Specifically, the gray matter of adults with dyslexia was symmetrically distributed over one particular region of the STS, the temporal voice area, whereas normal readers showed a clear rightward gray matter asymmetry in this area. We also identified a region in the left posterior STG in which the white matter distribution asymmetry was correlated to speech-in-noise comprehension abilities in dyslexic adults. These results provide further information concerning the morphological alterations observed in dyslexia, revealing the presence of both gray and white matter distribution anomalies and the

  14. Employing image processing techniques for cancer detection using microarray images.

    Science.gov (United States)

    Dehghan Khalilabad, Nastaran; Hassanpour, Hamid

    2017-02-01

    Microarray technology is a powerful genomic tool for simultaneously studying and analyzing the behavior of thousands of genes. The analysis of images obtained from this technology plays a critical role in the detection and treatment of diseases. The aim of the current study is to develop an automated system for analyzing data from microarray images in order to detect cancerous cases. The proposed system consists of three main phases, namely image processing, data mining, and the detection of the disease. The image processing phase performs operations such as refining image rotation, gridding (locating genes) and extracting raw data from images the data mining includes normalizing the extracted data and selecting the more effective genes. Finally, via the extracted data, cancerous cell is recognized. To evaluate the performance of the proposed system, microarray database is employed which includes Breast cancer, Myeloid Leukemia and Lymphomas from the Stanford Microarray Database. The results indicate that the proposed system is able to identify the type of cancer from the data set with an accuracy of 95.45%, 94.11%, and 100%, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Prognostic implication of p27Kip1, Skp2 and Cks1 expression in renal cell carcinoma: a tissue microarray study

    Directory of Open Access Journals (Sweden)

    Wang Facheng

    2008-10-01

    Full Text Available Abstract Background p27Kip1 plays a major role as a negative regulator of the cell cycle. The regulation of p27Kip1 degradation is mediated by its specific ubiquitin ligase subunits S-phase kinase protein (Skp 2 and cyclin-dependent kinase subunit (Cks 1. However, little is known regarding the prognostic utility of p27Kip1, Skp2 and Cks1 expression in renal cell carcinoma. Methods Immunohistochemistry was performed for p27Kip1, Skp2 and Cks1 in tissue microarrays of 482 renal cell carcinomas with follow-up. The data were correlated with clinicopathological features. The univariate and multivariate survival analyses were also performed to determine their prognostic significance. Results Immunoreactivity of p27Kip1, Skp2 and Cks1 was noted in 357, 71 and 82 patients, respectively. Skp2 and Cks1 expression were not noted in chromophobe cancers. A strong correlation was found between Skp2 and Cks1 expression (P Kip1 levels (P = 0.006 and P Kip1 expression and Skp2 expression were correlated with larger tumor size and higher stage, as well as tumor necrosis. Cks1 expression was only correlated with tumor size. In univariate analysis, low p27Kip1 expression, Skp2 and Cks1 expression were all associated with a poor prognosis, while in multivariate analysis, only low p27Kip1 expression were independent prognostic factors for both cancer specific survival and recurrence-free survival in patients with RCC. Conclusion Our results suggest that immunohistochemical expression levels of p27Kip1, Skp2 and Cks1 may serve as markers with prognostic value in renal cell carcinoma.

  16. Cell-cycle and suppressor proteins expression in uterine cervix in HIV/HPV co-infection: comparative study by tissue micro-array (TMA)

    International Nuclear Information System (INIS)

    Nicol, Alcina F; Pirmez, Claude; Pires, Andréa Rodrigues Cordovil; Souza, Simone R de; Nuovo, Gerard J; Grinsztejn, Beatriz; Tristão, Aparecida; Russomano, Fabio B; Velasque, Luciane; Silva, José R Lapa e

    2008-01-01

    The oncoproteins of human papillomavirus (HPVs) directly effect cell-cycle control. We hypothesize that regulatory and cell cycle protein expression might be additionally modified in the cervix of HIV/HPV co-infected women. We analyzed the expression of Rb, p27, VEGF and Elf-1 transcriptor factor by immunohistochemistry in 163 paraffin-embeded cervical samples using Tissue Micro-Array (TMA) and correlated this to HIV-1 and HPV infection. HIV/HPV co-infection was associated with a significant increase in expression (p < 0.001) of VEGF and p27 in both low and high grade CIN when compared to the cervices of women infected by HPV alone. Decreased Rb expression was evident with increased CIN grade in the cervices of women infected with HPV alone (p = 0.003 average of cells/mm 2 in CIN I: 17.9, CIN II/III: 4.8, and tumor 3.9). Rb expression increased 3-fold for both low and high grade CIN with HPV/HIV-1 co-infection compared to HPV infection alone but did not reach statistical significance. There was a significant increase in Elf-1 expression in HPV+/HIV- women with CIN II/III and tumor (average of cells/mm 2 in CIN I: 63.8; CIN II/III: 115.7 and tumor: 112.0, p = 0.005), in comparison to controls. Co-infection of HPV and HIV leads to significant increase in the VEGF and p27 expression when compared to HPV+/HIV-negative infection that could facilitate viral persistence and invasive tumor development

  17. Cell-cycle and suppressor proteins expression in uterine cervix in HIV/HPV co-infection: comparative study by tissue micro-array (TMA).

    Science.gov (United States)

    Nicol, Alcina F; Pires, Andréa Rodrigues Cordovil; de Souza, Simone R; Nuovo, Gerard J; Grinsztejn, Beatriz; Tristão, Aparecida; Russomano, Fabio B; Velasque, Luciane; Lapa e Silva, José R; Pirmez, Claude

    2008-10-07

    The oncoproteins of human papillomavirus (HPVs) directly effect cell-cycle control. We hypothesize that regulatory and cell cycle protein expression might be additionally modified in the cervix of HIV/HPV co-infected women. We analyzed the expression of Rb, p27, VEGF and Elf-1 transcriptor factor by immunohistochemistry in 163 paraffin-embeded cervical samples using Tissue Micro-Array (TMA) and correlated this to HIV-1 and HPV infection. HIV/HPV co-infection was associated with a significant increase in expression (p < 0.001) of VEGF and p27 in both low and high grade CIN when compared to the cervices of women infected by HPV alone. Decreased Rb expression was evident with increased CIN grade in the cervices of women infected with HPV alone (p = 0.003 average of cells/mm2 in CIN I: 17.9, CIN II/III: 4.8, and tumor 3.9). Rb expression increased 3-fold for both low and high grade CIN with HPV/HIV-1 co-infection compared to HPV infection alone but did not reach statistical significance. There was a significant increase in Elf-1 expression in HPV+/HIV- women with CIN II/III and tumor (average of cells/mm2 in CIN I: 63.8; CIN II/III: 115.7 and tumor: 112.0, p = 0.005), in comparison to controls. Co-infection of HPV and HIV leads to significant increase in the VEGF and p27 expression when compared to HPV+/HIV-negative infection that could facilitate viral persistence and invasive tumor development.

  18. Annotating breast cancer microarray samples using ontologies

    Science.gov (United States)

    Liu, Hongfang; Li, Xin; Yoon, Victoria; Clarke, Robert

    2008-01-01

    As the most common cancer among women, breast cancer results from the accumulation of mutations in essential genes. Recent advance in high-throughput gene expression microarray technology has inspired researchers to use the technology to assist breast cancer diagnosis, prognosis, and treatment prediction. However, the high dimensionality of microarray experiments and public access of data from many experiments have caused inconsistencies which initiated the development of controlled terminologies and ontologies for annotating microarray experiments, such as the standard microarray Gene Expression Data (MGED) ontology (MO). In this paper, we developed BCM-CO, an ontology tailored specifically for indexing clinical annotations of breast cancer microarray samples from the NCI Thesaurus. Our research showed that the coverage of NCI Thesaurus is very limited with respect to i) terms used by researchers to describe breast cancer histology (covering 22 out of 48 histology terms); ii) breast cancer cell lines (covering one out of 12 cell lines); and iii) classes corresponding to the breast cancer grading and staging. By incorporating a wider range of those terms into BCM-CO, we were able to indexed breast cancer microarray samples from GEO using BCM-CO and MGED ontology and developed a prototype system with web interface that allows the retrieval of microarray data based on the ontology annotations. PMID:18999108

  19. Simulation of microarray data with realistic characteristics

    Directory of Open Access Journals (Sweden)

    Lehmussola Antti

    2006-07-01

    Full Text Available Abstract Background Microarray technologies have become common tools in biological research. As a result, a need for effective computational methods for data analysis has emerged. Numerous different algorithms have been proposed for analyzing the data. However, an objective evaluation of the proposed algorithms is not possible due to the lack of biological ground truth information. To overcome this fundamental problem, the use of simulated microarray data for algorithm validation has been proposed. Results We present a microarray simulation model which can be used to validate different kinds of data analysis algorithms. The proposed model is unique in the sense that it includes all the steps that affect the quality of real microarray data. These steps include the simulation of biological ground truth data, applying biological and measurement technology specific error models, and finally simulating the microarray slide manufacturing and hybridization. After all these steps are taken into account, the simulated data has realistic biological and statistical characteristics. The applicability of the proposed model is demonstrated by several examples. Conclusion The proposed microarray simulation model is modular and can be used in different kinds of applications. It includes several error models that have been proposed earlier and it can be used with different types of input data. The model can be used to simulate both spotted two-channel and oligonucleotide based single-channel microarrays. All this makes the model a valuable tool for example in validation of data analysis algorithms.

  20. Translating microarray data for diagnostic testing in childhood leukaemia

    International Nuclear Information System (INIS)

    Hoffmann, Katrin; Firth, Martin J; Beesley, Alex H; Klerk, Nicholas H de; Kees, Ursula R

    2006-01-01

    Recent findings from microarray studies have raised the prospect of a standardized diagnostic gene expression platform to enhance accurate diagnosis and risk stratification in paediatric acute lymphoblastic leukaemia (ALL). However, the robustness as well as the format for such a diagnostic test remains to be determined. As a step towards clinical application of these findings, we have systematically analyzed a published ALL microarray data set using Robust Multi-array Analysis (RMA) and Random Forest (RF). We examined published microarray data from 104 ALL patients specimens, that represent six different subgroups defined by cytogenetic features and immunophenotypes. Using the decision-tree based supervised learning algorithm Random Forest (RF), we determined a small set of genes for optimal subgroup distinction and subsequently validated their predictive power in an independent patient cohort. We achieved very high overall ALL subgroup prediction accuracies of about 98%, and were able to verify the robustness of these genes in an independent panel of 68 specimens obtained from a different institution and processed in a different laboratory. Our study established that the selection of discriminating genes is strongly dependent on the analysis method. This may have profound implications for clinical use, particularly when the classifier is reduced to a small set of genes. We have demonstrated that as few as 26 genes yield accurate class prediction and importantly, almost 70% of these genes have not been previously identified as essential for class distinction of the six ALL subgroups. Our finding supports the feasibility of qRT-PCR technology for standardized diagnostic testing in paediatric ALL and should, in conjunction with conventional cytogenetics lead to a more accurate classification of the disease. In addition, we have demonstrated that microarray findings from one study can be confirmed in an independent study, using an entirely independent patient cohort

  1. A Postmortem Study of Frontal and Temporal Gyri Thickness and Cell Number in Human Obesity.

    Science.gov (United States)

    Gómez-Apo, Erick; García-Sierra, Adrián; Silva-Pereyra, Juan; Soto-Abraham, Virgilia; Mondragón-Maya, Alejandra; Velasco-Vales, Verónica; Pescatello, Linda S

    2018-01-01

    This study aimed to compare cortex thickness and neuronal cell density in postmortem brain tissue from people with overweight or obesity and normal weight. The cortex thickness and neuron density of eight donors with overweight or obesity (mean = 31.6 kg/m 2 ; SD = 4.35; n = 8; 6 male) and eight donors with normal weight (mean = 21.8 kg/m 2 ; SD = 1.5; n = 8; 5 male) were compared. All participants were Mexican and lived in Mexico City. Randomly selected thickness measures of different cortex areas from the frontal and temporal lobes were analyzed based on high-resolution real-size photographs. A histological analysis of systematic-random fields was used to quantify the number of neurons in postmortem left and right of the first, second, and third gyri of frontal and temporal lobe brain samples. No statistical difference was found in cortical thickness between donors with overweight or obesity and individuals with normal weight. A smaller number of neurons was found among the donors with overweight or obesity than the donors with normal weight at different frontal and temporal areas. A lower density of neurons is associated with overweight or obesity. The morphological basis for structural brain changes in obesity requires further investigation. © 2017 The Obesity Society.

  2. Right temporal cortical hypertrophy in resilience to trauma: an MRI study.

    Science.gov (United States)

    Nilsen, André Sevenius; Hilland, Eva; Kogstad, Norunn; Heir, Trond; Hauff, Edvard; Lien, Lars; Endestad, Tor

    2016-01-01

    In studies employing physiological measures such as magnetic resonance imaging (MRI), it is often hard to distinguish what constitutes risk-resilience factors to posttraumatic stress disorder (PTSD) following trauma exposure and what the effects of trauma exposure and PTSD are. We aimed to investigate whether there were observable morphological differences in cortical and sub-cortical regions of the brain, 7-8 years after a single potentially traumatic event. Twenty-four participants, who all directly experienced the 2004 Indian Ocean Tsunami, and 25 controls, underwent structural MRI using a 3T scanner. We generated cortical thickness maps and parcellated sub-cortical volumes for analysis. We observed greater cortical thickness for the trauma-exposed participants relative to controls, in a right lateralized temporal lobe region including anterior fusiform gyrus, and superior, middle, and inferior temporal gyrus. We observed greater thickness in the right temporal lobe which might indicate that the region could be implicated in resilience to the long-term effects of a traumatic event. We hypothesize this is due to altered emotional semantic memory processing. However, several methodological and confounding issues warrant caution in interpretation of the results.

  3. Parietal and temporal activity during a multimodal dance video game: an fNIRS study.

    Science.gov (United States)

    Tachibana, Atsumichi; Noah, J Adam; Bronner, Shaw; Ono, Yumie; Onozuka, Minoru

    2011-10-03

    Using functional near infrared spectroscopy (fNIRS) we studied how playing a dance video game employs coordinated activation of sensory-motor integration centers of the superior parietal lobe (SPL) and superior temporal gyrus (STG). Subjects played a dance video game, in a block design with 30s of activity alternating with 30s of rest, while changes in oxy-hemoglobin (oxy-Hb) levels were continuously measured. The game was modified to compare difficult (4-arrow), simple (2-arrow), and stepping conditions. Oxy-Hb levels were greatest with increased task difficulty. The quick-onset, trapezoidal time-course increase in SPL oxy-Hb levels reflected the on-off neuronal response of spatial orienting and rhythmic motor timing that were required during the activity. Slow-onset, bell-shaped increases in oxy-Hb levels observed in STG suggested the gradually increasing load of directing multisensory information to downstream processing centers associated with motor behavior and control. Differences in temporal relationships of SPL and STG oxy-Hb concentration levels may reflect the functional roles of these brain structures during the task period. NIRS permits insights into temporal relationships of cortical hemodynamics during real motor tasks. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  4. Right temporal cortical hypertrophy in resilience to trauma: an MRI study

    Directory of Open Access Journals (Sweden)

    André Sevenius Nilsen

    2016-07-01

    Full Text Available Background: In studies employing physiological measures such as magnetic resonance imaging (MRI, it is often hard to distinguish what constitutes risk-resilience factors to posttraumatic stress disorder (PTSD following trauma exposure and what the effects of trauma exposure and PTSD are. Objective: We aimed to investigate whether there were observable morphological differences in cortical and sub-cortical regions of the brain, 7–8 years after a single potentially traumatic event. Methods: Twenty-four participants, who all directly experienced the 2004 Indian Ocean Tsunami, and 25 controls, underwent structural MRI using a 3T scanner. We generated cortical thickness maps and parcellated sub-cortical volumes for analysis. Results: We observed greater cortical thickness for the trauma-exposed participants relative to controls, in a right lateralized temporal lobe region including anterior fusiform gyrus, and superior, middle, and inferior temporal gyrus. Conclusions: We observed greater thickness in the right temporal lobe which might indicate that the region could be implicated in resilience to the long-term effects of a traumatic event. We hypothesize this is due to altered emotional semantic memory processing. However, several methodological and confounding issues warrant caution in interpretation of the results.

  5. Design of the real time systems using temporal logic specifications: a case study

    Directory of Open Access Journals (Sweden)

    A. Ursu

    1996-07-01

    Full Text Available An implementation method for real time systems is proposed in this article. The implementation starts with the design of the functional specifications of the systems behaviour. The functional specifications are introduced as a set of rules describing the partial time ordering of the actions performed by the system. These rules are then written in terms of temporal logic formulae. The temporal logic formulae are checked using Z.Manna-P.Wolper satisfiability analysis procedure [1]. It is known that this procedure generates a state-graph which can be regarded as a state- based automaton of the system. The sate-based automaton is used then to generate the dual (inverted automaton of the system. The dual automaton is called action-based automaton and can be created using the procedure proposed by authors in [4,5]. Using the action-based automaton of the system the design method introduced in [5,6] is applied to implement the system driver in a systematic manner which can be computerised. The method proposed in this paper is an efficient complementation and generalisation of the results [4,5,6] mentioned above. The method is used for a case study. An elevator control system is designed using the proposed method. The design is carried out in a systematic manner which includes: a design of functional specifications, b design of temporal logic specifications, c satisfiability analysis of temporal logic specifications, d design of the state-based automaton of the specifications, e design of the action-based automaton of the system, f design of the transition activation conditions, g design of the action activation conditions, h design of the functional model of the elevator control system, i implementation of the elevator's actions, j design of the elevator control system driver.

  6. Microarrays: Molecular allergology and nanotechnology for personalised medicine (II).

    Science.gov (United States)

    Lucas, J M

    2010-01-01

    Progress in nanotechnology and DNA recombination techniques have produced tools for the diagnosis and investigation of allergy at molecular level. The most advanced examples of such progress are the microarray techniques, which have been expanded not only in research in the field of proteomics but also in application to the clinical setting. Microarrays of allergic components offer results relating to hundreds of allergenic components in a single test, and using a small amount of serum which can be obtained from capillary blood. The availability of new molecules will allow the development of panels including new allergenic components and sources, which will require evaluation for clinical use. Their application opens the door to component-based diagnosis, to the holistic perception of sensitisation as represented by molecular allergy, and to patient-centred medical practice by allowing great diagnostic accuracy and the definition of individualised immunotherapy for each patient. The present article reviews the application of allergenic component microarrays to allergology for diagnosis, management in the form of specific immunotherapy, and epidemiological studies. A review is also made of the use of protein and gene microarray techniques in basic research and in allergological diseases. Lastly, an evaluation is made of the challenges we face in introducing such techniques to clinical practice, and of the future perspectives of this new technology. Copyright 2010 SEICAP. Published by Elsevier Espana. All rights reserved.

  7. See what you eat--broad GMO screening with microarrays.

    Science.gov (United States)

    von Götz, Franz

    2010-03-01

    Despite the controversy of whether genetically modified organisms (GMOs) are beneficial or harmful for humans, animals, and/or ecosystems, the number of cultivated GMOs is increasing every year. Many countries and federations have implemented safety and surveillance systems for GMOs. Potent testing technologies need to be developed and implemented to monitor the increasing number of GMOs. First, these GMO tests need to be comprehensive, i.e., should detect all, or at least the most important, GMOs on the market. This type of GMO screening requires a high degree of parallel tests or multiplexing. To date, DNA microarrays have the highest number of multiplexing capabilities when nucleic acids are analyzed. This trend article focuses on the evolution of DNA microarrays for GMO testing. Over the last 7 years, combinations of multiplex PCR detection and microarray detection have been developed to qualitatively assess the presence of GMOs. One example is the commercially available DualChip GMO (Eppendorf, Germany; http://www.eppendorf-biochip.com), which is the only GMO screening system successfully validated in a multicenter study. With use of innovative amplification techniques, promising steps have recently been taken to make GMO detection with microarrays quantitative.

  8. Microarray expression profiling of human dental pulp from single subject.

    Science.gov (United States)

    Tete, Stefano; Mastrangelo, Filiberto; Scioletti, Anna Paola; Tranasi, Michelangelo; Raicu, Florina; Paolantonio, Michele; Stuppia, Liborio; Vinci, Raffaele; Gherlone, Enrico; Ciampoli, Cristian; Sberna, Maria Teresa; Conti, Pio

    2008-01-01

    Microarray is a recently developed simultaneous analysis of expression patterns of thousand of genes. The aim of this research was to evaluate the expression profile of human healthy dental pulp in order to find the presence of genes activated and encoding for proteins involved in the physiological process of human dental pulp. We report data obtained by analyzing expression profiles of human tooth pulp from single subjects, using an approach based on the amplification of the total RNA. Experiments were performed on a high-density array able to analyse about 21,000 oligonucleotide sequences of about 70 bases in duplicate, using an approach based on the amplification of the total RNA from the pulp of a single tooth. Obtained data were analyzed using the S.A.M. system (Significance Analysis of Microarray) and genes were merged according to their molecular functions and biological process by the Onto-Express software. The microarray analysis revealed 362 genes with specific pulp expression. Genes showing significant high expression were classified in genes involved in tooth development, protoncogenes, genes of collagen, DNAse, Metallopeptidases and Growth factors. We report a microarray analysis, carried out by extraction of total RNA from specimens of healthy human dental pulp tissue. This approach represents a powerful tool in the study of human normal and pathological pulp, allowing minimization of the genetic variability due to the pooling of samples from different individuals.

  9. Microarray analysis in the archaeon Halobacterium salinarum strain R1.

    Directory of Open Access Journals (Sweden)

    Jens Twellmeyer

    Full Text Available BACKGROUND: Phototrophy of the extremely halophilic archaeon Halobacterium salinarum was explored for decades. The research was mainly focused on the expression of bacteriorhodopsin and its functional properties. In contrast, less is known about genome wide transcriptional changes and their impact on the physiological adaptation to phototrophy. The tool of choice to record transcriptional profiles is the DNA microarray technique. However, the technique is still rarely used for transcriptome analysis in archaea. METHODOLOGY/PRINCIPAL FINDINGS: We developed a whole-genome DNA microarray based on our sequence data of the Hbt. salinarum strain R1 genome. The potential of our tool is exemplified by the comparison of cells growing under aerobic and phototrophic conditions, respectively. We processed the raw fluorescence data by several stringent filtering steps and a subsequent MAANOVA analysis. The study revealed a lot of transcriptional differences between the two cell states. We found that the transcriptional changes were relatively weak, though significant. Finally, the DNA microarray data were independently verified by a real-time PCR analysis. CONCLUSION/SIGNIFICANCE: This is the first DNA microarray analysis of Hbt. salinarum cells that were actually grown under phototrophic conditions. By comparing the transcriptomics data with current knowledge we could show that our DNA microarray tool is well applicable for transcriptome analysis in the extremely halophilic archaeon Hbt. salinarum. The reliability of our tool is based on both the high-quality array of DNA probes and the stringent data handling including MAANOVA analysis. Among the regulated genes more than 50% had unknown functions. This underlines the fact that haloarchaeal phototrophy is still far away from being completely understood. Hence, the data recorded in this study will be subject to future systems biology analysis.

  10. Comparison of gene coverage of mouse oligonucleotide microarray platforms

    Directory of Open Access Journals (Sweden)

    Medrano Juan F

    2006-03-01

    Full Text Available Abstract Background The increasing use of DNA microarrays for genetical genomics studies generates a need for platforms with complete coverage of the genome. We have compared the effective gene coverage in the mouse genome of different commercial and noncommercial oligonucleotide microarray platforms by performing an in-house gene annotation of probes. We only used information about probes that is available from vendors and followed a process that any researcher may take to find the gene targeted by a given probe. In order to make consistent comparisons between platforms, probes in each microarray were annotated with an Entrez Gene id and the chromosomal position for each gene was obtained from the UCSC Genome Browser Database. Gene coverage was estimated as the percentage of Entrez Genes with a unique position in the UCSC Genome database that is tested by a given microarray platform. Results A MySQL relational database was created to store the mapping information for 25,416 mouse genes and for the probes in five microarray platforms (gene coverage level in parenthesis: Affymetrix430 2.0 (75.6%, ABI Genome Survey (81.24%, Agilent (79.33%, Codelink (78.09%, Sentrix (90.47%; and four array-ready oligosets: Sigma (47.95%, Operon v.3 (69.89%, Operon v.4 (84.03%, and MEEBO (84.03%. The differences in coverage between platforms were highly conserved across chromosomes. Differences in the number of redundant and unspecific probes were also found among arrays. The database can be queried to compare specific genomic regions using a web interface. The software used to create, update and query the database is freely available as a toolbox named ArrayGene. Conclusion The software developed here allows researchers to create updated custom databases by using public or proprietary information on genes for any organisms. ArrayGene allows easy comparisons of gene coverage between microarray platforms for any region of the genome. The comparison presented here

  11. Autoregressive-model-based missing value estimation for DNA microarray time series data.

    Science.gov (United States)

    Choong, Miew Keen; Charbit, Maurice; Yan, Hong

    2009-01-01

    Missing value estimation is important in DNA microarray data analysis. A number of algorithms have been developed to solve this problem, but they have several limitations. Most existing algorithms are not able to deal with the situation where a particular time point (column) of the data is missing entirely. In this paper, we present an autoregressive-model-based missing value estimation method (ARLSimpute) that takes into account the dynamic property of microarray temporal data and the local similarity structures in the data. ARLSimpute is especially effective for the situation where a particular time point contains many missing values or where the entire time point is missing. Experiment results suggest that our proposed algorithm is an accurate missing value estimator in comparison with other imputation methods on simulated as well as real microarray time series datasets.

  12. Gene Expression and Microarray Investigation of Dendrobium ...

    African Journals Online (AJOL)

    blood glucose > 16.7 mmol/L were used as the model group and treated with Dendrobium mixture. (DEN ... Keywords: Diabetes, Gene expression, Dendrobium mixture, Microarray testing ..... homeostasis in airway smooth muscle. Am J.

  13. SLIMarray: Lightweight software for microarray facility management

    Directory of Open Access Journals (Sweden)

    Marzolf Bruz

    2006-10-01

    Full Text Available Abstract Background Microarray core facilities are commonplace in biological research organizations, and need systems for accurately tracking various logistical aspects of their operation. Although these different needs could be handled separately, an integrated management system provides benefits in organization, automation and reduction in errors. Results We present SLIMarray (System for Lab Information Management of Microarrays, an open source, modular database web application capable of managing microarray inventories, sample processing and usage charges. The software allows modular configuration and is well suited for further development, providing users the flexibility to adapt it to their needs. SLIMarray Lite, a version of the software that is especially easy to install and run, is also available. Conclusion SLIMarray addresses the previously unmet need for free and open source software for managing the logistics of a microarray core facility.

  14. Washing scaling of GeneChip microarray expression

    Directory of Open Access Journals (Sweden)

    Krohn Knut

    2010-05-01

    Full Text Available Abstract Background Post-hybridization washing is an essential part of microarray experiments. Both the quality of the experimental washing protocol and adequate consideration of washing in intensity calibration ultimately affect the quality of the expression estimates extracted from the microarray intensities. Results We conducted experiments on GeneChip microarrays with altered protocols for washing, scanning and staining to study the probe-level intensity changes as a function of the number of washing cycles. For calibration and analysis of the intensity data we make use of the 'hook' method which allows intensity contributions due to non-specific and specific hybridization of perfect match (PM and mismatch (MM probes to be disentangled in a sequence specific manner. On average, washing according to the standard protocol removes about 90% of the non-specific background and about 30-50% and less than 10% of the specific targets from the MM and PM, respectively. Analysis of the washing kinetics shows that the signal-to-noise ratio doubles roughly every ten stringent washing cycles. Washing can be characterized by time-dependent rate constants which reflect the heterogeneous character of target binding to microarray probes. We propose an empirical washing function which estimates the survival of probe bound targets. It depends on the intensity contribution due to specific and non-specific hybridization per probe which can be estimated for each probe using existing methods. The washing function allows probe intensities to be calibrated for the effect of washing. On a relative scale, proper calibration for washing markedly increases expression measures, especially in the limit of small and large values. Conclusions Washing is among the factors which potentially distort expression measures. The proposed first-order correction method allows direct implementation in existing calibration algorithms for microarray data. We provide an experimental

  15. DNA microarray-based PCR ribotyping of Clostridium difficile.

    Science.gov (United States)

    Schneeberg, Alexander; Ehricht, Ralf; Slickers, Peter; Baier, Vico; Neubauer, Heinrich; Zimmermann, Stefan; Rabold, Denise; Lübke-Becker, Antina; Seyboldt, Christian

    2015-02-01

    This study presents a DNA microarray-based assay for fast and simple PCR ribotyping of Clostridium difficile strains. Hybridization probes were designed to query the modularly structured intergenic spacer region (ISR), which is also the template for conventional and PCR ribotyping with subsequent capillary gel electrophoresis (seq-PCR) ribotyping. The probes were derived from sequences available in GenBank as well as from theoretical ISR module combinations. A database of reference hybridization patterns was set up from a collection of 142 well-characterized C. difficile isolates representing 48 seq-PCR ribotypes. The reference hybridization patterns calculated by the arithmetic mean were compared using a similarity matrix analysis. The 48 investigated seq-PCR ribotypes revealed 27 array profiles that were clearly distinguishable. The most frequent human-pathogenic ribotypes 001, 014/020, 027, and 078/126 were discriminated by the microarray. C. difficile strains related to 078/126 (033, 045/FLI01, 078, 126, 126/FLI01, 413, 413/FLI01, 598, 620, 652, and 660) and 014/020 (014, 020, and 449) showed similar hybridization patterns, confirming their genetic relatedness, which was previously reported. A panel of 50 C. difficile field isolates was tested by seq-PCR ribotyping and the DNA microarray-based assay in parallel. Taking into account that the current version of the microarray does not discriminate some closely related seq-PCR ribotypes, all isolates were typed correctly. Moreover, seq-PCR ribotypes without reference profiles available in the database (ribotype 009 and 5 new types) were correctly recognized as new ribotypes, confirming the performance and expansion potential of the microarray. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  16. Integrated olfactory receptor and microarray gene expression databases

    Directory of Open Access Journals (Sweden)

    Crasto Chiquito J

    2007-06-01

    Full Text Available Abstract Background Gene expression patterns of olfactory receptors (ORs are an important component of the signal encoding mechanism in the olfactory system since they determine the interactions between odorant ligands and sensory neurons. We have developed the Olfactory Receptor Microarray Database (ORMD to house OR gene expression data. ORMD is integrated with the Olfactory Receptor Database (ORDB, which is a key repository of OR gene information. Both databases aim to aid experimental research related to olfaction. Description ORMD is a Web-accessible database that provides a secure data repository for OR microarray experiments. It contains both publicly available and private data; accessing the latter requires authenticated login. The ORMD is designed to allow users to not only deposit gene expression data but also manage their projects/experiments. For example, contributors can choose whether to make their datasets public. For each experiment, users can download the raw data files and view and export the gene expression data. For each OR gene being probed in a microarray experiment, a hyperlink to that gene in ORDB provides access to genomic and proteomic information related to the corresponding olfactory receptor. Individual ORs archived in ORDB are also linked to ORMD, allowing users access to the related microarray gene expression data. Conclusion ORMD serves as a data repository and project management system. It facilitates the study of microarray experiments of gene expression in the olfactory system. In conjunction with ORDB, ORMD integrates gene expression data with the genomic and functional data of ORs, and is thus a useful resource for both olfactory researchers and the public.

  17. Seeded Bayesian Networks: Constructing genetic networks from microarray data

    Directory of Open Access Journals (Sweden)

    Quackenbush John

    2008-07-01

    Full Text Available Abstract Background DNA microarrays and other genomics-inspired technologies provide large datasets that often include hidden patterns of correlation between genes reflecting the complex processes that underlie cellular metabolism and physiology. The challenge in analyzing large-scale expression data has been to extract biologically meaningful inferences regarding these processes – often represented as networks – in an environment where the datasets are often imperfect and biological noise can obscure the actual signal. Although many techniques have been developed in an attempt to address these issues, to date their ability to extract meaningful and predictive network relationships has been limited. Here we describe a method that draws on prior information about gene-gene interactions to infer biologically relevant pathways from microarray data. Our approach consists of using preliminary networks derived from the literature and/or protein-protein interaction data as seeds for a Bayesian network analysis of microarray results. Results Through a bootstrap analysis of gene expression data derived from a number of leukemia studies, we demonstrate that seeded Bayesian Networks have the ability to identify high-confidence gene-gene interactions which can then be validated by comparison to other sources of pathway data. Conclusion The use of network seeds greatly improves the ability of Bayesian Network analysis to learn gene interaction networks from gene expression data. We demonstrate that the use of seeds derived from the biomedical literature or high-throughput protein-protein interaction data, or the combination, provides improvement over a standard Bayesian Network analysis, allowing networks involving dynamic processes to be deduced from the static snapshots of biological systems that represent the most common source of microarray data. Software implementing these methods has been included in the widely used TM4 microarray analysis package.

  18. Cochlear implant benefits in deafness rehabilitation: PET study of temporal voice Activations

    Energy Technology Data Exchange (ETDEWEB)

    Coez, A.; Zilbovicius, M. [CEA, Serv Hosp Frederic Joliot, INSERM, Res Unit Neuroimaging and Psychiat, U797, IFR49, F-91406 Orsay (France); Zilbovicius, M.; Syrota, A.; Samson, Y. [CEA, DSV, DRM, Serv Hosp Frederic Joliot, F-91406 Orsay (France); Bizaguet, E. [Lab Correct Audit, Paris (France); Coez, A. [Univ Paris Sud 11, Paris (France); Ferrary, E.; Bouccara, D.; Mosnier, I.; Sterkers, O. [INSERM, Unit M 867, Paris (France); Ambert-Dahan, E. [Hop Beaujon, Serv ORL Chirurg Cervicofaciale, AP-HP, Clichy (France); Ferrary, E.; Bouccara, D.; Mosnier, I.; Sterkers, O. [Inst Fed Rech Claude Bernard Physiol et Pathol, IFR02, Paris (France); Samson, Y. [Hop La Pitie Salpetriere, Serv Urgences Cerebro-vasc, AP-HP, Paris (France); Samson, Y. [Univ Paris 06, Paris (France); Sterkers, O. [Univ Denis Diderot Paris 7, Paris (France)

    2008-07-01

    Cochlear implants may improve the medical and social prognosis of profound deafness. Nevertheless, some patients have experienced poor results without any clear explanations. One correlate may be an alteration in cortical voice processing. To test this hypothesis, we studied the activation of human temporal voice areas (TVA) using a well-standardized PET paradigm adapted from previous functional MRI (fMRI) studies. Methods: A PET H{sub 2}{sup 15}O activation study was performed on 3 groups of adult volunteers: normal-hearing control subjects (n 6) and cochlear-implanted post-lingually deaf patients with {>=}2 y of cochlear implant experience, with intelligibility scores in the 'Lafon monosyllabic task' {>=}80% (Good group; n 6) or {<=}20% (Poor group; n 6). Relative cerebral blood flow was measured in 3 conditions: rest, passive listening to human voice, and non-voice stimuli. Results: Compared with silence, the activations induced by non-voice stimuli were bilaterally located in the superior temporal regions in all groups. However these activations were significantly and similarly reduced in both cochlear implant groups, whereas control subjects showed supplementary activations. Compared with non-voice, the voice stimuli induced bilateral activation of the TVA along the superior temporal sulcus (STS) in both the control and the Good groups. In contrast, these activations were not detected in the Poor group, which showed only left unilateral middle STS activation. Conclusion: These results suggest that PET is an adequate method to explore cochlear implant benefits and that this benefit could be linked to the activation of the TVA. (authors)

  19. Cochlear implant benefits in deafness rehabilitation: PET study of temporal voice Activations

    International Nuclear Information System (INIS)

    Coez, A.; Zilbovicius, M.; Zilbovicius, M.; Syrota, A.; Samson, Y.; Bizaguet, E.; Coez, A.; Ferrary, E.; Bouccara, D.; Mosnier, I.; Sterkers, O.; Ambert-Dahan, E.; Ferrary, E.; Bouccara, D.; Mosnier, I.; Sterkers, O.; Samson, Y.; Samson, Y.; Sterkers, O.

    2008-01-01

    Cochlear implants may improve the medical and social prognosis of profound deafness. Nevertheless, some patients have experienced poor results without any clear explanations. One correlate may be an alteration in cortical voice processing. To test this hypothesis, we studied the activation of human temporal voice areas (TVA) using a well-standardized PET paradigm adapted from previous functional MRI (fMRI) studies. Methods: A PET H 2 15 O activation study was performed on 3 groups of adult volunteers: normal-hearing control subjects (n 6) and cochlear-implanted post-lingually deaf patients with ≥2 y of cochlear implant experience, with intelligibility scores in the 'Lafon monosyllabic task' ≥80% (Good group; n 6) or ≤20% (Poor group; n 6). Relative cerebral blood flow was measured in 3 conditions: rest, passive listening to human voice, and non-voice stimuli. Results: Compared with silence, the activations induced by non-voice stimuli were bilaterally located in the superior temporal regions in all groups. However these activations were significantly and similarly reduced in both cochlear implant groups, whereas control subjects showed supplementary activations. Compared with non-voice, the voice stimuli induced bilateral activation of the TVA along the superior temporal sulcus (STS) in both the control and the Good groups. In contrast, these activations were not detected in the Poor group, which showed only left unilateral middle STS activation. Conclusion: These results suggest that PET is an adequate method to explore cochlear implant benefits and that this benefit could be linked to the activation of the TVA. (authors)

  20. Placement of single tooth implant in healed socket with immediate temporization: Clinical study

    Directory of Open Access Journals (Sweden)

    Jeevan Lata

    2012-01-01

    Full Text Available Introduction: Edentulous condition inadequately compensated for, by dentures, impair oral function and is accompanied by reduced self–confidence. In a continued effort to achieve these goals, implant dentistry was introduced. Immediate temporization is somehow a recent concept, which allows the maintenance of soft tissue contours, along with interdental alveolar contours. Aims and Obectives: Aims of the present study were to study the placement of implant in the post-extracted healed tooth socket of anterior maxilla and to evaluate the feasibility of early function on implants placed. Materials and Methods: In the present study, HI-TECH IMPLANTS TRX-OP one-piece immediate loading implant system with the built on abutment has been used.Immediate temporisation has been done and results have been evaluated in terms of stability, gingival health, esthetics, marginal bone loss, patient′s psychological attitude, and satisfaction.
Results: Out of eight implants, 6 successfully healed whereas 2 implants suffered failure
Conclusion: Overall conclusion drawn from the study is, immediate temporization is a successful method providing psychological, financial and emotional benefits to the patient.

  1. Temporal networks

    Science.gov (United States)

    Holme, Petter; Saramäki, Jari

    2012-10-01

    A great variety of systems in nature, society and technology-from the web of sexual contacts to the Internet, from the nervous system to power grids-can be modeled as graphs of vertices coupled by edges. The network structure, describing how the graph is wired, helps us understand, predict and optimize the behavior of dynamical systems. In many cases, however, the edges are not continuously active. As an example, in networks of communication via e-mail, text messages, or phone calls, edges represent sequences of instantaneous or practically instantaneous contacts. In some cases, edges are active for non-negligible periods of time: e.g., the proximity patterns of inpatients at hospitals can be represented by a graph where an edge between two individuals is on throughout the time they are at the same ward. Like network topology, the temporal structure of edge activations can affect dynamics of systems interacting through the network, from disease contagion on the network of patients to information diffusion over an e-mail network. In this review, we present the emergent field of temporal networks, and discuss methods for analyzing topological and temporal structure and models for elucidating their relation to the behavior of dynamical systems. In the light of traditional network theory, one can see this framework as moving the information of when things happen from the dynamical system on the network, to the network itself. Since fundamental properties, such as the transitivity of edges, do not necessarily hold in temporal networks, many of these methods need to be quite different from those for static networks. The study of temporal networks is very interdisciplinary in nature. Reflecting this, even the object of study has many names-temporal graphs, evolving graphs, time-varying graphs, time-aggregated graphs, time-stamped graphs, dynamic networks, dynamic graphs, dynamical graphs, and so on. This review covers different fields where temporal graphs are considered

  2. Cerebral blood flow in temporal lobe epilepsy: a partial volume correction study

    Energy Technology Data Exchange (ETDEWEB)

    Giovacchini, Giampiero [University Milano-Bicocca, Milan (Italy); Bonwetsch, Robert; Theodore, William H. [National Institute of Neurological Diseases and Strokes, Clinical Epilepsy Section, Bethesda, MD (United States); Herscovitch, Peter [National Institutes of Health, PET Department, Clinical Center, Bethesda, MD (United States); Carson, Richard E. [Yale PET Center, New Haven, CT (United States)

    2007-12-15

    Previous studies in temporal lobe epilepsy (TLE) have shown that, owing to brain atrophy, positron emission tomography (PET) can overestimate deficits in measures of cerebral function such as glucose metabolism (CMR{sub glu}) and neuroreceptor binding. The magnitude of this effect on cerebral blood flow (CBF) is unexplored. The aim of this study was to assess CBF deficits in TLE before and after magnetic resonance imaging-based partial volume correction (PVC). Absolute values of CBF for 21 TLE patients and nine controls were computed before and after PVC. In TLE patients, quantitative CMR{sub glu} measurements also were obtained. Before PVC, regional values of CBF were significantly (p<0.05) lower in TLE patients than in controls in all regions, except the fusiform gyrus contralateral to the epileptic focus. After PVC, statistical significance was maintained in only four regions: ipsilateral inferior temporal cortex, bilateral insula and contralateral amygdala. There was no significant difference between patients and controls in CBF asymmetry indices (AIs) in any region before or after PVC. In TLE patients, AIs for CBF were significantly smaller than for CMR{sub glu} in middle and inferior temporal cortex, fusiform gyrus and hippocampus both before and after PVC. A significant positive relationship between disease duration and AIs for CMR{sub glu}, but not CBF, was detected in hippocampus and amygdala, before but not after PVC. PVC should be used for PET CBF measurements in patients with TLE. Reduced blood flow, in contrast to glucose metabolism, is mainly due to structural changes. (orig.)

  3. Study of temporal variation of radon concentrations in public drinking water supplies

    International Nuclear Information System (INIS)

    York, E.L.

    1995-01-01

    The Environmental Protection Agency (EPA) has proposed a Maximum Contaminant Level (MCL) for radon-222 in public drinking water supplies of 300 pCi/L. Proposed monitoring requirements include collecting quarterly grab samples for the first year, then annual samples for the remainder of the compliance cycle provided first year quarterly samples average below the MCL. The focus of this research was to study the temporal variation of groundwater radon concentrations to investigate how reliably one can predict an annual average radon concentration based on the results of grab samples. Using a open-quotes slow-flowclose quotes collection method and liquid scintillation analysis, biweekly water samples were taken from ten public water supply wells in North Carolina (6 month - 11 month sampling periods). Based on study results, temporal variations exist in groundwater radon concentrations. Statistical analysis performed on the data indicates that grab samples taken from each of the ten wells during the study period would exhibit groundwater radon concentrations within 30% of their average radon concentration

  4. Uropathogenic Escherichia coli virulence genes: invaluable approaches for designing DNA microarray probes.

    Science.gov (United States)

    Jahandeh, Nadia; Ranjbar, Reza; Behzadi, Payam; Behzadi, Elham

    2015-01-01

    The pathotypes of uropathogenic Escherichia coli (UPEC) cause different types of urinary tract infections (UTIs). The presence of a wide range of virulence genes in UPEC enables us to design appropriate DNA microarray probes. These probes, which are used in DNA microarray technology, provide us with an accurate and rapid diagnosis and definitive treatment in association with UTIs caused by UPEC pathotypes. The main goal of this article is to introduce the UPEC virulence genes as invaluable approaches for designing DNA microarray probes. Main search engines such as Google Scholar and databases like NCBI were searched to find and study several original pieces of literature, review articles, and DNA gene sequences. In parallel with in silico studies, the experiences of the authors were helpful for selecting appropriate sources and writing this review article. There is a significant variety of virulence genes among UPEC strains. The DNA sequences of virulence genes are fabulous patterns for designing microarray probes. The location of virulence genes and their sequence lengths influence the quality of probes. The use of selected virulence genes for designing microarray probes gives us a wide range of choices from which the best probe candidates can be chosen. DNA microarray technology provides us with an accurate, rapid, cost-effective, sensitive, and specific molecular diagnostic method which is facilitated by designing microarray probes. Via these tools, we are able to have an accurate diagnosis and a definitive treatment regarding UTIs caused by UPEC pathotypes.

  5. A STUDY ON EFFICACY OF MANUAL SMALL INCISION CATARACT SURGERY BY TEMPORAL APPROACH

    Directory of Open Access Journals (Sweden)

    Vinodhini Kannan

    2018-01-01

    Full Text Available BACKGROUND Manual Small Incision Cataract Surgery (MSICS is a well-known technique of cataract surgery owing to its advantage of a selfsealing suture less incision with least surgically induced astigmatism at a low cost. It is a safe, simple, consistent, stable and cost-effective technique with various modifications that involve site, size, type of incision and method of nucleus delivery. One such modification is Temporal Incision MSICS, where the cataract surgery is done by a temporal approach, which is equally good compared to the superior incision. This study was done retrospectively to analyse the visual outcome of patients operated by Manual SICS - Temporal Approach, using the WHO criteria and to establish its efficacy as a good surgical technique. MATERIALS AND METHODS Records of patients operated for senile cataract by a single surgeon by Temporal MSICS using a temporal sclerocorneal incision of 6-6.5 mm, during a 1-year period, were analysed retrospectively. Post-operative followup records of POD-1 and subsequent follow-ups at 1 st week and 6 th week were recorded for visual outcome. RESULTS Out of the 83 cases analysed retrospectively, majority of them were found to be between 61-70 years with a female Preponderance. Most of the cases were found to have senile immature cataract (55 patients, with Grade III nuclear sclerosis (52 cases. The pre-operative visual acuity was poor <6/60 in 72 cases (86.7% and borderline in 11 cases (14.5%. 55 cases (66.3% had a 6.5 mm scleral incision and the remaining 28 cases (33.7% had a 6 mm incision. Average duration of surgery noted was 8.35 minutes. Striate Keratopathy was the most common 1 st POD complication followed by corneal oedema. Striate keratopathy was the most common complication at the 1 st week followup followed by pigment dispersion. Majority of cases (76 cases were found to have been complication free at the end of 6 weeks. At the end of 6 weeks post-operatively as per records, 80 cases

  6. Evaluation of the utility of temporal subtraction images in successive whole-body bone scans: a prospective clinical study

    International Nuclear Information System (INIS)

    Shiraishi, J.; Appelbaum, D.; Pu, Y.; Engelmann, R.; Li Qiang; Doi, K.

    2007-01-01

    We have begun a prospective clinical study for evaluating the clinical utility of temporal subtraction images in successive whole-body bone scans. The computerized temporal subtraction technique has been developed in order to highlight interval changes of abnormal lesions due to skeletal metastases, primary bone tumors, osteomyelitis, and fractures. In our initial preliminary results of the prospective study which was started on November 22, 2006 in our hospital, radiologists reported some interval changes which were not recognized in the initial standard readings, but were obvious when temporal subtraction images were viewed. The usefulness of the temporal subtraction images will be investigated in terms of its clinical utility by the prospective clinical study. (orig.)

  7. Spatial and temporal aspects of grain accumulation costs for ethanol production: An Australian case study

    International Nuclear Information System (INIS)

    Anderton, Nikki; Kingwell, Ross

    2008-01-01

    Ethanol production is increasingly commonplace in many grain-producing regions. This paper uses the grain-producing region of south-western Australia to illustrate spatial and temporal aspects of grain accumulation costs for ethanol production. Specifically, this study examines how price variability of various wheat grades, combined with spatial and temporal variability in production of those grades, affects the costs of grain accumulation. These costs are the main components of an ethanol plant's operating costs so lessening these costs can offer a comparative advantage for a plant owner. Logistics models based on mathematical programming are constructed for a range of plant sizes and locations for ethanol production. Modelling results identify low-cost sites that generate cost savings, in present value terms, of between 5 and 7.5 per cent, depending on plant size, over the 9-year study period. At all locations, small to medium-sized plants offer advantages of lower and less variable costs of grain accumulation. Yet, all locations and all plant sizes are characterised by marked volatility in the cost of grain accumulation. The profitability of ethanol production based on wheat in this region of Australia is particularly exposed to any prolonged period of high grain prices relative to petroleum prices, given current biofuel-policy settings in Australia. (author)

  8. Cerebral blood flow in temporal lobe epilepsy: a partial volume correction study

    International Nuclear Information System (INIS)

    Giovacchini, Giampiero; Bonwetsch, Robert; Theodore, William H.; Herscovitch, Peter; Carson, Richard E.

    2007-01-01

    Previous studies in temporal lobe epilepsy (TLE) have shown that, owing to brain atrophy, positron emission tomography (PET) can overestimate deficits in measures of cerebral function such as glucose metabolism (CMR glu ) and neuroreceptor binding. The magnitude of this effect on cerebral blood flow (CBF) is unexplored. The aim of this study was to assess CBF deficits in TLE before and after magnetic resonance imaging-based partial volume correction (PVC). Absolute values of CBF for 21 TLE patients and nine controls were computed before and after PVC. In TLE patients, quantitative CMR glu measurements also were obtained. Before PVC, regional values of CBF were significantly (p glu in middle and inferior temporal cortex, fusiform gyrus and hippocampus both before and after PVC. A significant positive relationship between disease duration and AIs for CMR glu , but not CBF, was detected in hippocampus and amygdala, before but not after PVC. PVC should be used for PET CBF measurements in patients with TLE. Reduced blood flow, in contrast to glucose metabolism, is mainly due to structural changes. (orig.)

  9. Anterior temporal white matter lesions in myotonic dystrophy with intellectual impairment: an MRI and neuropathological study

    International Nuclear Information System (INIS)

    Ogata, A.; Tashiro, K.; Terae, S.; Fujita, M.

    1998-01-01

    We studied 12 patients with myotonic dystrophy using MRI and the Mini-mental state examination (MMSE), to see it specific MRI findings were associated with intellectual impairment. We also compared them with the neuropathological findings in an autopsy case of MD with intellectual impairment. Mild intellectual impairment was found in 8 of the 12 patients. On T 2-weighted and proton density-weighted images, high-intensity areas were seen in cerebral white matter in 10 of the 12 patients. In seven of these, anterior temporal white-matter lesions (ATWML) were found; all seven had mild intellectual impairment (MMSE 22-26), whereas none of the four patients with normal mentation had ATWML. In only one of the eight patients with intellectual impairment were white-matter lesions not found. Pathological findings were severe loss and disordered arrangement of myelin sheaths and axons in addition to heterotopic neurons within anterior temporal white matter. Bilateral ATWML might be a factor for intellectual impairment in MD. The retrospective pathological study raised the possibility that the ATWML are compatible with focal dysplasia of white matter. (orig.)

  10. Study of temporal quantum correlations in decohering B and K meson systems

    Science.gov (United States)

    Naikoo, Javid; Alok, Ashutosh Kumar; Banerjee, Subhashish

    2018-03-01

    In this work we study temporal quantum correlations, quantified by Leggett-Garg (LG) and LG-type inequalities, in the B and K meson systems. We use the tools of open quantum systems to incorporate the effect of decoherence which is quantified by a single phenomenological parameter. The effect of C P violation is also included in our analysis. We find that the LG inequality is violated for both B and K meson systems, the violation being most prominent in the case of K mesons and least for Bs system. Since the systems with no coherence do not violate LGI, incorporating decoherence is expected to decrease the extent of violation of LGI and is clearly brought out in our results. We show that the expression for the LG functions depends upon an additional term, apart from the experimentally measurable meson transition probabilities. This term vanishes in the limit of zero decoherence. On the other hand, the LG-type parameter can be directly expressed in terms of transition probabilities, making it a more appropriate observable for studying temporal quantum correlations in neutral meson systems.

  11. Testing a Microarray to Detect and Monitor Toxic Microalgae in Arcachon Bay in France

    Directory of Open Access Journals (Sweden)

    Linda K. Medlin

    2013-03-01

    Full Text Available Harmful algal blooms (HABs occur worldwide, causing health problems and economic damages to fisheries and tourism. Monitoring agencies are therefore essential, yet monitoring is based only on time-consuming light microscopy, a level at which a correct identification can be limited by insufficient morphological characters. The project MIDTAL (Microarray Detection of Toxic Algae—an FP7-funded EU project—used rRNA genes (SSU and LSU as a target on microarrays to identify toxic species. Furthermore, toxins were detected with a newly developed multiplex optical Surface Plasmon Resonance biosensor (Multi SPR and compared with an enzyme-linked immunosorbent assay (ELISA. In this study, we demonstrate the latest generation of MIDTAL microarrays (version 3 and show the correlation between cell counts, detected toxin and microarray signals from field samples taken in Arcachon Bay in France in 2011. The MIDTAL microarray always detected more potentially toxic species than those detected by microscopic counts. The toxin detection was even more sensitive than both methods. Because of the universal nature of both toxin and species microarrays, they can be used to detect invasive species. Nevertheless, the MIDTAL microarray is not completely universal: first, because not all toxic species are on the chip, and second, because invasive species, such as Ostreopsis, already influence European coasts.

  12. Identification of potential biomarkers from microarray experiments using multiple criteria optimization

    International Nuclear Information System (INIS)

    Sánchez-Peña, Matilde L; Isaza, Clara E; Pérez-Morales, Jaileene; Rodríguez-Padilla, Cristina; Castro, José M; Cabrera-Ríos, Mauricio

    2013-01-01

    Microarray experiments are capable of determining the relative expression of tens of thousands of genes simultaneously, thus resulting in very large databases. The analysis of these databases and the extraction of biologically relevant knowledge from them are challenging tasks. The identification of potential cancer biomarker genes is one of the most important aims for microarray analysis and, as such, has been widely targeted in the literature. However, identifying a set of these genes consistently across different experiments, researches, microarray platforms, or cancer types is still an elusive endeavor. Besides the inherent difficulty of the large and nonconstant variability in these experiments and the incommensurability between different microarray technologies, there is the issue of the users having to adjust a series of parameters that significantly affect the outcome of the analyses and that do not have a biological or medical meaning. In this study, the identification of potential cancer biomarkers from microarray data is casted as a multiple criteria optimization (MCO) problem. The efficient solutions to this problem, found here through data envelopment analysis (DEA), are associated to genes that are proposed as potential cancer biomarkers. The method does not require any parameter adjustment by the user, and thus fosters repeatability. The approach also allows the analysis of different microarray experiments, microarray platforms, and cancer types simultaneously. The results include the analysis of three publicly available microarray databases related to cervix cancer. This study points to the feasibility of modeling the selection of potential cancer biomarkers from microarray data as an MCO problem and solve it using DEA. Using MCO entails a new optic to the identification of potential cancer biomarkers as it does not require the definition of a threshold value to establish significance for a particular gene and the selection of a normalization

  13. Analyses of Aloe polysaccharides using carbohydrate microarray profiling

    DEFF Research Database (Denmark)

    Isager Ahl, Louise; Grace, Olwen M; Pedersen, Henriette Lodberg

    2018-01-01

    As the popularity of Aloe vera extracts continues to rise, a desire to fully understand the individual polymer components of the leaf mesophyll, their relation to one another and the effects they have on the human body are increasing. Polysaccharides present in the leaf mesophyll have been...... identified as the components responsible for the biological activities of Aloe vera, and they have been widely studied in the past decades. However, the commonly used methods do not provide the desired platform to conduct large comparative studies of polysaccharide compositions as most of them require...... a complete or near-complete fractionation of the polymers. The objective for this study was to assess whether carbohydrate microarrays could be used for the high-throughput analysis of cell wall polysaccharides in Aloe leaf mesophyll. The method we chose is known as Comprehensive Microarray Polymer Profiling...

  14. Statistical study of spatio-temporal distribution of precursor solar flares associated with major flares

    Science.gov (United States)

    Gyenge, N.; Ballai, I.; Baranyi, T.

    2016-07-01

    The aim of the present investigation is to study the spatio-temporal distribution of precursor flares during the 24 h interval preceding M- and X-class major flares and the evolution of follower flares. Information on associated (precursor and follower) flares is provided by Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI). Flare list, while the major flares are observed by the Geostationary Operational Environmental Satellite (GOES) system satellites between 2002 and 2014. There are distinct evolutionary differences between the spatio-temporal distributions of associated flares in about one-day period depending on the type of the main flare. The spatial distribution was characterized by the normalized frequency distribution of the quantity δ (the distance between the major flare and its precursor flare normalized by the sunspot group diameter) in four 6 h time intervals before the major event. The precursors of X-class flares have a double-peaked spatial distribution for more than half a day prior to the major flare, but it changes to a lognormal-like distribution roughly 6 h prior to the event. The precursors of M-class flares show lognormal-like distribution in each 6 h subinterval. The most frequent sites of the precursors in the active region are within a distance of about 0.1 diameter of sunspot group from the site of the major flare in each case. Our investigation shows that the build-up of energy is more effective than the release of energy because of precursors.

  15. Apolipoprotein E in Temporal Lobe Epilepsy: A Case-Control Study

    Science.gov (United States)

    Kumar, Amit; Tripathi, Manjari; Pandey, Ravindra M.; Ramakrishnan, Lakshmy; Srinivas, M.; Luthra, Kalpana

    2006-01-01

    Purpose: To investigate the relationship of apolipoprotein E (apoE) genotype, plasma levels of apoE and lipids in temporal lobe epilepsy (TLE) patients in Asian Indians. Status of plasma levels of Apo E in epilepsy patients has not been reported till date. Methods: ApoE gene polymorphism was analyzed in 58 patients with temporal lobe epilepsy (TLE) and 57 age and sex approximated controls using Polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP). Levels of plasma apoE and lipids were measured using ELISA and enzymatic kits respectively. Results: The distribution of ApoE genotype in epilepsy patients and controls was comparable. Higher levels of plasma ApoE were observed in TLE patients as compared to controls (p = 0.0001). Individuals with plasma levels of apoE > 190 mg/L were at 20 times higher odds (95%CI = 2.46–163.34, p = 0.005), while those with levels of apoE between 150–190 mg/L were at 4.9 times higher odds (95% CI = 1.85–13.9, p = 0.001), to develop TLE. Conclusions: We have observed for the first time, high levels of plasma apoE in epilepsy patients. The findings of this case-control study suggest that apolipoprotein E may play an important role in epilepsy. PMID:17264404

  16. Neuropsychological outcomes after Gamma Knife radiosurgery for mesial temporal lobe epilepsy: a prospective multicenter study.

    Science.gov (United States)

    Quigg, Mark; Broshek, Donna K; Barbaro, Nicholas M; Ward, Mariann M; Laxer, Kenneth D; Yan, Guofen; Lamborn, Kathleen

    2011-05-01

    To assess outcomes of language, verbal memory, cognitive efficiency and mental flexibility, mood, and quality of life (QOL) in a prospective, multicenter pilot study of Gamma Knife radiosurgery (RS) for mesial temporal lobe epilepsy (MTLE). RS, randomized to 20 Gy or 24 Gy comprising 5.5-7.5 ml at the 50% isodose volume, was performed on mesial temporal structures of patients with unilateral MTLE. Neuropsychological evaluations were performed at preoperative baseline, and mean change scores were described at 12 and 24 months postoperatively. QOL data were also available at 36 months. Thirty patients were treated and 26 were available for the final 24-month neuropsychological evaluation. Language (Boston Naming Test), verbal memory (California Verbal Learning Test and Logical Memory subtest of the Wechsler Memory Scale-Revised), cognitive efficiency and mental flexibility (Trail Making Test), and mood (Beck Depression Inventory) did not differ from baseline. QOL scores improved at 24 and 36 months, with those patients attaining seizure remission by month 24s accounting for the majority of the improvement. The serial changes in cognitive outcomes, mood, and QOL are unremarkable following RS for MTLE. RS may provide an alternative to open surgery, especially in those patients at risk of cognitive impairment or who desire a noninvasive alternative to open surgery. Wiley Periodicals, Inc. © 2011 International League Against Epilepsy.

  17. Epileptogenicity of cortical dysplasia in temporal lobe dual pathology: an electrophysiological study with invasive recordings.

    Science.gov (United States)

    Fauser, Susanne; Schulze-Bonhage, Andreas

    2006-01-01

    Hippocampal sclerosis is often associated with macroscopic or microscopic dysplasia in the temporal neocortex (TN). The relevance of such a dual pathology with regard to epileptogenesis is unclear. This study investigates the role of both pathologies in the generation of ictal and interictal activity. Ictal (113 seizures) and interictal data from invasive EEG recordings with simultaneous depth electrodes in the hippocampus and subdural electrodes over the TN were analysed retrospectively in 12 patients with variable degrees of hippocampal sclerosis and different types of histologically confirmed temporal cortical dysplasia [all male, age at epilepsy onset 25 Hz) and repetitive sharp waves. The interictal patterns over the TN were similar to those seen over extratemporal focal cortical dysplasias. Simultaneous recordings from the hippocampus and the TN strongly suggest that dysplastic tissue in the TN is often epileptogenic. The quantitative contribution of the hippocampus to seizure generation corresponded with the degree of hippocampal pathology, whereas different subtypes of cortical dysplasia did not affect its relative contribution to seizure generation and even mild forms of dysplasia were epileptogenic.

  18. Temporal dynamics of disgust and morality: an event-related potential study.

    Directory of Open Access Journals (Sweden)

    Qun Yang

    Full Text Available Disgust is argued to be an emotion that motivates the avoidance of disease-causing entities in the physical domain and unacceptable behaviors in the social-moral domain. Empirical work from behavioral, physiological and brain imaging studies suggests moral judgments are strongly modulated by disgust feelings. Yet, it remains unclear how they are related in the time course of neural processing. Examining the temporal order of disgust emotion and morality could help to clarify the role of disgust in moral judgments. In the present research, a Go/No-Go paradigm was employed to evoke lateralized readiness potentials (LRPs to investigate the temporal order of physical disgust and moral information processing. Participants were asked to give a "yes" or "no" response regarding the physical disgust and moral wrongness of a social act. The results showed that the evaluation of moral information was processed prior to that of physical disgust information. This suggests that moral information is available earlier than physical disgust, and provides more data on the biological heterogeneity between disgust and morality in terms of the time course of neural activity. The findings implicate that physical disgust emotion may not be necessary for people to make moral judgments. They also suggest that some of our moral experience may be more fundamental (than physical disgust experience to our survival and development, as humans spend a considerable amount of time engaging in social interaction.

  19. Temporal, seasonal and weather effects on cycle volume: an ecological study

    Directory of Open Access Journals (Sweden)

    Tin Tin Sandar

    2012-03-01

    Full Text Available Abstract Background Cycling has the potential to provide health, environmental and economic benefits but the level of cycling is very low in New Zealand and many other countries. Adverse weather is often cited as a reason why people do not cycle. This study investigated temporal and seasonal variability in cycle volume and its association with weather in Auckland, New Zealand's largest city. Methods Two datasets were used: automated cycle count data collected on Tamaki Drive in Auckland by using ZELT Inductive Loop Eco-counters and weather data (gust speed, rain, temperature, sunshine duration available online from the National Climate Database. Analyses were undertaken using data collected over one year (1 January to 31 December 2009. Normalised cycle volumes were used in correlation and regression analyses to accommodate differences by hour of the day and day of the week and holiday. Results In 2009, 220,043 bicycles were recorded at the site. There were significant differences in mean hourly cycle volumes by hour of the day, day type and month of the year (p p Conclusions There are temporal and seasonal variations in cycle volume in Auckland and weather significantly influences hour-to-hour and day-to-day variations in cycle volume. Our findings will help inform future cycling promotion activities in Auckland.

  20. A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

    NARCIS (Netherlands)

    Sontrop, H.M.J.; Moerland, P.D.; Van den Ham, R.; Reinders, M.J.T.; Verhaegh, W.F.J.

    2009-01-01

    Background: Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for

  1. A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

    NARCIS (Netherlands)

    Sontrop, Herman M. J.; Moerland, Perry D.; van den Ham, René; Reinders, Marcel J. T.; Verhaegh, Wim F. J.

    2009-01-01

    Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the

  2. Study of the dependence of resolution temporal activity for a Philips gemini TF PET/CT scanner by applying a statistical analysis of time series

    International Nuclear Information System (INIS)

    Sanchez Merino, G.; Cortes Rpdicio, J.; Lope Lope, R.; Martin Gonzalez, T.; Garcia Fidalgo, M. A.

    2013-01-01

    The aim of the present work is to study the dependence of temporal resolution with the activity using statistical techniques applied to the series of values time series measurements of temporal resolution during daily equipment checks. (Author)

  3. Nanotechnology: moving from microarrays toward nanoarrays.

    Science.gov (United States)

    Chen, Hua; Li, Jun

    2007-01-01

    Microarrays are important tools for high-throughput analysis of biomolecules. The use of microarrays for parallel screening of nucleic acid and protein profiles has become an industry standard. A few limitations of microarrays are the requirement for relatively large sample volumes and elongated incubation time, as well as the limit of detection. In addition, traditional microarrays make use of bulky instrumentation for the detection, and sample amplification and labeling are quite laborious, which increase analysis cost and delays the time for obtaining results. These problems limit microarray techniques from point-of-care and field applications. One strategy for overcoming these problems is to develop nanoarrays, particularly electronics-based nanoarrays. With further miniaturization, higher sensitivity, and simplified sample preparation, nanoarrays could potentially be employed for biomolecular analysis in personal healthcare and monitoring of trace pathogens. In this chapter, it is intended to introduce the concept and advantage of nanotechnology and then describe current methods and protocols for novel nanoarrays in three aspects: (1) label-free nucleic acids analysis using nanoarrays, (2) nanoarrays for protein detection by conventional optical fluorescence microscopy as well as by novel label-free methods such as atomic force microscopy, and (3) nanoarray for enzymatic-based assay. These nanoarrays will have significant applications in drug discovery, medical diagnosis, genetic testing, environmental monitoring, and food safety inspection.

  4. Integrative missing value estimation for microarray data.

    Science.gov (United States)

    Hu, Jianjun; Li, Haifeng; Waterman, Michael S; Zhou, Xianghong Jasmine

    2006-10-12

    Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. We present the integrative Missing Value Estimation method (iMISS) by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS) imputation algorithm by up to 15% improvement in our benchmark tests. We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

  5. Integrative missing value estimation for microarray data

    Directory of Open Access Journals (Sweden)

    Zhou Xianghong

    2006-10-01

    Full Text Available Abstract Background Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. Results We present the integrative Missing Value Estimation method (iMISS by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS imputation algorithm by up to 15% improvement in our benchmark tests. Conclusion We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

  6. Xylella fastidiosa gene expression analysis by DNA microarrays

    OpenAIRE

    Travensolo,Regiane F.; Carareto-Alves,Lucia M.; Costa,Maria V.C.G.; Lopes,Tiago J.S.; Carrilho,Emanuel; Lemos,Eliana G.M.

    2009-01-01

    Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcrip...

  7. Microarray analysis of gene expression profiles in ripening pineapple fruits.

    Science.gov (United States)

    Koia, Jonni H; Moyle, Richard L; Botella, Jose R

    2012-12-18

    Pineapple (Ananas comosus) is a tropical fruit crop of significant commercial importance. Although the physiological changes that occur during pineapple fruit development have been well characterized, little is known about the molecular events that occur during the fruit ripening process. Understanding the molecular basis of pineapple fruit ripening will aid the development of new varieties via molecular breeding or genetic modification. In this study we developed a 9277 element pineapple microarray and used it to profile gene expression changes that occur during pineapple fruit ripening. Microarray analyses identified 271 unique cDNAs differentially expressed at least 1.5-fold between the mature green and mature yellow stages of pineapple fruit ripening. Among these 271 sequences, 184 share significant homology with genes encoding proteins of known function, 53 share homology with genes encoding proteins of unknown function and 34 share no significant homology with any database accession. Of the 237 pineapple sequences with homologs, 160 were up-regulated and 77 were down-regulated during pineapple fruit ripening. DAVID Functional Annotation Cluster (FAC) analysis of all 237 sequences with homologs revealed confident enrichment scores for redox activity, organic acid metabolism, metalloenzyme activity, glycolysis, vitamin C biosynthesis, antioxidant activity and cysteine peptidase activity, indicating the functional significance and importance of these processes and pathways during pineapple fruit development. Quantitative real-time PCR analysis validated the microarray expression results for nine out of ten genes tested. This is the first report of a microarray based gene expression study undertaken in pineapple. Our bioinformatic analyses of the transcript profiles have identified a number of genes, processes and pathways with putative involvement in the pineapple fruit ripening process. This study extends our knowledge of the molecular basis of pineapple fruit

  8. Printing Proteins as Microarrays for High-Throughput Function Determination

    Science.gov (United States)

    MacBeath, Gavin; Schreiber, Stuart L.

    2000-09-01

    Systematic efforts are currently under way to construct defined sets of cloned genes for high-throughput expression and purification of recombinant proteins. To facilitate subsequent studies of protein function, we have developed miniaturized assays that accommodate extremely low sample volumes and enable the rapid, simultaneous processing of thousands of proteins. A high-precision robot designed to manufacture complementary DNA microarrays was used to spot proteins onto chemically derivatized glass slides at extremely high spatial densities. The proteins attached covalently to the slide surface yet retained their ability to interact specifically with other proteins, or with small molecules, in solution. Three applications for protein microarrays were demonstrated: screening for protein-protein interactions, identifying the substrates of protein kinases, and identifying the protein targets of small molecules.

  9. Nanomedicine, microarrays and their applications in clinical microbiology

    Directory of Open Access Journals (Sweden)

    Özcan Deveci

    2010-12-01

    Full Text Available Growing interest in the future medical applications of nanotechnology is leading to the emergence of a new scientific field that called as “nanomedicine”. Nanomedicine may be defined as the investigating, treating, reconstructing and controlling human biology and health at the molecular level, using engineered nanodevices and nanostructures. Microarray technology is a revolutionary tool for elucidating roles of genes in infectious diseases, shifting from traditional methods of research to integrated approaches. This technology has great potential to provide medical diagnosis, monitor treatment and help in the development of new tools for infectious disease prevention and/or management. The aim of this paper is to provide an overview of the current application of microarray platforms and nanomedicine in the study of experimental microbiology and the impact of this technology in clinical settings.

  10. A cluster merging method for time series microarray with production values.

    Science.gov (United States)

    Chira, Camelia; Sedano, Javier; Camara, Monica; Prieto, Carlos; Villar, Jose R; Corchado, Emilio

    2014-09-01

    A challenging task in time-course microarray data analysis is to cluster genes meaningfully combining the information provided by multiple replicates covering the same key time points. This paper proposes a novel cluster merging method to accomplish this goal obtaining groups with highly correlated genes. The main idea behind the proposed method is to generate a clustering starting from groups created based on individual temporal series (representing different biological replicates measured in the same time points) and merging them by taking into account the frequency by which two genes are assembled together in each clustering. The gene groups at the level of individual time series are generated using several shape-based clustering methods. This study is focused on a real-world time series microarray task with the aim to find co-expressed genes related to the production and growth of a certain bacteria. The shape-based clustering methods used at the level of individual time series rely on identifying similar gene expression patterns over time which, in some models, are further matched to the pattern of production/growth. The proposed cluster merging method is able to produce meaningful gene groups which can be naturally ranked by the level of agreement on the clustering among individual time series. The list of clusters and genes is further sorted based on the information correlation coefficient and new problem-specific relevant measures. Computational experiments and results of the cluster merging method are analyzed from a biological perspective and further compared with the clustering generated based on the mean value of time series and the same shape-based algorithm.

  11. Tissue Microarray TechnologyA Brief Review

    Directory of Open Access Journals (Sweden)

    Ramya S Vokuda

    2018-01-01

    Full Text Available In this era of modern revolutionisation in the field of medical laboratory technology, everyone is aiming at taking the innovations from laboratory to bed side. One such technique that is most relevant to the pathologic community is Tissue Microarray (TMA technology. This is becoming quite popular amongst all the members of this family, right from laboratory scientists to clinicians and residents to technologists. The reason for this technique to gain popularity is attributed to its cost effectiveness and time saving protocols. Though, every technique is accompanied by disadvantages, the benefits out number them. This technique is very versatile as many downstream molecular assays such as immunohistochemistry, cytogenetic studies, Fluorescent In situ-Hybridisation (FISH etc., can be carried out on a single slide with multiple numbers of samples. It is a very practical approach that aids effectively to identify novel biomarkers in cancer diagnostics and therapeutics. It helps in assessing the molecular markers on a large scale very quickly. Also, the quality assurance protocols in pathological laboratory has exploited TMA to a great extent. However, the application of TMA technology is beyond oncology. This review shall focus on the different aspects of this technology such as construction of TMA, instrumentation, types, advantages and disadvantages and utilisation of the technique in various disease conditions.

  12. Tissue Microarray Analysis Applied to Bone Diagenesis.

    Science.gov (United States)

    Mello, Rafael Barrios; Silva, Maria Regina Regis; Alves, Maria Teresa Seixas; Evison, Martin Paul; Guimarães, Marco Aurelio; Francisco, Rafaella Arrabaca; Astolphi, Rafael Dias; Iwamura, Edna Sadayo Miazato

    2017-01-04

    Taphonomic processes affecting bone post mortem are important in forensic, archaeological and palaeontological investigations. In this study, the application of tissue microarray (TMA) analysis to a sample of femoral bone specimens from 20 exhumed individuals of known period of burial and age at death is described. TMA allows multiplexing of subsamples, permitting standardized comparative analysis of adjacent sections in 3-D and of representative cross-sections of a large number of specimens. Standard hematoxylin and eosin, periodic acid-Schiff and silver methenamine, and picrosirius red staining, and CD31 and CD34 immunohistochemistry were applied to TMA sections. Osteocyte and osteocyte lacuna counts, percent bone matrix loss, and fungal spheroid element counts could be measured and collagen fibre bundles observed in all specimens. Decalcification with 7% nitric acid proceeded more rapidly than with 0.5 M EDTA and may offer better preservation of histological and cellular structure. No endothelial cells could be detected using CD31 and CD34 immunohistochemistry. Correlation between osteocytes per lacuna and age at death may reflect reported age-related responses to microdamage. Methodological limitations and caveats, and results of the TMA analysis of post mortem diagenesis in bone are discussed, and implications for DNA survival and recovery considered.

  13. Effect of emotional arousal on inter-temporal decision-making: an fMRI study.

    Science.gov (United States)

    Sohn, Jin-Hun; Kim, Hyo-Eun; Sohn, Sunju; Seok, Ji-Woo; Choi, Damee; Watanuki, Shigeki

    2015-03-07

    Previous research has shown that emotion can significantly impact decision-making in humans. The current study examined whether or not and how situationally induced emotion influences people to make inter-temporal choices. Affective pictures were used as experiment stimuli to provoke emotion, immediately followed by subjects' performance of a delay-discounting task to measure impulsivity during functional magnetic resonance imaging. Results demonstrate a subsequent process of increased impulsive decision-making following a prior exposure to both high positive and negative arousal stimuli, compared to the experiment subjects' experiences with neutral stimuli. Findings indicate that increased impulsive decision-making behaviors can occur with high arousal and can be characterized by decreased activities in the cognitive control regions such as prefronto-parietal regions. These results suggest that 'stabilization of high emotional arousal' may facilitate a reduction of impulsive decision-making and implementation of longer term goals.

  14. A functional MRI study of language networks in left medial temporal lobe epilepsy

    International Nuclear Information System (INIS)

    Yu Aihong; Wang Xiaoyi; Xu Guoqing; Li Yongjie; Qin Wen; Li Kuncheng; Wang, Yuping

    2011-01-01

    Purpose: The purpose of this study was to investigate the abnormality of language networks in left medial temporal lobe epilepsy (MTLE) using fMRI. Materials and methods: Eight patients with left MTLE and 15 healthy subjects were evaluated. An auditory semantic judgment (AJ) paradigm was used. The fMRI data were collected on a 3T MR system and analyzed by AFNI (analysis of functional neuroimages) to generate the activation map. Results: Behavioral data showed that the reaction time of the left MTLE patients was significantly longer than that of controls on the AJ task (t = -3.396, P < 0.05). The left MTLE patients also exhibited diffusively decreased activation in the AJ task. Right hemisphere dominance of Broca's and Wernicke's areas was demonstrated in left MTLE patients. Conclusions: Long-term activation of spikes in left MTLE patients results in language impairment, which is associated with an abnormality of the brain neural network.

  15. Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

    Science.gov (United States)

    Guzzi, Pietro Hiram; Cannataro, Mario

    2013-08-01

    A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power

  16. Discovering biological progression underlying microarray samples.

    Directory of Open Access Journals (Sweden)

    Peng Qiu

    2011-04-01

    Full Text Available In biological systems that undergo processes such as differentiation, a clear concept of progression exists. We present a novel computational approach, called Sample Progression Discovery (SPD, to discover patterns of biological progression underlying microarray gene expression data. SPD assumes that individual samples of a microarray dataset are related by an unknown biological process (i.e., differentiation, development, cell cycle, disease progression, and that each sample represents one unknown point along the progression of that process. SPD aims to organize the samples in a manner that reveals the underlying progression and to simultaneously identify subsets of genes that are responsible for that progression. We demonstrate the performance of SPD on a variety of microarray datasets that were generated by sampling a biological process at different points along its progression, without providing SPD any information of the underlying process. When applied to a cell cycle time series microarray dataset, SPD was not provided any prior knowledge of samples' time order or of which genes are cell-cycle regulated, yet SPD recovered the correct time order and identified many genes that have been associated with the cell cycle. When applied to B-cell differentiation data, SPD recovered the correct order of stages of normal B-cell differentiation and the linkage between preB-ALL tumor cells with their cell origin preB. When applied to mouse embryonic stem cell differentiation data, SPD uncovered a landscape of ESC differentiation into various lineages and genes that represent both generic and lineage specific processes. When applied to a prostate cancer microarray dataset, SPD identified gene modules that reflect a progression consistent with disease stages. SPD may be best viewed as a novel tool for synthesizing biological hypotheses because it provides a likely biological progression underlying a microarray dataset and, perhaps more importantly, the

  17. A Comparative Study of Feature Selection Methods for the Discriminative Analysis of Temporal Lobe Epilepsy

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    Chunren Lai

    2017-12-01

    Full Text Available It is crucial to differentiate patients with temporal lobe epilepsy (TLE from the healthy population and determine abnormal brain regions in TLE. The cortical features and changes can reveal the unique anatomical patterns of brain regions from structural magnetic resonance (MR images. In this study, structural MR images from 41 patients with left TLE, 34 patients with right TLE, and 58 normal controls (NC were acquired, and four kinds of cortical measures, namely cortical thickness, cortical surface area, gray matter volume (GMV, and mean curvature, were explored for discriminative analysis. Three feature selection methods including the independent sample t-test filtering, the sparse-constrained dimensionality reduction model (SCDRM, and the support vector machine-recursive feature elimination (SVM-RFE were investigated to extract dominant features among the compared groups for classification using the support vector machine (SVM classifier. The results showed that the SVM-RFE achieved the highest performance (most classifications with more than 84% accuracy, followed by the SCDRM, and the t-test. Especially, the surface area and GMV exhibited prominent discriminative ability, and the performance of the SVM was improved significantly when the four cortical measures were combined. Additionally, the dominant regions with higher classification weights were mainly located in the temporal and the frontal lobe, including the entorhinal cortex, rostral middle frontal, parahippocampal cortex, superior frontal, insula, and cuneus. This study concluded that the cortical features provided effective information for the recognition of abnormal anatomical patterns and the proposed methods had the potential to improve the clinical diagnosis of TLE.

  18. Universal ligation-detection-reaction microarray applied for compost microbes

    Directory of Open Access Journals (Sweden)

    Romantschuk Martin

    2008-12-01

    Full Text Available Abstract Background Composting is one of the methods utilised in recycling organic communal waste. The composting process is dependent on aerobic microbial activity and proceeds through a succession of different phases each dominated by certain microorganisms. In this study, a ligation-detection-reaction (LDR based microarray method was adapted for species-level detection of compost microbes characteristic of each stage of the composting process. LDR utilises the specificity of the ligase enzyme to covalently join two adjacently hybridised probes. A zip-oligo is attached to the 3'-end of one probe and fluorescent label to the 5'-end of the other probe. Upon ligation, the probes are combined in the same molecule and can be detected in a specific location on a universal microarray with complementary zip-oligos enabling equivalent hybridisation conditions for all probes. The method was applied to samples from Nordic composting facilities after testing and optimisation with fungal pure cultures and environmental clones. Results Probes targeted for fungi were able to detect 0.1 fmol of target ribosomal PCR product in an artificial reaction mixture containing 100 ng competing fungal ribosomal internal transcribed spacer (ITS area or herring sperm DNA. The detection level was therefore approximately 0.04% of total DNA. Clone libraries were constructed from eight compost samples. The LDR microarray results were in concordance with the clone library sequencing results. In addition a control probe was used to monitor the per-spot hybridisation efficiency on the array. Conclusion This study demonstrates that the LDR microarray method is capable of sensitive and accurate species-level detection from a complex microbial community. The method can detect key species from compost samples, making it a basis for a tool for compost process monitoring in industrial facilities.

  19. A data-driven study of temporal adverbials as discourse segmentation markers

    Directory of Open Access Journals (Sweden)

    Marie-Paule Péry-Woodley

    2009-06-01

    Full Text Available De nombreuses études en linguistique et en psycholinguistique considèrent les adverbiaux temporels situés en position initiale de phrase comme de “bons” marqueurs de segmentation du discours. Cet article propose une analyse en corpus de leur capacité à signaler une discontinuité dans le discours (déplacement ou rupture. Nous portons ici une attention toute particulière aux configurations discursives dans lesquelles apparaissent les adverbiaux temporels à l'initiale en considérant deux autres traits : la position textuelle (relative à la structure du document et le type d'expressions sujet apparaissant dans la même phrase que l'adverbial. Notre méthodologie se base sur un corpus diversifié et étiqueté, représentant un volume de données relativement important pour le domaine. Le va-et-vient entre analyses quantitatives et qualitatives nous permet d'explorer comparativement selon différents types de textes les configurations discursives auxquelles participent les adverbiaux temporels à l'initiale. Au vu de nos résultats, il semble que les adverbiaux temporels signalent une discontinuité uniquement dans certaines configurations, ce qui signifie qu'ils ne constituent pas en eux-mêmes des marqueurs de segmentation.Many linguistic and psycholinguistic studies present sentence-initial temporal adverbials as “good” markers of discourse segmentation. This paper proposes a corpus-based evaluation of their potential to signal discontinuity such as a discourse break or shift. We look in particular at how temporal adverbials interact with other features, such as position in the text (in relation to document structure, and type of referring expression as grammatical subject in the host sentence. Our methodology calls upon a large diversified tagged corpus, and combines quantitative and qualitative approaches in order to systematically explore these configurations and their relation to text-type. Temporal adverbials are shown in

  20. The use of microarrays in microbial ecology

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer

  1. 3D Biomaterial Microarrays for Regenerative Medicine

    DEFF Research Database (Denmark)

    Gaharwar, Akhilesh K.; Arpanaei, Ayyoob; Andresen, Thomas Lars

    2015-01-01

    Three dimensional (3D) biomaterial microarrays hold enormous promise for regenerative medicine because of their ability to accelerate the design and fabrication of biomimetic materials. Such tissue-like biomaterials can provide an appropriate microenvironment for stimulating and controlling stem...... for tissue engineering and drug screening applications....... cell differentiation into tissue-specifi c lineages. The use of 3D biomaterial microarrays can, if optimized correctly, result in a more than 1000-fold reduction in biomaterials and cells consumption when engineering optimal materials combinations, which makes these miniaturized systems very attractive...

  2. Development and application of a microarray meter tool to optimize microarray experiments

    Directory of Open Access Journals (Sweden)

    Rouse Richard JD

    2008-07-01

    Full Text Available Abstract Background Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter' tool which assesses the inherent variations associated with microarray measurement prior to embarking on large scale projects. Findings The microarray meter consists of nucleic acid targets (reference and dynamic range control and probe components. Different plate designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization using three robots equipped with capillary printing pins. Discussion The generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variations associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a a measure of variability in the signal intensities, b a measure of the signal dynamic range and c a measure of variability of the spot morphologies.

  3. Quantitative magnetic resonance imaging study on patients with temporal lobe epilepsy

    International Nuclear Information System (INIS)

    Senzaki, Akira; Okubo, Yoshiro; Matsuura, Masato; Toru, Michio; Abe, Tetsuo; Asai, Kunihiko; Moriiwa, Motoi.

    1993-01-01

    In 30 patients with temporal lobe epilepsy who had no visual abnormality on either CT or MRI, cerebral changes especially in the mesial temporal region were examined. The findings were compared with those in 20 normal volunteers. In epileptic patients, the mesial temporal region was significantly smaller and T1-weighted values in this region were significantly higher, as compared with the controls. In the group of epilepsy, atrophy especially in the hippocampal and tonsillar regions and increased water content were suggested. Regarding the bilateral difference in the size of the mesial temporal region, there was no significant difference between the group of epilepsy and the control group. The group of epilepsy seemed to have bilateral changes in the mesial temporal region. In 9 patients with the present or past history of organic delusional (schizophrenia-like) disorder, the coronal section of the third ventricle was significantly large, suggesting the likelihood of structural changes surrounding the third ventricle. (N.K.)

  4. Anterior temporal face patches: A meta-analysis and empirical study

    Directory of Open Access Journals (Sweden)

    Rebecca J. Von Der Heide

    2013-02-01

    Full Text Available Studies of nonhuman primates have reported face sensitive patches in the ventral anterior temporal lobes (ATL. In humans, ATL resection or damage causes an associative prosopagnosia in which face perception is intact but face memory is compromised. Some fMRI studies have extended these findings using famous and familiar faces. However, it is unclear whether these regions in the human ATL are in locations comparable to those reported in non-human primates, typically using unfamiliar faces. We present the results of two studies of person memory: a meta-analysis of existing fMRI studies and an empirical fMRI study using optimized imaging parameters. Both studies showed left-lateralized ATL activations to familiar individuals while novel faces activated the right ATL. Activations to famous faces were quite ventral, similar to what has been reported in monkeys. These findings suggest that face memory-sensitive patches in the human ATL are in the ventral/polar ATL.

  5. Constructing Tissue Microarrays: Protocols and Methods Considering Potential Advantages and Disadvantages for Downstream Use.

    Science.gov (United States)

    Bingle, Lynne; Fonseca, Felipe P; Farthing, Paula M

    2017-01-01

    Tissue microarrays were first constructed in the 1980s but were used by only a limited number of researchers for a considerable period of time. In the last 10 years there has been a dramatic increase in the number of publications describing the successful use of tissue microarrays in studies aimed at discovering and validating biomarkers. This, along with the increased availability of both manual and automated microarray builders on the market, has encouraged even greater use of this novel and powerful tool. This chapter describes the basic techniques required to build a tissue microarray using a manual method in order that the theory behind the practical steps can be fully explained. Guidance is given to ensure potential disadvantages of the technique are fully considered.

  6. Construction of a cDNA microarray derived from the ascidian Ciona intestinalis.

    Science.gov (United States)

    Azumi, Kaoru; Takahashi, Hiroki; Miki, Yasufumi; Fujie, Manabu; Usami, Takeshi; Ishikawa, Hisayoshi; Kitayama, Atsusi; Satou, Yutaka; Ueno, Naoto; Satoh, Nori

    2003-10-01

    A cDNA microarray was constructed from a basal chordate, the ascidian Ciona intestinalis. The draft genome of Ciona has been read and inferred to contain approximately 16,000 protein-coding genes, and cDNAs for transcripts of 13,464 genes have been characterized and compiled as the "Ciona intestinalis Gene Collection Release I". In the present study, we constructed a cDNA microarray of these 13,464 Ciona genes. A preliminary experiment with Cy3- and Cy5-labeled probes showed extensive differential gene expression between fertilized eggs and larvae. In addition, there was a good correlation between results obtained by the present microarray analysis and those from previous EST analyses. This first microarray of a large collection of Ciona intestinalis cDNA clones should facilitate the analysis of global gene expression and gene networks during the embryogenesis of basal chordates.

  7. Improvement in the amine glass platform by bubbling method for a DNA microarray.

    Science.gov (United States)

    Jee, Seung Hyun; Kim, Jong Won; Lee, Ji Hyeong; Yoon, Young Soo

    2015-01-01

    A glass platform with high sensitivity for sexually transmitted diseases microarray is described here. An amino-silane-based self-assembled monolayer was coated on the surface of a glass platform using a novel bubbling method. The optimized surface of the glass platform had highly uniform surface modifications using this method, as well as improved hybridization properties with capture probes in the DNA microarray. On the basis of these results, the improved glass platform serves as a highly reliable and optimal material for the DNA microarray. Moreover, in this study, we demonstrated that our glass platform, manufactured by utilizing the bubbling method, had higher uniformity, shorter processing time, lower background signal, and higher spot signal than the platforms manufactured by the general dipping method. The DNA microarray manufactured with a glass platform prepared using bubbling method can be used as a clinical diagnostic tool.

  8. Temporal Trends in Enterobacter Species Bloodstream Infection: A Population-Based Study, 1998-2007

    Science.gov (United States)

    Al-Hasan, Majdi N.; Lahr, Brian D.; Eckel-Passow, Jeanette E.; Baddour, Larry M.

    2010-01-01

    Enterobacter species are the fourth most common cause of gram-negative bloodstream infection (BSI). We examined temporal changes and seasonal variation in the incidence rate of Enterobacter spp. BSI, estimated 28-day and 1-year mortality, and determined in vitro antimicrobial resistance rates of Enterobacter spp. bloodstream isolates in Olmsted County, Minnesota, from 1/1/1998 to 12/31/2007. Multivariable Poisson regression was used to examine temporal changes and seasonal variation in incidence rate and Kaplan-Meier method to estimate 28-day and 1-year mortality. The median age of patients with Enterobacter spp. BSI was 58 years and 53% were female. The overall age- and gender-adjusted incidence rate of Enterobacter spp. BSI was 3.3/100,000 person-years (95% confidence interval [CI]: 2.3-4.4). There was a linear trend of increasing incidence rate from 0.8 (95% CI: 0-1.9) to 6.2 (95% CI: 3.0-9.3) per 100,000 person-years between 1998 and 2007 (p=0.002). There was no significant difference in the incidence rate of Enterobacter spp. BSI during the warmest four months compared to the remainder of the year (incidence rate ratio 1.06 [95% CI: 0.47-2.01]). The overall 28-day and 1-year mortality rates of Enterobacter spp. BSI were 21% (95% CI: 8-34%) and 38% (95% CI: 22-53%), respectively. Up to 13% of Enterobacter spp. bloodstream isolates were resistant to third-generation cephalosporins. To our knowledge, this is the first population-based study to describe the epidemiology and outcome of Enterobacter spp. BSI. The increase in incidence rate of Enterobacter spp. BSI over the past decade, coupled with its associated antimicrobial resistance, dictate more investigation of this syndrome. PMID:20518795

  9. Temporal bone trauma: correlative study between CT findings and clinical manifestations

    International Nuclear Information System (INIS)

    Kim, Jung Hee; Kim, Hyung Jin; Kim, Jae Hyoung

    1994-01-01

    To assess how accurately computed tomography (CT) can demonstrate the abnormal findings which are believed to cause the clinical signs and symptoms of hearing loss (HL), vertigo and facial paralysis (FP) in patients with temporal bone trauma. The authors studied CT scans of 39 ears in 35 patients with temporal bone trauma. CT scans were performed with 1-1.5 mm slice thickness and table incrementation. Both axial and coronal scans were obtained in 32 patients and in three patients only axial scans were obtained. We analyzed CT with special reference to the structural abnormalities of the external auditory canal, middle ear cavity, bony labyrinth, and facial nerve canal, and correlated these findings with the actual clinical signs and symptoms. As to hearing loss, we evaluated 32 ears in which pure tone audiometry or brainstem evoked response audiometry had been performed. With respect to the specific types of HL, CT accurately showed the abnormalities in 84% (16/19) in conductive HL, 100% (2/2) in sensorineural HL, and 25% (2/8) for mixed HL. When we categorized HL simply as conductive and sensorineural, assuming that mixed be the result of combined conductive and sensorineural HL, CT demonstrated the abnormalities in 89% (24/27) for conductive HL and 50% (5/10) for sensorineural HL. Concerning vertigo and FP, CT demonstrated abnormalities in 67%(4/6), and 29% (4/14), respectively. Except for conductive HL, CT seems to have a variable degree of limitation for the demonstration of the structural abnormalities resulting sensorineural HL, vertigo or facial paralysis. It is imperative to correlate the CT findings with the signs and symptoms in those clinical settings

  10. Temporal bone trauma: correlative study between CT findings and clinical manifestations

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jung Hee; Kim, Hyung Jin; Kim, Jae Hyoung [College of Medicine, Gyeongsang National University, Jinju (Korea, Republic of)

    1994-11-15

    To assess how accurately computed tomography (CT) can demonstrate the abnormal findings which are believed to cause the clinical signs and symptoms of hearing loss (HL), vertigo and facial paralysis (FP) in patients with temporal bone trauma. The authors studied CT scans of 39 ears in 35 patients with temporal bone trauma. CT scans were performed with 1-1.5 mm slice thickness and table incrementation. Both axial and coronal scans were obtained in 32 patients and in three patients only axial scans were obtained. We analyzed CT with special reference to the structural abnormalities of the external auditory canal, middle ear cavity, bony labyrinth, and facial nerve canal, and correlated these findings with the actual clinical signs and symptoms. As to hearing loss, we evaluated 32 ears in which pure tone audiometry or brainstem evoked response audiometry had been performed. With respect to the specific types of HL, CT accurately showed the abnormalities in 84% (16/19) in conductive HL, 100% (2/2) in sensorineural HL, and 25% (2/8) for mixed HL. When we categorized HL simply as conductive and sensorineural, assuming that mixed be the result of combined conductive and sensorineural HL, CT demonstrated the abnormalities in 89% (24/27) for conductive HL and 50% (5/10) for sensorineural HL. Concerning vertigo and FP, CT demonstrated abnormalities in 67%(4/6), and 29% (4/14), respectively. Except for conductive HL, CT seems to have a variable degree of limitation for the demonstration of the structural abnormalities resulting sensorineural HL, vertigo or facial paralysis. It is imperative to correlate the CT findings with the signs and symptoms in those clinical settings.

  11. Morphometrical Study of the Temporal Bone and Auditory Ossicles in Guinea Pig

    Directory of Open Access Journals (Sweden)

    Ahmadali Mohammadpour

    2011-03-01

    Full Text Available In this research, anatomical descriptions of the structure of the temporal bone and auditory ossicles have been performed based on dissection of ten guinea pigs. The results showed that, in guinea pig temporal bone was similar to other animals and had three parts; squamous, tympanic and petrous .The tympanic part was much better developed and consisted of oval shaped tympanic bulla with many recesses in tympanic cavity. The auditory ossicles of guinea pig concluded of three small bones; malleus, incus and stapes but the head of the malleus and the body of incus were fused and forming a malleoincudal complex. The average of morphometric parameters showed that the malleus was 3.53 ± 0.22 mm in total length. In addition to head and handle, the malleus had two distinct process; lateral and muscular. The incus had a total length 1.23 ± 0.02mm. It had long and short crus although the long crus was developed better than short crus. The lenticular bone was a round bone that articulated with the long crus of incus. The stapes had a total length 1.38 ± 0.04mm. The anterior crus(0.86 ± 0.08mm was larger than posterior crus (0.76 ± 0.08mm. It is concluded that, in the guinea pig, the malleus and the incus are fused, forming a junction called incus-malleus, while in the other animals these are separate bones. The stapes is larger and has a triangular shape and the anterior and posterior crus are thicker than other rodents. Therefore, for otological studies, the guinea pig is a good lab animal.

  12. Revascularization of the upper posterior circulation with the anterior temporal artery: an anatomical feasibility study.

    Science.gov (United States)

    Tayebi Meybodi, Ali; Lawton, Michael T; Griswold, Dylan; Mokhtari, Pooneh; Payman, Andre; Tabani, Halima; Yousef, Sonia; Benet, Arnau

    2017-09-22

    OBJECTIVE In various disease processes, including unclippable aneurysms, a bypass to the upper posterior circulation (UPC) including the superior cerebellar artery (SCA) and posterior cerebral artery (PCA) may be needed. Various revascularization options exist, but the role of intracranial (IC) donors has not been scrutinized. The objective of this study was to evaluate the anatomical feasibility of utilizing the anterior temporal artery (ATA) for revascularization of the UPC. METHODS ATA-SCA and ATA-PCA bypasses were performed on 14 cadaver specimens. After performing an orbitozygomatic craniotomy and opening the basal cisterns, the ATA was divided at the M 3 -M 4 junction and mobilized to the crural cistern to complete an end-to-side bypass to the SCA and PCA. The length of the recipient artery between the anastomosis and origin was measured. RESULTS Seventeen ATAs were found. Successful anastomosis was performed in 14 (82%) of the ATAs. The anastomosis point on the PCA was 14.2 mm from its origin on the basilar artery. The SCA anastomosis point was 10.1 mm from its origin. Three ATAs did not reach the UPC region due to a common opercular origin with the middle temporal artery. The ATA-SCA bypass was also applied to the management of an incompletely coiled SCA aneurysm. CONCLUSIONS The ATA is a promising IC donor for UPC revascularization. The ATA is exposed en route to the proximal SCA and PCA through the pterional-orbitozygomatic approach. Also, the end-to-side anastomosis provides an efficient and straightforward bypass without the need to harvest a graft or perform multiple or difficult anastomoses.

  13. The course of language functions after temporal lobe epilepsy surgery: a prospective study.

    Science.gov (United States)

    Giovagnoli, A R; Parente, A; Didato, G; Manfredi, V; Deleo, F; Tringali, G; Villani, F

    2016-12-01

    Anterior temporal lobectomy (ATL) within the language-dominant hemisphere can impair naming. This prospective study examined the pre-operative to post-operative course of different language components, clarifying which changes are relevant within the short-term and long-term outcome of language. Patients with drug-resistant temporal lobe epilepsy (TLE) were evaluated using the Token, Boston Naming and Word Fluency tests assessing sentence comprehension and word-finding on visual, semantic or phonemic cues. A total of 106 patients were evaluated before and 6 months, 1 and 2 years after ATL; 60 patients were also evaluated after 5 years and 38 controls were assessed at baseline. Seizure outcome was comparable between the left and right TLE patients. Before surgery, naming and word fluency were impaired in the left and right TLE patients, whereas sentence comprehension was normal. After left or right ATL, word fluency progressively improved, naming showed early worsening and late improvement after left ATL and progressive improvement after right ATL, and sentence comprehension did not change. At the 5-year follow-up, naming improvement was clinically significant in 31% and 71% of the left and right TLE patients, respectively. Pre-operative naming, ATL laterality, schooling, and post-operative seizure frequency and number of antiepileptic drugs predicted post-operative naming. Pre-operative word fluency and schooling predicted post-operative word fluency. Left or right TLE can impair word-finding but not sentence comprehension. After ATL, word-finding may improve for a long time, depending on TLE laterality, seizure control and mental reserve. These findings may clarify prognosis prior to treatment. © 2016 EAN.

  14. Fuzzy support vector machine for microarray imbalanced data classification

    Science.gov (United States)

    Ladayya, Faroh; Purnami, Santi Wulan; Irhamah

    2017-11-01

    DNA microarrays are data containing gene expression with small sample sizes and high number of features. Furthermore, imbalanced classes is a common problem in microarray data. This occurs when a dataset is dominated by a class which have significantly more instances than the other minority classes. Therefore, it is needed a classification method that solve the problem of high dimensional and imbalanced data. Support Vector Machine (SVM) is one of the classification methods that is capable of handling large or small samples, nonlinear, high dimensional, over learning and local minimum issues. SVM has been widely applied to DNA microarray data classification and it has been shown that SVM provides the best performance among other machine learning methods. However, imbalanced data will be a problem because SVM treats all samples in the same importance thus the results is bias for minority class. To overcome the imbalanced data, Fuzzy SVM (FSVM) is proposed. This method apply a fuzzy membership to each input point and reformulate the SVM such that different input points provide different contributions to the classifier. The minority classes have large fuzzy membership so FSVM can pay more attention to the samples with larger fuzzy membership. Given DNA microarray data is a high dimensional data with a very large number of features, it is necessary to do feature selection first using Fast Correlation based Filter (FCBF). In this study will be analyzed by SVM, FSVM and both methods by applying FCBF and get the classification performance of them. Based on the overall results, FSVM on selected features has the best classification performance compared to SVM.

  15. Dynamic, electronically switchable surfaces for membrane protein microarrays.

    Science.gov (United States)

    Tang, C S; Dusseiller, M; Makohliso, S; Heuschkel, M; Sharma, S; Keller, B; Vörös, J

    2006-02-01

    Microarray technology is a powerful tool that provides a high throughput of bioanalytical information within a single experiment. These miniaturized and parallelized binding assays are highly sensitive and have found widespread popularity especially during the genomic era. However, as drug diagnostics studies are often targeted at membrane proteins, the current arraying technologies are ill-equipped to handle the fragile nature of the protein molecules. In addition, to understand the complex structure and functions of proteins, different strategies to immobilize the probe molecules selectively onto a platform for protein microarray are required. We propose a novel approach to create a (membrane) protein microarray by using an indium tin oxide (ITO) microelectrode array with an electronic multiplexing capability. A polycationic, protein- and vesicle-resistant copolymer, poly(l-lysine)-grafted-poly(ethylene glycol) (PLL-g-PEG), is exposed to and adsorbed uniformly onto the microelectrode array, as a passivating adlayer. An electronic stimulation is then applied onto the individual ITO microelectrodes resulting in the localized release of the polymer thus revealing a bare ITO surface. Different polymer and biological moieties are specifically immobilized onto the activated ITO microelectrodes while the other regions remain protein-resistant as they are unaffected by the induced electrical potential. The desorption process of the PLL-g-PEG is observed to be highly selective, rapid, and reversible without compromising on the integrity and performance of the conductive ITO microelectrodes. As such, we have successfully created a stable and heterogeneous microarray of biomolecules by using selective electronic addressing on ITO microelectrodes. Both pharmaceutical diagnostics and biomedical technology are expected to benefit directly from this unique method.

  16. DNA microarray technique for detecting food-borne pathogens

    Directory of Open Access Journals (Sweden)

    Xing GAO

    2012-08-01

    Full Text Available Objective To study the application of DNA microarray technique for screening and identifying multiple food-borne pathogens. Methods The oligonucleotide probes were designed by Clustal X and Oligo 6.0 at the conserved regions of specific genes of multiple food-borne pathogens, and then were validated by bioinformatic analyses. The 5' end of each probe was modified by amino-group and 10 Poly-T, and the optimized probes were synthesized and spotted on aldehyde-coated slides. The bacteria DNA template incubated with Klenow enzyme was amplified by arbitrarily primed PCR, and PCR products incorporated into Aminoallyl-dUTP were coupled with fluorescent dye. After hybridization of the purified PCR products with DNA microarray, the hybridization image and fluorescence intensity analysis was acquired by ScanArray and GenePix Pro 5.1 software. A series of detection conditions such as arbitrarily primed PCR and microarray hybridization were optimized. The specificity of this approach was evaluated by 16 different bacteria DNA, and the sensitivity and reproducibility were verified by 4 food-borne pathogens DNA. The samples of multiple bacteria DNA and simulated water samples of Shigella dysenteriae were detected. Results Nine different food-borne bacteria were successfully discriminated under the same condition. The sensitivity of genomic DNA was 102 -103pg/ μl, and the coefficient of variation (CV of the reproducibility of assay was less than 15%. The corresponding specific hybridization maps of the multiple bacteria DNA samples were obtained, and the detection limit of simulated water sample of Shigella dysenteriae was 3.54×105cfu/ml. Conclusions The DNA microarray detection system based on arbitrarily primed PCR can be employed for effective detection of multiple food-borne pathogens, and this assay may offer a new method for high-throughput platform for detecting bacteria.

  17. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L. gene expression oligonucleotide microarray.

    Directory of Open Access Journals (Sweden)

    Paula Fernandez

    Full Text Available Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de. The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons. The resulting Sunflower Unigen Resource (SUR version 1.0 was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01 allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  18. DNA Microarray Technologies: A Novel Approach to Geonomic Research

    Energy Technology Data Exchange (ETDEWEB)

    Hinman, R.; Thrall, B.; Wong, K,

    2002-01-01

    A cDNA microarray allows biologists to examine the expression of thousands of genes simultaneously. Researchers may analyze the complete transcriptional program of an organism in response to specific physiological or developmental conditions. By design, a cDNA microarray is an experiment with many variables and few controls. One question that inevitably arises when working with a cDNA microarray is data reproducibility. How easy is it to confirm mRNA expression patterns? In this paper, a case study involving the treatment of a murine macrophage RAW 264.7 cell line with tumor necrosis factor alpha (TNF) was used to obtain a rough estimate of data reproducibility. Two trials were examined and a list of genes displaying either a > 2-fold or > 4-fold increase in gene expression was compiled. Variations in signal mean ratios between the two slides were observed. We can assume that erring in reproducibility may be compensated by greater inductive levels of similar genes. Steps taken to obtain results included serum starvation of cells before treatment, tests of mRNA for quality/consistency, and data normalization.

  19. Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.

    Science.gov (United States)

    Dai, Yilin; Guo, Ling; Li, Meng; Chen, Yi-Bu

    2012-06-08

    Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results. We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs. Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.

  20. Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

    Science.gov (United States)

    Zhang, Wenqian; Yu, Ying; Hertwig, Falk; Thierry-Mieg, Jean; Zhang, Wenwei; Thierry-Mieg, Danielle; Wang, Jian; Furlanello, Cesare; Devanarayan, Viswanath; Cheng, Jie; Deng, Youping; Hero, Barbara; Hong, Huixiao; Jia, Meiwen; Li, Li; Lin, Simon M; Nikolsky, Yuri; Oberthuer, André; Qing, Tao; Su, Zhenqiang; Volland, Ruth; Wang, Charles; Wang, May D; Ai, Junmei; Albanese, Davide; Asgharzadeh, Shahab; Avigad, Smadar; Bao, Wenjun; Bessarabova, Marina; Brilliant, Murray H; Brors, Benedikt; Chierici, Marco; Chu, Tzu-Ming; Zhang, Jibin; Grundy, Richard G; He, Min Max; Hebbring, Scott; Kaufman, Howard L; Lababidi, Samir; Lancashire, Lee J; Li, Yan; Lu, Xin X; Luo, Heng; Ma, Xiwen; Ning, Baitang; Noguera, Rosa; Peifer, Martin; Phan, John H; Roels, Frederik; Rosswog, Carolina; Shao, Susan; Shen, Jie; Theissen, Jessica; Tonini, Gian Paolo; Vandesompele, Jo; Wu, Po-Yen; Xiao, Wenzhong; Xu, Joshua; Xu, Weihong; Xuan, Jiekun; Yang, Yong; Ye, Zhan; Dong, Zirui; Zhang, Ke K; Yin, Ye; Zhao, Chen; Zheng, Yuanting; Wolfinger, Russell D; Shi, Tieliu; Malkas, Linda H; Berthold, Frank; Wang, Jun; Tong, Weida; Shi, Leming; Peng, Zhiyu; Fischer, Matthias

    2015-06-25

    Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. We also find that RNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. To systematically compare the power of RNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (RNA-seq vs. microarrays), RNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models. We demonstrate that RNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while RNA-seq and microarray-based models perform similarly in clinical endpoint prediction. Our findings may be valuable to guide future studies on the development of gene expression-based predictive models and their implementation in clinical practice.

  1. A follow-up MRI study of the fusiform gyrus and middle and inferior temporal gyri in schizophrenia spectrum.

    Science.gov (United States)

    Takahashi, Tsutomu; Zhou, Shi-Yu; Nakamura, Kazue; Tanino, Ryoichiro; Furuichi, Atsushi; Kido, Mikio; Kawasaki, Yasuhiro; Noguchi, Kyo; Seto, Hikaru; Kurachi, Masayoshi; Suzuki, Michio

    2011-12-01

    While longitudinal magnetic resonance imaging (MRI) studies have demonstrated progressive gray matter reduction of the superior temporal gyrus (STG) during the early phases of schizophrenia, it remains largely unknown whether other temporal lobe structures also exhibit similar progressive changes and whether these changes, if present, are specific to schizophrenia among the spectrum disorders. In this longitudinal MRI study, the gray matter volumes of the fusiform, middle temporal, and inferior temporal gyri were measured at baseline and follow-up scans (mean inter-scan interval=2.7 years) in 18 patients with first-episode schizophrenia, 13 patients with schizotypal disorder, and 20 healthy controls. Both schizophrenia and schizotypal patients had a smaller fusiform gyrus than controls bilaterally at both time points, whereas no group difference was found in the middle and inferior temporal gyri. In the longitudinal comparison, the schizophrenia patients showed significant fusiform gyrus reduction (left, -2.6%/year; right, -2.3%/year) compared with schizotypal patients (left: -0.4%/year; right: -0.2%/year) and controls (left: 0.1%/year; right: 0.0%/year). However, the middle and inferior temporal gyri did not exhibit significant progressive gray matter change in all diagnostic groups. In the schizophrenia patients, a higher cumulative dose of antipsychotics during follow-up was significantly correlated with less severe gray matter reduction in the left fusiform gyrus. The annual gray matter loss of the fusiform gyrus did not correlate with that of the STG previously reported in the same subjects. Our findings suggest regional specificity of the progressive gray matter reduction in the temporal lobe structures, which might be specific to overt schizophrenia within the schizophrenia spectrum. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Insomnia and Its Temporal Association with Academic Performance among University Students: A Cross-Sectional Study

    Directory of Open Access Journals (Sweden)

    Yohannes Gebreegziabhere Haile

    2017-01-01

    Full Text Available Introduction. Studies show that 9.4% to 38.2% of university students are suffering from insomnia. However, research data in developing countries is limited. Thus, the aim of the study was to assess insomnia and its temporal association with academic performance. Methods and Materials. Institution based cross-sectional study was conducted with 388 students at Debre Berhan University. Data were collected at the nine colleges. Logistic and linear regression analysis was performed for modeling insomnia and academic performance with a p value threshold of 0.05, respectively. Data were entered using EPI-data version 3.1 and analyzed using SPSS version 20. Results. The prevalence of insomnia was 61.6%. Field of study (p value = 0.01, worshiping frequency (p value = 0.048, marital status (p value = 0.03, and common mental disorder (p value < 0.001 were identified associated factors of insomnia. There was no significant association between insomnia and academic performance (p value = 0.53, β = −0.04. Insomnia explained 1.2% (r2 = 0.012 of the difference in academic performance between students. Conclusions. Nearly 3 out of 5 students had insomnia. We recommended that universities would endorse sleep quality and mental health illness screening programs for students.

  3. Insomnia and Its Temporal Association with Academic Performance among University Students: A Cross-Sectional Study.

    Science.gov (United States)

    Haile, Yohannes Gebreegziabhere; Alemu, Sisay Mulugeta; Habtewold, Tesfa Dejenie

    2017-01-01

    Studies show that 9.4% to 38.2% of university students are suffering from insomnia. However, research data in developing countries is limited. Thus, the aim of the study was to assess insomnia and its temporal association with academic performance. Institution based cross-sectional study was conducted with 388 students at Debre Berhan University. Data were collected at the nine colleges. Logistic and linear regression analysis was performed for modeling insomnia and academic performance with a p value threshold of 0.05, respectively. Data were entered using EPI-data version 3.1 and analyzed using SPSS version 20. The prevalence of insomnia was 61.6%. Field of study ( p value = 0.01), worshiping frequency ( p value = 0.048), marital status ( p value = 0.03), and common mental disorder ( p value academic performance ( p value = 0.53, β = -0.04). Insomnia explained 1.2% ( r 2 = 0.012) of the difference in academic performance between students. Nearly 3 out of 5 students had insomnia. We recommended that universities would endorse sleep quality and mental health illness screening programs for students.

  4. Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays

    Directory of Open Access Journals (Sweden)

    Wu Xiaogang

    2012-06-01

    Full Text Available In many cases, crucial genes show relatively slight changes between groups of samples (e.g. normal vs. disease, and many genes selected from microarray differential analysis by measuring the expression level statistically are also poorly annotated and lack of biological significance. In this paper, we present an innovative approach - network expansion and pathway enrichment analysis (NEPEA for integrative microarray analysis. We assume that organized knowledge will help microarray data analysis in significant ways, and the organized knowledge could be represented as molecular interaction networks or biological pathways. Based on this hypothesis, we develop the NEPEA framework based on network expansion from the human annotated and predicted protein interaction (HAPPI database, and pathway enrichment from the human pathway database (HPD. We use a recently-published microarray dataset (GSE24215 related to insulin resistance and type 2 diabetes (T2D as case study, since this study provided a thorough experimental validation for both genes and pathways identified computationally from classical microarray analysis and pathway analysis. We perform our NEPEA analysis for this dataset based on the results from the classical microarray analysis to identify biologically significant genes and pathways. Our findings are not only consistent with the original findings mostly, but also obtained more supports from other literatures.

  5. Principles of gene microarray data analysis.

    Science.gov (United States)

    Mocellin, Simone; Rossi, Carlo Riccardo

    2007-01-01

    The development of several gene expression profiling methods, such as comparative genomic hybridization (CGH), differential display, serial analysis of gene expression (SAGE), and gene microarray, together with the sequencing of the human genome, has provided an opportunity to monitor and investigate the complex cascade of molecular events leading to tumor development and progression. The availability of such large amounts of information has shifted the attention of scientists towards a nonreductionist approach to biological phenomena. High throughput technologies can be used to follow changing patterns of gene expression over time. Among them, gene microarray has become prominent because it is easier to use, does not require large-scale DNA sequencing, and allows for the parallel quantification of thousands of genes from multiple samples. Gene microarray technology is rapidly spreading worldwide and has the potential to drastically change the therapeutic approach to patients affected with tumor. Therefore, it is of paramount importance for both researchers and clinicians to know the principles underlying the analysis of the huge amount of data generated with microarray technology.

  6. Detection of selected plant viruses by microarrays

    OpenAIRE

    HRABÁKOVÁ, Lenka

    2013-01-01

    The main aim of this master thesis was the simultaneous detection of four selected plant viruses ? Apple mosaic virus, Plum pox virus, Prunus necrotic ringspot virus and Prune harf virus, by microarrays. The intermediate step in the process of the detection was optimizing of multiplex polymerase chain reaction (PCR).

  7. LNA-modified isothermal oligonucleotide microarray for ...

    Indian Academy of Sciences (India)

    2014-10-20

    Oct 20, 2014 ... the advent of DNA microarray techniques (Lee et al. 2007). ... atoms of ribose to form a bicyclic ribosyl structure. It is the .... 532 nm and emission at 570 nm. The signal ..... sis and validation using real-time PCR. Nucleic Acids ...

  8. Gene Expression Analysis Using Agilent DNA Microarrays

    DEFF Research Database (Denmark)

    Stangegaard, Michael

    2009-01-01

    Hybridization of labeled cDNA to microarrays is an intuitively simple and a vastly underestimated process. If it is not performed, optimized, and standardized with the same attention to detail as e.g., RNA amplification, information may be overlooked or even lost. Careful balancing of the amount ...

  9. Microarrays (DNA Chips) for the Classroom Laboratory

    Science.gov (United States)

    Barnard, Betsy; Sussman, Michael; BonDurant, Sandra Splinter; Nienhuis, James; Krysan, Patrick

    2006-01-01

    We have developed and optimized the necessary laboratory materials to make DNA microarray technology accessible to all high school students at a fraction of both cost and data size. The primary component is a DNA chip/array that students "print" by hand and then analyze using research tools that have been adapted for classroom use. The…

  10. Fusion of multi-temporal Airborne Snow Observatory (ASO) lidar data for mountainous vegetation ecosystems studies.

    Science.gov (United States)

    Ferraz, A.; Painter, T. H.; Saatchi, S.; Bormann, K. J.

    2016-12-01

    Fusion of multi-temporal Airborne Snow Observatory (ASO) lidar data for mountainous vegetation ecosystems studies The NASA Jet Propulsion Laboratory developed the Airborne Snow Observatory (ASO), a coupled scanning lidar system and imaging spectrometer, to quantify the spatial distribution of snow volume and dynamics over mountains watersheds (Painter et al., 2015). To do this, ASO weekly over-flights mountainous areas during snowfall and snowmelt seasons. In addition, there are additional flights in snow-off conditions to calculate Digital Terrain Models (DTM). In this study, we focus on the reliability of ASO lidar data to characterize the 3D forest vegetation structure. The density of a single point cloud acquisition is of nearly 1 pt/m2, which is not optimal to properly characterize vegetation. However, ASO covers a given study site up to 14 times a year that enables computing a high-resolution point cloud by merging single acquisitions. In this study, we present a method to automatically register ASO multi-temporal lidar 3D point clouds. Although flight specifications do not change between acquisition dates, lidar datasets might have significant planimetric shifts due to inaccuracies in platform trajectory estimation introduced by the GPS system and drifts of the IMU. There are a large number of methodologies that address the problem of 3D data registration (Gressin et al., 2013). Briefly, they look for common primitive features in both datasets such as buildings corners, structures like electric poles, DTM breaklines or deformations. However, they are not suited for our experiment. First, single acquisition point clouds have low density that makes the extraction of primitive features difficult. Second, the landscape significantly changes between flights due to snowfall and snowmelt. Therefore, we developed a method to automatically register point clouds using tree apexes as keypoints because they are features that are supposed to experience little change

  11. The efficacy of microarray screening for autosomal recessive retinitis pigmentosa in routine clinical practice

    Science.gov (United States)

    van Huet, Ramon A. C.; Pierrache, Laurence H.M.; Meester-Smoor, Magda A.; Klaver, Caroline C.W.; van den Born, L. Ingeborgh; Hoyng, Carel B.; de Wijs, Ilse J.; Collin, Rob W. J.; Hoefsloot, Lies H.

    2015-01-01

    Purpose To determine the efficacy of multiple versions of a commercially available arrayed primer extension (APEX) microarray chip for autosomal recessive retinitis pigmentosa (arRP). Methods We included 250 probands suspected of arRP who were genetically analyzed with the APEX microarray between January 2008 and November 2013. The mode of inheritance had to be autosomal recessive according to the pedigree (including isolated cases). If the microarray identified a heterozygous mutation, we performed Sanger sequencing of exons and exon–intron boundaries of that specific gene. The efficacy of this microarray chip with the additional Sanger sequencing approach was determined by the percentage of patients that received a molecular diagnosis. We also collected data from genetic tests other than the APEX analysis for arRP to provide a detailed description of the molecular diagnoses in our study cohort. Results The APEX microarray chip for arRP identified the molecular diagnosis in 21 (8.5%) of the patients in our cohort. Additional Sanger sequencing yielded a second mutation in 17 patients (6.8%), thereby establishing the molecular diagnosis. In total, 38 patients (15.2%) received a molecular diagnosis after analysis using the microarray and additional Sanger sequencing approach. Further genetic analyses after a negative result of the arRP microarray (n = 107) resulted in a molecular diagnosis of arRP (n = 23), autosomal dominant RP (n = 5), X-linked RP (n = 2), and choroideremia (n = 1). Conclusions The efficacy of the commercially available APEX microarray chips for arRP appears to be low, most likely caused by the limitations of this technique and the genetic and allelic heterogeneity of RP. Diagnostic yields up to 40% have been reported for next-generation sequencing (NGS) techniques that, as expected, thereby outperform targeted APEX analysis. PMID:25999674

  12. Functional neuroimaging studies of episodic memory. Functional dissociation in the medial temporal lobe structures

    International Nuclear Information System (INIS)

    Tsukiura, Takashi

    2008-01-01

    Previous functional neuroimaging studies have demonstrated the critical role of the medial temporal lobe (MTL) regions in the encoding and retrieval of episodic memory. It has also been shown that an emotional factor in human memory enhances episodic encoding and retrieval. However, there is little evidence regarding the specific contribution of each MTL region to the relational, contextual, and emotional processes of episodic memory. The goal of this review article is to identify differential activation patterns of the processes between MTL regions. Results from functional neuroimaging studies of episodic memory show that the hippocampus is involved in encoding the relation between memory items, whereas the entorhinal and perirhinal cortices (anterior parahippocampal gyrus) contribute to the encoding of a single item. Additionally, the parahippocampal cortex (posterior parahippocampal gyrus) is selectively activated during the processing of contextual information of episodic memory. A similar pattern of functional dissociation is found in episodic memory retrieval. Functional neuroimaging has also shown that emotional information of episodic memory enhances amygdala-MTL correlations and that this enhancement is observed during both the encoding and retrieval of emotional memories. These findings from pervious neuroimaging studies suggest that different MTL regions could organize memory for personally experienced episodes via the 'relation' and 'context' factors of episodic memory, and that the emotional factor of episodes could modulate the functional organization in the MTL regions. (author)

  13. Comparative study of cocoa black ants temporal population distribution utilizing geospatial analysis

    Science.gov (United States)

    Adnan, N. A.; Bakar, S.; Mazlan, A. H.; Yusoff, Z. Mohd; Rasam, A. R. Abdul

    2018-02-01

    Cocoa plantation also subjected to diseases and pests infestation. Some pests not only reduced the yield but also inhibit the growth of trees. Therefore, the Malaysia Cocoa Board (MCB) has explored Cocoa Black Ants (CBA) as one of their biological control mechanism to reduce the pest infestation of the Cocoa Pod Borer (CPB). CPB is capable to cause damage to cocoa beans, and later on will reduce the quality of dried cocoa beans. This study tries to integrate the use of geospatial analysis in understanding population distribution pattern of CBA to enhance its capability in controlling CPB infestation. Two objectives of the study are i) to generate temporal CBA distribution of cocoa plantation for two different blocks, and ii) to compare visually the CBA population distribution pattern with the aid of geospatial technique. This study managed to find the CBA population pattern which indicated spatially modest amount of low pattern distribution in February of 2007 until reaching the highest levels of ant populations in September 2007 and decreasing by the end of the year in 2009 for two different blocks (i.e 10B and 18A). Therefore, the usage of GIS is important to explain the CBA pattern population in the mature cocoa field. This finding might to be used as an indicator to examine the optimum distribution of CBA, which needed as a biological control agent against the CPB in the future.

  14. Prominent increased calcineurin immunoreactivity in the superior temporal gyrus in schizophrenia: A postmortem study.

    Science.gov (United States)

    Wada, Akira; Kunii, Yasuto; Matsumoto, Jyunya; Hino, Mizuki; Yang, Qiaohui; Niwa, Shin-Ichi; Yabe, Hirooki

    2017-01-01

    Many neuroimaging studies have demonstrated structural changes in the superior temporal gyrus (STG) in patients with schizophrenia. Several postmortem studies have reported on the pathogenesis of schizophrenia, but few reports have investigated alterations in molecules in the STG. In addition, several studies have suggested that calcineurin (CaN) inadequacy may be a risk factor for schizophrenia, but no reports about CaN expression in the STG in schizophrenia have been published. We compared the density of CaN-immunoreactive (CaN-IR) neurons in the STG from 11 patients with schizophrenia with that of 11 sex- and age-matched controls. We used immunohistochemical analysis with rabbit polyclonal antibodies against human CaN. In the STG, the density of CaN-IR neurons in layers II - VI in the group with schizophrenia was significantly higher than that in the control group. Our results confirmed pathological changes in the STG in patients with schizophrenia, suggesting that alterations in the CaN pathway play a role in the pathogenesis of schizophrenia. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  15. Regional and temporal differences in gene expression of LH(BETA)T(AG) retinoblastoma tumors.

    Science.gov (United States)

    Houston, Samuel K; Pina, Yolanda; Clarke, Jennifer; Koru-Sengul, Tulay; Scott, William K; Nathanson, Lubov; Schefler, Amy C; Murray, Timothy G

    2011-07-23

    The purpose of this study was to evaluate by microarray the hypothesis that LH(BETA)T(AG) retinoblastoma tumors exhibit regional and temporal variations in gene expression. LH(BETA)T(AG) mice aged 12, 16, and 20 weeks were euthanatized (n = 9). Specimens were taken from five tumor areas (apex, anterior lateral, center, base, and posterior lateral). Samples were hybridized to gene microarrays. The data were preprocessed and analyzed, and genes with a P 2.5 were considered to be differentially expressed. Differentially expressed genes were analyzed for overlap with known networks by using pathway analysis tools. There were significant temporal (P regional differences in gene expression for LH(BETA)T(AG) retinoblastoma tumors. At P 2.5, there were significant changes in gene expression of 190 genes apically, 84 genes anterolaterally, 126 genes posteriorly, 56 genes centrally, and 134 genes at the base. Differentially expressed genes overlapped with known networks, with significant involvement in regulation of cellular proliferation and growth, response to oxygen levels and hypoxia, regulation of cellular processes, cellular signaling cascades, and angiogenesis. There are significant temporal and regional variations in the LH(BETA)T(AG) retinoblastoma model. Differentially expressed genes overlap with key pathways that may play pivotal roles in murine retinoblastoma development. These findings suggest the mechanisms involved in tumor growth and progression in murine retinoblastoma tumors and identify pathways for analysis at a functional level, to determine significance in human retinoblastoma. Microarray analysis of LH(BETA)T(AG) retinal tumors showed significant regional and temporal variations in gene expression, including dysregulation of genes involved in hypoxic responses and angiogenesis.

  16. Locating the scala media in the fixed human temporal bone for therapeutic access: a preliminary study.

    Science.gov (United States)

    Pau, H; Fagan, P; Oleskevich, S

    2006-11-01

    To investigate the location of the scala media in relation to the round window niche in human temporal bones. Ten human temporal bones were investigated by radical mastoidectomy and promontory drill-out. Temporal bone laboratory. The distance from the scala media to the anterior edge of the round window niche, measured by Fisch's stapedectomy measuring cylinders. The scala media was identified at the transection point of a vertical line 1.6 to 2.2 mm (mean=1.8 mm; standard deviation=0.2) anterior to the anterior edge of the round window niche and a horizontal line 0.2 mm inferior to the lower border of the oval window. This report demonstrates the point of entry into the scala media via the promontory in fixed temporal bone models, which may provide a site of entry for stem cells and gene therapy insertion.

  17. Iconic memory and parietofrontal network: fMRI study using temporal integration.

    Science.gov (United States)

    Saneyoshi, Ayako; Niimi, Ryosuke; Suetsugu, Tomoko; Kaminaga, Tatsuro; Yokosawa, Kazuhiko

    2011-08-03

    We investigated the neural basis of iconic memory using functional magnetic resonance imaging. The parietofrontal network of selective attention is reportedly relevant to readout from iconic memory. We adopted a temporal integration task that requires iconic memory but not selective attention. The results showed that the task activated the parietofrontal network, confirming that the network is involved in readout from iconic memory. We further tested a condition in which temporal integration was performed by visual short-term memory but not by iconic memory. However, no brain region revealed higher activation for temporal integration by iconic memory than for temporal integration by visual short-term memory. This result suggested that there is no localized brain region specialized for iconic memory per se.

  18. MRI-based brain structure volumes in temporal lobe epilepsy patients and their unaffected siblings: a preliminary study.

    LENUS (Irish Health Repository)

    Scanlon, Cathy

    2013-01-01

    Investigating the heritability of brain structure may be useful in simplifying complicated genetic studies in temporal lobe epilepsy (TLE). A preliminary study is presented to determine if volume deficits of candidate brain structures present at a higher rate in unaffected siblings than controls subjects.

  19. Application of a New Genetic Deafness Microarray for Detecting Mutations in the Deaf in China.

    Directory of Open Access Journals (Sweden)

    Hong Wu

    Full Text Available The aim of this study was to evaluate the GoldenGate microarray as a diagnostic tool and to elucidate the contribution of the genes on this array to the development of both nonsyndromic and syndromic sensorineural hearing loss in China.We developed a microarray to detect 240 mutations underlying syndromic and nonsyndromic sensorineural hearing loss. The microarray was then used for analysis of 382 patients with nonsyndromic sensorineural hearing loss (including 15 patients with enlarged vestibular aqueduct syndrome, 21 patients with Waardenburg syndrome, and 60 unrelated controls. Subsequently, we analyzed the sensitivity, specificity, and reproducibility of this new approach after Sanger sequencing-based verification, and also determined the contribution of the genes on this array to the development of distinct hearing disorders.The sensitivity and specificity of the microarray chip were 98.73% and 98.34%, respectively. Genetic defects were identified in 61.26% of the patients with nonsyndromic sensorineural hearing loss, and 9 causative genes were identified. The molecular etiology was confirmed in 19.05% and 46.67% of the patients with Waardenburg syndrome and enlarged vestibular aqueduct syndrome, respectively.Our new mutation-based microarray comprises an accurate and comprehensive genetic tool for the detection of sensorineural hearing loss. This microarray-based detection method could serve as a first-pass screening (before next-generation-sequencing screening for deafness-causing mutations in China.

  20. The detection and differentiation of canine respiratory pathogens using oligonucleotide microarrays.

    Science.gov (United States)

    Wang, Lih-Chiann; Kuo, Ya-Ting; Chueh, Ling-Ling; Huang, Dean; Lin, Jiunn-Horng

    2017-05-01

    Canine respiratory diseases are commonly seen in dogs along with co-infections with multiple respiratory pathogens, including viruses and bacteria. Virus infections in even vaccinated dogs were also reported. The clinical signs caused by different respiratory etiological agents are similar, which makes differential diagnosis imperative. An oligonucleotide microarray system was developed in this study. The wild type and vaccine strains of canine distemper virus (CDV), influenza virus, canine herpesvirus (CHV), Bordetella bronchiseptica and Mycoplasma cynos were detected and differentiated simultaneously on a microarray chip. The detection limit is 10, 10, 100, 50 and 50 copy numbers for CDV, influenza virus, CHV, B. bronchiseptica and M. cynos, respectively. The clinical test results of nasal swab samples showed that the microarray had remarkably better efficacy than the multiplex PCR-agarose gel method. The positive detection rate of microarray and agarose gel was 59.0% (n=33) and 41.1% (n=23) among the 56 samples, respectively. CDV vaccine strain and pathogen co-infections were further demonstrated by the microarray but not by the multiplex PCR-agarose gel. The oligonucleotide microarray provides a highly efficient diagnosis alternative that could be applied to clinical usage, greatly assisting in disease therapy and control. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.

    Science.gov (United States)

    Chockalingam, Sriram; Aluru, Maneesha; Aluru, Srinivas

    2016-09-19

    Pre-processing of microarray data is a well-studied problem. Furthermore, all popular platforms come with their own recommended best practices for differential analysis of genes. However, for genome-scale network inference using microarray data collected from large public repositories, these methods filter out a considerable number of genes. This is primarily due to the effects of aggregating a diverse array of experiments with different technical and biological scenarios. Here we introduce a pre-processing pipeline suitable for inferring genome-scale gene networks from large microarray datasets. We show that partitioning of the available microarray datasets according to biological relevance into tissue- and process-specific categories significantly extends the limits of downstream network construction. We demonstrate the effectiveness of our pre-processing pipeline by inferring genome-scale networks for the model plant Arabidopsis thaliana using two different construction methods and a collection of 11,760 Affymetrix ATH1 microarray chips. Our pre-processing pipeline and the datasets used in this paper are made available at http://alurulab.cc.gatech.edu/microarray-pp.

  2. Magnetic resonance in the diagnostic imaging study of mesial temporal sclerosis

    International Nuclear Information System (INIS)

    Pastor, E.; Sanchez, J. C.; Rodriguez, I.; Altuzarra, A.; Machado, F.; Aguilar, D.

    2001-01-01

    Mesial temporal sclerosis (MTS) consists of hippocampal atrophy and gliosis and is the most common cause of temporal lobe epilepsy. The objective of the authors was to establish a magnetic resonance imaging (MRI) protocol for its diagnosis. A prospective study was carried out in 72 patients with drug resistant complex partial seizures (42 women and 30 men ranging in age from 6 to 66 year: mean: 30 years). Using a 1.5-Tesla magnet, paracoronal sections were made in hippocampi for T1-weighted inversion-recovery images and volume measurements, fluid-attenuated inversion-recovery (FLAIR) and T2 relaxometry. A control group of 30 health volunteers was included in the study. MTS was considered to be indicated by the presence of atrophy and hyperintensity in hippocampi on T2-weighted images. There were no differences among the hippocampi of the healthy individuals. The confidence intervals (mean± 1.96 SD) were 4169 mm''3-5911 mm''3 for volume of right side, 4097 mm''3-5940 mm''3 for volume of left side and 98-113 ms for T2 relaxation time. MTS was detected in 40 patients (55.5%): 23 cases involving the left side, 13 involving the right and 4 cases of bilateral asymmetric involvement. The 95% confidence intervals for the diagnostic validity of the results (sensitivity/specificity) were (88.8%-97.2%)/(87.6%-96.4%) for T1 volumetry, (88.8%-97.2%)(95.7%-100.3%) for FLAIR and (85.4%-96.6%)/(85.4%-96.6%) for T2 relaxometry. In 5 cases of MTS, astrophy of other extra hippocampal structures was also observed, and MTS was associated with an extra hippocampal lesion (dual pathology), especially neurona migration disorders, in 8 patients. Seventeen patients (23.5%) presented lesions without MTS (tumors, cortical dysplasias and heterotopias) and there was no MRI evidence of anomalies in 15 (21%). Twenty-five patients underwent surgical treatment: 20 with MTS (19 diagnosed according to MRI and one in whom there had been no abnormal findings), 4 with tumors and 1 with a ballooned cell

  3. Comparative Study of Temporal Aspects of Data Collection Using Remote Database vs. Abstract Database in WSN

    Directory of Open Access Journals (Sweden)

    Abderrahmen BELFKIH

    2015-06-01

    Full Text Available The real-time aspect is an important factor for Wireless Sensor Network (WSN applications, which demand a timely data delivery, to reflect the current state of the environment. However, most existing works in the field of sensor networks are only interested in data processing and energy consumption, to improve the lifetime of WSN. Extensive researches have been done on data processing in WSN. Some works have been interested in improving data collection methods, and others have focused on various query processing techniques. In recent years, the query processing using abstract database technology like Cougar and TinyDB has shown efficient results in many researches. This paper presents a study of timing properties through two data processing techniques for WSN. The first is based on a warehousing approach, in which data are collected and stored on a remote database. The second is based on query processing using an abstract database like TinyDB. This study has allowed us to identify some factors which enhance the respect of temporal constraints.

  4. Usefulness of temporal bone prototype for drilling training: A prospective study.

    Science.gov (United States)

    Aussedat, C; Venail, F; Nguyen, Y; Lescanne, E; Marx, M; Bakhos, D

    2017-12-01

    Dissection of cadaveric temporal bones (TBs) is considered the gold standard for surgical training in otology. For many reasons, access to the anatomical laboratory and cadaveric TBs is difficult for some facilities. The aim of this prospective and comparative study was to evaluate the usefulness of a physical TB prototype for drilling training in residency. Prospective study. Tertiary referral centre. Thirty-four residents were included. Seventeen residents (mean age 26.7±1.6) drilled on only cadaveric TBs ("traditional" group), in the traditional training method, while seventeen residents (mean age 26.5±1.7) drilled first on a prototype and then on a cadaveric TB ("prototype" group). Drilling performance was assessed using a validated scale. Residents completed a mastoid image before and after each drilling to enable evaluation of mental representations of the mastoidectomy. No differences were observed between the groups with respect to age, drilling experience and level of residency. Regarding drilling performance, we found a significant difference across the groups, with a better score in the prototype group (P=.0007). For mental representation, the score was statistically improved (P=.0003) after drilling in both groups, suggesting that TB drilling improves the mental representation of the mastoidectomy whether prototype or cadaveric TB is used. The TB prototype improves the drilling performance and mental representation of the mastoidectomy in the young resident population. A drilling simulation with virtual or physical systems seems to be a beneficial tool to improve TB drilling. © 2017 John Wiley & Sons Ltd.

  5. A study on temporal variation of elemental composition in tree barks used as air pollution indicators

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Eliane C.; Saiki, Mitiko, E-mail: eliane_csantos@yahoo.com.br, E-mail: mitiko@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2015-07-01

    The study of air pollution using biological matrices has shown that tree barks may be used as biomonitor due to accumulation of aerosol particles on its porous surface. The bark elemental composition can provide information on pollution sources as well as characterize the aerial pollutants from a wide geographical region. The aim of this study was to investigate the variation in elemental composition in barks with time of exposure. Tree barks from Tipuana (Tipuana tipu) and Sibipiruna (Caesalpinia peltophoroides) species were collected in February 2013 and July 2014 in the city of São Paulo. For analysis, the barks were cleaned, grated, ground and analyzed by neutron activation analysis (NAA). Aliquots of samples and synthetic standards of elements were irradiated with thermal neutron flux at the IEA-R1 nuclear research reactor and after a suitable decay time, the induced gamma activities were analyzed by gamma spectrometry. The elements As, Br, Ca, Co, Cr, Cs, Fe, K, La, Rb, Sb, Sc and Zn were determined and the results indicated variability in the concentrations depending on the element, sampling period and also on tree species, indicating that there are not very well defined temporal trends. The quality control of the analytical results evaluated by analyzing INCT Virginia Tobacco Leaves certified reference material (CRM) presented values of |z-score| < 2, indicating that the procedure of NAA applied is suitable for the analyses. (author)

  6. A study on temporal variation of elemental composition in tree barks used as air pollution indicators

    International Nuclear Information System (INIS)

    Santos, Eliane C.; Saiki, Mitiko

    2015-01-01

    The study of air pollution using biological matrices has shown that tree barks may be used as biomonitor due to accumulation of aerosol particles on its porous surface. The bark elemental composition can provide information on pollution sources as well as characterize the aerial pollutants from a wide geographical region. The aim of this study was to investigate the variation in elemental composition in barks with time of exposure. Tree barks from Tipuana (Tipuana tipu) and Sibipiruna (Caesalpinia peltophoroides) species were collected in February 2013 and July 2014 in the city of São Paulo. For analysis, the barks were cleaned, grated, ground and analyzed by neutron activation analysis (NAA). Aliquots of samples and synthetic standards of elements were irradiated with thermal neutron flux at the IEA-R1 nuclear research reactor and after a suitable decay time, the induced gamma activities were analyzed by gamma spectrometry. The elements As, Br, Ca, Co, Cr, Cs, Fe, K, La, Rb, Sb, Sc and Zn were determined and the results indicated variability in the concentrations depending on the element, sampling period and also on tree species, indicating that there are not very well defined temporal trends. The quality control of the analytical results evaluated by analyzing INCT Virginia Tobacco Leaves certified reference material (CRM) presented values of |z-score| < 2, indicating that the procedure of NAA applied is suitable for the analyses. (author)

  7. Temporal trends in management and outcomes of testicular cancer: A population-based study.

    Science.gov (United States)

    Leveridge, Michael J; Siemens, D Robert; Brennan, Kelly; Izard, Jason P; Karim, Safiya; An, Howard; Mackillop, William J; Booth, Christopher M

    2018-04-16

    Treatment guidelines for early-stage testicular cancer have increasingly recommended de-escalation of therapy with surveillance strategies. This study was designed to describe temporal trends in routine clinical practice and to determine whether de-escalation of therapy is associated with inferior survival in the general population. The Ontario Cancer Registry was linked to electronic records of treatment to identify all patients diagnosed with testicular cancer treated with orchiectomy in Ontario during 2000-2010. Treatment after orchiectomy was classified as radiotherapy (RT), retroperitoneal lymph node dissection (RPLND), chemotherapy, or none. Surveillance was defined as no identified treatment within 90 days of orchiectomy. Overall survival (OS) and cancer-specific survival (CSS) were measured from the date of orchiectomy. The study population included 1564 and 1086 cases of seminomas and nonseminoma germ cell tumors (NSGCTs), respectively. Among patients with seminomas, there was a significant increase in the proportion of patients with no treatment within 90 days of orchiectomy (from 56% to 84%; P testicular cancer in routine practice since 2000. Long-term survival in routine practice is excellent and has not decreased with the uptake of surveillance strategies. Cancer 2018. © 2018 American Cancer Society. © 2018 American Cancer Society.

  8. Lead Pollution Remanence in an Urban River System: A multi-scale temporal and spatial study

    Directory of Open Access Journals (Sweden)

    Ayrault S.

    2013-04-01

    Full Text Available This work aims at studying the fate of sediments contaminated with tetraethyl Pb from leaded gasoline using a two-dimension upscaling approach, from a small urban subcatchment, the Orge River (900 km2 to the whole Seine River basin (64700 km2, in France. In France, the leaded gasoline reduction started in 1986 and leaded gasoline was completely banned after 2000. This work aims at assessing whether the ban of leaded gasoline is related to changes in Pb contamination sources of these river suspended sediment particles (SPM and bed sediment. Sediment cores and samples collected in the course of previous research projects of the Seine River contamination were used as temporal archives. The study of the isotopic lead ratio showed the fast decrease of the contamination of urban river suspended particulate matter due to the “gasoline” lead source from 2000 to 2011. This source mostly disappeared in the SPM from the Seine River basin that includes urban areas but also agricultural and industrial activities. Nevertheless, it is still present in the small urban catchment of the Orge River. The results on bed sediments showed a different pattern, where the “gasoline” source is still active in densely populated areas, either in the Seine River in the 20 km downstream Paris, or along the Orge River.

  9. Systematic study of association of four GABAergic genes: glutamic acid decarboxylase 1 gene, glutamic acid decarboxylase 2 gene, GABA(B) receptor 1 gene and GABA(A) receptor subunit beta2 gene, with schizophrenia using a universal DNA microarray.

    Science.gov (United States)

    Zhao, Xu; Qin, Shengying; Shi, Yongyong; Zhang, Aiping; Zhang, Jing; Bian, Li; Wan, Chunling; Feng, Guoyin; Gu, Niufan; Zhang, Guangqi; He, Guang; He, Lin

    2007-07-01

    Several studies have suggested the dysfunction of the GABAergic system as a risk factor in the pathogenesis of schizophrenia. In the present study, case-control association analysis was conducted in four GABAergic genes: two glutamic acid decarboxylase genes (GAD1 and GAD2), a GABA(A) receptor subunit beta2 gene (GABRB2) and a GABA(B) receptor 1 gene (GABBR1). Using a universal DNA microarray procedure we genotyped a total of 20 SNPs on the above four genes in a study involving 292 patients and 286 controls of Chinese descent. Statistically significant differences were observed in the allelic frequencies of the rs187269C/T polymorphism in the GABRB2 gene (P=0.0450, chi(2)=12.40, OR=1.65) and the -292A/C polymorphism in the GAD1 gene (P=0.0450, chi(2)=14.64 OR=1.77). In addition, using an electrophoretic mobility shift assay (EMSA), we discovered differences in the U251 nuclear protein binding to oligonucleotides representing the -292 SNP on the GAD1 gene, which suggests that the -292C allele has reduced transcription factor binding efficiency compared with the 292A allele. Using the multifactor-dimensionality reduction method (MDR), we found that the interactions among the rs187269C/T polymorphism in the GABRB2 gene, the -243A/G polymorphism in the GAD2 gene and the 27379C/T and 661C/T polymorphisms in the GAD1 gene revealed a significant association with schizophrenia (Pschizophrenia in the Chinese population.

  10. Microarray BASICA: Background Adjustment, Segmentation, Image Compression and Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jianping Hua

    2004-01-01

    Full Text Available This paper presents microarray BASICA: an integrated image processing tool for background adjustment, segmentation, image compression, and analysis of cDNA microarray images. BASICA uses a fast Mann-Whitney test-based algorithm to segment cDNA microarray images, and performs postprocessing to eliminate the segmentation irregularities. The segmentation results, along with the foreground and background intensities obtained with the background adjustment, are then used for independent compression of the foreground and background. We introduce a new distortion measurement for cDNA microarray image compression and devise a coding scheme by modifying the embedded block coding with optimized truncation (EBCOT algorithm (Taubman, 2000 to achieve optimal rate-distortion performance in lossy coding while still maintaining outstanding lossless compression performance. Experimental results show that the bit rate required to ensure sufficiently accurate gene expression measurement varies and depends on the quality of cDNA microarray images. For homogeneously hybridized cDNA microarray images, BASICA is able to provide from a bit rate as low as 5 bpp the gene expression data that are 99% in agreement with those of the original 32 bpp images.

  11. Developing a comprehensive presurgical functional MRI protocol for patients with intractable temporal lobe epilepsy: a pilot study

    International Nuclear Information System (INIS)

    Deblaere, K.; Vandemaele, P.; Achten, E.; Backes, W.H.; Hofman, P.; Wilmink, J.; Boon, P.A.; Vonck, K.; Boon, P.; Troost, J.; Vermeulen, J.; Aldenkamp, A.

    2002-01-01

    Our aim was to put together and test a comprehensive functional MRI (fMRI) protocol which could compete with the intracarotid amytal (IAT) or Wada test for the localisation of language and memory function in patients with intractable temporal lobe epilepsy. The protocol was designed to be performed in under 1 h on a standard 1.5 tesla imager. We used five paradigms to test nine healthy right-handed subjects: complex scene-encoding, picture-naming, reading, word-generation and semantic-decision tasks. The combination of these tasks generated two activation maps related to memory in the mesial temporal lobes, and three language-related maps of activation in a major part of the known language network. The functional maps from the encoding and naming tasks showed typical and symmetrical posterior mesial temporal lobe activation related to memory in all subjects. Only four of nine subjects also showed symmetrical anterior hippocampal activation. Language lateralisation was best with the word generation and reading paradigms and proved possible in all subjects. The reading paradigm enables localisation of language function in the left anterior temporal pole and middle temporal gyrus, areas typically resected during epilepsy surgery. The combined results of this comprehensive f MRI protocol are adequate for a comparative study with the IAT in patients with epilepsy being assessed for surgery. (orig.)

  12. Developing a comprehensive presurgical functional MRI protocol for patients with intractable temporal lobe epilepsy: a pilot study

    Energy Technology Data Exchange (ETDEWEB)

    Deblaere, K.; Vandemaele, P.; Achten, E. [MRI Department -1 K12, Department of Radiology, Ghent University Hospital, De Pintelaan 185, 9000 Ghent (Belgium); Backes, W.H.; Hofman, P.; Wilmink, J. [Department of Neuroradiology, University Hospital Maastricht, Postbus 5800, 6202 AZ Maastricht (Netherlands); Boon, P.A.; Vonck, K. [Department of Neurology, Ghent University Hospital, De Pintelaan 185, 9000 Ghent (Belgium); Boon, P. [Department of Medical Psychology, University Hospital Maastricht (Netherlands); Troost, J. [Department of Neurology, University Hospital Maastricht (Netherlands); Vermeulen, J. [S.E.I.N Heemstede, Psychological Laboratory, Achterweg 5, 2103 SW Heemstede (Netherlands); Aldenkamp, A. [Epilepsy Center ' Kempenhaeghe' , Postbus 61, 5900 AB Heeze (Netherlands)

    2002-08-01

    Our aim was to put together and test a comprehensive functional MRI (fMRI) protocol which could compete with the intracarotid amytal (IAT) or Wada test for the localisation of language and memory function in patients with intractable temporal lobe epilepsy. The protocol was designed to be performed in under 1 h on a standard 1.5 tesla imager. We used five paradigms to test nine healthy right-handed subjects: complex scene-encoding, picture-naming, reading, word-generation and semantic-decision tasks. The combination of these tasks generated two activation maps related to memory in the mesial temporal lobes, and three language-related maps of activation in a major part of the known language network. The functional maps from the encoding and naming tasks showed typical and symmetrical posterior mesial temporal lobe activation related to memory in all subjects. Only four of nine subjects also showed symmetrical anterior hippocampal activation. Language lateralisation was best with the word generation and reading paradigms and proved possible in all subjects. The reading paradigm enables localisation of language function in the left anterior temporal pole and middle temporal gyrus, areas typically resected during epilepsy surgery. The combined results of this comprehensive f MRI protocol are adequate for a comparative study with the IAT in patients with epilepsy being assessed for surgery. (orig.)

  13. Simultaneity and Temporal Order Judgments Are Coded Differently and Change With Age: An Event-Related Potential Study

    Directory of Open Access Journals (Sweden)

    Aysha Basharat

    2018-04-01

    Full Text Available Multisensory integration is required for a number of daily living tasks where the inability to accurately identify simultaneity and temporality of multisensory events results in errors in judgment leading to poor decision-making and dangerous behavior. Previously, our lab discovered that older adults exhibited impaired timing of audiovisual events, particularly when making temporal order judgments (TOJs. Simultaneity judgments (SJs, however, were preserved across the lifespan. Here, we investigate the difference between the TOJ and SJ tasks in younger and older adults to assess neural processing differences between these two tasks and across the lifespan. Event-related potentials (ERPs were studied to determine between-task and between-age differences. Results revealed task specific differences in perceiving simultaneity and temporal order, suggesting that each task may be subserved via different neural mechanisms. Here, auditory N1 and visual P1 ERP amplitudes confirmed that unisensory processing of audiovisual stimuli did not differ between the two tasks within both younger and older groups, indicating that performance differences between tasks arise either from multisensory integration or higher-level decision-making. Compared to younger adults, older adults showed a sustained higher auditory N1 ERP amplitude response across SOAs, suggestive of broader response properties from an extended temporal binding window. Our work provides compelling evidence that different neural mechanisms subserve the SJ and TOJ tasks and that simultaneity and temporal order perception are coded differently and change with age.

  14. An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

    Science.gov (United States)

    2012-01-01

    Background The combination of chromatin immunoprecipitation with two-channel microarray technology enables genome-wide mapping of binding sites of DNA-interacting proteins (ChIP-on-chip) or sites with methylated CpG di-nucleotides (DNA methylation microarray). These powerful tools are the gateway to understanding gene transcription regulation. Since the goals of such studies, the sample preparation procedures, the microarray content and study design are all different from transcriptomics microarrays, the data pre-processing strategies traditionally applied to transcriptomics microarrays may not be appropriate. Particularly, the main challenge of the normalization of "regulation microarrays" is (i) to make the data of individual microarrays quantitatively comparable and (ii) to keep the signals of the enriched probes, representing DNA sequences from the precipitate, as distinguishable as possible from the signals of the un-enriched probes, representing DNA sequences largely absent from the precipitate. Results We compare several widely used normalization approaches (VSN, LOWESS, quantile, T-quantile, Tukey's biweight scaling, Peng's method) applied to a selection of regulation microarray datasets, ranging from DNA methylation to transcription factor binding and histone modification studies. Through comparison of the data distributions of control probes and gene promoter probes before and after normalization, and assessment of the power to identify known enriched genomic regions after normalization, we demonstrate that there are clear differences in performance between normalization procedures. Conclusion T-quantile normalization applied separately on the channels and Tukey's biweight scaling outperform other methods in terms of the conservation of enriched and un-enriched signal separation, as well as in identification of genomic regions known to be enriched. T-quantile normalization is preferable as it additionally improves comparability between microarrays. In

  15. Diffusion Monte Carlo study on temporal evolution of entropy and free energy in nonequilibrium processes.

    Science.gov (United States)

    Tanaka, Shigenori

    2016-03-07

    A computational scheme to describe the temporal evolution of thermodynamic functions in stochastic nonequilibrium processes of isothermal classical systems is proposed on the basis of overdamped Langevin equation under given potential and temperature. In this scheme the associated Fokker-Planck-Smoluchowski equation for the probability density function is transformed into the imaginary-time Schrödinger equation with an effective Hamiltonian. The propagator for the time-dependent wave function is expressed in the framework of the path integral formalism, which can thus represent the dynamical behaviors of nonequilibrium molecular systems such as those conformational changes observed in protein folding and ligand docking. The present study then employs the diffusion Monte Carlo method to efficiently simulate the relaxation dynamics of wave function in terms of random walker distribution, which in the long-time limit reduces to the ground-state eigenfunction corresponding to the equilibrium Boltzmann distribution. Utilizing this classical-quantum correspondence, we can describe the relaxation processes of thermodynamic functions as an approach to the equilibrium state with the lowest free energy. Performing illustrative calculations for some prototypical model potentials, the temporal evolutions of enthalpy, entropy, and free energy of the classical systems are explicitly demonstrated. When the walkers initially start from a localized configuration in one- or two-dimensional harmonic or double well potential, the increase of entropy usually dominates the relaxation dynamics toward the equilibrium state. However, when they start from a broadened initial distribution or go into a steep valley of potential, the dynamics are driven by the decrease of enthalpy, thus causing the decrease of entropy associated with the spatial localization. In the cases of one- and two-dimensional asymmetric double well potentials with two minimal points and an energy barrier between them

  16. HER2/neu (c-erbB-2) gene amplification and protein expression are rare in uterine cervical neoplasia: a tissue microarray study of 814 archival specimens

    DEFF Research Database (Denmark)

    Lesnikova, Iana; Lidang, Marianne; Hamilton-Dutoit, Stephen

    2009-01-01

    intraepithelial neoplasia (CIN)1 (n = 262), CIN2 (n = 230), CIN3 (n = 186) and invasive carcinoma (n = 136), for HER2/neu protein expression by immunohistochemistry (IHC) and for HER2/neu gene amplification by chromogenic in situ hybridization (CISH). We found moderate or strong immunohistochemical positivity...... and invasive cervical carcinoma specimens. When present, Her-2/neu positivity is more commonly seen in higher grades of cervical dysplasia and in carcinoma. However, this large TMA study shows that HER2/neu oncoprotein expression and HER2/neu gene amplification overall are uncommon events in cervical neoplasia....... This provides compelling evidence that HER2/neu plays no major role in the development and progression of cervical neoplasia....

  17. Hyperphosphorylated tau in patients with refractory epilepsy correlates with cognitive decline: a study of temporal lobe resections.

    Science.gov (United States)

    Tai, Xin You; Koepp, Matthias; Duncan, John S; Fox, Nick; Thompson, Pamela; Baxendale, Sallie; Liu, Joan Y W; Reeves, Cheryl; Michalak, Zuzanna; Thom, Maria

    2016-09-01

    SEE BERNASCONI DOI101093/AWW202 FOR A SCIENTIFIC COMMENTARY ON THIS ARTICLE: Temporal lobe epilepsy, the most prevalent form of chronic focal epilepsy, is associated with a high prevalence of cognitive impairment but the responsible underlying pathological mechanisms are unknown. Tau, the microtubule-associated protein, is a hallmark of several neurodegenerative diseases including Alzheimer's disease and chronic traumatic encephalopathy. We hypothesized that hyperphosphorylated tau pathology is associated with cognitive decline in temporal lobe epilepsy and explored this through clinico-pathological study. We first performed pathological examination on tissue from 33 patients who had undergone temporal lobe resection between ages 50 and 65 years to treat drug-refractory temporal lobe epilepsy. We identified hyperphosphorylated tau protein using AT8 immunohistochemistry and compared this distribution to Braak patterns of Alzheimer's disease and patterns of chronic traumatic encephalopathy. We quantified tau pathology using a modified tau score created specifically for analysis of temporal lobectomy tissue and the Braak staging, which was limited without extra-temporal brain areas available. Next, we correlated tau pathology with pre- and postoperative cognitive test scores and clinical risk factors including age at time of surgery, duration of epilepsy, history of secondary generalized seizures, history of head injury, handedness and side of surgery. Thirty-one of 33 cases (94%) showed hyperphosphorylated tau pathology in the form of neuropil threads and neurofibrillary tangles and pre-tangles. Braak stage analysis showed 12% of our epilepsy cohort had a Braak staging III-IV compared to an age-matched non-epilepsy control group from the literature (8%). We identified a mixture of tau pathology patterns characteristic of Alzheimer's disease and chronic traumatic encephalopathy. We also found unusual patterns of subpial tau deposition, sparing of the hippocampus and

  18. Differential effects of selective frankincense (Ru Xiang) essential oil versus non-selective sandalwood (Tan Xiang) essential oil on cultured bladder cancer cells: a microarray and bioinformatics study

    Science.gov (United States)

    2014-01-01

    Background Frankincense (Boswellia carterii, known as Ru Xiang in Chinese) and sandalwood (Santalum album, known as Tan Xiang in Chinese) are cancer preventive and therapeutic agents in Chinese medicine. Their biologically active ingredients are usually extracted from frankincense by hydrodistillation and sandalwood by distillation. This study aims to investigate the anti-proliferative and pro-apoptotic activities of frankincense and sandalwood essential oils in cultured human bladder cancer cells. Methods The effects of frankincense (1,400–600 dilutions) (v/v) and sandalwood (16,000–7,000 dilutions) (v/v) essential oils on cell viability were studied in established human bladder cancer J82 cells and immortalized normal human bladder urothelial UROtsa cells using a colorimetric XTT cell viability assay. Genes that responded to essential oil treatments in human bladder cancer J82 cells were identified using the Illumina Expression BeadChip platform and analyzed for enriched functions and pathways. The chemical compositions of the essential oils were determined by gas chromatography–mass spectrometry. Results Human bladder cancer J82 cells were more sensitive to the pro-apoptotic effects of frankincense essential oil than the immortalized normal bladder UROtsa cells. In contrast, sandalwood essential oil exhibited a similar potency in suppressing the viability of both J82 and UROtsa cells. Although frankincense and sandalwood essential oils activated common pathways such as inflammatory interleukins (IL-6 signaling), each essential oil had a unique molecular action on the bladder cancer cells. Heat shock proteins and histone core proteins were activated by frankincense essential oil, whereas negative regulation of protein kinase activity and G protein-coupled receptors were activated by sandalwood essential oil treatment. Conclusion The effects of frankincense and sandalwood essential oils on J82 cells and UROtsa cells involved different mechanisms leading to

  19. A functional MRI study of language networks in left medial temporal lobe epilepsy

    Energy Technology Data Exchange (ETDEWEB)

    Yu Aihong, E-mail: yuaihong163@tom.com [Department of Radiology, the 4th Medical College of Peking University, Beijing Jishuitan Hospital, Beijing 100035 (China); Wang Xiaoyi; Xu Guoqing [Beijing Normal University, State Key Laboratory of Cognitive Neuroscience and Learning, Beijing 100875 (China); Li Yongjie [Beijing Institute of Functional Neurosurgery, Xuanwu Hospital, Capital University of Medical Sciences, Beijing 100053 (China); Qin Wen; Li Kuncheng [Department of Radiology, Xuanwu Hospital, Capital University of Medical Sciences (China); Wang, Yuping [Department of Neurology, Xuanwu Hospital, Capital University of Medical Sciences (China)

    2011-11-15

    Purpose: The purpose of this study was to investigate the abnormality of language networks in left medial temporal lobe epilepsy (MTLE) using fMRI. Materials and methods: Eight patients with left MTLE and 15 healthy subjects were evaluated. An auditory semantic judgment (AJ) paradigm was used. The fMRI data were collected on a 3T MR system and analyzed by AFNI (analysis of functional neuroimages) to generate the activation map. Results: Behavioral data showed that the reaction time of the left MTLE patients was significantly longer than that of controls on the AJ task (t = -3.396, P < 0.05). The left MTLE patients also exhibited diffusively decreased activation in the AJ task. Right hemisphere dominance of Broca's and Wernicke's areas was demonstrated in left MTLE patients. Conclusions: Long-term activation of spikes in left MTLE patients results in language impairment, which is associated with an abnormality of the brain neural network.

  20. On the temporal dynamics of sign production: An ERP study in Catalan Sign Language (LSC).

    Science.gov (United States)

    Baus, Cristina; Costa, Albert

    2015-06-03

    This study investigates the temporal dynamics of sign production and how particular aspects of the signed modality influence the early stages of lexical access. To that end, we explored the electrophysiological correlates associated to sign frequency and iconicity in a picture signing task in a group of bimodal bilinguals. Moreover, a subset of the same participants was tested in the same task but naming the pictures instead. Our results revealed that both frequency and iconicity influenced lexical access in sign production. At the ERP level, iconicity effects originated very early in the course of signing (while absent in the spoken modality), suggesting a stronger activation of the semantic properties for iconic signs. Moreover, frequency effects were modulated by iconicity, suggesting that lexical access in signed language is determined by the iconic properties of the signs. These results support the idea that lexical access is sensitive to the same phenomena in word and sign production, but its time-course is modulated by particular aspects of the modality in which a lexical item will be finally articulated. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Effect of seizure on hippocampus in mesial temporal lobe epilepsy and neocortical epilepsy: an MRS study

    International Nuclear Information System (INIS)

    Lee, S.K.; Kim, D.W.; Kim, K.K.; Chung, C.K.; Song, I.C.; Chang, K.H.

    2005-01-01

    This study was performed to evaluate the effect of seizures on the bilateral hippocampus in mesial temporal lobe epilepsy (mTLE) and neocortical epilepsy by single voxel proton magnetic resonance spectroscopy (MRS). Forty-one patients with mTLE having unilateral hippocampal sclerosis and 43 patients with a neocortical epilepsy who underwent subsequent epilepsy surgery were recruited. Ninety-five percent confidence intervals of N-acetyl aspartate/choline (NAA/Cho) and NAA/creatine (NAA/Cr) ratios in 20 healthy control subjects were used as threshold values to determine abnormal NAA/Cho and NAA/Cr. NAA/Cho and NAA/Cr were significantly lower in the ipsilateral hippocampus of mTLE and neocortical epilepsy. Using asymmetry indices for patients with bilaterally abnormal ratios of NAA/Cho and NAA/Cr in addition to using unilateral abnormal ratio, the seizure focus was correctly lateralized in 65.9% of patients with mTLE and 48.8% of neocortical epilepsy patients. Bilateral NAA/Cho abnormality was significantly related to a poor surgical outcome in mTLE. No significant relationship was found between the results of NAA/Cho or NAA/Cr and surgical outcome in neocortical epilepsy. The mean contralateral NAA/Cr ratio of the hippocampus in mTLE was significantly lower in patients with a history of secondary generalized tonic-clonic seizure (SGTCS) than in those without. (orig.)

  2. Study of the spatial and temporal variability of local ecosystems and glaciers of the Antisana Volcano

    Directory of Open Access Journals (Sweden)

    Mauricio Valladares Borja

    2014-12-01

    Full Text Available (Received: 2014/10/31 - Accepted: 2014/12/15The scientific interest in climate change allowed to uncover evidence demonstrating a general warming trend caused by human activities. Facts such as rising sea levels, extreme weather events and retreat of glaciers, are indicators of the presence of alterations of normal weather patterns. In Ecuador, the Antisana is a stratovolcano of strategic importance affecting the climate of the region, in the functioning of the surrounding ecosystems. It is also a reserve of water for the population of the Metropolitan District of Quito (DMQ. The glaciers of the tropical volcano are also suffering the effects of global warming. Its decline over time is of concern and should be analyzed. The present research work performed a spatial and temporal study based on historical series of aerial photographs taken between 1956 and 2011, through geo-processing capabilities of geographic information systems (GIS. The results show a significant decrease in the glaciers of the Antisana Volcano and significant changes in the surrounding local ecological formations.

  3. Effect of seizure on hippocampus in mesial temporal lobe epilepsy and neocortical epilepsy: an MRS study

    Energy Technology Data Exchange (ETDEWEB)

    Lee, S.K.; Kim, D.W.; Kim, K.K. [Seoul National University College of Medicine, Seoul National University Hospital, Department of Neurology, Chongno ku, Seoul (Korea); Chung, C.K. [Seoul National University College of Medicine, Seoul National University Hospital, Department of Neurosurgery, Chongno ku, Seoul (Korea); Song, I.C.; Chang, K.H. [Seoul National University College of Medicine, Seoul National University Hospital, Department of Radiology, Chongno ku, Seoul (Korea)

    2005-12-01

    This study was performed to evaluate the effect of seizures on the bilateral hippocampus in mesial temporal lobe epilepsy (mTLE) and neocortical epilepsy by single voxel proton magnetic resonance spectroscopy (MRS). Forty-one patients with mTLE having unilateral hippocampal sclerosis and 43 patients with a neocortical epilepsy who underwent subsequent epilepsy surgery were recruited. Ninety-five percent confidence intervals of N-acetyl aspartate/choline (NAA/Cho) and NAA/creatine (NAA/Cr) ratios in 20 healthy control subjects were used as threshold values to determine abnormal NAA/Cho and NAA/Cr. NAA/Cho and NAA/Cr were significantly lower in the ipsilateral hippocampus of mTLE and neocortical epilepsy. Using asymmetry indices for patients with bilaterally abnormal ratios of NAA/Cho and NAA/Cr in addition to using unilateral abnormal ratio, the seizure focus was correctly lateralized in 65.9% of patients with mTLE and 48.8% of neocortical epilepsy patients. Bilateral NAA/Cho abnormality was significantly related to a poor surgical outcome in mTLE. No significant relationship was found between the results of NAA/Cho or NAA/Cr and surgical outcome in neocortical epilepsy. The mean contralateral NAA/Cr ratio of the hippocampus in mTLE was significantly lower in patients with a history of secondary generalized tonic-clonic seizure (SGTCS) than in those without. (orig.)

  4. Dynamic computed tomography based on spatio-temporal analysis in acute stroke: Preliminary study

    Energy Technology Data Exchange (ETDEWEB)

    Park, Ha Young; Pyeon, Do Yeong; Kim, Da Hye; Jung, Young Jin [Dongseo University, Busan (Korea, Republic of)

    2016-12-15

    Acute stroke is a one of common disease that require fast diagnosis and treatment to save patients life. however, the acute stroke may cause lifelong disability due to brain damage with no prompt surgical procedure. In order to diagnose the Stroke, brain perfusion CT examination and possible rapid implementation of 3D angiography has been widely used. However, a low-dose technique should be applied for the examination since a lot of radiation exposure to the patient may cause secondary damage for the patients. Therefore, the degradation of the measured CT images may interferes with a clinical check in that blood vessel shapes o n the CT image are significantly affected by gaussian noise. In this study, we employed the spatio-temporal technique to analyze dynamic (brain perfusion) CT data to improve an image quality for successful clinical diagnosis. As a results, proposed technique could remove gaussian noise successfully, demonstrated a possibility of new image segmentation technique for CT angiography. Qualitative evaluation was conducted by skilled radiological technologists, indicated significant quality improvement of dynamic CT images. the proposed technique will be useful tools as a clinical application for brain perfusion CT examination.

  5. Reproducibility of qualitative assessments of temporal lobe atrophy in MRI studies.

    Science.gov (United States)

    Sarria-Estrada, S; Acevedo, C; Mitjana, R; Frascheri, L; Siurana, S; Auger, C; Rovira, A

    2015-01-01

    To determine the reproducibility of the Scheltens visual rating scale in establishing atrophy of the medial temporal lobe. We used coronal T1-weighted inversion recovery sequences on a 1.5 Tesla MRI scanner to study 25 patients with clinically diagnosed Alzheimer's disease or mild cognitive decline and 25 subjects without cognitive decline. Five neuroradiologists trained to apply the Scheltens visual rating scale analyzed the images. We used the interclass correlation coefficient to evaluate interrater and intrarater agreement. Raters scored 20 (80%) of the 25 patients with mild cognitive decline or Alzheimer's disease between 2 and 4; by contrast, they scored 21 (84%) of the 25 subjects without cognitive decline between 0 and 1. The interrater agreement was consistently greater than 0.82, with a 95% confidence interval of (0.7-0.9). The intrarater agreement ranged from 0.82 to 0.87, with a 95% confidence interval of (0.56-0.93). The Scheltens visual rating scale is reproducible among observers, and this finding supports its use in clinical practice. Copyright © 2013 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

  6. Stria vascularis and cochlear hair cell changes in syphilis: A human temporal bone study.

    Science.gov (United States)

    Hızlı, Ömer; Kaya, Serdar; Hızlı, Pelin; Paparella, Michael M; Cureoglu, Sebahattin

    2016-12-01

    To observe any changes in stria vascularis and cochlear hair cells in patients with syphilis. We examined 13 human temporal bone samples from 8 patients with syphilis (our syphilis group), as well as 12 histopathologically normal samples from 9 age-matched patients without syphilis (our control group). We compared, between the two groups, the mean area of the stria vascularis (measured with conventional light microscopy connected to a personal computer) and the mean percentage of cochlear hair cell loss (obtained from cytocochleograms). In our syphilis group, only 1 (7.7%) of the 13 samples had precipitate in the endolymphatic or perilymphatic spaces; 8 (61.5%) of the samples revealed the presence of endolymphatic hydrops (4 cochlear, 4 saccular). The mean area of the stria vascularis did not significantly differ, in any turn of the cochlea, between the 2 groups (P>0.1). However, we did find significant differences between the 2 groups in the mean percentage of outer hair cells in the apical turn (Psyphilis group, we observed either complete loss of the organ of Corti or a flattened organ of Corti without any cells in addition to the absence of both outer and inner hair cells. In this study, syphilis led either to complete loss of the organ of Corti or to significant loss of cochlear hair cells, in addition to cochleosaccular hydrops. But the area of the stria vascularis did not change. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. Spatio-temporal study of carbon sequestration through piscicultural practice at East Kolkata Wetland.

    Science.gov (United States)

    Pal, Sudin; Chattopadhyay, Buddhadeb; Mukhopadhyay, Subhra Kumar

    2016-09-01

    The present study focus the variation of carbon concentrations within three trophic level i.e., primary producer (phytoplankton), primary consumers (zooplankton) and secondary consumers (fish) in three selected ponds at East Kolkata Wetland area. Depending on the amount and frequency of wastewater input, physico-chemical characteristics of pond, species richness, predator-prey interactions and pond wise different piscicultural practices, the amount of carbon sequestration varied spatially. Significant temporal variations were also observed in each trophic level of these three selected East Kolkata Wetland pond ecosystems. On average primary producers were sequestered 2038.6 ± 244.8mg C m-3 d-1 whereas 307 ± 19.3 mg C m-3 and 11531.4 ± 318.2mg C m-3 was sequestered by primary and secondary consumers, respectively. In Kolkata and its nearby districts over 90% of the production was marked from the East Kolkata Wetland area. Consequently, a significant amount of sequestered carbon was exported from the East Kolkata Wetland ecosystem in the form of fish and this continuous system might increase the carbon sequestration efficiency of the aquatic ecosystem.

  8. Whole-Genome Microarray and Gene Deletion Studies Reveal Regulation of the Polyhydroxyalkanoate Production Cycle by the Stringent Response in Ralstonia eutropha H16

    Energy Technology Data Exchange (ETDEWEB)

    Brigham, CJ; Speth, DR; Rha, C; Sinskey, AJ

    2012-10-22

    Poly(3-hydroxybutyrate) (PHB) production and mobilization in Ralstonia eutropha are well studied, but in only a few instances has PHB production been explored in relation to other cellular processes. We examined the global gene expression of wild-type R. eutropha throughout the PHB cycle: growth on fructose, PHB production using fructose following ammonium depletion, and PHB utilization in the absence of exogenous carbon after ammonium was resupplied. Our results confirm or lend support to previously reported results regarding the expression of PHB-related genes and enzymes. Additionally, genes for many different cellular processes, such as DNA replication, cell division, and translation, are selectively repressed during PHB production. In contrast, the expression levels of genes under the control of the alternative sigma factor sigma(54) increase sharply during PHB production and are repressed again during PHB utilization. Global gene regulation during PHB production is strongly reminiscent of the gene expression pattern observed during the stringent response in other species. Furthermore, a ppGpp synthase deletion mutant did not show an accumulation of PHB, and the chemical induction of the stringent response with DL-norvaline caused an increased accumulation of PHB in the presence of ammonium. These results indicate that the stringent response is required for PHB accumulation in R. eutropha, helping to elucidate a thus-far-unknown physiological basis for this process.

  9. Gene expression profiles of lung adenocarcinoma linked to histopathological grading and survival but not to EGF-R status: a microarray study

    Directory of Open Access Journals (Sweden)

    Passlick Bernward

    2010-03-01

    Full Text Available Abstract Background Several different gene expression signatures have been proposed to predict response to therapy and clinical outcome in lung adenocarcinoma. Herein, we investigate if elements of published gene sets can be reproduced in a small dataset, and how gene expression profiles based on limited sample size relate to clinical parameters including histopathological grade and EGFR protein expression. Methods Affymetrix Human Genome U133A platform was used to obtain gene expression profiles of 28 pathologically and clinically annotated adenocarcinomas of the lung. EGFR status was determined by fluorescent in situ hybridization and immunohistochemistry. Results Using unsupervised clustering algorithms, the predominant gene expression signatures correlated with the histopathological grade but not with EGFR protein expression as detected by immunohistochemistry. In a supervised analysis, the signature of high grade tumors but not of EGFR overexpressing cases showed significant enrichment of gene sets reflecting MAPK activation and other potential signaling cascades downstream of EGFR. Out of four different previously published gene sets that had been linked to prognosis, three showed enrichment in the gene expression signature associated with favorable prognosis. Conclusions In this dataset, histopathological tumor grades but not EGFR status were associated with dominant gene expression signatures and gene set enrichment reflecting oncogenic pathway activation, suggesting that high immunohistochemistry EGFR scores may not necessarily be linked to downstream effects that cause major changes in gene expression patterns. Published gene sets showed association with patient survival; however, the small sample size of this study limited the options for a comprehensive validation of previously reported prognostic gene expression signatures.

  10. Temporal dynamics of cortical and subcortical responses to apomorphine in Parkinson disease: an H2(15)O PET study

    NARCIS (Netherlands)

    Hosey, Lara A.; Thompson, Jennifer L. W.; Metman, Leonard Verhagen; van den Munckhof, Pepyn; Braun, Allen R.

    2005-01-01

    H2(15)O positron emission tomography (PET) was used to study the temporal course of central nervous system (CNS) responses to apomorphine in patients with idiopathic Parkinson disease (PD). Agonist-induced changes in regional cerebral blood flow (rCBF) were evaluated within

  11. Magnetic resonance in the diagnostic imaging study of mesial temporal sclerosis; Diagnostico por imagen con resonancia magnetica de la esclerosis temporal mesial

    Energy Technology Data Exchange (ETDEWEB)

    Pastor, E; Sanchez, J C; Rodriguez, I; Altuzarra, A; Machado, F [Hospital Universitario Virgen de las Nieves. Granada (Spain); Aguilar, D [Hospital Clinico Universitario San Cecilio. Granada (Spain)

    2001-07-01

    Mesial temporal sclerosis (MTS) consists of hippocampal atrophy and gliosis and is the most common cause of temporal lobe epilepsy. The objective of the authors was to establish a magnetic resonance imaging (MRI) protocol for its diagnosis. A prospective study was carried out in 72 patients with drug resistant complex partial seizures (42 women and 30 men ranging in age from 6 to 66 year: mean: 30 years). Using a 1.5-Tesla magnet, paracoronal sections were made in hippocampi for T1-weighted inversion-recovery images and volume measurements, fluid-attenuated inversion-recovery (FLAIR) and T2 relaxometry. A control group of 30 health volunteers was included in the study. MTS was considered to be indicated by the presence of atrophy and hyperintensity in hippocampi on T2-weighted images. There were no differences among the hippocampi of the healthy individuals. The confidence intervals (mean{+-} 1.96 SD) were 4169 mm''3-5911 mm''3 for volume of right side, 4097 mm''3-5940 mm''3 for volume of left side and 98-113 ms for T2 relaxation time. MTS was detected in 40 patients (55.5%): 23 cases involving the left side, 13 involving the right and 4 cases of bilateral asymmetric involvement. The 95% confidence intervals for the diagnostic validity of the results (sensitivity/specificity) were (88.8%-97.2%)/(87.6%-96.4%) for T1 volumetry, (88.8%-97.2%)(95.7%-100.3%) for FLAIR and (85.4%-96.6%)/(85.4%-96.6%) for T2 relaxometry. In 5 cases of MTS, astrophy of other extra hippocampal structures was also observed, and MTS was associated with an extra hippocampal lesion (dual pathology), especially neurona migration disorders, in 8 patients. Seventeen patients (23.5%) presented lesions without MTS (tumors, cortical dysplasias and heterotopias) and there was no MRI evidence of anomalies in 15 (21%). Twenty-five patients underwent surgical treatment: 20 with MTS (19 diagnosed according to MRI and one in whom there had been no abnormal findings), 4 with tumors and 1 with a ballooned

  12. Magnetic resonance in the diagnostic imaging study of mesial temporal sclerosis; Diagnostico por imagen con resonancia magnetica de la esclerosis temporal mesial

    Energy Technology Data Exchange (ETDEWEB)

    Pastor, E.; Sanchez, J. C.; Rodriguez, I.; Altuzarra, A.; Machado, F. [Hospital Universitario Virgen de las Nieves. Granada (Spain); Aguilar, D. [Hospital Clinico Universitario San Cecilio. Granada (Spain)

    2001-07-01

    Mesial temporal sclerosis (MTS) consists of hippocampal atrophy and gliosis and is the most common cause of temporal lobe epilepsy. The objective of the authors was to establish a magnetic resonance imaging (MRI) protocol for its diagnosis. A prospective study was carried out in 72 patients with drug resistant complex partial seizures (42 women and 30 men ranging in age from 6 to 66 year: mean: 30 years). Using a 1.5-Tesla magnet, paracoronal sections were made in hippocampi for T1-weighted inversion-recovery images and volume measurements, fluid-attenuated inversion-recovery (FLAIR) and T2 relaxometry. A control group of 30 health volunteers was included in the study. MTS was considered to be indicated by the presence of atrophy and hyperintensity in hippocampi on T2-weighted images. There were no differences among the hippocampi of the healthy individuals. The confidence intervals (mean{+-} 1.96 SD) were 4169 mm''3-5911 mm''3 for volume of right side, 4097 mm''3-5940 mm''3 for volume of left side and 98-113 ms for T2 relaxation time. MTS was detected in 40 patients (55.5%): 23 cases involving the left side, 13 involving the right and 4 cases of bilateral asymmetric involvement. The 95% confidence intervals for the diagnostic validity of the results (sensitivity/specificity) were (88.8%-97.2%)/(87.6%-96.4%) for T1 volumetry, (88.8%-97.2%)(95.7%-100.3%) for FLAIR and (85.4%-96.6%)/(85.4%-96.6%) for T2 relaxometry. In 5 cases of MTS, astrophy of other extra hippocampal structures was also observed, and MTS was associated with an extra hippocampal lesion (dual pathology), especially neurona migration disorders, in 8 patients. Seventeen patients (23.5%) presented lesions without MTS (tumors, cortical dysplasias and heterotopias) and there was no MRI evidence of anomalies in 15 (21%). Twenty-five patients underwent surgical treatment: 20 with MTS (19 diagnosed according to MRI and one in whom there had been no abnormal findings

  13. Design issues in toxicogenomics using DNA microarray experiment

    International Nuclear Information System (INIS)

    Lee, Kyoung-Mu; Kim, Ju-Han; Kang, Daehee

    2005-01-01

    The methods of toxicogenomics might be classified into omics study (e.g., genomics, proteomics, and metabolomics) and population study focusing on risk assessment and gene-environment interaction. In omics study, microarray is the most popular approach. Genes falling into several categories (e.g., xenobiotics metabolism, cell cycle control, DNA repair etc.) can be selected up to 20,000 according to a priori hypothesis. The appropriate type of samples and species should be selected in advance. Multiple doses and varied exposure durations are suggested to identify those genes clearly linked to toxic response. Microarray experiments can be affected by numerous nuisance variables including experimental designs, sample extraction, type of scanners, etc. The number of slides might be determined from the magnitude and variance of expression change, false-positive rate, and desired power. Instead, pooling samples is an alternative. Online databases on chemicals with known exposure-disease outcomes and genetic information can aid the interpretation of the normalized results. Gene function can be inferred from microarray data analyzed by bioinformatics methods such as cluster analysis. The population study often adopts hospital-based or nested case-control design. Biases in subject selection and exposure assessment should be minimized, and confounding bias should also be controlled for in stratified or multiple regression analysis. Optimal sample sizes are dependent on the statistical test for gene-to-environment or gene-to-gene interaction. The design issues addressed in this mini-review are crucial in conducting toxicogenomics study. In addition, integrative approach of exposure assessment, epidemiology, and clinical trial is required

  14. Cerebral infarction secondary to temporal lobe herniation in head trauma: a CT study

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jae Hyoung; Park, Eui Dong; Kim, Hyung Jin; Han, Jong Woo; Chung, Sung Hoon; Ha, Choong Kun; Kim, Jae Il [College of Medicine, Gyeongsang National University, Jinju (Korea, Republic of)

    1992-11-15

    Cerebral infarction is a known complication of temporal lobe herniation caused by a traumatic intracranial lesion. To ascertain the frequency, time of recognition, and influence on mortality of posttraumatic cerebral infarction secondary to temporal lobe herniation, we retrospectively reviewed brain CT scans and clinical records of 55 patients who had CT and clinical signs of temporal lobe herniation on admission date. Cerebral infarctions were recognized in seven (12.7%) patients on CT scans taken within two days after admission (mean: 1.3 days). Cerebral infarctions were in the terrtiories of the posterior cerebral artery in all seven patients, two of whom had infarctions of the anterior choroidal artery as well. Mortality (71.4%) for these seven patients was not statistically significant from that (50%) of patients without cerebral infarction admitted with the same range of Glasgow Coma Scale score. The result suggests that such cerebral infarction dose not greatly influence patient's mortality.

  15. DNA Microarrays in Comparative Genomics and Transcriptomics

    DEFF Research Database (Denmark)

    Willenbrock, Hanni

    2007-01-01

    at identifying the exact breakpoints where DNA has been gained or lost. In this thesis, three popular methods are compared and a realistic simulation model is presented for generating artificial data with known breakpoints and known DNA copy number. By using simulated data, we obtain a realistic evaluation......During the past few years, innovations in the DNA sequencing technology has led to an explosion in available DNA sequence information. This has revolutionized biological research and promoted the development of high throughput analysis methods that can take advantage of the vast amount of sequence...... data. For this, the DNA microarray technology has gained enormous popularity due to its ability to measure the presence or the activity of thousands of genes simultaneously. Microarrays for high throughput data analyses are not limited to a few organisms but may be applied to everything from bacteria...

  16. Immobilization Techniques for Microarray: Challenges and Applications

    Directory of Open Access Journals (Sweden)

    Satish Balasaheb Nimse

    2014-11-01

    Full Text Available The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.

  17. Facilitating RNA structure prediction with microarrays.

    Science.gov (United States)

    Kierzek, Elzbieta; Kierzek, Ryszard; Turner, Douglas H; Catrina, Irina E

    2006-01-17

    Determining RNA secondary structure is important for understanding structure-function relationships and identifying potential drug targets. This paper reports the use of microarrays with heptamer 2'-O-methyl oligoribonucleotides to probe the secondary structure of an RNA and thereby improve the prediction of that secondary structure. When experimental constraints from hybridization results are added to a free-energy minimization algorithm, the prediction of the secondary structure of Escherichia coli 5S rRNA improves from 27 to 92% of the known canonical base pairs. Optimization of buffer conditions for hybridization and application of 2'-O-methyl-2-thiouridine to enhance binding and improve discrimination between AU and GU pairs are also described. The results suggest that probing RNA with oligonucleotide microarrays can facilitate determination of secondary structure.

  18. Plasmonically amplified fluorescence bioassay with microarray format

    Science.gov (United States)

    Gogalic, S.; Hageneder, S.; Ctortecka, C.; Bauch, M.; Khan, I.; Preininger, Claudia; Sauer, U.; Dostalek, J.

    2015-05-01

    Plasmonic amplification of fluorescence signal in bioassays with microarray detection format is reported. A crossed relief diffraction grating was designed to couple an excitation laser beam to surface plasmons at the wavelength overlapping with the absorption and emission bands of fluorophore Dy647 that was used as a label. The surface of periodically corrugated sensor chip was coated with surface plasmon-supporting gold layer and a thin SU8 polymer film carrying epoxy groups. These groups were employed for the covalent immobilization of capture antibodies at arrays of spots. The plasmonic amplification of fluorescence signal on the developed microarray chip was tested by using interleukin 8 sandwich immunoassay. The readout was performed ex situ after drying the chip by using a commercial scanner with high numerical aperture collecting lens. Obtained results reveal the enhancement of fluorescence signal by a factor of 5 when compared to a regular glass chip.

  19. Familiarity and recollection vs representational models of medial temporal lobe structures: A single-case study.

    Science.gov (United States)

    Lacot, Emilie; Vautier, Stéphane; Kőhler, Stefan; Pariente, Jérémie; Martin, Chris B; Puel, Michèle; Lotterie, Jean-Albert; Barbeau, Emmanuel J

    2017-09-01

    Although it is known that medial temporal lobe (MTL) structures support declarative memory, the fact these structures have different architectonics and circuitry suggests they may also play different functional roles. Selective lesions of MTL structures offer an opportunity to understand these roles. We report, in this study, on JMG, a patient who presents highly unusual lesions that completely affected all MTL structures except for the right hippocampus and parts of neighbouring medial parahippocampal cortex. We first demonstrate that JMG shows preserved recall for visual material on 5 experimental tasks. This finding suggests that his right hippocampus is functional, even though it appears largely disconnected from most of its MTL afferents. In contrast, JMG performed very poorly, as compared to control subjects, on 7 tasks of visual recognition memory for single items. Although he sometimes performed above chance, neither familiarity nor recollection appeared fully preserved. These results indicate that extrahippocampal structures, damaged bilaterally in JMG, perform critical operations for item recognition; and that the hippocampus cannot take over that role, including recollection, when these structures are largely damaged. Finally, in a set of 3 recognition memory tasks with scenes as stimuli, JMG performed at the level of control participants and obtained normal indices of familiarity and recollection. Overall, our findings suggest that the right hippocampus and remnants of parahippocampal cortex can support recognition memory for scenes in the absence of preserved item-recognition memory. The patterns of dissociations, which we report in the present study, provide support for a representational account of the functional organization of MTL structures. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Temporal changes in cortical activation during conditioned pain modulation (CPM), a LORETA study.

    Science.gov (United States)

    Moont, Ruth; Crispel, Yonatan; Lev, Rina; Pud, Dorit; Yarnitsky, David

    2011-07-01

    For most healthy subjects, both subjective pain ratings and pain-evoked potentials are attenuated under conditioned pain modulation (CPM; formerly termed diffuse noxious inhibitory controls, or DNIC). Although essentially spinal-bulbar, this inhibition is under cortical control. This is the first study to observe temporal as well as spatial changes in cortical activations under CPM. Specifically, we aimed to investigate the interplay of areas involved in the perception and processing of pain and those involved in controlling descending inhibition. We examined brief consecutive poststimulus time windows of 50 ms using a method of source-localization from pain evoked potentials, sLORETA. This enabled determination of dynamic changes in localized cortical generators evoked by phasic noxious heat stimuli to the left volar forearm in healthy young males, with and without conditioning hot-water pain to the right hand. We found a CPM effect characterized by an initial increased activation in the orbitofrontal cortex (OFC) and amygdala at 250-300 ms poststimulus, which was correlated with the extent of psychophysical pain reduction. This was followed by reduced activations in the primary and secondary somatosensory cortices, supplementary motor area, posterior insula, and anterior cingulate cortex from 400 ms poststimulus. Our findings show that the prefrontal pain-controlling areas of OFC and amygdala increase their activity in parallel with subjective pain reduction under CPM, and that this increased activity occurs prior to reductions in activations of the pain sensory areas. In conclusion, achieving pain inhibition by the CPM process seems to be under control of the OFC and the amygdala. Copyright © 2011 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.

  1. Predictors of meaningful improvement in quality of life after temporal lobe epilepsy surgery: A prospective study.

    Science.gov (United States)

    Pauli, Carla; Schwarzbold, Marcelo Liborio; Diaz, Alexandre Paim; de Oliveira Thais, Maria Emilia Rodrigues; Kondageski, Charles; Linhares, Marcelo Neves; Guarnieri, Ricardo; de Lemos Zingano, Bianca; Ben, Juliana; Nunes, Jean Costa; Markowitsch, Hans Joachim; Wolf, Peter; Wiebe, Samuel; Lin, Katia; Walz, Roger

    2017-05-01

    To investigate prospectively the independent predictors of a minimum clinically important change (MCIC) in quality of life (QOL) after anterior temporal lobectomy (ATL) for drug-resistant mesial temporal lobe epilepsy related to hippocampal sclerosis (MTLE-HS) in Brazilian patients. Multiple binary logistic regression analysis was performed to identify the clinical, demographic, radiologic, and electrophysiologic variables independently associated with MCIC in the Quality of Life in Epilepsy-31 Inventory (QOLIE-31) overall score 1 year after ATL in 77 consecutive patients with unilateral MTLE-HS. The overall QOLIE-31 score and all its subscale scores increased significantly (p Epilepsy.

  2. Geiger mode avalanche photodiodes for microarray systems

    Science.gov (United States)

    Phelan, Don; Jackson, Carl; Redfern, R. Michael; Morrison, Alan P.; Mathewson, Alan

    2002-06-01

    New Geiger Mode Avalanche Photodiodes (GM-APD) have been designed and characterized specifically for use in microarray systems. Critical parameters such as excess reverse bias voltage, hold-off time and optimum operating temperature have been experimentally determined for these photon-counting devices. The photon detection probability, dark count rate and afterpulsing probability have been measured under different operating conditions. An active- quench circuit (AQC) is presented for operating these GM- APDs. This circuit is relatively simple, robust and has such benefits as reducing average power dissipation and afterpulsing. Arrays of these GM-APDs have already been designed and together with AQCs open up the possibility of having a solid-state microarray detector that enables parallel analysis on a single chip. Another advantage of these GM-APDs over current technology is their low voltage CMOS compatibility which could allow for the fabrication of an AQC on the same device. Small are detectors have already been employed in the time-resolved detection of fluorescence from labeled proteins. It is envisaged that operating these new GM-APDs with this active-quench circuit will have numerous applications for the detection of fluorescence in microarray systems.

  3. Temporal pole signal abnormality on MR imaging in temporal lobe epilepsy with hippocampal sclerosis: a fluid-attenuated inversion-recovery study; Anormalidade de sinal na imagem por RM do polo temporal na epilepsia do lobo temporal com esclerose hipocampal: um estudo pela sequencia inversao recuperacao com supressao da agua livre (FLAIR)

    Energy Technology Data Exchange (ETDEWEB)

    Carrete Junior, Henrique; Abdala, Nitamar; Szjenfeld, Jacob; Nogueira, Roberto Gomes [Universidade Federal de Sao Paulo (UNIFESP-EPM), Sao Paulo, SP (Brazil). Dept. de Diagnostico por Imagem; Lin, Katia; Caboclo, Luis Otavio; Centeno, Ricardo Silva; Sakamoto, Americo Ceiki; Yacubian, Elza Marcia Targas [Universidade Federal de Sao Paulo (UNIFESP-EPM), Sao Paulo, SP (Brazil). Dept. de Neurologia e Neurocirurgia

    2007-09-15

    Objective: To determine the frequency and regional involvement of temporal pole signal abnormality (TPA) in patients with hippocampal sclerosis (HS) using fluid-attenuated inversion-recovery (FLAIR) MR imaging, and to correlate this feature with history. Method: Coronal FLAIR images of the temporal pole were assessed in 120 patients with HS and in 30 normal subjects, to evaluate gray-white matter demarcation. Results: Ninety (75%) of 120 patients had associated TPA. The HS side made difference regarding the presence of TPA, with a left side prevalence (p=0.04, {chi}{sup 2} test). The anteromedial zone of temporal pole was affected in 27 (30%) out of 90 patients. In 63 (70%) patients the lateral zone were also affected. Patients with TPA were younger at seizure onset (p=0.018), but without association with duration of epilepsy. Conclusion: Our FLAIR study show temporal pole signal abnormality in 3/4 of patients with HS, mainly seen on the anteromedial region, with a larger prevalence when the left hippocampus was involved. (author)

  4. The PowerAtlas: a power and sample size atlas for microarray experimental design and research

    Directory of Open Access Journals (Sweden)

    Wang Jelai

    2006-02-01

    Full Text Available Abstract Background Microarrays permit biologists to simultaneously measure the mRNA abundance of thousands of genes. An important issue facing investigators planning microarray experiments is how to estimate the sample size required for good statistical power. What is the projected sample size or number of replicate chips needed to address the multiple hypotheses with acceptable accuracy? Statistical methods exist for calculating power based upon a single hypothesis, using estimates of the variability in data from pilot studies. There is, however, a need for methods to estimate power and/or required sample sizes in situations where multiple hypotheses are being tested, such as in microarray experiments. In addition, investigators frequently do not have pilot data to estimate the sample sizes required for microarray studies. Results To address this challenge, we have developed a Microrarray PowerAtlas 1. The atlas enables estimation of statistical power by allowing investigators to appropriately plan studies by building upon previous studies that have similar experimental characteristics. Currently, there are sample sizes and power estimates based on 632 experiments from Gene Expression Omnibus (GEO. The PowerAtlas also permits investigators to upload their own pilot data and derive power and sample size estimates from these data. This resource will be updated regularly with new datasets from GEO and other databases such as The Nottingham Arabidopsis Stock Center (NASC. Conclusion This resource provides a valuable tool for investigators who are planning efficient microarray studies and estimating required sample sizes.

  5. Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient.

    Science.gov (United States)

    Yao, Jianchao; Chang, Chunqi; Salmi, Mari L; Hung, Yeung Sam; Loraine, Ann; Roux, Stanley J

    2008-06-18

    Currently, clustering with some form of correlation coefficient as the gene similarity metric has become a popular method for profiling genomic data. The Pearson correlation coefficient and the standard deviation (SD)-weighted correlation coefficient are the two most widely-used correlations as the similarity metrics in clustering microarray data. However, these two correlations are not optimal for analyzing replicated microarray data generated by most laboratories. An effective correlation coefficient is needed to provide statistically sufficient analysis of replicated microarray data. In this study, we describe a novel correlation coefficient, shrinkage correlation coefficient (SCC), that fully exploits the similarity between the replicated microarray experimental samples. The methodology considers both the number of replicates and the variance within each experimental group in clustering expression data, and provides a robust statistical estimation of the error of replicated microarray data. The value of SCC is revealed by its comparison with two other correlation coefficients that are currently the most widely-used (Pearson correlation coefficient and SD-weighted correlation coefficient) using statistical measures on both synthetic expression data as well as real gene expression data from Saccharomyces cerevisiae. Two leading clustering methods, hierarchical and k-means clustering were applied for the comparison. The comparison indicated that using SCC achieves better clustering performance. Applying SCC-based hierarchical clustering to the replicated microarray data obtained from germinating spores of the fern Ceratopteris richardii, we discovered two clusters of genes with shared expression patterns during spore germination. Functional analysis suggested that some of the genetic mechanisms that control germination in such diverse plant lineages as mosses and angiosperms are also conserved among ferns. This study shows that SCC is an alternative to the Pearson

  6. A prospective study of the immunophenotype and temporal changes in the histologic lesions of canine demodicosis.

    Science.gov (United States)

    Caswell, J L; Yager, J A; Parker, W M; Moore, P F

    1997-07-01

    Mural folliculitis is a consistent histologic lesion of canine demodicosis. The objective of this study was to describe the immunophenotype and to evaluate temporal changes in histologic lesions of demodicosis during the course of therapy. Five dogs with demodicosis were examined and biopsied biweekly for up to 14 weeks; three dogs were evaluated once only. Lymphocyte subsets infiltrating the lesions were quantified using immunohistochemistry to detect CD3, CD21, CD4, and CD8 antigens. Lymphocyte subsets in blood were analyzed from four dogs using flow cytometry. Mural folliculitis was always present during clinically active disease. In contrast, following resolution of clinical lesions, perifolliculitis and/or perifollicular granulomas were present but mural folliculitis was absent. Most lymphocytes infiltrating the follicular epithelium in lesions of mural folliculitis were CD3+ and CD8+; the ratio of CD4+ :CD8+ cells in this epithelium was 0.032. In contrast, the perifollicular dermis contained approximately equal numbers of CD4+ cells and CD8+ cells, with slightly fewer CD21+B cells. In peripheral blood, the ratio of CD4+:CD8+ lymphocytes was reduced and the percentage of CD8+ cells was increased in three of four dogs. These results indicate that mural folliculitis is a consistent lesion of clinically active canine demodicosis and is characterized by infiltration of the follicular epithelium by CD3+ CD8+ T lymphocytes. These lymphocytes are cytotoxic T cells, which may mediate the injury to the follicular epithelium in demodicosis. Alternatively, CD8+ T cells may play a role in resistance to Demodex canis infection or may represent a deleterious immune response in dogs that develop demodicosis.

  7. Sad facial cues inhibit temporal attention: evidence from an event-related potential study.

    Science.gov (United States)

    Kong, Xianxian; Chen, Xiaoqiang; Tan, Bo; Zhao, Dandan; Jin, Zhenlan; Li, Ling

    2013-06-19

    We examined the influence of different emotional cues (happy or sad) on temporal attention (short or long interval) using behavioral as well as event-related potential recordings during a Stroop task. Emotional stimuli cued short and long time intervals, inducing 'sad-short', 'sad-long', 'happy-short', and 'happy-long' conditions. Following the intervals, participants performed a numeric Stroop task. Behavioral results showed the temporal attention effects in the sad-long, happy-long, and happy-short conditions, in which valid cues quickened the reaction times, but not in the sad-short condition. N2 event-related potential components showed sad cues to have decreased activity for short intervals compared with long intervals, whereas happy cues did not. Taken together, these findings provide evidence for different modulation of sad and happy facial cues on temporal attention. Furthermore, sad cues inhibit temporal attention, resulting in longer reaction time and decreased neural activity in the short interval by diverting more attentional resources.

  8. Apolipoprotein E in Temporal Lobe Epilepsy: A Case-Control Study

    Directory of Open Access Journals (Sweden)

    Amit Kumar

    2006-01-01

    Full Text Available Purpose: To investigate the relationship of apolipoprotein E (apoE genotype, plasma levels of apoE and lipids in temporal lobe epilepsy (TLE patients in Asian Indians. Status of plasma levels of Apo E in epilepsy patients has not been reported till date.

  9. The time course of temporal preparation in an applied setting: a study of gaming behavior

    NARCIS (Netherlands)

    Los, S.A.; Hoorn, J.F.; Grin, M.; van den Burg, E.

    2013-01-01

    We examined the time course of temporal preparation in the practice of computer gaming. Participants held an infrared rifle to shoot animated figures ("terrorists") that appeared from an elevator that opened briefly after the sound of a bell. The sound was either loud or soft and the interval

  10. Classification of prostate cancer grade using temporal ultrasound: in vivo feasibility study

    Science.gov (United States)

    Ghavidel, Sahar; Imani, Farhad; Khallaghi, Siavash; Gibson, Eli; Khojaste, Amir; Gaed, Mena; Moussa, Madeleine; Gomez, Jose A.; Siemens, D. Robert; Leveridge, Michael; Chang, Silvia; Fenster, Aaron; Ward, Aaron D.; Abolmaesumi, Purang; Mousavi, Parvin

    2016-03-01

    Temporal ultrasound has been shown to have high classification accuracy in differentiating cancer from benign tissue. In this paper, we extend the temporal ultrasound method to classify lower grade Prostate Cancer (PCa) from all other grades. We use a group of nine patients with mostly lower grade PCa, where cancerous regions are also limited. A critical challenge is to train a classifier with limited aggressive cancerous tissue compared to low grade cancerous tissue. To resolve the problem of imbalanced data, we use Synthetic Minority Oversampling Technique (SMOTE) to generate synthetic samples for the minority class. We calculate spectral features of temporal ultrasound data and perform feature selection using Random Forests. In leave-one-patient-out cross-validation strategy, an area under receiver operating characteristic curve (AUC) of 0.74 is achieved with overall sensitivity and specificity of 70%. Using an unsupervised learning approach prior to proposed method improves sensitivity and AUC to 80% and 0.79. This work represents promising results to classify lower and higher grade PCa with limited cancerous training samples, using temporal ultrasound.

  11. ASPECTUAL INFLUENCE ON TEMPORAL RELATIONS: A CASE STUDY OF THE EXPERIENTIAL GUO IN MANDARINE

    Directory of Open Access Journals (Sweden)

    Jiun-Shiung Wu

    2009-12-01

    Full Text Available This paper examines how the temporal relation between a clause containing the experiential guo and an adjacent clause is determined. Mandarin is a language not morphologically marked for tenses (e.g., Lin 2006, and therefore, tenses cannot help in determining temporal relations in Mandarin. However, Mandarin has a rich aspectual system. This paper argues that the experiential guo indirectly influences temporal relations via rhetorical relations by either specifying a default rhetorical relation, or by constraining the circumstances under which a certain rhetorical relation can connect a clause with guo to an adjacent clause. This paper also argues that the default rhetorical relation and the constraints are determined by the aspectual properties of the experiential marker. Other information, such as discourse connectors, lexical information, etc., can override the default rhetorical relation indicated by guo and specifies a rhetorical relation. Therefore, this paper concludes that in Mandarin aspect markers can indirectly affect temporal relations by means of rhetorical relations, a result consistent with Wu’s (2005b paper on the perfective marker le in Mandarin, and Wu’s (2007b, 2004 work on the progressive marker zai and the durative marker zhe.

  12. Temporal lobe epilepsy with varying severity: MRI study of 222 patients

    International Nuclear Information System (INIS)

    Lehericy, S.; Hasboun, D.; Dormont, D.; Marsault, C.; Semah, F.; Baulac, M.; Clemenceau, S.; Granat, O.

    1997-01-01

    MRI was performed in 222 consecutive adult patients with temporal lobe epilepsy of varying severity from January 1991 to May 1993. The diagnosis of hippocampal sclerosis was established visually by three independent observers. The accuracy of visual assessment of hippocampal asymmetry was compared with volumetric measurements. Neuropathological correlations were obtained in 63 patients with refractory seizures. Temporal lobe abnormalities were observed in 180 patients (81 %) as follows: hippocampal sclerosis in 122 (55 %); developmental abnormalities in 16 (7.2 %); tumours in 15 (6.8 %); scars in 11 (5 %); cavernous angiomas in 10 (4.5 %); miscellaneous lesions in 6. MRI was normal or showed unrelated changes in 42 patients (19 %). Visual assessment correctly lateralised hippocampal sclerosis in 79 of the 84 patients measured (94 %). Temporal lobectomy confirmed the MRI data (side and aetiology) in all 63 operated patients. Patients with normal MRI had an older age of seizure onset and were more often drug-responsive than patients with hippocampal sclerosis. MRI showed temporal lobe abnormalities in 81 % of epileptic patients with varying severity with good neuropathological correlation. Patients with normal MRI had a less severe form of the disease. (orig.)

  13. Temporal evolution of event-related desynchronization in acute stroke: A pilot study

    NARCIS (Netherlands)

    Tangwiriyasakul, Chayanin; Verhagen, Rens; Rutten, Wim; van Putten, Michel Johannes Antonius Maria

    2014-01-01

    Objective Assessment of event-related desynchronization (ERD) may assist in predicting recovery from stroke and rehabilitation, for instance in BCI applications. Here, we explore the temporal evolution of ERD during stroke recovery. Methods Ten stroke patients and eleven healthy controls were

  14. Five-Year Neuropsychological Outcome after Stereotactic Radiofrequency Amygdalohippocampectomy for Mesial Temporal Lobe Epilepsy: Longitudinal Study

    Czech Academy of Sciences Publication Activity Database

    Krámská, L.; Vojtěch, Z.; Lukavský, Jiří; Stará, M.; Malíková, H.

    2017-01-01

    Roč. 95, č. 3 (2017), s. 149-157 ISSN 1011-6125 Institutional support: RVO:68081740 Keywords : Cognitive outcome * Memory * Temporal lobe epilepsy * Stereotactic surgery Subject RIV: FH - Neurology OBOR OECD: Psychology (including human - machine relations) Impact factor: 1.692, year: 2016

  15. Children with a History of SLI Show Reduced Sensitivity to Audiovisual Temporal Asynchrony: An ERP Study

    Science.gov (United States)

    Kaganovich, Natalya; Schumaker, Jennifer; Leonard, Laurence B.; Gustafson, Dana; Macias, Danielle

    2014-01-01

    Purpose: The authors examined whether school-age children with a history of specific language impairment (H-SLI), their peers with typical development (TD), and adults differ in sensitivity to audiovisual temporal asynchrony and whether such difference stems from the sensory encoding of audiovisual information. Method: Fifteen H-SLI children, 15…

  16. Advances in temporal logic

    CERN Document Server

    Fisher, Michael; Gabbay, Dov; Gough, Graham

    2000-01-01

    Time is a fascinating subject that has captured mankind's imagination from ancient times to the present. It has been, and continues to be studied across a wide range of disciplines, from the natural sciences to philosophy and logic. More than two decades ago, Pnueli in a seminal work showed the value of temporal logic in the specification and verification of computer programs. Today, a strong, vibrant international research community exists in the broad community of computer science and AI. This volume presents a number of articles from leading researchers containing state-of-the-art results in such areas as pure temporal/modal logic, specification and verification, temporal databases, temporal aspects in AI, tense and aspect in natural language, and temporal theorem proving. Earlier versions of some of the articles were given at the most recent International Conference on Temporal Logic, University of Manchester, UK. Readership: Any student of the area - postgraduate, postdoctoral or even research professor ...

  17. Glycoprofiling of Early Gastric Cancer Using Lectin Microarray Technology.

    Science.gov (United States)

    Li, Taijie; Mo, Cuiju; Qin, Xue; Li, Shan; Liu, Yinkun; Liu, Zhiming

    2018-01-01

    Recently, studies have reported that protein glycosylation plays an important role in the occurrence and development of cancer. Gastric cancer is a common cancer with high morbidity and mortality owing to most gastric cancers are discovered only at an advanced stage. Here, we aim to discover novel specific serum glycanbased biomarkers for gastric cancer. A lectin microarray with 50 kinds of tumor-associated lectin was used to detect the glycan profiles of serum samples between early gastric cancer and healthy controls. Then lectin blot was performed to validate the differences. The result of the lectin microarray showed that the signal intensities of 13 lectins showed significant differences between the healthy controls and early gastric cancer. Compared to the healthy, the normalized fluorescent intensities of the lectins PWA, LEL, and STL were significantly increased, and it implied that their specifically recognized GlcNAc showed an especially elevated expression in early gastric cancer. Moreover, the binding affinity of the lectins EEL, RCA-II, RCA-I, VAL, DSA, PHA-L, UEA, and CAL were higher in the early gastric cancer than in healthy controls. These glycan structures containing GalNAc, terminal Galβ 1-4 GlcNAc, Tri/tetraantennary N-glycan, β-1, 6GlcNAc branching structure, α-linked fucose residues, and Tn antigen were elevated in gastric cancer. While the two lectins CFL GNL reduced their binding ability. In addition, their specifically recognized N-acetyl-D-galactosamine structure and (α-1,3) mannose residues were decreased in early gastric cancer. Furthermore, lectin blot results of LEL, STL, PHA-L, RCA-I were consistent with the results of the lectin microarray. The findings of our study clarify the specific alterations for glycosylation during the pathogenesis of gastric cancer. The specific high expression of GlcNAc structure may act as a potential early diagnostic marker for gastric cancer.

  18. Automatic temporal expectancy: a high-density event-related potential study.

    Directory of Open Access Journals (Sweden)

    Giovanni Mento

    Full Text Available How we compute time is not fully understood. Questions include whether an automatic brain mechanism is engaged in temporally regular environmental structure in order to anticipate events, and whether this can be dissociated from task-related processes, including response preparation, selection and execution. To investigate these issues, a passive temporal oddball task requiring neither time-based motor response nor explicit decision was specifically designed and delivered to participants during high-density, event-related potentials recording. Participants were presented with pairs of audiovisual stimuli (S1 and S2 interspersed with an Inter-Stimulus Interval (ISI that was manipulated according to an oddball probabilistic distribution. In the standard condition (70% of trials, the ISI lasted 1,500 ms, while in the two alternative, deviant conditions (15% each, it lasted 2,500 and 3,000 ms. The passive over-exposition to the standard ISI drove participants to automatically and progressively create an implicit temporal expectation of S2 onset, reflected by the time course of the Contingent Negative Variation response, which always peaked in correspondence to the point of S2 maximum expectation and afterwards inverted in polarity towards the baseline. Brain source analysis of S1- and ISI-related ERP activity revealed activation of sensorial cortical areas and the supplementary motor area (SMA, respectively. In particular, since the SMA time course synchronised with standard ISI, we suggest that this area is the major cortical generator of the temporal CNV reflecting an automatic, action-independent mechanism underlying temporal expectancy.

  19. Cognitive Functioning in Temporal Lobe Epilepsy: A BOLD-fMRI Study.

    Science.gov (United States)

    Guo, Lili; Bai, Genji; Zhang, Hui; Lu, Daoyan; Zheng, Jiyong; Xu, Gang

    2017-12-01

    We aimed to analyze the association between resting-state functional magnetic resonance imaging (re-fMRI) and cognitive function (including language, executive, and memory functions) in temporal lobe epilepsy (TLE) patients, which will help to explore the mechanism of brain function in patients. 15 TLE patients and 15 non-TLE patients were recruited. All subjects underwent neuropsychological testing and memory functional evaluation. Changes in verbal intelligence quotient (VIQ), performance intelligence quotient (PIQ), full intelligence quotient (FIQ), and memory quotient (MQ) were compared between two groups. Re-fMRI data were also collected from two groups to evaluate these changes. Each individual score of neuropsychological testing and memory functional evaluation were higher in control group, which was statistically different (all P temporal gyrus back, right superior temporal gyrus, left cerebellum, left angular gyrus, left wedge anterior lobe, and left central back; while the negatively activated brain regions were left prefrontal, right cerebellum, right corner back, and right anterior cingulate gyrus. During the language task, the activated brain regions of the TLE patients were right prefrontal lobe, the lateral temporal gyri, the left cerebellum, left cornu laterale gyrus, left precuneus, and the left postcentral gyrus, whereas the negatively activated brain areas were the left prefrontal cortex, the right cerebellum, right cornu laterale gyrus, and the right anterior cingulate gyrus. During the executive task, epilepsy patients showed activation difference in right prefrontal and right frontal lobe and right brain, left superior temporal gyrus, and right cerebellum anterior lobe compared with the control group; no negatively activated differences in brain areas. During the memory task, the difference lay in bilateral anterior cingulate gyrus and bilateral wedge anterior lobe while the negatively activated brain areas were the left inferior frontal

  20. Visual and auditory socio-cognitive perception in unilateral temporal lobe epilepsy in children and adolescents: a prospective controlled study.

    Science.gov (United States)

    Laurent, Agathe; Arzimanoglou, Alexis; Panagiotakaki, Eleni; Sfaello, Ignacio; Kahane, Philippe; Ryvlin, Philippe; Hirsch, Edouard; de Schonen, Scania

    2014-12-01

    A high rate of abnormal social behavioural traits or perceptual deficits is observed in children with unilateral temporal lobe epilepsy. In the present study, perception of auditory and visual social signals, carried by faces and voices, was evaluated in children or adolescents with temporal lobe epilepsy. We prospectively investigated a sample of 62 children with focal non-idiopathic epilepsy early in the course of the disorder. The present analysis included 39 children with a confirmed diagnosis of temporal lobe epilepsy. Control participants (72), distributed across 10 age groups, served as a control group. Our socio-perceptual evaluation protocol comprised three socio-visual tasks (face identity, facial emotion and gaze direction recognition), two socio-auditory tasks (voice identity and emotional prosody recognition), and three control tasks (lip reading, geometrical pattern and linguistic intonation recognition). All 39 patients also benefited from a neuropsychological examination. As a group, children with temporal lobe epilepsy performed at a significantly lower level compared to the control group with regards to recognition of facial identity, direction of eye gaze, and emotional facial expressions. We found no relationship between the type of visual deficit and age at first seizure, duration of epilepsy, or the epilepsy-affected cerebral hemisphere. Deficits in socio-perceptual tasks could be found independently of the presence of deficits in visual or auditory episodic memory, visual non-facial pattern processing (control tasks), or speech perception. A normal FSIQ did not exempt some of the patients from an underlying deficit in some of the socio-perceptual tasks. Temporal lobe epilepsy not only impairs development of emotion recognition, but can also impair development of perception of other socio-perceptual signals in children with or without intellectual deficiency. Prospective studies need to be designed to evaluate the results of appropriate re

  1. Spatial distribution and temporal changes of pulmonary thallium uptake in myocardial perfusion studies

    International Nuclear Information System (INIS)

    Mannting, F.

    1990-01-01

    Spatial distribution and temporal changes in pulmonary thallium (Tl) uptake were assessed in 24 normal subjects and 35 patients with coronary artery disease (CAD). In studies carried out directly after stress and 3 h later, pulmonary Tl uptake was assessed as body surface area corrected absolute pulmonary uptake in the upper, middle and lower right lung regions, and in the total right lung and upper left lung. Pulmonary/myocardial (PM) uptake ratios for these 5 regions were calculated by mean pulmonary/mean background-corrected myocardial uptake. Additionally, wash-out was assessed for each region and for the myocardium. In normal subjects, the inital pulmonary Tl uptake, the PM ratios and Tl wash-out were greater in the lower lung regions than in the upper. In the late studies, no significant differences in Tl content or PM ratios were found among the regions. In patients with CAD, initial pulmonary Tl putake and PM ratios were greater in the lower than in the upper regions, and higher than for the normal subjects in all pulmonary regions (P<0.001). Tl wash-out was significantly higher in the low and middle regions versus the upper region (P<0.001) and higher in all regions than in normal subjects (P<0.001). In the late studies no significant differences in Tl content or PM ratios were found between any pulmonary regions. Pulmonary Tl content was, in all regions, higher in CAD than in normal subjects (P<0.01), as were the PM ratios (P<0.001). In conclusion, in normal subjects as well as in patients with CAD, pulmonary Tl uptake is greatest in the lower lung regions. Absolute pulmonary Tl uptake, PM ratios and pulmonary wash-out are greater in all lung regions in patients with CAD. Lower myocardial uptake may be the more important factor in producting the increased PM ratios in patients with CAD. Pulmonary redistribution is complete after 3-4 h. These characteristics strongly affect pulmonary Tl uptake ratios and wash-out assessments. (orig.)

  2. Determinants and Temporal Trends of Perfluoroalkyl Substances in Pregnant Women: The Hokkaido Study on Environment and Children’s Health

    OpenAIRE

    Meng-Shan Tsai; Chihiro Miyashita; Atsuko Araki; Sachiko Itoh; Yu Ait Bamai; Houman Goudarzi; Emiko Okada; Ikuko Kashino; Hideyuki Matsuura; Reiko Kishi

    2018-01-01

    Perfluoroalkyl substances (PFAS) are persistent bio-accumulative chemicals that impact the health of pregnant women and their children. PFAS derive from environmental and consumer products, which depend on human lifestyle, socioeconomic characteristics, and time variation. Here, we aimed to explore the temporal trends of PFAS in pregnant women and the characteristics related to maternal PFAS concentration. Our study is part of the Hokkaido Study on Environment and Children’s Health, the Hokka...

  3. Quantitative inference of dynamic regulatory pathways via microarray data

    Directory of Open Access Journals (Sweden)

    Chen Bor-Sen

    2005-03-01

    Full Text Available Abstract Background The cellular signaling pathway (network is one of the main topics of organismic investigations. The intracellular interactions between genes in a signaling pathway are considered as the foundation of functional genomics. Thus, what genes and how much they influence each other through transcriptional binding or physical interactions are essential problems. Under the synchronous measures of gene expression via a microarray chip, an amount of dynamic information is embedded and remains to be discovered. Using a systematically dynamic modeling approach, we explore the causal relationship among genes in cellular signaling pathways from the system biology approach. Results In this study, a second-order dynamic model is developed to describe the regulatory mechanism of a target gene from the upstream causality point of view. From the expression profile and dynamic model of a target gene, we can estimate its upstream regulatory function. According to this upstream regulatory function, we would deduce the upstream regulatory genes with their regulatory abilities and activation delays, and then link up a regulatory pathway. Iteratively, these regulatory genes are considered as target genes to trace back their upstream regulatory genes. Then we could construct the regulatory pathway (or network to the genome wide. In short, we can infer the genetic regulatory pathways from gene-expression profiles quantitatively, which can confirm some doubted paths or seek some unknown paths in a regulatory pathway (network. Finally, the proposed approach is validated by randomly reshuffling the time order of microarray data. Conclusion We focus our algorithm on the inference of regulatory abilities of the identified causal genes, and how much delay before they regulate the downstream genes. With this information, a regulatory pathway would be built up using microarray data. In the present study, two signaling pathways, i.e. circadian regulatory

  4. A probabilistic framework for microarray data analysis: fundamental probability models and statistical inference.

    Science.gov (United States)

    Ogunnaike, Babatunde A; Gelmi, Claudio A; Edwards, Jeremy S

    2010-05-21

    Gene expression studies generate large quantities of data with the defining characteristic that the number of genes (whose expression profiles are to be determined) exceed the number of available replicates by several orders of magnitude. Standard spot-by-spot analysis still seeks to extract useful information for each gene on the basis of the number of available replicates, and thus plays to the weakness of microarrays. On the other hand, because of the data volume, treating the entire data set as an ensemble, and developing theoretical distributions for these ensembles provides a framework that plays instead to the strength of microarrays. We present theoretical results that under reasonable assumptions, the distribution of microarray intensities follows the Gamma model, with the biological interpretations of the model parameters emerging naturally. We subsequently establish that for each microarray data set, the fractional intensities can be represented as a mixture of Beta densities, and develop a procedure for using these results to draw statistical inference regarding differential gene expression. We illustrate the results with experimental data from gene expression studies on Deinococcus radiodurans following DNA damage using cDNA microarrays. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  5. Assessing the Clinical Utility of SNP Microarray for Prader-Willi Syndrome due to Uniparental Disomy.

    Science.gov (United States)

    Santoro, Stephanie L; Hashimoto, Sayaka; McKinney, Aimee; Mihalic Mosher, Theresa; Pyatt, Robert; Reshmi, Shalini C; Astbury, Caroline; Hickey, Scott E

    2017-01-01

    Maternal uniparental disomy (UPD) 15 is one of the molecular causes of Prader-Willi syndrome (PWS), a multisystem disorder which presents with neonatal hypotonia and feeding difficulty. Current diagnostic algorithms differ regarding the use of SNP microarray to detect PWS. We retrospectively examined the frequency with which SNP microarray could identify regions of homozygosity (ROH) in patients with PWS. We determined that 7/12 (58%) patients with previously confirmed PWS by methylation analysis and microsatellite-positive UPD studies had ROH (>10 Mb) by SNP microarray. Additional assessment of 5,000 clinical microarrays, performed from 2013 to present, determined that only a single case of ROH for chromosome 15 was not caused by an imprinting disorder or identity by descent. We observed that ROH for chromosome 15 is rarely incidental and strongly associated with hypotonic infants having features of PWS. Although UPD microsatellite studies remain essential to definitively establish the presence of UPD, SNP microarray has important utility in the timely diagnostic algorithm for PWS. © 2017 S. Karger AG, Basel.

  6. A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy

    Directory of Open Access Journals (Sweden)

    Archer Kellie J

    2008-02-01

    Full Text Available Abstract Background With the popularity of DNA microarray technology, multiple groups of researchers have studied the gene expression of similar biological conditions. Different methods have been developed to integrate the results from various microarray studies, though most of them rely on distributional assumptions, such as the t-statistic based, mixed-effects model, or Bayesian model methods. However, often the sample size for each individual microarray experiment is small. Therefore, in this paper we present a non-parametric meta-analysis approach for combining data from independent microarray studies, and illustrate its application on two independent Affymetrix GeneChip studies that compared the gene expression of biopsies from kidney transplant recipients with chronic allograft nephropathy (CAN to those with normal functioning allograft. Results The simulation study comparing the non-parametric meta-analysis approach to a commonly used t-statistic based approach shows that the non-parametric approach has better sensitivity and specificity. For the application on the two CAN studies, we identified 309 distinct genes that expressed differently in CAN. By applying Fisher's exact test to identify enriched KEGG pathways among those genes called differentially expressed, we found 6 KEGG pathways to be over-represented among the identified genes. We used the expression measurements of the identified genes as predictors to predict the class labels for 6 additional biopsy samples, and the predicted results all conformed to their pathologist diagnosed class labels. Conclusion We present a new approach for combining data from multiple independent microarray studies. This approach is non-parametric and does not rely on any distributional assumptions. The rationale behind the approach is logically intuitive and can be easily understood by researchers not having advanced training in statistics. Some of the identified genes and pathways have been

  7. Novel evaluation metrics for sparse spatio-temporal point process hotspot predictions - a crime case study

    OpenAIRE

    Adepeju, M.; Rosser, G.; Cheng, T.

    2016-01-01

    Many physical and sociological processes are represented as discrete events in time and space. These spatio-temporal point processes are often sparse, meaning that they cannot be aggregated and treated with conventional regression models. Models based on the point process framework may be employed instead for prediction purposes. Evaluating the predictive performance of these models poses a unique challenge, as the same sparseness prevents the use of popular measures such as the root mean squ...

  8. The Executive Functions in Frontal and Temporal Lobes: A Flanker Task Intracerebral Recording Study

    Czech Academy of Sciences Publication Activity Database

    Rusnáková, S.; Daniel, P.; Chládek, Jan; Jurák, Pavel; Rektor, I.

    2011-01-01

    Roč. 28, č. 1 (2011), s. 30-35 ISSN 0736-0258 R&D Projects: GA ČR(CZ) GA102/05/0402 Institutional research plan: CEZ:AV0Z20650511 Keywords : generator of P3 * temporal neocortex * orbitofrontal cortex * flanker test * neurocognitive network Subject RIV: FA - Cardiovascular Diseases incl. Cardiotharic Surgery Impact factor: 1.451, year: 2011

  9. The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays

    Directory of Open Access Journals (Sweden)

    Brazma Alvis

    2010-03-01

    Full Text Available Abstract Background Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Results The IronChip Evaluation Package (ICEP is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. Conclusions ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see "Additional Files" section and at: http://www.alice-dsl.net/evgeniy.vainshtein/ICEP/

  10. Integration of microarray analysis into the clinical diagnosis of hematological malignancies: How much can we improve cytogenetic testing?

    Science.gov (United States)

    Peterson, Jess F.; Aggarwal, Nidhi; Smith, Clayton A.; Gollin, Susanne M.; Surti, Urvashi; Rajkovic, Aleksandar; Swerdlow, Steven H.; Yatsenko, Svetlana A.

    2015-01-01

    Purpose To evaluate the clinical utility, diagnostic yield and rationale of integrating microarray analysis in the clinical diagnosis of hematological malignancies in comparison with classical chromosome karyotyping/fluorescence in situ hybridization (FISH). Methods G-banded chromosome analysis, FISH and microarray studies using customized CGH and CGH+SNP designs were performed on 27 samples from patients with hematological malignancies. A comprehensive comparison of the results obtained by three methods was conducted to evaluate benefits and limitations of these techniques for clinical diagnosis. Results Overall, 89.7% of chromosomal abnormalities identified by karyotyping/FISH studies were also detectable by microarray. Among 183 acquired copy number alterations (CNAs) identified by microarray, 94 were additional findings revealed in 14 cases (52%), and at least 30% of CNAs were in genomic regions of diagnostic/prognostic significance. Approximately 30% of novel alterations detected by microarray were >20 Mb in size. Balanced abnormalities were not detected by microarray; however, of the 19 apparently “balanced” rearrangements, 55% (6/11) of recurrent and 13% (1/8) of non-recurrent translocations had alterations at the breakpoints discovered by microarray. Conclusion Microarray technology enables accurate, cost-effective and time-efficient whole-genome analysis at a resolution significantly higher than that of conventional karyotyping and FISH. Array-CGH showed advantage in identification of cryptic imbalances and detection of clonal aberrations in population of non-dividing cancer cells and samples with poor chromosome morphology. The integration of microarray analysis into the cytogenetic diagnosis of hematologic malignancies has the potential to improve patient management by providing clinicians with additional disease specific and potentially clinically actionable genomic alterations. PMID:26299921

  11. Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays.

    Science.gov (United States)

    Chao, Jie; Li, Zhenhua; Li, Jing; Peng, Hongzhen; Su, Shao; Li, Qian; Zhu, Changfeng; Zuo, Xiaolei; Song, Shiping; Wang, Lianhui; Wang, Lihua

    2016-07-15

    Microarrays of biomolecules hold great promise in the fields of genomics, proteomics, and clinical assays on account of their remarkably parallel and high-throughput assay capability. However, the fluorescence detection used in most conventional DNA microarrays is still limited by sensitivity. In this study, we have demonstrated a novel universal and highly sensitive platform for fluorescent detection of sequence specific DNA at the femtomolar level by combining dextran-coated microarrays with hybridization chain reaction (HCR) signal amplification. Three-dimensional dextran matrix was covalently coated on glass surface as the scaffold to immobilize DNA recognition probes to increase the surface binding capacity and accessibility. DNA nanowire tentacles were formed on the matrix surface for efficient signal amplification by capturing multiple fluorescent molecules in a highly ordered way. By quantifying microscopic fluorescent signals, the synergetic effects of dextran and HCR greatly improved sensitivity of DNA microarrays, with a detection limit of 10fM (1×10(5) molecules). This detection assay could recognize one-base mismatch with fluorescence signals dropped down to ~20%. This cost-effective microarray platform also worked well with samples in serum and thus shows great potential for clinical diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Extended analysis of benchmark datasets for Agilent two-color microarrays

    Directory of Open Access Journals (Sweden)

    Kerr Kathleen F

    2007-10-01

    Full Text Available Abstract Background As part of its broad and ambitious mission, the MicroArray Quality Control (MAQC project reported the results of experiments using External RNA Controls (ERCs on five microarray platforms. For most platforms, several different methods of data processing were considered. However, there was no similar consideration of different methods for processing the data from the Agilent two-color platform. While this omission is understandable given the scale of the project, it can create the false impression that there is consensus about the best way to process Agilent two-color data. It is also important to consider whether ERCs are representative of all the probes on a microarray. Results A comparison of different methods of processing Agilent two-color data shows substantial differences among methods for low-intensity genes. The sensitivity and specificity for detecting differentially expressed genes varies substantially for different methods. Analysis also reveals that the ERCs in the MAQC data only span the upper half of the intensity range, and therefore cannot be representative of all genes on the microarray. Conclusion Although ERCs demonstrate good agreement between observed and expected log-ratios on the Agilent two-color platform, such an analysis is incomplete. Simple loess normalization outperformed data processing with Agilent's Feature Extraction software for accurate identification of differentially expressed genes. Results from studies using ERCs should not be over-generalized when ERCs are not representative of all probes on a microarray.

  13. Fabrication of protein microarrays for alpha fetoprotein detection by using a rapid photo-immobilization process

    Directory of Open Access Journals (Sweden)

    Sirasa Yodmongkol

    2016-03-01

    Full Text Available In this study, protein microarrays based on sandwich immunoassays are generated to quantify the amount of alpha fetoprotein (AFP in blood serum. For chip generation a mixture of capture antibody and a photoactive copolymer consisting of N,N-dimethylacrylamide (DMAA, methacryloyloxy benzophenone (MaBP, and Na-4-styrenesulfonate (SSNa was spotted onto unmodified polymethyl methacrylate (PMMA substrates. Subsequently to printing of the microarray, the polymer and protein were photochemically cross-linked and the forming, biofunctionalized hydrogels simultaneously bound to the chip surface by short UV- irradiation. The obtained biochip was incubated with AFP antigen, followed by biotinylated AFP antibody and streptavidin-Cy5 and the fluorescence signal read-out. The developed microarray biochip covers the range of AFP in serum samples such as maternal serum in the range of 5 and 100 ng/ml. The chip production process is based on a fast and simple immobilization process, which can be applied to conventional plastic surfaces. Therefore, this protein microarray production process is a promising method to fabricate biochips for AFP screening processes. Keywords: Photo-immobilization, Protein microarray, Alpha fetoprotein, Hydrogel, 3D surface, Down syndrome

  14. A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

    Directory of Open Access Journals (Sweden)

    Pląder Wojciech

    2011-09-01

    Full Text Available Abstract Plastids are small organelles equipped with their own genomes (plastomes. Although these organelles are involved in numerous plant metabolic pathways, current knowledge about the transcriptional activity of plastomes is limited. To solve this problem, we constructed a plastid tiling microarray (PlasTi-microarray consisting of 1629 oligonucleotide probes. The oligonucleotides were designed based on the cucumber chloroplast genomic sequence and targeted both strands of the plastome in a non-contiguous arrangement. Up to 4 specific probes were designed for each gene/exon, and the intergenic regions were covered regularly, with 70-nt intervals. We also developed a protocol for direct chemical labeling and hybridization of as little as 2 micrograms of chloroplast RNA. We used this protocol for profiling the expression of the cucumber chloroplast plastome on the PlasTi-microarray. Owing to the high sequence similarity of plant plastomes, the newly constructed microarray can be used to study plants other than cucumber. Comparative hybridization of chloroplast transcriptomes from cucumber, Arabidopsis, tomato and spinach showed that the PlasTi-microarray is highly versatile.

  15. Improvement in the amine glass platform by bubbling method for a DNA microarray

    Directory of Open Access Journals (Sweden)

    Jee SH

    2015-10-01

    Full Text Available Seung Hyun Jee,1 Jong Won Kim,2 Ji Hyeong Lee,2 Young Soo Yoon11Department of Chemical and Biological Engineering, Gachon University, Seongnam, Gyeonggi, Republic of Korea; 2Genomics Clinical Research Institute, LabGenomics Co., Ltd., Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of KoreaAbstract: A glass platform with high sensitivity for sexually transmitted diseases microarray is described here. An amino-silane-based self-assembled monolayer was coated on the surface of a glass platform using a novel bubbling method. The optimized surface of the glass platform had highly uniform surface modifications using this method, as well as improved hybridization properties with capture probes in the DNA microarray. On the basis of these results, the improved glass platform serves as a highly reliable and optimal material for the DNA microarray. Moreover, in this study, we demonstrated that our glass platform, manufactured by utilizing the bubbling method, had higher uniformity, shorter processing time, lower background signal, and higher spot signal than the platforms manufactured by the general dipping method. The DNA microarray manufactured with a glass platform prepared using bubbling method can be used as a clinical diagnostic tool. Keywords: DNA microarray, glass platform, bubbling method, self-assambled monolayer

  16. Multiplex RT-PCR and Automated Microarray for Detection of Eight Bovine Viruses.

    Science.gov (United States)

    Lung, O; Furukawa-Stoffer, T; Burton Hughes, K; Pasick, J; King, D P; Hodko, D

    2017-12-01

    Microarrays can be a useful tool for pathogen detection as it allow for simultaneous interrogation of the presence of a large number of genetic sequences in a sample. However, conventional microarrays require extensive manual handling and multiple pieces of equipment for printing probes, hybridization, washing and signal detection. In this study, a reverse transcription (RT)-PCR with an accompanying novel automated microarray for simultaneous detection of eight viruses that affect cattle [vesicular stomatitis virus (VSV), bovine viral diarrhoea virus type 1 and type 2, bovine herpesvirus 1, bluetongue virus, malignant catarrhal fever virus, rinderpest virus (RPV) and parapox viruses] is described. The assay accurately identified a panel of 37 strains of the target viruses and identified a mixed infection. No non-specific reactions were observed with a panel of 23 non-target viruses associated with livestock. Vesicular stomatitis virus was detected as early as 2 days post-inoculation in oral swabs from experimentally infected animals. The limit of detection of the microarray assay was as low as 1 TCID 50 /ml for RPV. The novel microarray platform automates the entire post-PCR steps of the assay and integrates electrophoretic-driven capture probe printing in a single user-friendly instrument that allows array layout and assay configuration to be user-customized on-site. © 2016 Her Majesty the Queen in Right of Canada.

  17. On the classification techniques in data mining for microarray data classification

    Science.gov (United States)

    Aydadenta, Husna; Adiwijaya

    2018-03-01

    Cancer is one of the deadly diseases, according to data from WHO by 2015 there are 8.8 million more deaths caused by cancer, and this will increase every year if not resolved earlier. Microarray data has become one of the most popular cancer-identification studies in the field of health, since microarray data can be used to look at levels of gene expression in certain cell samples that serve to analyze thousands of genes simultaneously. By using data mining technique, we can classify the sample of microarray data thus it can be identified with cancer or not. In this paper we will discuss some research using some data mining techniques using microarray data, such as Support Vector Machine (SVM), Artificial Neural Network (ANN), Naive Bayes, k-Nearest Neighbor (kNN), and C4.5, and simulation of Random Forest algorithm with technique of reduction dimension using Relief. The result of this paper show performance measure (accuracy) from classification algorithm (SVM, ANN, Naive Bayes, kNN, C4.5, and Random Forets).The results in this paper show the accuracy of Random Forest algorithm higher than other classification algorithms (Support Vector Machine (SVM), Artificial Neural Network (ANN), Naive Bayes, k-Nearest Neighbor (kNN), and C4.5). It is hoped that this paper can provide some information about the speed, accuracy, performance and computational cost generated from each Data Mining Classification Technique based on microarray data.

  18. Improved microarray-based decision support with graph encoded interactome data.

    Directory of Open Access Journals (Sweden)

    Anneleen Daemen

    Full Text Available In the past, microarray studies have been criticized due to noise and the limited overlap between gene signatures. Prior biological knowledge should therefore be incorporated as side information in models based on gene expression data to improve the accuracy of diagnosis and prognosis in cancer. As prior knowledge, we investigated interaction and pathway information from the human interactome on different aspects of biological systems. By exploiting the properties of kernel methods, relations between genes with similar functions but active in alternative pathways could be incorporated in a support vector machine classifier based on spectral graph theory. Using 10 microarray data sets, we first reduced the number of data sources relevant for multiple cancer types and outcomes. Three sources on metabolic pathway information (KEGG, protein-protein interactions (OPHID and miRNA-gene targeting (microRNA.org outperformed the other sources with regard to the considered class of models. Both fixed and adaptive approaches were subsequently considered to combine the three corresponding classifiers. Averaging the predictions of these classifiers performed best and was significantly better than the model based on microarray data only. These results were confirmed on 6 validation microarray sets, with a significantly improved performance in 4 of them. Integrating interactome data thus improves classification of cancer outcome for the investigated microarray technologies and cancer types. Moreover, this strategy can be incorporated in any kernel method or non-linear version of a non-kernel method.

  19. Spatial and temporal superresolution concepts to study plasma membrane organization by single molecule fluorescence techniques

    International Nuclear Information System (INIS)

    Ruprecht, V.

    2010-01-01

    molecules over multiple images. Proof-of-principles experiments on a fluid bilayer system, a quantitative assessment of the method and statistical estimates for the detection of rare events are presented. A different approach to catch molecular interactions of membrane components relies on analyzing brightness values of fluorescent spots in one color single molecule images. In this case the brightness value of observed spots is a direct measure for the number of fluorescent molecules within a molecular complex. The method was applied to study the homo-association of fluorescent lipid analogues in the live cell plasma membrane of living Cho and Jakarta T cells. The obtained results suggest the presence of stable lipid nano platforms in the live cell plasma membrane that are sensitive to cholesterol extraction and temperature elevation. Fluorescence correlation spectroscopy is discussed as a complementary single molecule approach to unravel dynamic processes in the cellular plasma membrane. A theoretical study supported by Monte Carlo simulations is presented that demonstrates the potential of spot variation fluorescence correlation spectroscopy (sv-FCS) to measure transient confinement times of plasma membrane constituents. Effects due to the underlying distribution of trapping times, trap mobility and the size of the confinement structure are also characterized. In comparison to conventional FCS measurements performed at a single laser beam waist the presented FCS concept features improved temporal resolution to access confinement times below the characteristic diffusion time of a tracer through the focal spot. (author) [de

  20. Design of a covalently bonded glycosphingolipid microarray

    DEFF Research Database (Denmark)

    Arigi, Emma; Blixt, Klas Ola; Buschard, Karsten

    2012-01-01

    , the major classes of plant and fungal GSLs. In this work, a prototype "universal" GSL-based covalent microarray has been designed, and preliminary evaluation of its potential utility in assaying protein-GSL binding interactions investigated. An essential step in development involved the enzymatic release...... of the fatty acyl moiety of the ceramide aglycone of selected mammalian GSLs with sphingolipid N-deacylase (SCDase). Derivatization of the free amino group of a typical lyso-GSL, lyso-G(M1), with a prototype linker assembled from succinimidyl-[(N-maleimidopropionamido)-diethyleneglycol] ester and 2...

  1. Linking probe thermodynamics to microarray quantification

    International Nuclear Information System (INIS)

    Li, Shuzhao; Pozhitkov, Alexander; Brouwer, Marius

    2010-01-01

    Understanding the difference in probe properties holds the key to absolute quantification of DNA microarrays. So far, Langmuir-like models have failed to link sequence-specific properties to hybridization signals in the presence of a complex hybridization background. Data from washing experiments indicate that the post-hybridization washing has no major effect on the specifically bound targets, which give the final signals. Thus, the amount of specific targets bound to probes is likely determined before washing, by the competition against nonspecific binding. Our competitive hybridization model is a viable alternative to Langmuir-like models. (comment)

  2. How the RNA isolation method can affect microRNA microarray results

    DEFF Research Database (Denmark)

    Podolska, Agnieszka; Kaczkowski, Bogumil; Litman, Thomas

    2011-01-01

    RNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results...... that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.......The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform micro...

  3. DNA Microarray Data Analysis: A Novel Biclustering Algorithm Approach

    Directory of Open Access Journals (Sweden)

    Tewfik Ahmed H

    2006-01-01

    Full Text Available Biclustering algorithms refer to a distinct class of clustering algorithms that perform simultaneous row-column clustering. Biclustering problems arise in DNA microarray data analysis, collaborative filtering, market research, information retrieval, text mining, electoral trends, exchange analysis, and so forth. When dealing with DNA microarray experimental data for example, the goal of biclustering algorithms is to find submatrices, that is, subgroups of genes and subgroups of conditions, where the genes exhibit highly correlated activities for every condition. In this study, we develop novel biclustering algorithms using basic linear algebra and arithmetic tools. The proposed biclustering algorithms can be used to search for all biclusters with constant values, biclusters with constant values on rows, biclusters with constant values on columns, and biclusters with coherent values from a set of data in a timely manner and without solving any optimization problem. We also show how one of the proposed biclustering algorithms can be adapted to identify biclusters with coherent evolution. The algorithms developed in this study discover all valid biclusters of each type, while almost all previous biclustering approaches will miss some.

  4. Systematic interpretation of microarray data using experiment annotations

    Directory of Open Access Journals (Sweden)

    Frohme Marcus

    2006-12-01

    Full Text Available Abstract Background Up to now, microarray data are mostly assessed in context with only one or few parameters characterizing the experimental conditions under study. More explicit experiment annotations, however, are highly useful for interpreting microarray data, when available in a statistically accessible format. Results We provide means to preprocess these additional data, and to extract relevant traits corresponding to the transcription patterns under study. We found correspondence analysis particularly well-suited for mapping such extracted traits. It visualizes associations both among and between the traits, the hereby annotated experiments, and the genes, revealing how they are all interrelated. Here, we apply our methods to the systematic interpretation of radioactive (single channel and two-channel data, stemming from model organisms such as yeast and drosophila up to complex human cancer samples. Inclusion of technical parameters allows for identification of artifacts and flaws in experimental design. Conclusion Biological and clinical traits can act as landmarks in transcription space, systematically mapping the variance of large datasets from the predominant changes down toward intricate details.

  5. Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data.

    Science.gov (United States)

    Tan, Qihua; Thomassen, Mads; Burton, Mark; Mose, Kristian Fredløv; Andersen, Klaus Ejner; Hjelmborg, Jacob; Kruse, Torben

    2017-06-06

    Modeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health.

  6. SPATIAL-TEMPORAL ANALYSIS OF OPENSTREETMAP DATA AFTER NATURAL DISASTERS: A CASE STUDY OF HAITI UNDER HURRICANE MATTHEW

    Directory of Open Access Journals (Sweden)

    J. Xu

    2017-09-01

    Full Text Available Volunteered geographic information (VGI has been widely adopted as an alternative for authoritative geographic information in disaster management considering its up-to-date data. OpenStreetMap, in particular, is now aiming at crisis mapping for humanitarian purpose. This paper illustrated that natural disaster played an essential role in updating OpenStreetMap data after Haiti was hit by Hurricane Matthew in October, 2016. Spatial-temporal analysis of updated OSM data was conducted in this paper. Correlation of features was also studied to figure out whether updates of data were coincidence or the results of the hurricane. Spatial pattern matched the damaged areas and temporal changes fitted the time when disaster occurred. High level of correlation values of features were recorded when hurricane occurred, suggesting that updates in data were led by the hurricane.

  7. Spatial-Temporal Analysis of Openstreetmap Data after Natural Disasters: a Case Study of Haiti Under Hurricane Matthew

    Science.gov (United States)

    Xu, J.; Li, L.; Zhou, Q.

    2017-09-01

    Volunteered geographic information (VGI) has been widely adopted as an alternative for authoritative geographic information in disaster management considering its up-to-date data. OpenStreetMap, in particular, is now aiming at crisis mapping for humanitarian purpose. This paper illustrated that natural disaster played an essential role in updating OpenStreetMap data after Haiti was hit by Hurricane Matthew in October, 2016. Spatial-temporal analysis of updated OSM data was conducted in this paper. Correlation of features was also studied to figure out whether updates of data were coincidence or the results of the hurricane. Spatial pattern matched the damaged areas and temporal changes fitted the time when disaster occurred. High level of correlation values of features were recorded when hurricane occurred, suggesting that updates in data were led by the hurricane.

  8. The Tölz Temporal Topography Study: mapping the visual field across the life span. Part I: the topography of light detection and temporal-information processing.

    Science.gov (United States)

    Poggel, Dorothe A; Treutwein, Bernhard; Calmanti, Claudia; Strasburger, Hans

    2012-08-01

    Temporal performance parameters vary across the visual field. Their topographical distributions relative to each other and relative to basic visual performance measures and their relative change over the life span are unknown. Our goal was to characterize the topography and age-related change of temporal performance. We acquired visual field maps in 95 healthy participants (age: 10-90 years): perimetric thresholds, double-pulse resolution (DPR), reaction times (RTs), and letter contrast thresholds. DPR and perimetric thresholds increased with eccentricity and age; the periphery showed a more pronounced age-related increase than the center. RT increased only slightly and uniformly with eccentricity. It remained almost constant up to the age of 60, a marked change occurring only above 80. Overall, age was a poor predictor of functionality. Performance decline could be explained only in part by the aging of the retina and optic media. In Part II, we therefore examine higher visual and cognitive functions.

  9. Design of an Enterobacteriaceae Pan-genome Microarray Chip

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana; Ussery, David

    2010-01-01

    -density microarray chip has been designed, using 116 Enterobacteriaceae genome sequences, taking into account the enteric pan-genome. Probes for the microarray were checked in silico and performance of the chip, based on experimental strains from four different genera, demonstrate a relatively high ability...... to distinguish those strains on genus, species, and pathotype/serovar levels. Additionally, the microarray performed well when investigating which genes were found in a given strain of interest. The Enterobacteriaceae pan-genome microarray, based on 116 genomes, provides a valuable tool for determination...

  10. Comparative analysis of MR imaging, Ictal SPECT and EEG in temporal lobe epilepsy: a prospective IAEA multi-center study

    Energy Technology Data Exchange (ETDEWEB)

    Zaknun, John J. [University Hospital of Innsbruck, Department of Nuclear Medicine, Innsbruck (Austria); International Atomic Energy Agency (IAEA), Nuclear Medicine Section, Division of Human Health, Vienna (Austria); IAEA, Nuclear Medicine Section, Division of Human Health, Wagramer Strasse 5, P.O. Box 100, Wien (Austria); Bal, Chandrasekhar [All India Institute of Medical Sciences, Department of Nuclear Medicine, New Delhi (India); Maes, Alex [Katholieke Universiteit Leuven, Leuven (Belgium); AZ Groeninge, Department of Nuclear Medicine, Kortrijk (Belgium); Tepmongkol, Supatporn [Chulalongkorn University, Nuclear Medicine Division, Department of Radiology, Bangkok (Thailand); Vazquez, Silvia [Instituto de Investigaciones Neurologicas, FLENI, Department of Radiology, Buenos Aires (Argentina); Dupont, Patrick [Katholieke Universiteit Leuven, Leuven (Belgium); Dondi, Maurizio [Ospedale Maggiore, Department of Nuclear Medicine, Bologna (Italy); International Atomic Energy Agency (IAEA), Nuclear Medicine Section, Division of Human Health, Vienna (Austria)

    2008-01-15

    MR imaging, ictal single-photon emission CT (SPECT) and ictal EEG play important roles in the presurgical localization of epileptic foci. This multi-center study was established to investigate whether the complementary role of perfusion SPECT, MRI and EEG for presurgical localization of temporal lobe epilepsy could be confirmed in a prospective setting involving centers from India, Thailand, Italy and Argentina. We studied 74 patients who underwent interictal and ictal EEG, interictal and ictal SPECT and MRI before surgery of the temporal lobe. In all but three patients, histology was reported. The clinical outcome was assessed using Engel's classification. Sensitivity values of all imaging modalities were calculated, and the add-on value of SPECT was assessed. Outcome (Engel's classification) in 74 patients was class I, 89%; class II, 7%; class III, 3%; and IV, 1%. Regarding the localization of seizure origin, sensitivity was 84% for ictal SPECT, 70% for ictal EEG, 86% for MRI, 55% for interictal SPECT and 40% for interictal EEG. Add-on value of ictal SPECT was shown by its ability to correctly localize 17/22 (77%) of the seizure foci missed by ictal EEG and 8/10 (80%) of the seizure foci not detected by MRI. This prospective multi-center trial, involving centers from different parts of the world, confirms that ictal perfusion SPECT is an effective diagnostic modality for correctly identifying seizure origin in temporal lobe epilepsy, providing complementary information to ictal EEG and MRI. (orig.)

  11. Comparative analysis of MR imaging, Ictal SPECT and EEG in temporal lobe epilepsy: a prospective IAEA multi-center study

    International Nuclear Information System (INIS)

    Zaknun, John J.; Bal, Chandrasekhar; Maes, Alex; Tepmongkol, Supatporn; Vazquez, Silvia; Dupont, Patrick; Dondi, Maurizio

    2008-01-01

    MR imaging, ictal single-photon emission CT (SPECT) and ictal EEG play important roles in the presurgical localization of epileptic foci. This multi-center study was established to investigate whether the complementary role of perfusion SPECT, MRI and EEG for presurgical localization of temporal lobe epilepsy could be confirmed in a prospective setting involving centers from India, Thailand, Italy and Argentina. We studied 74 patients who underwent interictal and ictal EEG, interictal and ictal SPECT and MRI before surgery of the temporal lobe. In all but three patients, histology was reported. The clinical outcome was assessed using Engel's classification. Sensitivity values of all imaging modalities were calculated, and the add-on value of SPECT was assessed. Outcome (Engel's classification) in 74 patients was class I, 89%; class II, 7%; class III, 3%; and IV, 1%. Regarding the localization of seizure origin, sensitivity was 84% for ictal SPECT, 70% for ictal EEG, 86% for MRI, 55% for interictal SPECT and 40% for interictal EEG. Add-on value of ictal SPECT was shown by its ability to correctly localize 17/22 (77%) of the seizure foci missed by ictal EEG and 8/10 (80%) of the seizure foci not detected by MRI. This prospective multi-center trial, involving centers from different parts of the world, confirms that ictal perfusion SPECT is an effective diagnostic modality for correctly identifying seizure origin in temporal lobe epilepsy, providing complementary information to ictal EEG and MRI. (orig.)

  12. Quantifying temporal trends in fisheries abundance using Bayesian dynamic linear models: A case study of riverine Smallmouth Bass populations

    Science.gov (United States)

    Schall, Megan K.; Blazer, Vicki S.; Lorantas, Robert M.; Smith, Geoffrey; Mullican, John E.; Keplinger, Brandon J.; Wagner, Tyler

    2018-01-01

    Detecting temporal changes in fish abundance is an essential component of fisheries management. Because of the need to understand short‐term and nonlinear changes in fish abundance, traditional linear models may not provide adequate information for management decisions. This study highlights the utility of Bayesian dynamic linear models (DLMs) as a tool for quantifying temporal dynamics in fish abundance. To achieve this goal, we quantified temporal trends of Smallmouth Bass Micropterus dolomieu catch per effort (CPE) from rivers in the mid‐Atlantic states, and we calculated annual probabilities of decline from the posterior distributions of annual rates of change in CPE. We were interested in annual declines because of recent concerns about fish health in portions of the study area. In general, periods of decline were greatest within the Susquehanna River basin, Pennsylvania. The declines in CPE began in the late 1990s—prior to observations of fish health problems—and began to stabilize toward the end of the time series (2011). In contrast, many of the other rivers investigated did not have the same magnitude or duration of decline in CPE. Bayesian DLMs provide information about annual changes in abundance that can inform management and are easily communicated with managers and stakeholders.

  13. Experimentally induced thyrotoxicosis leads to increased connectivity in temporal lobe structures: a resting state fMRI study.

    Science.gov (United States)

    Göttlich, Martin; Heldmann, Marcus; Göbel, Anna; Dirk, Anna-Luise; Brabant, Georg; Münte, Thomas F

    2015-06-01

    Adult onset hyperthyroidism may impact on different cognitive domains, including attention and concentration, memory, perceptual function, language and executive function. Previous PET studies implicated changed functionality of limbic regions, the temporal and frontal lobes in hyperthyroidism, whereas it is unknown whether cognitive effects of hyperthyroidism may be due to changed brain connectivity. This study aimed to investigate the effect of experimentally induced short-term hyperthyroidism thyrotoxicosis on resting-state functional connectivity using functional magnetic resonance imaging. Twenty-nine healthy male right-handed subjects were examined twice, once prior and once after 8 weeks of oral administration of 250 μg levothyroxine per day. Resting-state fMRI was subjected to graph-theory based analysis methods to investigate whole-brain intrinsic functional connectivity. Despite a lack of subjective changes noticed by the subjects significant thyrotoxicosis was confirmed in all subjects. This induced a significant increase in resting-state functional connectivity specifically in the rostral temporal lobes (0.05 FDR corrected at the cluster level), which is caused by an increased connectivity to the cognitive control network. The increased connectivity between temporal poles and the cognitive control network shown here under experimental conditions supports an important function of thyroid hormones in the regulation of paralimbic structures. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Characterization of adjacent breast tumors using oligonucleotide microarrays

    International Nuclear Information System (INIS)

    Unger, Meredith A; Rishi, Mazhar; Clemmer, Virginia B; Hartman, Jennifer L; Keiper, Elizabeth A; Greshock, Joel D; Chodosh, Lewis A; Liebman, Michael N; Weber, Barbara L

    2001-01-01

    Current methodology often cannot distinguish second primary breast cancers from multifocal disease, a potentially important distinction for clinical management. In the present study we evaluated the use of oligonucleotide-based microarray analysis in determining the clonality of tumors by comparing gene expression profiles. Total RNA was extracted from two tumors with no apparent physical connection that were located in the right breast of an 87-year-old woman diagnosed with invasive ductal carcinoma (IDC). The RNA was hybridized to the Affymetrix Human Genome U95A Gene Chip ® (12,500 known human genes) and analyzed using the Gene Chip Analysis Suite ® 3.3 (Affymetrix, Inc, Santa Clara, CA, USA) and JMPIN ® 3.2.6 (SAS Institute, Inc, Cary, NC, USA). Gene expression profiles of tumors from five additional patients were compared in order to evaluate the heterogeneity in gene expression between tumors with similar clinical characteristics. The adjacent breast tumors had a pairwise correlation coefficient of 0.987, and were essentially indistinguishable by microarray analysis. Analysis of gene expression profiles from different individuals, however, generated a pairwise correlation coefficient of 0.710. Transcriptional profiling may be a useful diagnostic tool for determining tumor clonality and heterogeneity, and may ultimately impact on therapeutic decision making

  15. Screening for C3 deficiency in newborns using microarrays.

    Directory of Open Access Journals (Sweden)

    Magdalena Janzi

    Full Text Available BACKGROUND: Dried blood spot samples (DBSS from newborns are widely used in neonatal screening for selected metabolic diseases and diagnostic possibilities for additional disorders are continuously being evaluated. Primary immunodeficiency disorders comprise a group of more than one hundred diseases, several of which are fatal early in life. Yet, a majority of the patients are not diagnosed due to lack of high-throughput screening methods. METHODOLOGY/PRINCIPAL FINDINGS: We have previously developed a system using reverse phase protein microarrays for analysis of IgA levels in serum samples. In this study, we extended the applicability of the method to include determination of complement component C3 levels in eluates from DBSS collected at birth. Normal levels of C3 were readily detected in 269 DBSS from healthy newborns, while no C3 was detected in sera and DBSS from C3 deficient patients. CONCLUSIONS/SIGNIFICANCE: The findings suggest that patients with deficiencies of specific serum proteins can be identified by analysis of DBSS using reverse phase protein microarrays.

  16. Data Integration for Microarrays: Enhanced Inference for Gene Regulatory Networks

    Directory of Open Access Journals (Sweden)

    Alina Sîrbu

    2015-05-01

    Full Text Available Microarray technologies have been the basis of numerous important findings regarding gene expression in the few last decades. Studies have generated large amounts of data describing various processes, which, due to the existence of public databases, are widely available for further analysis. Given their lower cost and higher maturity compared to newer sequencing technologies, these data continue to be produced, even though data quality has been the subject of some debate. However, given the large volume of data generated, integration can help overcome some issues related, e.g., to noise or reduced time resolution, while providing additional insight on features not directly addressed by sequencing methods. Here, we present an integration test case based on public Drosophila melanogaster datasets (gene expression, binding site affinities, known interactions. Using an evolutionary computation framework, we show how integration can enhance the ability to recover transcriptional gene regulatory networks from these data, as well as indicating which data types are more important for quantitative and qualitative network inference. Our results show a clear improvement in performance when multiple datasets are integrated, indicating that microarray data will remain a valuable and viable resource for some time to come.

  17. Fuzzy C-means method for clustering microarray data.

    Science.gov (United States)

    Dembélé, Doulaye; Kastner, Philippe

    2003-05-22

    Clustering analysis of data from DNA microarray hybridization studies is essential for identifying biologically relevant groups of genes. Partitional clustering methods such as K-means or self-organizing maps assign each gene to a single cluster. However, these methods do not provide information about the influence of a given gene for the overall shape of clusters. Here we apply a fuzzy partitioning method, Fuzzy C-means (FCM), to attribute cluster membership values to genes. A major problem in applying the FCM method for clustering microarray data is the choice of the fuzziness parameter m. We show that the commonly used value m = 2 is not appropriate for some data sets, and that optimal values for m vary widely from one data set to another. We propose an empirical method, based on the distribution of distances between genes in a given data set, to determine an adequate value for m. By setting threshold levels for the membership values, genes which are tigthly associated to a given cluster can be selected. Using a yeast cell cycle data set as an example, we show that this selection increases the overall biological significance of the genes within the cluster. Supplementary text and Matlab functions are available at http://www-igbmc.u-strasbg.fr/fcm/

  18. Data Integration for Microarrays: Enhanced Inference for Gene Regulatory Networks.

    Science.gov (United States)

    Sîrbu, Alina; Crane, Martin; Ruskin, Heather J

    2015-05-14

    Microarray technologies have been the basis of numerous important findings regarding gene expression in the few last decades. Studies have generated large amounts of data describing various processes, which, due to the existence of public databases, are widely available for further analysis. Given their lower cost and higher maturity compared to newer sequencing technologies, these data continue to be produced, even though data quality has been the subject of some debate. However, given the large volume of data generated, integration can help overcome some issues related, e.g., to noise or reduced time resolution, while providing additional insight on features not directly addressed by sequencing methods. Here, we present an integration test case based on public Drosophila melanogaster datasets (gene expression, binding site affinities, known interactions). Using an evolutionary computation framework, we show how integration can enhance the ability to recover transcriptional gene regulatory networks from these data, as well as indicating which data types are more important for quantitative and qualitative network inference. Our results show a clear improvement in performance when multiple datasets are integrated, indicating that microarray data will remain a valuable and viable resource for some time to come.

  19. Classification of mislabelled microarrays using robust sparse logistic regression.

    Science.gov (United States)

    Bootkrajang, Jakramate; Kabán, Ata

    2013-04-01

    Previous studies reported that labelling errors are not uncommon in microarray datasets. In such cases, the training set may become misleading, and the ability of classifiers to make reliable inferences from the data is compromised. Yet, few methods are currently available in the bioinformatics literature to deal with this problem. The few existing methods focus on data cleansing alone, without reference to classification, and their performance crucially depends on some tuning parameters. In this article, we develop a new method to detect mislabelled arrays simultaneously with learning a sparse logistic regression classifier. Our method may be seen as a label-noise robust extension of the well-known and successful Bayesian logistic regression classifier. To account for possible mislabelling, we formulate a label-flipping process as part of the classifier. The regularization parameter is automatically set using Bayesian regularization, which not only saves the computation time that cross-validation would take, but also eliminates any unwanted effects of label noise when setting the regularization parameter. Extensive experiments with both synthetic data and real microarray datasets demonstrate that our approach is able to counter the bad effects of labelling errors in terms of predictive performance, it is effective at identifying marker genes and simultaneously it detects mislabelled arrays to high accuracy. The code is available from http://cs.bham.ac.uk/∼jxb008. Supplementary data are available at Bioinformatics online.

  20. Microfluidic extraction and microarray detection of biomarkers from cancer tissue slides

    Science.gov (United States)

    Nguyen, H. T.; Dupont, L. N.; Jean, A. M.; Géhin, T.; Chevolot, Y.; Laurenceau, E.; Gijs, M. A. M.

    2018-03-01

    We report here a new microfluidic method allowing for the quantification of human epidermal growth factor receptor 2 (HER2) expression levels from formalin-fixed breast cancer tissues. After partial extraction of proteins from the tissue slide, the extract is routed to an antibody (Ab) microarray for HER2 titration by fluorescence. Then the HER2-expressing cell area is evaluated by immunofluorescence (IF) staining of the tissue slide and used to normalize the fluorescent HER2 signal measured from the Ab microarray. The number of HER2 gene copies measured by fluorescence in situ hybridization (FISH) on an adjacent tissue slide is concordant with the normalized HER2 expression signal. This work is the first study implementing biomarker extraction and detection from cancer tissue slides using microfluidics in combination with a microarray system, paving the way for further developments towards multiplex and precise quantification of cancer biomarkers.

  1. Microarray-based genotyping of Salmonella: Inter-laboratory evaluation of reproducibility and standardization potential

    DEFF Research Database (Denmark)

    Grønlund, Hugo Ahlm; Riber, Leise; Vigre, Håkan

    2011-01-01

    Bacterial food-borne infections in humans caused by Salmonella spp. are considered a crucial food safety issue. Therefore, it is important for the risk assessments of Salmonella to consider the genomic variationamong different isolates in order to control pathogen-induced infections. Microarray...... critical methodology parameters that differed between the two labs were identified. These related to printing facilities, choice of hybridization buffer,wash buffers used following the hybridization and choice of procedure for purifying genomic DNA. Critical parameters were randomized in a four......DNA and different wash buffers. However, less agreement (Kappa=0.2–0.6) between microarray results were observed when using different hybridization buffers, indicating this parameter as being highly criticalwhen transferring a standard microarray assay between laboratories. In conclusion, this study indicates...

  2. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

    KAUST Repository

    Boopathi, Pon Arunachalam

    2016-10-09

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

  3. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

    KAUST Repository

    Boopathi, Pon Arunachalam; Subudhi, Amit; Middha, Sheetal; Acharya, Jyoti; Mugasimangalam, Raja Chinnadurai; Kochar, Sanjay Kumar; Kochar, Dhanpat Kumar; Das, Ashis

    2016-01-01

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

  4. Temporal Glare

    DEFF Research Database (Denmark)

    Ritschel, Tobias; Ihrke, Matthias; Frisvad, Jeppe Revall

    2009-01-01

    Glare is a consequence of light scattered within the human eye when looking at bright light sources. This effect can be exploited for tone mapping since adding glare to the depiction of high-dynamic range (HDR) imagery on a low-dynamic range (LDR) medium can dramatically increase perceived contra...... to initially static HDR images. By conducting psychophysical studies, we validate that our method improves perceived brightness and that dynamic glare-renderings are often perceived as more attractive depending on the chosen scene.......Glare is a consequence of light scattered within the human eye when looking at bright light sources. This effect can be exploited for tone mapping since adding glare to the depiction of high-dynamic range (HDR) imagery on a low-dynamic range (LDR) medium can dramatically increase perceived contrast....... Even though most, if not all, subjects report perceiving glare as a bright pattern that fluctuates in time, up to now it has only been modeled as a static phenomenon. We argue that the temporal properties of glare are a strong means to increase perceived brightness and to produce realistic...

  5. Psychiatric comorbidity in epilepsy: a study comparing patients with mesial temporal sclerosis and juvenile myoclonic epilepsy.

    Science.gov (United States)

    Filho, Gerardo Maria de Araújo; Rosa, Vivianne Pellegrino; Lin, Katia; Caboclo, Luís Otávio Sales Ferreira; Sakamoto, Américo Ceiki; Yacubian, Elza Márcia Targas

    2008-07-01

    We evaluated the frequency of psychiatric disorders (PDs) in a homogenous series of patients with temporal lobe epilepsy with mesial temporal sclerosis (TLE-MTS), as compared with patients with juvenile myoclonic epilepsy (JME), aiming to determine possible differences in psychiatric diagnoses between these two epileptic syndromes. Data from 170 patients with refractory TLE-MTS and from 100 patients with JME were reviewed and compared. The prevalence of PDs was high in both groups of patients with epilepsy: PDs were present in 85 patients with TLE-MTS (50%) and 49 patients with JME (49%). Among the TLE-MTS group, mood (25.8%), psychotic (15.8%), and anxiety (14.1%) disorders were the most frequent diagnoses, whereas anxiety and mood disorders (23 and 19%, respectively) were the most common among patients with JME. Psychoses were significantly associated with MTS (P<0.01) and anxiety disorders with JME (P<0.05). These findings suggest the existence of an anatomic correlation between PDs and brain structures involved in both epilepsy syndromes.

  6. Is there temporal variation on solid waste stranding in mangroves? A case study in Ratones mangrove, Florianopolis, Brazil

    Directory of Open Access Journals (Sweden)

    Bianca Pinto Vieira

    2013-03-01

    Full Text Available Mangrove areas are decreasing around the world due to population increase. The most damaging activities include embankments, shrimp farming, and dumping of wastes. The temporal and spatial stranding patterns of solid waste are important to establish probable sources and understand their role in the dispersion of organisms through natural areas. In this study, we analyze temporal variation of solid waste stranding in Ratones mangrove, northwestern of Santa Catarina Island (Brazil. Samplings were carried out monthly during one year in four different areas. In each area, two 50 m2 random plots were sampled per month. All solid waste strands on the plots were removed, quantified, and qualified. Plastic and nylon items (both made of petroleum represented 80% of waste stranding. There were significant differences in temporal stranding with regard to plastic, but not to nylon. Wastes were found in all samples throughout the year, and some areas are more affected than others. Places with dense edges of Spartina alterniflora Loisel (Poaceae seem to have less solid waste inside mangrove forest, perhaps due to the effect of grass acting as a mesh barrier. The results reflected concerns with conservation, considering that these coastal ecosystems are impacted by waste dumping throughout the year, with highest concentration within important nursery points.

  7. a Comparison Study of Different Kernel Functions for Svm-Based Classification of Multi-Temporal Polarimetry SAR Data

    Science.gov (United States)

    Yekkehkhany, B.; Safari, A.; Homayouni, S.; Hasanlou, M.

    2014-10-01

    In this paper, a framework is developed based on Support Vector Machines (SVM) for crop classification using polarimetric features extracted from multi-temporal Synthetic Aperture Radar (SAR) imageries. The multi-temporal integration of data not only improves the overall retrieval accuracy but also provides more reliable estimates with respect to single-date data. Several kernel functions are employed and compared in this study for mapping the input space to higher Hilbert dimension space. These kernel functions include linear, polynomials and Radial Based Function (RBF). The method is applied to several UAVSAR L-band SAR images acquired over an agricultural area near Winnipeg, Manitoba, Canada. In this research, the temporal alpha features of H/A/α decomposition method are used in classification. The experimental tests show an SVM classifier with RBF kernel for three dates of data increases the Overall Accuracy (OA) to up to 3% in comparison to using linear kernel function, and up to 1% in comparison to a 3rd degree polynomial kernel function.

  8. The temporal relationship between alcohol, marijuana, angry affect, and dating violence perpetration: A daily diary study with female college students.

    Science.gov (United States)

    Shorey, Ryan C; Stuart, Gregory L; Moore, Todd M; McNulty, James K

    2014-06-01

    Although a robust literature documents a positive association between alcohol and intimate partner violence (IPV), there is limited temporal research on this relation. Moreover, the role of marijuana in influencing IPV has been mixed. Thus, the primary aim of the current study was to examine the temporal relationship between alcohol and marijuana use and dating violence perpetration. A secondary aim was to examine whether angry affect moderated the temporal relation between alcohol and marijuana use and IPV perpetration. Participants were college women who had consumed alcohol in the previous month and were in a dating relationship (N = 173). For up to 90 consecutive days, women completed daily surveys that assessed their alcohol use, marijuana use, angry affect (anger, hostility, and irritation), and violence perpetration (psychological and physical). On alcohol use days, marijuana use days, and with increases in angry affect, the odds of psychological aggression increased. Only alcohol use days and increases in angry affect increased the odds of physical aggression. Moreover, the main effects of alcohol and marijuana use on aggression were moderated by angry affect. Alcohol was positively associated with psychological and physical aggression when angry affect was high, but was unrelated to aggression when angry affect was low. Marijuana use was associated with psychological aggression when angry affect was high. Findings advance our understanding of the proximal effect of alcohol and marijuana use on dating violence, including the potential moderating effect of angry affect on this relation.

  9. Nutrients and toxin producing phytoplankton control algal blooms - a spatio-temporal study in a noisy environment.

    Science.gov (United States)

    Sarkar, Ram Rup; Malchow, Horst

    2005-12-01

    A phytoplankton-zooplankton prey-predator model has been investigated for temporal, spatial and spatio-temporal dissipative pattern formation in a deterministic and noisy environment, respectively. The overall carrying capacity for the phytoplankton population depends on the nutrient level. The role of nutrient concentrations and toxin producing phytoplankton for controlling the algal blooms has been discussed. The local analysis yields a number of stationary and/or oscillatory regimes and their combinations. Correspondingly interesting is the spatio-temporal behaviour, modelled by stochastic reaction-diffusion equations. The present study also reveals the fact that the rate of toxin production by toxin producing phytoplankton (TPP) plays an important role for controlling oscillations in the plankton system. We also observe that different mortality functions of zooplankton due to TPP have significant influence in controlling oscillations, coexistence, survival or extinction of the zoo-plankton population. External noise can enhance the survival and spread of zooplankton that would go extinct in the deterministic system due to a high rate of toxin production.

  10. Evaluation of a gene information summarization system by users during the analysis process of microarray datasets

    Directory of Open Access Journals (Sweden)

    Cohen Aaron

    2009-02-01

    Full Text Available Abstract Background Summarization of gene information in the literature has the potential to help genomics researchers translate basic research into clinical benefits. Gene expression microarrays have been used to study biomarkers for disease and discover novel types of therapeutics and the task of finding information in journal articles on sets of genes is common for translational researchers working with microarray data. However, manually searching and scanning the literature references returned from PubMed is a time-consuming task for scientists. We built and evaluated an automatic summarizer of information on genes studied in microarray experiments. The Gene Information Clustering and Summarization System (GICSS is a system that integrates two related steps of the microarray data analysis process: functional gene clustering and gene information gathering. The system evaluation was conducted during the process of genomic researchers analyzing their own experimental microarray datasets. Results The clusters generated by GICSS were validated by scientists during their microarray analysis process. In addition, presenting sentences in the abstract provided significantly more important information to the users than just showing the title in the default PubMed format. Conclusion The evaluation results suggest that GICSS can be useful for researchers in genomic area. In addition, the hybrid evaluation method, partway between intrinsic and extrinsic system evaluation, may enable researchers to gauge the true usefulness of the tool for the scientists in their natural analysis workflow and also elicit suggestions for future enhancements. Availability GICSS can be accessed online at: http://ir.ohsu.edu/jianji/index.html

  11. In silico design and performance of peptide microarrays for breast cancer tumour-auto-antibody testing

    Directory of Open Access Journals (Sweden)

    Andreas Weinhäusel

    2012-06-01

    Full Text Available The simplicity and potential of minimally invasive testing using sera from patients makes auto-antibody based biomarkers a very promising tool for use in cancer diagnostics. Protein microarrays have been used for the identification of such auto-antibody signatures. Because high throughput protein expression and purification is laborious, synthetic peptides might be a good alternative for microarray generation and multiplexed analyses. In this study, we designed 1185 antigenic peptides, deduced from proteins expressed by 642 cDNA expression clones found to be sero-reactive in both breast tumour patients and controls. The sero-reactive proteins and the corresponding peptides were used for the production of protein and peptide microarrays. Serum samples from females with benign and malignant breast tumours and healthy control sera (n=16 per group were then analysed. Correct classification of the serum samples on peptide microarrays were 78% for discrimination of ‘malignant versus healthy controls’, 72% for ‘benign versus malignant’ and 94% for ‘benign versus controls’. On protein arrays, correct classification for these contrasts was 69%, 59% and 59%, respectively. The over-representation analysis of the classifiers derived from class prediction showed enrichment of genes associated with ribosomes, spliceosomes, endocytosis and the pentose phosphate pathway. Sequence analyses of the peptides with the highest sero-reactivity demonstrated enrichment of the zinc-finger domain. Peptides’ sero-reactivities were found negatively correlated with hydrophobicity and positively correlated with positive charge, high inter-residue protein contact energies and a secondary structure propensity bias. This study hints at the possibility of using in silico designed antigenic peptide microarrays as an alternative to protein microarrays for the improvement of tumour auto-antibody based diagnostics.

  12. Independent effects of bottom-up temporal expectancy and top-down spatial attention. An audiovisual study using rhythmic cueing.

    Directory of Open Access Journals (Sweden)

    Alexander eJones

    2015-01-01

    Full Text Available Selective attention to a spatial location has shown enhance perception and facilitate behaviour for events at attended locations. However, selection relies not only on where but also when an event occurs. Recently, interest has turned to how intrinsic neural oscillations in the brain entrain to rhythms in our environment, and, stimuli appearing in or out of synch with a rhythm have shown to modulate perception and performance. Temporal expectations created by rhythms and spatial attention are two processes which have independently shown to affect stimulus processing but it remains largely unknown how, and if, they interact. In four separate tasks, this study investigated the effects of voluntary spatial attention and bottom-up temporal expectations created by rhythms in both unimodal and crossmodal conditions. In each task the participant used an informative cue, either colour or pitch, to direct their covert spatial attention to the left or right, and respond as quickly as possible to a target. The lateralized target (visual or auditory was then presented at the attended or unattended side. Importantly, although not task relevant, the cue was a rhythm of either flashes or beeps. The target was presented in or out of sync (early or late with the rhythmic cue. The results showed participants were faster responding to spatially attended compared to unattended targets in all tasks. Moreover, there was an effect of rhythmic cueing upon response times in both unimodal and crossmodal conditions. Responses were faster to targets presented in sync with the rhythm compared to when they appeared too early in both crossmodal tasks. That is, rhythmic stimuli in one modality influenced the temporal expectancy in the other modality, suggesting temporal expectancies created by rhythms are crossmodal. Interestingly, there was no interaction between top-down spatial attention and rhythmic cueing in any task suggesting these two processes largely influenced

  13. Serious limitations of the QTL/Microarray approach for QTL gene discovery

    Directory of Open Access Journals (Sweden)

    Warden Craig H

    2010-07-01

    Full Text Available Abstract Background It has been proposed that the use of gene expression microarrays in nonrecombinant parental or congenic strains can accelerate the process of isolating individual genes underlying quantitative trait loci (QTL. However, the effectiveness of this approach has not been assessed. Results Thirty-seven studies that have implemented the QTL/microarray approach in rodents were reviewed. About 30% of studies showed enrichment for QTL candidates, mostly in comparisons between congenic and background strains. Three studies led to the identification of an underlying QTL gene. To complement the literature results, a microarray experiment was performed using three mouse congenic strains isolating the effects of at least 25 biometric QTL. Results show that genes in the congenic donor regions were preferentially selected. However, within donor regions, the distribution of differentially expressed genes was homogeneous once gene density was accounted for. Genes within identical-by-descent (IBD regions were less likely to be differentially expressed in chromosome 2, but not in chromosomes 11 and 17. Furthermore, expression of QTL regulated in cis (cis eQTL showed higher expression in the background genotype, which was partially explained by the presence of single nucleotide polymorphisms (SNP. Conclusions The literature shows limited successes from the QTL/microarray approach to identify QTL genes. Our own results from microarray profiling of three congenic strains revealed a strong tendency to select cis-eQTL over trans-eQTL. IBD regions had little effect on rate of differential expression, and we provide several reasons why IBD should not be used to discard eQTL candidates. In addition, mismatch probes produced false cis-eQTL that could not be completely removed with the current strains genotypes and low probe density microarrays. The reviewed studies did not account for lack of coverage from the platforms used and therefore removed genes

  14. Identification of potential prognostic markers for vulvar cancer using immunohistochemical staining of tissue microarrays.

    NARCIS (Netherlands)

    Fons, G.; Burger, M.P.; Kate, F.J. ten; Velden, J. van der

    2007-01-01

    The aim of this study is to determine immunohistochemical markers with prognostic significance for disease-specific survival in patients with squamous cell cancer of the vulva. The study material consisted of slides and paraffin blocks of 50 vulvectomy specimens. A tissue microarray was constructed

  15. Study of the dependence of resolution temporal activity for a Philips gemini TF PET/CT scanner by applying a statistical analysis of time series; Estudio de la dependencia de la resolucion temporal con la actividad para un escaner PET-TAC philips gemini TF aplicando un analisis estadistico de series temporales

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez Merino, G.; Cortes Rpdicio, J.; Lope Lope, R.; Martin Gonzalez, T.; Garcia Fidalgo, M. A.

    2013-07-01

    The aim of the present work is to study the dependence of temporal resolution with the activity using statistical techniques applied to the series of values time series measurements of temporal resolution during daily equipment checks. (Author)

  16. Exploring the use of internal and externalcontrols for assessing microarray technical performance

    Directory of Open Access Journals (Sweden)

    Game Laurence

    2010-12-01

    Full Text Available Abstract Background The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies. Results A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes" was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification. External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC metrics. Conclusions These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray

  17. Immunohistochemistry - Microarray Analysis of Patients with Peritoneal Metastases of Appendiceal or Colorectal Origin

    Directory of Open Access Journals (Sweden)

    Danielle E Green

    2015-01-01

    Full Text Available BackgroundThe value of immunohistochemistry (IHC-microarray analysis of pathological specimens in the management of patients is controversial although preliminary data suggests potential benefit. We describe the characteristics of patients undergoing a commercially available IHC-microarray method in patients with peritoneal metastases (PM and the feasibility of this technique in this population.MethodsWe retrospectively analyzed consecutive patients with pathologically confirmed PM from appendiceal or colorectal primary who underwent Caris Molecular IntelligenceTM testing. IHC, microarray, FISH and mutational analysis were included and stratified by PCI score, histology and treatment characteristics. Statistical analysis was performed using non-parametric tests.ResultsOur study included 5 patients with appendiceal and 11 with colorectal PM. The median age of patients was 51 (IQR 39-65 years, with 11(68% female. The median PCI score of the patients was 17(IQR 10-25. Hyperthermic intra-peritoneal chemoperfusion (HIPEC was performed in 4 (80% patients with appendiceal primary tumors and 4 (36% with colorectal primary. KRAS mutations were encountered in 40% of appendiceal vs. 30% colorectal tumors, while BRAF mutations were seen in 40% of colorectal PM and none of the patients with appendiceal PM (p=0.06. IHC biomarker expression was not significantly different between the two primaries. Sufficient tumor for microarray analysis was found in 44% (n=7 patients, which was not associated with previous use of chemotherapy (p>0.20 for 5-FU/LV, Irinotecan and Oxaliplatin.ConclusionsIn a small sample of patients with peritoneal metastases, the feasibility and results of IHC-microarray staining based on a commercially available test is reported. The apparent high incidence of the BRAF mutation in patients with PM may potentially offer opportunities for novel therapeutics and suggest that IHC-microarray is a method that can be used in this population.

  18. Towards the integration, annotation and association of historical microarray experiments with RNA-seq.

    Science.gov (United States)

    Chavan, Shweta S; Bauer, Michael A; Peterson, Erich A; Heuck, Christoph J; Johann, Donald J

    2013-01-01

    Transcriptome analysis by microarrays has produced important advances in biomedicine. For instance in multiple myeloma (MM), microarray approaches led to the development of an effective disease subtyping via cluster assignment, and a 70 gene risk score. Both enabled an improved molecular understanding of MM, and have provided prognostic information for the purposes of clinical management. Many researchers are now transitioning to Next Generation Sequencing (NGS) approaches and RNA-seq in particular, due to its discovery-based nature, improved sensitivity, and dynamic range. Additionally, RNA-seq allows for the analysis of gene isoforms, splice variants, and novel gene fusions. Given the voluminous amounts of historical microarray data, there is now a need to associate and integrate microarray and RNA-seq data via advanced bioinformatic approaches. Custom software was developed following a model-view-controller (MVC) approach to integrate Affymetrix probe set-IDs, and gene annotation information from a variety of sources. The tool/approach employs an assortment of strategies to integrate, cross reference, and associate microarray and RNA-seq datasets. Output from a variety of transcriptome reconstruction and quantitation tools (e.g., Cufflinks) can be directly integrated, and/or associated with Affymetrix probe set data, as well as necessary gene identifiers and/or symbols from a diversity of sources. Strategies are employed to maximize the annotation and cross referencing process. Custom gene sets (e.g., MM 70 risk score (GEP-70)) can be specified, and the tool can be directly assimilated into an RNA-seq pipeline. A novel bioinformatic approach to aid in the facilitation of both annotation and association of historic microarray data, in conjunction with richer RNA-seq data, is now assisting with the study of MM cancer biology.

  19. Moving Toward Integrating Gene Expression Profiling into High-throughput Testing:A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium

    Science.gov (United States)

    Microarray profiling of chemical-induced effects is being increasingly used in medium and high-throughput formats. In this study, we describe computational methods to identify molecular targets from whole-genome microarray data using as an example the estrogen receptor α (ERα), ...

  20. Carbon nanoparticles as detection labels in antibody microarrays. Detection of genes encoding virulence factors in Shiga toxin-producing Escherichia coli.

    NARCIS (Netherlands)

    Noguera, P.S.; Posthuma-Trumpie, G.A.; Tuil, Van M.; Wal, van der F.J.; Boer, De A.; Moers, A.P.H.A.; Amerongen, Van A.

    2011-01-01

    The present study demonstrates that carbon nanoparticles (CNPs) can be used as labels in microarrays. CNPs were used in nucleic acid microarray immunoassays (NAMIAs) for the detection of different Shiga toxin-producing Escherichia coli (STEC) virulence factors: four genes specific for STEC (vt1,

  1. Construction and temporal behaviour study of multi RLC intense light pulses for dermatological applications.

    Science.gov (United States)

    Hamoudi, Walid K; Ismail, Raid A; Shakir, Hussein A

    2017-10-01

    Driving a flash lamp in an intense pulsed light system requires a high-voltage DC power supply, capacitive energy storage and a flash lamp triggering unit. Single, double, triple and quadruple-mesh discharge and triggering circuits were constructed to provide intense light pulses of variable energy and time durations. The system was treated as [Formula: see text] circuit in some cases and [Formula: see text] circuit in others with a light pulse profile following the temporal behaviour of the exciting current pulse. Distributing the energy delivered to one lamp onto a number of LC meshes permitted longer current pulses, and consequently increased the light pulse length. Positive results were obtained when using the system to treat skin wrinkles.

  2. Cognitive function fifty-six years after surgical treatment of temporal lobe epilepsy: A case study

    Directory of Open Access Journals (Sweden)

    Sarah Jane Banks

    2014-01-01

    Our investigation at 56 postoperative years focused on cognitive skills, with some emphasis on learning and memory; a clinical examination was also performed, and the anatomical extent of the resection was determined on 3-Tesla magnetic resonance imaging. Four age- and IQ-appropriate women were tested as healthy control subjects. The patient showed material-specific impairments in language and verbal memory compared with the control subjects and also compared with her own earlier performance, but her performance on other cognitive tasks did not differ from that of the control subjects. Thus, her specific deficits had worsened over time, and she was also impaired compared with healthy individuals of her age, but her deficits remained confined to the verbal sphere, consistent with her temporal lobe seizure focus and surgery.

  3. Study on temporal and spatial variations of urban land use based on land change data

    Science.gov (United States)

    Jiang, Ping; Liu, Yanfang; Fan, Min; Zhang, Yang

    2009-10-01

    With the rapid development of urbanization, demands of urban land increase in succession, hence, to analyze temporal and spatial variations of urban land use becomes more and more important. In this paper, the principle of trend surface analysis and formula of urban land sprawl index ( ULSI) are expatiated at first, and then based on land change data of Jiayu county, the author fits quadratic trend surface by choosing urban land area as dependent variable and urbanization and GDP as independent variables from 1996 to 2006, draws isoline of trend surface and residual values; and then urban land sprawl indexes of towns are calculated on the basis of urban land area of 1996 and 2006 and distribution map of ULSI is plotted. After analyzing those results, we can conclude that there is consanguineous relationship between urban land area and urbanization, economic level etc.

  4. ePRISM: A case study in multiple proxy and mixed temporal resolution integration

    Science.gov (United States)

    Robinson, Marci M.; Dowsett, Harry J.

    2010-01-01

    As part of the Pliocene Research, Interpretation and Synoptic Mapping (PRISM) Project, we present the ePRISM experiment designed I) to provide climate modelers with a reconstruction of an early Pliocene warm period that was warmer than the PRISM interval (similar to 3.3 to 3.0 Ma), yet still similar in many ways to modern conditions and 2) to provide an example of how best to integrate multiple-proxy sea surface temperature (SST) data from time series with varying degrees of temporal resolution and age control as we begin to build the next generation of PRISM, the PRISM4 reconstruction, spanning a constricted time interval. While it is possible to tie individual SST estimates to a single light (warm) oxygen isotope event, we find that the warm peak average of SST estimates over a narrowed time interval is preferential for paleoclimate reconstruction as it allows for the inclusion of more records of multiple paleotemperature proxies.

  5. A phantom study on temporal and subband Minimum Variance adaptive beamforming

    DEFF Research Database (Denmark)

    Diamantis, Konstantinos; Voxen, Iben Holfort; Greenaway, Alan H.

    2014-01-01

    This paper compares experimentally temporal and subband implementations of the Minimum Variance (MV) adaptive beamformer for medical ultrasound imaging. The performance of the two approaches is tested by comparing wire phantom measurements, obtained by the research ultrasound scanner SARUS. A 7 MHz...... BK8804 linear transducer was used to scan a wire phantom in which wires are separated by 10 mm. Performance is then evaluated by the lateral Full-Width-Half-Maximum (FWHM), the Peak Sidelobe Level (PSL), and the computational load. Beamformed single emission responses are also compared with those...... from conventional Delay-and-Sum (DAS) beamformer. FWHM measured at the depth of 46.6 mm, is 0.02 mm (0.09λ) for both adaptive methods while the corresponding values for Hanning and Boxcar weights are 0.64 and 0.44 mm respectively. Between the MV beamformers a -2 dB difference in PSL is noticed in favor...

  6. Complete gene expression profiling of Saccharopolyspora erythraea using GeneChip DNA microarrays

    Directory of Open Access Journals (Sweden)

    Bordoni Roberta

    2007-11-01

    Full Text Available Abstract Background The Saccharopolyspora erythraea genome sequence, recently published, presents considerable divergence from those of streptomycetes in gene organization and function, confirming the remarkable potential of S. erythraea for producing many other secondary metabolites in addition to erythromycin. In order to investigate, at whole transcriptome level, how S. erythraea genes are modulated, a DNA microarray was specifically designed and constructed on the S. erythraea strain NRRL 2338 genome sequence, and the expression profiles of 6494 ORFs were monitored during growth in complex liquid medium. Results The transcriptional analysis identified a set of 404 genes, whose transcriptional signals vary during growth and characterize three distinct phases: a rapid growth until 32 h (Phase A; a growth slowdown until 52 h (Phase B; and another rapid growth phase from 56 h to 72 h (Phase C before the cells enter the stationary phase. A non-parametric statistical method, that identifies chromosomal regions with transcriptional imbalances, determined regional organization of transcription along the chromosome, highlighting differences between core and non-core regions, and strand specific patterns of expression. Microarray data were used to characterize the temporal behaviour of major functional classes and of all the gene clusters for secondary metabolism. The results confirmed that the ery cluster is up-regulated during Phase A and identified six additional clusters (for terpenes and non-ribosomal peptides that are clearly regulated in later phases. Conclusion The use of a S. erythraea DNA microarray improved specificity and sensitivity of gene expression analysis, allowing a global and at the same time detailed picture of how S. erythraea genes are modulated. This work underlines the importance of using DNA microarrays, coupled with an exhaustive statistical and bioinformatic analysis of the results, to understand the transcriptional

  7. Spatial and temporal variation of particulate matter characteristics within office buildings - The OFFICAIR study.

    Science.gov (United States)

    Szigeti, Tamás; Dunster, Christina; Cattaneo, Andrea; Spinazzè, Andrea; Mandin, Corinne; Le Ponner, Eline; de Oliveira Fernandes, Eduardo; Ventura, Gabriela; Saraga, Dikaia E; Sakellaris, Ioannis A; de Kluizenaar, Yvonne; Cornelissen, Eric; Bartzis, John G; Kelly, Frank J

    2017-06-01

    In the frame of the OFFICAIR project, office buildings were investigated across Europe to assess how the office workers are exposed to different particulate matter (PM) characteristics (i.e. PM 2.5 mass concentration, particulate oxidative potential (OP) based on ascorbate and reduced glutathione depletion, trace element concentration and total particle number concentration (PNC)) within the buildings. Two offices per building were investigated during the working hours (5 consecutive days; 8h per day) in two campaigns. Differences were observed for all parameters across the office buildings. Our results indicate that the monitoring of the PM 2.5 mass concentration in different offices within a building might not reflect the spatial variation of the health relevant PM characteristics such as particulate OP or the concentration of certain trace elements (e.g., Cu, Fe), since larger differences were apparent within a building for these parameters compared to that obtained for the PM 2.5 mass concentration in many cases. The temporal variation was larger for almost all PM characteristics (except for the concentration of Mn) than the spatial differences within the office buildings. These findings indicate that repeated or long-term monitoring campaigns are necessary to have information about the temporal variation of the PM characteristics. However, spatial variation in exposure levels within an office building may cause substantial differences in total exposure in the long term. We did not find strong associations between the investigated indoor activities such as printing or windows opening and the PNC values. This might be caused by the large number of factors affecting PNC indoors and outdoors. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Temporal resolution of orientation-defined texture segregation: a VEP study.

    Science.gov (United States)

    Lachapelle, Julie; McKerral, Michelle; Jauffret, Colin; Bach, Michael

    2008-09-01

    Orientation is one of the visual dimensions that subserve figure-ground discrimination. A spatial gradient in orientation leads to "texture segregation", which is thought to be concurrent parallel processing across the visual field, without scanning. In the visual-evoked potential (VEP) a component can be isolated which is related to texture segregation ("tsVEP"). Our objective was to evaluate the temporal frequency dependence of the tsVEP to compare processing speed of low-level features (e.g., orientation, using the VEP, here denoted llVEP) with texture segregation because of a recent literature controversy in that regard. Visual-evoked potentials (VEPs) were recorded in seven normal adults. Oriented line segments of 0.1 degrees x 0.8 degrees at 100% contrast were presented in four different arrangements: either oriented in parallel for two homogeneous stimuli (from which were obtained the low-level VEP (llVEP)) or with a 90 degrees orientation gradient for two textured ones (from which were obtained the texture VEP). The orientation texture condition was presented at eight different temporal frequencies ranging from 7.5 to 45 Hz. Fourier analysis was used to isolate low-level components at the pattern-change frequency and texture-segregation components at half that frequency. For all subjects, there was lower high-cutoff frequency for tsVEP than for llVEPs, on average 12 Hz vs. 17 Hz (P = 0.017). The results suggest that the processing of feature gradients to extract texture segregation requires additional processing time, resulting in a lower fusion frequency.

  9. Shared probe design and existing microarray reanalysis using PICKY

    Directory of Open Access Journals (Sweden)

    Chou Hui-Hsien

    2010-04-01

    Full Text Available Abstract Background Large genomes contain families of highly similar genes that cannot be individually identified by microarray probes. This limitation is due to thermodynamic restrictions and cannot be resolved by any computational method. Since gene annotations are updated more frequently than microarrays, another common issue facing microarray users is that existing microarrays must be routinely reanalyzed to determine probes that are still useful with respect to the updated annotations. Results PICKY 2.0 can design shared probes for sets of genes that cannot be individually identified using unique probes. PICKY 2.0 uses novel algorithms to track sharable regions among genes and to strictly distinguish them from other highly similar but nontarget regions during thermodynamic comparisons. Therefore, PICKY does not sacrifice the quality of shared probes when choosing them. The latest PICKY 2.1 includes the new capability to reanalyze existing microarray probes against updated gene sets to determine probes that are still valid to use. In addition, more precise nonlinear salt effect estimates and other improvements are added, making PICKY 2.1 more versatile to microarray users. Conclusions Shared probes allow expressed gene family members to be detected; this capability is generally more desirable than not knowing anything about these genes. Shared probes also enable the design of cross-genome microarrays, which facilitate multiple species identification in environmental samples. The new nonlinear salt effect calculation significantly increases the precision of probes at a lower buffer salt concentration, and the probe reanalysis function improves existing microarray result interpretations.

  10. A Critical Perspective On Microarray Breast Cancer Gene Expression Profiling

    NARCIS (Netherlands)

    Sontrop, H.M.J.

    2015-01-01

    Microarrays offer biologists an exciting tool that allows the simultaneous assessment of gene expression levels for thousands of genes at once. At the time of their inception, microarrays were hailed as the new dawn in cancer biology and oncology practice with the hope that within a decade diseases

  11. Uses of Dendrimers for DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Jean-Pierre Majoral

    2006-08-01

    Full Text Available Biosensors such as DNA microarrays and microchips are gaining an increasingimportance in medicinal, forensic, and environmental analyses. Such devices are based onthe detection of supramolecular interactions called hybridizations that occur betweencomplementary oligonucleotides, one linked to a solid surface (the probe, and the other oneto be analyzed (the target. This paper focuses on the improvements that hyperbranched andperfectly defined nanomolecules called dendrimers can provide to this methodology. Twomain uses of dendrimers for such purpose have been described up to now; either thedendrimer is used as linker between the solid surface and the probe oligonucleotide, or thedendrimer is used as a multilabeled entity linked to the target oligonucleotide. In the firstcase the dendrimer generally induces a higher loading of probes and an easier hybridization,due to moving away the solid phase. In the second case the high number of localized labels(generally fluorescent induces an increased sensitivity, allowing the detection of smallquantities of biological entities.

  12. Bystander effect: Biological endpoints and microarray analysis

    Energy Technology Data Exchange (ETDEWEB)

    Chaudhry, M. Ahmad [Department of Medical Laboratory and Radiation Sciences, College of Nursing and Health Sciences, University of Vermont, 302 Rowell Building, Burlington, VT 05405 (United States) and DNA Microarray Facility, University of Vermont, Burlington, VT 05405 (United States)]. E-mail: mchaudhr@uvm.edu

    2006-05-11

    In cell populations exposed to ionizing radiation, the biological effects occur in a much larger proportion of cells than are estimated to be traversed by radiation. It has been suggested that irradiated cells are capable of providing signals to the neighboring unirradiated cells resulting in damage to these cells. This phenomenon is termed the bystander effect. The bystander effect induces persistent, long-term, transmissible changes that result in delayed death and neoplastic transformation. Because the bystander effect is relevant to carcinogenesis, it could have significant implications for risk estimation for radiation exposure. The nature of the bystander effect signal and how it impacts the unirradiated cells remains to be elucidated. Examination of the changes in gene expression could provide clues to understanding the bystander effect and could define the signaling pathways involved in sustaining damage to these cells. The microarray technology serves as a tool to gain insight into the molecular pathways leading to bystander effect. Using medium from irradiated normal human diploid lung fibroblasts as a model system we examined gene expression alterations in bystander cells. The microarray data revealed that the radiation-induced gene expression profile in irradiated cells is different from unirradiated bystander cells suggesting that the pathways leading to biological effects in the bystander cells are different from the directly irradiated cells. The genes known to be responsive to ionizing radiation were observed in irradiated cells. Several genes were upregulated in cells receiving media from irradiated cells. Surprisingly no genes were found to be downregulated in these cells. A number of genes belonging to extracellular signaling, growth factors and several receptors were identified in bystander cells. Interestingly 15 genes involved in the cell communication processes were found to be upregulated. The induction of receptors and the cell

  13. Bystander effect: Biological endpoints and microarray analysis

    International Nuclear Information System (INIS)

    Chaudhry, M. Ahmad

    2006-01-01

    In cell populations exposed to ionizing radiation, the biological effects occur in a much larger proportion of cells than are estimated to be traversed by radiation. It has been suggested that irradiated cells are capable of providing signals to the neighboring unirradiated cells resulting in damage to these cells. This phenomenon is termed the bystander effect. The bystander effect induces persistent, long-term, transmissible changes that result in delayed death and neoplastic transformation. Because the bystander effect is relevant to carcinogenesis, it could have significant implications for risk estimation for radiation exposure. The nature of the bystander effect signal and how it impacts the unirradiated cells remains to be elucidated. Examination of the changes in gene expression could provide clues to understanding the bystander effect and could define the signaling pathways involved in sustaining damage to these cells. The microarray technology serves as a tool to gain insight into the molecular pathways leading to bystander effect. Using medium from irradiated normal human diploid lung fibroblasts as a model system we examined gene expression alterations in bystander cells. The microarray data revealed that the radiation-induced gene expression profile in irradiated cells is different from unirradiated bystander cells suggesting that the pathways leading to biological effects in the bystander cells are different from the directly irradiated cells. The genes known to be responsive to ionizing radiation were observed in irradiated cells. Several genes were upregulated in cells receiving media from irradiated cells. Surprisingly no genes were found to be downregulated in these cells. A number of genes belonging to extracellular signaling, growth factors and several receptors were identified in bystander cells. Interestingly 15 genes involved in the cell communication processes were found to be upregulated. The induction of receptors and the cell

  14. Lipid Microarray Biosensor for Biotoxin Detection.

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Anup K.; Throckmorton, Daniel J.; Moran-Mirabal, Jose C.; Edel, Joshua B.; Meyer, Grant D.; Craighead, Harold G.

    2006-05-01

    We present the use of micron-sized lipid domains, patterned onto planar substrates and within microfluidic channels, to assay the binding of bacterial toxins via total internal reflection fluorescence microscopy (TIRFM). The lipid domains were patterned using a polymer lift-off technique and consisted of ganglioside-populated DSPC:cholesterol supported lipid bilayers (SLBs). Lipid patterns were formed on the substrates by vesicle fusion followed by polymer lift-off, which revealed micron-sized SLBs containing either ganglioside GT1b or GM1. The ganglioside-populated SLB arrays were then exposed to either Cholera toxin subunit B (CTB) or Tetanus toxin fragment C (TTC). Binding was assayed on planar substrates by TIRFM down to 1 nM concentration for CTB and 100 nM for TTC. Apparent binding constants extracted from three different models applied to the binding curves suggest that binding of a protein to a lipid-based receptor is strongly affected by the lipid composition of the SLB and by the substrate on which the bilayer is formed. Patterning of SLBs inside microfluidic channels also allowed the preparation of lipid domains with different compositions on a single device. Arrays within microfluidic channels were used to achieve segregation and selective binding from a binary mixture of the toxin fragments in one device. The binding and segregation within the microfluidic channels was assayed with epifluorescence as proof of concept. We propose that the method used for patterning the lipid microarrays on planar substrates and within microfluidic channels can be easily adapted to proteins or nucleic acids and can be used for biosensor applications and cell stimulation assays under different flow conditions. KEYWORDS. Microarray, ganglioside, polymer lift-off, cholera toxin, tetanus toxin, TIRFM, binding constant.4

  15. cDNA microarray screening in food safety

    International Nuclear Information System (INIS)

    Roy, Sashwati; Sen, Chandan K.

    2006-01-01

    The cDNA microarray technology and related bioinformatics tools presents a wide range of novel application opportunities. The technology may be productively applied to address food safety. In this mini-review article, we present an update highlighting the late breaking discoveries that demonstrate the vitality of cDNA microarray technology as a tool to analyze food safety with reference to microbial pathogens and genetically modified foods. In order to bring the microarray technology to mainstream food safety, it is important to develop robust user-friendly tools that may be applied in a field setting. In addition, there needs to be a standardized process for regulatory agencies to interpret and act upon microarray-based data. The cDNA microarray approach is an emergent technology in diagnostics. Its values lie in being able to provide complimentary molecular insight when employed in addition to traditional tests for food safety, as part of a more comprehensive battery of tests

  16. Development and application of an oligonucleotide microarray and real-time quantitative PCR for detection of wastewater bacterial pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dae-Young [National Water Research Institute, Environment Canada, 867 Lakeshore Road, Burlington, Ontario, L7R 4A6 (Canada)], E-mail: daeyoung.lee@ec.gc.ca; Lauder, Heather; Cruwys, Heather; Falletta, Patricia [National Water Research Institute, Environment Canada, 867 Lakeshore Road, Burlington, Ontario, L7R 4A6 (Canada); Beaudette, Lee A. [Environmental Science and Technology Centre, Environment Canada, 335 River Road South, Ottawa, Ontario, K1A 0H3 (Canada)], E-mail: lee.beaudette@ec.gc.ca

    2008-07-15

    Conventional microbial water quality test methods are well known for their technical limitations, such as lack of direct pathogen detection capacity and low throughput capability. The microarray assay has recently emerged as a promising alternative for environmental pathogen monitoring. In this study, bacterial pathogens were detected in municipal wastewater using a microarray equipped with short oligonucleotide probes targeting 16S rRNA sequences. To date, 62 probes have been designed against 38 species, 4 genera, and 1 family of pathogens. The detection sensitivity of the microarray for a waterborne pathogen Aeromonas hydrophila was determined to be approximately 1.0% of the total DNA, or approximately 10{sup 3}A. hydrophila cells per sample. The efficacy of the DNA microarray was verified in a parallel study where pathogen genes and E. coli cells were enumerated using real-time quantitative PCR (qPCR) and standard membrane filter techniques, respectively. The microarray and qPCR successfully detected multiple wastewater pathogen species at different stages of the disinfection process (i.e. secondary effluents vs. disinfected final effluents) and at two treatment plants employing different disinfection methods (i.e. chlorination vs. UV irradiation). This result demonstrates the effectiveness of the DNA microarray as a semi-quantitative, high throughput pathogen monitoring tool for municipal wastewater.

  17. Gaussian mixture clustering and imputation of microarray data.

    Science.gov (United States)

    Ouyang, Ming; Welsh, William J; Georgopoulos, Panos

    2004-04-12

    In microarray experiments, missing entries arise from blemishes on the chips. In large-scale studies, virtually every chip contains some missing entries and more than 90% of the genes are affected. Many analysis methods require a full set of data. Either those genes with missing entries are excluded, or the missing entries are filled with estimates prior to the analyses. This study compares methods of missing value estimation. Two evaluation metrics of imputation accuracy are employed. First, the root mean squared error measures the difference between the true values and the imputed values. Second, the number of mis-clustered genes measures the difference between clustering with true values and that with imputed values; it examines the bias introduced by imputation to clustering. The Gaussian mixture clustering with model averaging imputation is superior to all other imputation methods, according to both evaluation metrics, on both time-series (correlated) and non-time series (uncorrelated) data sets.

  18. Versatile High Resolution Oligosaccharide Microarrays for Plant Glycobiology and Cell Wall Research

    DEFF Research Database (Denmark)

    Pedersen, Henriette Lodberg; Fangel, Jonatan Ulrik; McCleary, Barry

    2012-01-01

    Microarrays are powerful tools for high throughput analysis, and hundreds or thousands of molecular interactions can be assessed simultaneously using very small amounts of analytes. Nucleotide microarrays are well established in plant research, but carbohydrate microarrays are much less establish...

  19. The Relative Importance of Spatial Versus Temporal Structure in the Perception of Biological Motion: An Event-Related Potential Study

    Science.gov (United States)

    Hirai, Masahiro; Hiraki, Kazuo

    2006-01-01

    We investigated how the spatiotemporal structure of animations of biological motion (BM) affects brain activity. We measured event-related potentials (ERPs) during the perception of BM under four conditions: normal spatial and temporal structure; scrambled spatial and normal temporal structure; normal spatial and scrambled temporal structure; and…

  20. Microarray analysis of gender- and parasite-specific gene transcription in Strongyloides ratti

    NARCIS (Netherlands)

    Evans, Helen; Mello, Luciane V.; Fang, Yongxiang; Wit, Ernst; Thompson, Fiona J.; Viney, Mark E.; Paterson, Steve

    2008-01-01

    The molecular mechanisms by which parasitic nematodes reproduce and have adapted to life within a host are unclear. In the present study, microarray analysis was used to explore differential transcription among the different stages and sexes of Strongyloides ratti, a parasitic nematode of brown

  1. Development of a biosensor microarray towards food screening using imaging surface plasmon resonance

    NARCIS (Netherlands)

    Rebe, S.; Bremer, M.G.E.G.; Giesbers, M.; Norde, W.

    2008-01-01

    In this study we examined the possibilities of implementing direct and competitive immunoassay formats for small and large molecule detection on a microarray, using IBIS imaging surface plasmon resonance (iSPR) system. First, IBIS iSPR optics performance was evaluated. Using a glycerol calibration

  2. Development of a biosensor microarray towards food screening, using imaging surface plasmon resonance

    NARCIS (Netherlands)

    Raz, Sabina Rebe; Bremer, Maria G. E. G.; Giesbers, Marcel; Norde, Willem

    2008-01-01

    In this study we examined the possibilities of implementing direct and competitive immunoassay formats for small and large molecule detection on a microarray, using IBIS imaging surface plasmon resonance (iSPR) system. First, IBIS iSPR optics performance was evaluated. Using a glycerol calibration

  3. Chromosomal microarrays testing in children with developmental disabilities and congenital anomalies

    Directory of Open Access Journals (Sweden)

    Guillermo Lay-Son

    2015-04-01

    Full Text Available OBJECTIVES: Clinical use of microarray-based techniques for the a