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Sample records for temporal microarray study

  1. 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

  2. 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.

  3. Identification of temporal association rules from time-series microarray data sets.

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    Nam, Hojung; Lee, KiYoung; Lee, Doheon

    2009-03-19

    One of the most challenging problems in mining gene expression data is to identify how the expression of any particular gene affects the expression of other genes. To elucidate the relationships between genes, an association rule mining (ARM) method has been applied to microarray gene expression data. However, a conventional ARM method has a limit on extracting temporal dependencies between gene expressions, though the temporal information is indispensable to discover underlying regulation mechanisms in biological pathways. In this paper, we propose a novel method, referred to as temporal association rule mining (TARM), which can extract temporal dependencies among related genes. A temporal association rule has the form [gene A upward arrow, gene B downward arrow] --> (7 min) [gene C upward arrow], which represents that high expression level of gene A and significant repression of gene B followed by significant expression of gene C after 7 minutes. The proposed TARM method is tested with Saccharomyces cerevisiae cell cycle time-series microarray gene expression data set. In the parameter fitting phase of TARM, the fitted parameter set [threshold = +/- 0.8, support >or= 3 transactions, confidence >or= 90%] with the best precision score for KEGG cell cycle pathway has been chosen for rule mining phase. With the fitted parameter set, numbers of temporal association rules with five transcriptional time delays (0, 7, 14, 21, 28 minutes) are extracted from gene expression data of 799 genes, which are pre-identified cell cycle relevant genes. From the extracted temporal association rules, associated genes, which play same role of biological processes within short transcriptional time delay and some temporal dependencies between genes with specific biological processes are identified. In this work, we proposed TARM, which is an applied form of conventional ARM. TARM showed higher precision score than Dynamic Bayesian network and Bayesian network. Advantages of TARM are

  4. Near-optimal designs for dual channel microarray studies

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    Wit, Ernst; Nobile, Agostino; Khanin, Raya

    2005-01-01

    Much biological and medical research employs microarray studies to monitor gene expression levels across a wide range of organisms and under many experimental conditions. Dual channel microarrays are a common platform and allow two samples to be measured simultaneously. A frequently used design uses

  5. Tissue microarray construction for salivary gland tumors study

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    Paiva-Fonseca, Felipe; de-Almeida, Oslei P.; Ayroza-Rangel, Ana L C.

    2013-01-01

    Objective: To describe and discuss the design, building and usefulness of tissue microarray (TMA) blocks for the study of salivary gland tumors (SGTs). Study Design: Two hundred thirty-eight formalin-fixed, paraffin-embedded SGTs were arranged in blocks of TMA using a manual tissue arrayer. Three representative cores of 1.0, 2.0 or 3.0mm were taken from each original block and their characteristics were analyzed and described. Results: It was created 12 TMA blocks that presented highly representative neoplastic cylinders. However, those neoplasias rich in cystic spaces such as mucoepidermoid carcinoma and Warthin tumor presented more difficulties to be sampled, as the neoplastic tissue available was scarce. Tissue damage and loss during TMA construction was estimated as 3.7%. Conclusion: Representative areas of SGTs, with relatively small loss of tissue, can be obtained with the construction of TMA blocks for molecular studies. However, tumors rich in cystic spaces present more difficulties to be adequately sampled. Key words:Tissue microarray, tma, salivary gland tumors, immunohistochemistry. PMID:22926480

  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. Gene expression profiling in cluster headache: a pilot microarray study.

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    Sjöstrand, Christina; Duvefelt, Kristina; Steinberg, Anna; Remahl, Ingela Nilsson; Waldenlind, Elisabet; Hillert, Jan

    2006-01-01

    from this pilot microarray study provide a basis for further studies in CH.

  8. Tissue microarray use for immunohistochemical study of ameloblastoma.

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    Neves-Silva, Rodrigo; Fonseca, Felipe Paiva; de Jesus, Adriana Souza; Pontes, Hélder Antônio Rebelo; Rocha, André Caroli; Brandão, Thais Bianca; Vargas, Pablo Agustin; Lopes, Márcio Ajudarte; de Almeida, Oslei Paes; Santos-Silva, Alan Roger

    2016-10-01

    Ameloblastoma is a locally aggressive odontogenic tumor with high rates of recurrence. To better understand the molecular basis of ameloblastoma, tissue microarray (TMA) may represent a useful tool. However, despite TMA has been considered a high-throughput technique for different human neoplasms, it remains to be validated in the ameloblastoma context. Therefore, the objective of this study was to validate TMA for immunohistochemical study of ameloblastoma, determining its most appropriate design. Forty cases of ameloblastoma were manually distributed in two TMA blocks assembled in triplicate containing 1.0- and 2.0-mm cores (20 cases each). Immunohistochemistry for cytokeratins 14 and 19, and Bcl-2 and Ki-67 was performed, and semiquantitative analysis was performed. Results obtained with TMA sections were compared to their corresponding conventional whole-section slides (CWSS). Kappa statistical test demonstrated that both 1.0- and 2.0-mm cores assessed as duplicate or triplicate significantly correlated with CWSS, with higher levels obtained using Ki67 (k = 0.98, 0.97, 0.88, 0.87) and CK19 (k = 0.62, 0.58, 0.85, 0.85). There was no significant difference between 1.0- and 2.0-mm cores, and between duplicate and triplicate values. 1.0-mm TMA showed a higher index of core loss (33.74% vs. 4.99%). Using a manual arrayer, it was demonstrated that 1.0-mm TMA arranged in duplicate is a valid method for ameloblastoma immunohistochemical study with satisfactory levels of agreement between TMA cylinders and CWSS. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Microarray image segmentation using additional dye--an experimental study.

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    Gupta, Rashi; Ruosaari, Salla; Kulathinal, Sangita; Hollmén, Jaakko; Auvinen, Petri

    2007-01-01

    The DNA microarray technique allows monitoring the expression levels of thousands of genes simultaneously. A single DNA microarray experiment involves a number of error-prone manual and automated processes, which influence the results and have an impact on the subsequent stages of analysis. Typical problems of arrays are pinning errors while probe printing and the corruption of spots by noise patches. These errors should be detected at the time of image analysis in order to prevent the erroneous intensities from ending up in the analysis and inference stages. In this paper we introduce the concept (referred to as SybrSpot) of utilizing information provided by an additional dye, SYBR green RNA II, for segmentation of gene expression microarrays. Owing to the effective binding of the SYBR green RNA II to the array probes, an image with high signal-to-noise ratio is obtained. This image is used to learn about the spot quality and to flag spots which are not reliably hybridized and corrupted by noise. Further, we compare SybrSpot with GenePix and demonstrate that SybrSpot performs better than GenePix when flagging spots with no probes or weak probes. The code is available upon request to authors.

  10. 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

  11. mRNA expression in rabbit experimental aneurysms: a study using gene chip microarrays.

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    Mangrum, W I; Farassati, F; Kadirvel, R; Kolbert, C P; Raghavakaimal, S; Dai, D; Ding, Y H; Grill, D; Khurana, V G; Kallmes, D F

    2007-05-01

    The molecular characteristics of intracranial aneurysms are still poorly documented. A rabbit elastase aneurysm model has been helpful in the evaluation of devices and strategies involved in endovascular treatment of aneurysms. The goal of this project was to document the molecular changes, assessed by gene chip microarrays, associated with the creation of aneurysms in this model compared with the contralateral carotid artery. A microarray of rabbit genes of interest was constructed using rabbit nucleotide sequences from GenBank. Elastase-induced saccular aneurysms were created at the origin of the right common carotid artery in 4 rabbits. Twelve weeks after aneurysm creation, RNA was isolated from the aneurysm as well as the contralateral common carotid artery and used for microarray experiments. Reverse transcription-polymerase chain reaction (RT-PCR) was performed on 1 animal as a confirmatory test. Ninety-six (46%) of 209 genes in the microarray were differentially expressed in the rabbit aneurysm compared with the contralateral common carotid artery. In general, differential gene expression followed specific molecular pathways. Similarities were found between rabbit aneurysms and human intracranial aneurysms, including increased metalloproteinase activity and decreased production of the extracellular matrix. RT-PCR results confirmed the differential expression found by the gene chip microarray. The molecular characteristics of the rabbit elastase-induced saccular aneurysm are described. The rabbit aneurysm model shares some molecular features with human intracranial aneurysms. Future studies can use the rabbit model and the new rabbit gene chip microarray to study the molecular aspects of saccular aneurysms.

  12. Genomic Microarray in Fetuses with Early Growth Restriction: A Multicenter Study.

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    Borrell, Antoni; Grande, Maribel; Meler, Eva; Sabrià, Joan; Mazarico, Edurne; Muñoz, Anna; Rodriguez-Revenga, Laia; Badenas, Cèlia; Figueras, Francesc

    2017-01-01

    Little information is available about the risk of microdeletion and microduplication syndromes in fetal growth restriction (FGR) with a normal karyotype. To assess the incremental yield of genomic microarray over conventional karyotyping in fetuses with early growth restriction. Genomic microarray was prospectively performed in fetuses with early growth restriction defined as a fetal weight below the 3rd percentile estimated before 32 weeks of pregnancy, and a normal quantitative fluorescent polymerase chain reaction result. The incremental yield of genomic microarray was defined by the rate of fetuses presenting with a pathogenic copy number variant below 10 Mb. Among 133 fetuses with early FGR, a 6.8% (95% CI: 2.5-11.0) incremental yield of genomic microarray over karyotyping was observed. This incremental yield was 4.8% (95% CI: 0.2-9.3) in isolated FGR, 10% (95% CI: 0-20.7) in FGR with nonstructural anomalies, and 10.5% (95% CI: 0-24.3) in FGR with structural anomalies. Our multicenter study reveals that 6.8% of fetuses with early growth restriction present with submicroscopic anomalies after common aneuploidies were excluded. Even when FGR is observed as an isolated finding, genomic microarray analysis should be considered after or instead of karyotyping, due to its 4.8% incremental yield. © 2016 S. Karger AG, Basel.

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

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    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

  14. 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.

  15. 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 microarray analysis is a reliable and high-resolution technology and should be used as the first-tier test for prenatal diagnosis of congenital heart disease in clinical practice. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Screening of FGF target genes in Xenopus by microarray: temporal dissection of the signalling pathway using a chemical inhibitor.

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    Chung, Hyeyoung A; Hyodo-Miura, Junko; Kitayama, Atsushi; Terasaka, Chie; Nagamune, Teruyuki; Ueno, Naoto

    2004-08-01

    Microarray is a powerful tool for analysing gene expression patterns in genome-wide view and has greatly contributed to our understanding of spatiotemporal embryonic development at the molecular level. Members of FGF (fibroblast growth factor) family play important roles in embryogenesis, e.g. in organogenesis, proliferation, differentiation, cell migration, angiogenesis, and wound healing. To dissect spatiotemporally the versatile roles of FGF during embryogenesis, we profiled gene expression in Xenopus embryo explants treated with SU5402, a chemical inhibitor specific to FGF receptor 1 (FGFR1), by microarray. We identified 38 genes that were down-regulated and 5 that were up-regulated in response to SU5402 treatment from stage 10.5-11.5 and confirmed their FGF-dependent transcription with RT-PCR analysis and whole-mount in situ hybridization (WISH). Among the 43 genes, we identified 26 as encoding novel proteins and investigated their spatial expression pattern by WISH. Genes whose expression patterns were similar to FGFR1 were further analysed to test whether any of them represented functional FGF target molecules. Here, we report two interesting genes: one is a component of the canonical Ras-MAPK pathway, similar to mammalian mig6 (mitogen-inducible gene 6) acting in muscle differentiation; the other, similar to GPCR4 (G-protein coupled receptor 4), is a promising candidate for a gastrulation movement regulator. These results demonstrate that our approach is a promising strategy for scanning the genes that are essential for the regulation of a diverse array of developmental processes.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Carbohydrate microarrays

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    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-based technol......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......-based technology has been widely employed for rapid analysis of the glycan binding properties of lectins and antibodies, the quantitative measurements of glycan-protein interactions, detection of cells and pathogens, identification of disease-related anti-glycan antibodies for diagnosis, and fast assessment...

  3. A study of inter-lab and inter-platform agreement of DNA microarray data

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    Wilson Carole

    2005-05-01

    Full Text Available Abstract As gene expression profile data from DNA microarrays accumulate rapidly, there is a natural need to compare data across labs and platforms. Comparisons of microarray data can be quite challenging due to data complexity and variability. Different labs may adopt different technology platforms. One may ask about the degree of agreement we can expect from different labs and different platforms. To address this question, we conducted a study of inter-lab and inter-platform agreement of microarray data across three platforms and three labs. The statistical measures of consistency and agreement used in this paper are the Pearson correlation, intraclass correlation, kappa coefficients, and a measure of intra-transcript correlation. The three platforms used in the present paper were Affymetrix GeneChip, custom cDNA arrays, and custom oligo arrays. Using the within-platform variability as a benchmark, we found that these technology platforms exhibited an acceptable level of agreement, but the agreement between two technologies within the same lab was greater than that between two labs using the same technology. The consistency of replicates in each experiment varies from lab to lab. When there is high consistency among replicates, different technologies show good agreement within and across labs using the same RNA samples. On the other hand, the lab effect, especially when confounded with the RNA sample effect, plays a bigger role than the platform effect on data agreement.

  4. Design of a combinatorial dna microarray for protein-dnainteraction studies

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    Mintseris, Julian; Eisen, Michael B.

    2006-07-07

    Background: Discovery of precise specificity oftranscription factors is an important step on the way to understandingthe complex mechanisms of gene regulation in eukaryotes. Recently,doublestranded protein-binding microarrays were developed as apotentially scalable approach to tackle transcription factor binding siteidentification. Results: Here we present an algorithmic approach toexperimental design of a microarray that allows for testing fullspecificity of a transcription factor binding to all possible DNA bindingsites of a given length, with optimally efficient use of the array. Thisdesign is universal, works for any factor that binds a sequence motif andis not species-specific. Furthermore, simulation results show that dataproduced with the designed arrays is easier to analyze and would resultin more precise identification of binding sites. Conclusion: In thisstudy, we present a design of a double stranded DNA microarray forprotein-DNA interaction studies and show that our algorithm allowsoptimally efficient use of the arrays for this purpose. We believe such adesign will prove useful for transcription factor binding siteidentification and other biological problems.

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

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    Ballerstedt, Hendrik; Volkers, Rita J. M.; Mars, Astrid E.; Hallsworth, John E.; Santos, Vitor A. Martins dos; Puchalka, Ja?ek; van Duuren, Joost; Eggink, Gerrit; Timmis, Ken N.; de Bont, Jan A. M.; Wery, Jan

    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 transcriptomics studies of other Pseudomonas strains was investigated. To this end, microarray hybridizations were performed with genomic DNAs of subcultures of P. putida KT2440 (DSM6125), the type...

  6. DNA Microarrays

    Science.gov (United States)

    Nguyen, C.; Gidrol, X.

    Genomics has revolutionised biological and biomedical research. This revolution was predictable on the basis of its two driving forces: the ever increasing availability of genome sequences and the development of new technology able to exploit them. Up until now, technical limitations meant that molecular biology could only analyse one or two parameters per experiment, providing relatively little information compared with the great complexity of the systems under investigation. This gene by gene approach is inadequate to understand biological systems containing several thousand genes. It is essential to have an overall view of the DNA, RNA, and relevant proteins. A simple inventory of the genome is not sufficient to understand the functions of the genes, or indeed the way that cells and organisms work. For this purpose, functional studies based on whole genomes are needed. Among these new large-scale methods of molecular analysis, DNA microarrays provide a way of studying the genome and the transcriptome. The idea of integrating a large amount of data derived from a support with very small area has led biologists to call these chips, borrowing the term from the microelectronics industry. At the beginning of the 1990s, the development of DNA chips on nylon membranes [1, 2], then on glass [3] and silicon [4] supports, made it possible for the first time to carry out simultaneous measurements of the equilibrium concentration of all the messenger RNA (mRNA) or transcribed RNA in a cell. These microarrays offer a wide range of applications, in both fundamental and clinical research, providing a method for genome-wide characterisation of changes occurring within a cell or tissue, as for example in polymorphism studies, detection of mutations, and quantitative assays of gene copies. With regard to the transcriptome, it provides a way of characterising differentially expressed genes, profiling given biological states, and identifying regulatory channels.

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

  11. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

    Science.gov (United States)

    Shi, Leming; Campbell, Gregory; Jones, Wendell D; Campagne, Fabien; Wen, Zhining; Walker, Stephen J; Su, Zhenqiang; Chu, Tzu-Ming; Goodsaid, Federico M; Pusztai, Lajos; Shaughnessy, John D; Oberthuer, André; Thomas, Russell S; Paules, Richard S; Fielden, Mark; Barlogie, Bart; Chen, Weijie; Du, Pan; Fischer, Matthias; Furlanello, Cesare; Gallas, Brandon D; Ge, Xijin; Megherbi, Dalila B; Symmans, W Fraser; Wang, May D; Zhang, John; Bitter, Hans; Brors, Benedikt; Bushel, Pierre R; Bylesjo, Max; Chen, Minjun; Cheng, Jie; Cheng, Jing; Chou, Jeff; Davison, Timothy S; Delorenzi, Mauro; Deng, Youping; Devanarayan, Viswanath; Dix, David J; Dopazo, Joaquin; Dorff, Kevin C; Elloumi, Fathi; Fan, Jianqing; Fan, Shicai; Fan, Xiaohui; Fang, Hong; Gonzaludo, Nina; Hess, Kenneth R; Hong, Huixiao; Huan, Jun; Irizarry, Rafael A; Judson, Richard; Juraeva, Dilafruz; Lababidi, Samir; Lambert, Christophe G; Li, Li; Li, Yanen; Li, Zhen; Lin, Simon M; Liu, Guozhen; Lobenhofer, Edward K; Luo, Jun; Luo, Wen; McCall, Matthew N; Nikolsky, Yuri; Pennello, Gene A; Perkins, Roger G; Philip, Reena; Popovici, Vlad; Price, Nathan D; Qian, Feng; Scherer, Andreas; Shi, Tieliu; Shi, Weiwei; Sung, Jaeyun; Thierry-Mieg, Danielle; Thierry-Mieg, Jean; Thodima, Venkata; Trygg, Johan; Vishnuvajjala, Lakshmi; Wang, Sue Jane; Wu, Jianping; Wu, Yichao; Xie, Qian; Yousef, Waleed A; Zhang, Liang; Zhang, Xuegong; Zhong, Sheng; Zhou, Yiming; Zhu, Sheng; Arasappan, Dhivya; Bao, Wenjun; Lucas, Anne Bergstrom; Berthold, Frank; Brennan, Richard J; Buness, Andreas; Catalano, Jennifer G; Chang, Chang; Chen, Rong; Cheng, Yiyu; Cui, Jian; Czika, Wendy; Demichelis, Francesca; Deng, Xutao; Dosymbekov, Damir; Eils, Roland; Feng, Yang; Fostel, Jennifer; Fulmer-Smentek, Stephanie; Fuscoe, James C; Gatto, Laurent; Ge, Weigong; Goldstein, Darlene R; Guo, Li; Halbert, Donald N; Han, Jing; Harris, Stephen C; Hatzis, Christos; Herman, Damir; Huang, Jianping; Jensen, Roderick V; Jiang, Rui; Johnson, Charles D; Jurman, Giuseppe; Kahlert, Yvonne; Khuder, Sadik A; Kohl, Matthias; Li, Jianying; Li, Li; Li, Menglong; Li, Quan-Zhen; Li, Shao; Li, Zhiguang; Liu, Jie; Liu, Ying; Liu, Zhichao; Meng, Lu; Madera, Manuel; Martinez-Murillo, Francisco; Medina, Ignacio; Meehan, Joseph; Miclaus, Kelci; Moffitt, Richard A; Montaner, David; Mukherjee, Piali; Mulligan, George J; Neville, Padraic; Nikolskaya, Tatiana; Ning, Baitang; Page, Grier P; Parker, Joel; Parry, R Mitchell; Peng, Xuejun; Peterson, Ron L; Phan, John H; Quanz, Brian; Ren, Yi; Riccadonna, Samantha; Roter, Alan H; Samuelson, Frank W; Schumacher, Martin M; Shambaugh, Joseph D; Shi, Qiang; Shippy, Richard; Si, Shengzhu; Smalter, Aaron; Sotiriou, Christos; Soukup, Mat; Staedtler, Frank; Steiner, Guido; Stokes, Todd H; Sun, Qinglan; Tan, Pei-Yi; Tang, Rong; Tezak, Zivana; Thorn, Brett; Tsyganova, Marina; Turpaz, Yaron; Vega, Silvia C; Visintainer, Roberto; von Frese, Juergen; Wang, Charles; Wang, Eric; Wang, Junwei; Wang, Wei; Westermann, Frank; Willey, James C; Woods, Matthew; Wu, Shujian; Xiao, Nianqing; Xu, Joshua; Xu, Lei; Yang, Lun; Zeng, Xiao; Zhang, Jialu; Zhang, Li; Zhang, Min; Zhao, Chen; Puri, Raj K; Scherf, Uwe; Tong, Weida; Wolfinger, Russell D

    2010-08-01

    Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans. In total, >30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. We found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  14. Assessing the utility of confirmatory studies following identification of large-scale genomic imbalances by microarray.

    Science.gov (United States)

    Sanmann, Jennifer N; Pickering, Diane L; Golden, Denae M; Stevens, Jadd M; Hempel, Thomas E; Althof, Pamela A; Wiggins, Michele L; Starr, Lois J; Davé, Bhavana J; Sanger, Warren G

    2015-11-01

    The identification of clinically relevant genomic dosage anomalies assists in accurate diagnosis, prognosis, and medical management of affected individuals. Technological advancements within the field, such as the advent of microarray, have markedly increased the resolution of detection; however, clinical laboratories have maintained conventional techniques for confirmation of genomic imbalances identified by microarray to ensure diagnostic accuracy. In recent years the utility of this confirmatory testing of large-scale aberrations has been questioned but has not been scientifically addressed. We retrospectively reviewed 519 laboratory cases with genomic imbalances meeting reportable criteria by microarray and subsequently confirmed with a second technology, primarily fluorescence in situ hybridization. All genomic imbalances meeting reportable criteria detected by microarray were confirmed with a second technology. Microarray analysis generated no false-positive results. Confirmatory testing of large-scale genomic imbalances (deletion of ≥150 kb, duplication of ≥500 kb) solely for the purpose of microarray verification may be unwarranted. In some cases, however, adjunct testing is necessary to overcome limitations inherent to microarray. A recommended clinical strategy for adjunct testing following identified genomic imbalances using microarray is detailed.

  15. 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

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

    Science.gov (United States)

    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.

  17. Effects on human transcriptome of mutated BRCA1 BRCT domain: A microarray study

    International Nuclear Information System (INIS)

    Iofrida, Caterina; Melissari, Erika; Mariotti, Veronica; Guglielmi, Chiara; Guidugli, Lucia; Caligo, Maria Adelaide; Pellegrini, Silvia

    2012-01-01

    BRCA1 (breast cancer 1, early onset) missense mutations have been detected in familial breast and ovarian cancers, but the role of these variants in cancer predisposition is often difficult to ascertain. In this work, the molecular mechanisms affected in human cells by two BRCA1 missense variants, M1775R and A1789T, both located in the second BRCT (BRCA1 C Terminus) domain, have been investigated. Both these variants were isolated from familial breast cancer patients and the study of their effect on yeast cell transcriptome has previously provided interesting clues to their possible role in the pathogenesis of breast cancer. We compared by Human Whole Genome Microarrays the expression profiles of HeLa cells transfected with one or the other variant and HeLa cells transfected with BRCA1 wild-type. Microarray data analysis was performed by three comparisons: M1775R versus wild-type (M1775RvsWT-contrast), A1789T versus wild-type (A1789TvsWT-contrast) and the mutated BRCT domain versus wild-type (MutvsWT-contrast), considering the two variants as a single mutation of BRCT domain. 201 differentially expressed genes were found in M1775RvsWT-contrast, 313 in A1789TvsWT-contrast and 173 in MutvsWT-contrast. Most of these genes mapped in pathways deregulated in cancer, such as cell cycle progression and DNA damage response and repair. Our results represent the first molecular evidence of the pathogenetic role of M1775R, already proposed by functional studies, and give support to a similar role for A1789T that we first hypothesized based on the yeast cell experiments. This is in line with the very recently suggested role of BRCT domain as the main effector of BRCA1 tumor suppressor activity

  18. Molecular Signature of Cancer at Gene Level or Pathway Level? Case Studies of Colorectal Cancer and Prostate Cancer Microarray Data

    Directory of Open Access Journals (Sweden)

    Jiajia Chen

    2013-01-01

    Full Text Available With recent advances in microarray technology, there has been a flourish in genome-scale identification of molecular signatures for cancer. However, the differentially expressed genes obtained by different laboratories are highly divergent. The present discrepancy at gene level indicates a need for a novel strategy to obtain more robust signatures for cancer. In this paper we hypothesize that (1 the expression signatures of different cancer microarray datasets are more similar at pathway level than at gene level; (2 the comparability of the cancer molecular mechanisms of different individuals is related to their genetic similarities. In support of the hypotheses, we summarized theoretical and experimental evidences, and conducted case studies on colorectal and prostate cancer microarray datasets. Based on the above assumption, we propose that reliable cancer signatures should be investigated in the context of biological pathways, within a cohort of genetically homogeneous population. It is hoped that the hypotheses can guide future research in cancer mechanism and signature discovery.

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

    Science.gov (United States)

    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.

  20. Processing Temporal Constraints: An ERP Study

    Science.gov (United States)

    Baggio, Giosue

    2008-01-01

    This article investigates how linguistic expressions of time--in particular, temporal adverbs and verb tense morphemes--are used to establish temporal reference at the level of brain physiology. First, a formal semantic analysis of tense and temporal adverbs is outlined. It is argued that computing temporal reference amounts to solving a…

  1. 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

    Directory of Open Access Journals (Sweden)

    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.

  2. 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

  3. Economic methods used in fabrication of tissue microarray: A pilot study.

    Science.gov (United States)

    Srinath, Sahana; Kendole, Rohit Kumar; Gopinath, Pavana; Krishnappa, Srinath; Vishwanath, S K

    2016-01-01

    Tissue microarray (TMA) is a method of harvesting small disks of tissue from a range of standard paraffin tissue blocks and placing them in an array on a recipient paraffin block such that hundreds of cases can be analyzed simultaneously by using only a few microliters of antibody in immunohistochemistry as a single experiment. The TMA construction done with the help of automated tissue arrayer or commercially available rubber molds are expensive. This study involved the fabrication of TMA using rubber-based additional silicone mold constructed in the department and comparison of this method with two other methods of fabricating TMA. The TMA mold was fabricated using silicone material in the department. The recipient blocks were prepared. The tissue core prepared from donor blocks were inserted into the recipient blocks. The sections taken from this were compared with the TMA using double-sided adhesive tape technique and TMA by punching out holes in prefabricated dummy paraffin recipient block for insertion of tissue core. The TMA using a mold made of silicone showed more advantages than other two methods. Fabricating TMA mold using silicone in the department is inexpensive and yet efficient.

  4. 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...... 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...

  5. Nanotechnologies in protein microarrays.

    Science.gov (United States)

    Krizkova, Sona; Heger, Zbynek; Zalewska, Marta; Moulick, Amitava; Adam, Vojtech; Kizek, Rene

    2015-01-01

    Protein microarray technology became an important research tool for study and detection of proteins, protein-protein interactions and a number of other applications. The utilization of nanoparticle-based materials and nanotechnology-based techniques for immobilization allows us not only to extend the surface for biomolecule immobilization resulting in enhanced substrate binding properties, decreased background signals and enhanced reporter systems for more sensitive assays. Generally in contemporarily developed microarray systems, multiple nanotechnology-based techniques are combined. In this review, applications of nanoparticles and nanotechnologies in creating protein microarrays, proteins immobilization and detection are summarized. We anticipate that advanced nanotechnologies can be exploited to expand promising fields of proteins identification, monitoring of protein-protein or drug-protein interactions, or proteins structures.

  6. Optimal Design of Genetic Studies of Gene Expression With Two-Color Microarrays in Outbred Crosses

    NARCIS (Netherlands)

    Lam, Alex C.; Fu, Jingyuan; Jansen, Ritsert C.; Haley, Chris S.; de Koning, Dirk-Jan

    2008-01-01

    Combining global gene-expression profiling and genetic analysis of natural allelic variation (genetical genomics) has great potential in dissecting the genetic pathways underlying complex phenotypes. Efficient use of microarrays is paramount in experimental design as the cost. of conducting this

  7. A comprehensive microarray-based DNA methylation study of 367 hematological neoplasms.

    Directory of Open Access Journals (Sweden)

    Jose I Martin-Subero

    2009-09-01

    Full Text Available Alterations in the DNA methylation pattern are a hallmark of leukemias and lymphomas. However, most epigenetic studies in hematologic neoplasms (HNs have focused either on the analysis of few candidate genes or many genes and few HN entities, and comprehensive studies are required.Here, we report for the first time a microarray-based DNA methylation study of 767 genes in 367 HNs diagnosed with 16 of the most representative B-cell (n = 203, T-cell (n = 30, and myeloid (n = 134 neoplasias, as well as 37 samples from different cell types of the hematopoietic system. Using appropriate controls of B-, T-, or myeloid cellular origin, we identified a total of 220 genes hypermethylated in at least one HN entity. In general, promoter hypermethylation was more frequent in lymphoid malignancies than in myeloid malignancies, being germinal center mature B-cell lymphomas as well as B and T precursor lymphoid neoplasias those entities with highest frequency of gene-associated DNA hypermethylation. We also observed a significant correlation between the number of hypermethylated and hypomethylated genes in several mature B-cell neoplasias, but not in precursor B- and T-cell leukemias. Most of the genes becoming hypermethylated contained promoters with high CpG content, and a significant fraction of them are targets of the polycomb repressor complex. Interestingly, T-cell prolymphocytic leukemias show low levels of DNA hypermethylation and a comparatively large number of hypomethylated genes, many of them showing an increased gene expression.We have characterized the DNA methylation profile of a wide range of different HNs entities. As well as identifying genes showing aberrant DNA methylation in certain HN subtypes, we also detected six genes--DBC1, DIO3, FZD9, HS3ST2, MOS, and MYOD1--that were significantly hypermethylated in B-cell, T-cell, and myeloid malignancies. These might therefore play an important role in the development of different HNs.

  8. The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies

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    Reinders Marcel JT

    2006-03-01

    Full Text Available Abstract Background Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers. Results Using two publicly available datasets, i.e., gene-expression data of 285 patients with Acute Myeloid Leukemia (AML, Affymetrix HG-U133A GeneChip and 42 samples of tumor tissue of the embryonal central nervous system (CNS, Affymetrix HuGeneFL GeneChip, we tested the effect of the four pre-processing strategies mentioned above, on (1 expression level measurements, (2 detection of differential expression, (3 cluster analysis and (4 classification of samples. In most cases, the effect of pre-processing is relatively small compared to other choices made in an analysis for the AML dataset, but has a more profound effect on the outcome of the CNS dataset. Analyses on individual probe sets, such as testing for differential expression, are affected most; supervised, multivariate analyses such as classification are far less sensitive to pre-processing. Conclusion Using two experimental datasets, we show that the choice of pre-processing method is of relatively minor influence on the final analysis outcome of large microarray studies whereas it can have important effects on the results of a smaller study. The data source (platform, tissue homogeneity, RNA quality is potentially of bigger importance than the choice of pre-processing method.

  9. Offering pregnant women different levels of genetic information from prenatal chromosome microarray: a prospective study.

    Science.gov (United States)

    Halliday, Jane L; Muller, Cecile; Charles, Taryn; Norris, Fiona; Kennedy, Joanne; Lewis, Sharon; Meiser, Bettina; Donath, Susan; Stark, Zornitza; McGillivray, George; Menezes, Melody; Smith, Sian K; Forster, Della; Walker, Susan; Pertile, Mark; Amor, David J

    2018-02-06

    This study aimed to examine the choice pregnant women make about the amount of fetal genetic information they want from chromosome microarray. Women having invasive prenatal testing in the absence of fetal structural abnormality were recruited in Victoria, Australia. A decision aid for women described 'targeted' analysis as reporting only copy number variants implicated in a highly penetrant and well-described phenotype and 'extended' as additionally reporting variants of uncertain or unknown significance. Participant's choice and demographics were collected by survey before chorionic villus sampling or amniocentesis; psychological data were also collected then and again about 10 days after receiving results. High-resolution single-nucleotide polymorphism array analysis was performed, and a clinical review committee assessed variants for reporting before returning results to participants. Sixty-six participants (59.5%) chose extended analysis and 45 (40.5%) targeted. Choosing extended information was associated with (1) indication for prenatal diagnosis: maternal age alone (adjusted odds ratio (adjOR) 9.6, 95% confidence interval (CI): 1.4-66.0, p= 0.02), or 'other' indication (adjOR 7.1, 95% CI: 1.5-33.1, p= 0.01)); (2) >12 months to conceive (adjOR 4.1, 95% CI: 1.0-17.7, p= 0.05); and (3) Asian background (adjOR 4.67, 95% CI: 1.0-21.0, p= 0.04). No adverse psychological impact occurred in either group. We conclude that offering pregnant women different levels of fetal genetic analysis is warranted, alongside decision support.

  10. Changes in gene expression linked with adult reproductive diapause in a northern malt fly species: a candidate gene microarray study

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    Hoikkala Anneli

    2010-02-01

    Full Text Available Abstract Background Insect diapause is an important biological process which involves many life-history parameters important for survival and reproductive fitness at both individual and population level. Drosophila montana, a species of D. virilis group, has a profound photoperiodic reproductive diapause that enables the adult flies to survive through the harsh winter conditions of high latitudes and altitudes. We created a custom-made microarray for D. montana with 101 genes known to affect traits important in diapause, photoperiodism, reproductive behaviour, circadian clock and stress tolerance in model Drosophila species. This array gave us a chance to filter out genes showing expression changes during photoperiodic reproductive diapause in a species adapted to live in northern latitudes with high seasonal changes in environmental conditions. Results Comparisons among diapausing, reproducing and young D. montana females revealed expression changes in 24 genes on microarray; for example in comparison between diapausing and reproducing females one gene (Drosophila cold acclimation gene, Dca showed up-regulation and 15 genes showed down-regulation in diapausing females. Down-regulation of seven of these genes was specific to diapause state while in five genes the expression changes were linked with the age of the females rather than with their reproductive status. Also, qRT-PCR experiments confirmed couch potato (cpo gene to be involved in diapause of D. montana. Conclusions A candidate gene microarray proved to offer a practical and cost-effective way to trace genes that are likely to play an important role in photoperiodic reproductive diapause and further in adaptation to seasonally varying environmental conditions. The present study revealed two genes, Dca and cpo, whose role in photoperiodic diapause in D. montana is worth of studying in more details. Also, further studies using the candidate gene microarray with more specific experimental

  11. A comprehensive study design reveals treatment- and transcript abundance–dependent concordance between RNA-seq and microarray data

    Science.gov (United States)

    Wang, Charles; Gong, Binsheng; Bushel, Pierre R.; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Xu, Joshua; Fang, Hong; Hong, Huixiao; Shen, Jie; Su, Zhenqiang; Meehan, Joe; Li, Xiaojin; Yang, Lu; Li, Haiqing; Łabaj, Paweł P.; Kreil, David P.; Megherbi, Dalila; Florian, Caiment; Gaj, Stan; van Delft, Joost; Kleinjans, Jos; Scherer, Andreas; Viswanath, Devanarayan; Wang, Jian; Yang, Yong; Qian, Hui-Rong; Lancashire, Lee J.; Bessarabova, Marina; Nikolsky, Yuri; Furlanello, Cesare; Chierici, Marco; Albanese, Davide; Jurman, Giuseppe; Riccadonna, Samantha; Filosi, Michele; Visintainer, Roberto; Zhang, Ke K.; Li, Jianying; Hsieh, Jui-Hua; Svoboda, Daniel L.; Fuscoe, James C.; Deng, Youping; Shi, Leming; Paules, Richard S.; Auerbach, Scott S.; Tong, Weida

    2014-01-01

    RNA-seq facilitates unbiased genome-wide gene-expression profiling. However, its concordance with the well-established microarray platform must be rigorously assessed for confident uses in clinical and regulatory application. Here we use a comprehensive study design to generate Illumina RNA-seq and Affymetrix microarray data from the same set of liver samples of rats under varying degrees of perturbation by 27 chemicals representing multiple modes of action (MOA). The cross-platform concordance in terms of differentially expressed genes (DEGs) or enriched pathways is highly correlated with treatment effect size, gene-expression abundance and the biological complexity of the MOA. RNA-seq outperforms microarray (90% versus 76%) in DEG verification by quantitative PCR and the main gain is its improved accuracy for low expressed genes. Nonetheless, predictive classifiers derived from both platforms performed similarly. Therefore, the endpoint studied and its biological complexity, transcript abundance, and intended application are important factors in transcriptomic research and for decision-making. PMID:25150839

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    Chalmel Frédéric

    2007-08-01

    Full Text Available Abstract 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

  14. 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

  15. Tissue microarrays analysis in chondrosarcomas: light microscopy, immunohistochemistry and xenograft study.

    Science.gov (United States)

    Machado, Isidro; Giner, Francisco; Mayordomo, Empar; Carda, Carmen; Navarro, Samuel; Llombart-Bosch, Antonio

    2008-07-15

    Chondrosarcoma (Chs) is the third most frequent primary malignant tumour of bone and can be primary or secondary, the latter results mainly from the malignant transformation of a benign pre-existing tumour. All the cases diagnosed as Chs (primary tumours, recurrences and/or metastasis and xenotransplanted Chs) from the files of our Department were collected. Only cases with paraffin blocks available were selected (Total 32 cases). Six Tissue Microarrays (TMAs) were performed and all the cases and biopsies were distributed into the following groups: a) only paraffin block available from primary and/or metastatic tumours (3 TMAs), b) paraffin block available from primary and/or metastatic tumours as well as from the corresponding Nude mice xenotransplant (2 TMAs), c) only paraffin block available from xenotransplanted Chs (1 TMA). A reclassification of all the cases was performed; in addition, conventional hematoxylin-eosin as well as immunohistochemistry staining (S100, SOX-9, Ki-67, BCL-2, p53, p16, CK, CD99, Survivin and Caveolin) was analyzed in all the TMA. The distribution of the cases according to the histopathological pattern and the location of tumours were as follows: fourteen Grade I Chs (all primaries), two primary Grade II Chs, ten Grade III Chs (all primaries), five dedifferentiated Chs (four primaries and one primary with metastasis), and two Chs from cell cultures (Ch grade III). One recurrent extraskeletal myxoid Chs was included as a control in the TMA. Although there was heterogeneity in immunohistochemistry results of the different material analyzed, S100, SOX-9, Caveolin and Survivin were more expressed. The number of passages in xenotransplants fluctuated between 1 and 13. Curiously, in Grade I Chs, these implanted tumours hardly grew, and the number of passages did not exceed one. The study of Chs by means of TMA techniques is very important because it will improve the assessment of different antibodies applied in the immunohistochemical assays

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

    Directory of Open Access Journals (Sweden)

    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.

  17. Use of phenotype microarrays to study the effect of acquisition of resistance to antimicrobials in bacterial physiology.

    Science.gov (United States)

    Reales-Calderon, Jose A; Blanco, Paula; Alcalde-Rico, Manuel; Corona, Fernando; Lira, Felipe; Hernando-Amado, Sara; Bernardini, Alejandra; Sánchez, María B; Martínez, José L

    It is widely accepted that the acquisition of resistance to antimicrobials confers a fitness cost. Different works have shown that the effect of acquiring resistance in bacterial physiology may be more specific than previously thought. Study of these specific changes may help to predict the outcome of resistant organisms in different ecosystems. In addition to changing bacterial physiology, acquisition of resistance either increases or reduces susceptibility to other antimicrobials. In the current article, we review recent information on the effect of acquiring resistance upon bacterial physiology, with a specific focus on studies using phenotype microarray technology. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

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

    DEFF Research Database (Denmark)

    Jouffe, Vincent; Rowe, Suzanne; Liaubet, Laurence

    2009-01-01

    of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH) Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide...... 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) Results: Different approaches to localize the differentially expressed (DE) genes to the pig genome...

  19. 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

  20. Microarray study of single nucleotide polymorphisms and expression of ATP-binding cassette genes in breast tumors

    Science.gov (United States)

    Tsyganov, M. M.; Ibragimova, M. K.; Karabut, I. V.; Freydin, M. B.; Choinzonov, E. L.; Litvyakov, N. V.

    2015-11-01

    Our previous research establishes that changes of expression of the ATP-binding cassette genes family is connected with the neoadjuvant chemotherapy effect. However, the mechanism of regulation of resistance gene expression remains unclear. As many researchers believe, single nucleotide polymorphisms can be involved in this process. Thereupon, microarray analysis is used to study polymorphisms in ATP-binding cassette genes. It is thus found that MDR gene expression is connected with 5 polymorphisms, i.e. rs241432, rs241429, rs241430, rs3784867, rs59409230, which participate in the regulation of expression of own genes.

  1. 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

  2. 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

  3. Contributions to Statistical Problems Related to Microarray Data

    Science.gov (United States)

    Hong, Feng

    2009-01-01

    Microarray is a high throughput technology to measure the gene expression. Analysis of microarray data brings many interesting and challenging problems. This thesis consists three studies related to microarray data. First, we propose a Bayesian model for microarray data and use Bayes Factors to identify differentially expressed genes. Second, we…

  4. Nonstationary temporal Wiener filtering of gated blood pool studies

    International Nuclear Information System (INIS)

    King, M.A.; Miller, T.R.; Doherty, P.W.; Bianco, J.A.

    1985-01-01

    Temporal filtering of dynamic images can significantly improve the image quality of gated blood pool (GBP) studies and serves as a necessary preprocessing step in the formation of cardiac functional images based on derivatives of pixel time activity curves. Generally, either linear combination of the frames, or a simple frequency domain low pass filter have been employed. The work described in this paper introduces the Wiener temporal filter which adjusts to match the temporal characteristic of the image at each pixel. For temporal data degraded by signal-dependent Poisson noise, the frequency domain form of the filter is presented. Use of nonstationary temporal Wiener filtering was found to improve the quality of cines formed from GBP studies and yielded better separation of cardiac from non-cardiac regions in functional images the peak ejection and filling rates

  5. 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.

  6. A Growth Curve Model with Fractional Polynomials for Analysing Incomplete Time-Course Data in Microarray Gene Expression Studies

    Science.gov (United States)

    Tan, Qihua; Thomassen, Mads; Hjelmborg, Jacob v. B.; Clemmensen, Anders; Andersen, Klaus Ejner; Petersen, Thomas K.; McGue, Matthew; Christensen, Kaare; Kruse, Torben A.

    2011-01-01

    Identifying the various gene expression response patterns is a challenging issue in expression microarray time-course experiments. Due to heterogeneity in the regulatory reaction among thousands of genes tested, it is impossible to manually characterize a parametric form for each of the time-course pattern in a gene by gene manner. We introduce a growth curve model with fractional polynomials to automatically capture the various time-dependent expression patterns and meanwhile efficiently handle missing values due to incomplete observations. For each gene, our procedure compares the performances among fractional polynomial models with power terms from a set of fixed values that offer a wide range of curve shapes and suggests a best fitting model. After a limited simulation study, the model has been applied to our human in vivo irritated epidermis data with missing observations to investigate time-dependent transcriptional responses to a chemical irritant. Our method was able to identify the various nonlinear time-course expression trajectories. The integration of growth curves with fractional polynomials provides a flexible way to model different time-course patterns together with model selection and significant gene identification strategies that can be applied in microarray-based time-course gene expression experiments with missing observations. PMID:21966290

  7. Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson's disease: a comparison of 33 human and animal studies.

    Science.gov (United States)

    Oerton, Erin; Bender, Andreas

    2017-03-23

    As the popularity of transcriptomic analysis has grown, the reported lack of concordance between different studies of the same condition has become a growing concern, raising questions as to the representativeness of different study types, such as non-human disease models or studies of surrogate tissues, to gene expression in the human condition. In a comparison of 33 microarray studies of Parkinson's disease, correlation and clustering analyses were used to determine the factors influencing concordance between studies, including agreement between different tissue types, different microarray platforms, and between neurotoxic and genetic disease models and human Parkinson's disease. Concordance over all studies is low, with correlation of only 0.05 between differential gene expression signatures on average, but increases within human patients and studies of the same tissue type, rising to 0.38 for studies of human substantia nigra. Agreement of animal models, however, is dependent on model type. Studies of brain tissue from Parkinson's disease patients (specifically the substantia nigra) form a distinct group, showing patterns of differential gene expression noticeably different from that in non-brain tissues and animal models of Parkinson's disease; while comparison with other brain diseases (Alzheimer's disease and brain cancer) suggests that the mixed study types display a general signal of neurodegenerative disease. A meta-analysis of these 33 microarray studies demonstrates the greater ability of studies in humans and highly-affected tissues to identify genes previously known to be associated with Parkinson's disease. The observed clustering and concordance results suggest the existence of a 'characteristic' signal of Parkinson's disease found in significantly affected human tissues in humans. These results help to account for the consistency (or lack thereof) so far observed in microarray studies of Parkinson's disease, and act as a guide to the selection of

  8. 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.

  9. CGH microarray studies in idiopathic developmental/cognitive impairment: association of historical and clinical features and the De Vries Score

    Directory of Open Access Journals (Sweden)

    Promilla Perattur

    2011-05-01

    Full Text Available Objective. Studies have confirmed that copy number variations (CNV in the human genome contribute to the etiology of mental retardation/ development delay/ congenital anomalies. We sought to evaluate the use of a microarray in the context of a clinical genetics practice, to determine if there were any specific clinical findings that predict the discovery of a CNV. Patients and methods. 334 cases with idiopathic mental retardation/impairment/development delay/disability or a combination of these findings were studied using array comparative genomic hybridization (Signature Chip Version 4. The subjects had previously had a non diagnostic medical genetics evaluation. Clinical findings were collated by a chart review. Each patient was scored according to a previously published clinical checklist by de Vries and colleagues. Results. Of 334 patients, 8 were excluded due to a syndromic diagnosis being established by clinical and/or microarray testing. Out of the remaining 326 patients, 33 (10% showed CNVs, of which 5 were maternally inherited, 4 paternally inherited, 11 were de novo, and the origin of 13 remained unknown. The mean de Vries score was greater in the CNV group than in the non CNV group (4.17 and 3.95, respectively. No patient in the CNV group had a score of less than 3, while in the non CNV group, 12% of patients had scores less than 3. Conclusions. The De Vries clinical score was higher in CNV cases compared to those with no CNV (p=0.04 but this difference is unlikely to be clinically meaningful. Several features reached statistical significance of p<0.05 but we were unable to delineate patterns of features that might increase the yield of positive CNV results.

  10. Comparing gene discovery from Affymetrix GeneChip microarrays and Clontech PCR-select cDNA subtraction: a case study

    Science.gov (United States)

    Cao, Wuxiong; Epstein, Charles; Liu, Hong; DeLoughery, Craig; Ge, Nanxiang; Lin, Jieyi; Diao, Rong; Cao, Hui; Long, Fan; Zhang, Xin; Chen, Yangde; Wright, Paul S; Busch, Steve; Wenck, Michelle; Wong, Karen; Saltzman, Alan G; Tang, Zhihua; Liu, Li; Zilberstein, Asher

    2004-01-01

    Background Several high throughput technologies have been employed to identify differentially regulated genes that may be molecular targets for drug discovery. Here we compared the sets of differentially regulated genes discovered using two experimental approaches: a subtracted suppressive hybridization (SSH) cDNA library methodology and Affymetrix GeneChip® technology. In this "case study" we explored the transcriptional pattern changes during the in vitro differentiation of human monocytes to myeloid dendritic cells (DC), and evaluated the potential for novel gene discovery using the SSH methodology. Results The same RNA samples isolated from peripheral blood monocyte precursors and immature DC (iDC) were used for GeneChip microarray probing and SSH cDNA library construction. 10,000 clones from each of the two-way SSH libraries (iDC-monocytes and monocytes-iDC) were picked for sequencing. About 2000 transcripts were identified for each library from 8000 successful sequences. Only 70% to 75% of these transcripts were represented on the U95 series GeneChip microarrays, implying that 25% to 30% of these transcripts might not have been identified in a study based only on GeneChip microarrays. In addition, about 10% of these transcripts appeared to be "novel", although these have not yet been closely examined. Among the transcripts that are also represented on the chips, about a third were concordantly discovered as differentially regulated between iDC and monocytes by GeneChip microarray transcript profiling. The remaining two thirds were either not inferred as differentially regulated from GeneChip microarray data, or were called differentially regulated but in the opposite direction. This underscores the importance both of generating reciprocal pairs of SSH libraries, and of real-time RT-PCR confirmation of the results. Conclusions This study suggests that SSH could be used as an alternative and complementary transcript profiling tool to GeneChip microarrays

  11. Compressive Sensing DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Sheikh Mona A

    2009-01-01

    Full Text Available Compressive sensing microarrays (CSMs are DNA-based sensors that operate using group testing and compressive sensing (CS principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed.

  12. 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

  13. 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.

  14. 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)

  15. Microarray analysis of gene expression during bacteriophage T4 infection.

    Science.gov (United States)

    Luke, Kimberly; Radek, Agnes; Liu, XiuPing; Campbell, John; Uzan, Marc; Haselkorn, Robert; Kogan, Yakov

    2002-08-01

    Genomic microarrays were used to examine the complex temporal program of gene expression exhibited by bacteriophage T4 during the course of development. The microarray data confirm the existence of distinct early, middle, and late transcriptional classes during the bacteriophage replicative cycle. This approach allows assignment of previously uncharacterized genes to specific temporal classes. The genomic expression data verify many promoter assignments and predict the existence of previously unidentified promoters.

  16. Health status, infection and disease in California sea lions (Zalophus californianus) studied using a canine microarray platform and machine-learning approaches.

    Science.gov (United States)

    Mancia, Annalaura; Ryan, James C; Chapman, Robert W; Wu, Qingzhong; Warr, Gregory W; Gulland, Frances M D; Van Dolah, Frances M

    2012-04-01

    Conservation biologists face many challenges in assessing health, immune status and infectious diseases in protected species. These challenges include unpredictable sample populations, diverse genetic and environmental backgrounds of the animals, as well as the practical, legal and ethical issues involved in experimentation. The use of whole genome scale transcriptomics with animal samples obtained in a minimally invasive manner is an approach that shows promise for health assessment. In this study we assessed the utility of a microarray to identify changes in gene expression predictive of health status by interrogating blood samples from California sea lions (Zalophus californianus) in rehabilitation. A custom microarray was developed from the commercially available dog microarray (Canis familiaris) by selecting probes that demonstrated reliable cross-hybridization with RNA in sea lion blood. This custom microarray was used for the analysis of RNA from 73 sea lion blood samples, from animals with a broad spectrum of health changes. Both traditional classifying techniques and newer artificial neural network approaches correctly classified sea lions with respect to health status, primarily distinguishing between leptospirosis infection and domoic acid exposure. Real time PCR validation for a small set of genes, followed by sequencing, showed good correlation with array results and high identity (96-98%) between the dog and sea lion sequences. This approach to health status classification shows promise for disease identification in a clinical setting, and assessment of health status of wildlife. Published by Elsevier Ltd.

  17. 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

  18. 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

  19. 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

  20. Temporal clauses with conditional value in legal language (contrastive study

    Directory of Open Access Journals (Sweden)

    Iva Svobodová

    2017-12-01

    Full Text Available This study is a summary of a qualitative and quantitative linguistic investigation of the Portuguese and Brazilian Penal Code, and contains important results pertaining to the temporal clauses introduced by the connector quando. We focused on its semantic conditional features, suggesting the name pseudo-temporal clauses for these hypotactic constructions and observe the relation between the occurrence of different verbal modes and the semantic interpretation. We verify, in both the texts, the temporal clauses introduced by quando have an evident conditional value. On the other side, the compared texts are different regarding the selection of the verbal mode. The Portuguese Penal Code preferred, evidently, the subjunctive mode and in the Brazilian one the indicative mode. We explained this divergence by semantic and pragmatic factors.

  1. DNA Microarray Technology

    Science.gov (United States)

    ... this page. En Español: Tecnología de micromatriz de ADN DNA Microarray Technology What is a DNA microarray? ... this page. En Español: Tecnología de micromatriz de ADN Get Email Updates Privacy Copyright Contact Accessibility Plug- ...

  2. 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.

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

    Science.gov (United States)

    Menzel, Ralph; Swain, Suresh C; Hoess, Sebastian; Claus, Evelyn; Menzel, Stefanie; Steinberg, Christian EW; Reifferscheid, Georg; Stürzenbaum, Stephen R

    2009-01-01

    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. PMID:19366437

  4. 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.

  5. Microarray Technology to Study the Role of Genetic Polymorphisms in Breast Cancer Risk

    National Research Council Canada - National Science Library

    Ozcelik, Hilmi

    2004-01-01

    .... In this study we took the candidate gene approach to study the association of 19 different genetic polymorphisms with breast cancer risk in a population-based sample using a high-throughput genotyping technology...

  6. Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study

    Directory of Open Access Journals (Sweden)

    Debashis Ghosh

    2008-01-01

    Full Text Available With an increasing number of cancer profiling studies assaying both transcript mRNA and copy number expression levels, a natural question then involves the potential to combine information across the two types of genomic data. In this article, we perform a study to assess the nature of association between the two types of data across several experiments. We report on several interesting findings: 1 global correlation between gene expression and copy number is relatively weak but consistent across studies; 2 there is strong evidence for a cis-dosage effect of copy number on gene expression; 3 segmenting the copy number levels helps to improve correlations.

  7. 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.

  8. 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...

  9. Comparing gene discovery from Affymetrix GeneChip microarrays and Clontech PCR-select cDNA subtraction: a case study

    Directory of Open Access Journals (Sweden)

    Wright Paul S

    2004-04-01

    Full Text Available Abstract Background Several high throughput technologies have been employed to identify differentially regulated genes that may be molecular targets for drug discovery. Here we compared the sets of differentially regulated genes discovered using two experimental approaches: a subtracted suppressive hybridization (SSH cDNA library methodology and Affymetrix GeneChip® technology. In this "case study" we explored the transcriptional pattern changes during the in vitro differentiation of human monocytes to myeloid dendritic cells (DC, and evaluated the potential for novel gene discovery using the SSH methodology. Results The same RNA samples isolated from peripheral blood monocyte precursors and immature DC (iDC were used for GeneChip microarray probing and SSH cDNA library construction. 10,000 clones from each of the two-way SSH libraries (iDC-monocytes and monocytes-iDC were picked for sequencing. About 2000 transcripts were identified for each library from 8000 successful sequences. Only 70% to 75% of these transcripts were represented on the U95 series GeneChip microarrays, implying that 25% to 30% of these transcripts might not have been identified in a study based only on GeneChip microarrays. In addition, about 10% of these transcripts appeared to be "novel", although these have not yet been closely examined. Among the transcripts that are also represented on the chips, about a third were concordantly discovered as differentially regulated between iDC and monocytes by GeneChip microarray transcript profiling. The remaining two thirds were either not inferred as differentially regulated from GeneChip microarray data, or were called differentially regulated but in the opposite direction. This underscores the importance both of generating reciprocal pairs of SSH libraries, and of real-time RT-PCR confirmation of the results. Conclusions This study suggests that SSH could be used as an alternative and complementary transcript profiling tool to

  10. 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.

  11. Progressive obesity leads to altered ovarian gene expression in the Lethal Yellow mouse: a microarray study

    Directory of Open Access Journals (Sweden)

    Brannian John

    2009-08-01

    Full Text Available Abstract Background Lethal yellow (LY; C57BL/6J Ay/a mice exhibit adult-onset obesity, altered metabolic regulation, and early reproductive senescence. The present study was designed to test the hypothesis that obese LY mice possess differences in expression of ovarian genes relative to age-matched lean mice. Methods 90- and 180-day-old LY and lean black (C57BL/6J a/a mice were suppressed with GnRH antagonist (Antide®, then stimulated with 5 IU eCG. cRNA derived from RNA extracts of whole ovarian homogenates collected 36 h post-eCG were run individually on Codelink Mouse Whole Genome Bioarrays (GE Healthcare Life Sciences. Results Fifty-two genes showed ≥ 2-fold differential (p Cyp51, and steroidogenic acute regulatory protein (Star. Fewer genes showed lower expression in LY mice, e.g. angiotensinogen. In contrast, none of these genes showed differential expression in 90-day-old LY and black mice, which are of similar body weight. Interestingly, 180-day-old LY mice had a 2-fold greater expression of 11beta-hydroxysteroid dehydrogenase type 1 (Hsd11b1 and a 2-fold lesser expression of 11beta-hydroxysteroid dehydrogenase type 2 (Hsd11b2, differences not seen in 90-day-old mice. Consistent with altered Hsd11b gene expression, ovarian concentrations of corticosterone (C were elevated in aging LY mice relative to black mice, but C levels were similar in young LY and black mice. Conclusion The data suggest that reproductive dysfunction in aging obese mice is related to modified intraovarian gene expression that is directly related to acquired obesity.

  12. 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

  13. Women's preference for non-invasive prenatal DNA testing versus chromosomal microarray after screening for Down syndrome: a prospective study.

    Science.gov (United States)

    Cheng, Yky; Leung, W C; Leung, T Y; Choy, K W; Chiu, Rwk; Lo, T-K; Kwok, K Y; Sahota, D S

    2018-03-01

    To examine preferences for follow-up testing in women screened with high or intermediate risk for Down syndrome in the first or second trimester. Prospective cohort study. Three public hospitals in Hong Kong, China. Women with pregnancies termed as high risk (≥1:250; HR) or intermediate risk (1:251-1200; IR) for Down syndrome. Women with pregnancies screened as HR were offered the choices of: (1) an invasive test plus chromosomal microarray (CMA) to obtain more detailed fetal genetic information; (2) non-invasive cell-free prenatal DNA screening (NIPT) to detect trisomies 13, 18 and 21, and to avoid procedure-related miscarriage; and (3) to decline any further testing. Women received standardised counselling informing them that the reporting times were identical, the procedure miscarriage risk was 0.1-0.2% and that there was no charge for screening. Women with IR pregnancies (1:251-1200) were offered NIPT as a secondary screening test. Uptake rate for NIPT. Three hundred and forty-seven women had pregnancies deemed as HR; 344 (99.1%) women opted for follow-up testing, 216 (62.2%) of whom chose NIPT. Five hundred and seven of 614 women (82.6%) with IR risk chose NIPT. Seven (21%) of 34 women with nuchal translucency ≥3.5 mm opted for NIPT. In a setting where reporting times are similar and there is no cost difference between options, approximately 60% of women with pregnancies classed as HR would opt for NIPT, offering simple but limited aneuploidy assessment, over a diagnostic procedure with comprehensive and more detailed assessment. 60% of pregnant Chinese women prefer NIPT over CMA when screened as high risk for Down syndrome. © 2018 Royal College of Obstetricians and Gynaecologists.

  14. 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.

  15. 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.

  16. 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.

  17. PMD: A Resource for Archiving and Analyzing Protein Microarray data.

    Science.gov (United States)

    Xu, Zhaowei; Huang, Likun; Zhang, Hainan; Li, Yang; Guo, Shujuan; Wang, Nan; Wang, Shi-Hua; Chen, Ziqing; Wang, Jingfang; Tao, Sheng-Ce

    2016-01-27

    Protein microarray is a powerful technology for both basic research and clinical study. However, because there is no database specifically tailored for protein microarray, the majority of the valuable original protein microarray data is still not publically accessible. To address this issue, we constructed Protein Microarray Database (PMD), which is specifically designed for archiving and analyzing protein microarray data. In PMD, users can easily browse and search the entire database by experimental name, protein microarray type, and sample information. Additionally, PMD integrates several data analysis tools and provides an automated data analysis pipeline for users. With just one click, users can obtain a comprehensive analysis report for their protein microarray data. The report includes preliminary data analysis, such as data normalization, candidate identification, and an in-depth bioinformatics analysis of the candidates, which include functional annotation, pathway analysis, and protein-protein interaction network analysis. PMD is now freely available at www.proteinmicroarray.cn.

  18. The Stanford Microarray Database

    Science.gov (United States)

    Sherlock, Gavin; Hernandez-Boussard, Tina; Kasarskis, Andrew; Binkley, Gail; Matese, John C.; Dwight, Selina S.; Kaloper, Miroslava; Weng, Shuai; Jin, Heng; Ball, Catherine A.; Eisen, Michael B.; Spellman, Paul T.; Brown, Patrick O.; Botstein, David; Cherry, J. Michael

    2001-01-01

    The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two immediate goals for SMD are to serve as a storage site for microarray data from ongoing research at Stanford University, and to facilitate the public dissemination of that data once published, or released by the researcher. Of paramount importance is the connection of microarray data with the biological data that pertains to the DNA deposited on the microarray (genes, clones etc.). SMD makes use of many public resources to connect expression information to the relevant biology, including SGD [Ball,C.A., Dolinski,K., Dwight,S.S., Harris,M.A., Issel-Tarver,L., Kasarskis,A., Scafe,C.R., Sherlock,G., Binkley,G., Jin,H. et al. (2000) Nucleic Acids Res., 28, 77–80], YPD and WormPD [Costanzo,M.C., Hogan,J.D., Cusick,M.E., Davis,B.P., Fancher,A.M., Hodges,P.E., Kondu,P., Lengieza,C., Lew-Smith,J.E., Lingner,C. et al. (2000) Nucleic Acids Res., 28, 73–76], Unigene [Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Nucleic Acids Res., 28, 10–14], dbEST [Boguski,M.S., Lowe,T.M. and Tolstoshev,C.M. (1993) Nature Genet., 4, 332–333] and SWISS-PROT [Bairoch,A. and Apweiler,R. (2000) Nucleic Acids Res., 28, 45–48] and can be accessed at http://genome-www.stanford.edu/microarray. PMID:11125075

  19. Respiratory Tularemia:Francisella Tularensisand Microarray Probe Designing.

    Science.gov (United States)

    Ranjbar, Reza; Behzadi, Payam; Mammina, Caterina

    2016-01-01

    Francisella tularensis ( F. tularensis ) is the etiological microorganism for tularemia. There are different forms of tularemia such as respiratory tularemia. Respiratory tularemia is the most severe form of tularemia with a high rate of mortality; if not treated. Therefore, traditional microbiological tools and Polymerase Chain Reaction (PCR) are not useful for a rapid, reliable, accurate, sensitive and specific diagnosis. But, DNA microarray technology does. DNA microarray technology needs to appropriate microarray probe designing. The main goal of this original article was to design suitable long oligo microarray probes for detection and identification of F. tularensis . For performing this research, the complete genomes of F. tularensis subsp. tularensis FSC198, F. tularensis subsp. holarctica LVS, F. tularensis subsp. mediasiatica , F. tularensis subsp. novicida ( F. novicida U112), and F. philomiragia subsp. philomiragia ATCC 25017 were studied via NCBI BLAST tool, GView and PanSeq Servers and finally the microarray probes were produced and processed via AlleleID 7.7 software and Oligoanalyzer tool, respectively. In this in silico investigation, a number of long oligo microarray probes were designed for detecting and identifying F. tularensis . Among these probes, 15 probes were recognized as the best candidates for microarray chip designing. Calibrated microarray probes reduce the biasis of DNA microarray technology as an advanced, rapid, accurate and cost-effective molecular diagnostic tool with high specificity and sensitivity. Professional microarray probe designing provides us with much more facility and flexibility regarding preparation of a microarray diagnostic chip.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. Studying the protein expression in human B lymphoblastoid cells exposed to 1.8-GHz (GSM) radiofrequency radiation (RFR) with protein microarray.

    Science.gov (United States)

    Zhijian, Chen; Xiaoxue, Li; Wei, Zheng; Yezhen, Lu; Jianlin, Lou; Deqiang, Lu; Shijie, Chen; Lifen, Jin; Jiliang, He

    2013-03-29

    In the present study, the protein microarray was used to investigate the protein expression in human B-cell lymphoblastoid cells intermittently exposed to 1.8-GHz GSM radiofrequency radiation (RFR) at the specific absorption rate (SAR) of 2.0 W/kg for 24 h. The differential expression of 27 proteins was found, which were related to DNA damage repair, apoptosis, oncogenesis, cell cycle and proliferation (ratio >1.5-fold, PRFR exposure group (PRFR on DNA damage/repair and cell apoptosis. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. 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.

  6. Auditory temporal processing in healthy aging: a magnetoencephalographic study

    Directory of Open Access Journals (Sweden)

    Manemann Elisabeth

    2009-04-01

    Full Text Available Abstract Background Impaired speech perception is one of the major sequelae of aging. In addition to peripheral hearing loss, central deficits of auditory processing are supposed to contribute to the deterioration of speech perception in older individuals. To test the hypothesis that auditory temporal processing is compromised in aging, auditory evoked magnetic fields were recorded during stimulation with sequences of 4 rapidly recurring speech sounds in 28 healthy individuals aged 20 – 78 years. Results The decrement of the N1m amplitude during rapid auditory stimulation was not significantly different between older and younger adults. The amplitudes of the middle-latency P1m wave and of the long-latency N1m, however, were significantly larger in older than in younger participants. Conclusion The results of the present study do not provide evidence for the hypothesis that auditory temporal processing, as measured by the decrement (short-term habituation of the major auditory evoked component, the N1m wave, is impaired in aging. The differences between these magnetoencephalographic findings and previously published behavioral data might be explained by differences in the experimental setting between the present study and previous behavioral studies, in terms of speech rate, attention, and masking noise. Significantly larger amplitudes of the P1m and N1m waves suggest that the cortical processing of individual sounds differs between younger and older individuals. This result adds to the growing evidence that brain functions, such as sensory processing, motor control and cognitive processing, can change during healthy aging, presumably due to experience-dependent neuroplastic mechanisms.

  7. 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

  8. Study Time: Heidegger and the Temporality of Education

    Science.gov (United States)

    Lewis, Tyson E.

    2017-01-01

    In this article, the author argues that the question of educational time is absolutely essential in contemporary debates concerning the fate of the university. In order to examine the nature of educational time, this article first outlines Heidegger's distinction between temporality and Temporality. Second, the author makes a clarification between…

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

    Directory of Open Access Journals (Sweden)

    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.

  10. Robust Microarray Image Processing

    OpenAIRE

    Novikov, Eugene; Barillot, Emmanuel

    2007-01-01

    In this work we have presented a complete solution for robust, high-throughput, two-color microarray image processing comprising procedures for automatic spot localization, spot quantification and spot quality control. The spot localization algorithm is fully automatic and robust with respect to deviations from perfect spot alignment and contamination. As an input, it requires only the common array design parameters: number of blocks and number of spots in the x and y directions of the array....

  11. Studying the protein expression in human B lymphoblastoid cells exposed to 1.8-GHz (GSM) radiofrequency radiation (RFR) with protein microarray

    International Nuclear Information System (INIS)

    Zhijian, Chen; Xiaoxue, Li; Wei, Zheng; Yezhen, Lu; Jianlin, Lou; Deqiang, Lu; Shijie, Chen; Lifen, Jin; Jiliang, He

    2013-01-01

    Highlights: ► Protein microarray shows the differential expression of 27 proteins induced by RFR. ► RPA32 related to DNA repair is down-regulated in Western blot. ► p73 related to cell genome stability and apoptosis is up-regulated in Western blot. -- Abstract: In the present study, the protein microarray was used to investigate the protein expression in human B-cell lymphoblastoid cells intermittently exposed to 1.8-GHz GSM radiofrequency radiation (RFR) at the specific absorption rate (SAR) of 2.0 W/kg for 24 h. The differential expression of 27 proteins was found, which were related to DNA damage repair, apoptosis, oncogenesis, cell cycle and proliferation (ratio >1.5-fold, P < 0.05). The results validated with Western blot assay indicated that the expression of RPA32 was significantly down-regulated (P < 0.05) while the expression of p73 was significantly up-regulated in RFR exposure group (P < 0.05). Because of the crucial roles of those proteins in DNA repair and cell apoptosis, the results of present investigation may explain the biological effects of RFR on DNA damage/repair and cell apoptosis

  12. 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.

  13. Cone Beam CT Study of Temporal Crest Canal.

    Science.gov (United States)

    Hasani, Mahvash; Shahidi, Shoaleh; Shamszade, Shahrzad Alsadat

    2018-03-01

    It is crucial for clinicians to be certain about the location of mandibular canal and determine any anatomical variants relevant to it. The temporal crest canal (TCC) is a rare anatomical variant of mandibular canal that lack of awareness about its presence can complicate surgical procedures. This study investigated the anatomical characteristics and prevalence of the TCC using CBCT. This descriptive cross-section study evaluated 327 CBCTs (654 sides) from all the patients with various problems. TCC on sagittal and axial plans were identified and then classified into two types based on their configuration. The prevalence of TCC was calculated amongst men and women. Six TCC (0.91%) were observed in 654 sides. We observed all 6 TCCs in females. One case (0.30%) was bilateral TCC, and the remaining four (1.22%) cases were unilateral TCC (two on the left and two on the right side). Considering the classification of TCC, five sides had presentation of type I and one case was type II based on Kawai et al . study. Three-dimensional images of CBCT data are useful in confirming the presence of TCC. TCC is considered as a clinically significant structure; therefore, this variation should be carefully investigated using reconstructed CBCT images.

  14. Temporal distance and discrimination: an audit study in academia.

    Science.gov (United States)

    Milkman, Katherine L; Akinola, Modupe; Chugh, Dolly

    2012-07-01

    Through a field experiment set in academia (with a sample of 6,548 professors), we found that decisions about distant-future events were more likely to generate discrimination against women and minorities (relative to Caucasian males) than were decisions about near-future events. In our study, faculty members received e-mails from fictional prospective doctoral students seeking to schedule a meeting either that day or in 1 week; students' names signaled their race (Caucasian, African American, Hispanic, Indian, or Chinese) and gender. When the requests were to meet in 1 week, Caucasian males were granted access to faculty members 26% more often than were women and minorities; also, compared with women and minorities, Caucasian males received more and faster responses. However, these patterns were essentially eliminated when prospective students requested a meeting that same day. Our identification of a temporal discrimination effect is consistent with the predictions of construal-level theory and implies that subtle contextual shifts can alter patterns of race- and gender-based discrimination.

  15. Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation.

    Science.gov (United States)

    Richard, Arianne C; Lyons, Paul A; Peters, James E; Biasci, Daniele; Flint, Shaun M; Lee, James C; McKinney, Eoin F; Siegel, Richard M; Smith, Kenneth G C

    2014-08-04

    Although numerous investigations have compared gene expression microarray platforms, preprocessing methods and batch correction algorithms using constructed spike-in or dilution datasets, there remains a paucity of studies examining the properties of microarray data using diverse biological samples. Most microarray experiments seek to identify subtle differences between samples with variable background noise, a scenario poorly represented by constructed datasets. Thus, microarray users lack important information regarding the complexities introduced in real-world experimental settings. The recent development of a multiplexed, digital technology for nucleic acid measurement enables counting of individual RNA molecules without amplification and, for the first time, permits such a study. Using a set of human leukocyte subset RNA samples, we compared previously acquired microarray expression values with RNA molecule counts determined by the nCounter Analysis System (NanoString Technologies) in selected genes. We found that gene measurements across samples correlated well between the two platforms, particularly for high-variance genes, while genes deemed unexpressed by the nCounter generally had both low expression and low variance on the microarray. Confirming previous findings from spike-in and dilution datasets, this "gold-standard" comparison demonstrated signal compression that varied dramatically by expression level and, to a lesser extent, by dataset. Most importantly, examination of three different cell types revealed that noise levels differed across tissues. Microarray measurements generally correlate with relative RNA molecule counts within optimal ranges but suffer from expression-dependent accuracy bias and precision that varies across datasets. We urge microarray users to consider expression-level effects in signal interpretation and to evaluate noise properties in each dataset independently.

  16. Microfluidic Methods for Protein Microarrays

    OpenAIRE

    Hartmann, Michael

    2010-01-01

    Protein microarray technology has an enormous potential for in vitro diagnostics (IVD)1. Miniaturized and parallelized immunoassays are powerful tools to measure dozens of parameters from minute amounts of sample, whilst only requiring small amounts of reagent. Protein microarrays have become well-established research tools in basic and applied research and the first diagnostic products are already released on the market. However, in order for protein microarrays to become broadly accepted to...

  17. 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

  18. 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

  19. 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

  20. Correlation of Aggregatibacter actinomycetemcomitans detection with clinical/immunoinflammatory profile of localized aggressive periodontitis using a 16S rRNA microarray method: a cross-sectional study.

    Directory of Open Access Journals (Sweden)

    Patricia F Gonçalves

    Full Text Available The objective of this study was to determine whether the detection of Aggregatibacter actinomycetemcomitans (Aa correlates with the clinical and immunoinflammatory profile of Localized Aggressive Periodontitis (LAP, as determined by by 16S rRNA gene-based microarray.Subgingival plaque samples from the deepest diseased site of 30 LAP patients [PD ≥ 5 mm, BoP and bone loss] were analyzed by 16S rRNA gene-based microarrays. Gingival crevicular fluid (GCF samples were analyzed for 14 cyto/chemokines. Peripheral blood was obtained and stimulated in vitro with P.gingivalis and E.coli to evaluate inflammatory response profiles. Plasma lipopolysaccharide (LPS levels were also measured.Aa was detected in 56% of LAP patients and was shown to be an indicator for different bacterial community structures (p0.05. Clinical parameters and serum LPS levels were similar between groups. However, Aa-non-detected GCF contained higher concentration of IL-8 than Aa-detected sites (p<0.05. TNFα and IL1β were elevated upon E.coli LPS stimulation of peripheral blood cells derived from patients with Aa-detected sites.Our findings demonstrate that the detection of Aa in LAP affected sites, did not correlate with clinical severity of the disease at the time of sampling in this cross-sectional study, although it did associate with lower local levels of IL-8, a different subgingival bacterial profile and elevated LPS-induced levels of TNFα and IL1β.

  1. Hybridization and Selective Release of DNA Microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J; Benett, W; Mukerjee, E; Dzenitis, J; Wheeler, E K

    2011-11-29

    DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy

  2. Memory reorganization following anterior temporal lobe resection: a longitudinal functional MRI study.

    Science.gov (United States)

    Bonelli, Silvia B; Thompson, Pamela J; Yogarajah, Mahinda; Powell, Robert H W; Samson, Rebecca S; McEvoy, Andrew W; Symms, Mark R; Koepp, Matthias J; Duncan, John S

    2013-06-01

    Anterior temporal lobe resection controls seizures in 50-60% of patients with intractable temporal lobe epilepsy but may impair memory function, typically verbal memory following left, and visual memory following right anterior temporal lobe resection. Functional reorganization can occur within the ipsilateral and contralateral hemispheres. We investigated the reorganization of memory function in patients with temporal lobe epilepsy before and after left or right anterior temporal lobe resection and the efficiency of postoperative memory networks. We studied 46 patients with unilateral medial temporal lobe epilepsy (25/26 left hippocampal sclerosis, 16/20 right hippocampal sclerosis) before and after anterior temporal lobe resection on a 3 T General Electric magnetic resonance imaging scanner. All subjects had neuropsychological testing and performed a functional magnetic resonance imaging memory encoding paradigm for words, pictures and faces, testing verbal and visual memory in a single scanning session, preoperatively and again 4 months after surgery. Event-related analysis revealed that patients with left temporal lobe epilepsy had greater activation in the left posterior medial temporal lobe when successfully encoding words postoperatively than preoperatively. Greater pre- than postoperative activation in the ipsilateral posterior medial temporal lobe for encoding words correlated with better verbal memory outcome after left anterior temporal lobe resection. In contrast, greater postoperative than preoperative activation in the ipsilateral posterior medial temporal lobe correlated with worse postoperative verbal memory performance. These postoperative effects were not observed for visual memory function after right anterior temporal lobe resection. Our findings provide evidence for effective preoperative reorganization of verbal memory function to the ipsilateral posterior medial temporal lobe due to the underlying disease, suggesting that it is the capacity

  3. 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

  4. 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.

  5. A comparative study of genome-wide SNP, CGH microarray and protein expression analysis to explore genotypic and phenotypic mechanisms of acquired antiestrogen resistance in breast cancer.

    Science.gov (United States)

    Johnson, Neil; Speirs, Valerie; Curtin, Nicola J; Hall, Andrew G

    2008-09-01

    Allelic imbalance is a common feature of many malignancies. We have measured allelic imbalance in genomic DNA from the breast cancer cell lines T47D, MDA-MB-231, two antiestrogen sensitive (MCF7N and MCF7L) and two resistant MCF7 cell lines (MMU2 and LCC9) using single nucleotide polymorphism (SNP) oligonucleotide microarrays. DNA from MCF7(L) and MMU2 cells was also analysed by comparative genome hybridisation (CGH) to compare with SNP microarray data. Proteins previously determined to be involved in disease progression were quantified by Western blot and compared to array data. The SNP and CGH array both detected cytogenetic abnormalities commonly found in breast cancer: amplification of chromosomes 11q13-14.1, 17q and 20q containing cyclin D1, BCAS1 and 3 (Breast Cancer Amplified Sequence) and AIB1 (Amplified in Breast cancer) genes; losses at 6q, 9p and X chromosomes, which included ERalpha (Estrogen Receptor alpha) and p16 ( INK4A ) genes. However the SNP chip array data additionally identified regions of loss of heterozygosity (LOH) followed by duplication of the remaining allele-uniparental disomy (UPD). Good concordance between SNP arrays and CGH analyses was observed, however there was poor correlation between gene copy number and protein levels between the cell lines. There were reductions in ERalpha, cyclin D1 and p27 protein levels whilst p21 protein levels were elevated in antiestrogen resistant MCF7 cell lines. Although protein levels varied there was no difference in gene copy number. This study shows SNP and CGH array analysis are powerful tools for analysis of allelic imbalance in breast cancer. However, the antiestrogen resistant phenotype was likely to be due to changes in gene expression and protein degradation rather than in altered gene copy number.

  6. Microarray-based Detection of Antibiotic Resisteance Genes in Salmonella

    NARCIS (Netherlands)

    Hoek, van A.H.A.M.; Aarts, H.J.M.

    2008-01-01

    In the presented study, 143 Salmonella isolates belonging to 26 different serovars were screened for the presence of antibiotic resistance genes by microarray analysis. The microarray contained a total of 223 oligonucleotides representing genes encoding for resistance to the following antibiotic

  7. 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...

  8. DNA Microarray-Based Diagnostics.

    Science.gov (United States)

    Marzancola, Mahsa Gharibi; Sedighi, Abootaleb; Li, Paul C H

    2016-01-01

    The DNA microarray technology is currently a useful biomedical tool which has been developed for a variety of diagnostic applications. However, the development pathway has not been smooth and the technology has faced some challenges. The reliability of the microarray data and also the clinical utility of the results in the early days were criticized. These criticisms added to the severe competition from other techniques, such as next-generation sequencing (NGS), impacting the growth of microarray-based tests in the molecular diagnostic market.Thanks to the advances in the underlying technologies as well as the tremendous effort offered by the research community and commercial vendors, these challenges have mostly been addressed. Nowadays, the microarray platform has achieved sufficient standardization and method validation as well as efficient probe printing, liquid handling and signal visualization. Integration of various steps of the microarray assay into a harmonized and miniaturized handheld lab-on-a-chip (LOC) device has been a goal for the microarray community. In this respect, notable progress has been achieved in coupling the DNA microarray with the liquid manipulation microsystem as well as the supporting subsystem that will generate the stand-alone LOC device.In this chapter, we discuss the major challenges that microarray technology has faced in its almost two decades of development and also describe the solutions to overcome the challenges. In addition, we review the advancements of the technology, especially the progress toward developing the LOC devices for DNA diagnostic applications.

  9. 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

  10. Temporal query of attribute-value patient data: utilizing the constraints of clinical studies

    Science.gov (United States)

    Deshpande, Aniruddha M.; Brandt, Cynthia; Nadkarni, Prakash M.

    2010-01-01

    Summary We describe an interface and architecture for ad hoc temporal query of TrialDB, a clinical study data management system (CSDMS). A clinical study focuses primarily on the effect of therapy on a group of patients, who have individually enrolled in a study at different times. Relative times (chronological offsets from the time of enrollment) are therefore more useful than absolute times when collectively describing therapeutic or adverse events. For logistic reasons, study parameter values are typically recorded at fixed relative times (‘study events’), which serve as timestamps and can be used by CSDMS temporal query algorithms to simplify temporal computations. The entity-attribute-value model of clinical data storage, used by both CSDMSs and clinical patient record systems, complicates temporal query. To apply temporal operators, data for parameters of interest must first be transiently converted into conventional relational form, with one column per parameter. PMID:12706183

  11. 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

  12. Single-species microarrays and comparative transcriptomics.

    Directory of Open Access Journals (Sweden)

    Frédéric J J Chain

    Full Text Available BACKGROUND: Prefabricated expression microarrays are currently available for only a few species but methods have been proposed to extend their application to comparisons between divergent genomes. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that the hybridization intensity of genomic DNA is a poor basis on which to select unbiased probes on Affymetrix expression arrays for studies of comparative transcriptomics, and that doing so produces spurious results. We used the Affymetrix Xenopus laevis microarray to evaluate expression divergence between X. laevis, X. borealis, and their F1 hybrids. When data are analyzed with probes that interrogate only sequences with confirmed identity in both species, we recover results that differ substantially analyses that use genomic DNA hybridizations to select probes. CONCLUSIONS/SIGNIFICANCE: Our findings have implications for the experimental design of comparative expression studies that use single-species microarrays, and for our understanding of divergent expression in hybrid clawed frogs. These findings also highlight important limitations of single-species microarrays for studies of comparative transcriptomics of polyploid species.

  13. 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.

  14. Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm

    Directory of Open Access Journals (Sweden)

    Malyj Wasyl

    2005-08-01

    Full Text Available Abstract Background Life processes are determined by the organism's genetic profile and multiple environmental variables. However the interaction between these factors is inherently non-linear 1. Microarray data is one representation of the nonlinear interactions among genes and genes and environmental factors. Still most microarray studies use linear methods for the interpretation of nonlinear data. In this study, we apply Isomap, a nonlinear method of dimensionality reduction, to analyze three independent large Affymetrix high-density oligonucleotide microarray data sets. Results Isomap discovered low-dimensional structures embedded in the Affymetrix microarray data sets. These structures correspond to and help to interpret biological phenomena present in the data. This analysis provides examples of temporal, spatial, and functional processes revealed by the Isomap algorithm. In a spinal cord injury data set, Isomap discovers the three main modalities of the experiment – location and severity of the injury and the time elapsed after the injury. In a multiple tissue data set, Isomap discovers a low-dimensional structure that corresponds to anatomical locations of the source tissues. This model is capable of describing low- and high-resolution differences in the same model, such as kidney-vs.-brain and differences between the nuclei of the amygdala, respectively. In a high-throughput drug screening data set, Isomap discovers the monocytic and granulocytic differentiation of myeloid cells and maps several chemical compounds on the two-dimensional model. Conclusion Visualization of Isomap models provides useful tools for exploratory analysis of microarray data sets. In most instances, Isomap models explain more of the variance present in the microarray data than PCA or MDS. Finally, Isomap is a promising new algorithm for class discovery and class prediction in high-density oligonucleotide data sets.

  15. 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.

  16. 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...

  17. Microarray technology: a promising tool in nutrigenomics.

    Science.gov (United States)

    Masotti, Andrea; Da Sacco, Letizia; Bottazzo, Gian Franco; Alisi, Anna

    2010-08-01

    Microarray technology is a powerful tool for the global evaluation of gene expression profiles in tissues and for understanding many of the factors controlling the regulation of gene transcription. This technique not only provides a considerable amount of information on markers and predictive factors that may potentially characterize a specific clinical picture, but also promises new applications for therapy. One of the most recent applications of microarrays concerns nutritional genomics. Nutritional genomics, known as nutrigenomics, aims to identify and understand mechanisms of molecular interaction between nutrients and/or other dietary bioactive compounds and the genome. Actually, many nutrigenomic studies utilize new approaches such as microarrays, genomics, and bioinformatics to understand how nutrients influence gene expression. The coupling of these new technologies with nutrigenomics promises to lead to improvements in diet and health. In fact, it may provide new information which can be used to ameliorate dietary regimens and to discover novel natural agents for the treatment of important diseases such as diabetes and cancer. This critical review gives an overview of the clinical relevance of a nutritional approach to several important diseases, and proposes the use of microarray for nutrigenomic studies.

  18. 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

  19. Microarray platform for omics analysis

    Science.gov (United States)

    Mecklenburg, Michael; Xie, Bin

    2001-09-01

    Microarray technology has revolutionized genetic analysis. However, limitations in genome analysis has lead to renewed interest in establishing 'omic' strategies. As we enter the post-genomic era, new microarray technologies are needed to address these new classes of 'omic' targets, such as proteins, as well as lipids and carbohydrates. We have developed a microarray platform that combines self- assembling monolayers with the biotin-streptavidin system to provide a robust, versatile immobilization scheme. A hydrophobic film is patterned on the surface creating an array of tension wells that eliminates evaporation effects thereby reducing the shear stress to which biomolecules are exposed to during immobilization. The streptavidin linker layer makes it possible to adapt and/or develop microarray based assays using virtually any class of biomolecules including: carbohydrates, peptides, antibodies, receptors, as well as them ore traditional DNA based arrays. Our microarray technology is designed to furnish seamless compatibility across the various 'omic' platforms by providing a common blueprint for fabricating and analyzing arrays. The prototype microarray uses a microscope slide footprint patterned with 2 by 96 flat wells. Data on the microarray platform will be presented.

  20. Genetic profile of Egyptian hepatocellular-carcinoma associated with hepatitis C virus Genotype 4 by 15 K cDNA microarray: Preliminary study

    Directory of Open Access Journals (Sweden)

    Mansour Tarek

    2008-10-01

    Full Text Available Abstract Background Hepatocellular carcinoma (HCC is a preventable disease rather than a curable one, since there is no well-documented effective treatment modality until now, making the molecular study of this disease mandatory. Findings We studied gene expression profile of 17 Egyptian HCC patients associated with HCV genotype-4 infection by c-DNA microarray. Out of the 15,660 studied genes, 446 were differentially expressed; 180 of them were up regulated and 134 were down regulated. Seventeen genes out of the 180 up-regulated genes are involved in 28 different pathways. Protein phosphatase 3 (PPP3R1 is involved in 10 different pathways followed by fibroblast growth factor receptor 1 (FGFR1, Cas-Br-M ecotropic retroviral transforming sequence b (CBLB, spleen tyrosine kinase (SYK involved in three pathways; bone morphogenetic protein 8a (BMP8A, laminin alpha 3 (LAMA3, cell division cycle 23 (CDC23 involved in 2 pathways and NOTCH4 which regulate Notch signaling pathway. On the other hand, 25 out of the 134 down-regulated genes are involved in 20 different pathways. Integrin alpha V alpha polypeptide antigen CD51 (ITGVA is involved in 4 pathways followed by lymphotoxin alpha (TNF superfamily, member 1 (LTA involved in 3 pathways and alpha-2-macroglobulin (A2M, phosphorylase kinase alpha 2-liver (PHKA2 and MAGI1 membrane associated guanylate kinase 1 (MAGI1 involved in 2 pathways. In addition, 22 genes showed significantly differential expression between HCC cases with cirrhosis and without cirrhosis. Confirmation analysis was performed on subsets of these genes by RT-PCR, including some up-regulated genes such as CDK4, Bax, NOTCH4 and some down-regulated genes such as ISGF3G, TNF, and VISA. Conclusion This is the first preliminary study on gene expression profile in Egyptian HCC patients associated with HCV-Genotype-4 using the cDNA microarray. The identified genes could provide a new gate for prognostic and diagnostic markers for HCC associated

  1. 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.

  2. Shrinkage covariance matrix approach for microarray data

    Science.gov (United States)

    Karjanto, Suryaefiza; Aripin, Rasimah

    2013-04-01

    Microarray technology was developed for the purpose of monitoring the expression levels of thousands of genes. A microarray data set typically consists of tens of thousands of genes (variables) from just dozens of samples due to various constraints including the high cost of producing microarray chips. As a result, the widely used standard covariance estimator is not appropriate for this purpose. One such technique is the Hotelling's T2 statistic which is a multivariate test statistic for comparing means between two groups. It requires that the number of observations (n) exceeds the number of genes (p) in the set but in microarray studies it is common that n Hotelling's T2 statistic with the shrinkage approach is proposed to estimate the covariance matrix for testing differential gene expression. The performance of this approach is then compared with other commonly used multivariate tests using a widely analysed diabetes data set as illustrations. The results across the methods are consistent, implying that this approach provides an alternative to existing techniques.

  3. Evaluating different methods of microarray data normalization

    Directory of Open Access Journals (Sweden)

    Ferreira Carlos

    2006-10-01

    Full Text Available Abstract Background With the development of DNA hybridization microarray technologies, nowadays it is possible to simultaneously assess the expression levels of thousands to tens of thousands of genes. Quantitative comparison of microarrays uncovers distinct patterns of gene expression, which define different cellular phenotypes or cellular responses to drugs. Due to technical biases, normalization of the intensity levels is a pre-requisite to performing further statistical analyses. Therefore, choosing a suitable approach for normalization can be critical, deserving judicious consideration. Results Here, we considered three commonly used normalization approaches, namely: Loess, Splines and Wavelets, and two non-parametric regression methods, which have yet to be used for normalization, namely, the Kernel smoothing and Support Vector Regression. The results obtained were compared using artificial microarray data and benchmark studies. The results indicate that the Support Vector Regression is the most robust to outliers and that Kernel is the worst normalization technique, while no practical differences were observed between Loess, Splines and Wavelets. Conclusion In face of our results, the Support Vector Regression is favored for microarray normalization due to its superiority when compared to the other methods for its robustness in estimating the normalization curve.

  4. Dissociations between Spatial and Temporal Order Memory: A Neuropsychological Patient Study.

    Science.gov (United States)

    Kant, Neeltje; van Zandvoort, Martine J E; van den Berg, Esther; Frijns, Catharina J M; Kappelle, L Jaap; Postma, Albert

    2017-05-01

    In complex real life situations, memories for temporal and spatial information are naturally linked since sequential events coincide in time and space. Whether this connection is inseparable or instead whether these processes are functionally dissociable was investigated in this patient study. Spatial object-location and temporal order memory tasks were administered to 36 stroke patients and 44 healthy control participants. On group level, patients with a stroke in the left hemisphere performed worse on temporal order memory, compared to the control participants. On individual level, using a multiple case-study approach, a clear pattern of dissociations was found between memory for temporal and for spatial features. These findings indicate that location and temporal order memory contain functionally separable processes. This adds to our understanding of how context information is processed in human memory. (JINS, 2017, 23, 421-430).

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

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    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.

  6. Microarray expression in peri-implant tissue next to different titanium implant surfaces predicts clinical outcomes: a split-mouth study.

    Science.gov (United States)

    Menini, M; Dellepiane, E; Baldi, D; Longobardi, M G; Pera, P; Izzotti, A

    2017-09-01

    This split-mouth study evaluated miRNA expression of tissues around implants with different surface treatments. Each patient of the sample (five men and five women) received two implants (one control and one test) into an edentulous quadrant to support fixed partial dentures. The control implants (Osseotite) had a dual acid-etched (DAE) surface in the apical portion and a machined coronal part, test implants (Full Osseotite, FOSS) were completely DAE. Machined healing abutments were placed on control implants and DAE abutments on test ones. All implants were assigned codes for blinding. Standardized periapical radiographs were taken at baseline, 2 and 6 months, and 1 year after surgery. Plaque index (PI), bleeding on probing (BOP), and probing depth (PD) were recorded at 3 and 6 weeks, and 2, 3, 6, and 12 months post-implant placement. After 3 months, a mini-invasive sample of soft tissue was collected from seven patients (four women and three men) for miRNA microarray analysis. Control implants showed greater bone resorption (BR) and lower PI: this was not statistically significant. No statistically significant differences in BOP and PD appeared. miRNA modulated by implant surfaces as well as by other clinical conditions has been identified. miRNA microarray analysis revealed that: (i) implant sites with low PI and absence of BOP had a miRNA expression profile similar to those with plaque and absence of BOP; sites with high PI and high BOP had a different profile. (ii) Implant sites with BOP presented similar profiles independently from implant surface. (iii) Implant sites with high PI and normal BR differed from others for miRNA expression profile. (iv) Implant sites with normal BR despite high BOP differed from others. This profile resembled that of FOSS implants. (v) Implant surface affected BR; groups having similar BR clusterized differently according to the implant type. DAE surfaces induced lower BR and more plaque accumulation: This did not affect the

  7. 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 (pAuditory 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.

  8. Identifying Fishes through DNA Barcodes and Microarrays.

    Science.gov (United States)

    Kochzius, Marc; Seidel, Christian; Antoniou, Aglaia; Botla, Sandeep Kumar; Campo, Daniel; Cariani, Alessia; Vazquez, Eva Garcia; Hauschild, Janet; Hervet, Caroline; Hjörleifsdottir, Sigridur; Hreggvidsson, Gudmundur; Kappel, Kristina; Landi, Monica; Magoulas, Antonios; Marteinsson, Viggo; Nölte, Manfred; Planes, Serge; Tinti, Fausto; Turan, Cemal; Venugopal, Moleyur N; Weber, Hannes; Blohm, Dietmar

    2010-09-07

    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.

  9. Identifying Fishes through DNA Barcodes and Microarrays.

    Directory of Open Access Journals (Sweden)

    Marc Kochzius

    Full Text Available BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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.

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

    Directory of Open Access Journals (Sweden)

    Kelli Anderson

    Full Text Available 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.

  11. A Human Lectin Microarray for Sperm Surface Glycosylation Analysis *

    Science.gov (United States)

    Sun, Yangyang; Cheng, Li; Gu, Yihua; Xin, Aijie; Wu, Bin; Zhou, Shumin; Guo, Shujuan; Liu, Yin; Diao, Hua; Shi, Huijuan; Wang, Guangyu; Tao, Sheng-ce

    2016-01-01

    Glycosylation is one of the most abundant and functionally important protein post-translational modifications. As such, technology for efficient glycosylation analysis is in high demand. Lectin microarrays are a powerful tool for such investigations and have been successfully applied for a variety of glycobiological studies. However, most of the current lectin microarrays are primarily constructed from plant lectins, which are not well suited for studies of human glycosylation because of the extreme complexity of human glycans. Herein, we constructed a human lectin microarray with 60 human lectin and lectin-like proteins. All of the lectins and lectin-like proteins were purified from yeast, and most showed binding to human glycans. To demonstrate the applicability of the human lectin microarray, human sperm were probed on the microarray and strong bindings were observed for several lectins, including galectin-1, 7, 8, GalNAc-T6, and ERGIC-53 (LMAN1). These bindings were validated by flow cytometry and fluorescence immunostaining. Further, mass spectrometry analysis showed that galectin-1 binds several membrane-associated proteins including heat shock protein 90. Finally, functional assays showed that binding of galectin-8 could significantly enhance the acrosome reaction within human sperms. To our knowledge, this is the first construction of a human lectin microarray, and we anticipate it will find wide use for a range of human or mammalian studies, alone or in combination with plant lectin microarrays. PMID:27364157

  12. 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.

  13. Replicable and Coupled Changes in Innate and Adaptive Immune Gene Expression in Two Case-Control Studies of Blood Microarrays in Major Depressive Disorder.

    Science.gov (United States)

    Leday, Gwenaël G R; Vértes, Petra E; Richardson, Sylvia; Greene, Jonathan R; Regan, Tim; Khan, Shahid; Henderson, Robbie; Freeman, Tom C; Pariante, Carmine M; Harrison, Neil A; Perry, V Hugh; Drevets, Wayne C; Wittenberg, Gayle M; Bullmore, Edward T

    2018-01-01

    Peripheral inflammation is often associated with major depressive disorder (MDD), and immunological biomarkers of depression remain a focus of investigation. We used microarray data on whole blood from two independent case-control studies of MDD: the GlaxoSmithKline-High-Throughput Disease-specific target Identification Program [GSK-HiTDiP] study (113 patients and 57 healthy control subjects) and the Janssen-Brain Resource Company study (94 patients and 100 control subjects). Genome-wide differential gene expression analysis (18,863 probes) resulted in a p value for each gene in each study. A Bayesian method identified the largest p-value threshold (q = .025) associated with twice the number of genes differentially expressed in both studies compared with the number of coincidental case-control differences expected by chance. A total of 165 genes were differentially expressed in both studies with concordant direction of fold change. The 90 genes overexpressed (or UP genes) in MDD were significantly enriched for immune response to infection, were concentrated in a module of the gene coexpression network associated with innate immunity, and included clusters of genes with correlated expression in monocytes, monocyte-derived dendritic cells, and neutrophils. In contrast, the 75 genes underexpressed (or DOWN genes) in MDD were associated with the adaptive immune response and included clusters of genes with correlated expression in T cells, natural killer cells, and erythroblasts. Consistently, the MDD patients with overexpression of UP genes also had underexpression of DOWN genes (correlation > .70 in both studies). MDD was replicably associated with proinflammatory activation of the peripheral innate immune system, coupled with relative inactivation of the adaptive immune system, indicating the potential of transcriptional biomarkers for immunological stratification of patients with depression. Copyright © 2017 Society of Biological Psychiatry. Published by Elsevier

  14. 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.

  15. Protein microarray-mediated detection of antienterovirus antibodies in serum.

    Science.gov (United States)

    Zhang, Aiying; Xiu, Bingshui; Zhang, Heqiu; Li, Ning

    2016-04-01

    To utilize prokaryotic gene expression and protein microarray to develop and evaluate a sensitive, accurate protein microarray assay for detecting antienterovirus antibodies in serum samples from patients with hand, foot and mouth disease (HFMD). Enterovirus 71 (EV71) and coxsackievirus A16 (CA16), two common causative agents for HFMD, were used for assay development. Serum was collected from patients with HFMD and healthy controls. EV71 and CA16 VP1 and VP3 genes were expressed in transfected Escherichia coli; the resultant VP1 and 3 proteins were used in a microarray assay for human serum EV71 and CA16 immunoglobulin (Ig) M and IgG. To validate the microarray assay, serum samples were tested for EV71 IgM using enzyme-linked immunosorbent assay (ELISA). Out of 50 patients with HFMD, EV71 IgM and CA16 IgM was detected in 80% and 44% of serum samples, respectively, using protein microarray, and EV71 IgM was detected in 78% of samples using ELISA. Protein microarray and ELISA showed 100% specificity for EV71-IgM detection. The protein microarray assay developed in the present study shows potential as a sensitive technique for detecting EV71 IgM in serum samples from patients with HFMD. © The Author(s) 2016.

  16. 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

  17. A genome-wide study of cytogenetic changes in colorectal cancer using SNP microarrays: opportunities for future personalized treatment.

    Directory of Open Access Journals (Sweden)

    Farzana Jasmine

    Full Text Available In colorectal cancer (CRC, chromosomal instability (CIN is typically studied using comparative-genomic hybridization (CGH arrays. We studied paired (tumor and surrounding healthy fresh frozen tissue from 86 CRC patients using Illumina's Infinium-based SNP array. This method allowed us to study CIN in CRC, with simultaneous analysis of copy number (CN and B-allele frequency (BAF--a representation of allelic composition. These data helped us to detect mono-allelic and bi-allelic amplifications/deletion, copy neutral loss of heterozygosity, and levels of mosaicism for mixed cell populations, some of which can not be assessed with other methods that do not measure BAF. We identified associations between CN abnormalities and different CRC phenotypes (histological diagnosis, location, tumor grade, stage, MSI and presence of lymph node metastasis. We showed commonalities between regions of CN change observed in CRC and the regions reported in previous studies of other solid cancers (e.g. amplifications of 20q, 13q, 8q, 5p and deletions of 18q, 17p and 8p. From Therapeutic Target Database, we identified relevant drugs, targeted to the genes located in these regions with CN changes, approved or in trials for other cancers and common diseases. These drugs may be considered for future therapeutic trials in CRC, based on personalized cytogenetic diagnosis. We also found many regions, harboring genes, which are not currently targeted by any relevant drugs that may be considered for future drug discovery studies. Our study shows the application of high density SNP arrays for cytogenetic study in CRC and its potential utility for personalized treatment.

  18. A New Way to Introduce Microarray Technology in a Lecture/Laboratory Setting by Studying the Evolution of This Modern Technology

    Science.gov (United States)

    Rowland-Goldsmith, Melissa

    2009-01-01

    DNA microarray is an ordered grid containing known sequences of DNA, which represent many of the genes in a particular organism. Each DNA sequence is unique to a specific gene. This technology enables the researcher to screen many genes from cells or tissue grown in different conditions. We developed an undergraduate lecture and laboratory…

  19. Study of microarray time series data based on Forward-Backward Linear Prediction and Singular Value Decomposition.

    Science.gov (United States)

    Choong, Miew Keen; Levy, David; Yan, Hong

    2009-01-01

    We propose a method to analyse the periodicities of gene expression profiles based on the spectral domain approach. Our spectral reconstruction method outperforms three other recently proposed methods, which do not require any prior knowledge. It is proven that an alternative method for studying cell-cycle regulation is possible even where very little prior knowledge is available. We also investigate the potential of combining signals with similar frequency components to form an overdetermined system of equations, and use least squares solution to estimate the spectral frequency. Results show that this new method is able to estimate the peak frequency more accurately.

  20. 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....

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

    Science.gov (United States)

    Rojas-Caraballo, Jose; López-Abán, Julio; Fernández-Soto, Pedro; Vicente, Belén; Collía, Francisco; Muro, Antonio

    2015-12-01

    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].

  2. 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].

  3. A growth curve model with fractional polynomials for analysing incomplete time-course data in microarray gene expression studies

    DEFF Research Database (Denmark)

    Tan, Qihua; Thomassen, Mads; Hjelmborg, Jacob V B

    2011-01-01

    -course pattern in a gene by gene manner. We introduce a growth curve model with fractional polynomials to automatically capture the various time-dependent expression patterns and meanwhile efficiently handle missing values due to incomplete observations. For each gene, our procedure compares the performances...... among fractional polynomial models with power terms from a set of fixed values that offer a wide range of curve shapes and suggests a best fitting model. After a limited simulation study, the model has been applied to our human in vivo irritated epidermis data with missing observations to investigate...... time-dependent transcriptional responses to a chemical irritant. Our method was able to identify the various nonlinear time-course expression trajectories. The integration of growth curves with fractional polynomials provides a flexible way to model different time-course patterns together with model...

  4. 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.

  5. 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

  6. Asymmetrical Blood Flow in the Temporal Lobe in the Charles Bonnet Syndrome: Serial Neuroimaging Study

    Directory of Open Access Journals (Sweden)

    N. Adachi

    1994-01-01

    Full Text Available Clinical features and results of neuroimagings of an 86 year old woman with the Charles Bonnet syndrome are reported. She had become completely blind bilaterally due to cataracts and glaucoma. Shortly after an operation for cataracts, she developed visual hallucinations which lasted for 22 years. She had no deterioration of intelligence. Computed tomography (CT and magnetic resonance imaging (MRI showed moderate generalized atrophy, particularly of the temporal lobes. A serial single photon emission computed tomography (SPECT study during visual hallucinations demonstrated hyperperfusion in the left temporal region and the basal ganglia and hypoperfusion in the right temporal region. These findings suggest that asymmetrical blood flow, particularly in the temporal regions, may be correlated with visual hallucination in the Charles Bonnet syndrome.

  7. Endocrine-disrupting potentials of equine estrogens equilin, equilenin, and their metabolites, in the medaka Oryzias latipes: in silico and DNA microarray studies.

    Science.gov (United States)

    Uchida, Masaya; Ishibashi, Hiroshi; Yamamoto, Ryoko; Koyanagi, Akiko; Kusano, Teruhiko; Tominaga, Nobuaki; Ishibashi, Yasuhiro; Arizono, Koji

    2015-09-01

    Although several previous studies have demonstrated the presence of equine estrogens in the aquatic environment, limited data are currently available on the endocrine-disrupting potentials in fish and the risks they pose to aquatic organisms. To investigate the interactions of major equine estrogens equilin (Eq) and equilenin (Eqn), as well as their metabolites 17α-dihydroequilin, 17β-dihydroequilin, 17α-dihydroequilenin and 17β-dihydroequilenin, with the estrogen receptor α (ERα) of medaka (Oryzias latipes), a three-dimensional model of the ligand-binding domain (LBD) of ERα was built in silico, and docking simulations were performed. The docking simulation analysis indicated that the interaction of 17β-dihydroequilenin with the ERα LBD is the most potent, followed by those of 17α-dihydroequilin and 17β-dihydroequilin, whereas those of Eq and Eqn were least potent. We further analyzed gene expression profiles in the livers of male medaka exposed to Eq and Eqn. A DNA microarray representing 6000 genes revealed that 24-h exposure to Eq and Eqn (100 ng/L) upregulated the expression of 6 and 34 genes in the livers of males, respectively. Genes upregulated by Eq included the estrogenic biomarker genes vitellogenins and choriogenins, suggesting the estrogenic potential of Eq. In contrast, Eqn exposure upregulated several cancer-related genes, such as mediator complex subunit 16 and RAS oncogene family members, suggesting a carcinogenic potential for Eqn. These results suggest that equine estrogens may have not only endocrine-disrupting potentials via the ERα signaling pathway but also carcinogenic potency in male medaka. Copyright © 2015 John Wiley & Sons, Ltd.

  8. Weighted analysis of general microarray experiments

    Directory of Open Access Journals (Sweden)

    Kristiansson Erik

    2007-10-01

    Full Text Available Abstract Background In DNA microarray experiments, measurements from different biological samples are often assumed to be independent and to have identical variance. For many datasets these assumptions have been shown to be invalid and typically lead to too optimistic p-values. A method called WAME has been proposed where a variance is estimated for each sample and a covariance is estimated for each pair of samples. The current version of WAME is, however, limited to experiments with paired design, e.g. two-channel microarrays. Results The WAME procedure is extended to general microarray experiments, making it capable of handling both one- and two-channel datasets. Two public one-channel datasets are analysed and WAME detects both unequal variances and correlations. WAME is compared to other common methods: fold-change ranking, ordinary linear model with t-tests, LIMMA and weighted LIMMA. The p-value distributions are shown to differ greatly between the examined methods. In a resampling-based simulation study, the p-values generated by WAME are found to be substantially more correct than the alternatives when a relatively small proportion of the genes is regulated. WAME is also shown to have higher power than the other methods. WAME is available as an R-package. Conclusion The WAME procedure is generalized and the limitation to paired-design microarray datasets is removed. The examined other methods produce invalid p-values in many cases, while WAME is shown to produce essentially valid p-values when a relatively small proportion of genes is regulated. WAME is also shown to have higher power than the examined alternative methods.

  9. Metadata management and semantics in microarray repositories.

    Science.gov (United States)

    Kocabaş, F; Can, T; Baykal, N

    2011-12-01

    The number of microarray and other high-throughput experiments on primary repositories keeps increasing as do the size and complexity of the results in response to biomedical investigations. Initiatives have been started on standardization of content, object model, exchange format and ontology. However, there are backlogs and inability to exchange data between microarray repositories, which indicate that there is a great need for a standard format and data management. We have introduced a metadata framework that includes a metadata card and semantic nets that make experimental results visible, understandable and usable. These are encoded in syntax encoding schemes and represented in RDF (Resource Description Frame-word), can be integrated with other metadata cards and semantic nets, and can be exchanged, shared and queried. We demonstrated the performance and potential benefits through a case study on a selected microarray repository. We concluded that the backlogs can be reduced and that exchange of information and asking of knowledge discovery questions can become possible with the use of this metadata framework.

  10. 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.

  11. 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...

  12. A Comparative Study of Reservoir Computing for Temporal Signal Processing

    OpenAIRE

    Goudarzi, Alireza; Banda, Peter; Lakin, Matthew R.; Teuscher, Christof; Stefanovic, Darko

    2014-01-01

    Reservoir computing (RC) is a novel approach to time series prediction using recurrent neural networks. In RC, an input signal perturbs the intrinsic dynamics of a medium called a reservoir. A readout layer is then trained to reconstruct a target output from the reservoir's state. The multitude of RC architectures and evaluation metrics poses a challenge to both practitioners and theorists who study the task-solving performance and computational power of RC. In addition, in contrast to tradit...

  13. Design and analysis of mismatch probes for long oligonucleotide microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Zhou, Jizhong

    2008-08-15

    Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.

  14. Microarray Developed on Plastic Substrates.

    Science.gov (United States)

    Bañuls, María-José; Morais, Sergi B; Tortajada-Genaro, Luis A; Maquieira, Ángel

    2016-01-01

    There is a huge potential interest to use synthetic polymers as versatile solid supports for analytical microarraying. Chemical modification of polycarbonate (PC) for covalent immobilization of probes, micro-printing of protein or nucleic acid probes, development of indirect immunoassay, and development of hybridization protocols are described and discussed.

  15. 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.

  16. Profiling In Situ Microbial Community Structure with an Amplification Microarray

    Science.gov (United States)

    Knickerbocker, Christopher; Bryant, Lexi; Golova, Julia; Wiles, Cory; Williams, Kenneth H.; Peacock, Aaron D.; Long, Philip E.

    2013-01-01

    The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO3−) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. PMID:23160129

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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

  3. The Clinical Utility of a Single-Nucleotide Polymorphism Microarray in Patients With Epilepsy at a Tertiary Medical Center.

    Science.gov (United States)

    Hrabik, Sarah A; Standridge, Shannon M; Greiner, Hansel M; Neilson, Derek E; Pilipenko, Valentina V; Zimmerman, Sarah L; Connor, Jessica A; Spaeth, Christine G

    2015-11-01

    Microarray testing has revolutionized clinical cytogenetics, as it provides a significantly higher resolution and greater clinical yield than karyotype analysis. This study assessed the clinical utility of single-nucleotide polymorphism microarray in patients with epilepsy. Study subjects were patients between the ages of birth to 23 years who were diagnosed with epilepsy and had a microarray performed at Cincinnati Children's Hospital Medical Center. Statistical analysis explored the association of microarray results and brain magnetic resonance imaging (MRI), seizure type, and structural malformations. Approximately 17.7% (26/147) of participants had an abnormal microarray as defined by laboratory guidelines. There were no differences in frequency of abnormal brain MRI or seizure type between the abnormal and normal microarray groups. There was a higher prevalence of musculoskeletal malformations (P microarrays. Clinicians should consider microarray analysis in individuals who have epilepsy, especially in combination with musculoskeletal malformation or cardiovascular malformation. © The Author(s) 2015.

  4. 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.

  5. 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...

  6. Galeal flap based on superficial temporal vessels for oral cavity and pharynx reconstruction: an anatomical study

    Directory of Open Access Journals (Sweden)

    Fabio Pinto

    2008-01-01

    Full Text Available PURPOSE: Despite the advances in microvascular free tissue transfer for intraoral reconstruction, this surgery is not recommended for all patients. In specific cases, the pedicled temporoparietal galeal flap may be an option for reconstructive procedures in the head and neck regions. The objective of this paper is to present the anatomical aspects of a galeal flap based on the superficial temporal vessels and to test its potential for reconstructing diverse sites of the oral cavity and pharynx. METHODS: We performed 40 dissections on 34 fresh adult cadavers. The flap vascular anatomy was studied by injecting latex into the superficial temporal vessels. A standardized square-shape flap measuring 10 x 10 cm², pedicled on the superficial temporal vessels, was raised. Oral cavity and oropharynx reconstruction simulations were performed after flap transposition into the mouth by passing it under the zygomatic arch. Hypopharyngeal reconstruction was tested by transposing the flap to the neck under the facial nerve. RESULTS: After latex injection, a rich vascular network over the temporoparietal galea was observed directly from the superficial temporal artery, and a well-vascularized flap based on this vessel was raised. In the reconstruction simulations, the flap was shown to be suitable for the coverage of hypothetical defects in most oral cavity and pharyngeal sites, mainly the retromolar trigone, tonsil area, and buccal mucosa. CONCLUSIONS: A galeal flap based on the superficial temporal vessels presents favorable anatomical characteristics for oral cavity and pharyngeal reconstruction.

  7. 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.

  8. An exploratory study of temporal integration in the peripheral retina of myopes

    Science.gov (United States)

    Macedo, Antonio F.; Encarnação, Tito J.; Vilarinho, Daniel; Baptista, António M. G.

    2017-08-01

    The visual system takes time to respond to visual stimuli, neurons need to accumulate information over a time span in order to fire. Visual information perceived by the peripheral retina might be impaired by imperfect peripheral optics leading to myopia development. This study explored the effect of eccentricity, moderate myopia and peripheral refraction in temporal visual integration. Myopes and emmetropes showed similar performance at detecting briefly flashed stimuli in different retinal locations. Our results show evidence that moderate myopes have normal visual integration when refractive errors are corrected with contact lens; however, the tendency to increased temporal integration thresholds observed in myopes deserves further investigation.

  9. Project Temporalities

    DEFF Research Database (Denmark)

    Tryggestad, Kjell; Justesen, Lise; Mouritsen, Jan

    2013-01-01

    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...... into account. This may require investments in new project management technologies. Originality/value – This paper adds to the literatures on project temporalities and stakeholder theory by connecting them to the question of non-human stakeholders and to project management technologies.......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...

  10. The Temporal Properties of E-Learning: An Exploratory Study of Academics' Conceptions

    Science.gov (United States)

    Martins, Jorge; Nunes, Miguel Baptista

    2016-01-01

    Purpose: The purpose of this paper is to present the results of an exploratory study that investigates Portuguese academics' conceptions concerning the temporal properties of e-learning, in the context of traditional Higher Education Institutions. Design/methodology/approach: Grounded Theory methodology was used to systematically analyse data…

  11. 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.

  12. 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.

  13. 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...

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

    Directory of Open Access Journals (Sweden)

    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.

  15. 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.

  16. Precision Profiling and Components of Variability Analysis for Affymetrix Microarray Assays Run in a Clinical Context

    OpenAIRE

    Daly, Thomas M.; Dumaual, Carmen M.; Dotson, Crystal A.; Farmen, Mark W.; Kadam, Sunil K.; Hockett, Richard D.

    2005-01-01

    Although gene expression profiling using microarray technology is widely used in research environments, adoption of microarray testing in clinical laboratories is currently limited. In an attempt to determine how such assays would perform in a clinical laboratory, we evaluated the analytical variability of Affymetrix microarray probesets using two generations of human Affymetrix chips (U95Av2 and U133A). The study was designed to mimic potential clinical applications by using multiple operato...

  17. Gene expression risk signatures maintain prognostic power in multiple myeloma despite microarray probe set translation

    DEFF Research Database (Denmark)

    Hermansen, N E U; Borup, R; Andersen, M K

    2016-01-01

    INTRODUCTION: Gene expression profiling (GEP) risk models in multiple myeloma are based on 3'-end microarrays. We hypothesized that GEP risk signatures could retain prognostic power despite being translated and applied to whole-transcript microarray data. METHODS: We studied CD138-positive bone...... signatures maintain significant prognostic power in HDT myeloma patients. We suggest probe set matching for GEP risk signature translation as part of the efforts towards a microarray-independent GEP risk standard. (ClicinalTrials.gov identifier: NCT00639054)....

  18. New oligonucleotide microarray for rapid diagnosis of avian viral diseases.

    Science.gov (United States)

    Sultankulova, Kulyaisan T; Kozhabergenov, Nurlan S; Strochkov, Vitaliy M; Burashev, Yerbol D; Shorayeva, Kamshat A; Chervyakova, Olga V; Rametov, Nurkuisa M; Sandybayev, Nurlan T; Sansyzbay, Abylay R; Orynbayev, Mukhit B

    2017-04-05

    We developed a new oligonucleotide microarray comprising 16 identical subarrays for simultaneous rapid detection of avian viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious bursal disease virus (IBDV) in single- and mixed-virus infections. The objective of the study was to develop an oligonucleotide microarray for rapid diagnosis of avian diseases that would be used in the course of mass analysis for routine epidemiological surveillance owing to its ability to test one specimen for several infections. The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescent-labelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. Sensitivity and specificity of the developed microarray was evaluated with use of 122 specimens of biological material: 44 cloacal swabs from sick birds and 78 tissue specimens from dead wild and domestic birds, as well as with use of 15 AIV, NDV, IBV and IBDV strains, different in their origin, epidemiological and biological characteristics (RIBSP Microbial Collection). This microarray demonstrates high diagnostic sensitivity (99.16% within 95% CI limits 97.36-100%) and specificity (100%). Specificity of the developed technique was confirmed by direct sequencing of NP and M (AIV), VP2 (IBDV), S1 (IBV), NP (NDV) gene fragments. Diagnostic effectiveness of the developed DNA microarray is 99.18% and therefore it can be used in mass survey for specific detection of AIV, NDV, IBV and IBDV circulating in the region in the course of epidemiological surveillance. Rather simple method for rapid diagnosis of avian viral diseases that several times shortens duration of assay versus classical diagnostic

  19. DNA Microarray Detection of 18 Important Human Blood Protozoan Species.

    Science.gov (United States)

    Chen, Mu-Xin; Ai, Lin; Chen, Jun-Hu; Feng, Xin-Yu; Chen, Shao-Hong; Cai, Yu-Chun; Lu, Yan; Zhou, Xiao-Nong; Chen, Jia-Xu; Hu, Wei

    2016-12-01

    Accurate detection of blood protozoa from clinical samples is important for diagnosis, treatment and control of related diseases. In this preliminary study, a novel DNA microarray system was assessed for the detection of Plasmodium, Leishmania, Trypanosoma, Toxoplasma gondii and Babesia in humans, animals, and vectors, in comparison with microscopy and PCR data. Developing a rapid, simple, and convenient detection method for protozoan detection is an urgent need. The microarray assay simultaneously identified 18 species of common blood protozoa based on the differences in respective target genes. A total of 20 specific primer pairs and 107 microarray probes were selected according to conserved regions which were designed to identify 18 species in 5 blood protozoan genera. The positive detection rate of the microarray assay was 91.78% (402/438). Sensitivity and specificity for blood protozoan detection ranged from 82.4% (95%CI: 65.9% ~ 98.8%) to 100.0% and 95.1% (95%CI: 93.2% ~ 97.0%) to 100.0%, respectively. Positive predictive value (PPV) and negative predictive value (NPV) ranged from 20.0% (95%CI: 2.5% ~ 37.5%) to 100.0% and 96.8% (95%CI: 95.0% ~ 98.6%) to 100.0%, respectively. Youden index varied from 0.82 to 0.98. The detection limit of the DNA microarrays ranged from 200 to 500 copies/reaction, similar to PCR findings. The concordance rate between microarray data and DNA sequencing results was 100%. Overall, the newly developed microarray platform provides a convenient, highly accurate, and reliable clinical assay for the determination of blood protozoan species.

  20. 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.

  1. Inference of selection based on temporal genetic differentiation in the study of highly polymorphic multigene families.

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    Mark McMullan

    Full Text Available The co-evolutionary arms race between host immune genes and parasite virulence genes is known as Red Queen dynamics. Temporal fluctuations in allele frequencies, or the 'turnover' of alleles at immune genes, are concordant with predictions of the Red Queen hypothesis. Such observations are often taken as evidence of host-parasite co-evolution. Here, we use computer simulations of the Major Histocompatibility Complex (MHC of guppies (Poecilia reticulata to study the turnover rate of alleles (temporal genetic differentiation, G'(ST. Temporal fluctuations in MHC allele frequencies can be ≥≤order of magnitude larger than changes observed at neutral loci. Although such large fluctuations in the MHC are consistent with Red Queen dynamics, simulations show that other demographic and population genetic processes can account for this observation, these include: (1 overdominant selection, (2 fluctuating population size within a metapopulation, and (3 the number of novel MHC alleles introduced by immigrants when there are multiple duplicated genes. Synergy between these forces combined with migration rate and the effective population size can drive the rapid turnover in MHC alleles. We posit that rapid allelic turnover is an inherent property of highly polymorphic multigene families and that it cannot be taken as evidence of Red Queen dynamics. Furthermore, combining temporal samples in spatial F(ST outlier analysis may obscure the signal of selection.

  2. 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.

  3. 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.

  4. 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.

  5. Statistical implications of pooling RNA samples for microarray experiments

    Directory of Open Access Journals (Sweden)

    Landfield Philip W

    2003-06-01

    Full Text Available Abstract Background Microarray technology has become a very important tool for studying gene expression profiles under various conditions. Biologists often pool RNA samples extracted from different subjects onto a single microarray chip to help defray the cost of microarray experiments as well as to correct for the technical difficulty in getting sufficient RNA from a single subject. However, the statistical, technical and financial implications of pooling have not been explicitly investigated. Results Modeling the resulting gene expression from sample pooling as a mixture of individual responses, we derived expressions for the experimental error and provided both upper and lower bounds for its value in terms of the variability among individuals and the number of RNA samples pooled. Using "virtual" pooling of data from real experiments and computer simulations, we investigated the statistical properties of RNA sample pooling. Our study reveals that pooling biological samples appropriately is statistically valid and efficient for microarray experiments. Furthermore, optimal pooling design(s can be found to meet statistical requirements while minimizing total cost. Conclusions Appropriate RNA pooling can provide equivalent power and improve efficiency and cost-effectiveness for microarray experiments with a modest increase in total number of subjects. Pooling schemes in terms of replicates of subjects and arrays can be compared before experiments are conducted.

  6. 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.

  7. Generalization of temporal order detection skill learning: two experimental studies of children with dyslexia

    Directory of Open Access Journals (Sweden)

    C.F.B. Murphy

    2010-04-01

    Full Text Available The objective of this study was to investigate the phenomenon of learning generalization of a specific skill of auditory temporal processing (temporal order detection in children with dyslexia. The frequency order discrimination task was applied to children with dyslexia and its effect after training was analyzed in the same trained task and in a different task (duration order discrimination involving the temporal order discrimination too. During study 1, one group of subjects with dyslexia (N = 12; mean age = 10.9 ± 1.4 years was trained and compared to a group of untrained dyslexic children (N = 28; mean age = 10.4 ± 2.1 years. In study 2, the performance of a trained dyslexic group (N = 18; mean age = 10.1 ± 2.1 years was compared at three different times: 2 months before training, at the beginning of training, and at the end of training. Training was carried out for 2 months using a computer program responsible for training frequency ordering skill. In study 1, the trained group showed significant improvement after training only for frequency ordering task compared to the untrained group (P < 0.001. In study 2, the children showed improvement in the last interval in both frequency ordering (P < 0.001 and duration ordering (P = 0.01 tasks. These results showed differences regarding the presence of learning generalization of temporal order detection, since there was generalization of learning in only one of the studies. The presence of methodological differences between the studies, as well as the relationship between trained task and evaluated tasks, are discussed.

  8. Tumor classification ranking from microarray data

    Directory of Open Access Journals (Sweden)

    Kijsanayothin Phongphun

    2008-09-01

    Full Text Available Abstract Background Gene expression profiles based on microarray data are recognized as potential diagnostic indices of cancer. Molecular tumor classifications resulted from these data and learning algorithms have advanced our understanding of genetic changes associated with cancer etiology and development. However, classifications are not always perfect and in such cases the classification rankings (likelihoods of correct class predictions can be useful for directing further research (e.g., by deriving inferences about predictive indicators or prioritizing future experiments. Classification ranking is a challenging problem, particularly for microarray data, where there is a huge number of possible regulated genes with no known rating function. This study investigates the possibility of making tumor classification more informative by using a method for classification ranking that requires no additional ranking analysis and maintains relatively good classification accuracy. Results Microarray data of 11 different types and subtypes of cancer were analyzed using MDR (Multi-Dimensional Ranker, a recently developed boosting-based ranking algorithm. The number of predictor genes in all of the resulting classification models was at most nine, a huge reduction from the more than 12 thousands genes in the majority of the expression samples. Compared to several other learning algorithms, MDR gives the greatest AUC (area under the ROC curve for the classifications of prostate cancer, acute lymphoblastic leukemia (ALL and four ALL subtypes: BCR-ABL, E2A-PBX1, MALL and TALL. SVM (Support Vector Machine gives the highest AUC for the classifications of lung, lymphoma, and breast cancers, and two ALL subtypes: Hyperdiploid > 50 and TEL-AML1. MDR gives highly competitive results, producing the highest average AUC, 91.01%, and an average overall accuracy of 90.01% for cancer expression analysis. Conclusion Using the classification rankings from MDR is a simple

  9. 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

  10. Mortality burden of diurnal temperature range and its temporal changes: A multi-country study.

    Science.gov (United States)

    Lee, Whanhee; Bell, Michelle L; Gasparrini, Antonio; Armstrong, Ben G; Sera, Francesco; Hwang, Sunghee; Lavigne, Eric; Zanobetti, Antonella; Coelho, Micheline de Sousa Zanotti Stagliorio; Saldiva, Paulo Hilario Nascimento; Osorio, Samuel; Tobias, Aurelio; Zeka, Ariana; Goodman, Patrick G; Forsberg, Bertil; Rocklöv, Joacim; Hashizume, Masahiro; Honda, Yasushi; Guo, Yue-Liang Leon; Seposo, Xerxes; Van Dung, Do; Dang, Tran Ngoc; Tong, Shilu; Guo, Yuming; Kim, Ho

    2018-01-01

    Although diurnal temperature range (DTR) is a key index of climate change, few studies have reported the health burden of DTR and its temporal changes at a multi-country scale. Therefore, we assessed the attributable risk fraction of DTR on mortality and its temporal variations in a multi-country data set. We collected time-series data covering mortality and weather variables from 308 cities in 10 countries from 1972 to 2013. The temporal change in DTR-related mortality was estimated for each city with a time-varying distributed lag model. Estimates for each city were pooled using a multivariate meta-analysis. The results showed that the attributable fraction of total mortality to DTR was 2.5% (95% eCI: 2.3-2.7%) over the entire study period. In all countries, the attributable fraction increased from 2.4% (2.1-2.7%) to 2.7% (2.4-2.9%) between the first and last study years. This study found that DTR has significantly contributed to mortality in all the countries studied, and this attributable fraction has significantly increased over time in the USA, the UK, Spain, and South Korea. Therefore, because the health burden of DTR is not likely to reduce in the near future, countermeasures are needed to alleviate its impact on human health. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Advanced Data Mining of Leukemia Cells Micro-Arrays

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    Ryan M. Pierce

    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.

  12. Tissue Microarray: A rapidly evolving diagnostic and research tool

    Science.gov (United States)

    Jawhar, Nazar M.T.

    2009-01-01

    Tissue microarray is a recent innovation in the field of pathology. A microarray contains many small representative tissue samples from hundreds of different cases assembled on a single histologic slide, and therefore allows high throughput analysis of multiple specimens at the same time. Tissue microarrays are paraffin blocks produced by extracting cylindrical tissue cores from different paraffin donor blocks and re-embedding these into a single recipient (microarray) block at defined array coordinates. Using this technique, up to 1000 or more tissue samples can be arrayed into a single paraffin block. It can permit simultaneous analysis of molecular targets at the DNA, mRNA, and protein levels under identical, standardized conditions on a single glass slide, and also provide maximal preservation and use of limited and irreplaceable archival tissue samples. This versatile technique, in which data analysis is automated facilitates retrospective and prospective human tissue studies. It is a practical and effective tool for high-throughput molecular analysis of tissues that is helping to identify new diagnostic and prognostic markers and targets in human cancers, and has a range of potential applications in basic research, prognostic oncology and drug discovery. This article summarizes the technical aspects of tissue microarray construction and sectioning, advantages, application, and limitations. PMID:19318744

  13. Comparative analysis of genomic signal processing for microarray data clustering.

    Science.gov (United States)

    Istepanian, Robert S H; Sungoor, Ala; Nebel, Jean-Christophe

    2011-12-01

    Genomic signal processing is a new area of research that combines advanced digital signal processing methodologies for enhanced genetic data analysis. It has many promising applications in bioinformatics and next generation of healthcare systems, in particular, in the field of microarray data clustering. In this paper we present a comparative performance analysis of enhanced digital spectral analysis methods for robust clustering of gene expression across multiple microarray data samples. Three digital signal processing methods: linear predictive coding, wavelet decomposition, and fractal dimension are studied to provide a comparative evaluation of the clustering performance of these methods on several microarray datasets. The results of this study show that the fractal approach provides the best clustering accuracy compared to other digital signal processing and well known statistical methods.

  14. 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...... from a direct comparison of two treatments (dye-balanced). While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using...

  15. 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.

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    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

  18. 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)

  19. 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.

  20. The EADGENE Microarray Data Analysis Workshop

    OpenAIRE

    de Koning, Dirk-Jan; Jaffrézic, Florence; Lund, Mogens Sandø; Watson, Michael; Channing, Caroline; Hulsegge, Ina; Pool, Marco; Buitenhuis, Bart; Hedegaard, Jakob; Hornshøj, Henrik; Jiang, Li; Sørensen, Peter; Marot, Guillemette; Delmas, Céline; Lê Cao, Kim-Anh

    2007-01-01

    Abstract 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 microarra...

  1. D-MaPs - DNA-microarray projects: Web-based software for multi-platform microarray analysis.

    Science.gov (United States)

    Carazzolle, Marcelo F; Herig, Taís S; Deckmann, Ana C; Pereira, Gonçalo A G

    2009-07-01

    The web application D-Maps provides a user-friendly interface to researchers performing studies based on microarrays. The program was developed to manage and process one- or two-color microarray data obtained from several platforms (currently, GeneTAC, ScanArray, CodeLink, NimbleGen and Affymetrix). Despite the availability of many algorithms and many software programs designed to perform microarray analysis on the internet, these usually require sophisticated knowledge of mathematics, statistics and computation. D-maps was developed to overcome the requirement of high performance computers or programming experience. D-Maps performs raw data processing, normalization and statistical analysis, allowing access to the analyzed data in text or graphical format. An original feature presented by D-Maps is GEO (Gene Expression Omnibus) submission format service. The D-MaPs application was already used for analysis of oligonucleotide microarrays and PCR-spotted arrays (one- and two-color, laser and light scanner). In conclusion, D-Maps is a valuable tool for microarray research community, especially in the case of groups without a bioinformatic core.

  2. D-MaPs - DNA-microarray projects: web-based software for multi-platform microarray analysis

    Directory of Open Access Journals (Sweden)

    Marcelo F. Carazzolle

    2009-01-01

    Full Text Available The web application D-Maps provides a user-friendly interface to researchers performing studies based on microarrays. The program was developed to manage and process one- or two-color microarray data obtained from several platforms (currently, GeneTAC, ScanArray, CodeLink, NimbleGen and Affymetrix. Despite the availability of many algorithms and many software programs designed to perform microarray analysis on the internet, these usually require sophisticated knowledge of mathematics, statistics and computation. D-maps was developed to overcome the requirement of high performance computers or programming experience. D-Maps performs raw data processing, normalization and statistical analysis, allowing access to the analyzed data in text or graphical format. An original feature presented by D-Maps is GEO (Gene Expression Omnibus submission format service. The D-MaPs application was already used for analysis of oligonucleotide microarrays and PCR-spotted arrays (one- and two-color, laser and light scanner. In conclusion, D-Maps is a valuable tool for microarray research community, especially in the case of groups without a bioinformatic core.

  3. Microarray time course experiments: finding profiles.

    Science.gov (United States)

    Irigoien, Itziar; Vives, Sergi; Arenas, Concepción

    2011-01-01

    Time course studies with microarray techniques and experimental replicates are very useful in biomedical research. We present, in replicate experiments, an alternative approach to select and cluster genes according to a new measure for association between genes. First, the procedure normalizes and standardizes the expression profile of each gene, and then, identifies scaling parameters that will further minimize the distance between replicates of the same gene. Then, the procedure filters out genes with a flat profile, detects differences between replicates, and separates genes without significant differences from the rest. For this last group of genes, we define a mean profile for each gene and use it to compute the distance between two genes. Next, a hierarchical clustering procedure is proposed, a statistic is computed for each cluster to determine its compactness, and the total number of classes is determined. For the rest of the genes, those with significant differences between replicates, the procedure detects where the differences between replicates lie, and assigns each gene to the best fitting previously identified profile or defines a new profile. We illustrate this new procedure using simulated data and a representative data set arising from a microarray experiment with replication, and report interesting results.

  4. Additive risk survival model with microarray data

    Directory of Open Access Journals (Sweden)

    Huang Jian

    2007-06-01

    Full Text Available Abstract Background Microarray techniques survey gene expressions on a global scale. Extensive biomedical studies have been designed to discover subsets of genes that are associated with survival risks for diseases such as lymphoma and construct predictive models using those selected genes. In this article, we investigate simultaneous estimation and gene selection with right censored survival data and high dimensional gene expression measurements. Results We model the survival time using the additive risk model, which provides a useful alternative to the proportional hazards model and is adopted when the absolute effects, instead of the relative effects, of multiple predictors on the hazard function are of interest. A Lasso (least absolute shrinkage and selection operator type estimate is proposed for simultaneous estimation and gene selection. Tuning parameter is selected using the V-fold cross validation. We propose Leave-One-Out cross validation based methods for evaluating the relative stability of individual genes and overall prediction significance. Conclusion We analyze the MCL and DLBCL data using the proposed approach. A small number of probes represented on the microarrays are identified, most of which have sound biological implications in lymphoma development. The selected probes are relatively stable and the proposed approach has overall satisfactory prediction power.

  5. DNA microarray data and contextual analysis of correlation graphs

    Directory of Open Access Journals (Sweden)

    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.

  6. Screening of cDNA libraries on glass slide microarrays.

    Science.gov (United States)

    Berger, Dave K; Crampton, Bridget G; Hein, Ingo; Vos, Wiesner

    2007-01-01

    A quantitative screening method was developed to evaluate the quality of cDNA libraries constructed by suppression subtraction hybridization (SSH) or other enrichment techniques. The SSH technique was adapted to facilitate screening of the resultant library on a small number of glass slide microarrays. A simple data analysis pipeline named SSHscreen using "linear models for microarray data" (limma) functions in the R computing environment was developed to identify clones in the cDNA libraries that are significantly differentially expressed, and to determine if they were rare or abundant in the original treated sample. This approach facilitates the choice of clones from the cDNA library for further analysis, such as DNA sequencing, Northern blotting, RT-PCR, or detailed expression profiling using a custom cDNA microarray. Furthermore, this strategy is particularly useful for studies of nonmodel organisms for which there is little genome sequence information.

  7. 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...

  8. "Harshlighting" small blemishes on microarrays

    Directory of Open Access Journals (Sweden)

    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.

  9. 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

  10. Advanced bionics thin lateral and Helix II electrodes: a temporal bone study.

    Science.gov (United States)

    Wright, Charles G; Roland, Peter S; Kuzma, Janusz

    2005-11-01

    This study was performed to evaluate the insertional properties of two cochlear implant electrodes recently developed by Advanced Bionics Corporation. Anatomic study using human cadaveric temporal bones. The electrode prototypes we tested are the Thin Lateral and Helix II arrays, which incorporate features designed to minimize insertional trauma. A total of eight electrodes (4 of each prototype) were evaluated after insertion into freshly fixed temporal bones. The electrodes were inserted by way of standard cochleostomies, and the specimens were subsequently dissected to assess electrode position, insertion depth, and intracochlear trauma. Quantitative data regarding insertion depths and contact distances from the modiolus are presented for all electrodes tested. The mean insertion depths were 368 degrees for the Thin Lateral electrodes, which are designed to approximate the lateral cochlear wall, and 436 degrees for the Helix II electrodes, which occupy a more medial position in the scala tympani. No evidence of insertional trauma was observed with either electrode. The ease of insertion and absence of trauma were confirmed during additional trials in which electrode behavior was directly observed during insertion into previously opened cochleas. Both electrodes performed favorably in our human temporal bone trials, and both arrays appear promising for clinical use, especially in patients with residual hearing in whom atraumatic insertion is an important objective.

  11. 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.

  12. Clinical performance of non-invasive prenatal testing (NIPT) using targeted cell-free DNA analysis in maternal plasma with microarrays or next generation sequencing (NGS) is consistent across multiple controlled clinical studies.

    Science.gov (United States)

    Stokowski, Renee; Wang, Eric; White, Karen; Batey, Annette; Jacobsson, Bo; Brar, Herb; Balanarasimha, Madhumitha; Hollemon, Desiree; Sparks, Andrew; Nicolaides, Kypros; Musci, Thomas J

    2015-12-01

    To evaluate the clinical performance of non-invasive prenatal testing for trisomy 21, 18, and 13 using targeted cell-free DNA (cfDNA) analysis. Targeted cfDNA analysis using DANSR™ and FORTE™ with microarray quantitation was used to evaluate the risk of trisomy 21, 18, and 13 in blinded samples from 799 singleton, twin, natural, and IVF pregnancies. Subjects either had fetal chromosome evaluation by karyotype, FISH, QF-PCR, or karyotype for newborns with suspected aneuploidy at birth. The results of targeted cfDNA analysis were compared to clinical genetic testing outcomes to assess clinical performance. Targeted cfDNA analysis with microarray quantification identified 107/108 trisomy 21 cases (99.1%), 29/30 trisomy 18 cases (96.7%), and 12/12 trisomy 13 cases (100%). The specificity was 100% for all three trisomies. Combining this data with all published clinical performance studies using DANSR/FORTE methodology for greater than 23 000 pregnancies, the sensitivity of targeted cfDNA analysis was calculated to be greater than 99% for trisomy 21, 97% for trisomy 18, and 94% for trisomy 13. Specificity for each trisomy was greater than 99.9%. Targeted cfDNA analysis demonstrates consistently high sensitivity and extremely low false positive rates for common autosomal trisomies in pregnancy across quantitation platforms. © 2015 Ariosa Diagnostics Inc. Prenatal Diagnosis published by John Wiley & Sons, Ltd.

  13. 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

  14. 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

  15. Microarray Assisted Gene Discovery in Ulcerative Colitis

    DEFF Research Database (Denmark)

    Brusgaard, Klaus

    ), and microarray based expression studies. In IBD the increased production of chemo attractants from the inflamed microenvironment results in recruitment of activated CD4+ T lymphocytes which results in tissue damage. Where Th1 cell-derived cytokines has been reported to be essential mediators in CD with high (IFN...... on the activation of different downstream pathways. Thus it seems that different genetic backgrounds can lead to similar clinical manifestations, and as well determines the susceptibility to IBD. In the previous micro array based expression studies on UC the main target has been to point to new candidate genes...... based on analysis of the main up or down regulated genes in the dataset. The majority of the studies are hampered by a relatively shortcoming of the numbers of genes analysed on the particular array. In this study the main target has been to point to clusters of genes involved in biochemical pathways...

  16. Microarray-based large scale detection of single feature ...

    Indian Academy of Sciences (India)

    2015-12-08

    Dec 8, 2015 ... Hybridization and data quality. The five genotypes such as JKC703, JKC725, JKC737,. JKC777 and JKC783 were used in the present study. To assess our microarray intensity data, the raw intensity data of only PM probes/features of cotton cultivars were log2 transformed and studied by density plots, and ...

  17. 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.

  18. 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.

  19. 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.

  20. Simulation study on the spatial and temporal characteristics of focused microwave beam discharge in nitrogen

    Science.gov (United States)

    Yang, Wei; Zhou, Qianhong; Dong, Zhiwei

    2018-01-01

    This paper reports a simulation study on a focused microwave (frequency 9.4 GHz, pulse width 2.5 μs, and peak electric field 1.2 kV/cm) discharge in 200 Pa nitrogen. A one-dimensional (1D) fluid model is based on the wave equation for the microwave field propagating through the gas breakdown plasma, the continuity equations for electron, ion and neutral particle densities, and the energy balance equations for mean electron temperature, and nitrogen vibrational and translational temperatures. These equations are numerically solved in a self-consistent manner with a simplified plasma chemistry set, in which the reaction rates involving electrons are calculated from the electron energy distribution function (EEDF) using a two-term expansion method. The spatial and temporal characteristics of the focused microwave breakdown in nitrogen are demonstrated, which include the amplitude of the microwave electric field, and the densities and temperatures of the plasma components. The temporal evolution of the plasma electron density agrees reasonably well with that measured with a microwave interferometer. The spatial-temporal distributions of metastable states are discussed on the plasma chemistry and the character of mean electron temperature. The spatially integrated N2(C3) density shows similar trends with the measured temporal intensity of optical emission spectroscopy, except for a time delay of 100-300 ns. The quantitative discrepancies are explained in light of limitations of the 1D model with a two-term expansion of EEDF. The theoretical model is found to describe the gas breakdown plasma generated by focused microwave beams at least qualitatively.

  1. 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.

  2. 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.

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

    Indian Academy of Sciences (India)

    2014-10-20

    Oct 20, 2014 ... To achieve high detection specificity, we fabricated an isothermal microarray ... diagnosis, drug screening, food inspection, agricultural prod- uct monitoring ..... printed with probes B1, B2 and B3 for Bacillus licheniformis (image 1), and microarray analysis of Bacillus licheniformis PCR products amplified ...

  4. Diagnostic and analytical applications of protein microarrays

    DEFF Research Database (Denmark)

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

    2005-01-01

    years. A genome-scale protein microarray has been demonstrated for identifying protein-protein interactions as well as for rapid identification of protein binding to a particular drug. Furthermore, protein microarrays have been shown as an efficient tool in cancer profiling, detection of bacteria...

  5. Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations.

    Science.gov (United States)

    Hume, David A; Summers, Kim M; Raza, Sobia; Baillie, J Kenneth; Freeman, Thomas C

    2010-06-01

    Very large microarray datasets showing gene expression across multiple tissues and cell populations provide a window on the transcriptional networks that underpin the differences in functional activity between biological systems. Clusters of co-expressed genes provide lineage markers, candidate regulators of cell function and, by applying the principle of guilt by association, candidate functions for genes of currently unknown function. We have analysed a dataset comprising pure cell populations from hemopoietic and non-hemopoietic cell types (http://biogps.gnf.org). Using a novel network visualisation and clustering approach, we demonstrate that it is possible to identify very tight expression signatures associated specifically with embryonic stem cells, mesenchymal cells and hematopoietic lineages. Selected examples validate the prediction that gene function can be inferred by co-expression. One expression cluster was enriched in phagocytes, which, alongside endosome-lysosome constituents, contains genes that may make up a 'pathway' for phagocyte differentiation. Promoters of these genes are enriched for binding sites for the ETS/PU.1 and MITF families. Another cluster was associated with the production of a specific extracellular matrix, with high levels of gene expression shared by cells of mesenchymal origin (fibroblasts, adipocytes, osteoblasts and myoblasts). We discuss the limitations placed upon such data by the presence of alternative promoters with distinct tissue specificity within many protein-coding genes. Copyright 2010 Elsevier Inc. All rights reserved.

  6. Evaluation of Ki67 expression across distinct categories of breast cancer specimens: a population-based study of matched surgical specimens, core needle biopsies and tissue microarrays.

    Directory of Open Access Journals (Sweden)

    Gøril Knutsvik

    Full Text Available Tumor cell proliferation in breast cancer is strongly prognostic and may also predict response to chemotherapy. However, there is no consensus on counting areas or cut-off values for patient stratification. Our aim was to assess the matched level of proliferation by Ki67 when using different tissue categories (whole sections, WS; core needle biopsies, CNB; tissue microarrays, TMA, and the corresponding prognostic value.We examined a retrospective, population-based series of breast cancer (n = 534 from the Norwegian Breast Cancer Screening Program. The percentage of Ki67 positive nuclei was evaluated by visual counting on WS (n = 534, CNB (n = 154 and TMA (n = 459.The median percentage of Ki67 expression was 18% on WS (hot-spot areas, 13% on CNB, and 7% on TMA, and this difference was statistically significant in paired cases. Increased Ki67 expression by all evaluation methods was associated with aggressive tumor features (large tumor diameter, high histologic grade, ER negativity and reduced patient survival.There is a significant difference in tumor cell proliferation by Ki67 across different sample categories. Ki67 is prognostic over a wide range of cut-off points and for different sample types, although Ki67 results derived from TMA sections are lower compared with those obtained using specimens from a clinical setting. Our findings indicate that specimen specific cut-off values should be applied for practical use.

  7. Evaluation of Ki67 expression across distinct categories of breast cancer specimens: a population-based study of matched surgical specimens, core needle biopsies and tissue microarrays.

    Science.gov (United States)

    Knutsvik, Gøril; Stefansson, Ingunn M; Aziz, Sura; Arnes, Jarle; Eide, Johan; Collett, Karin; Akslen, Lars A

    2014-01-01

    Tumor cell proliferation in breast cancer is strongly prognostic and may also predict response to chemotherapy. However, there is no consensus on counting areas or cut-off values for patient stratification. Our aim was to assess the matched level of proliferation by Ki67 when using different tissue categories (whole sections, WS; core needle biopsies, CNB; tissue microarrays, TMA), and the corresponding prognostic value. We examined a retrospective, population-based series of breast cancer (n = 534) from the Norwegian Breast Cancer Screening Program. The percentage of Ki67 positive nuclei was evaluated by visual counting on WS (n = 534), CNB (n = 154) and TMA (n = 459). The median percentage of Ki67 expression was 18% on WS (hot-spot areas), 13% on CNB, and 7% on TMA, and this difference was statistically significant in paired cases. Increased Ki67 expression by all evaluation methods was associated with aggressive tumor features (large tumor diameter, high histologic grade, ER negativity) and reduced patient survival. There is a significant difference in tumor cell proliferation by Ki67 across different sample categories. Ki67 is prognostic over a wide range of cut-off points and for different sample types, although Ki67 results derived from TMA sections are lower compared with those obtained using specimens from a clinical setting. Our findings indicate that specimen specific cut-off values should be applied for practical use.

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

    Directory of Open Access Journals (Sweden)

    Russomano Fabio B

    2008-10-01

    Full Text Available Abstract Background 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. Methods 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. Results HIV/HPV co-infection was associated with a significant increase in expression (p 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/mm2 in CIN I: 63.8; CIN II/III: 115.7 and tumor: 112.0, p = 0.005, in comparison to controls. Conclusion 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.

  9. Immunohistochemical detection of 3 viral infections in paraffin-embedded tissue from mink (Mustela vison): a tissue-microarray-based study

    Science.gov (United States)

    Hammer, Anne Sofie; Dietz, Hans Henrik; Hamilton-Dutoit, Stephen

    2007-01-01

    Immunohistochemical (IHC) assays were developed and tested for the detection of 3 viral infections in archived paraffin-embedded mink tissue. Specimens had been obtained from mink with diagnoses of acute Aleutian disease (AD), mink parvoviral enteritis (MVE), or canine distemper (CD) made by means of routine diagnostic procedures. To improve the efficiency and reduce the costs of IHC analyses, tissue microarray (TMA) technology was used. Representative cores 2 mm in diameter from each tissue specimen and from positive- and negative-control specimens were collected in a TMA block. Immunohistochemical reactions to viral antigens were assessed and graded. Positive reactions were found in 91% of the 32 specimens from mink with AD, 53% to 80% of the 60 specimens from mink with MVE, and all 66 of the specimens from mink with CD. To validate the use of TMAs, the IHC methods were applied to whole-mount paraffin-embedded sections of 10 of the positive specimens for each disease, together with whole-mount sections of small intestine and lung tissue from 2 healthy mink. The IHC grading of the TMA cores and the whole-mount sections from the same animal corresponded completely. These results suggest that IHC demonstration of viral antigen allows rapid and reliable diagnosis of the 3 viral infections in mink and is a potential supplement to histologic diagnostic procedures. The TMA technique proved useful for screening large numbers of samples for expression of specific viral antigens, while reducing overall costs. PMID:17193876

  10. 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...

  11. 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.

  12. Review Article: Current Knowledge on Microarray Technology - An ...

    African Journals Online (AJOL)

    The completion of whole genome sequencing projects has led to a rapid increase in the availability of genetic information. In the field of transcriptomics, the emergence of microarray-based technologies and the design of DNA biochips allow high-throughput studies of RNA expression in cell and tissue at a given moment.

  13. Evaluation of prognostic indicators using validated canine insulinoma tissue microarrays

    NARCIS (Netherlands)

    Buishand, Floryne O; Visser, Judith; Kik, Marja; Gröne, Andrea; Keesler, Rebekah I; Briaire-de Bruijn, Inge H; Kirpensteijn, Jolle

    Tissue microarray (TMA) technology allows analysis of multiple tumour samples simultaneously on a single slide. The aim of the present study was to develop and assess a TMA containing 32 primary canine insulinomas and 13 insulinoma metastases. The results of histopathological and immunohistochemical

  14. 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)

  15. 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)

  16. 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.

  17. A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis.

    Science.gov (United States)

    Chalmers, Andrew D; Goldstone, Kim; Smith, James C; Gilchrist, Mike; Amaya, Enrique; Papalopulu, Nancy

    2005-03-01

    Microarrays have great potential for the study of developmental biology. As a model system Xenopus is well suited for making the most of this potential. However, Xenopus laevis has undergone a genome wide duplication meaning that most genes are represented by two paralogues. This causes a number of problems. Most importantly the presence of duplicated genes mean that a X. laevis microarray will have less or even half the coverage of a similar sized microarray from the closely related but diploid frog Xenopus tropicalis. However, to date, X. laevis is the most commonly used amphibian system for experimental embryology. Therefore, we have tested if a microarray based on sequences from X. tropicalis will work across species using RNA from X. laevis. We produced a pilot oligonucleotide microarray based on sequences from X. tropicalis. The microarray was used to identify genes whose expression levels changed during early X. tropicalis development. The same assay was then carried out using RNA from X. laevis. The cross species experiments gave similar results to those using X. tropicalis RNA. This was true at the whole microarray level and for individual genes, with most genes giving similar results using RNA from X. laevis and X. tropicalis. Furthermore, the overlap in genes identified between a X. laevis and a X. tropicalis set of experiments was only 12% less than the overlap between two sets of X. tropicalis experiments. Therefore researchers can work with X. laevis and still make use of the advantages offered by X. tropicalis microarrays.

  18. Fully Automated Complementary DNA Microarray Segmentation using a Novel Fuzzy-based Algorithm.

    Science.gov (United States)

    Saberkari, Hamidreza; Bahrami, Sheyda; Shamsi, Mousa; Amoshahy, Mohammad Javad; Ghavifekr, Habib Badri; Sedaaghi, Mohammad Hossein

    2015-01-01

    DNA microarray is a powerful approach to study simultaneously, the expression of 1000 of genes in a single experiment. The average value of the fluorescent intensity could be calculated in a microarray experiment. The calculated intensity values are very close in amount to the levels of expression of a particular gene. However, determining the appropriate position of every spot in microarray images is a main challenge, which leads to the accurate classification of normal and abnormal (cancer) cells. In this paper, first a preprocessing approach is performed to eliminate the noise and artifacts available in microarray cells using the nonlinear anisotropic diffusion filtering method. Then, the coordinate center of each spot is positioned utilizing the mathematical morphology operations. Finally, the position of each spot is exactly determined through applying a novel hybrid model based on the principle component analysis and the spatial fuzzy c-means clustering (SFCM) algorithm. Using a Gaussian kernel in SFCM algorithm will lead to improving the quality in complementary DNA microarray segmentation. The performance of the proposed algorithm has been evaluated on the real microarray images, which is available in Stanford Microarray Databases. Results illustrate that the accuracy of microarray cells segmentation in the proposed algorithm reaches to 100% and 98% for noiseless/noisy cells, respectively.

  19. 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.)

  20. How We Think about Temporal Words: A Gestural Priming Study in English and Chinese

    Directory of Open Access Journals (Sweden)

    Melvin M. R. Ng

    2017-06-01

    Full Text Available Spatial metaphors are used to represent and reason about time. Such metaphors are typically arranged along the sagittal axis in most languages. For example, in English, “The future lies ahead of us” and “We look back on our past.” This is less straightforward for Chinese. Specifically, both the past and future can either be behind or ahead. The present study aims to explore these cross-linguistic differences by priming auditory targets (e.g., tomorrow with either a congruent (i.e., pointing forwards or incongruent (i.e., pointing backwards gesture. Two groups of college-age young adult participants (English and Chinese speakers made temporal classifications of words after watching a gestural prime. If speakers represent time along the sagittal axis, they should respond faster if the auditory target is preceded with a gesture indicating a congruent vs. incongruent spatial location. Results showed that English speakers responded faster to congruent gesture-word pairs than to incongruent pairs, mirroring spatio-temporal metaphors commonly recruited to talk about time in their native language. However, such an effect of congruency was not found for Chinese speakers. These findings suggest that while the spatio-temporal metaphors commonly recruited to talk about time help to structure the mental timelines of English speakers, the varying instances in how time is represented along the sagittal axis in Chinese may lead to a more variable mental timeline as well. In addition, our findings demonstrate that gestures may not only be a means of accessing concrete concepts in the mind, as shown in previous studies, but may be used to access abstract ones as well.

  1. 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

  2. The expression of c-Met pathway components in unclassified pleomorphic sarcoma/malignant fibrous histiocytoma (UPS/MFH): a tissue microarray study.

    Science.gov (United States)

    Lahat, Guy; Zhang, Pingyu; Zhu, Quan-Sheng; Torres, Keila; Ghadimi, Markus; Smith, Kerrington D; Wang, Wei-Lien; Lazar, Alexander J; Lev, Dina

    2011-09-01

    Subclassification of undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma (UPS/MFH) into distinct biological cohorts based on the expression patterns of molecular markers can identify patient subsets with especially unfavourable clinical outcomes. Identification of molecular prognosticators amenable for drug targeting can facilitate rational development of UPS/MFH tailored therapies. The aim was to evaluate expression of c-Met pathway components in a large cohort of UPS/MFH samples. An immunohistochemical analysis for hepatocyte growth factor (HGF), c-Met, phospho-c-Met (pc-Met), phospho-mitogen-activated protein kinase kinase (MAPKK) also known as mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) kinase (p-MEK) and phospho-protein kinase B (p-AKT) was performed on a clinically annotated tissue microarray of 158 UPS/MFH samples. Univariable and multivariable analyses were conducted to evaluate the correlation of molecular variables with UPS/MFH disease specific survival. All evaluated markers were expressed in UPS/MFH to varying levels. Most importantly, strong HGF, pc-Met, p-MEK and p-AKT expression correlated significantly with dismal patient outcome on univariable statistical analysis. Expression of p-MEK and p-AKT remained statistically significant independent prognosticators on multivariable analysis. c-Met pathway components and especially p-MEK and p-AKT are potential prognostic biomarkers for UPS/MFH; their inclusion in future molecular-based staging systems should be evaluated. Furthermore, novel approaches targeting HGF, c-Met, MEK/extracellular-regulated kinase (ERK) and/or AKT should be considered for a subset of UPS/MFH patients. © 2011 Blackwell Publishing Limited.

  3. 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.

  4. 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.

  5. A Versatile Microarray Immobilization Strategy Based on a Biorthogonal Reaction Between Tetrazine and Trans-Cyclooctene.

    Science.gov (United States)

    Wang, Ping; Gao, Liqian; Lei, Haipeng; Lee, Su Seong; Yao, Shao Q; Sun, Hongyan

    2017-01-01

    Given its increasing importance in transforming biomedical research in recent years, microarray technology has become highly popular as a powerful screening platform in detecting biomolecule interactions, discovering new inhibitors, and identifying biomarkers as well as diagnosing disease. The success of microarray technology in various biological applications is highly dependent on the accessibility, the functionality, and the density of the surface bound biomolecules. Therefore, compound immobilization represents a critical step for the successful implementation of microarray screening. Herein we describe a fast and site-specific microarray immobilization approach by using trans-cyclooctene-tetrazine ligation. This approach not only ensures fast immobilization and uniform display of biomolecules, but also allows the optimum orientation of biomolecules after immobilization. All these excellent properties facilitate subsequent interactions of the biomolecules and their interacting partners during the screening process. We envision that the immobilization strategy described here can find useful applications in many other microarray related studies.

  6. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    York, Emma L. [Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Environmental Sciences and Engineering

    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 "slow-flow" 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.

  8. Surface Subsidence Analysis by Multi-Temporal InSAR and GRACE: A Case Study in Beijing

    OpenAIRE

    Guo, Jiming; Zhou, Lv; Yao, Chaolong; Hu, Jiyuan

    2016-01-01

    The aim of this study was to investigate the relationship between surface subsidence and groundwater changes. To investigate this relationship, we first analyzed surface subsidence. This paper presents the results of a case study of surface subsidence in Beijing from 1 August 2007 to 29 September 2010. The Multi-temporal Interferometric Synthetic Aperture Radar (multi-temporal InSAR) technique, which can simultaneously detect point-like stable reflectors (PSs) and distributed scatterers (DSs)...

  9. 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

  10. Microarray-integrated optoelectrofluidic immunoassay system.

    Science.gov (United States)

    Han, Dongsik; Park, Je-Kyun

    2016-05-01

    A microarray-based analytical platform has been utilized as a powerful tool in biological assay fields. However, an analyte depletion problem due to the slow mass transport based on molecular diffusion causes low reaction efficiency, resulting in a limitation for practical applications. This paper presents a novel method to improve the efficiency of microarray-based immunoassay via an optically induced electrokinetic phenomenon by integrating an optoelectrofluidic device with a conventional glass slide-based microarray format. A sample droplet was loaded between the microarray slide and the optoelectrofluidic device on which a photoconductive layer was deposited. Under the application of an AC voltage, optically induced AC electroosmotic flows caused by a microarray-patterned light actively enhanced the mass transport of target molecules at the multiple assay spots of the microarray simultaneously, which reduced tedious reaction time from more than 30 min to 10 min. Based on this enhancing effect, a heterogeneous immunoassay with a tiny volume of sample (5 μl) was successfully performed in the microarray-integrated optoelectrofluidic system using immunoglobulin G (IgG) and anti-IgG, resulting in improved efficiency compared to the static environment. Furthermore, the application of multiplex assays was also demonstrated by multiple protein detection.

  11. 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

  12. Study of spectro-temporal variation in paleo-climatic marine proxy records using wavelet transformations

    Science.gov (United States)

    Pandey, Chhavi P.

    2017-10-01

    Wavelet analysis is a powerful mathematical and computational tool to study periodic phenomena in time series particu-larly in the presence of potential frequency changes in time. Continuous wavelet transformation (CWT) provides localised spectral information of the analysed dataset and in particular useful to study multiscale, nonstationary processes occurring over finite spatial and temporal domains. In the present work, oxygen-isotope ratio from the plantonic foraminifera species (viz. Globigerina bul-loides and Globigerinoides ruber) acquired from the broad central plateau of the Maldives ridge situated in south-eastern Arabian sea have been used as climate proxy. CWT of the time series generated using both the biofacies indicate spectro-temporal varia-tion of the natural climatic cycles. The dominant period resembles to the period of Milankovitch glacial-interglacial cycle. Apart from that, various other cycles are present in the time series. The results are in good agreement with the astronomical theory of paleoclimates and can provide better visualisation of Indian summer monsoon in the context of climate change.

  13. 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)

  14. 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.)

  15. 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.

  16. Spotted cotton oligonucleotide microarrays for gene expression analysis

    Directory of Open Access Journals (Sweden)

    Nettleton Dan

    2007-03-01

    Full Text Available Abstract Background Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Results Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome and previously studied cotton genes, transcription factors, and genes with homology to Arabidopsis. A small portion of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from fiber-specific cDNA libraries, the microarray has direct application for analysis of the fiber transcriptome. To illustrate the utility of the microarray, we hybridized labeled bud and leaf cDNAs from G. hirsutum and demonstrate technical consistency of results. Conclusion The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info.

  17. 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.

  18. 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.

  19. 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.

  20. Applications of heparin and heparan sulfate microarrays.

    Science.gov (United States)

    Yin, Jian; Seeberger, Peter H

    2010-01-01

    Carbohydrate microarrays have become crucial tools for revealing the biological interactions and functions of glycans, primarily because the microarray format enables the investigation of large numbers of carbohydrates at a time. Heparan sulfate (HS) and heparin are the most structurally complex glycosaminoglycans (GAGs). In this chapter, we describe the preparation of a small library of HS/heparin oligosaccharides, and the fabrication of HS/heparin microarrays that have been used to establish HS/heparin-binding profiles. Fibroblast growth factors (FGFs), natural cytotoxicity receptors (NCRs), and chemokines were screened to illuminate the very important biological functions of these glycans. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  1. Fuzzy clustering analysis of microarray data.

    Science.gov (United States)

    Han, Lixin; Zeng, Xiaoqin; Yan, Hong

    2008-10-01

    Fuzzy clustering is a useful tool for identifying relevant subsets of microarray data. This paper proposes a fuzzy clustering method for microarray data analysis. An advantage of the method is that it used a combination of the fuzzy c-means and the principal component analysis to identify the groups of genes that show similar expression patterns. It allows a gene to belong to more than a gene expression pattern with different membership grades. The method is suitable for the analysis of large amounts of noisy microarray data.

  2. Pineal function: impact of microarray analysis

    DEFF Research Database (Denmark)

    Klein, David C; Bailey, Michael J; Carter, David A

    2009-01-01

    Microarray analysis has provided a new understanding of pineal function by identifying genes that are highly expressed in this tissue relative to other tissues and also by identifying over 600 genes that are expressed on a 24-h schedule. This effort has highlighted surprising similarity to the re......Microarray analysis has provided a new understanding of pineal function by identifying genes that are highly expressed in this tissue relative to other tissues and also by identifying over 600 genes that are expressed on a 24-h schedule. This effort has highlighted surprising similarity...... foundation that microarray analysis has provided will broadly support future research on pineal function....

  3. A genome-wide 20 K citrus microarray for gene expression analysis

    Directory of Open Access Journals (Sweden)

    Gadea Jose

    2008-07-01

    Full Text Available Abstract Background Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genome-wide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant. Results We have designed and constructed a publicly available genome-wide cDNA microarray that include 21,081 putative unigenes of citrus. As a functional companion to the microarray, a web-browsable database 1 was created and populated with information about the unigenes represented in the microarray, including cDNA libraries, isolated clones, raw and processed nucleotide and protein sequences, and results of all the structural and functional annotation of the unigenes, like general description, BLAST hits, putative Arabidopsis orthologs, microsatellites, putative SNPs, GO classification and PFAM domains. We have performed a Gene Ontology comparison with the full set of Arabidopsis proteins to estimate the genome coverage of the microarray. We have also performed microarray hybridizations to check its usability. Conclusion This new cDNA microarray replaces the first 7K microarray generated two years ago and allows gene expression analysis at a more global scale. We have followed a rational design to minimize cross-hybridization while maintaining its utility for different citrus species. Furthermore, we also provide access to a website with full structural and functional annotation of the unigenes represented in the microarray, along with the ability to use this site to directly perform gene expression analysis using standard tools at different publicly available servers. Furthermore, we show how this microarray offers a good representation of the citrus genome and present the usefulness of this genomic tool for global

  4. Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data

    Directory of Open Access Journals (Sweden)

    Martinez M Juanita

    2005-05-01

    Full Text Available Abstract Background Commercial microarray scanners and software cannot distinguish between spectrally overlapping emission sources, and hence cannot accurately identify or correct for emissions not originating from the labeled cDNA. We employed our hyperspectral microarray scanner coupled with multivariate data analysis algorithms that independently identify and quantitate emissions from all sources to investigate three artifacts that reduce the accuracy and reliability of microarray data: skew toward the green channel, dye separation, and variable background emissions. Results Here we demonstrate that several common microarray artifacts resulted from the presence of emission sources other than the labeled cDNA that can dramatically alter the accuracy and reliability of the array data. The microarrays utilized in this study were representative of a wide cross-section of the microarrays currently employed in genomic research. These findings reinforce the need for careful attention to detail to recognize and subsequently eliminate or quantify the presence of extraneous emissions in microarray images. Conclusion Hyperspectral scanning together with multivariate analysis offers a unique and detailed understanding of the sources of microarray emissions after hybridization. This opportunity to simultaneously identify and quantitate contaminant and background emissions in microarrays markedly improves the reliability and accuracy of the data and permits a level of quality control of microarray emissions previously unachievable. Using these tools, we can not only quantify the extent and contribution of extraneous emission sources to the signal, but also determine the consequences of failing to account for them and gain the insight necessary to adjust preparation protocols to prevent such problems from occurring.

  5. 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.

  6. Independent component analysis of Alzheimer's DNA microarray gene expression data

    Directory of Open Access Journals (Sweden)

    Vanderburg Charles R

    2009-01-01

    Full Text Available Abstract Background Gene microarray technology is an effective tool to investigate the simultaneous activity of multiple cellular pathways from hundreds to thousands of genes. However, because data in the colossal amounts generated by DNA microarray technology are usually complex, noisy, high-dimensional, and often hindered by low statistical power, their exploitation is difficult. To overcome these problems, two kinds of unsupervised analysis methods for microarray data: principal component analysis (PCA and independent component analysis (ICA have been developed to accomplish the task. PCA projects the data into a new space spanned by the principal components that are mutually orthonormal to each other. The constraint of mutual orthogonality and second-order statistics technique within PCA algorithms, however, may not be applied to the biological systems studied. Extracting and characterizing the most informative features of the biological signals, however, require higher-order statistics. Results ICA is one of the unsupervised algorithms that can extract higher-order statistical structures from data and has been applied to DNA microarray gene expression data analysis. We performed FastICA method on DNA microarray gene expression data from Alzheimer's disease (AD hippocampal tissue samples and consequential gene clustering. Experimental results showed that the ICA method can improve the clustering results of AD samples and identify significant genes. More than 50 significant genes with high expression levels in severe AD were extracted, representing immunity-related protein, metal-related protein, membrane protein, lipoprotein, neuropeptide, cytoskeleton protein, cellular binding protein, and ribosomal protein. Within the aforementioned categories, our method also found 37 significant genes with low expression levels. Moreover, it is worth noting that some oncogenes and phosphorylation-related proteins are expressed in low levels. In

  7. 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

  8. 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.

  9. 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.

  10. 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...

  11. Suture restriction of the temporal bone as a risk factor for acute otitis media in children: cohort study

    Directory of Open Access Journals (Sweden)

    Morin Chantal

    2012-11-01

    Full Text Available Abstract Background Eustachian tube (ET dysfunction plays an important role in the pathogenesis of acute otitis media (AOM. Unfortunately, there is a lack of knowledge about the exact role of the ET’s bony support, the temporal bone, on occurrence of AOM. This study investigates whether severe suture restriction of the temporal bone is a risk factor for development of AOM in young children. Methods Using a prospective cohort design, 64 children aged 6 to 18 months without prior history of AOM were followed during the cold season (September 2009 to April 2010. Temporal bone status (categorized as with or without severe suture restriction was evaluated using palpation and a cranial bone mobility test. Information about potential baseline confounders and risk factors for AOM (gender, age, birth weight, gestational age, use of pacifier, daycare attendance, presence of siblings, low socioeconomic status, breastfeeding ≥ 6 months, parental smoking and history of upper respiratory tract infection were also collected. Occurrence of AOM diagnosed by physicians blinded to temporal bone status was the main outcome. Data were analyzed using hierarchical linear and nonlinear (multilevel models. Results Severe suture restriction of the temporal bone was identified in 23 children (35.9%. At least one AOM episode was diagnosed in 14 (48.3% of the ears associated with temporal bones previously identified as having severe suture restriction and in 28 (28.3% of those without severe suture restriction. Higher risk for AOM was explained by severe suture restriction of the temporal bone (adjusted relative risk (RR, 2.26, 95% CI 1.43 to 2.91, p Conclusions The study results indicate that severe suture restriction of the temporal bone is a risk factor for AOM in young children. Subsequent intervention studies are needed to determine if this mechanical risk factor can be modified in young children.

  12. Estimating Pollutant Concentration Maps at Multiple Spatial and Temporal Scales for Exposure Studies

    Science.gov (United States)

    Tan, Si

    Chronic exposure to high concentrations of pollutants such as NO2 and ultrafine particles is associated with negative health effects. Studies of exposure to these pollutants require estimates of concentrations at temporal and spatial scales relevant to exposure calculations. We have developed and applied methods to construct these concentration "maps" by using a combination of measurements and modeled results. To estimate concentration patterns at the urban scale of tens of kilometers we have formulated a Lagrangian model to estimate concentrations of NOx, NO2, and O3 over a domain extending over hundreds of kilometers. The model is evaluated with data collected at 21 regional monitoring stations in the San Joaquin Valley Air Basin during 2005. The model provides adequate descriptions of the spatial and temporal variation of concentrations of NO2, and NOx. We then use "residual" Kriging to combine the results from the dispersion model with observed concentrations to produce realistic concentration maps. To estimate concentration patterns at scales of tens of meters in urban areas we developed a dispersion model that accounts for the effects of local building morphology on dispersion. The data used to evaluate the model was collected in field studies conducted in Los Angeles, California. The studies measured ultrafine particle concentrations and associated micrometeorology at several locations with different building morphologies. Surface concentrations in urban areas are primarily controlled by vertical dispersion, which depends on the street aspect ratio, defined as the ratio of the equivalent building height to the street width, and the vertical turbulent velocity sigma w. The presence of buildings increases the concentrations due to local traffic emissions relative to open areas. Since routine measurements of micrometeorological variables are usually not available in urban areas, we have developed models that allow us to estimate urban surface variables using

  13. Diagnostic and analytical applications of protein microarrays.

    Science.gov (United States)

    Dufva, Martin; Christensen, Claus 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 past 5 years. A genome-scale protein microarray has been demonstrated for identifying protein-protein interactions as well as for rapid identification of protein binding to a particular drug. Furthermore, protein microarrays have been shown as an efficient tool in cancer profiling, detection of bacteria and toxins, identification of allergen reactivity and autoantibodies. They have also demonstrated the ability to measure the absolute concentration of small molecules. Besides their capacity for parallel diagnostics, microarrays can be more sensitive than traditional methods such as enzyme-linked immunosorbent assay, mass spectrometry or high-performance liquid chromatography-based assays. However, for protein and antibody arrays to be successfully introduced into diagnostics, the biochemistry of immunomicroarrays must be better characterized and simplified, they must be validated in a clinical setting and be amenable to automation or integrated into easy-to-use systems, such as micrototal analysis systems or point-of-care devices.

  14. Use of cranial surface anatomic fiducials for interactive image-guided navigation in the temporal bone: a cadaveric study.

    Science.gov (United States)

    Vrionis, F D; Foley, K T; Robertson, J H; Shea, J J

    1997-04-01

    Because of the intricate anatomy of the temporal bone, we examined the feasibility and reliability of cranial surface anatomic fiducials to register computed tomographic images of the temporal bone by using a frameless image-guided system. One-millimeter thick computed tomographic slices and the smallest possible field of view were used to register 10 dry and 10 fresh temporal bones from cadavers. The fiducials used for registration included the umbo of the tympanic membrane, emissary foramina, the asterion, various sutures, the tip of the mastoid process, and Henle's spine. Mean initial fiducial registration error ranged from 0.6 to 0.7 mm, and was reduced to 0.5 and 0.4 mm for the dry cranial and cadaveric studies, respectively, by eliminating or reregistering inexact fiducials. Mean target localization error ranged from 0.91 to 2.44 mm for superficial structures of the temporal bone in the dry cranial specimens and from 0.71 to 1.52 mm for deep structures such as the facial nerve, semicircular canals and ossicles in the cadaveric study. Interactive image-guided navigation in the temporal bone is possible with registration of cranial surface anatomic fiducials. It may be useful to the neurosurgeon and otologist in identifying critical anatomic structures of the temporal bone encountered during the translabyrinthine, retrolabyrinthine presigmoid, and suboccipital approaches.

  15. Spatial and temporal assessment of orofacial somatosensory sensitivity: a methodological study

    DEFF Research Database (Denmark)

    Thygesen, Torben; Nørholt, Sven Erik; Jensen, John

    2007-01-01

    AIMS: To evaluate the sensitivity and reproducibility of a multimodal psychophysical technique for the assessment of both spatial and temporal changes in somatosensory function after an infraorbital nerve block. METHODS: Sixteen healthy volunteers with a mean (+/- SD) age of 22.5 +/- 3.4 years...... of somatosensory function was carried out before the injection (baseline) and after 30 and 60 minutes on both the anesthetized and contralateral (control) side. In addition, the applicability of the psychophysical techniques was tested in pilot experiments in 2 patients before maxillary osteotomy and 3 months...... matrices allowed a spatial description of somatosensory sensitivity. This method may be valuable for studies on changes in somatosensory sensitivity following trauma or orthognathic surgery on the maxilla....

  16. 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.

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  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. Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies.

    Science.gov (United States)

    Domanova, Westa; Krycer, James; Chaudhuri, Rima; Yang, Pengyi; Vafaee, Fatemeh; Fazakerley, Daniel; Humphrey, Sean; James, David; Kuncic, Zdenka

    2016-01-01

    , and provide evidence suggesting IRS-1 S265 as a novel Akt site. KSR-LIVE is an open-access algorithm that allows users to dissect phosphorylation signaling within a specific biological context, with the potential to be included in the standard analysis workflow for studying temporal high-throughput signal transduction data.

  1. Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies.

    Directory of Open Access Journals (Sweden)

    Westa Domanova

    linear consensus motif, and provide evidence suggesting IRS-1 S265 as a novel Akt site. KSR-LIVE is an open-access algorithm that allows users to dissect phosphorylation signaling within a specific biological context, with the potential to be included in the standard analysis workflow for studying temporal high-throughput signal transduction data.

  2. Temporal abstraction for feature extraction: a comparative case study in prediction from intensive care monitoring data

    NARCIS (Netherlands)

    Verduijn, Marion; Sacchi, Lucia; Peek, Niels; Bellazzi, Riccardo; de Jonge, Evert; de Mol, Bas A. J. M.

    2007-01-01

    OBJECTIVES: To compare two temporal abstraction procedures for the extraction of meta features from monitoring data. Feature extraction prior to predictive modeling is a common strategy in prediction from temporal data. A fundamental dilemma in this strategy, however, is the extent to which the

  3. An FMRI study of the neural systems involved in visually cued auditory top-down spatial and temporal attention.

    Directory of Open Access Journals (Sweden)

    Chunlin Li

    Full Text Available Top-down attention to spatial and temporal cues has been thoroughly studied in the visual domain. However, because the neural systems that are important for auditory top-down temporal attention (i.e., attention based on time interval cues remain undefined, the differences in brain activity between directed attention to auditory spatial location (compared with time intervals are unclear. Using fMRI (magnetic resonance imaging, we measured the activations caused by cue-target paradigms by inducing the visual cueing of attention to an auditory target within a spatial or temporal domain. Imaging results showed that the dorsal frontoparietal network (dFPN, which consists of the bilateral intraparietal sulcus and the frontal eye field, responded to spatial orienting of attention, but activity was absent in the bilateral frontal eye field (FEF during temporal orienting of attention. Furthermore, the fMRI results indicated that activity in the right ventrolateral prefrontal cortex (VLPFC was significantly stronger during spatial orienting of attention than during temporal orienting of attention, while the DLPFC showed no significant differences between the two processes. We conclude that the bilateral dFPN and the right VLPFC contribute to auditory spatial orienting of attention. Furthermore, specific activations related to temporal cognition were confirmed within the superior occipital gyrus, tegmentum, motor area, thalamus and putamen.

  4. 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.)

  5. 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.

  6. Representation of spatial and temporal variability in large-domain hydrological models: case study for a mesoscale pre-Alpine basin

    NARCIS (Netherlands)

    Melsen, Lieke; Teuling, Adriaan; Torfs, Paul; Zappa, Massimiliano; Mizukami, Naoki; Clark, Martyn; Uijlenhoet, Remko

    2016-01-01

    The transfer of parameter sets over different temporal and spatial resolutions is common practice in many large-domain hydrological modelling studies. The degree to which parameters are transferable across temporal and spatial resolutions is an indicator of how well spatial and temporal variability

  7. 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

  8. Study of temporal evolution of emission spectrum in a steeply rising submillimeter burst

    International Nuclear Information System (INIS)

    Li, Jian-Ping; Zhou, Ai-Hua; Wang, Xin-Dong

    2016-01-01

    The temporal evolution of a spectrum during a steeply rising submillimeter (THz) burst that occurred on 2003 November 2 was investigated in detail for the first time. Observations show that the flux density of the THz spectrum increased steeply with frequency above 200 GHz. Their average rising rates reached a value of 235 sfu GHz −1 (corresponding to spectral index α of 4.8) during the burst. The flux densities reached about 4 000 and 70 000 sfu at 212 and 405 GHz at the maximum phase, respectively. The emissions at 405 GHz maintained such a continuous high level that they largely exceeded the peak values of the microwave (MW) spectra during the main phase. Our studies suggest that only energetic electrons with a low-energy cutoff of ∼1 MeV and number density of ∼10 6 –10 8 cm −3 can produce such a strong and steeply rising THz component via gyrosynchrotron radiation based on numerical simulations of burst spectra in the case of a nonuniform magnetic field. The electron number density N, derived from our numerical fits to the THz temporal evolution spectra, increased substantially from 8 × 10 6 to 4 × 10 8 cm −3 , i.e., the N value increased 50 times during the rise phase. During the decay phase it decreased to 7 × 10 7 cm −3 , i.e., it decreased by about five times from the maximum phase. The total electron number decreased an order of magnitude from the maximum phase to the decay phase. Nevertheless, the variation in amplitude of N is only about one time in the MW emission source during this burst, and the total electron number did not decrease but increased by about 20% during the decay phase. Interestingly, we find that the THz source radius decreased by about 24% while the MW source radius, on the contrary, increased by 28% during the decay phase. (paper)

  9. Spatio-temporal precipitation error propagation in runoff modelling: a case study in central Sweden

    Directory of Open Access Journals (Sweden)

    J. Olsson

    2006-01-01

    Full Text Available The propagation of spatio-temporal errors in precipitation estimates to runoff errors in the output from the conceptual hydrological HBV model was investigated. The study region was the Gimån catchment in central Sweden, and the period year 2002. Five precipitation sources were considered: NWP model (H22, weather radar (RAD, precipitation gauges (PTH, and two versions of a mesoscale analysis system (M11, M22. To define the baseline estimates of precipitation and runoff, used to define seasonal precipitation and runoff biases, the mesoscale climate analysis M11 was used. The main precipitation biases were a systematic overestimation of precipitation by H22, in particular during winter and early spring, and a pronounced local overestimation by RAD during autumn, in the western part of the catchment. These overestimations in some cases exceeded 50% in terms of seasonal subcatchment relative accumulated volume bias, but generally the bias was within ±20%. The precipitation data from the different sources were used to drive the HBV model, set up and calibrated for two stations in Gimån, both for continuous simulation during 2002 and for forecasting of the spring flood peak. In summer, autumn and winter all sources agreed well. In spring H22 overestimated the accumulated runoff volume by ~50% and peak discharge by almost 100%, owing to both overestimated snow depth and precipitation during the spring flood. PTH overestimated spring runoff volumes by ~15% owing to overestimated winter precipitation. The results demonstrate how biases in precipitation estimates may exhibit a substantial space-time variability, and may further become either magnified or reduced when applied for hydrological purposes, depending on both temporal and spatial variations in the catchment. Thus, the uncertainty in precipitation estimates should preferably be specified as a function of both time and space.

  10. 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

  11. Flow-pattern Guided Fabrication of High-density Barcode Antibody Microarray.

    Science.gov (United States)

    Ramirez, Lisa S; Wang, Jun

    2016-01-06

    Antibody microarray as a well-developed technology is currently challenged by a few other established or emerging high-throughput technologies. In this report, we renovate the antibody microarray technology by using a novel approach for manufacturing and by introducing new features. The fabrication of our high-density antibody microarray is accomplished through perpendicularly oriented flow-patterning of single stranded DNAs and subsequent conversion mediated by DNA-antibody conjugates. This protocol outlines the critical steps in flow-patterning DNA, producing and purifying DNA-antibody conjugates, and assessing the quality of the fabricated microarray. The uniformity and sensitivity are comparable with conventional microarrays, while our microarray fabrication does not require the assistance of an array printer and can be performed in most research laboratories. The other major advantage is that the size of our microarray units is 10 times smaller than that of printed arrays, offering the unique capability of analyzing functional proteins from single cells when interfacing with generic microchip designs. This barcode technology can be widely employed in biomarker detection, cell signaling studies, tissue engineering, and a variety of clinical applications.

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

    Science.gov (United States)

    Kegel, Jessica U; Del Amo, Yolanda; Costes, Laurence; Medlin, Linda K

    2013-03-05

    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.

  13. 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.

  14. 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...

  15. Design of custom oligonucleotide microarrays for single species or interspecies hybrids using Array Oligo Selector.

    Science.gov (United States)

    Caudy, Amy A

    2011-01-01

    New technologies for DNA sequencing have made it feasible to determine the genome sequence of any organism of interest. This sequence is the resource required to create tools for downstream studies, including DNA microarrays. A number of vendors can produce DNA microarrays containing customer-specified sequences, allowing investigators to design and order arrays customized for any species of interest. Freely available, user-friendly computer programs are available for designing microarray probes. These design programs can be used to create probes that distinguish between two related genomes, allowing investigation of gene expression or gene representation in intra- or interspecies hybrids or in samples containing DNA from multiple species.

  16. 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

  17. 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.

  18. 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.

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

    Science.gov (United States)

    Alemu, Sisay Mulugeta

    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 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 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. PMID:28752093

  20. 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.

  1. Microarray is an efficient tool for circRNA profiling.

    Science.gov (United States)

    Li, Shasha; Teng, Shuaishuai; Xu, Junquan; Su, Guannan; Zhang, Yu; Zhao, Jianqing; Zhang, Suwei; Wang, Haiyan; Qin, Wenyan; Lu, Zhi John; Guo, Yong; Zhu, Qianyong; Wang, Dong

    2018-02-03

    Circular RNAs (circRNAs) are emerging as a new class of endogenous and regulatory noncoding RNAs in latest years. With the widespread application of RNA sequencing (RNA-seq) technology and bioinformatics prediction, large numbers of circRNAs have been identified. However, at present, we lack a comprehensive characterization of all these circRNAs in interested samples. In this study, we integrated 87 935 circRNAs sequences that cover most of circRNAs identified till now represented in circBase to design microarray probes targeting back-splice site of each circRNA to profile expression of those circRNAs. By comparing the circRNA detection efficiency of RNA-seq with this circRNA microarray, we revealed that microarray is more efficient than RNA-seq for circRNA profiling. Then, we found ∼80 000 circRNAs were expressed in cervical tumors and matched normal tissues, and ∼25 000 of them were differently expressed. Notably, many of these circRNAs detected by this microarray can be validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR) or RNA-seq. Strikingly, as many as ∼18 000 circRNAs could be robustly detected in cell-free plasma samples, and the expression of ∼2700 of them differed after surgery for tumor removal. Our findings provided a comprehensive and genome-wide characterization of circRNAs in paired normal tissues and tumors and plasma samples from multiple individuals. In addition, we also provide a rich resource with 41 microarray data sets and 10 RNA-seq data sets and strong evidences for circRNA expression in cervical cancer. In conclusion, circRNAs could be efficiently profiled by circRNA microarray to target their reported back-splice sites in interested samples. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  2. 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.

  3. 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.

  4. 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)

  5. Advancing microarray assembly with acoustic dispensing technology.

    Science.gov (United States)

    Wong, E Y; Diamond, S L

    2009-01-01

    In the assembly of microarrays and microarray-based chemical assays and enzymatic bioassays, most approaches use pins for contact spotting. Acoustic dispensing is a technology capable of nanoliter transfers by using acoustic energy to eject liquid sample from an open source well. Although typically used for well plate transfers, when applied to microarraying, it avoids the drawbacks of undesired physical contact with the sample; difficulty in assembling multicomponent reactions on a chip by readdressing, a rigid mode of printing that lacks patterning capabilities; and time-consuming wash steps. We demonstrated the utility of acoustic dispensing by delivering human cathepsin L in a drop-on-drop fashion into individual 50-nanoliter, prespotted reaction volumes to activate enzyme reactions at targeted positions on a microarray. We generated variable-sized spots ranging from 200 to 750 microm (and higher) and handled the transfer of fluorescent bead suspensions with increasing source well concentrations of 0.1 to 10 x 10(8) beads/mL in a linear fashion. There are no tips that can clog, and liquid dispensing CVs are generally below 5%. This platform expands the toolbox for generating analytical arrays and meets needs associated with spatially addressed assembly of multicomponent microarrays on the nanoliter scale.

  6. Tissue microarray profiling in human heart failure.

    Science.gov (United States)

    Lal, Sean; Nguyen, Lisa; Tezone, Rhenan; Ponten, Fredrik; Odeberg, Jacob; Li, Amy; Dos Remedios, Cristobal

    2016-09-01

    Tissue MicroArrays (TMAs) are a versatile tool for high-throughput protein screening, allowing qualitative analysis of a large number of samples on a single slide. We have developed a customizable TMA system that uniquely utilizes cryopreserved human cardiac samples from both heart failure and donor patients to produce formalin-fixed paraffin-embedded sections. Confirmatory upstream or downstream molecular studies can then be performed on the same (biobanked) cryopreserved tissue. In a pilot study, we applied our TMAs to screen for the expression of four-and-a-half LIM-domain 2 (FHL2), a member of the four-and-a-half LIM family. This protein has been implicated in the pathogenesis of heart failure in a variety of animal models. While FHL2 is abundant in the heart, not much is known about its expression in human heart failure. For this purpose, we generated an affinity-purified rabbit polyclonal anti-human FHL2 antibody. Our TMAs allowed high-throughput profiling of FHL2 protein using qualitative and semiquantitative immunohistochemistry that proved complementary to Western blot analysis. We demonstrated a significant relative reduction in FHL2 protein expression across different forms of human heart failure. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Study Addiction: A Cross-Cultural Longitudinal Study Examining Temporal Stability and Predictors of Its Changes

    OpenAIRE

    Atroszko, Pawe? Andrzej; Andreassen, Cecilie Schou; Griffiths, Mark D.; Pallesen, St?le

    2016-01-01

    Background and aims: "Study addiction" has recently been conceptualized as a behavioral addiction and defined within the framework of work addiction. Using a newly developed measure to assess this construct, the Bergen Study Addiction Scale (BStAS), the present study examined the 1-year stability of study addiction and factors related to changes in this construct over time, and is the first longitudinal investigation of study addiction thus far. \\ud Methods: The BStAS and the Ten Item Persona...

  8. 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.

  9. 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

  10. Predictability of Persistent Frequent Attendance in Primary Care: A Temporal and Geographical Validation Study

    Science.gov (United States)

    Smits, Frans T.; Brouwer, Henk J.; Zwinderman, Aeilko H.; van den Akker, Marjan; van Steenkiste, Ben; Mohrs, Jacob; Schene, Aart H.; van Weert, Henk C.; ter Riet, Gerben

    2013-01-01

    Background Frequent attenders are patients who visit their general practitioner exceptionally frequently. Frequent attendance is usually transitory, but some frequent attenders become persistent. Clinically, prediction of persistent frequent attendance is useful to target treatment at underlying diseases or problems. Scientifically it is useful for the selection of high-risk populations for trials. We previously developed a model to predict which frequent attenders become persistent. Aim To validate an existing prediction model for persistent frequent attendance that uses information solely from General Practitioners’ electronic medical records. Methods We applied the existing model (N = 3,045, 2003–2005) to a later time frame (2009–2011) in the original derivation network (N = 4,032, temporal validation) and to patients of another network (SMILE; 2007–2009, N = 5,462, temporal and geographical validation). Model improvement was studied by adding three new predictors (presence of medically unexplained problems, prescriptions of psychoactive drugs and antibiotics). Finally, we derived a model on the three data sets combined (N = 12,539). We expressed discrimination using histograms of the predicted values and the concordance-statistic (c-statistic) and calibration using the calibration slope (1 = ideal) and Hosmer-Lemeshow tests. Results The existing model (c-statistic 0.67) discriminated moderately with predicted values between 7.5 and 50 percent and c-statistics of 0.62 and 0.63, for validation in the original network and SMILE network, respectively. Calibration (0.99 originally) was better in SMILE than in the original network (slopes 0.84 and 0.65, respectively). Adding information on the three new predictors did not importantly improve the model (c-statistics 0.64 and 0.63, respectively). Performance of the model based on the combined data was similar (c-statistic 0.65). Conclusion This external validation study showed that

  11. Predictability of persistent frequent attendance in primary care: a temporal and geographical validation study.

    Directory of Open Access Journals (Sweden)

    Frans T Smits

    Full Text Available BACKGROUND: Frequent attenders are patients who visit their general practitioner exceptionally frequently. Frequent attendance is usually transitory, but some frequent attenders become persistent. Clinically, prediction of persistent frequent attendance is useful to target treatment at underlying diseases or problems. Scientifically it is useful for the selection of high-risk populations for trials. We previously developed a model to predict which frequent attenders become persistent. AIM: To validate an existing prediction model for persistent frequent attendance that uses information solely from General Practitioners' electronic medical records. METHODS: We applied the existing model (N = 3,045, 2003-2005 to a later time frame (2009-2011 in the original derivation network (N = 4,032, temporal validation and to patients of another network (SMILE; 2007-2009, N = 5,462, temporal and geographical validation. Model improvement was studied by adding three new predictors (presence of medically unexplained problems, prescriptions of psychoactive drugs and antibiotics. Finally, we derived a model on the three data sets combined (N = 12,539. We expressed discrimination using histograms of the predicted values and the concordance-statistic (c-statistic and calibration using the calibration slope (1 = ideal and Hosmer-Lemeshow tests. RESULTS: The existing model (c-statistic 0.67 discriminated moderately with predicted values between 7.5 and 50 percent and c-statistics of 0.62 and 0.63, for validation in the original network and SMILE network, respectively. Calibration (0.99 originally was better in SMILE than in the original network (slopes 0.84 and 0.65, respectively. Adding information on the three new predictors did not importantly improve the model (c-statistics 0.64 and 0.63, respectively. Performance of the model based on the combined data was similar (c-statistic 0.65. CONCLUSION: This external validation study showed that

  12. Low-Cost Peptide Microarrays for Mapping Continuous Antibody Epitopes.

    Science.gov (United States)

    McBride, Ryan; Head, Steven R; Ordoukhanian, Phillip; Law, Mansun

    2016-01-01

    With the increasing need for understanding antibody specificity in antibody and vaccine research, pepscan assays provide a rapid method for mapping and profiling antibody responses to continuous epitopes. We have developed a relatively low-cost method to generate peptide microarray slides for studying antibody binding. Using a setup of an IntavisAG MultiPep RS peptide synthesizer, a Digilab MicroGrid II 600 microarray printer robot, and an InnoScan 1100 AL scanner, the method allows the interrogation of up to 1536 overlapping, alanine-scanning, and mutant peptides derived from the target antigens. Each peptide is tagged with a polyethylene glycol aminooxy terminus to improve peptide solubility, orientation, and conjugation efficiency to the slide surface.

  13. Impact of temporal variation on design and analysis of mouse knockout phenotyping studies.

    Directory of Open Access Journals (Sweden)

    Natasha A Karp

    Full Text Available A significant challenge facing high-throughput phenotyping of in-vivo knockout mice is ensuring phenotype calls are robust and reliable. Central to this problem is selecting an appropriate statistical analysis that models both the experimental design (the workflow and the way control mice are selected for comparison with knockout animals and the sources of variation. Recently we proposed a mixed model suitable for small batch-oriented studies, where controls are not phenotyped concurrently with mutants. Here we evaluate this method both for its sensitivity to detect phenotypic effects and to control false positives, across a range of workflows used at mouse phenotyping centers. We found the sensitivity and control of false positives depend on the workflow. We show that the phenotypes in control mice fluctuate unexpectedly between batches and this can cause the false positive rate of phenotype calls to be inflated when only a small number of batches are tested, when the effect of knockout becomes confounded with temporal fluctuations in control mice. This effect was observed in both behavioural and physiological assays. Based on this analysis, we recommend two approaches (workflow and accompanying control strategy and associated analyses, which would be robust, for use in high-throughput phenotyping pipelines. Our results show the importance in modelling all sources of variability in high-throughput phenotyping studies.

  14. Monitoring studies should consider temporal variability to reveal relations between cyanobacterial abundance and environmental variables

    Directory of Open Access Journals (Sweden)

    JULIANA WOJCIECHOWSKI

    2015-09-01

    Full Text Available One of the main goals of monitoring cyanobacteria blooms in aquatic environments is to reveal the relationship between cyanobacterial abundance and environmental variables. Studies typically correlate data that were simultaneously sampled. However, samplings occur sparsely over time and may not reveal the short-term responses of cyanobacterial abundance to environmental changes. In this study, we tested the hypothesis that stronger cyanobacteria x environment relationships in monitoring are found when the temporal variability of sampling points is incorporated in the statistical analyses. To this end, we investigated relationships between cyanobacteria and seven environmental variables that were sampled twice yearly for three years across 11 reservoirs, and data from an intensive monitoring in one of these reservoirs. Poor correlations were obtained when correlating data simultaneously sampled. In fact, the 'highly recurrent' role of phosphorus in cyanobacteria blooms is not properly observed in all sampling periods. On the other hand, the strongest correlation values for the total phosphorus x cyanobacteria relationship were observed when we used the variation of sampling points. We have also shown that environment variables better explain cyanobacteria when a time lag is considered. We conclude that, in cyanobacteria monitoring, the best approach to reveal determinants of cyanobacteria blooms is to consider environmental variability.

  15. 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)

  16. 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)

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.)

  2. 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.)

  3. Fish 'n' chips: the use of microarrays for aquatic toxicology.

    Science.gov (United States)

    Denslow, Nancy D; Garcia-Reyero, Natàlia; Barber, David S

    2007-03-01

    Gene expression analysis is changing the way that we look at toxicity, allowing toxicologists to perform parallel analyses of entire transcriptomes. While this technology is not as advanced in aquatic toxicology as it is for mammalian models, it has shown promise for determining modes of action, identifying biomarkers and developing "signatures" of chemicals that can be used for field and mixture studies. A major hurdle for the use of microarrays in aquatic toxicology is the lack of sequence information for non-model species. Custom arrays based on gene libraries enriched for genes that are expressed in response to specific contaminants have been used with excellent success for some non-model species, suggesting that this approach will work well for ecotoxicology and spurring on the sequencing of cDNA libraries for species of interest. New sequencing technology and development of repositories for gene expression data will accelerate the use of microarrays in aquatic toxicology. Notwithstanding the preliminary successes that have been achieved even with partial cDNA libraries printed on arrays, ecological samples present elevated challenges for this technology due to the high degree of variation of the samples. Furthermore, recent studies that show nonlinear toxic responses for ecological species underscore the necessity of establishing time and dose dependence of effects on gene expression and comparing these results with traditional markers of toxicity. To realize the full potential of microarrays, researchers must do the experiments required to bridge the gap between the 'omics' technologies and traditional toxicology to demonstrate that microarrays have predictive value in ecotoxicology.

  4. 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

  5. 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

  6. 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

  7. 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 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.

  8. 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.

  9. 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.

  10. A multicrystal diffraction data-collection approach for studying structural dynamics with millisecond temporal resolution

    Directory of Open Access Journals (Sweden)

    Robin Schubert

    2016-11-01

    Full Text Available Many biochemical processes take place on timescales ranging from femtoseconds to seconds. Accordingly, any time-resolved experiment must be matched to the speed of the structural changes of interest. Therefore, the timescale of interest defines the requirements of the X-ray source, instrumentation and data-collection strategy. In this study, a minimalistic approach for in situ crystallization is presented that requires only a few microlitres of sample solution containing a few hundred crystals. It is demonstrated that complete diffraction data sets, merged from multiple crystals, can be recorded within only a few minutes of beamtime and allow high-resolution structural information of high quality to be obtained with a temporal resolution of 40 ms. Global and site-specific radiation damage can be avoided by limiting the maximal dose per crystal to 400 kGy. Moreover, analysis of the data collected at higher doses allows the time-resolved observation of site-specific radiation damage. Therefore, our approach is well suited to observe structural changes and possibly enzymatic reactions in the low-millisecond regime.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

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

    Science.gov (United States)

    Tin Tin, Sandar; Woodward, Alistair; Robinson, Elizabeth; Ameratunga, Shanthi

    2012-03-08

    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. 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. 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 weather variables significantly influenced hourly and daily cycle volumes (p 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.

  16. Temporal Trends in Rainwater Tank Suicides in Rijeka, Croatia-A 30-year Study.

    Science.gov (United States)

    Ferenčić, Antun; Šoša, Ivan; Cuculic, Drazen; Stemberga, Valter; Byard, Roger W

    2017-11-06

    Although drowning in rainwater tanks is a generally rare phenomenon, this method for suicide has been observed in parts of Croatia. Review of autopsy records at the University of Rijeka, Croatia, was undertaken from 1987 to 2016 to examine this phenomenon. Of 469 drowning deaths, there were 35 suicides in rainwater tanks (7.5%). Overall drowning deaths showed no temporal trends. In contrast, suicidal drownings in rain water tanks showed a marked decline over the years, with 15 cases in 1987-1991, seven in 1992-1996, six in 1997-2001, six in 2002-2006, one in 2007-2011, and none in 2012-2016. Thus, suicidal drowning cases as a percentage of overall drownings dropped from 18% to zero (p<0.001). This study reports a very unusual method of suicide that may have occurred because of the ready availability of large water reservoirs in homes. The recent fall in numbers may relate to less reliance on domestic reservoirs of water. © 2017 American Academy of Forensic Sciences.

  17. Direct labeling of serum proteins by fluorescent dye for antibody microarray.

    Science.gov (United States)

    Klimushina, M V; Gumanova, N G; Metelskaya, V A

    2017-05-06

    Analysis of serum proteome by antibody microarray is used to identify novel biomarkers and to study signaling pathways including protein phosphorylation and protein-protein interactions. Labeling of serum proteins is important for optimal performance of the antibody microarray. Proper choice of fluorescent label and optimal concentration of protein loaded on the microarray ensure good quality of imaging that can be reliably scanned and processed by the software. We have optimized direct serum protein labeling using fluorescent dye Arrayit Green 540 (Arrayit Corporation, USA) for antibody microarray. Optimized procedure produces high quality images that can be readily scanned and used for statistical analysis of protein composition of the serum. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Identification of chromosomal errors in human preimplantation embryos with oligonucleotide DNA microarray.

    Directory of Open Access Journals (Sweden)

    Lifeng Liang

    Full Text Available A previous study comparing the performance of different platforms for DNA microarray found that the oligonucleotide (oligo microarray platform containing 385K isothermal probes had the best performance when evaluating dosage sensitivity, precision, specificity, sensitivity and copy number variations border definition. Although oligo microarray platform has been used in some research fields and clinics, it has not been used for aneuploidy screening in human embryos. The present study was designed to use this new microarray platform for preimplantation genetic screening in the human. A total of 383 blastocysts from 72 infertility patients with either advanced maternal age or with previous miscarriage were analyzed after biopsy and microarray. Euploid blastocysts were transferred to patients and clinical pregnancy and implantation rates were measured. Chromosomes in some aneuploid blastocysts were further analyzed by fluorescence in-situ hybridization (FISH to evaluate accuracy of the results. We found that most (58.1% of the blastocysts had chromosomal abnormalities that included single or multiple gains and/or losses of chromosome(s, partial chromosome deletions and/or duplications in both euploid and aneuploid embryos. Transfer of normal euploid blastocysts in 34 cycles resulted in 58.8% clinical pregnancy and 54.4% implantation rates. Examination of abnormal blastocysts by FISH showed that all embryos had matching results comparing microarray and FISH analysis. The present study indicates that oligo microarray conducted with a higher resolution and a greater number of probes is able to detect not only aneuploidy, but also minor chromosomal abnormalities, such as partial chromosome deletion and/or duplication in human embryos. Preimplantation genetic screening of the aneuploidy by DNA microarray is an advanced technology used to select embryos for transfer and improved embryo implantation can be obtained after transfer of the screened normal

  19. 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.

  20. Segmentation and intensity estimation for microarray images with saturated pixels

    Directory of Open Access Journals (Sweden)

    Yang Yan

    2011-11-01

    Full Text Available Abstract Background Microarray image analysis processes scanned digital images of hybridized arrays to produce the input spot-level data for downstream analysis, so it can have a potentially large impact on those and subsequent analysis. Signal saturation is an optical effect that occurs when some pixel values for highly expressed genes or peptides exceed the upper detection threshold of the scanner software (216 - 1 = 65, 535 for 16-bit images. In practice, spots with a sizable number of saturated pixels are often flagged and discarded. Alternatively, the saturated values are used without adjustments for estimating spot intensities. The resulting expression data tend to be biased downwards and can distort high-level analysis that relies on these data. Hence, it is crucial to effectively correct for signal saturation. Results We developed a flexible mixture model-based segmentation and spot intensity estimation procedure that accounts for saturated pixels by incorporating a censored component in the mixture model. As demonstrated with biological data and simulation, our method extends the dynamic range of expression data beyond the saturation threshold and is effective in correcting saturation-induced bias when the lost information is not tremendous. We further illustrate the impact of image processing on downstream classification, showing that the proposed method can increase diagnostic accuracy using data from a lymphoma cancer diagnosis study. Conclusions The presented method adjusts for signal saturation at the segmentation stage that identifies a pixel as part of the foreground, background or other. The cluster membership of a pixel can be altered versus treating saturated values as truly observed. Thus, the resulting spot intensity estimates may be more accurate than those obtained from existing methods that correct for saturation based on already segmented data. As a model-based segmentation method, our procedure is able to identify inner

  1. 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.

  2. SPATIAL-TEMPORAL DYNAMICS OF URBAN FIRE INCIDENTS: A CASE STUDY OF NANJING, CHINA

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    J. Yao

    2016-06-01

    Full Text Available Fire and rescue service is one of the fundamental public services provided by government in order to protect people, properties and environment from fires and other disasters, and thus promote a safer living environment. Well understanding spatial-temporal dynamics of fire incidents can offer insights for potential determinants of various fire events and enable better fire risk estimation, assisting future allocation of prevention resources and strategic planning of mitigation programs. Using a 12-year (2002-2013 dataset containing the urban fire events in Nanjing, China, this research explores the spatial-temporal dynamics of urban fire incidents. A range of exploratory spatial data analysis (ESDA approaches and tools, such as spatial kernel density and co-maps, are employed to examine the spatial, temporal and spatial-temporal variations of the fire events. Particular attention has been paid to two types of fire incidents: residential properties and local facilities, due to their relatively higher occurrence frequencies. The results demonstrated that the amount of urban fire has greatly increased in the last decade and spatial-temporal distribution of fire events vary among different incident types, which implies varying impact of potential influencing factors for further investigation.

  3. Spatial-Temporal Dynamics of Urban Fire Incidents: a Case Study of Nanjing, China

    Science.gov (United States)

    Yao, J.; Zhang, X.

    2016-06-01

    Fire and rescue service is one of the fundamental public services provided by government in order to protect people, properties and environment from fires and other disasters, and thus promote a safer living environment. Well understanding spatial-temporal dynamics of fire incidents can offer insights for potential determinants of various fire events and enable better fire risk estimation, assisting future allocation of prevention resources and strategic planning of mitigation programs. Using a 12-year (2002-2013) dataset containing the urban fire events in Nanjing, China, this research explores the spatial-temporal dynamics of urban fire incidents. A range of exploratory spatial data analysis (ESDA) approaches and tools, such as spatial kernel density and co-maps, are employed to examine the spatial, temporal and spatial-temporal variations of the fire events. Particular attention has been paid to two types of fire incidents: residential properties and local facilities, due to their relatively higher occurrence frequencies. The results demonstrated that the amount of urban fire has greatly increased in the last decade and spatial-temporal distribution of fire events vary among different incident types, which implies varying impact of potential influencing factors for further investigation.

  4. Microarrays of near-field optical probes with adjustable dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Chovin, A. [Laboratoire d' Analyse Chimique par Reconnaissance Moleculaire, Universite Bordeaux I, ENSCPB, 16 avenue Pey-Berland, 33607 Pessac (France); Garrigue, P. [Laboratoire d' Analyse Chimique par Reconnaissance Moleculaire, Universite Bordeaux I, ENSCPB, 16 avenue Pey-Berland, 33607 Pessac (France); Pecastaings, G. [Centre de Recherche Paul Pascal-CNRS, 115 avenue du Dr Schweitzer, 33600 Pessac (France); Saadaoui, H. [Centre de Recherche Paul Pascal-CNRS, 115 avenue du Dr Schweitzer, 33600 Pessac (France); Manek-Hoenninger, I. [Centre Lasers Intenses et Applications, Universite Bordeaux I, 351 Cours de la Liberation, 33405 Talence (France)]. E-mail: manek@celia.u-bordeaux1.fr; Sojic, N. [Laboratoire d' Analyse Chimique par Reconnaissance Moleculaire, Universite Bordeaux I, ENSCPB, 16 avenue Pey-Berland, 33607 Pessac (France)]. E-mail: sojic@enscpb.fr

    2006-01-15

    We present the fabrication and the characterization of high-density microarrays comprising thousands of near-field optical probes. Two types of microarrays have been prepared by adapting the SNOM methodology: arrays of uncoated fiber nanotips (i.e. apertureless probes) and arrays of apertures with adjustable subwavelength dimensions. Such arrays were fabricated by retaining the coherent structure of monomode optical fiber bundles and therefore keeping their imaging properties. The size of the apertures in a microarray was tuned at the nanometer scale by modifying the fabrication parameters. Far-field characterization of these near-field probe arrays shows completely different behavior depending both on their architecture and on their characteristic size. The angular distribution of the far-field intensity transmitted through the aperture arrays is used to determine the optical size of such diffracting apertures. Aperture radii ranging from 95 to 250 nm were found in good agreement with SEM data. Furthermore, each nanoaperture of the array is optically independent in the far-field regime. Eventually, this study demonstrates potential applications of these imaging arrays as parallel near-field optical probes in both configurations (apertureless and with apertures)

  5. Microarrays of near-field optical probes with adjustable dimensions.

    Science.gov (United States)

    Chovin, A; Garrigue, P; Pecastaings, G; Saadaoui, H; Manek-Hönninger, I; Sojic, N

    2006-01-01

    We present the fabrication and the characterization of high-density microarrays comprising thousands of near-field optical probes. Two types of microarrays have been prepared by adapting the SNOM methodology: arrays of uncoated fiber nanotips (i.e. apertureless probes) and arrays of apertures with adjustable subwavelength dimensions. Such arrays were fabricated by retaining the coherent structure of monomode optical fiber bundles and therefore keeping their imaging properties. The size of the apertures in a microarray was tuned at the nanometer scale by modifying the fabrication parameters. Far-field characterization of these near-field probe arrays shows completely different behavior depending both on their architecture and on their characteristic size. The angular distribution of the far-field intensity transmitted through the aperture arrays is used to determine the optical size of such diffracting apertures. Aperture radii ranging from 95 to 250 nm were found in good agreement with SEM data. Furthermore, each nanoaperture of the array is optically independent in the far-field regime. Eventually, this study demonstrates potential applications of these imaging arrays as parallel near-field optical probes in both configurations (apertureless and with apertures).

  6. 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.

  7. Identification of Listeria species by microarray-based assay.

    Science.gov (United States)

    Volokhov, Dmitriy; Rasooly, Avraham; Chumakov, Konstantin; Chizhikov, Vladimir

    2002-12-01

    We have developed a rapid microarray-based assay for the reliable detection and discrimination of six species of the Listeria genus: L. monocytogenes, L. ivanovii, L. innocua, L. welshimeri, L. seeligeri, and L. grayi. The approach used in this study involves one-tube multiplex PCR amplification of six target bacterial virulence factor genes (iap, hly, inlB, plcA, plcB, and clpE), synthesis of fluorescently labeled single-stranded DNA, and hybridization to the multiple individual oligonucleotide probes specific for each Listeria species and immobilized on a glass surface. Results of the microarray analysis of 53 reference and clinical isolates of Listeria spp. demonstrated that this method allowed unambiguous identification of all six Listeria species based on sequence differences in the iap gene. Another virulence factor gene, hly, was used for detection and genotyping all L. monocytogenes, all L. ivanovii, and 8 of 11 L. seeligeri isolates. Other members of the genus Listeria and three L. seeligeri isolates did not contain the hly gene. There was complete agreement between the results of genotyping based on the hly and iap gene sequences. All L. monocytogenes isolates were found to be positive for the inlB, plcA, plcB, and clpE virulence genes specific only to this species. Our data on Listeria species analysis demonstrated that this microarray technique is a simple, rapid, and robust genotyping method that is also a potentially valuable tool for identification and characterization of bacterial pathogens in general.

  8. Sequence-dependent fluorescence of cyanine dyes on microarrays.

    Directory of Open Access Journals (Sweden)

    Christy Agbavwe

    Full Text Available Cy3 and Cy5 are among the most commonly used oligonucleotide labeling molecules. Studies of nucleic acid structure and dynamics use these dyes, and they are ubiquitous in microarray experiments. They are sensitive to their environment and have higher quantum yield when bound to DNA. The fluorescent intensity of terminal cyanine dyes is also known to be significantly dependent on the base sequence of the oligonucleotide. We have developed a very precise and high-throughput method to evaluate the sequence dependence of oligonucleotide labeling dyes using microarrays and have applied the method to Cy3 and Cy5. We used light-directed in-situ synthesis of terminally-labeled microarrays to determine the fluorescence intensity of each dye on all 1024 possible 5'-labeled 5-mers. Their intensity is sensitive to all five bases. Their fluorescence is higher with 5' guanines, and adenines in subsequent positions. Cytosine suppresses fluorescence. Intensity falls by half over the range of all 5-mers for Cy3, and two-thirds for Cy5. Labeling with 5'-biotin-streptavidin-Cy3/-Cy5 gives a completely different sequence dependence and greatly reduces fluorescence compared with direct terminal labeling.

  9. 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

  10. 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

    Directory of Open Access Journals (Sweden)

    Dai Yilin

    2012-06-01

    Full Text Available Abstract Background 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. Findings 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. Conclusion 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.

  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

  12. Using pre-existing microarray datasets to increase experimental power: application to insulin resistance.

    Directory of Open Access Journals (Sweden)

    Bernie J Daigle

    2010-03-01

    Full Text Available Although they have become a widely used experimental technique for identifying differentially expressed (DE genes, DNA microarrays are notorious for generating noisy data. A common strategy for mitigating the effects of noise is to perform many experimental replicates. This approach is often costly and sometimes impossible given limited resources; thus, analytical methods are needed which increase accuracy at no additional cost. One inexpensive source of microarray replicates comes from prior work: to date, data from hundreds of thousands of microarray experiments are in the public domain. Although these data assay a wide range of conditions, they cannot be used directly to inform any particular experiment and are thus ignored by most DE gene methods. We present the SVD Augmented Gene expression Analysis Tool (SAGAT, a mathematically principled, data-driven approach for identifying DE genes. SAGAT increases the power of a microarray experiment by using observed coexpression relationships from publicly available microarray datasets to reduce uncertainty in individual genes' expression measurements. We tested the method on three well-replicated human microarray datasets and demonstrate that use of SAGAT increased effective sample sizes by as many as 2.72 arrays. We applied SAGAT to unpublished data from a microarray study investigating transcriptional responses to insulin resistance, resulting in a 50% increase in the number of significant genes detected. We evaluated 11 (58% of these genes experimentally using qPCR, confirming the directions of expression change for all 11 and statistical significance for three. Use of SAGAT revealed coherent biological changes in three pathways: inflammation, differentiation, and fatty acid synthesis, furthering our molecular understanding of a type 2 diabetes risk factor. We envision SAGAT as a means to maximize the potential for biological discovery from subtle transcriptional responses, and we provide it as a

  13. Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability.

    Science.gov (United States)

    Uziela, Karolis; Honkela, Antti

    2015-01-01

    Rapidly growing public gene expression databases contain a wealth of data for building an unprecedentedly detailed picture of human biology and disease. This data comes from many diverse measurement platforms that make integrating it all difficult. Although RNA-sequencing (RNA-seq) is attracting the most attention, at present, the rate of new microarray studies submitted to public databases far exceeds the rate of new RNA-seq studies. There is clearly a need for methods that make it easier to combine data from different technologies. In this paper, we propose a new method for processing RNA-seq data that yields gene expression estimates that are much more similar to corresponding estimates from microarray data, hence greatly improving cross-platform comparability. The method we call PREBS is based on estimating the expression from RNA-seq reads overlapping the microarray probe regions, and processing these estimates with standard microarray summarisation algorithms. Using paired microarray and RNA-seq samples from TCGA LAML data set we show that PREBS expression estimates derived from RNA-seq are more similar to microarray-based expression estimates than those from other RNA-seq processing methods. In an experiment to retrieve paired microarray samples from a database using an RNA-seq query sample, gene signatures defined based on PREBS expression estimates were found to be much more accurate than those from other methods. PREBS also allows new ways of using RNA-seq data, such as expression estimation for microarray probe sets. An implementation of the proposed method is available in the Bioconductor package "prebs."

  14. Systematic review of accuracy of prenatal diagnosis for abnormal chromosome diseases by microarray technology.

    Science.gov (United States)

    Xu, H B; Yang, H; Liu, G; Chen, H

    2014-10-31

    The accuracy of prenatal diagnosis for abnormal chromosome diseases by chromosome microarray technology and karyotyping were compared. A literature search was carried out in the MEDLINE database with the keywords "chromosome" and "karyotype" and "genetic testing" and "prenatal diagnosis" and "oligonucleotide array sequence". The studies obtained were filtered by using the QUADAS tool, and studies conforming to the quality standard were fully analyzed. There was one paper conforming to the QUADAS standards including 4406 gravidas with adaptability syndromes of prenatal diagnosis including elderly parturient women, abnormal structure by type-B ultrasound, and other abnormalities. Microarray technology yielded successful diagnoses in 4340 cases (98.8%), and there was no need for tissue culture in 87.9% of the samples. All aneuploids and non-parallel translocations in 4282 cases of non-chimera identified by karyotyping could be detected using microarray analysis technology, whereas parallel translocations and fetal triploids could not be detected by microarray analysis technology. In the samples with normal karyotyping results, type-B ultrasound showed that 6% of chromosomal deficiencies or chromosome duplications could be detected by microarray technology, and the same abnormal chromosomes were detected in 1.7% of elderly parturient women and samples with positive serology screening results. In the prenatal diagnosis test, compared with karyotyping, microarray technology could identify the extra cell genetic information with clinical significance, aneuploids, and non-parallel translocations; however, its disadvantage is that it could not identify parallel translocations and triploids.

  15. Evaluation of a gene information summarization system by users during the analysis process of microarray datasets.

    Science.gov (United States)

    Yang, Jianji; Cohen, Aaron; Hersh, William

    2009-02-05

    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. 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. 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. GICSS can be accessed online at: http://ir.ohsu.edu/jianji/index.html.

  16. Spatio-temporal study of environmental nontuberculous mycobacteria isolated from Wardha district in Central India.

    Science.gov (United States)

    Mishra, Pranava S; Narang, Pratibha; Narang, Rahul; Goswami, Bidhan; Mendiratta, Deepak K

    2018-01-01

    During the last two decades, nontuberculous mycobacteria (NTM) have gained in importance but there is still a paucity of data, particularly for environmental isolates. We studied, over a period of two years, the spatio-temporal features of NTM isolates obtained from different environmental sources in Wardha district, India. A total of 1398 samples (699 each of soil and water) were tested and 170 (12.2%) yielded NTM isolates, including 123 from soil and 47 from water samples. Out of 170 NTM isolates, 107 (63%) belonged to potentially pathogenic mycobacteria (PPM) and 63 (37%) to the less pathogenic mycobacterial (LPM) group. Overall, maximum isolation was obtained in rainy season (20.3%) followed by winter (13.5%), post rainy (8.7%) and summer seasons (5.8%). Mycobacterium fortuitum, Mycobacterium gordonae and Mycobacterium avium complex (MAC) were common isolates followed by Mycobacterium flavescens, Mycobacterium scrofulaceum, Mycobacterium simiae and Mycobacterium marinum. From soil, isolation of NTM was highest from grounds used for community gatherings (42.8%) followed by soil from residential premises (27.7%) and near the wells (26.0%). From drinking water sources, highest NTM isolation was obtained from wells (15.4%) followed by treated water tanks (6.9%), household receptacles (6.3%), hand pumps (5.6%) and tap water supply (3.5%). Isolation from natural canal water was 6.6%, while from drainage and waste water ponds isolation was 8.3%. The results of the study revealed that in Wardha district, NTM are present both in the soil and drinking water. As NTM can be pathogenic, particularly in immune-compromised individuals, these can be of potential risk to the human population.

  17. Systematic study of high-order harmonic optimal control by temporal pulse shaping of laser pulses

    International Nuclear Information System (INIS)

    Boyko, O.; Valentin, C.; Mercier, B.; Coquelet, Ch.; Pascal, V.; Papalazarou, E.; Rey, G.; Balcou, Ph.

    2007-01-01

    We explore experimentally and numerically the physics underlying the optimization of high-order harmonic generation by intense laser pulses, whose temporal profile is tailored by a learning genetic algorithm. Based on a large set of optimization data obtained under different generation parameters, we show that the algorithm converges toward a class of very special profiles on the leading edge of the pulse. The behavior of the harmonic signal is then compared with theoretical simulations based on the time-dependent Schroedinger equation, allowing one to identify separately the role of microscopic and macroscopic phenomena in the temporal dynamics of high-harmonic generation and optimization

  18. 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

    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......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...

  19. Biological microarray interpretation : The rules of engagement

    NARCIS (Netherlands)

    Breitling, Rainer

    2006-01-01

    Gene expression microarrays are now established as a standard tool in biological and biochemical laboratories. Interpreting the masses of data generated by this technology poses a number of unusual new challenges. Over the past few years a consensus has begun to emerge concerning the most important

  20. Ecologically relevant stress resistance: from microarrays and ...

    Indian Academy of Sciences (India)

    2004-10-15

    Oct 15, 2004 ... Home; Journals; Journal of Biosciences; Volume 29; Issue 4. Ecologically relevant stress resistance: from microarrays and quantitative trait loci to candidate genes – A research plan and preliminary results using Drosophila as a model organism and climatic and genetic stress as model stresses.

  1. Design of a covalently bonded glycosphingolipid microarray

    DEFF Research Database (Denmark)

    Arigi, Emma; Blixt, Klas Ola; Buschard, Karsten

    2012-01-01

    Glycosphingolipids (GSLs) are well known ubiquitous constituents of all eukaryotic cell membranes, yet their normal biological functions are not fully understood. As with other glycoconjugates and saccharides, solid phase display on microarrays potentially provides an effective platform for in vi......Glycosphingolipids (GSLs) are well known ubiquitous constituents of all eukaryotic cell membranes, yet their normal biological functions are not fully understood. As with other glycoconjugates and saccharides, solid phase display on microarrays potentially provides an effective platform......, 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......-mercaptoethylamine, was also tested. Underivatized or linker-derivatized lyso-GSL were then immobilized on N-hydroxysuccinimide- or epoxide-activated glass microarray slides and probed with carbohydrate binding proteins of known or partially known specificities (i.e., cholera toxin B-chain; peanut agglutinin...

  2. 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...

  3. 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; Klevering, B Jeroen

    2015-01-01

    To determine the efficacy of multiple versions of a commercially available arrayed primer extension (APEX) microarray chip for autosomal recessive retinitis pigmentosa (arRP). 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. 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). 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.

  4. A method of microarray data storage using array data type.

    Science.gov (United States)

    Tsoi, Lam C; Zheng, W Jim

    2007-04-01

    A well-designed microarray database can provide valuable information on gene expression levels. However, designing an efficient microarray database with minimum space usage is not an easy task since designers need to integrate the microarray data with the information of genes, probe annotation, and the descriptions of each microarray experiment. Developing better methods to store microarray data can greatly improve the efficiency and usefulness of such data. A new schema is proposed to store microarray data by using array data type in an object-relational database management system--PostgreSQL. The implemented database can store all the microarray data from the same chip in an array data structure. The variable-length array data type in PostgreSQL can store microarray data from same chip. The implementation of our schema can help to increase the data retrieval and space efficiency.

  5. Microarray Analysis of Space-flown Murine Thymus Tissue

    Data.gov (United States)

    National Aeronautics and Space Administration — Microarray Analysis of Space-flown Murine Thymus Tissue Reveals Changes in Gene Expression Regulating Stress and Glucocorticoid Receptors. We used microarrays to...

  6. Instance-based concept learning from multiclass DNA microarray data

    Directory of Open Access Journals (Sweden)

    Dubitzky Werner

    2006-02-01

    Full Text Available Abstract Background Various statistical and machine learning methods have been successfully applied to the classification of DNA microarray data. Simple instance-based classifiers such as nearest neighbor (NN approaches perform remarkably well in comparison to more complex models, and are currently experiencing a renaissance in the analysis of data sets from biology and biotechnology. While binary classification of microarray data has been extensively investigated, studies involving multiclass data are rare. The question remains open whether there exists a significant difference in performance between NN approaches and more complex multiclass methods. Comparative studies in this field commonly assess different models based on their classification accuracy only; however, this approach lacks the rigor needed to draw reliable conclusions and is inadequate for testing the null hypothesis of equal performance. Comparing novel classification models to existing approaches requires focusing on the significance of differences in performance. Results We investigated the performance of instance-based classifiers, including a NN classifier able to assign a degree of class membership to each sample. This model alleviates a major problem of conventional instance-based learners, namely the lack of confidence values for predictions. The model translates the distances to the nearest neighbors into 'confidence scores'; the higher the confidence score, the closer is the considered instance to a pre-defined class. We applied the models to three real gene expression data sets and compared them with state-of-the-art methods for classifying microarray data of multiple classes, assessing performance using a statistical significance test that took into account the data resampling strategy. Simple NN classifiers performed as well as, or significantly better than, their more intricate competitors. Conclusion Given its highly intuitive underlying principles – simplicity

  7. Spatial mapping of temporal risk to improve prevention measures: A case study of dengue epidemic in Lahore.

    Science.gov (United States)

    Hafeez, Sidrah; Amin, Muhammad; Munir, Bilal Ahmed

    2017-06-01

    Dengue is identified as serious vector born infectious disease by WHO, threating around 2.5 billion people around the globe. Pakistan is facing dengue epidemic since 1994 but 2010 and 2011 dengue outbreaks were worst. During 2011 dengue outbreak 22,562 cases were reported and 363 died due to this fatal infection in Pakistan. In this study, Lahore District was chosen as it was severely affected in 2011 dengue outbreak with 14,000 reported cases and 300 deaths. There is no vaccine developed yet for the disease control, so only effective early warning, prevention and control measures can reduce the potential disease risk. This study proposes a method for detecting spatial autocorrelation of temporal dynamics of disease using Local Index of Spatial Autocorrelation (LISA) using three temporal indices: (a) how often the dengue cases occur, frequency index; (b) how long the epidemic wave prevails, duration index; (c) how significant dengue cases occur in successive periods, severity index. Overlay analysis of LISA value for each temporal index resulted in eight risk types. The mapping of spatio-temporal risk indices and their overlay analysis identified that 10.6% area of Lahore (184.3km 2 and population density 119,110persons/km 2 ) had high values for frequency, duration, and severity index (pSpatial risk identification by using local spatial-autocorrelation helps in identifying other possible causes of disease risk and further strategic planning for prevention and control measures. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Whiteboard icons to support the blood-test process in an emergency department: an observational study of temporal patterns.

    Science.gov (United States)

    Torkilsheyggi, Arnvør á; Hertzum, Morten; From, Gustav

    2013-01-01

    The competent treatment of emergency department (ED) patients requires an effective and efficient process for handling laboratory tests such as blood tests. This study investigates how ED clinicians go about the process, from ordering blood tests to acknowledging their results and, specifically, assesses the use of whiteboard icons to support this process. On the basis of observation and interviews we find that the blood-test process is intertwined with multiple other temporal patterns in ED work. The whiteboard icons, which indicate four temporally distinct steps in the blood-test process, support the nurses in maintaining the flow of patients through the ED and the physicians in assessing test results at timeouts. The main results of this study are, however, that the blood-test process is temporally and collaboratively complex, that the whiteboard icons pass by most of this complexity, that attending to the icons is yet another temporally sensitive activity to remember, and that whereas the assessment of test results is integral to patient treatment, the acknowledgement of having seen the results is a formal add-on, the responsibility for which is sometimes unclear.

  9. 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)

  10. A high resolution temporal study of phytoplankton bloom dynamics in the eutrophic Taw Estuary (SW England).

    Science.gov (United States)

    Maier, Gerald; Glegg, Gillian A; Tappin, Alan D; Worsfold, Paul J

    2012-09-15

    The Taw Estuary (SW England) is eutrophic as a result of enhanced nutrient inputs from its catchment. However, factors influencing the timing and extent of phytoplankton bloom formation are not fully understood in this system. In this study, high resolution chemical and biological sampling was undertaken in late-winter/spring and summer 2008 in order to gain further insights into bloom dynamics in the Taw Estuary. Temporal variations in chlorophyll a maxima in the upper and middle estuary during summer were controlled by river flow and tidal amplitude, with nutrient limitation probably less important. Concentrations of chlorophyll a were highest during low river flow and neap tides. Increased river flows advected the chlorophyll maximum to the outer estuary, and under highest river discharges, chlorophyll a concentrations were further reduced. This feature was even more pronounced when spring tides coincided with high flows. The main bloom species were the diatoms Asterionellopsis glacialis and Thalassiosira guillardii. Using two multivariate statistical techniques in combination, five distinct physical and biogeochemical states in the Taw estuarine waters were identified. These states can be summarised as: A(1), high chlorophyll a, high temperature, long residence times, nutrient depletion; A(2), strong coastal water influence; B(1), decreasing chlorophyll a, increasing river flow and/or spring tides; B(2), transitional between states A(1) and B(3); B(3), high river flow. It was thus possible to differentiate between contrasting environmental conditions that were either beneficial or detrimental for the development of algal blooms. A conceptual model of diatom - dominated primary production for the Taw Estuary is proposed which describes how physical controls (river flow, tidal state) moderate plankton biomass production in the upper and mid - estuarine regions. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. A synthetic dataset for spatio-temporal scaling studies in microwave remote sensing

    Science.gov (United States)

    Ebrahimi, H.; Liu, P. W.; Chakrabarti, S.; Judge, J.

    2017-12-01

    Passive microwave missions such as the SMAP and SMOS provide Soil Moisture (SM) information on a global basis at spatial resolution of 10s of km. These products have to be downscaled to field scales of 200 m-1 km for applications in hydrology and agriculture. Unfortunately, a dense network of field measurements is typically unavailable under the satellite footprint to evaluate the spatial scaling algorithms. An effective alternative is to develop a synthetic experiment for simulating SM observations at both satellite and field scales. In this study, we develop a simulation dataset for the state of Iowa based upon our previous methodology used to conduct synthetic experiments for heterogeneous landscapes with dynamic vegetation in north central Florida. Such a dataset will allow developing and evaluating spatio-temporal scaling algorithms. The dataset is developed for 162 SMAP pixels (320km X 560km) for corn, soybean, and bare soil land covers in Iowa, during two years, 2012 and 2015, where 2012 was a drier year than 2015. The crop growth and development will be simulated with the Decision Support for Agrotechnology Transfer (DSSAT) suite of crop models. The LSP-DSSAT-MB model have been calibrated with data from the Soil Moisture Active Passive Validation Experiment-2016. During the experiment, the University of Florida observed active and passive microwave signatures and concurrent soil and vegetation conditions for growing corn and soybean from May-September (SMAPVEX16-MicroWEX). The dataset has been generated at 200m, 1km, 5km, 10km, 25km, and 36km. The results show variability of soil moisture across the region for the two years.

  12. 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.

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

    Science.gov (United States)

    Wu, Hong; Feng, Yong; Jiang, Lu; Pan, Qian; Liu, Yalan; Liu, Chang; He, Chufeng; Chen, Hongsheng; Liu, Xueming; Hu, Chang; Hu, Yiqiao; Mei, Lingyun

    2016-01-01

    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.

  14. 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.

  15. Use of non-amplified RNA samples for microarray analysis of gene expression.

    Directory of Open Access Journals (Sweden)

    Hiroko Sudo

    Full Text Available Demand for high quality gene expression data has driven the development of revolutionary microarray technologies. The quality of the data is affected by the performance of the microarray platform as well as how the nucleic acid targets are prepared. The most common method for target nucleic acid preparation includes in vitro transcription amplification of the sample RNA. Although this method requires a small amount of starting material and is reported to have high reproducibility, there are also technical disadvantages such as amplification bias and the long, laborious protocol. Using RNA derived from human brain, breast and colon, we demonstrate that a non-amplification method, which was previously shown to be inferior, could be transformed to a highly quantitative method with a dynamic range of five orders of magnitude. Furthermore, the correlation coefficient calculated by comparing microarray assays using non-amplified samples with qRT-PCR assays was approximately 0.9, a value much higher than when samples were prepared using amplification methods. Our results were also compared with data from various microarray platforms studied in the MicroArray Quality Control (MAQC project. In combination with micro-columnar 3D-Gene™ microarray, this non-amplification method is applicable to a variety of genetic analyses, including biomarker screening and diagnostic tests for cancer.

  16. Microarray analysis reveals the actual specificity of enrichment media used for food safety assessment.

    Science.gov (United States)

    Kostić, Tanja; Stessl, Beatrix; Wagner, Martin; Sessitsch, Angela

    2011-06-01

    Microbial diagnostic microarrays are tools for simultaneous detection and identification of microorganisms in food, clinical, and environmental samples. In comparison to classic methods, microarray-based systems have the potential for high throughput, parallelism, and miniaturization. High specificity and high sensitivity of detection have been demonstrated. A microbial diagnostic microarray for the detection of the most relevant bacterial food- and waterborne pathogens and indicator organisms was developed and thoroughly validated. The microarray platform based on sequence-specific end labeling of oligonucleotides and the phylogenetically robust gyrB marker gene allowed a highly specific (resolution on genus and/or species level) and sensitive (0.1% relative and 10(4) CFU absolute sensitivity) detection of the target pathogens. In initial challenge studies of the applicability of microarray-based food analysis, we obtained results demonstrating the questionable specificity of standardized culture-dependent microbiological detection methods. Taking into consideration the importance of reliable food safety assessment methods, comprehensive performance assessment is essential. Results demonstrate the potential of this new pathogen diagnostic microarray to evaluate culture-based standard methods in microbiological food analysis.

  17. Temporal variability of ecological niches : A study on intertidal macrobenthic fauna

    NARCIS (Netherlands)

    Kraan, Casper; Aarts, Geert; Piersma, Theunis; Dormann, Carsten F.

    The determination of temporal niche dynamics under field conditions is an important component of a species' ecology. Recent developments in niche mapping, and the possibility to account for spatial autocorrelation in species distributions, hold promise for the statistical approach explored here.

  18. Temporal variability of ecological niches: a study on intertidal macrobenthic fauna

    NARCIS (Netherlands)

    Kraan, C.; Aarts, G.; Dormann, C.F.; Piersma, T.

    2013-01-01

    The determination of temporal niche dynamics under field conditions is an important component of a species' ecology. Recent developments in niche mapping, and the possibility to account for spatial autocorrelation in species distributions, hold promise for the statistical approach explored here.

  19. 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…

  20. 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.

    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

  1. 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

  2. Executive functions processed in the frontal and lateral temporal cortices: Intracerebral study

    Czech Academy of Sciences Publication Activity Database

    Bočková, H.; Chládek, Jan; Jurák, Pavel; Halámek, Josef; Rektor, I.

    2007-01-01

    Roč. 118, č. 12 (2007), s. 2625-2636 ISSN 1388-2457 R&D Projects: GA ČR(CZ) GA102/05/0402 Institutional research plan: CEZ:AV0Z20650511 Keywords : SEEG * executive functions * ERD/S * temporal neocortex Subject RIV: FH - Neurology Impact factor: 2.468, year: 2007

  3. Temporal organization of living organisms and problem of the reproducability of magnetobiological study results

    International Nuclear Information System (INIS)

    Martynyuk, V.S.

    1995-01-01

    The analysis of bad reproduction of experimental magnitobiological results was realized onto experimental data for extremely low frequency magnetic field influence on leucocytes level in animal blood. It was shown that one of the causes of bad experimental results reproduction is a dynamism of temporal organization parameters in animals that used as a biological control. 13 refs

  4. Techniques for studying gravity waves and turbulence: Horizontal, vertical and temporal resolution needed

    Science.gov (United States)

    Avery, S. K.; Carter, D. A.

    1983-01-01

    One of the most important atmospheric measurements that is needed is a measure of the gravity-wave spectrum. The MST radar has been investigated as means to measure the temporal resolution required to determine gravity-wave oscillations. The required vertical and horizontal resolution is dependent on the particular part of the gravity wave spectrum that is analyzed. Horizontal spacing is also discussed.

  5. 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.

  6. 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.

  7. 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

  8. 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

    of genetic variation on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and TopHat) on S288c genome, the capabilities of five different statistical methods to detect differential gene expression (baySeq, Cuffdiff, DESeq, edgeR and NOISeq) and we explored...... 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...

  9. The temporal evolution of pyroclast ejection velocity and exit trajectory, a laboratory case study.

    Science.gov (United States)

    Cigala, Valeria; Kueppers, Ulrich; José Peña Fernández, Juan; Sesterhenn, Jörn; Taddeucci, Jacopo; Dingwell, Donald Bruce

    2017-04-01

    Pyroclast ejection dynamics during explosive volcanic eruptions are highly variable. This variability is due to complex interaction among different parameters, which define the boundary conditions for a certain eruption. Scaled and controlled laboratory experiments come in hand to characterize the effect of specific physical parameters on the ejection dynamics. We focus, in particular, on the dynamics of pyroclasts ejection in the region just above the vent, also called gas-thrust region, for the case of impulsively released gas-pyroclast mixtures (i.e., unsteady eruptions). In this study, gas-particle mixtures were released in a series of shock-tube experiments with varying 1) tube length, 2) vent geometry, 3) gas-particle ratio, 4) initial temperature and 5) particle size distribution. The tube length was varied by changing the starting sample load, resulting in a gas-particle ratio of 1, 2.5 and 8, respectively. Thereby, the initial distance of the sample from the exit varied between 320, 230 and 140 mm, respectively, allowing for variable time for accelerating (and possibly decelerating) the particles prior to exit. Moreover, four vent geometries were employed, a nozzle with converging walls (5°), a cylinder and two funnels with walls diverging at 15° and 30° respectively. All of them are characterized by a value h/D=1.07, where h is the length between the throat and the lip of the vent and D is throat diameter. The experiments were performed at both 500°C and room temperature using particles from 2 to 0.125 mm in diameter. In all experiments, initial pressure was 15 MPa. High speed videos of the ejection behaviour were analyzed to obtain the temporal evolution of particle velocity and exit trajectory depending on boundary conditions. Max velocity of 300 m/s was observed together with a non-linear decay of exit velocity over time. The exit trajectories were found to deviate from the vertical by 5° to 45° and also display a non-linear evolution with time

  10. 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

  11. 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 ...

  12. 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

  13. GABA- and acetylcholine-related gene expression in blood correlate with tic severity and microarray evidence for alternative splicing in Tourette syndrome: a pilot study.

    Science.gov (United States)

    Tian, Yingfang; Gunther, Joan R; Liao, Isaac H; Liu, Dazhi; Ander, Bradley P; Stamova, Boryana S; Lit, Lisa; Jickling, Glen C; Xu, Huichun; Zhan, Xinhua; Sharp, Frank R

    2011-03-24

    Tourette syndrome (TS) is a complex childhood neurodevelopmental disorder characterized by motor and vocal tics. Recently, altered numbers of GABAergic-parvalbumin (PV) and cholinergic interneurons were observed in the basal ganglia of individuals with TS. Thus, we postulated that gamma-amino butyric acid (GABA)- and acetylcholine (ACh)-related genes might be associated with the pathophysiology of TS. Total RNA isolated from whole blood of 26 un-medicated TS subjects and 23 healthy controls (HC) was processed on Affymetrix Human Exon 1.0 ST arrays. Data were analyzed to identify genes whose expression correlated with tic severity in TS, and to identify genes differentially spliced in TS compared to HC subjects. Many genes (3627) correlated with tic severity in TS (p genes were significantly over-represented. Moreover, several GABA and ACh-related genes were predicted to be alternatively spliced in TS compared to HC including GABA receptors GABRA4 and GABRG1, the nicotinic ACh receptor CHRNA4 and cholinergic differentiation factor (CDF). This pilot study suggests that at least some of these GABA- and ACh-related genes observed in blood that correlate with tics or are alternatively spliced are involved in the pathophysiology of TS and tics. Copyright © 2010 Elsevier B.V. All rights reserved.

  14. High temporal resolution dynamic contrast-enhanced MRI at 7 Tesla: a feasibility study with mouse liver model.

    Science.gov (United States)

    Hartono, S; Thng, C H; Ng, Q S; Yong, C X; Yang, C-T; Shi, W; Chuang, K H; Koh, T S

    2011-01-01

    Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) has been widely applied to evaluate microcirculatory parameters in clinical settings. However, pre-clinical studies involving DCE-MRI of small animals remain challenging with the requirement for high spatial and temporal resolution for quantitative tracer kinetic analysis. This study illustrates the feasibility of applying a high temporal resolution (2 s) protocol for liver imaging in mice by analyzing the DCE-MRI datasets of mice liver with a dual-input two-compartment tracer kinetic model. Phantom studies were performed to validate the T(1) estimates derived by the proposed protocol before applying it in mice studies. The DCE-MRI datasets of mice liver were amendable to tracer kinetic analysis using a dual-input two-compartment model. Estimated micro-circulatory parameters were consistent with liver physiology, indicating viability of applying the technique for pre-clinical drug developments.

  15. 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 < .001); the use of RT decreased over time (from 38% to 8%; P < .001); and the use of chemotherapy remained stable (from 6% to 9%; P = .289). Practice patterns 90 days after orchiectomy remained stable over time among patients with NSGCTs: from 51% to 57% for no treatment (P = .435), from 43% to 43% for chemotherapy (P = .336), and from 9% to 3% for RPLND (P = .476). The OS rates for the entire cohort at 5 and 10 years were 97% and 96%, respectively; the CSS rates were 98% and 98%, respectively. There was no significant change in OS or CSS for patients with seminomas or NSGCTs during the study period. There has been substantial de-escalation in the treatment of 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.

  16. 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

  17. Surface Subsidence Analysis by Multi-Temporal InSAR and GRACE: A Case Study in Beijing.

    Science.gov (United States)

    Guo, Jiming; Zhou, Lv; Yao, Chaolong; Hu, Jiyuan

    2016-09-14

    The aim of this study was to investigate the relationship between surface subsidence and groundwater changes. To investigate this relationship, we first analyzed surface subsidence. This paper presents the results of a case study of surface subsidence in Beijing from 1 August 2007 to 29 September 2010. The Multi-temporal Interferometric Synthetic Aperture Radar (multi-temporal InSAR) technique, which can simultaneously detect point-like stable reflectors (PSs) and distributed scatterers (DSs), was used to retrieve the subsidence magnitude and distribution in Beijing using 18 ENVISAT ASAR images. The multi-temporal InSAR-derived subsidence was verified by leveling at an accuracy better than 5 mm/year. Based on the verified multi-temporal InSAR results, a prominent uneven subsidence was identified in Beijing. Specifically, most of the subsidence velocities in the downtown area were within 10 mm/year, and the largest subsidence was detected in Tongzhou, with velocities exceeding 140 mm/year. Furthermore, Gravity Recovery and Climate Experiment (GRACE) data were used to derive the groundwater change series and trend. By comparison with the multi-temporal InSAR-derived subsidence results, the long-term decreasing trend between groundwater changes and surface subsidence showed a relatively high consistency, and a significant impact of groundwater changes on the surface subsidence was identified. Additionally, the spatial distribution of the subsidence funnel was partially consistent with that of groundwater depression, i.e., the former possessed a wider range than the latter. Finally, the relationship between surface subsidence and groundwater changes was determined.

  18. Surface Subsidence Analysis by Multi-Temporal InSAR and GRACE: A Case Study in Beijing

    Directory of Open Access Journals (Sweden)

    Jiming Guo

    2016-09-01

    Full Text Available The aim of this study was to investigate the relationship between surface subsidence and groundwater changes. To investigate this relationship, we first analyzed surface subsidence. This paper presents the results of a case study of surface subsidence in Beijing from 1 August 2007 to 29 September 2010. The Multi-temporal Interferometric Synthetic Aperture Radar (multi-temporal InSAR technique, which can simultaneously detect point-like stable reflectors (PSs and distributed scatterers (DSs, was used to retrieve the subsidence magnitude and distribution in Beijing using 18 ENVISAT ASAR images. The multi-temporal InSAR-derived subsidence was verified by leveling at an accuracy better than 5 mm/year. Based on the verified multi-temporal InSAR results, a prominent uneven subsidence was identified in Beijing. Specifically, most of the subsidence velocities in the downtown area were within 10 mm/year, and the largest subsidence was detected in Tongzhou, with velocities exceeding 140 mm/year. Furthermore, Gravity Recovery and Climate Experiment (GRACE data were used to derive the groundwater change series and trend. By comparison with the multi-temporal InSAR-derived subsidence results, the long-term decreasing trend between groundwater changes and surface subsidence showed a relatively high consistency, and a significant impact of groundwater changes on the surface subsidence was identified. Additionally, the spatial distribution of the subsidence funnel was partially consistent with that of groundwater depression, i.e., the former possessed a wider range than the latter. Finally, the relationship between surface subsidence and groundwater changes was determined.

  19. An ANOCEF genomic and transcriptomic microarray study of the response to radiotherapy or to alkylating first-line chemotherapy in glioblastoma patients

    Directory of Open Access Journals (Sweden)

    Ducray François

    2010-09-01

    Full Text Available Abstract Background The molecular characteristics associated with the response to treatment in glioblastomas (GBMs remain largely unknown. We performed a retrospective study to assess the genomic characteristics associated with the response of GBMs to either first-line chemotherapy or radiation therapy. The gene expression (n = 56 and genomic profiles (n = 67 of responders and non-responders to first-line chemotherapy or radiation therapy alone were compared on Affymetrix Plus 2 gene expression arrays and BAC CGH arrays. Results According to Verhaak et al.'s classification system, mesenchymal GBMs were more likely to respond to radiotherapy than to first-line chemotherapy, whereas classical GBMs were more likely to respond to first-line chemotherapy than to radiotherapy. In patients treated with radiation therapy alone, the response was associated with differential expression of microenvironment-associated genes; the expression of hypoxia-related genes was associated with short-term progression-free survival ( 10 months. Consistently, infiltration of the tumor by both CD3 and CD68 cells was significantly more frequent in responders to radiotherapy than in non-responders. In patients treated with first-line chemotherapy, the expression of stem-cell genes was associated with resistance to chemotherapy, and there was a significant association between response to treatment and p16 locus deletions. Consistently, in an independent data set of patients treated with either radiotherapy alone or with both radiotherapy and adjuvant chemotherapy, we found that patients with the p16 deletion benefited from adjuvant chemotherapy regardless of their MGMT promoter methylation status, whereas in patients without the p16 deletion, this benefit was only observed in patients with a methylated MGMT promoter. Conclusion Differential expression of microenvironment genes and p16 locus deletion are associated with responses to radiation therapy and to first

  20. Sequential interim analyses of survival data in DNA microarray experiments

    Directory of Open Access Journals (Sweden)

    Jung Klaus

    2011-04-01

    Full Text Available Abstract Background Discovery of biomarkers that are correlated with therapy response and thus with survival is an important goal of medical research on severe diseases, e.g. cancer. Frequently, microarray studies are performed to identify genes of which the expression levels in pretherapeutic tissue samples are correlated to survival times of patients. Typically, such a study can take several years until the full planned sample size is available. Therefore, interim analyses are desirable, offering the possibility of stopping the study earlier, or of performing additional laboratory experiments to validate the role of the detected genes. While many methods correcting the multiple testing bias introduced by interim analyses have been proposed for studies of one single feature, there are still open questions about interim analyses of multiple features, particularly of high-dimensional microarray data, where the number of features clearly exceeds the number of samples. Therefore, we examine false discovery rates and power rates in microarray experiments performed during interim analyses of survival studies. In addition, the early stopping based on interim results of such studies is evaluated. As stop criterion we employ the achieved average power rate, i.e. the proportion of detected true positives, for which a new estimator is derived and compared to existing estimators. Results In a simulation study, pre-specified levels of the false discovery rate are maintained in each interim analysis, where reduced levels as used in classical group sequential designs of one single feature are not necessary. Average power rates increase with each interim analysis, and many studies can be stopped prior to their planned end when a certain pre-specified power rate is achieved. The new estimator for the power rate slightly deviates from the true power rate but is comparable to other estimators. Conclusions Interim analyses of microarray experiments can provide

  1. 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

  2. Lagrangian study of temporal changes of a surface flow through the Kamchatka Strait

    OpenAIRE

    Prants, S. V.; Andreev, A. G.; Uleysky, M. Yu.; Budyansky, M. V.

    2014-01-01

    Using Lagrangian methods we analyze a 20-year-long estimate of water flux through the Kamchatka Strait in the northern North Pacific based on AVISO velocity field. It sheds new light on the flux pattern and its variability on annual and monthly time scales. Strong seasonality in surface outflow through the strait could be explained by temporal changes in the wind stress over the northern and western Bering Sea slopes. Interannual changes in a surface outflow through the Kamchatka Strait corre...

  3. RNA-seq and microarray complement each other in transcriptome profiling

    Science.gov (United States)

    2012-01-01

    Background RNA-seq and microarray are the two popular methods employed for genome-wide transcriptome profiling. Current comparison studies have shown that transcriptome quantified by these two methods correlated well. However, none of them have addressed if they complement each other, considering the strengths and the limitations inherent with them. The pivotal requirement to address this question is the knowledge of a well known data set. In this regard, HrpX regulome from pathogenic bacteria serves as an ideal choice as the target genes of HrpX transcription factor are well studied due to their central role in pathogenicity. Results We compared the performance of RNA-seq and microarray in their ability to detect known HrpX target genes by profiling the transcriptome from the wild-type and the hrpX mutant strains of γ-Proteobacterium Xanthomonas citri subsp. citri. Our comparative analysis indicated that gene expression levels quantified by RNA-seq and microarray well-correlated both at absolute as well as relative levels (Spearman correlation-coefficient, rs > 0.76). Further, the expression levels quantified by RNA-seq and microarray for the significantly differentially expressed genes (DEGs) also well-correlated with qRT-PCR based quantification (rs = 0.58 to 0.94). Finally, in addition to the 55 newly identified DEGs, 72% of the already known HrpX target genes were detected by both RNA-seq and microarray, while, the remaining 28% could only be detected by either one of the methods. Conclusions This study has significantly advanced our understanding of the regulome of the critical transcriptional factor HrpX. RNA-seq and microarray together provide a more comprehensive picture of HrpX regulome by uniquely identifying new DEGs. Our study demonstrated that RNA-seq and microarray complement each other in transcriptome profiling. PMID:23153100

  4. A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly.

    Science.gov (United States)

    Goralski, Michal; Sobieszczanska, Paula; Obrepalska-Steplowska, Aleksandra; Swiercz, Aleksandra; Zmienko, Agnieszka; Figlerowicz, Marek

    2016-01-01

    Nicotiana benthamiana has been widely used in laboratories around the world for studying plant-pathogen interactions and posttranscriptional gene expression silencing. Yet the exploration of its transcriptome has lagged behind due to the lack of both adequate sequence information and genome-wide analysis tools, such as DNA microarrays. Despite the increasing use of high-throughput sequencing technologies, the DNA microarrays still remain a popular gene expression tool, because they are cheaper and less demanding regarding bioinformatics skills and computational effort. We designed a gene expression microarray with 103,747 60-mer probes, based on two recently published versions of N. benthamiana transcriptome (v.3 and v.5). Both versions were reconstructed from RNA-Seq data of non-strand-specific pooled-tissue libraries, so we defined the sense strand of the contigs prior to designing the probe. To accomplish this, we combined a homology search against Arabidopsis thaliana proteins and hybridization to a test 244k microarray containing pairs of probes, which represented individual contigs. We identified the sense strand in 106,684 transcriptome contigs and used this information to design an Nb-105k microarray on an Agilent eArray platform. Following hybridization of RNA samples from N. benthamiana roots and leaves we demonstrated that the new microarray had high specificity and sensitivity for detection of differentially expressed transcripts. We also showed that the data generated with the Nb-105k microarray may be used to identify incorrectly assembled contigs in the v.5 transcriptome, by detecting inconsistency in the gene expression profiles, which is indicated using multiple microarray probes that match the same v.5 primary transcripts. We provided a complete design of an oligonucleotide microarray that may be applied to the research of N. benthamiana transcriptome. This, in turn, will allow the N. benthamiana research community to take full advantage of

  5. Viral diagnosis in Indian livestock using customized microarray chips.

    Science.gov (United States)

    Yadav, Brijesh S; Pokhriyal, Mayank; Ratta, Barkha; Kumar, Ajay; Saxena, Meeta; Sharma, Bhaskar

    2015-01-01

    Viral diagnosis in Indian livestock using customized microarray chips is gaining momentum in recent years. Hence, it is possible to design customized microarray chip for viruses infecting livestock in India. Customized microarray chips identified Bovine herpes virus-1 (BHV-1), Canine Adeno Virus-1 (CAV-1), and Canine Parvo Virus-2 (CPV-2) in clinical samples. Microarray identified specific probes were further confirmed using RT-PCR in all clinical and known samples. Therefore, the application of microarray chips during viral disease outbreaks in Indian livestock is possible where conventional methods are unsuitable. It should be noted that customized application requires a detailed cost efficiency calculation.

  6. High-resolution microarray in the assessment of fetal anomalies detected by ultrasound.

    Science.gov (United States)

    Charan, Poonam; Woodrow, Nicole; Walker, Sue P; Ganesamoorthy, Devika; McGillivray, George; Palma-Dias, Ricardo

    2014-02-01

    The main aim of this study was to determine the feasibility of using high-resolution microarray to assist with prenatal diagnosis of ultrasound-detected fetal abnormality and to describe the frequency of abnormal results in different categories of fetal anomalies. Prospective cross-sectional study was conducted on women diagnosed with a fetal anomaly (ies) between February 2009 and December 2011 who were offered testing by microarray analysis (Affymetrix 2.7M SNP) and fluorescent in situ hybridisation (FISH) instead of standard karyotyping. Fetal anomalies were categorised according to organ system involvement. One hundred and eighteen women consented to testing with microarray. Eleven of one hundred eighteen (9.3%) cases had aneuploidy detected by FISH. Of the remaining 107, 23 (21.5%) had an abnormality detected on microarray, only three of which would have been detected using the combination of six-probe FISH and banded karyotype. The maximum expected yield for six-probe FISH and karyotype was thus 14/118 (11.8%), compared to 34/118 (28.8%), P microarray, 10 (43%) were pathogenic, six (26%) were long continuous stretches of homozygosity and seven (30%) were of uncertain significance. The maximum yield was in cases with cardiovascular (100%); multiple (40%); central nervous system (CNS) (25%) and skeletal (9%) abnormalities. This study has confirmed the feasibility of translation of microarray into clinical practice. 11.8% (14/118) of the cases would have a genetic basis of an abnormality with a FISH and banded karyotype. This figure is approximately tripled to 28.8% (34/118) if we offer FISH and microarray. High yield for imbalances are multiple, cardiovascular, CNS and skeletal abnormalities. © 2014 The Royal Australian and New Zealand College of Obstetricians and Gynaecologists.

  7. 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.

  8. Studies of spatial and temporal disorder in macroscopic systems. Final report, April 1, 1993--May 31, 1998

    Energy Technology Data Exchange (ETDEWEB)

    Howes, F.A.; Stein, D.L.

    1998-06-01

    This document constitutes the final report of research conducted under the DOE grant {open_quotes}Studies of Spatial and Temporal Disorder in Macroscopic Systems{close_quotes}. There are three sections to this report, each describing research in a different general area, and a bibliography consisting of published journal articles reporting that research. The three sections are: the weak-noise characteristic boundary exit problem; spin glasses and other systems with quenched disorder; and dynamical problems arising from protein biophysics.

  9. Disrupted Structural and Functional Networks and Their Correlation with Alertness in Right Temporal Lobe Epilepsy: A Graph Theory Study

    Directory of Open Access Journals (Sweden)

    Wenyu Jiang

    2017-05-01

    Full Text Available Previous studies have shown that temporal lobe epilepsy (TLE involves abnormal structural or functional connectivity in specific brain areas. However, limited comprehensive studies have been conducted on TLE associated changes in the topological organization of structural and functional networks. Additionally, epilepsy is associated with impairment in alertness, a fundamental component of attention. In this study, structural networks were constructed using diffusion tensor imaging tractography, and functional networks were obtained from resting-state functional MRI temporal series correlations in 20 right temporal lobe epilepsy (rTLE patients and 19 healthy controls. Global network properties were computed by graph theoretical analysis, and correlations were assessed between global network properties and alertness. The results from these analyses showed that rTLE patients exhibit abnormal small-world attributes in structural and functional networks. Structural networks shifted toward more regular attributes, but functional networks trended toward more random attributes. After controlling for the influence of the disease duration, negative correlations were found between alertness, small-worldness, and the cluster coefficient. However, alertness did not correlate with either the characteristic path length or global efficiency in rTLE patients. Our findings show that disruptions of the topological construction of brain structural and functional networks as well as small-world property bias are associated with deficits in alertness in rTLE patients. These data suggest that reorganization of brain networks develops as a mechanism to compensate for altered structural and functional brain function during disease progression.

  10. Analyzing microarray data using quantitative association rules.

    Science.gov (United States)

    Georgii, Elisabeth; Richter, Lothar; Rückert, Ulrich; Kramer, Stefan

    2005-09-01

    We tackle the problem of finding regularities in microarray data. Various data mining tools, such as clustering, classification, Bayesian networks and association rules, have been applied so far to gain insight into gene-expression data. Association rule mining techniques used so far work on discretizations of the data and cannot account for cumulative effects. In this paper, we investigate the use of quantitative association rules that can operate directly on numeric data and represent cumulative effects of variables. Technically speaking, this type of quantitative association rules based on half-spaces can find non-axis-parallel regularities. We performed a variety of experiments testing the utility of quantitative association rules for microarray data. First of all, the results should be statistically significant and robust against fluctuations in the data. Next, the approach should be scalable in the number of variables, which is important for such high-dimensional data. Finally, the rules should make sense biologically and be sufficiently different from rules found in regular association rule mining working with discretizations. In all of these dimensions, the proposed approach performed satisfactorily. Therefore, quantitative association rules based on half-spaces should be considered as a tool for the analysis of microarray gene-expression data. The code is available from the authors on request.

  11. A New Distribution Family for Microarray Data

    Directory of Open Access Journals (Sweden)

    Diana Mabel Kelmansky

    2017-02-01

    Full Text Available The traditional approach with microarray data has been to apply transformations that approximately normalize them, with the drawback of losing the original scale. The alternative stand point taken here is to search for models that fit the data, characterized by the presence of negative values, preserving their scale; one advantage of this strategy is that it facilitates a direct interpretation of the results. A new family of distributions named gpower-normal indexed by p∈R is introduced and it is proven that these variables become normal or truncated normal when a suitable gpower transformation is applied. Expressions are given for moments and quantiles, in terms of the truncated normal density. This new family can be used to model asymmetric data that include non-positive values, as required for microarray analysis. Moreover, it has been proven that the gpower-normal family is a special case of pseudo-dispersion models, inheriting all the good properties of these models, such as asymptotic normality for small variances. A combined maximum likelihood method is proposed to estimate the model parameters, and it is applied to microarray and contamination data. Rcodes are available from the authors upon request.

  12. 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.

  13. Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction.

    Science.gov (United States)

    Behzadi, Payam; Najafi, Ali; Behzadi, Elham; Ranjbar, Reza

    2016-01-01

    Urinary tract infections are predominant diseases which may be caused by different pathogenic microorganisms, particularly Escherichia coli (E.coli). DNA microarray technology is an accurate, rapid, sensitive, and specific diagnostic tool which may lead to definite diagnosis and treatment of several infectious diseases. DNA microarray is a multi-process method in which probe designing plays an important. Therefore, the authors of the present study have tried to design a range of effective and proper long oligo microarray probes for detection and identification of different strains of pathogenic E.coli and in particular, uropathogenic E.coli (UPEC). E.coli O26 H11 11368 uid41021 was selected as the standard strain for probe designing. This strain encompasses the largest nucleotide sequence and the most number of genes among other pathogenic strains of E.coli. For performing this in silico survey, NCBI database, GReview Server, PanSeq Server, Oligoanalyzer tool, and AlleleID 7.7 were used to design accurate, appropriate, effective, and flexible long oligo microarray probes. Moreover, the genome of E.coli and its closely related microorganisms were compared. In this study, 15 long oligo microarray probes were designed for detecting and identifying different strains of E.coli such as UPEC. These probes possessed the best physico-chemical characteristics. The functional and structural properties of the designed probes were recognized by practical tools and softwares. The use of reliable advanced technologies and methodologies for probe designing guarentees the high quality of microarray probes and makes DNA microarray technology more flexible and an effective diagnostic technique.

  14. Identifying Cancer Biomarkers From Microarray Data Using Feature Selection and Semisupervised Learning.

    Science.gov (United States)

    Chakraborty, Debasis; Maulik, Ujjwal

    2014-01-01

    Microarrays have now gone from obscurity to being almost ubiquitous in biological research. At the same time, the statistical methodology for microarray analysis has progressed from simple visual assessments of results to novel algorithms for analyzing changes in expression profiles. In a micro-RNA (miRNA) or gene-expression profiling experiment, the expression levels of thousands of genes/miRNAs are simultaneously monitored to study the effects of certain treatments, diseases, and developmental stages on their expressions. Microarray-based gene expression profiling can be used to identify genes, whose expressions are changed in response to pathogens or other organisms by comparing gene expression in infected to that in uninfected cells or tissues. Recent studies have revealed that patterns of altered microarray expression profiles in cancer can serve as molecular biomarkers for tumor diagnosis, prognosis of disease-specific outcomes, and prediction of therapeutic responses. Microarray data sets containing expression profiles of a number of miRNAs or genes are used to identify biomarkers, which have dysregulation in normal and malignant tissues. However, small sample size remains a bottleneck to design successful classification methods. On the other hand, adequate number of microarray data that do not have clinical knowledge can be employed as additional source of information. In this paper, a combination of kernelized fuzzy rough set (KFRS) and semisupervised support vector machine (S(3)VM) is proposed for predicting cancer biomarkers from one miRNA and three gene expression data sets. Biomarkers are discovered employing three feature selection methods, including KFRS. The effectiveness of the proposed KFRS and S(3)VM combination on the microarray data sets is demonstrated, and the cancer biomarkers identified from miRNA data are reported. Furthermore, biological significance tests are conducted for miRNA cancer biomarkers.

  15. THEME: a web tool for loop-design microarray data analysis.

    Science.gov (United States)

    Chen, Chaang-Ray; Shu, Wun-Yi; Tsai, Min-Lung; Cheng, Wei-Chung; Hsu, Ian C

    2012-02-01

    A number of recent studies have shown that loop-design is more efficient than reference control design. Data analysis for loop-design microarray experiments is commonly undertaken using linear models and statistical tests. These techniques require specialized knowledge in statistical programming. However, limited loop-design web-based tools are available. We have developed the THEME (Tsing Hua Engine of Microarray Experiment) that exploits all necessary data analysis tools for loop-design microarray studies. THEME allows users to construct linear models and to apply multiple user-defined statistical tests of hypotheses for detection of DEG (differentially expressed genes). Users can modify entries of design matrix for experimental design as well as that of contrast matrix for statistical tests of hypotheses. The output of multiple user-defined statistical tests of hypotheses, DEG lists, can be cross-validated. The web platform provides data assessment and visualization tools that significantly assist users when evaluating the performance of microarray experimental procedures. THEME is also a MIAME (Minimal Information About a Microarray Experiment) compliant system, which enables users to export formatted files for GEO (Gene Expression Omnibus) submission. THEME offers comprehensive web services to biologists for data analysis of loop-design microarray experiments. This web-based resource is especially useful for core facility service as well as collaboration projects when researchers are not at the same site. Data analysis procedures, starting from uploading raw data files to retrieving DEG lists, can be flexibly operated with natural workflows. These features make THEME a reliable and powerful on-line system for data analysis of loop-design microarrays. The THEME server is available at http://metadb.bmes.nthu.edu.tw/theme/. Copyright © 2011 Elsevier Ltd. All rights reserved.

  16. MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs.

    Science.gov (United States)

    Sacan, Ahmet; Ferhatosmanoglu, Nilgun; Ferhatosmanoglu, Hakan

    2009-09-22

    Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments that can help minimize the errors in the resulting inferences has recently received increasing attention. However, a general and scalable search tool and a corresponding database of optimal designs were still missing. An efficient and scalable search method for finding near-optimal dual-channel microarray designs, based on a greedy hill-climbing optimization strategy, has been developed. It is empirically shown that this method can successfully and efficiently find near-optimal designs. Additionally, an improved interwoven loop design construction algorithm has been developed to provide an easily computable general class of near-optimal designs. Finally, in order to make the best results readily available to biologists, a continuously evolving catalog of near-optimal designs is provided. A new search algorithm and database for near-optimal microarray designs have been developed. The search tool and the database are accessible via the World Wide Web at http://db.cse.ohio-state.edu/MicroarrayDesigner. Source code and binary distributions are available for academic use upon request.

  17. MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs

    Directory of Open Access Journals (Sweden)

    Ferhatosmanoglu Nilgun

    2009-09-01

    Full Text Available Abstract Background Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments that can help minimize the errors in the resulting inferences has recently received increasing attention. However, a general and scalable search tool and a corresponding database of optimal designs were still missing. Description An efficient and scalable search method for finding near-optimal dual-channel microarray designs, based on a greedy hill-climbing optimization strategy, has been developed. It is empirically shown that this method can successfully and efficiently find near-optimal designs. Additionally, an improved interwoven loop design construction algorithm has been developed to provide an easily computable general class of near-optimal designs. Finally, in order to make the best results readily available to biologists, a continuously evolving catalog of near-optimal designs is provided. Conclusion A new search algorithm and database for near-optimal microarray designs have been developed. The search tool and the database are accessible via the World Wide Web at http://db.cse.ohio-state.edu/MicroarrayDesigner. Source code and binary distributions are available for academic use upon request.

  18. 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.

  19. 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.

  20. Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach.

    Science.gov (United States)

    Pan, Yi-Shin; Lee, Yun-Shien; Lee, Yung-Lin; Lee, Wei-Chen; Hsieh, Sen-Yung

    2006-05-31

    The main limitation in performing genome-wide gene-expression profiling is the assay of low-expression genes. Approaches with high throughput and high sensitivity for assaying low-expression transcripts are urgently needed for functional genomic studies. Combination of the suppressive subtractive hybridization (SSH) and cDNA microarray techniques using the subtracted cDNA clones as probes printed on chips has greatly improved the efficiency for fishing out the differentially expressed clones and has been used before. However, it remains tedious and inefficient sequencing works for identifying genes including the great number of redundancy in the subtracted amplicons, and sacrifices the original advantages of high sensitivity of SSH in profiling low-expression transcriptomes. We modified the previous combination of SSH and microarray methods by directly using the subtracted amplicons as targets to hybridize the pre-made cDNA microarrays (named as "SSH/microarray"). mRNA prepared from three pairs of hepatoma and non-hepatoma liver tissues was subjected to the SSH/microarray assays, as well as directly to regular cDNA microarray assays for comparison. As compared to the original SSH and microarray combination assays, the modified SSH/microarray assays allowed for much easier inspection of the subtraction efficiency and identification of genes in the subtracted amplicons without tedious and inefficient sequencing work. On the other hand, 5015 of the 9376 genes originally filtered out by the regular cDNA microarray assays because of low expression became analyzable by the SSH/microarray assays. Moreover, the SSH/microarray assays detected about ten times more (701 vs. 69) HCC differentially expressed genes (at least a two-fold difference and P SSH/microarray approaches resulted in identifying many differentially expressed genes implicated in the regulation of cell cycle, cell death, signal transduction and cell morphogenesis, suggesting the involvement of multi

  1. STUDI ANALISIS VARIASI TEMPORAL KANDUNGAN UAP AIR MENGGUNAKAN DATA PENGAMATAN GPS

    Directory of Open Access Journals (Sweden)

    Fikri Bamahry

    2015-02-01

    Full Text Available Pengamatan kandungan uap air yang teliti di atmosfer masih menjadi pekerjaan yang belum terselesaikan oleh para peneliti atmosfer. Dikarenakan pergerakan kandungan uap air yang cepat baik temporal maupun spasialnya di atmosfer, pengamatan kandungan uap air yang akurat sangat sulit dilakukan. Global Positioning System atau yang lebih dikenal dengan sebutan GPS telah menawarkan metode baru untuk kandungan uap air yang ada di atmosfer secara akurat. Dengan memanfaatan hitungan estimasi perlambatan dan pembelokan sinyal GPS di lapisan troposfer serta dilengkapi dengan data pengukuran meteorologi permukaan, kita dapat mengetahui berapa kandungan uap air yang ada di atmosfer dengan akurat. Pada penelitian ini digunakan 8 (delapan stasiun GPS CORS Badan Informasi Geospasial (BIG untuk mengestimasi kandungan uap air di sekitar wilayah lokasi penelitian, diantara lain: Tuban, Lamongan, Mojokerto, Surabaya, Nganjuk, Malang, Pasuruan, dan Sampang. Zenith Tropospheric Delay (ZTD yang diestimasi dari pengamatan GPS ini diekstraksi menjadi kandungan uap air menggunkan data meteorologi permukaan. Data kandungan uap air yang didapatkan dari pengamatan GPS di Surabaya memiliki korelasi yang baik dengan hasil pengamatan meteorologi konvensial, yaitu balon radiosonde. Dengan nilai bias 0,761 mm dan korelasi 98,3%, perbandingan data tersebut dapat dikatakan baik. Dari hasil plotting grafik variasi temporal, didapatkan informasi bahwa rerata kandungan uap air bulanan pada musim kemarau (Mei – Oktober 2012 berada antara 20 – 45 mm, sedangkan pada musim hujan (November-April 2012 berada antara 45 – 65 mm. Baik dari grafik variasi temporal kandungan uap air dan hasil penggambaran variasi spasial didapatkan informasi bahwa bulan terkering pada tahun 2012 adalah bulan Agustus, dan bulan terbasah pada tahun 2012 adalah bulan Januari. Hal ini dimungkinkan karena pengaruh siklus Monsoon Asia-Australia yang mempengaruhi cuaca dan iklim di Indonesia.

  2. Spatio-temporal characteristics of Agulhas leakage: a model inter-comparison study

    Science.gov (United States)

    Holton, L.; Deshayes, J.; Backeberg, B. C.; Loveday, B. R.; Hermes, J. C.; Reason, C. J. C.

    2017-04-01

    Investigating the variability of Agulhas leakage, the volume transport of water from the Indian Ocean to the South Atlantic Ocean, is highly relevant due to its potential contribution to the Atlantic Meridional Overturning Circulation as well as the global circulation of heat and salt and hence global climate. Quantifying Agulhas leakage is challenging due to the non-linear nature of this process; current observations are insufficient to estimate its variability and ocean models all have biases in this region, even at high resolution . An Eulerian threshold integration method is developed to examine the mechanisms of Agulhas leakage variability in six ocean model simulations of varying resolution. This intercomparison, based on the circulation and thermohaline structure at the Good Hope line, a transect to the south west of the southern tip of Africa , is used to identify features that are robust regardless of the model used and takes into account the thermohaline biases of each model. When determined by a passive tracer method, 60 % of the magnitude of Agulhas leakage is captured and more than 80 % of its temporal fluctuations, suggesting that the method is appropriate for investigating the variability of Agulhas leakage. In all simulations but one, the major driver of variability is associated with mesoscale features passing through the section. High resolution ({<} 1/10°) hindcast models agree on the temporal (2-4 cycles per year) and spatial (300-500 km) scales of these features corresponding to observed Agulhas Rings. Coarser resolution models ({<} 1/4°) reproduce similar time scale of variability of Agulhas leakage in spite of their difficulties in representing the Agulhas rings properties. A coarser resolution climate model (2°) does not resolve the spatio-temporal mechanism of variability of Agulhas leakage. Hence it is expected to underestimate the contribution of Agulhas Current System to climate variability.

  3. Identification of Listeria Species by Microarray-Based Assay

    OpenAIRE

    Volokhov, Dmitriy; Rasooly, Avraham; Chumakov, Konstantin; Chizhikov, Vladimir

    2002-01-01

    We have developed a rapid microarray-based assay for the reliable detection and discrimination of six species of the Listeria genus: L. monocytogenes, L. ivanovii, L. innocua, L. welshimeri, L. seeligeri, and L. grayi. The approach used in this study involves one-tube multiplex PCR amplification of six target bacterial virulence factor genes (iap, hly, inlB, plcA, plcB, and clpE), synthesis of fluorescently labeled single-stranded DNA, and hybridization to the multiple individual oligonucleot...

  4. 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.

  5. The effect of delayed auditory feedback on activity in the temporal lobe while speaking: a positron emission tomography study.

    Science.gov (United States)

    Takaso, Hideki; Eisner, Frank; Wise, Richard Js; Scott, Sophie K

    2010-04-01

    Delayed auditory feedback is a technique that can improve fluency in stutterers, while disrupting fluency in many nonstuttering individuals. The aim of this study was to determine the neural basis for the detection of and compensation for such a delay, and the effects of increases in the delay duration. Positron emission tomography was used to image regional cerebral blood flow changes, an index of neural activity, and to assess the influence of increasing amounts of delay. Delayed auditory feedback led to increased activation in the bilateral superior temporal lobes, extending into posterior-medial auditory areas. Similar peaks in the temporal lobe were sensitive to increases in the amount of delay. A single peak in the temporal parietal junction responded to the amount of delay but not to the presence of a delay (relative to no delay). This study permitted distinctions to be made between the neural response to hearing one's voice at a delay and the neural activity that correlates with this delay. Notably, all the peaks showed some influence of the amount of delay. This result confirms a role for the posterior, sensorimotor "how" system in the production of speech under conditions of delayed auditory feedback.

  6. 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.)

  7. Study of Spatio-Temporal Immunofluorescence on Bead Patterns in a Microfluidic Channel

    Science.gov (United States)

    Sivagnanam, Venkataragavalu; Yang, Hui; Gijs, Martin A. M.

    2010-12-01

    We performed a direct immunoassay inside a microfluidic channel on patterned streptavidin-coated beads, which captured fluorescently-labeled biotin target molecules from a continuous flow. We arranged the beads in a dot array at the bottom of the channel and demonstrated their position- and flow rate-dependent fluorescence. As the target analyte gets gradually depleted from the flow when passing downstream the channel, the highest fluorescence intensity was observed on the most upstream positioned dot patterns. We propose a simple analytical convection model to explain this spatio-temporal fluorescence.

  8. DNA Microarray for Detection of Gastrointestinal Viruses

    Science.gov (United States)

    Martínez, Miguel A.; Soto-del Río, María de los Dolores; Gutiérrez, Rosa María; Chiu, Charles Y.; Greninger, Alexander L.; Contreras, Juan Francisco; López, Susana; Arias, Carlos F.

    2014-01-01

    Gastroenteritis is a clinical illness of humans and other animals that is characterized by vomiting and diarrhea and caused by a variety of pathogens, including viruses. An increasing number of viral species have been associated with gastroenteritis or have been found in stool samples as new molecular tools have been developed. In this work, a DNA microarray capable in theory of parallel detection of more than 100 viral species was developed and tested. Initial validation was done with 10 different virus species, and an additional 5 species were validated using clinical samples. Detection limits of 1 × 103 virus particles of Human adenovirus C (HAdV), Human astrovirus (HAstV), and group A Rotavirus (RV-A) were established. Furthermore, when exogenous RNA was added, the limit for RV-A detection decreased by one log. In a small group of clinical samples from children with gastroenteritis (n = 76), the microarray detected at least one viral species in 92% of the samples. Single infection was identified in 63 samples (83%), and coinfection with more than one virus was identified in 7 samples (9%). The most abundant virus species were RV-A (58%), followed by Anellovirus (15.8%), HAstV (6.6%), HAdV (5.3%), Norwalk virus (6.6%), Human enterovirus (HEV) (9.2%), Human parechovirus (1.3%), Sapporo virus (1.3%), and Human bocavirus (1.3%). To further test the specificity and sensitivity of the microarray, the results were verified by reverse transcription-PCR (RT-PCR) detection of 5 gastrointestinal viruses. The RT-PCR assay detected a virus in 59 samples (78%). The microarray showed good performance for detection of RV-A, HAstV, and calicivirus, while the sensitivity for HAdV and HEV was low. Furthermore, some discrepancies in detection of mixed infections were observed and were addressed by reverse transcription-quantitative PCR (RT-qPCR) of the viruses involved. It was observed that differences in the amount of genetic material favored the detection of the most abundant

  9. Human conchal cartilage and temporal fascia: an evidence-based roadmap from rhinoplasty to an in vivo study and beyond.

    Science.gov (United States)

    Cimpean, Anca Maria; Crăiniceanu, Zorin; Mihailovici, Dorina; Bratu, Tiberiu; Raica, Marius

    2014-01-01

    Conchal cartilage or cartilage/ temporal fascia composite grafting (DC-F) used for rhinoplasty is applied by plastic surgeons for reconstructive purposes. Previous studies on experimental models such as mice or rabbits have elucidated on the late events following grafting, with tissue specimens being harvested two months after implantation. Early microscopic and molecular events following DC-F grafting are completely unknown. We designed a chick embryo chorioallantoic membrane model for human grafts study, regarding the dynamic observation of graft survival and its mutual interrelation with the chick embryo chorioallantoic membrane microenvironment. The DC-F graft preserved its cartilage component in a normal state compared to cartilage graft-only because of protective factors provided by temporal fascia. Its strong adherence to the cartilage, lack of angiogenic factors and high content of collagen IV-derived fragments with anti-angiogenic effects make the temporal fascia a good protective tissue to prevent implanted cartilage degeneration. The cartilage graft produced high inflammation, stromal fibrosis and activated angiogenic cascade through VEGF-mediated pathways followed by cartilage degeneration. Also, high content of podoplanin from conchal cartilage chondrocytes exerted a major role in inflammation accompanying cartilage graft. The presently employed experimental model allowed us to characterize the early histological and molecular events triggered by temporal fascia, cartilage or composite graft DC-F implanted on chick embryo chorioallantoic membrane. Our microscopic and molecular observations may help explain some post-surgical complications generated after using cartilage alone as biomaterial for nasal augmentation, supporting the use of DC-F composite graft, with the aim to reduce unwanted post-surgical events. Copyright © 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  10. SNP Microarray in FISH Negative Clinically Suspected 22q11.2 Microdeletion Syndrome

    Science.gov (United States)

    Jain, Manish; Kalsi, Amanpreet Kaur

    2016-01-01

    The present study evaluated the role of SNP microarray in 101 cases of clinically suspected FISH negative (noninformative/normal) 22q11.2 microdeletion syndrome. SNP microarray was carried out using 300 K HumanCytoSNP-12 BeadChip array or CytoScan 750 K array. SNP microarray identified 8 cases of 22q11.2 microdeletions and/or microduplications in addition to cases of chromosomal abnormalities and other pathogenic/likely pathogenic CNVs. Clinically suspected specific deletions (22q11.2) were detectable in approximately 8% of cases by SNP microarray, mostly from FISH noninformative cases. This study also identified several LOH/AOH loci with known and well-defined UPD (uniparental disomy) disorders. In conclusion, this study suggests more strict clinical criteria for FISH analysis. However, if clinical criteria are few or doubtful, in particular newborn/neonate in intensive care, SNP microarray should be the first screening test to be ordered. FISH is ideal test for detecting mosaicism, screening family members, and prenatal diagnosis in proven families. PMID:27051557

  11. SNP Microarray in FISH Negative Clinically Suspected 22q11.2 Microdeletion Syndrome.

    Science.gov (United States)

    Halder, Ashutosh; Jain, Manish; Kalsi, Amanpreet Kaur

    2016-01-01

    The present study evaluated the role of SNP microarray in 101 cases of clinically suspected FISH negative (noninformative/normal) 22q11.2 microdeletion syndrome. SNP microarray was carried out using 300 K HumanCytoSNP-12 BeadChip array or CytoScan 750 K array. SNP microarray identified 8 cases of 22q11.2 microdeletions and/or microduplications in addition to cases of chromosomal abnormalities and other pathogenic/likely pathogenic CNVs. Clinically suspected specific deletions (22q11.2) were detectable in approximately 8% of cases by SNP microarray, mostly from FISH noninformative cases. This study also identified several LOH/AOH loci with known and well-defined UPD (uniparental disomy) disorders. In conclusion, this study suggests more strict clinical criteria for FISH analysis. However, if clinical criteria are few or doubtful, in particular newborn/neonate in intensive care, SNP microarray should be the first screening test to be ordered. FISH is ideal test for detecting mosaicism, screening family members, and prenatal diagnosis in proven families.

  12. SNP Microarray in FISH Negative Clinically Suspected 22q11.2 Microdeletion Syndrome

    Directory of Open Access Journals (Sweden)

    Ashutosh Halder

    2016-01-01

    Full Text Available The present study evaluated the role of SNP microarray in 101 cases of clinically suspected FISH negative (noninformative/normal 22q11.2 microdeletion syndrome. SNP microarray was carried out using 300 K HumanCytoSNP-12 BeadChip array or CytoScan 750 K array. SNP microarray identified 8 cases of 22q11.2 microdeletions and/or microduplications in addition to cases of chromosomal abnormalities and other pathogenic/likely pathogenic CNVs. Clinically suspected specific deletions (22q11.2 were detectable in approximately 8% of cases by SNP microarray, mostly from FISH noninformative cases. This study also identified several LOH/AOH loci with known and well-defined UPD (uniparental disomy disorders. In conclusion, this study suggests more strict clinical criteria for FISH analysis. However, if clinical criteria are few or doubtful, in particular newborn/neonate in intensive care, SNP microarray should be the first screening test to be ordered. FISH is ideal test for detecting mosaicism, screening family members, and prenatal diagnosis in proven families.

  13. 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.

  14. Phenotype microarray profiling of the antibacterial activity of red cabbage

    Directory of Open Access Journals (Sweden)

    Hafidh RR

    2012-06-01

    Full Text Available Background: Functional food can be a potent source of wide array of biocomonents with antimicrobial activity. We investigated the antibacterial activity of red cabbage (RC extract on Gram negative and positive ATCC strains. Most intersting, we, for the first time, explored and analysed the complete phenotypic profile of RC-treated bacteria using Omnilog Phenotype Microarray. Results: This study revealed that the phenotype microarray (PM screen was a valuable tool in the search for compounds and their antibacterial mechanisms that can inhibit bacterial growth by affecting certain metabolic pathways. It was shown that RC exerted remarkable antibacterial effect on S. aureus and E. coli bacteria, and PM showed a wide range phenotypic profile of the exerted RC antibacterial activity. RC targeted the peptide, carbon, nutriontional assembly, and sulfur metbolic pathways altogether. The peptidoglycan synthesis pathway was inferred to be targeted by RC extract at a metabolic point different from other available cell wall-targeting drugs; these could be hot targets for the discovery of new therapy for many problematic microbes.Conclusions: Taken together, the phenotype microarray for functional food and medicinal plants can be a very useful tool for profiling their antimicrobial activity. Moreover, extracts of functional food can exert antibacterial activity by hitting a wide range of metabolic pathways, at the same time leading to very difficult condition for bacteria to rapidly develop resistance. Therefore, using functional foods or medicinal plants as such, or as extracts, can be superior on mono-targeting antibiotics if the optimal concentrations and conditions of these functional foods were sought.

  15. 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

    2012-11-01

    Full Text Available http://dx.doi.org/10.5007/2175-7925.2013v26n1p79 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 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.

  16. 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.

  17. 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.

  18. Decrease in temporal gyrus gray matter volume in first-episode, early onset schizophrenia: an MRI study.

    Directory of Open Access Journals (Sweden)

    Jinsong Tang

    Full Text Available BACKGROUND: Loss of gray matter has been previously found in early-onset schizophrenic patients. However, there are no consistent findings between studies due to different methods used to measure grey matter volume/density and influences of confounding factors. METHODS: The volume of gray matter (GM was measured in 29 first episode early-onset schizophrenia (EOS and 34 well-matched healthy controls by using voxel-based morphometry (VBM. Psychotic symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS. The correlations between the GM volume and PANSS scores, age of psychosis onset, duration of psychosis, and chlorpromazine (CPZ equivalent value were investigated. RESULTS: Relative to healthy subjects, the patients with first episode EOS showed significantly lower GM volume in the left middle and superior temporal gyrus. The loss of GM volume negatively correlated with PANSS-positive symptoms (p = 0.002, but not with PANSS-negative symptoms, PANSS-general psychopathology, and PANSS-total score. No significant correlation was found between GM volume and age of psychosis onset, duration of psychosis, and CPZ equivalent value. CONCLUSION: Patients with first episode EOS have evidence of reduced GM in the left middle and superior temporal gyrus. Structural abnormalities in the left middle and superior temporal gyrus may contribute to the pathophysiology of schizophrenia.

  19. 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.

  20. 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.

  1. 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

  2. MIGS-GPU: Microarray Image Gridding and Segmentation on the GPU.

    Science.gov (United States)

    Katsigiannis, Stamos; Zacharia, Eleni; Maroulis, Dimitris

    2017-05-01

    Complementary DNA (cDNA) microarray is a powerful tool for simultaneously studying the expression level of thousands of genes. Nevertheless, the analysis of microarray images remains an arduous and challenging task due to the poor quality of the images that often suffer from noise, artifacts, and uneven background. In this study, the MIGS-GPU [Microarray Image Gridding and Segmentation on Graphics Processing Unit (GPU)] software for gridding and segmenting microarray images is presented. MIGS-GPU's computations are performed on the GPU by means of the compute unified device architecture (CUDA) in order to achieve fast performance and increase the utilization of available system resources. Evaluation on both real and synthetic cDNA microarray images showed that MIGS-GPU provides better performance than state-of-the-art alternatives, while the proposed GPU implementation achieves significantly lower computational times compared to the respective CPU approaches. Consequently, MIGS-GPU can be an advantageous and useful tool for biomedical laboratories, offering a user-friendly interface that requires minimum input in order to run.

  3. Merging microarray data, robust feature selection, and predicting prognosis in prostate cancer

    Directory of Open Access Journals (Sweden)

    Kevin R. Coombes

    2006-01-01

    Full Text Available Moti