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Sample records for microarrays normal eye

  1. Searching for biomarkers of developmental toxicity with microarrays: normal eye morphogenesis in rodent embryos

    SciTech Connect

    Nemeth, Kimberly A.; Singh, Amar V.; Knudsen, Thomas B. . E-mail: thomas.knudsen@louisville.edu

    2005-08-07

    Gene expression arrays reveal the potential linkage of altered gene expression with specific adverse effects leading to disease phenotypes. But how closely do microarray data reflect early physiological or pharmacological measures that predict toxic event(s)? To explore this issue, we have undertaken experiments in early mouse embryos exposed to various teratogens during neurulation stages with the aim of correlating large-scale changes in gene expression across the critical period during exposure. This study reports some of the large-scale changes in gene expression that can be detected in the optic rudiment of the developing mouse and rat embryo across the window of development during which the eye is exceedingly sensitive to teratogen-induced micro-/anophthalmia. Microarray analysis was performed on RNA from the headfold or ocular region at the optic vesicle and optic cup stages when the ocular primordium is enriched for Pax-6, a master control gene for eye morphogenesis. Statistical selection of differentially regulated genes and various clustering techniques identified groups of genes in upward or downward trajectories in the normal optic primordium during early eye development in mouse and rat species. We identified 165 genes with significant differential expression during eye development, and a smaller subset of 58 genes that showed a tight correlation between mouse-rat development. Significantly over-represented functional categories included fatty acid metabolism (up-regulated) and glycolysis (down-regulated). From studies such as these that benchmark large-scale gene expression during normal embryonic development, we may be able to identify the panel of biomarkers that best correlate with species differences and the risks for developmental toxicity.

  2. Tonometry of normal eyes in raptors.

    PubMed

    Stiles, J; Buyukmihci, N C; Farver, T B

    1994-04-01

    An applanation tonometer was used to estimate intraocular pressure in normal eyes of several species of raptors. No bird had active injury or illness, though some were nonreleasable to the wild because of previous injury. Mean (+/- SD) intraocular pressure was 20.6 (+/- 3.4) mm of Hg in red-tailed hawks (Buteo jamaicensis, n = 10), 20.8 (+/- 2.3) mm of Hg in Swainson's hawks (Buteo swainsoni, n = 6), 21.5 (+/- 3.0) mm of Hg in golden eagles (Aquila chrysaetos, n = 7), 20.6 (+/- 2.0) mm of Hg in bald eagles (Haliaeetus leucocephalus, n = 3), and 10.8 (+/- 3.6) mm of Hg in great horned owls (Bubo virginianus, n = 6). There was no significant difference in intraocular pressure between hawks and eagles. Mean pressure in great horned owls was significantly (P < 0.01) lower than pressure in hawks or eagles. Reliable intraocular pressure readings could not be obtained in barn owls (Tyto alba). PMID:8017692

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

    EPA Science Inventory

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

  4. Microarrays

    ERIC Educational Resources Information Center

    Plomin, Robert; Schalkwyk, Leonard C.

    2007-01-01

    Microarrays are revolutionizing genetics by making it possible to genotype hundreds of thousands of DNA markers and to assess the expression (RNA transcripts) of all of the genes in the genome. Microarrays are slides the size of a postage stamp that contain millions of DNA sequences to which single-stranded DNA or RNA can hybridize. This…

  5. Better performance through amblyopic than through normal eyes.

    PubMed

    Fahle, M; Bachmann, G

    1996-07-01

    Spatio-temporal interpolation reconstructs the (complete) motion path of objects presented discontinuously, e.g. under stroboscopic illumination or in television. Interpolative vernier stimuli were created by presenting two line segments with a temporal delay instead of a spatial offset. Ten amblyopic patients had to indicate whether the lower segment of the moving target was offset to the left or right relative to the upper segment. For five patients we also measured thresholds for a conventional moving vernier. Five normal subjects were measured with sharply focused and blurred interpolative verniers. At low velocities of interpolative vernier targets, results of amblyopic eyes are inferior to those of normal eyes. However, 9 out of 10 patients perform better using their amblyopic than using their normal eye at high velocities. In control subjects, blurred stimuli yield results similar to those of amblyopic eyes, indicating a similarity between (optical) blur and the mechanisms underlying amblyopia. Thresholds for conventional vernier targets of amblyopic observers, on the other hand, are constant over the whole velocity range for both normal and amblyopic eyes, with a better performance of the normal eye at all velocities. The consequences for models of amblyopia are discussed. PMID:8759433

  6. Microarray-based understanding of normal and malignant plasma cells

    PubMed Central

    De Vos, John; Hose, Dirk; Rème, Thierry; Tarte, Karin; Moreaux, Jérôme; Mahtouk, Karéne; Jourdan, Michel; Goldschmidt, Hartmut; Rossi, Jean-François; Cremer, Friedrich W.; Klein, Bernard

    2006-01-01

    Plasma cells develop from B-lymphocytes following stimulation by antigen and express a genetic program aimed at the synthesis of immunoglobulins. This program includes the induction of genes coding for transcription factors such as PRDM1 and XBP1, cell-surface molecules such as CD138/syndecan-1 and for the unfolded protein response (UPR). We review how the microarray technology has recently contributed to the understanding of the biology of this rare but essential cell population and its transformation into pre-malignant and malignant plasma cells. PMID:16623766

  7. RPE Cell and Sheet Properties in Normal and Diseased Eyes.

    PubMed

    Rashid, Alia; Bhatia, Shagun K; Mazzitello, Karina I; Chrenek, Micah A; Zhang, Qing; Boatright, Jeffrey H; Grossniklaus, Hans E; Jiang, Yi; Nickerson, John M

    2016-01-01

    Previous studies of human retinal pigment epithelium (RPE) morphology found spatial differences in density: a high density of cells in the macula, decreasing peripherally. Because the RPE sheet is not perfectly regular, we anticipate that there will be differences between conditions and when and where damage is most likely to begin. The purpose of this study is to establish relationships among RPE morphometrics in age, cell location, and disease of normal human and AMD eyes that highlight irregularities reflecting damage. Cadaveric eyes from 11 normal and 3 age-related macular degeneration (AMD) human donors ranging from 29 to 82 years of age were used. Borders of RPE cells were identified with phalloidin. RPE segmentation and analysis were conducted with CellProfiler. Exploration of spatial point patterns was conducted using the "spatstat" package of R. In the normal human eye, with increasing age, cell size increased, and cells lost their regular hexagonal shape. Cell density was higher in the macula versus periphery. AMD resulted in greater variability in size and shape of the RPE cell. Spatial point analysis revealed an ordered distribution of cells in normal and high spatial disorder in AMD eyes. Morphometrics of the RPE cell readily discriminate among young vs. old and normal vs. diseased in the human eye. The normal RPE sheet is organized in a regular array of cells, but AMD exhibited strong spatial irregularity. These findings reflect on the robust recovery of the RPE sheet after wounding and the circumstances under which it cannot recover. PMID:26427486

  8. CrossNorm: a novel normalization strategy for microarray data in cancers

    PubMed Central

    Cheng, Lixin; Lo, Leung-Yau; Tang, Nelson L. S.; Wang, Dong; Leung, Kwong-Sak

    2016-01-01

    Normalization is essential to get rid of biases in microarray data for their accurate analysis. Existing normalization methods for microarray gene expression data commonly assume a similar global expression pattern among samples being studied. However, scenarios of global shifts in gene expressions are dominant in cancers, making the assumption invalid. To alleviate the problem, here we propose and develop a novel normalization strategy, Cross Normalization (CrossNorm), for microarray data with unbalanced transcript levels among samples. Conventional procedures, such as RMA and LOESS, arbitrarily flatten the difference between case and control groups leading to biased gene expression estimates. Noticeably, applying these methods under the strategy of CrossNorm, which makes use of the overall statistics of the original signals, the results showed significantly improved robustness and accuracy in estimating transcript level dynamics for a series of publicly available datasets, including titration experiment, simulated data, spike-in data and several real-life microarray datasets across various types of cancers. The results have important implications for the past and the future cancer studies based on microarray samples with non-negligible difference. Moreover, the strategy can also be applied to other sorts of high-throughput data as long as the experiments have global expression variations between conditions. PMID:26732145

  9. Using RNA sample titrations to assess microarray platform performance and normalization techniques.

    PubMed

    Shippy, Richard; Fulmer-Smentek, Stephanie; Jensen, Roderick V; Jones, Wendell D; Wolber, Paul K; Johnson, Charles D; Pine, P Scott; Boysen, Cecilie; Guo, Xu; Chudin, Eugene; Sun, Yongming Andrew; Willey, James C; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Setterquist, Robert A; Wilson, Mike; Lucas, Anne Bergstrom; Novoradovskaya, Natalia; Papallo, Adam; Turpaz, Yaron; Baker, Shawn C; Warrington, Janet A; Shi, Leming; Herman, Damir

    2006-09-01

    We have assessed the utility of RNA titration samples for evaluating microarray platform performance and the impact of different normalization methods on the results obtained. As part of the MicroArray Quality Control project, we investigated the performance of five commercial microarray platforms using two independent RNA samples and two titration mixtures of these samples. Focusing on 12,091 genes common across all platforms, we determined the ability of each platform to detect the correct titration response across the samples. Global deviations from the response predicted by the titration ratios were observed. These differences could be explained by variations in relative amounts of messenger RNA as a fraction of total RNA between the two independent samples. Overall, both the qualitative and quantitative correspondence across platforms was high. In summary, titration samples may be regarded as a valuable tool, not only for assessing microarray platform performance and different analysis methods, but also for determining some underlying biological features of the samples.

  10. Quantitative analysis of p53 expression in human normal and cancer tissue microarray with global normalization method

    PubMed Central

    Idikio, Halliday A

    2011-01-01

    Tissue microarray based immunohistochemical staining and proteomics are important tools to create and validate clinically relevant cancer biomarkers. Immunohistochemical stains using formalin-fixed tissue microarray sections for protein expression are scored manually and semi-quantitatively. Digital image analysis methods remove some of the drawbacks of manual scoring but may need other methods such as normalization to provide across the board utility. In the present study, quantitative proteomics-based global normalization method was used to evaluate its utility in the analysis of p53 protein expression in mixed human normal and cancer tissue microarray. Global normalization used the mean or median of β-actin to calculate ratios of individual core stain intensities, then log transformed the ratios, calculate a mean or median and subtracted the value from the log of ratios. In the absence of global normalization of p53 protein expression, 44% (42 of 95) of tissue cores were positive using the median of intensity values and 40% (38 of 95) using the mean of intensities as cut-off points. With global normalization, p53 positive cores changed to 20% (19 of 95) when using median of intensities and 15.8%(15 of 95) when the mean of intensities were used. In conclusion, the global normalization method helped to define positive p53 staining in the tissue microarray set used. The method used helped to define clear cut-off points and confirmed all negatively stained tissue cores. Such normalization methods should help to better define clinically useful biomarkers. PMID:21738821

  11. Effect of data normalization on fuzzy clustering of DNA microarray data

    PubMed Central

    Kim, Seo Young; Lee, Jae Won; Bae, Jong Sung

    2006-01-01

    Background Microarray technology has made it possible to simultaneously measure the expression levels of large numbers of genes in a short time. Gene expression data is information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. Clustering is an important tool for finding groups of genes with similar expression patterns in microarray data analysis. However, hard clustering methods, which assign each gene exactly to one cluster, are poorly suited to the analysis of microarray datasets because in such datasets the clusters of genes frequently overlap. Results In this study we applied the fuzzy partitional clustering method known as Fuzzy C-Means (FCM) to overcome the limitations of hard clustering. To identify the effect of data normalization, we used three normalization methods, the two common scale and location transformations and Lowess normalization methods, to normalize three microarray datasets and three simulated datasets. First we determined the optimal parameters for FCM clustering. We found that the optimal fuzzification parameter in the FCM analysis of a microarray dataset depended on the normalization method applied to the dataset during preprocessing. We additionally evaluated the effect of normalization of noisy datasets on the results obtained when hard clustering or FCM clustering was applied to those datasets. The effects of normalization were evaluated using both simulated datasets and microarray datasets. A comparative analysis showed that the clustering results depended on the normalization method used and the noisiness of the data. In particular, the selection of the fuzzification parameter value for the FCM method was sensitive to the normalization method used for datasets with large variations across samples. Conclusion Lowess normalization is more robust for clustering of genes from general microarray data than the two common scale and location adjustment methods

  12. A New Modified Histogram Matching Normalization for Time Series Microarray Analysis

    PubMed Central

    Astola, Laura; Molenaar, Jaap

    2014-01-01

    Microarray data is often utilized in inferring regulatory networks. Quantile normalization (QN) is a popular method to reduce array-to-array variation. We show that in the context of time series measurements QN may not be the best choice for this task, especially not if the inference is based on continuous time ODE model. We propose an alternative normalization method that is better suited for network inference from time series data.

  13. SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis.

    PubMed

    Colantuoni, Carlo; Henry, George; Zeger, Scott; Pevsner, Jonathan

    2002-11-01

    SNOMAD is a collection of algorithms for the normalization and standardization of gene expression datasets derived from diverse biological and technological sources. In addition to conventional transformations and visualization tools, SNOMAD includes two non-linear transformations which correct for bias and variance which are non-uniformly distributed across the range of microarray element signal intensities: (1). Local mean normalization; and (2). Local variance correction (Z-score generation using a locally calculated standard deviation).

  14. Assessment of Corneal Epithelial Thickness in Asymmetric Keratoconic Eyes and Normal Eyes Using Fourier Domain Optical Coherence Tomography

    PubMed Central

    Cadarso, L.; Esteves, F.; Salgado-Borges, J.; Lopez, M.; Cadarso, C.

    2016-01-01

    Purpose. To compare the characteristics of asymmetric keratoconic eyes and normal eyes by Fourier domain optical coherence tomography (OCT) corneal mapping. Methods. Retrospective corneal and epithelial thickness OCT data for 74 patients were compared in three groups of eyes: keratoconic (n = 22) and normal fellow eyes (n = 22) in patients with asymmetric keratoconus and normal eyes (n = 104) in healthy subjects. Areas under the curve (AUC) of receiver operator characteristic (ROC) curves for each variable were compared across groups to indicate their discrimination capacity. Results. Three variables were found to differ significantly between fellow eyes and normal eyes (all p < 0.05): minimum corneal thickness, thinnest corneal point, and central corneal thickness. These variables combined showed a high discrimination power to differentiate fellow eyes from normal eyes indicated by an AUC of 0.840 (95% CI: 0.762–0.918). Conclusions. Our findings indicate that topographically normal fellow eyes in patients with very asymmetric keratoconus differ from the eyes of healthy individuals in terms of their corneal epithelial and pachymetry maps. This type of information could be useful for an early diagnosis of keratoconus in topographically normal eyes. PMID:27379181

  15. Assessment of Corneal Epithelial Thickness in Asymmetric Keratoconic Eyes and Normal Eyes Using Fourier Domain Optical Coherence Tomography.

    PubMed

    Catalan, S; Cadarso, L; Esteves, F; Salgado-Borges, J; Lopez, M; Cadarso, C

    2016-01-01

    Purpose. To compare the characteristics of asymmetric keratoconic eyes and normal eyes by Fourier domain optical coherence tomography (OCT) corneal mapping. Methods. Retrospective corneal and epithelial thickness OCT data for 74 patients were compared in three groups of eyes: keratoconic (n = 22) and normal fellow eyes (n = 22) in patients with asymmetric keratoconus and normal eyes (n = 104) in healthy subjects. Areas under the curve (AUC) of receiver operator characteristic (ROC) curves for each variable were compared across groups to indicate their discrimination capacity. Results. Three variables were found to differ significantly between fellow eyes and normal eyes (all p < 0.05): minimum corneal thickness, thinnest corneal point, and central corneal thickness. These variables combined showed a high discrimination power to differentiate fellow eyes from normal eyes indicated by an AUC of 0.840 (95% CI: 0.762-0.918). Conclusions. Our findings indicate that topographically normal fellow eyes in patients with very asymmetric keratoconus differ from the eyes of healthy individuals in terms of their corneal epithelial and pachymetry maps. This type of information could be useful for an early diagnosis of keratoconus in topographically normal eyes.

  16. Assessment of Corneal Epithelial Thickness in Asymmetric Keratoconic Eyes and Normal Eyes Using Fourier Domain Optical Coherence Tomography.

    PubMed

    Catalan, S; Cadarso, L; Esteves, F; Salgado-Borges, J; Lopez, M; Cadarso, C

    2016-01-01

    Purpose. To compare the characteristics of asymmetric keratoconic eyes and normal eyes by Fourier domain optical coherence tomography (OCT) corneal mapping. Methods. Retrospective corneal and epithelial thickness OCT data for 74 patients were compared in three groups of eyes: keratoconic (n = 22) and normal fellow eyes (n = 22) in patients with asymmetric keratoconus and normal eyes (n = 104) in healthy subjects. Areas under the curve (AUC) of receiver operator characteristic (ROC) curves for each variable were compared across groups to indicate their discrimination capacity. Results. Three variables were found to differ significantly between fellow eyes and normal eyes (all p < 0.05): minimum corneal thickness, thinnest corneal point, and central corneal thickness. These variables combined showed a high discrimination power to differentiate fellow eyes from normal eyes indicated by an AUC of 0.840 (95% CI: 0.762-0.918). Conclusions. Our findings indicate that topographically normal fellow eyes in patients with very asymmetric keratoconus differ from the eyes of healthy individuals in terms of their corneal epithelial and pachymetry maps. This type of information could be useful for an early diagnosis of keratoconus in topographically normal eyes. PMID:27379181

  17. Microarray Meta-Analysis and Cross-Platform Normalization: Integrative Genomics for Robust Biomarker Discovery

    PubMed Central

    Walsh, Christopher J.; Hu, Pingzhao; Batt, Jane; Dos Santos, Claudia C.

    2015-01-01

    The diagnostic and prognostic potential of the vast quantity of publicly-available microarray data has driven the development of methods for integrating the data from different microarray platforms. Cross-platform integration, when appropriately implemented, has been shown to improve reproducibility and robustness of gene signature biomarkers. Microarray platform integration can be conceptually divided into approaches that perform early stage integration (cross-platform normalization) versus late stage data integration (meta-analysis). A growing number of statistical methods and associated software for platform integration are available to the user, however an understanding of their comparative performance and potential pitfalls is critical for best implementation. In this review we provide evidence-based, practical guidance to researchers performing cross-platform integration, particularly with an objective to discover biomarkers. PMID:27600230

  18. Microarray Meta-Analysis and Cross-Platform Normalization: Integrative Genomics for Robust Biomarker Discovery

    PubMed Central

    Walsh, Christopher J.; Hu, Pingzhao; Batt, Jane; Dos Santos, Claudia C.

    2015-01-01

    The diagnostic and prognostic potential of the vast quantity of publicly-available microarray data has driven the development of methods for integrating the data from different microarray platforms. Cross-platform integration, when appropriately implemented, has been shown to improve reproducibility and robustness of gene signature biomarkers. Microarray platform integration can be conceptually divided into approaches that perform early stage integration (cross-platform normalization) versus late stage data integration (meta-analysis). A growing number of statistical methods and associated software for platform integration are available to the user, however an understanding of their comparative performance and potential pitfalls is critical for best implementation. In this review we provide evidence-based, practical guidance to researchers performing cross-platform integration, particularly with an objective to discover biomarkers.

  19. Analysis of hypertrophic and normal scar gene expression with cDNA microarrays.

    PubMed

    Tsou, R; Cole, J K; Nathens, A B; Isik, F F; Heimbach, D M; Engrav, L H; Gibran, N S

    2000-01-01

    Hypertrophic scar is one form of abnormal wound healing. Previous studies have suggested that hypertrophic scar formation results from altered gene expression of extracellular matrix molecules. A broadscale evaluation of gene expression in hypertrophic scars has not been reported. To better understand abnormalities in hypertrophic scar gene expression, we compared messenger RNA expression in hypertrophic scars, normal scars, and uninjured skin with the use of complementary (c)DNA microarrays. Total RNA was extracted from freshly excised human hypertrophic scars, normal scars, or uninjured skin and reverse transcribed into cDNA with the incorporation of [33P] deoxycytidine triphosphate. The resulting radioactive cDNA probes were hybridized onto cDNA microarrays of 4000 genes. Hybridization signals were normalized and analyzed. In the comparison of tissue samples, mean intensities were calculated for each gene within each group (hypertrophic scars, normal scars, and uninjured skin). Ratios of the mean intensities of hypertrophic scars to normal scars, hypertrophic scars to uninjured skin, and normal scars to uninjured skin were generated. A ratio that was greater than 1 indicated upregulation of any particular gene and a ratio that was less than 1 indicated downregulation of any particular gene. Our data indicated that 142 genes were overexpressed and 50 genes were underexpressed in normal scars compared with uninjured skin, 107 genes were overexpressed and 71 were underexpressed in hypertrophic scars compared with uninjured skin, and 44 genes were overexpressed and 124 were underexpressed in hypertrophic scars compared with normal scars. Our analysis of collagen, growth factor, and metalloproteinase gene expression confirmed that our molecular data were consistent with published biochemical and clinical observations of normal scars and hypertrophic scars. cDNA microarray analysis provides a powerful tool for the investigation of differential gene expression in

  20. [Cat eye syndrome with pituitary dwarfism and normal mental development].

    PubMed

    Pierson, M; Gilgenkrantz, S; Saborio, M

    1975-11-01

    In the so-called "cat-eye" syndrome are associated the following malformations: coloboma iridis, anal atresia, pre-auricular fistullae with an extra 47th chromosome of the G group type. About twenty cases have already been reported. Some are familial cases and some have the complete phenotype but without the extra chromosome. Even if the structure of the material of this element is doubtful, its responsability in the phenotype is likely. This case is reported since the patient has pituitary dwarfism and normal intelligence.

  1. A python module to normalize microarray data by the quantile adjustment method.

    PubMed

    Baber, Ibrahima; Tamby, Jean Philippe; Manoukis, Nicholas C; Sangaré, Djibril; Doumbia, Seydou; Traoré, Sekou F; Maiga, Mohamed S; Dembélé, Doulaye

    2011-06-01

    Microarray technology is widely used for gene expression research targeting the development of new drug treatments. In the case of a two-color microarray, the process starts with labeling DNA samples with fluorescent markers (cyanine 635 or Cy5 and cyanine 532 or Cy3), then mixing and hybridizing them on a chemically treated glass printed with probes, or fragments of genes. The level of hybridization between a strand of labeled DNA and a probe present on the array is measured by scanning the fluorescence of spots in order to quantify the expression based on the quality and number of pixels for each spot. The intensity data generated from these scans are subject to errors due to differences in fluorescence efficiency between Cy5 and Cy3, as well as variation in human handling and quality of the sample. Consequently, data have to be normalized to correct for variations which are not related to the biological phenomena under investigation. Among many existing normalization procedures, we have implemented the quantile adjustment method using the python computer language, and produced a module which can be run via an HTML dynamic form. This module is composed of different functions for data files reading, intensity and ratio computations and visualization. The current version of the HTML form allows the user to visualize the data before and after normalization. It also gives the option to subtract background noise before normalizing the data. The output results of this module are in agreement with the results of other normalization tools.

  2. Image analysis and data normalization procedures are crucial for microarray analyses.

    PubMed

    Kadanga, Ali Kpatcha; Leroux, Christine; Bonnet, Muriel; Chauvet, Stéphanie; Meunier, Bruno; Cassar-Malek, Isabelle; Hocquette, Jean-François

    2008-03-17

    This study was conducted with the aim of optimizing the experimental design of array experiments. We compared two image analysis and normalization procedures prior to data analysis using two experimental designs. For this, RNA samples from Charolais steers Longissimus thoracis muscle and subcutaneous adipose tissues were labeled and hybridized to a bovine 8,400 oligochip either in triplicate or in a dye-swap design. Image analysis and normalization were processed by either GenePix/MadScan or ImaGene/GeneSight. Statistical data analysis was then run using either the SAM method or a Student's t-test using a multiple test correction run on R 2.1 software. Our results show that image analysis and normalization procedure had an impact whereas the statistical methods much less influenced the outcome of differentially expressed genes. Image analysis and data normalization are thus an important aspect of microarray experiments, having a potentially significant impact on downstream analyses such as the identification of differentially expressed genes. This study provides indications on the choice of raw data preprocessing in microarray technology.

  3. Image Analysis and Data Normalization Procedures are Crucial for Microarray Analyses

    PubMed Central

    Kadanga, Ali Kpatcha; Leroux, Christine; Bonnet, Muriel; Chauvet, Stéphanie; Meunier, Bruno; Cassar-Malek, Isabelle; Hocquette, Jean-François

    2008-01-01

    This study was conducted with the aim of optimizing the experimental design of array experiments. We compared two image analysis and normalization procedures prior to data analysis using two experimental designs. For this, RNA samples from Charolais steers Longissimus thoracis muscle and subcutaneous adipose tissues were labeled and hybridized to a bovine 8,400 oligochip either in triplicate or in a dye-swap design. Image analysis and normalization were processed by either GenePix/MadScan or ImaGene/GeneSight. Statistical data analysis was then run using either the SAM method or a Student’s t-test using a multiple test correction run on R 2.1 software. Our results show that image analysis and normalization procedure had an impact whereas the statistical methods much less influenced the outcome of differentially expressed genes. Image analysis and data normalization are thus an important aspect of microarray experiments, having a potentially significant impact on downstream analyses such as the identification of differentially expressed genes. This study provides indications on the choice of raw data preprocessing in microarray technology. PMID:19787079

  4. Normal SPECT thallium-201 bull's-eye display: gender differences

    SciTech Connect

    Eisner, R.L.; Tamas, M.J.; Cloninger, K.; Shonkoff, D.; Oates, J.A.; Gober, A.M.; Dunn, D.W.; Malko, J.A.; Churchwell, A.L.; Patterson, R.E.

    1988-12-01

    The bull's-eye technique synthesizes three-dimensional information from single photon emission computed tomographic S TI images into two dimensions so that a patient's data can be compared quantitatively against a normal file. To characterize the normal database and to clarify differences between males and females, clinical data and exercise electrocardiography were used to identify 50 males and 50 females with less than 5% probability of coronary artery disease. Results show inhomogeneity of the S TI distributions at stress and delay: septal to lateral wall count ratios are less than 1.0 in both females and males; anterior to inferior wall count ratios are greater than 1.0 in males but are approximately equal to 1.0 in females. Washout rate is faster in females than males at the same peak exercise heart rate and systolic blood pressure, despite lower exercise time. These important differences suggest that quantitative analysis of single photon emission computed tomographic S TI images requires gender-matched normal files.

  5. "Per cell" normalization method for mRNA measurement by quantitative PCR and microarrays

    PubMed Central

    Kanno, Jun; Aisaki, Ken-ichi; Igarashi, Katsuhide; Nakatsu, Noriyuki; Ono, Atsushi; Kodama, Yukio; Nagao, Taku

    2006-01-01

    Background Transcriptome data from quantitative PCR (Q-PCR) and DNA microarrays are typically obtained from a fixed amount of RNA collected per sample. Therefore, variations in tissue cellularity and RNA yield across samples in an experimental series compromise accurate determination of the absolute level of each mRNA species per cell in any sample. Since mRNAs are copied from genomic DNA, the simplest way to express mRNA level would be as copy number per template DNA, or more practically, as copy number per cell. Results Here we report a method (designated the "Percellome" method) for normalizing the expression of mRNA values in biological samples. It provides a "per cell" readout in mRNA copy number and is applicable to both quantitative PCR (Q-PCR) and DNA microarray studies. The genomic DNA content of each sample homogenate was measured from a small aliquot to derive the number of cells in the sample. A cocktail of five external spike RNAs admixed in a dose-graded manner (dose-graded spike cocktail; GSC) was prepared and added to each homogenate in proportion to its DNA content. In this way, the spike mRNAs represented absolute copy numbers per cell in the sample. The signals from the five spike mRNAs were used as a dose-response standard curve for each sample, enabling us to convert all the signals measured to copy numbers per cell in an expression profile-independent manner. A series of samples was measured by Q-PCR and Affymetrix GeneChip microarrays using this Percellome method, and the results showed up to 90 % concordance. Conclusion Percellome data can be compared directly among samples and among different studies, and between different platforms, without further normalization. Therefore, "percellome" normalization can serve as a standard method for exchanging and comparing data across different platforms and among different laboratories. PMID:16571132

  6. Central and Peripheral Autorefraction Repeatability in Normal Eyes

    PubMed Central

    Moore, Kelly E.; Berntsen, David A.

    2014-01-01

    Purpose To determine the between-visit repeatability of peripheral autorefraction measurements using the Grand Seiko WAM-5500 in normal eyes. Methods Cycloplegic autorefraction of the right eye was measured on 25 myopic young adults using a modified Grand Seiko autorefractor. Measurements were made centrally (along the line of sight) and ±20°, ±30°, and ±40° from the line of sight in the horizontal meridian at two visits separated by 1 to 15 days. Five autorefraction measurements at each location were converted to vector space and averaged. Relative peripheral refraction (RPR) was calculated as the difference between the peripheral and central spherical equivalent (SE). Between-visit repeatability was evaluated by plotting the difference versus the mean of the measurements at the two visits (bias) and by calculating the 95% limits of agreement (LoA). Results The mean (±SD) age and SE refractive error centrally (at visit 1) were 24.0 ± 1.3 years and −3.45 ± 1.42 D, respectively. There was no significant between-visit bias for any refractive component evaluated (M, J0, J45, and RPR) at any location measured (all p>0.05). The 95% LoA of defocus (M) was ±0.21 D centrally and increased with increasing eccentricity to ±0.73 D and ±0.88 D at 40° nasally and temporally on the retina, respectively. The 95% LoA of RPR increased with increasing eccentricity to ±0.67 D and ±0.82 D at 40° nasally and temporally on the retina, respectively. Conclusions In normal eyes, the repeatability of cycloplegic autorefraction was best centrally and decreased as eccentricity increased; however, repeatability in the far periphery was still better than previously reported between-visit repeatability for foveal cycloplegic subjective refraction. With clear knowledge of the repeatability of on- and off-axis cycloplegic autorefraction with the Grand Seiko, peripheral measurements can be properly interpreted in longitudinal studies. PMID:25062133

  7. Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes

    PubMed Central

    Johnstone, Daniel M.; Riveros, Carlos; Heidari, Moones; Graham, Ross M.; Trinder, Debbie; Berretta, Regina; Olynyk, John K.; Scott, Rodney J.; Moscato, Pablo; Milward, Elizabeth A.

    2013-01-01

    While Illumina microarrays can be used successfully for detecting small gene expression changes due to their high degree of technical replicability, there is little information on how different normalization and differential expression analysis strategies affect outcomes. To evaluate this, we assessed concordance across gene lists generated by applying different combinations of normalization strategy and analytical approach to two Illumina datasets with modest expression changes. In addition to using traditional statistical approaches, we also tested an approach based on combinatorial optimization. We found that the choice of both normalization strategy and analytical approach considerably affected outcomes, in some cases leading to substantial differences in gene lists and subsequent pathway analysis results. Our findings suggest that important biological phenomena may be overlooked when there is a routine practice of using only one approach to investigate all microarray datasets. Analytical artefacts of this kind are likely to be especially relevant for datasets involving small fold changes, where inherent technical variation—if not adequately minimized by effective normalization—may overshadow true biological variation. This report provides some basic guidelines for optimizing outcomes when working with Illumina datasets involving small expression changes.

  8. Evaluation of normalization methods for cDNA microarray data by k-NN classification

    SciTech Connect

    Wu, Wei; Xing, Eric P; Myers, Connie; Mian, Saira; Bissell, Mina J

    2004-12-17

    Non-biological factors give rise to unwanted variations in cDNA microarray data. There are many normalization methods designed to remove such variations. However, to date there have been few published systematic evaluations of these techniques for removing variations arising from dye biases in the context of downstream, higher-order analytical tasks such as classification. Ten location normalization methods that adjust spatial- and/or intensity-dependent dye biases, and three scale methods that adjust scale differences were applied, individually and in combination, to five distinct, published, cancer biology-related cDNA microarray data sets. Leave-one-out cross-validation (LOOCV) classification error was employed as the quantitative end-point for assessing the effectiveness of a normalization method. In particular, a known classifier, k-nearest neighbor (k-NN), was estimated from data normalized using a given technique, and the LOOCV error rate of the ensuing model was computed. We found that k-NN classifiers are sensitive to dye biases in the data. Using NONRM and GMEDIAN as baseline methods, our results show that single-bias-removal techniques which remove either spatial-dependent dye bias (referred later as spatial effect) or intensity-dependent dye bias (referred later as intensity effect) moderately reduce LOOCV classification errors; whereas double-bias-removal techniques which remove both spatial- and intensity effect reduce LOOCV classification errors even further. Of the 41 different strategies examined, three two-step processes, IGLOESS-SLFILTERW7, ISTSPLINE-SLLOESS and IGLOESS-SLLOESS, all of which removed intensity effect globally and spatial effect locally, appear to reduce LOOCV classification errors most consistently and effectively across all data sets. We also found that the investigated scale normalization methods do not reduce LOOCV classification error. Using LOOCV error of k-NNs as the evaluation criterion, three double

  9. Cross-platform normalization of microarray and RNA-seq data for machine learning applications.

    PubMed

    Thompson, Jeffrey A; Tan, Jie; Greene, Casey S

    2016-01-01

    Large, publicly available gene expression datasets are often analyzed with the aid of machine learning algorithms. Although RNA-seq is increasingly the technology of choice, a wealth of expression data already exist in the form of microarray data. If machine learning models built from legacy data can be applied to RNA-seq data, larger, more diverse training datasets can be created and validation can be performed on newly generated data. We developed Training Distribution Matching (TDM), which transforms RNA-seq data for use with models constructed from legacy platforms. We evaluated TDM, as well as quantile normalization, nonparanormal transformation, and a simple log 2 transformation, on both simulated and biological datasets of gene expression. Our evaluation included both supervised and unsupervised machine learning approaches. We found that TDM exhibited consistently strong performance across settings and that quantile normalization also performed well in many circumstances. We also provide a TDM package for the R programming language. PMID:26844019

  10. Cross-platform normalization of microarray and RNA-seq data for machine learning applications.

    PubMed

    Thompson, Jeffrey A; Tan, Jie; Greene, Casey S

    2016-01-01

    Large, publicly available gene expression datasets are often analyzed with the aid of machine learning algorithms. Although RNA-seq is increasingly the technology of choice, a wealth of expression data already exist in the form of microarray data. If machine learning models built from legacy data can be applied to RNA-seq data, larger, more diverse training datasets can be created and validation can be performed on newly generated data. We developed Training Distribution Matching (TDM), which transforms RNA-seq data for use with models constructed from legacy platforms. We evaluated TDM, as well as quantile normalization, nonparanormal transformation, and a simple log 2 transformation, on both simulated and biological datasets of gene expression. Our evaluation included both supervised and unsupervised machine learning approaches. We found that TDM exhibited consistently strong performance across settings and that quantile normalization also performed well in many circumstances. We also provide a TDM package for the R programming language.

  11. Cross-platform normalization of microarray and RNA-seq data for machine learning applications

    PubMed Central

    Thompson, Jeffrey A.; Tan, Jie

    2016-01-01

    Large, publicly available gene expression datasets are often analyzed with the aid of machine learning algorithms. Although RNA-seq is increasingly the technology of choice, a wealth of expression data already exist in the form of microarray data. If machine learning models built from legacy data can be applied to RNA-seq data, larger, more diverse training datasets can be created and validation can be performed on newly generated data. We developed Training Distribution Matching (TDM), which transforms RNA-seq data for use with models constructed from legacy platforms. We evaluated TDM, as well as quantile normalization, nonparanormal transformation, and a simple log2 transformation, on both simulated and biological datasets of gene expression. Our evaluation included both supervised and unsupervised machine learning approaches. We found that TDM exhibited consistently strong performance across settings and that quantile normalization also performed well in many circumstances. We also provide a TDM package for the R programming language. PMID:26844019

  12. Immune-Signatures for Lung Cancer Diagnostics: Evaluation of Protein Microarray Data Normalization Strategies

    PubMed Central

    Brezina, Stefanie; Soldo, Regina; Kreuzhuber, Roman; Hofer, Philipp; Gsur, Andrea; Weinhaeusel, Andreas

    2015-01-01

    New minimal invasive diagnostic methods for early detection of lung cancer are urgently needed. It is known that the immune system responds to tumors with production of tumor-autoantibodies. Protein microarrays are a suitable highly multiplexed platform for identification of autoantibody signatures against tumor-associated antigens (TAA). These microarrays can be probed using 0.1 mg immunoglobulin G (IgG), purified from 10 µL of plasma. We used a microarray comprising recombinant proteins derived from 15,417 cDNA clones for the screening of 100 lung cancer samples, including 25 samples of each main histological entity of lung cancer, and 100 controls. Since this number of samples cannot be processed at once, the resulting data showed non-biological variances due to “batch effects”. Our aim was to evaluate quantile normalization, “distance-weighted discrimination” (DWD), and “ComBat” for their effectiveness in data pre-processing for elucidating diagnostic immune-signatures. “ComBat” data adjustment outperformed the other methods and allowed us to identify classifiers for all lung cancer cases versus controls and small-cell, squamous cell, large-cell, and adenocarcinoma of the lung with an accuracy of 85%, 94%, 96%, 92%, and 83% (sensitivity of 0.85, 0.92, 0.96, 0.88, 0.83; specificity of 0.85, 0.96, 0.96, 0.96, 0.83), respectively. These promising data would be the basis for further validation using targeted autoantibody tests.

  13. Comparisons of Robustness and Sensitivity between Cancer and Normal Cells by Microarray Data

    PubMed Central

    Chu, Liang-Hui; Chen, Bor-Sen

    2008-01-01

    Robustness is defined as the ability to uphold performance in face of perturbations and uncertainties, and sensitivity is a measure of the system deviations generated by perturbations to the system. While cancer appears as a robust but fragile system, few computational and quantitative evidences demonstrate robustness tradeoffs in cancer. Microarrays have been widely applied to decipher gene expression signatures in human cancer research, and quantification of global gene expression profiles facilitates precise prediction and modeling of cancer in systems biology. We provide several efficient computational methods based on system and control theory to compare robustness and sensitivity between cancer and normal cells by microarray data. Measurement of robustness and sensitivity by linear stochastic model is introduced in this study, which shows oscillations in feedback loops of p53 and demonstrates robustness tradeoffs that cancer is a robust system with some extreme fragilities. In addition, we measure sensitivity of gene expression to perturbations in other gene expression and kinetic parameters, discuss nonlinear effects in feedback loops of p53 and extend our method to robustness-based cancer drug design. PMID:19259409

  14. Hyperspectral microscopic analysis of normal, benign and carcinoma microarray tissue sections

    NASA Astrophysics Data System (ADS)

    Maggioni, Mauro; Davis, Gustave L.; Warner, Frederick J.; Geshwind, Frank B.; Coppi, Andreas C.; DeVerse, Richard A.; Coifman, Ronald R.

    2006-02-01

    We apply a unique micro-optoelectromechanical tuned light source and new algorithms to the hyper-spectral microscopic analysis of human colon biopsies. The tuned light prototype (Plain Sight Systems Inc.) transmits any combination of light frequencies, range 440nm 700nm, trans-illuminating H and E stained tissue sections of normal (N), benign adenoma (B) and malignant carcinoma (M) colon biopsies, through a Nikon Biophot microscope. Hyper-spectral photomicrographs, randomly collected 400X magnication, are obtained with a CCD camera (Sensovation) from 59 different patient biopsies (20 N, 19 B, 20 M) mounted as a microarray on a single glass slide. The spectra of each pixel are normalized and analyzed to discriminate among tissue features: gland nuclei, gland cytoplasm and lamina propria/lumens. Spectral features permit the automatic extraction of 3298 nuclei with classification as N, B or M. When nuclei are extracted from each of the 59 biopsies the average classification among N, B and M nuclei is 97.1%; classification of the biopsies, based on the average nuclei classification, is 100%. However, when the nuclei are extracted from a subset of biopsies, and the prediction is made on nuclei in the remaining biopsies, there is a marked decrement in performance to 60% across the 3 classes. Similarly the biopsy classification drops to 54%. In spite of these classification differences, which we believe are due to instrument and biopsy normalization issues, hyper-spectral analysis has the potential to achieve diagnostic efficiency needed for objective microscopic diagnosis.

  15. Optic nerve head perfusion in normal eyes and eyes with glaucoma using optical coherence tomography-based microangiography

    PubMed Central

    Chen, Chieh-Li; Bojikian, Karine D.; Gupta, Divakar; Wen, Joanne C.; Zhang, Qinqin; Xin, Chen; Kono, Rei; Mudumbai, Raghu C.; Johnstone, Murray A.; Chen, Philip P.

    2016-01-01

    Background To investigate the differences of perfusion in the optic nerve head (ONH) between normal and glaucomatous eyes using optical microangiography (OMAG) based optical coherence tomography (OCT) angiography technique. Methods One eye from each subject was scanned with a 68 kHz Cirrus 5000 HD-OCT-based OMAG prototype system centered at the ONH (Carl Zeiss Meditec Inc, Dublin, CA, USA). Microvascular images were generated from the OMAG dataset by detecting the differences in OCT signal between consecutive B-scans. The pre-laminar layer (preLC) was isolated by a semi-automatic segmentation program. En face OMAG images for preLC were generated using signals with highest blood flow signal intensity. ONH perfusion was quantified as flux, vessel area density, and normalized flux within the ONH. Standard t-tests were performed to analyze the ONH perfusion differences between normal and glaucomatous eyes. Linear regression models were constructed to analyze the correlation between ONH perfusion and other clinical measurements. Results Twenty normal and 21 glaucoma subjects were enrolled. Glaucomatous eyes had significantly lower ONH perfusion in preLC in all three perfusion metrics compared to normal eyes (P≤0.0003). Significant correlations between ONH perfusion and disease severity as well as structural changes were detected in glaucomatous eyes (P≤0.012). Conclusions ONH perfusion detected by OMAG showed significant differences between glaucoma and normal controls and was significantly correlated with disease severity and structural defects in glaucomatous eyes. ONH perfusion measurement using OMAG may provide useful information for detection and monitoring of glaucoma. PMID:27190764

  16. Retinal image degradation by optical aberrations and light scatter in normal and albino chick eyes

    NASA Astrophysics Data System (ADS)

    Tian, Yibin; Shieh, Kevin; Wildsoet, Christine F.

    2007-02-01

    Comprehensive evaluation of retinal image quality requires that light scatter as well as optical aberrations be considered. In investigating how retinal image degradation affects eye growth in the chick model of myopia, we developed a simple method based on Shack-Hartmann images for evaluating the effects of both monochromatic aberrations and light scatter on retinal image quality. We further evaluated our method in the current study by applying it to data collected from both normal chick eyes and albino eyes that were expected to show increased intraocular light scatter. To analyze light scatter in our method, each Shack-Hartmann dot is treated as a local point spread function (PSF) that is the convolution of a local scatter PSF and a lenslet diffraction PSF. The local scatter PSF is obtained by de-convolution, and is fitted with a circularly symmetric Gaussian function using nonlinear regressions. A whole-eye scatter PSF also can be derived from the local scatter PSFs for the analyzed pupil. Aberrations are analyzed using OSA standard Zernike polynomials, and aberration-related PSF calculated from reconstructed wavefront using fast Fourier transform. Modulation transfer functions (MTFs) are computed separately for aberration and scatter PSFs, and a whole-eye MTF is derived as the product of the two. This method was applied to 4 normal and 4 albino eyes. Compared to normal eyes, albino eyes were more aberrated and showed greater light scatter. As a result, overall retinal image degradation was much greater in albino eyes than in normal eyes, with the relative contribution to retinal image degradation of light scatter compared to aberrations also being greater for albino eyes.

  17. Eye Movements in Autistic, Mentally Retarded and Normal Young Children: Simultaneous Measurement by an Eye Camera System for Autistic Children (ECSA) and an Electro-Oculography (EOG).

    ERIC Educational Resources Information Center

    Itoh, Hideo

    1987-01-01

    Smooth pursuit eye movements and saccadic eye movements in Japanese autistic, mentally retarded, and normal young children were simultaneously measured by an eye camera system (ECS) and an electro-oculography (EOG) system. The ECS was developed in the laboratory of the Research Institute for the Education of Exceptional Children at Tokyo Gakugei…

  18. Saccadic eye movements of dyslexic and normal reading children.

    PubMed

    Biscaldi, M; Fischer, B; Aiple, F

    1994-01-01

    Twenty-four children made saccades in five noncognitive tasks. Two standard tasks required saccades to a single target presented randomly 4 deg to the right or left of a fixation point. Three other tasks required sequential saccades from the left to the right. 75 parameters of the eye-movement data were collected for each child. On the basis of their reading, writing, and other cognitive performances, twelve children were considered dyslexic and were divided into two groups (D1 and D2). Group statistical comparisons revealed significant differences between control and dyslexic subjects. In general, in the standard tasks the dyslexic subjects had poorer fixation quality, failed more often to hit the target at once, had smaller primary saccades, and had shorter reaction times to the left as compared with the control group. The control group and group D1 dyslexics showed an asymmetrical distribution of reaction times, but in opposite directions. Group D2 dyslexics made more anticipatory and express saccades, they undershot the target more often in comparison with the control group, and almost never overshot it. In the sequential tasks group D1 subjects made fewer and larger saccades in a shorter time and group D2 subjects had shorter fixation durations than the subjects of the control group.

  19. Tono-Pen tonometry in normal and in post-keratoplasty eyes.

    PubMed Central

    Geyer, O; Mayron, Y; Loewenstein, A; Neudorfer, M; Rothkoff, L; Lazar, M

    1992-01-01

    Oculab Tono-Pen tonometry was compared with Goldmann applanation tonometry in 82 eyes of 82 patients with normal corneas and in 54 eyes of 54 patients who had undergone penetrating keratoplasty and whose corneas did not preclude the use of Goldmann tonometer. We found that the intraocular pressure (IOP) in 48% of the eyes with normal corneas and in 57% after keratoplasty has different measurements with Goldmann and Tono-Pen pressures of 3 mm Hg or more. Despite the correlation between the Goldmann tonometer and the Tono-Pen in the group of eyes with normal corneas (r = 0.83) as well as in the group of eyes after keratoplasty (r = 0.79) the Tono-Pen tended to significantly overestimate the Goldmann tonometer reading (p < 0.0001). The mean difference between the two instruments was highest across the lower IOP range (< 9 mm Hg) in the group of eyes after keratoplasty. Because the mean absolute values of the paired differences between Goldmann and Tono-Pen measurements varied significantly across all IOP intervals it was not possible to establish a correction factor which could be used when comparing the two measurements. Based on this study the Tono-Pen consistently overestimated the actual IOP in an unpredictable manner. Where possible Goldmann measurements of the IOP are still to be preferred. PMID:1420058

  20. Ability of Cirrus™ HD-OCT Optic Nerve Head Parameters to Discriminate Normal from Glaucomatous Eyes

    PubMed Central

    Mwanza, Jean-Claude; Oakley, Jonathan D; Budenz, Donald L; Anderson, Douglas R

    2010-01-01

    Purpose To determine the ability of optic nerve head (ONH) parameters measured with spectral domain Cirrus™ HD-OCT to discriminate between normal and glaucomatous eyes and to compare them to the discriminating ability of peripapillary retinal nerve fiber layer (RNFL) thickness measurements performed with Cirrus™ HD-OCT. Design Evaluation of diagnostic test or technology. Participants Seventy-three subjects with glaucoma and one hundred and forty-six age-matched normal subjects. Methods Peripapillary ONH parameters and RNFL thickness were measured in one randomly selected eye of each participant within a 200×200 pixel A-scan acquired with Cirrus™ HD-OCT centered on the ONH. Main Outcome Measures ONH topographic parameters, peripapillary RNFL thickness, and the area under receiver operating characteristic curves (AUCs). Results For distinguishing normal from glaucomatous eyes, regardless of disease stage, the six best parameters (expressed as AUC) were vertical rim thickness (VRT, 0.963), rim area (RA, 0.962), RNFL thickness at clock-hour 7 (0.957), RNFL thickness of the inferior quadrant (0.953), vertical cup-to-disc ratio (VCDR, 0.951) and average RNFL thickness (0.950). The AUC for distinguishing between normal and eyes with mild glaucoma was greatest for RNFL thickness of clock-hour 7 (0.918), VRT (0.914), RA (0.912), RNFL thickness of inferior quadrant (0.895), average RNFL thickness (0.893) and VCDR (0.890). There were no statistically significant differences between AUCs for the best ONH parameters and RNFL thickness measurements (p > 0.05). Conclusions Cirrus™ HD-OCT ONH parameters are able to discriminate between eyes that are normal from those with glaucoma or even mild glaucoma. There is no difference in the ability of ONH parameters and RNFL thickness measurement, as measured with Cirrus™ OCT, to distinguish between normal and glaucomatous eyes. PMID:20920824

  1. Wavefront aberration statistics in normal eye populations: are they well described by the Kolmogorov model?

    PubMed

    Pailos, Eliseo; Bará, Salvador

    2014-06-01

    This Letter studies the statistics of wavefront aberrations in a sample of eyes with normal vision. Methods relying on the statistics of the measured wavefront slopes are used, not including the aberration estimation stage. Power-law aberration models, an extension of the Kolmogorov one, are rejected by χ2-tests performed on fits to the slope structure function data. This is due to the large weight of defocus and astigmatism variations in normal eyes. Models of only second-order changes are not ruled out. The results are compared with previous works in the area.

  2. Identification of Differential Gene Expression Profiles in Placentas from Preeclamptic Pregnancies Versus Normal Pregnancies by DNA Microarrays

    PubMed Central

    Chen, Haiying; Sun, Manni; Wang, He; Zhao, Ge; Wang, Xiaoshuang

    2012-01-01

    Abstract The purpose of this study was to perform a comprehensive analysis of gene expression profiles in placentas from preeclamptic pregnancies versus normal placentas. Placental tissues were obtained immediately after delivery from women with normal pregnancies (n=6) and patients with preeclampsia (n=6). The gene expression profile was assessed by oligonucleotide-based DNA microarrays and validated by quantitative real-time RT-PCR. Functional relationships and canonical pathways/networks of differentially-expressed genes were evaluated by GeneSpring™ GX 11.0 software, and ingenuity pathways analysis (IPA). A total of 939 genes were identified that differed significantly in expression: 483 genes were upregulated and 456 genes were downregulated in preeclamptic placentas compared with normal placentas (fold change ≥2 and p<0.05 by unpaired t-test corrected with Bonferroni multiple testing). The IPA revealed that the primary molecular functions of these genes are involved in cellular function and maintenance, cellular development, cell signaling, and lipid metabolism. Pathway analysis provided evidence that a number of biological pathways, including Notch, Wnt, NF-κB, and transforming growth factor-β (TGF-β) signaling pathways, were aberrantly regulated in preeclampsia. In conclusion, our microarray analysis represents a comprehensive list of placental gene expression profiles and various dysregulated signaling pathways that are altered in preeclampsia. These observations may provide the basis for developing novel predictive, diagnostic, and prognostic biomarkers of preeclampsia to improve reproductive outcomes and reduce the risk for subsequent cardiovascular disease. PMID:22702245

  3. Dynamic Characteristics of Saccadic Eye Movements in Normal and Mentally Retarded Children.

    ERIC Educational Resources Information Center

    Takahashi, Teruko; And Others

    1987-01-01

    Analysis of saccadic eye movements in 10 normal and 10 mentally retarded children (ages 13-15) suggested that retarded children may have difficulty in visual orientation. They followed a visual target on fewer than 50 percent of the trials, displaying frequent undershoot patterns and an average rising latency that was much longer than that of…

  4. Comparison of Microarray Platforms for Measuring Differential MicroRNA Expression in Paired Normal/Cancer Colon Tissues

    PubMed Central

    Callari, Maurizio; Dugo, Matteo; Musella, Valeria; Marchesi, Edoardo; Chiorino, Giovanna; Grand, Maurizia Mello; Pierotti, Marco Alessandro; Daidone, Maria Grazia; Canevari, Silvana; De Cecco, Loris

    2012-01-01

    Background Microarray technology applied to microRNA (miRNA) profiling is a promising tool in many research fields; nevertheless, independent studies characterizing the same pathology have often reported poorly overlapping results. miRNA analysis methods have only recently been systematically compared but only in few cases using clinical samples. Methodology/Principal Findings We investigated the inter-platform reproducibility of four miRNA microarray platforms (Agilent, Exiqon, Illumina, and Miltenyi), comparing nine paired tumor/normal colon tissues. The most concordant and selected discordant miRNAs were further studied by quantitative RT-PCR. Globally, a poor overlap among differentially expressed miRNAs identified by each platform was found. Nevertheless, for eight miRNAs high agreement in differential expression among the four platforms and comparability to qRT-PCR was observed. Furthermore, most of the miRNA sets identified by each platform are coherently enriched in data from the other platforms and the great majority of colon cancer associated miRNA sets derived from the literature were validated in our data, independently from the platform. Computational integration of miRNA and gene expression profiles suggested that anti-correlated predicted target genes of differentially expressed miRNAs are commonly enriched in cancer-related pathways and in genes involved in glycolysis and nutrient transport. Conclusions Technical and analytical challenges in measuring miRNAs still remain and further research is required in order to increase consistency between different microarray-based methodologies. However, a better inter-platform agreement was found by looking at miRNA sets instead of single miRNAs and through a miRNAs – gene expression integration approach. PMID:23028787

  5. Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data.

    PubMed

    Müller, Christian; Schillert, Arne; Röthemeier, Caroline; Trégouët, David-Alexandre; Proust, Carole; Binder, Harald; Pfeiffer, Norbert; Beutel, Manfred; Lackner, Karl J; Schnabel, Renate B; Tiret, Laurence; Wild, Philipp S; Blankenberg, Stefan; Zeller, Tanja; Ziegler, Andreas

    2016-01-01

    Technical variation plays an important role in microarray-based gene expression studies, and batch effects explain a large proportion of this noise. It is therefore mandatory to eliminate technical variation while maintaining biological variability. Several strategies have been proposed for the removal of batch effects, although they have not been evaluated in large-scale longitudinal gene expression data. In this study, we aimed at identifying a suitable method for batch effect removal in a large study of microarray-based longitudinal gene expression. Monocytic gene expression was measured in 1092 participants of the Gutenberg Health Study at baseline and 5-year follow up. Replicates of selected samples were measured at both time points to identify technical variability. Deming regression, Passing-Bablok regression, linear mixed models, non-linear models as well as ReplicateRUV and ComBat were applied to eliminate batch effects between replicates. In a second step, quantile normalization prior to batch effect correction was performed for each method. Technical variation between batches was evaluated by principal component analysis. Associations between body mass index and transcriptomes were calculated before and after batch removal. Results from association analyses were compared to evaluate maintenance of biological variability. Quantile normalization, separately performed in each batch, combined with ComBat successfully reduced batch effects and maintained biological variability. ReplicateRUV performed perfectly in the replicate data subset of the study, but failed when applied to all samples. All other methods did not substantially reduce batch effects in the replicate data subset. Quantile normalization plus ComBat appears to be a valuable approach for batch correction in longitudinal gene expression data.

  6. Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data.

    PubMed

    Müller, Christian; Schillert, Arne; Röthemeier, Caroline; Trégouët, David-Alexandre; Proust, Carole; Binder, Harald; Pfeiffer, Norbert; Beutel, Manfred; Lackner, Karl J; Schnabel, Renate B; Tiret, Laurence; Wild, Philipp S; Blankenberg, Stefan; Zeller, Tanja; Ziegler, Andreas

    2016-01-01

    Technical variation plays an important role in microarray-based gene expression studies, and batch effects explain a large proportion of this noise. It is therefore mandatory to eliminate technical variation while maintaining biological variability. Several strategies have been proposed for the removal of batch effects, although they have not been evaluated in large-scale longitudinal gene expression data. In this study, we aimed at identifying a suitable method for batch effect removal in a large study of microarray-based longitudinal gene expression. Monocytic gene expression was measured in 1092 participants of the Gutenberg Health Study at baseline and 5-year follow up. Replicates of selected samples were measured at both time points to identify technical variability. Deming regression, Passing-Bablok regression, linear mixed models, non-linear models as well as ReplicateRUV and ComBat were applied to eliminate batch effects between replicates. In a second step, quantile normalization prior to batch effect correction was performed for each method. Technical variation between batches was evaluated by principal component analysis. Associations between body mass index and transcriptomes were calculated before and after batch removal. Results from association analyses were compared to evaluate maintenance of biological variability. Quantile normalization, separately performed in each batch, combined with ComBat successfully reduced batch effects and maintained biological variability. ReplicateRUV performed perfectly in the replicate data subset of the study, but failed when applied to all samples. All other methods did not substantially reduce batch effects in the replicate data subset. Quantile normalization plus ComBat appears to be a valuable approach for batch correction in longitudinal gene expression data. PMID:27272489

  7. Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data

    PubMed Central

    Müller, Christian; Schillert, Arne; Röthemeier, Caroline; Trégouët, David-Alexandre; Proust, Carole; Binder, Harald; Pfeiffer, Norbert; Beutel, Manfred; Lackner, Karl J.; Schnabel, Renate B.; Tiret, Laurence; Wild, Philipp S.; Blankenberg, Stefan

    2016-01-01

    Technical variation plays an important role in microarray-based gene expression studies, and batch effects explain a large proportion of this noise. It is therefore mandatory to eliminate technical variation while maintaining biological variability. Several strategies have been proposed for the removal of batch effects, although they have not been evaluated in large-scale longitudinal gene expression data. In this study, we aimed at identifying a suitable method for batch effect removal in a large study of microarray-based longitudinal gene expression. Monocytic gene expression was measured in 1092 participants of the Gutenberg Health Study at baseline and 5-year follow up. Replicates of selected samples were measured at both time points to identify technical variability. Deming regression, Passing-Bablok regression, linear mixed models, non-linear models as well as ReplicateRUV and ComBat were applied to eliminate batch effects between replicates. In a second step, quantile normalization prior to batch effect correction was performed for each method. Technical variation between batches was evaluated by principal component analysis. Associations between body mass index and transcriptomes were calculated before and after batch removal. Results from association analyses were compared to evaluate maintenance of biological variability. Quantile normalization, separately performed in each batch, combined with ComBat successfully reduced batch effects and maintained biological variability. ReplicateRUV performed perfectly in the replicate data subset of the study, but failed when applied to all samples. All other methods did not substantially reduce batch effects in the replicate data subset. Quantile normalization plus ComBat appears to be a valuable approach for batch correction in longitudinal gene expression data. PMID:27272489

  8. hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine

    PubMed Central

    Falgreen, Steffen; Ellern Bilgrau, Anders; Brøndum, Rasmus Froberg; Hjort Jakobsen, Lasse; Have, Jonas; Lindblad Nielsen, Kasper; El-Galaly, Tarec Christoffer; Bødker, Julie Støve; Schmitz, Alexander; H. Young, Ken; Johnsen, Hans Erik; Dybkær, Karen; Bøgsted, Martin

    2016-01-01

    Background Dozens of omics based cancer classification systems have been introduced with prognostic, diagnostic, and predictive capabilities. However, they often employ complex algorithms and are only applicable on whole cohorts of patients, making them difficult to apply in a personalized clinical setting. Results This prompted us to create hemaClass.org, an online web application providing an easy interface to one-by-one RMA normalization of microarrays and subsequent risk classifications of diffuse large B-cell lymphoma (DLBCL) into cell-of-origin and chemotherapeutic sensitivity classes. Classification results for one-by-one array pre-processing with and without a laboratory specific RMA reference dataset were compared to cohort based classifiers in 4 publicly available datasets. Classifications showed high agreement between one-by-one and whole cohort pre-processsed data when a laboratory specific reference set was supplied. The website is essentially the R-package hemaClass accompanied by a Shiny web application. The well-documented package can be used to run the website locally or to use the developed methods programmatically. Conclusions The website and R-package is relevant for biological and clinical lymphoma researchers using affymetrix U-133 Plus 2 arrays, as it provides reliable and swift methods for calculation of disease subclasses. The proposed one-by-one pre-processing method is relevant for all researchers using microarrays. PMID:27701436

  9. Corneal Biomechanical Assessment Using Corneal Visualization Scheimpflug Technology in Keratoconic and Normal Eyes

    PubMed Central

    Huang, Yi-Fei; Wang, Li-Qiang; Bai, Hua; Wang, Qun; Jiang, Jing-Jing; Wu, Ying; Gao, Min

    2014-01-01

    Purpose. To compare the corneal biomechanical properties of keratoconic patients and age-matched controls using corneal visualization Scheimpflug technology (Corvis ST). Methods. Sixty keratoconic eyes from 47 keratoconus patients and 60 normal eyes from 60 controls were enrolled in this prospective study. Tomography and biomechanical parameters of all eyes were obtained with the Pentacam and Corvis ST, respectively. Intraocular pressure was measured using a Goldmann applanation tonometer. Results. The tomography and biomechanical parameters of the keratoconic corneas were significantly different from those of the normal corneas except for the anterior chamber angle, first applanation length, the highest concavity time, and peak distance. The deformation amplitude was the best predictive parameter (area under the curve: 0.882), with a sensitivity of 81.7%, although there was a significant overlap between keratoconic and normal corneas that ranged from 1.0 to 1.4 mm. In both the keratoconus and control groups, the deformation amplitude was negatively correlated with intraocular pressure, central corneal thickness, and corneal volume at 3 and 5 mm. Conclusions. Corvis ST offers an alternative method for measuring corneal biomechanical properties. The possibility of classifying keratoconus based on deformation amplitude deserves clinical attention. PMID:24800059

  10. Comparison of macular OCTs in right and left eyes of normal people

    NASA Astrophysics Data System (ADS)

    Mahmudi, Tahereh; Kafieh, Rahele; Rabbani, Hossein; Mehri dehnavi, Alireza; Akhlagi, Mohammadreza

    2014-03-01

    Retinal 3D Optical coherence tomography (OCT) is a non-invasive imaging modality in ocular diseases. Due to large volumes of OCT data, it is better to utilize automatic extraction of information from OCT images, such as total retinal thickness and retinal nerve fiber layer thickness (RNFLT). These two thickness values have become useful indices to indicate the progress of diseases like glaucoma, according to the asymmetry between two eyes of an individual. Furthermore, the loss of ganglion cells may not be diagnosable by other tests and even not be evaluated when we only consider the thickness of one eye (due to dramatic different thickness among individuals). This can justify our need to have a comparison between thicknesses of two eyes in symmetricity. Therefore, we have proposed an asymmetry analysis of the retinal nerve layer thickness and total retinal thickness around the macula in the normal Iranian population. In the first step retinal borders are segmented by diffusion map method and thickness profiles were made. Then we found the middle point of the macula by pattern matching scheme. RNFLT and retinal thickness are analyzed in 9 sectors and the mean and standard deviation of each sector in the right and left eye are obtained. The maximums of the average RNFL thickness in right and left eyes are seen in the perifoveal nasal, and the minimums are seen in the fovea. Tolerance limits in RNFL thickness is shown to be between 0.78 to 2.4 μm for 19 volunteers used in this study.

  11. Lamina Cribrosa Microarchitecture in Normal Monkey Eyes Part 1: Methods and Initial Results

    PubMed Central

    Lockwood, Howard; Reynaud, Juan; Gardiner, Stuart; Grimm, Jonathan; Libertiaux, Vincent; Downs, J. Crawford; Yang, Hongli; Burgoyne, Claude F.

    2015-01-01

    Purpose. To introduce quantitative postmortem lamina cribrosa (LC) microarchitecture (LMA) assessment and characterize beam diameter (BD), pore diameter (PD), and connective tissue volume fraction (CTVF) in 21 normal monkey eyes. Methods. Optic nerve heads (ONHs) underwent digital three-dimensional (3D) reconstruction and LC beam segmentation. Each beam and pore voxel was assigned a diameter based on the largest sphere that contained it before transformation to one of twelve 30° sectors in a common cylinder. Mean BD, PD, and CTVF within 12 central and 12 peripheral subsectors and within inner, middle, and outer LC depths were assessed for sector, subsector, and depth effects by analysis of variance using general estimating equations. Eye-specific LMA discordance (the pattern of lowest connective tissue density) was plotted for each parameter. Results. The ranges of mean BD, PD, and CTVF were 14.0 to 23.1 μm, 20.0 to 35.6 μm, and 0.247 to 0.638, respectively. Sector, subsector, and depth effects were significant (P < 0.01) for all parameters except subsector on CTVF. Beam diameter and CTVF were smaller and PD was larger within the superior-temporal (ST) and inferior-temporal (IT) sectors (P < 0.05). These differences were enhanced within the central versus peripheral subsectors. Beam diameter and CTVF were larger and PD was smaller (P < 0.05) within the middle LC layer. Lamina cribrosa microarchitecture discordance most commonly occurred within the ST and IT sectors, varied by eye, and generally diminished as CTVF increased. Conclusions. Our data support previous characterizations of diminished connective tissue density within the ST and IT ONH regions. The clinical importance of eye-specific LMA discordance warrants further study. PMID:25650423

  12. Fluorescein gonioangiography of the normal canine eye using a dSLR camera adaptor.

    PubMed

    Alario, Anthony F; Pirie, Christopher G

    2015-06-01

    The purpose of this study was to describe fluorescein gonioangiography (FGA) of the normal canine eye using a digital single lens reflex (dSLR) camera adaptor. Dogs were anesthetized using intravenous propofol. Imaging was performed using a Lovac Barkan goniolens, dSLR camera, dSLR camera adaptor, camera lens, and accessory flash. Twelve dogs with a mean age of 2.0 +/- 0.8 years were imaged. No characteristic angiographic phases were observed. Leakage from the peri-limbal capillary network was a common finding and occurred 7.7 +/- 2.2 s post injection in 9 (75%) dogs. In 3 (25%) dogs, filling of the circumferential ciliary artery was observed 10.3 +/- 2.8 s post injection. Dye leakage within the iris base and into the aqueous humor was demonstrated in 4 (33%) and 6 dogs (50%) respectively. No adverse events were noted. This study demonstrates FGA findings in normal canine eyes using a cost effective dSLR camera adaptor. PMID:25823859

  13. Characterization of human retinal vessel arborisation in normal and amblyopic eyes using multifractal analysis

    PubMed Central

    Tălu, Stefan; Vlăduţiu, Cristina; Lupaşcu, Carmen A.

    2015-01-01

    AIM To characterize the human retinal vessel arborisation in normal and amblyopic eyes using multifractal geometry and lacunarity parameters. METHODS Multifractal analysis using a box counting algorithm was carried out for a set of 12 segmented and skeletonized human retinal images, corresponding to both normal (6 images) and amblyopia states of the retina (6 images). RESULTS It was found that the microvascular geometry of the human retina network represents geometrical multifractals, characterized through subsets of regions having different scaling properties that are not evident in the fractal analysis. Multifractal analysis of the amblyopia images (segmented and skeletonized versions) show a higher average of the generalized dimensions (Dq) for q=0, 1, 2 indicating a higher degree of the tree-dimensional complexity associated with the human retinal microvasculature network whereas images of healthy subjects show a lower value of generalized dimensions indicating normal complexity of biostructure. On the other hand, the lacunarity analysis of the amblyopia images (segmented and skeletonized versions) show a lower average of the lacunarity parameter Λ than the corresponding values for normal images (segmented and skeletonized versions). CONCLUSION The multifractal and lacunarity analysis may be used as a non-invasive predictive complementary tool to distinguish amblyopic subjects from healthy subjects and hence this technique could be used for an early diagnosis of patients with amblyopia. PMID:26558216

  14. Repeatability and Reproducibility of Anterior Segment Measurements in Normal Eyes Using Dual Scheimpflug Analyzer

    PubMed Central

    Altıparmak, Zeynep; Yağcı, Ramazan; Güler, Emre; Arslanyılmaz, Zeynel; Canbal, Metin; Hepşen, İbrahim F.

    2015-01-01

    Objectives: To assess the repeatability and reproducibility of anterior segment measurements including aberrometric measurements provided by a dual Scheimpflug analyzer (Galilei) system in normal eyes. Materials and Methods: Three repeated consecutive measurements were taken by two independent examiners. The following were evaluated: total corneal power and posterior corneal power, corneal higher-order wavefront aberrations (6.0 mm pupil), pachymetry at the central, paracentral, and peripheral zones, and anterior chamber depth (ACD). Repeatability was assessed by calculating the within-subject standard deviation, precision, repeatability, and intraclass correlation coefficient (ICC). Bland-Altman analysis was used for assessing reproducibility. Results: Thirty eyes of 30 patients were included. The best ICC values were for corneal pachymetry and ACD. For both observers, acceptable ICC was also achieved for the other parameters, the only exceptions being posterior corneal astigmatism and total high order aberration. The 95% LoA (Limits of Agreement) values for all measurements showed small variability between the two examiners. Conclusion: The Galilei system provided reliable measurements of anterior segment parameters. Therefore, the instrument can be confidently used for routine clinical use and research purposes. PMID:27800242

  15. Optic Disc Perfusion in Primary Open Angle and Normal Tension Glaucoma Eyes Using Optical Coherence Tomography-Based Microangiography

    PubMed Central

    Wen, Joanne C.; Zhang, Qinqin; Xin, Chen; Gupta, Divakar; Mudumbai, Raghu C.; Johnstone, Murray A.; Wang, Ruikang K.; Chen, Philip P.

    2016-01-01

    Purpose To investigate optic disc perfusion differences in normal, primary open-angle glaucoma (POAG), and normal tension glaucoma (NTG) eyes using optical microangiography (OMAG) based optical coherence tomography (OCT) angiography technique. Design Cross-sectional, observational study. Subjects Twenty-eight normal, 30 POAG, and 31 NTG subjects. Methods One eye from each subject was scanned with a 68 kHz Cirrus HD-OCT 5,000-based OMAG prototype system centered at the optic nerve head (ONH) (Carl Zeiss Meditec Inc, Dublin, CA). Microvascular images were generated from the OMAG dataset by detecting the differences in OCT signal between consecutive B-scans. The pre-laminar layer (preLC) was isolated by a semi-automatic segmentation program. Main Outcome Measures Optic disc perfusion, quantified as flux, vessel area density, and normalized flux (flux normalized by the vessel area) within the ONH. Results Glaucomatous eyes had significantly lower optic disc perfusion in preLC in all three perfusion metrics (p<0.0001) compared to normal eyes. The visual field (VF) mean deviation (MD) and pattern standard deviation (PSD) were similar between the POAG and NTG groups, and no differences in optic disc perfusion were observed between POAG and NTG. Univariate analysis revealed significant correlation between optic disc perfusion and VF MD, VF PSD, and rim area in both POAG and NTG groups (p≤0.0288). However, normalized optic disc perfusion was correlated with some structural measures (retinal nerve fiber layer thickness and ONH cup/disc ratio) only in POAG eyes. Conclusions Optic disc perfusion detected with OMAG was significantly reduced in POAG and NTG groups compared to normal controls, but no difference was seen between POAG and NTG groups with similar levels of VF damage. Disc perfusion was significantly correlated with VF MD, VF PSD, and rim area in glaucomatous eyes. Vascular changes at the optic disc as measured using OMAG may provide useful information for

  16. Argon laser trabeculoplasty as a means of decreasing intraocular pressure from ''normal'' levels in glaucomatous eyes

    SciTech Connect

    Sharpe, E.D.; Simmons, R.J.

    1985-06-15

    The authors conducted a retrospective study of 67 patients (85 eyes) with severe glaucoma to determine whether argon laser trabeculoplasty could reduce intraocular pressures below the ''normal'' range. All patients had initial intraocular pressures of less than or equal to 19 mm Hg. Success was defined as a decrease in intraocular pressure of at least 20%, no increase in medications, stable visual field, and no subsequent glaucoma surgery. After an average follow-up period of 30 months, treatment was successful in 31 cases. One half of the failures occurred by six months and 11 failures (30%) occurred after 12 months. Sixteen patients were able to decrease their medications. Two patients achieved intraocular pressures between 6 and 9 mm Hg and 20 between 10 and 12 mm Hg.

  17. Variation of Laminar Depth in Normal Eyes With Age and Race

    PubMed Central

    Rhodes, Lindsay A.; Huisingh, Carrie; Johnstone, John; Fazio, Massimo; Smith, Brandon; Clark, Mark; Downs, J. Crawford; Owsley, Cynthia; Girard, Michael J. A.; Mari, Jean Martial; Girkin, Christopher

    2014-01-01

    Purpose. To determine if laminar depth (LD) and prelaminar tissue volume (PTV) are associated with age and race in healthy human eyes. Methods. Optic nerve head images from enhanced depth imaging spectral-domain optical coherence tomography of 166 normal eyes from 84 subjects of African descent (AD) and European descent (ED) were manually delineated to identify the principal surfaces: internal limiting membrane, Bruch's membrane (BM), anterior sclera (AS), and anterior surface of the lamina cribrosa. These four surfaces defined the LD and PTV using Bruch's membrane opening (BMO) and AS for reference structures. Generalized estimating equations were used to evaluate whether the effect of age on each outcome was differential by race. Results. When age was analyzed as a continuous variable, the interaction term between age and race was statistically significant for mean LDBMO (P = 0.015) and mean LDAS (P = 0.0062) after adjusting for axial length and BMO area. For every 1-year increase in age, the LDAS was greater on average by 1.78 μm in AD subjects and less by 1.71 μm in ED subjects. Mean PTV was lower in the older subjects (1248 × 106 μm3 AD, 881 × 106 μm3 ED) compared to the younger subjects (1316 × 106 μm3 AD, 1102 × 106 μm3 ED) in both groups. Conclusions. With increasing age, the LD changes differently across racial groups in normal subjects. The LD in ED subjects showed a significantly decreasing slope suggesting that the lamina moves anteriorly with age in this group. PMID:25414182

  18. Discrimination between normal and glaucomatous eyes with visual field and scanning laser polarimetry measurements

    PubMed Central

    Lauande-Pimentel, R.; Carvalho, R.; Oliveira, H.; Goncalves, D.; Silva, L.; Costa, V.

    2001-01-01

    AIM—To evaluate the ability of structural parameters (as determined by retinal nerve fibre layer (RNFL) measurements obtained with the scanning laser polarimeter (SLP-NFA/GDx)) and functional parameters (as determined by automated perimetry) to discriminate between normal and glaucomatous eyes.
METHODS—In a case-control study, a total of 91 normal subjects and 94 patients with glaucoma underwent automated perimetry and RNFL measurements obtained with the SLP. Three independent scans of each eye were obtained and a mean image was created and used for further analysis. Only one eye per individual was randomly included in the study. The sensitivity (Se) and specificity (Sp) of 12 RNFL parameters were calculated according to the SLP internal normative database. The Se and Sp of the visual field (VF) global indices and the glaucoma hemifield test (GHT) were also calculated according to the instrument's normative database. Receiver operator characteristic (ROC) curves were built for each SLP parameter and VF index. Fisher's linear discriminant formulas (LDFs) were developed for VF indices (VF LDF), SLP measurements (SLP LDF), and both examinations (combined LDF).
RESULTS—According to the SLP internal database, the parameters with better Se and Sp were: superior/nasal ratio (Se = 58.5%; Sp = 86.8%), and GDx the number (Se = 43.3%; Sp = 96.7%). The construction of an ROC curve for the number resulted in Se = 84% and Sp = 79%. The creation of LDFs improved both the sensitivities and specificities when compared with isolated parameters SLP LDF (Se = 90.4%; Sp = 82.4%), VF LDF (Se = 89.4%; Sp = 89.0%), and combined LDF (Se = 93.0%; Sp = 90.1%). The sensitivity to diagnose early and moderate glaucomatous damage observed with the GHT was lower than that obtained with the number (p<0.01).
CONCLUSIONS—Creation of LDFs enhanced the Se and Sp for both VF and SLP. Integration of SLP and VF in a combined LDF reached the highest Se/Sp relation

  19. Characterization of Choroidal Layers in Normal Aging Eyes Using Enface Swept-Source Optical Coherence Tomography

    PubMed Central

    Mullins, Robert F.; Baumal, Caroline R.; Mohler, Kathrin J.; Kraus, Martin F.; Liu, Jonathan; Badaro, Emmerson; Alasil, Tarek; Hornegger, Joachim; Fujimoto, James G.; Duker, Jay S.; Waheed, Nadia K.

    2015-01-01

    Purpose To characterize qualitative and quantitative features of the choroid in normal eyes using enface swept-source optical coherence tomography (SS-OCT). Methods Fifty-two eyes of 26 consecutive normal subjects were prospectively recruited to obtain multiple three-dimensional 12x12mm volumetric scans using a long-wavelength high-speed SS-OCT prototype. A motion-correction algorithm merged multiple SS-OCT volumes to improve signal. Retinal pigment epithelium (RPE) was segmented as the reference and enface images were extracted at varying depths every 4.13μm intervals. Systematic analysis of the choroid at different depths was performed to qualitatively assess the morphology of the choroid and quantify the absolute thicknesses as well as the relative thicknesses of the choroidal vascular layers including the choroidal microvasculature (choriocapillaris, terminal arterioles and venules; CC) and choroidal vessels (CV) with respect to the subfoveal total choroidal thickness (TC). Subjects were divided into two age groups: younger (<40 years) and older (≥40 years). Results Mean age of subjects was 41.92 (24-66) years. Enface images at the level of the RPE, CC, CV, and choroidal-scleral interface were used to assess specific qualitative features. In the younger age group, the mean absolute thicknesses were: TC 379.4μm (SD±75.7μm), CC 81.3μm (SD±21.2μm) and CV 298.1μm (SD±63.7μm). In the older group, the mean absolute thicknesses were: TC 305.0μm (SD±50.9μm), CC 56.4μm (SD±12.1μm) and CV 248.6μm (SD±49.7μm). In the younger group, the relative thicknesses of the individual choroidal layers were: CC 21.5% (SD±4.0%) and CV 78.4% (SD±4.0%). In the older group, the relative thicknesses were: CC 18.9% (SD±4.5%) and CV 81.1% (SD±4.5%). The absolute thicknesses were smaller in the older age group for all choroidal layers (TC p=0.006, CC p=0.0003, CV p=0.03) while the relative thickness was smaller only for the CC (p=0.04). Conclusions Enface SS-OCT at

  20. Pulsatile flow into the aqueous veins: Manifestations in normal and glaucomatous eyes

    PubMed Central

    Johnstone, Murray; Martin, Elizabeth; Jamil, Annisa

    2015-01-01

    The aqueous outflow system is unique because nowhere else can the pattern of flow of an extravascular fluid be directly observed as it returns to the vascular system. Such observations reveal that aqueous flow both from Schlemm’s canal into the aqueous veins and from the aqueous veins into the episcleral veins is pulsatile. Pulsatile aqueous flow mechanisms are observable in vivo not only in normal and but also in glaucomatous eyes. A series of specific patterns accompany the pulsatile mixing of aqueous with blood in the episcleral veins. These directly observable patterns of pulsatile flow are synchronous with intraocular pressure (IOP) transients induced by the cardiac pulse, blinking and eye movement. Patterns of pulsatile flow are altered by events that increase IOP such as pressure on the side of the eye, tonography and water drinking. Pulsatile flow stops when IOP is reduced below its resting level, but begins again when IOP returns to the resting level. Pulsatile flow reduction probably results from the intrinsic reduction of pulse amplitude at a lower IOP, and may thus provide a passive mechanism to maintain short-term homeostasis. Thus modulation of the pulsatile flow phenomenon appears to maintain a homeostatic IOP setpoint. Visible pulsatile flow abnormalities develop in glaucoma patients. Medications that reduce IOP through improvement in outflow do so through pulsatile flow mechanisms. Laboratory studies have demonstrated that cyclic stresses in outflow tissues alter signaling pathways, cytoskeletal responses, extracellular matrix composition and cytokine secretion. How physiologic pulse transients orchestrate cellular responses and how cellular responses identified in the laboratory may in turn regulate pulsatile aqueous outflow is unknown. Linkage of laboratory and in vivo observations await an improved understanding of how cellular and extracellular structures within the outflow system are able to generate an aqueous pulse wave. The purpose of the

  1. Profile and Determinants of Retinal Optical Intensity in Normal Eyes with Spectral Domain Optical Coherence Tomography

    PubMed Central

    Chen, Haoyu; Yang, Jianling; Shi, Fei; Zheng, Ce; Zhu, Weifang; Xiang, Dehui; Chen, Xinjian; Zhang, Mingzhi

    2016-01-01

    Purpose To investigate the profile and determinants of retinal optical intensity in normal subjects using 3D spectral domain optical coherence tomography (SD OCT). Methods A total of 231 eyes from 231 healthy subjects ranging in age from 18 to 80 years were included and underwent a 3D OCT scan. Forty-four eyes were randomly chosen to be scanned by two operators for reproducibility analysis. Distribution of optical intensity of each layer and regions specified by the Early Treatment of Diabetic Retinopathy Study (ETDRS) were investigated by analyzing the OCT raw data with our automatic graph-based algorithm. Univariate and multivariate analyses were performed between retinal optical intensity and sex, age, height, weight, spherical equivalent (SE), axial length, image quality, disc area and rim/disc area ratio (R/D area ratio). Results For optical intensity measurements, the intraclass correlation coefficient of each layer ranged from 0.815 to 0.941, indicating good reproducibility. Optical intensity was lowest in the central area of retinal nerve fiber layer, ganglion cell layer, inner plexiform layer, inner nuclear layer, outer plexiform layer and photoreceptor layer, except for the retinal pigment epithelium (RPE). Optical intensity was positively correlated with image quality in all retinal layers (0.553<β<0.851, p<0.01), and negatively correlated with age in most retinal layers (-0.362<β<-0.179, p<0.01), except for the RPE (β = 0.456, p<0.01), outer nuclear layer and photoreceptor layer (p>0.05). There was no relationship between retinal optical intensity and sex, height, weight, SE, axial length, disc area and R/D area ratio. Conclusions There was a specific pattern of distribution of retinal optical intensity in different regions. The optical intensity was affected by image quality and age. Image quality can be used as a reference for normalization. The effect of age needs to be taken into consideration when using OCT for diagnosis. PMID:26863010

  2. Rat Optic Nerve Head Anatomy within 3D Histomorphometric Reconstructions of Normal Control Eyes

    PubMed Central

    Pazos, Marta; Yang, Hongli; Gardiner, Stuart K.; Cepurna, William O.; Johnson, Elaine C.; Morrison, John C.; Burgoyne, Claude F.

    2015-01-01

    The purpose of this study is to three-dimensionally (3D) characterize the principal macroscopic and microscopic relationships within the rat optic nerve head (ONH) and quantify them in normal control eyes. Perfusion-fixed, trephinated ONH from 8 normal control eyes of 8 Brown Norway Rats were 3D histomorphometrically reconstructed, visualized, delineated and parameterized. The rat ONH consists of 2 scleral openings, (a superior neurovascular and inferior arterial) separated by a thin connective tissue strip we have termed the “scleral sling”. Within the superior opening, the nerve abuts a prominent extension of Bruch's Membrane (BM) superiorly and is surrounded by a vascular plexus, as it passes through the sclera, that is a continuous from the choroid into and through the dural sheath and contains the central retinal vein (CRV), (inferiorly). The inferior scleral opening contains the central retinal artery and three long posterior ciliary arteries which obliquely pass through the sclera to obtain the choroid. Bruch's Membrane Opening (BMO) is irregular and vertically elongated, enclosing the nerve (superiorly) and CRV and CRA (inferiorly). Overall mean BMO Depth, BMO Area, Choroidal Thickness and peripapillary Scleral Thickness were 29 μm, 56.5 × 103 μm2, 57 μm and 104 μm respectively. Mean anterior scleral canal opening (ASCO) and posterior scleral canal opening (PSCO) radii were 201 ± 15 μm and 204 ± 16 μm, respectively. Mean optic nerve area at the ASCO and PSCO were 46.3 × 103 ± 4.4 × 103 μm2 and 44.1 × 103 ± 4.5 × 103 μm2 respectively. In conclusion, the 3D complexity of the rat ONH and the extent to which it differs from the primate have been under-appreciated within previous 2D studies. Properly understood, these anatomic differences may provide new insights into the relative susceptibilities of the rat and primate ONH to elevated intraocular pressure. PMID:26021973

  3. Saccadic Eye Movements in Normal Children from 8 to 15 Years of Age: A Developmental Study of Visuospatial Attention.

    ERIC Educational Resources Information Center

    Ross, Randal G.; And Others

    1994-01-01

    This study used saccadic eye movements to assess visuospatial attention in 53 normal children (ages 8-15). Saccadic latency, the ability to suppress extraneous saccades during fixation, and the ability to inhibit task-provoked anticipatory saccades all improved with age. Developmental patterns varied by task. Analyses of age-related changes may be…

  4. Gonioscopic differences between eyes with primary open-angle glaucoma and normal eyes in subjects over the age of forty.

    PubMed Central

    Kimura, R; Levene, R Z

    1975-01-01

    Gonioscopy was performed on 110 patients with primary open-angle glaucoma over the age of 40 and an equal number of normal subjects matched by race and age. The frequency distribution of various angle features differed in two groups. In the glaucoma group there were more iris processes at all levels of insertion, a higher insertion of the iris root, and more trabecular pigmentation. We believe that a congenital angle anomaly is an important factor in the pathogenesis of the elevated intraocular pressure. PMID:1246817

  5. Analytical approach for selecting normalizing genes from a cDNA microarray platform to be used in q-RT-PCR assays: a cnidarian case study.

    PubMed

    Rodriguez-Lanetty, Mauricio; Phillips, Wendy S; Dove, Sophie; Hoegh-Guldberg, Ove; Weis, Virginia M

    2008-04-24

    Research in gene function using Quantitative Reverse Transcription PCR (q-RT-PCR) and microarray approaches are emerging and just about to explode in the field of coral and cnidarian biology. These approaches are showing the great potential to significantly advance our understanding of how corals respond to abiotic and biotic stresses, and how host cnidarians/dinoflagellates symbioses are maintained and regulated. With these genomic advances, however, new analytical challenges are also emerging, such as the normalization of gene expression data derived from q-RT-PCR. In this study, an effective analytical method is introduced to identify candidate housekeeping genes (HKG) from a sea anemone (Anthopleura elegantissima) cDNA microarray platform that can be used as internal control genes to normalize q-RT-PCR gene expression data. It is shown that the identified HKGs were stable among the experimental conditions tested in this study. The three most stables genes identified, in term of gene expression, were beta-actin, ribosomal protein L12, and a Poly(a) binding protein. The applications of these HKGs in other cnidarian systems are further discussed. PMID:17913235

  6. Safety evaluation of the aqueous extract Kothala himbutu (Salacia reticulata) stem in the hepatic gene expression profile of normal mice using DNA microarrays.

    PubMed

    Im, Ryanghyok; Mano, Hiroshi; Nakatani, Sachie; Shimizu, Jun; Wada, Masahiro

    2008-12-01

    Kothala himbutu is a traditional Ayurvedic medicinal plant used to treat diabetes. We aimed to evaluate the safety of an aqueous extract of Kothala himbutu stem (KTE) in normal mice. The mice were divided into two groups: one was administered KTE and the other distilled water for 3 weeks. During the test period, the groups showed no significant differences in body weight gain or plasma parameters, such as fasting blood glucose level, oral glucose tolerance test, or aspartate transaminase (AST) or alanine transaminase (ALT) activity. DNA microarray analysis revealed that expression of genes of known function, such as those for the stress response, ribosomal proteins, transcription, cell function, the inflammatory/immune response, and metabolism (xenobiotic, glutathione, etc.) remained largely unaffected by KTE. However some genes such as catechol-o-methyltransferase and succinyl-CoA synthetase were regulated by KTE, indicating that KTE is not toxic to normal mice and might be effective as a functional food. PMID:19060410

  7. Microarray analysis reveals the inhibition of nuclear factor-kappa B signaling by aristolochic acid in normal human kidney (HK-2) cells

    PubMed Central

    Chen, Ya-yin; Chiang, Su-yin; Wu, Hsiu-ching; Kao, Shung-te; Hsiang, Chien-yun; Ho, Tin-yun; Lin, Jaung-geng

    2010-01-01

    Aim: To study the molecular mechanism underlying the effect of aristolochic acid (AA), a major active component of plants from the Aristolochiaceae family using microarray analysis. Methods: Human kidney (HK-2) cells were treated with AA (0, 10, 30, and 90 μmol/L) for 24 h, and the cell viability was measured by a 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazolium bromide assay. Complementary DNA microarrays were used to investigate the gene expression pattern of HK-2 cells exposed to AA in triplicate. A quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assay was used to verify the microarray data for selected nuclear factor kappa B (NF-κB)-regulated genes. Furthermore, the subcellular localization of NF-κB p65 was visualized by immunofluorescence confocal microscopy in HK-2 cells. The NF-κB activity was examined by a luciferase reporter assay in HK-2/NF-κB transgenic cells. Results: AA exhibited a dose-dependent cytotoxic effect in HK-2 cells and induced alterations in the gene expression profiles related to the DNA damage response, DNA repair, macromolecule metabolic process, carbohydrate metabolic process, DNA metabolic process, apoptosis, cell cycle, and transcription. In addition, 9 biological pathways associated with immunomodulatory functions were down-regulated in AA-treated HK-2 cells. A network analysis revealed that NF-κB played a central role in the network topology. Among NF-κB-regulated genes, 8 differentially expressed genes were verified by qRT-PCR. The inhibition of NF-κB activity by AA was further confirmed by immunofluorescence confocal microscopy and by NF-κB luciferase reporter assay. Conclusion: Our data revealed that AA could suppress NF-κB activity in normal human cells, perhaps partially accounting for the reported anti-inflammatory effects of some plants from the genus Aristolochia. PMID:20139906

  8. Preface: The aging eye: normal changes, age-related diseases, and sight-saving approaches.

    PubMed

    Chader, Gerald J; Taylor, Allen

    2013-12-13

    This volume presents articles based on a workshop held June 14 to 16, 2013 in Rancho Palos Verde, CA sponsored by the Ocular Research Symposia Foundation (ORSF). The mission of the ORSF is to focus attention on unmet needs and current research opportunities in eye research with the objective of accelerating translation of research findings to effective clinical care. In this workshop, the subject of the "The Aging Eye" was addressed, including the prevalence of eye diseases in aging and the economic burden imposed by these diseases. New research work was highlighted on the genetics, biology, biochemistry, neurochemistry, and the impact of nutrition and the environment on function in the older eye. By identifying "low-hanging fruit" (i.e., the best opportunities for successful transition of laboratory research for the prevention of and new treatments and cures for ocular diseases), we seek to spur funding at both the basic research and clinical levels, resulting in sight-saving and sight-restoration measures in the near future.

  9. Normal Speed and Accuracy of Saccade and Vergence Eye Movements in Dyslexic Reader Children

    PubMed Central

    Bucci, Maria Pia; Vernet, Marine; Gerard, Christophe-Loïc; Kapoula, Zoï

    2009-01-01

    Objective. Latency of eye movements depends on cortical structures while speed of execution and accuracy depends mostly on subcortical brainstem structures. Prior studies reported in dyslexic reader children abnormalities of latencies of saccades (isolated and combined with vergence); such abnormalities were attributed to deficits of fixation control and of visual attention. In this study we examine speed and accuracy characteristics of horizontal eye movements in natural space (saccades, vergence and combined movements) in dyslexic reader children. Methods. Two paradigms are tested: gap paradigm (fixation offset 200 ms prior to target onset), producing shorter latencies, in both non-dyslexic reader and dyslexic reader children and simultaneous paradigm. Seventeen dyslexic reader children (mean age: 12 ± 0.08 years) and thirteen non-dyslexic reader children (mean age: 12 ± 1 years) were tested. Horizontal eye movements from both eyes were recorded simultaneously by a photoelectric device (Oculometer, Dr. Bouis). Results. For all movements tested (saccades, vergence, isolated or combined) and for both paradigms, the mean velocity and accuracy were similar in dyslexic readers and non-dyslexic readers; no significant difference was found. Conclusion. This negative but important result, suggests no dysfunction of brainstem ocular motor circuits in dyslexic readers. It contrasts results on latencies related to visual attention dysfunction at cortical level. PMID:20309415

  10. Preface: The aging eye: normal changes, age-related diseases and sight-saving approaches

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This volume presents chapters based on a workshop held on June 14-16, 2013 in Rancho Palos Verde, CA sponsored by the Ocular Research Symposia Foundation (ORSF). The mission of the ORSF is to focus attention on unmet needs and current research opportunities in eye research with the objective of acce...

  11. Comparison of Schlemm's canal's biological parameters in primary open-angle glaucoma and normal human eyes with swept source optical

    NASA Astrophysics Data System (ADS)

    Wang, Fei; Shi, Guohua; Li, Xiqi; Lu, Jing; Ding, Zhihua; Sun, Xinghuai; Jiang, Chunhui; Zhang, Yudong

    2012-11-01

    Thirty-seven normal and primary open angle glaucoma (POAG) subjects were noninvasively imaged by a tailor-made real-time anterior segment swept source optical coherence tomography (SS-OCT) to demonstrate the differences of the Schlemm's canal (SC) between POAG and normal eyes. After the cross-section images of the anterior chamber angle were acquired by SS-OCT, SC was confirmed by two independent masked observers and the average area, long diameter, and perimeter of the SC were measured. In normal subjects the circumference, area, and long diameter is 580.34±87.81 μm, 8023.89±1486.10 μ, and 272.83±49.39 μm, respectively, and these parameters were 393.25±98.04 μm, 3941.50±1210.69 μ, and 190.91±46.47 μm in the POAG subjects. The area of SC in the normal ones was significantly larger than that in POAG eyes (p<0.001), so as the long diameter and the perimeter (p<0.001 p<0.001).

  12. Relationship among Photopic Negative Response, Retinal Nerve Fiber Layer Thickness, and Visual Field between Normal and POAG Eyes

    PubMed Central

    Shen, Xiaoli; Huang, Lina; Fan, Ning; He, Jing

    2013-01-01

    Purpose. To determine the relationship among photopic negative response (PhNR) of the electroretinogram (ERG), retinal nerve fiber layer (RNFL) thickness, and the visual field in normal and glaucomatous patients. Methods. Thirty-eight normal volunteers and one hundred twenty-four patients with Primary open-angle glaucoma (POAG) were enrolled in the study. The PhNRs were elicited by white stimuli on a white background and red stimuli on a blue background. The visual field parameters were measured using the standard automated perimetry (SAP). The spectral domain optical coherence tomography (SD-OCT) was used to measure the retinal nerve fiber layer (RNFL) thickness around the optic disc. Results. The PhNR amplitude (W/W, B/R), MD, and mean RNFL thickness in POAG eyes were significantly lower than normal eyes (P = 0.001). The R value in Normal + Glaucomatous group was higher than that of the only glaucomatous group. The R values of PhNR amplitude (B/R) with MD and RNFL were higher than those of PhNR amplitude (W/W). Significant linear association was found in the relationship between RNFL thickness and PhNR amplitude (B/R) (R2 = 0.5, P = 0.001). However, significant curve associations were found in the relationship between MD and PhNR amplitude (B/R) and RNFL thickness (R2 = 0.525, 0.442, P = 0.001). Conclusions. The ganglion cell activity can be more efficiently evaluated with the PhNR elicited with a red than with a broadband stimulus. The linear relationship between the PhNR amplitude and RNFL thickness indicates that inner retinal function declines proportionately with neural loss in glaucomatous eyes. The PhNR and RNFLT are more objective tools to detect glaucomatous damage than visual field. PMID:24558598

  13. Morphometric measurement of Schlemm's canal in normal human eye using anterior segment swept source optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Shi, Guohua; Wang, Fei; Li, Xiqi; Lu, Jing; Ding, Zhihua; Sun, Xinghuai; Jiang, Chunhui; Zhang, Yudong

    2012-01-01

    We have used anterior segment swept source optical coherence tomography to measure Schlemm's canal (SC) morphometric values in the living human eye. Fifty healthy volunteers with 100 normal eyes were measured in the nasal and temporal side. Comparison with the published SC morphometric values of histologic sections proves the reliability of our results. The statistical results show that there are no significant differences between nasal and temporal SC with respect to their diameter, perimeter, and area in our study (diameter: t=0.122, p=0.903; perimeter: t=-0.003, p=0.998; area: t=-1.169, p=0.244); further, no significant differences in SC morphometric values are found between oculus sinister and oculus dexter (diameter: t=0.943, p=0.35; perimeter: t=1.346, p=0.18; area: t=1.501, p=0.135).

  14. A mass and solute balance model for tear volume and osmolarity in the normal and the dry eye.

    PubMed

    Gaffney, E A; Tiffany, J M; Yokoi, N; Bron, A J

    2010-01-01

    Tear hyperosmolarity is thought to play a key role in the mechanism of dry eye, a common symptomatic condition accompanied by visual disturbance, tear film instability, inflammation and damage to the ocular surface. We have constructed a model for the mass and solute balance of the tears, with parameter estimation based on extensive data from the literature which permits the influence of tear evaporation, lacrimal flux and blink rate on tear osmolarity to be explored. In particular the nature of compensatory events has been estimated in aqueous-deficient (ADDE) and evaporative (EDE) dry eye. The model reproduces observed osmolarities of the tear meniscus for the healthy eye and predicts a higher concentration in the tear film than meniscus in normal and dry eye states. The differential is small in the normal eye, but is significantly increased in dry eye, especially for the simultaneous presence of high meniscus concentration and low meniscus radius. This may influence the interpretation of osmolarity values obtained from meniscus samples since they need not fully reflect potential damage to the ocular surface caused by tear film hyperosmolarity. Interrogation of the model suggests that increases in blink rate may play a limited role in compensating for a rise in tear osmolarity in ADDE but that an increase in lacrimal flux, together with an increase in blink rate, may delay the development of hyperosmolarity in EDE. Nonetheless, it is predicted that tear osmolarity may rise to much higher levels in EDE than ADDE before the onset of tear film breakup, in the absence of events at the ocular surface which would independently compromise tear film stability. Differences in the predicted responses of the pre-ocular tears in ADDE compared to EDE or hybrid disease to defined conditions suggest that no single, empirically-accessible variable can act as a surrogate for tear film concentration and the potential for ocular surface damage. This emphasises the need to measure

  15. Preserve the (intraocular) environment: the importance of maintaining normal oxygen gradients in the eye.

    PubMed

    Beebe, David C; Shui, Ying-Bo; Siegfried, Carla J; Holekamp, Nancy M; Bai, Fang

    2014-05-01

    Oxygen levels in the eye are generally low and tightly regulated. Oxygen enters the eye largely by diffusion from retinal arterioles and through the cornea. In intact eyes, oxygen from the retinal arterioles diffuses into the vitreous body. There is a decreasing oxygen gradient from the retina to the lens, established by oxygen consumption by ascorbate in the vitreous fluid and lens metabolism. Age-related degeneration of the vitreous body or removal during vitrectomy exposes the posterior of the lens to increased oxygen, causing nuclear sclerotic cataracts. Lowering oxygen in the vitreous, as occurs in patients with ischemic diabetic retinopathy, protects against cataracts after vitrectomy. Vitrectomy and cataract surgery increase oxygen levels at the trabecular meshwork and with it the risk of open angle glaucoma. Two additional risk factors for glaucoma, African heritage and having a thinner cornea, are also associated with increased oxygen in the anterior chamber angle. Preservation of the vitreous body and the lens, two important oxygen consumers, would protect against nuclear sclerotic cataracts and open angle glaucoma. Delaying removal of the lens for as long as possible after vitrectomy would be an important step in delaying ocular hypertension and glaucoma progression. PMID:24687817

  16. Computed Tomography and Magnetic Resonance Anatomy of the Normal Orbit and Eye of the Horse.

    PubMed

    D'Août, C; Nisolle, J F; Navez, M; Perrin, R; Launois, T; Brogniez, L; Clegg, P; Hontoir, F; Vandeweerd, J M

    2015-10-01

    Traumatic and infectious diseases of the eye and orbit can occur in horses. For diagnosis and monitoring of such diseases, medical imaging is useful including computed tomography (CT) and magnetic resonance imaging (MRI). The aim of the current study was to describe CT and MRI anatomy of the equine orbit and ocular globe. The heads from four adult horses were scanned with a 6-slice Emotion 6 CT (Siemens, Erlangen), and a 3.0 Tesla Siemens Verio 6 MRI using T1 and T2-weighted sequences. To validate CT and MR reference images, these were compared with anatomical models and gross anatomical sections. The bony limits of the orbital cavity, the relationship of the orbit with sinuses and foramina of the skull were well identified by CT. MRI was useful to observe soft tissues and was able to identify adnexae of the ocular globe (eyelids, periorbital fat, extraocular muscles, lacrymal and tarsal glands). Although MRI was able to identify all components of the eye (including the posterior chamber), it could not differentiate sclera from choroid and retina. The only nerve identified was the optic nerve. Vessels were not seen in this series of cadaver heads. This study showed that CT and MRI are useful techniques to image the equine orbit and eye that can have clinical applications.

  17. Healthy Eyes

    MedlinePlus

    ... please turn Javascript on. Healthy Eyes Maintaining Your Vision Click for more information Taking good care of ... are qualified to perform eye exams. Aging and Vision Changes As you age, it is normal to ...

  18. Studies of the Ability to Hold the Eye in Eccentric Gaze: Measurements in Normal Subjects with the Head Erect

    NASA Technical Reports Server (NTRS)

    Reschke, Millard F.; Somers, Jeffrey T.; Feiveson, Alan H.; Leigh, R. John; Wood, Scott J.; Paloski, William H.; Kornilova, Ludmila

    2006-01-01

    We studied the ability to hold the eyes in eccentric horizontal or vertical gaze angles in 68 normal humans, age range 19-56. Subjects attempted to sustain visual fixation of a briefly flashed target located 30 in the horizontal plane and 15 in the vertical plane in a dark environment. Conventionally, the ability to hold eccentric gaze is estimated by fitting centripetal eye drifts by exponential curves and calculating the time constant (t(sub c)) of these slow phases of gazeevoked nystagmus. Although the distribution of time-constant measurements (t(sub c)) in our normal subjects was extremely skewed due to occasional test runs that exhibited near-perfect stability (large t(sub c) values), we found that log10(tc) was approximately normally distributed within classes of target direction. Therefore, statistical estimation and inference on the effect of target direction was performed on values of z identical with log10t(sub c). Subjects showed considerable variation in their eyedrift performance over repeated trials; nonetheless, statistically significant differences emerged: values of tc were significantly higher for gaze elicited to targets in the horizontal plane than for the vertical plane (P less than 10(exp -5), suggesting eccentric gazeholding is more stable in the horizontal than in the vertical plane. Furthermore, centrifugal eye drifts were observed in 13.3, 16.0 and 55.6% of cases for horizontal, upgaze and downgaze tests, respectively. Fifth percentile values of the time constant were estimated to be 10.2 sec, 3.3 sec and 3.8 sec for horizontal, upward and downward gaze, respectively. The difference between horizontal and vertical gazeholding may be ascribed to separate components of the velocity position neural integrator for eye movements, and to differences in orbital mechanics. Our statistical method for representing the range of normal eccentric gaze stability can be readily applied in a clinical setting to patients who were exposed to environments

  19. Heterogeneity of SPECT bull`s-eyes in normal dogs: Comparison of attenuation compensation algorithms

    SciTech Connect

    DiBella, E.V.R.; Eisner, R.L.; Schmarkey, L.S.; Barclay, A.B.; Patterson, R.E.; Nowak, D.J.; Lalush, D.S.; Tsui, B.M.W. ||

    1995-08-01

    In normal dogs, SPECT {sup 99m}Tc Sestamibi (MIBI) and {sup 201}Tl myocardial perfusion images reconstructed with filtered backprojection (FBP) show a large decrease of counts in the septal wall (S) compared to the lateral wall (L). The authors evaluated the iterative method of Chang at 0 and 1 iterations (Chang0 and Chang1), and the Maximum Likelihood-Expectation Maximization with attenuation compensation (ML-EM-ATN) algorithm on data acquired from 5 normal dogs and from simulated projection data using a homogeneous count-density model of a normal canine myocardium in the attenuation field measured in one dog. Mean counts in the S and L regions were calculated from maximum-count circumferential profile arrays. Their results demonstrate that ML-EM-ATN and Chang1 result in improved uniformity, as measured by the S/L ratio.

  20. Prenatal diagnosis of sub-microscopic partial trisomy 10q using chromosomal microarray analysis in a phenotypically abnormal fetus with normal karyotype.

    PubMed

    Browne, P C; Adam, S; Badr, M; Brooks, C R; Edwards, J; Walker, P; Mohamed, S; Gregg, A R

    2016-05-17

    Partial trisomy of the 10q region was originally reported in 1979 [1]. For 25 years, the diagnosis was made microscopically based on large, visible insertions in the region identified by karyotype analysis. Previous case reports have included both unbalanced translocations and large duplications/insertions in the 10q region [2]. Probands with partial trisomy 10q syndrome often have an abnormal phenotype that may include developmental delay [3-5], craniofacial abnormalities [3, 5], talipes (clubfoot) [2], microcephaly [2-4], or congenital heart disease [2-6]. Prenatal diagnoses by karyotype have been made following ultrasound diagnosis of sacrococcygeal teratoma [7], renal pyelectasis [3, 8-10], and other fetal abnormalities [4]. In this case, we report the first prenatal diagnosis of partial trisomy 10q (10q22.3-10q23.2) with a normal karyotype and an abnormal chromosomal microarray analysis (CMA). This is the smallest copy number variant (CNV) (7.5 Mb) in the 10q22.3-10q23.2 regions yet reported. PMID:27197934

  1. Normalization.

    ERIC Educational Resources Information Center

    Cuevas, Eduardo J.

    1997-01-01

    Discusses cornerstone of Montessori theory, normalization, which asserts that if a child is placed in an optimum prepared environment where inner impulses match external opportunities, the undeviated self emerges, a being totally in harmony with its surroundings. Makes distinctions regarding normalization, normalized, and normality, indicating how…

  2. Biophysical and Morphological Evaluation of Human Normal and Dry Eye Meibum Using Hot Stage Polarized Light Microscopy

    PubMed Central

    Butovich, Igor A.; Lu, Hua; McMahon, Anne; Ketelson, Howard; Senchyna, Michelle; Meadows, David; Campbell, Elaine; Molai, Mike; Linsenbardt, Emily

    2014-01-01

    Purpose. To study melting characteristics and the morphology of human and mouse meibum. Methods. Hot stage cross-polarized light microscopy (HSPM) and immunohistochemical approaches were used. Results. Isolated human meibum, and meibum of mice (either isolated or within the meibomian ducts of mice), were found to be in liquid-crystal state at physiological temperatures. Melting of both types of meibum started at approximately 10°C and was completed at approximately 40°C. Melting curves of isolated meibum and meibum inside the meibomian ducts were multiphasic with at least two or three clearly defined phase transition temperatures, typically at approximately 12 ± 2°C (minor transition), 21 ± 3°C, and 32 ± 3°C, regardless the source of meibum. Melting was highly cooperative in nature. Samples of abnormal human meibum collected from dry eye patients with meibomian gland dysfunction often showed an increased presence of nonlipid, nonmelting, nonbirefringent, chloroform-insoluble inclusions of a protein nature. The inclusions were positively stained for cytokeratins. The presence of these inclusions was semiquantitatively characterized using a newly proposed 0 to 4 scale. In the presence of large amounts of these inclusions, melting characteristics of meibum and its structural integrity were altered. Conclusions. HSPM is an effective tool that is suitable for biophysical and morphological evaluation of meibum. Morphological properties and melting characteristics of human meibum were found to be similar to those of mice. Abnormal meibum of many dry eye patients contained large quantities of nonlipid, protein-like inclusions, which were routinely absent in meibum of normal controls. PMID:24282231

  3. Color defect and color theory; studies of normal and colorblind persons, including a subject color-blind in one eye but not in the other.

    PubMed

    GRAHAM, C H; HSIA, Y

    1958-03-28

    It is important to find answers to two questions concerning the visual discriminations of dichromatic persons, especially deuteranopes: (i) Do such persons show a loss of sensitivity to various wavelengths of the spectrum as compared with normal subjects? (ii) What colors do they see? A number of experiments were performed on the first question. First, luminosity curves were determined on three groups of subjects, consisting respectively of five protanopes, six deuteranopes, and seven normal individuals. As compared with normal subjects, protanopes show a loss of luminosity in the red, whereas deuteranopes show a loss in the blue-to-green region of the spectrum (See 10). Second, we examined the luminosity curves of a subject whose right eye is classifiable (on the basis of color-mixture determinations) as normal and whose left eye is classifiable as dichromatic. (The hue discrimination curve for her dichromatic eye seemed comparable to the curve of the usual deuteranope except in the violet, where it manifested relatively good discrimination.) The luminosity function for this subject's dichromatic eye, determined by data on threshold and flicker, exhibits the same type of luminosity loss in the blue and green regions of the spectrum as was shown by our group of six deuteranopes. Only unilaterally dichromatic subjects can tell us how colors seen by a dichromatic eye appear to a normal eye. In the color-blind eye, our unilaterally dichromatic subject sees wavelengths below and above her neutral ("grey") point (which occurs at 502 mmicro) as, respectively, a blue equivalent to about 470 mmicro and a yellow equivalent to about 570 mmicro in her normal eye. The results on (i) luminosity loss and (ii) the seeing of wavelengths above 502 mmicro as yellow are considered theoretically. The seeing of yellow by deuteranopes and protanopes may be accounted for by an idea based on Leber-Fick transmation theory. It is proposed that the characteristic sensitivities of the red and

  4. RNA Microarray Analysis of Macroscopically Normal Articular Cartilage from Knees Undergoing Partial Medial Meniscectomy: Potential Prediction of the Risk for Developing Osteoarthritis

    PubMed Central

    Sandell, Linda J.; Zhang, Bo; Wright, Rick W.; Brophy, Robert H.

    2016-01-01

    Objectives (i) To provide baseline knowledge of gene expression in macroscopically normal articular cartilage, (ii) to test the hypothesis that age, body-mass-index (BMI), and sex are associated with cartilage RNA transcriptome, and (iii) to predict individuals at potential risk for developing “pre-osteoarthritis” (OA) based on screening of genetic risk-alleles associated with OA and gene transcripts differentially expressed between normal and OA cartilage. Design Healthy-appearing cartilage was obtained from the medial femoral notch of 12 knees with a meniscus tear undergoing arthroscopic partial meniscectomy. Cartilage had no radiographic, magnetic-resonance-imaging or arthroscopic evidence for degeneration. RNA was subjected to Affymetrix microarrays followed by validation of selected transcripts by microfluidic digital polymerase-chain-reaction. The underlying biological processes were explored computationally. Transcriptome-wide gene expression was probed for association with known OA genetic risk-alleles assembled from published literature and for comparison with gene transcripts differentially expressed between healthy and OA cartilage from other studies. Results We generated a list of 27,641 gene transcripts in healthy cartilage. Several gene transcripts representing numerous biological processes were correlated with age and BMI and differentially expressed by sex. Based on disease-specific Ingenuity Pathways Analysis, gene transcripts associated with aging were enriched for bone/cartilage disease while the gene expression profile associated with BMI was enriched for growth-plate calcification and OA. When segregated by genetic risk-alleles, two clusters of study patients emerged, one cluster containing transcripts predicted by risk studies. When segregated by OA-associated gene transcripts, three clusters of study patients emerged, one of which is remarkably similar to gene expression pattern in OA. Conclusions Our study provides a list of gene

  5. Eyes with Suspicious Appearance of the Optic Disc and Normal Intraocular Pressure: Using Clinical and Epidemiological Characteristics to Differentiate Those with and without Glaucoma

    PubMed Central

    Sousa, Marina C.; Dorairaj, Syril; Biteli, Luis G.

    2016-01-01

    Among all glaucoma suspects, eyes with optic nerve head features suspicious or suggestive of early glaucoma are probably those that offer the greatest challenge for clinicians. In contrast with the robust longitudinal data published on ocular hypertension, there is no specific management guideline for these patients. Therefore, evaluating eyes with suspicious optic disc appearance and normal intraocular pressure (IOP), we sought to investigate potential differences in clinical and epidemiological characteristics to differentiate those with normal-tension glaucoma (NTG) from those with presumed large physiological optic disc cups (pLPC). In this observational case-control study, we consecutively enrolled individuals with pLPC and NTG. All eyes had vertical cup-to-disc ratio (VCDR)≥0.6 and untreated IOP<21 mmHg. Glaucomatous eyes had reproducible visual field defects. Eyes with pLPC required normal visual fields and ≥30 months of follow-up with no evidence of glaucomatous neuropathy. Clinical and epidemiological parameters were compared between groups. Eighty-four individuals with pLPC and 40 NTG patients were included. Regarding our main results, NTG patients were significantly older and with a higher prevalence of Japanese descendants (p<0.01). Not only did pLPC eyes have smaller mean VCDR, but also larger optic discs (p≤0.04). There were no significant differences for gender, central corneal thickness, and spherical equivalent (p≥0.38). Significant odds ratios (OR) were found for race (OR = 2.42; for Japanese ancestry), age (OR = 1.05), VCDR (OR = 5.03), and disc size (OR = 0.04; p≤0.04). In conclusion, in patients with suspicious optic disc and normal IOP, those with older age, Japanese ancestry, smaller optic discs, and larger VCDR are more likely to have NTG, and therefore, deserve deeper investigation and closer monitoring. PMID:27433805

  6. Eye muscle repair - slideshow

    MedlinePlus

    ... page: //medlineplus.gov/ency/presentations/100062.htm Eye muscle repair - series—Normal anatomy To use the sharing ... the eyeball to the eye socket. The external muscles of the eye are found behind the conjunctiva. ...

  7. A novel rat model to study the functions of macrophages during normal development and pathophysiology of the eye.

    PubMed

    Hose, Stacey; Zigler, J Samuel; Sinha, Debasish

    2005-01-31

    Several studies have shown that macrophages play an active role in the initiation and completion of the programmed cell death process during development. Macrophages are called professional phagocytes, as their primary role is phagocytosis. The process of phagocytosis is complex and to date only poorly defined. It has also been postulated that macrophages around the developing lens likely migrate into the neural retina and differentiate into microglia after completion of their role as debris removers. We have identified ED1 immunopositive macrophages and CD11b/18 (OX-42) immunopositive macrophage-like cells in the vitreous chamber and sub-retinal space of a rat spontaneous mutation that we have termed Nuc1. The mutation appears to affect the programmed cell death process and is highly eye specific in its effects. While ED1 and ED2-immunopositive macrophages have previously been found surrounding the developing lens and are thought to play a role in the programmed regression of the tunica vasculosa lentis (part of the vascular structure present on the posterior surface of the lens during development), OX-42-immunopositive cells have not previously been identified in the vitreous chamber under normal or pathological conditions. Macrophage subpopulations surrounding the lens may differentiate into OX-42+ cells in Nuc1 following the release of lens material into the vitreous after the posterior capsule ruptures. In Nuc1 homozygotes, the posterior lens capsule ruptures before birth, causing lens material to be extruded into the vitreous compartment and damaging the tunica vasculosa lentis. Alternatively, OX-42+ cells may be recruited due to an inflammatory response both in the vitreous compartment and sub-retinal space. Inflammation is known to have an enhanced influx of phagocytic cells. Our data suggests that subpopulations of macrophages perform distinct functions in inducing apoptosis and phagocytic activity during normal conditions and in disease.

  8. Protein Microarrays

    NASA Astrophysics Data System (ADS)

    Ricard-Blum, S.

    Proteins are key actors in the life of the cell, involved in many physiological and pathological processes. Since variations in the expression of messenger RNA are not systematically correlated with variations in the protein levels, the latter better reflect the way a cell functions. Protein microarrays thus supply complementary information to DNA chips. They are used in particular to analyse protein expression profiles, to detect proteins within complex biological media, and to study protein-protein interactions, which give information about the functions of those proteins [3-9]. They have the same advantages as DNA microarrays for high-throughput analysis, miniaturisation, and the possibility of automation. Section 18.1 gives a brief overview of proteins. Following this, Sect. 18.2 describes how protein microarrays can be made on flat supports, explaining how proteins can be produced and immobilised on a solid support, and discussing the different kinds of substrate and detection method. Section 18.3 discusses the particular format of protein microarrays in suspension. The diversity of protein microarrays and their applications are then reported in Sect. 18.4, with applications to therapeutics (protein-drug interactions) and diagnostics. The prospects for future developments of protein microarrays are then outlined in the conclusion. The bibliography provides an extensive list of reviews and detailed references for those readers who wish to go further in this area. Indeed, the aim of the present chapter is not to give an exhaustive or detailed analysis of the state of the art, but rather to provide the reader with the basic elements needed to understand how proteins are designed and used.

  9. Symmetry Between the Right and Left Eyes of the Normal Retinal Nerve Fiber Layer Measured with Optical Coherence Tomography (An AOS Thesis)

    PubMed Central

    Budenz, Donald L.

    2008-01-01

    Purpose To determine the limits of the normal amount of interocular symmetry in retinal nerve fiber layer (RNFL) thickness measurements obtained with third-generation time domain optical coherence tomography (OCT3). Methods Both eyes of normal volunteers were scanned using the peripapillary standard and fast RNFL algorithms of OCT3. Results A total of 108 volunteers were included in the analysis. The mean ± standard deviation (SD) of age of the volunteers was 46.0 ± 15.0 years (range 20–82). Forty-two participants (39%) were male and 66 (61%) were female. Mean RNFL thickness correlated extremely well, with intraclass correlation coefficients of 0.89 for both algorithms (95% confidence interval [CI], 0.84–0.93). The mean RNFL thickness of the right eye measured 1.3 μm thicker than the left on the standard scan (SD 4.7, 95% CI 0.4–2.2, P = .004) and 1.2 μm on the fast scan (SD 5.2, 95% CI 0.1–2.2, P = .026). The 95% tolerance limits on the difference between the mean RNFL thicknesses of right minus left eye was −10.8 and +8.9 μm with the standard scan algorithm and −10.6 and +11.7 μm with the fast scan algorithm. Conclusions Mean RNFL thickness between the 2 eyes of normal individuals should not differ by more than approximately 9 to 12 μm, depending on which scanning algorithm of OCT3 is used and which eye measures thicker. Differences beyond this level suggest statistically abnormal asymmetry, which may represent early glaucomatous optic neuropathy. PMID:19277241

  10. Tissue Microarrays.

    PubMed

    Dancau, Ana-Maria; Simon, Ronald; Mirlacher, Martina; Sauter, Guido

    2016-01-01

    Modern next-generation sequencing and microarray technologies allow for the simultaneous analysis of all human genes on the DNA, RNA, miRNA, and methylation RNA level. Studies using such techniques have lead to the identification of hundreds of genes with a potential role in cancer or other diseases. The validation of all of these candidate genes requires in situ analysis of high numbers of clinical tissues samples. The tissue microarray technology greatly facilitates such analysis. In this method minute tissue samples (typically 0.6 mm in diameter) from up to 1000 different tissues can be analyzed on one microscope glass slide. All in situ methods suitable for histological studies can be applied to TMAs without major changes of protocols, including immunohistochemistry, fluorescence in situ hybridization, or RNA in situ hybridization. Because all tissues are analyzed simultaneously with the same batch of reagents, TMA studies provide an unprecedented degree of standardization, speed, and cost efficiency.

  11. Chromosome Microarray.

    PubMed

    Anderson, Sharon

    2016-01-01

    Over the last half century, knowledge about genetics, genetic testing, and its complexity has flourished. Completion of the Human Genome Project provided a foundation upon which the accuracy of genetics, genomics, and integration of bioinformatics knowledge and testing has grown exponentially. What is lagging, however, are efforts to reach and engage nurses about this rapidly changing field. The purpose of this article is to familiarize nurses with several frequently ordered genetic tests including chromosomes and fluorescence in situ hybridization followed by a comprehensive review of chromosome microarray. It shares the complexity of microarray including how testing is performed and results analyzed. A case report demonstrates how this technology is applied in clinical practice and reveals benefits and limitations of this scientific and bioinformatics genetic technology. Clinical implications for maternal-child nurses across practice levels are discussed. PMID:27276104

  12. Repeatability and Reproducibility of Retinal Nerve Fiber Layer Parameters Measured by Scanning Laser Polarimetry with Enhanced Corneal Compensation in Normal and Glaucomatous Eyes

    PubMed Central

    Ara, Mirian; Ferreras, Antonio; Pajarin, Ana B.; Calvo, Pilar; Figus, Michele; Frezzotti, Paolo

    2015-01-01

    Objective. To assess the intrasession repeatability and intersession reproducibility of peripapillary retinal nerve fiber layer (RNFL) thickness parameters measured by scanning laser polarimetry (SLP) with enhanced corneal compensation (ECC) in healthy and glaucomatous eyes. Methods. One randomly selected eye of 82 healthy individuals and 60 glaucoma subjects was evaluated. Three scans were acquired during the first visit to evaluate intravisit repeatability. A different operator obtained two additional scans within 2 months after the first session to determine intervisit reproducibility. The intraclass correlation coefficient (ICC), coefficient of variation (COV), and test-retest variability (TRT) were calculated for all SLP parameters in both groups. Results. ICCs ranged from 0.920 to 0.982 for intravisit measurements and from 0.910 to 0.978 for intervisit measurements. The temporal-superior-nasal-inferior-temporal (TSNIT) average was the highest (0.967 and 0.946) in normal eyes, while nerve fiber indicator (NFI; 0.982) and inferior average (0.978) yielded the best ICC in glaucomatous eyes for intravisit and intervisit measurements, respectively. All COVs were under 10% in both groups, except NFI. TSNIT average had the lowest COV (2.43%) in either type of measurement. Intervisit TRT ranged from 6.48 to 12.84. Conclusions. The reproducibility of peripapillary RNFL measurements obtained with SLP-ECC was excellent, indicating that SLP-ECC is sufficiently accurate for monitoring glaucoma progression. PMID:26185762

  13. Eye-Voice Span during Rapid Automatized Naming of Digits and Dice in Chinese Normal and Dyslexic Children

    ERIC Educational Resources Information Center

    Pan, Jinger; Yan, Ming; Laubrock, Jochen; Shu, Hua; Kliegl, Reinhold

    2013-01-01

    We measured Chinese dyslexic and control children's eye movements during rapid automatized naming (RAN) with alphanumeric (digits) and symbolic (dice surfaces) stimuli. Both types of stimuli required identical oral responses, controlling for effects associated with speech production. Results showed that naming dice was much slower than naming…

  14. Navigating public microarray databases.

    PubMed

    Penkett, Christopher J; Bähler, Jürg

    2004-01-01

    With the ever-escalating amount of data being produced by genome-wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this information to complement and enhance their own studies. Many groups have set up databases of expression data, ranging from large repositories, which are designed to comprehensively capture all published data, through to more specialized databases. The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide downstream analysis of normalized data from more focused studies and data sources. Here we provide a guide to the use of these public microarray resources.

  15. Evaluation of Central Corneal Thickness Using Corneal Dynamic Scheimpflug Analyzer Corvis ST and Comparison with Pentacam Rotating Scheimpflug System and Ultrasound Pachymetry in Normal Eyes.

    PubMed

    Yu, Ayong; Zhao, Weiqi; Savini, Giacomo; Huang, Zixu; Bao, Fangjun; Lu, Weicong; Wang, Qinmei; Huang, Jinhai

    2015-01-01

    Purpose. To assess the repeatability and reproducibility of central corneal thickness (CCT) measurements by corneal dynamic Scheimpflug analyzer Corvis ST in normal eyes and compare the agreement with Pentacam rotating Scheimpflug System and ultrasound pachymetry. Methods. 84 right eyes underwent Corvis ST measurements performed by two operators. The test-retest repeatability (TRT), within-subject coefficient of variation (CoV), and intraclass correlation coefficient (ICC) were used to evaluate the intraoperator repeatability and interoperator reproducibility. CCT measurements also were obtained from Pentacam and ultrasound pachymetry by the first operator. The agreement between the three devices was evaluated with 95% limits of agreement (LoA) and Bland-Altman plots. Results. Corvis ST showed high repeatability as indicated by TRT ≤ 13.0 μm, CoV < 0.9%, and ICC > 0.97. The interoperator reproducibility was also excellent. The CoV was <0.9%, and ICC was >0.97. Corvis ST showed significantly lower values than Pentacam and ultrasound pachymetry (P < 0.001). The 95% LoA between Corvis ST and Pentacam or ultrasound pachymetry were -15.8 to 9.5 μm and -27.9 to 12.3 μm, respectively. Conclusions. Corvis ST showed excellent repeatability and interoperator reproducibility of CCT measurements in normal eyes. Corvis ST is interchangeable with Pentacam but not with ultrasound pachymetry. PMID:26697213

  16. Evaluation of Central Corneal Thickness Using Corneal Dynamic Scheimpflug Analyzer Corvis ST and Comparison with Pentacam Rotating Scheimpflug System and Ultrasound Pachymetry in Normal Eyes

    PubMed Central

    Yu, Ayong; Zhao, Weiqi; Savini, Giacomo; Huang, Zixu; Bao, Fangjun; Lu, Weicong; Wang, Qinmei; Huang, Jinhai

    2015-01-01

    Purpose. To assess the repeatability and reproducibility of central corneal thickness (CCT) measurements by corneal dynamic Scheimpflug analyzer Corvis ST in normal eyes and compare the agreement with Pentacam rotating Scheimpflug System and ultrasound pachymetry. Methods. 84 right eyes underwent Corvis ST measurements performed by two operators. The test-retest repeatability (TRT), within-subject coefficient of variation (CoV), and intraclass correlation coefficient (ICC) were used to evaluate the intraoperator repeatability and interoperator reproducibility. CCT measurements also were obtained from Pentacam and ultrasound pachymetry by the first operator. The agreement between the three devices was evaluated with 95% limits of agreement (LoA) and Bland-Altman plots. Results. Corvis ST showed high repeatability as indicated by TRT ≤ 13.0 μm, CoV < 0.9%, and ICC > 0.97. The interoperator reproducibility was also excellent. The CoV was <0.9%, and ICC was >0.97. Corvis ST showed significantly lower values than Pentacam and ultrasound pachymetry (P < 0.001). The 95% LoA between Corvis ST and Pentacam or ultrasound pachymetry were −15.8 to 9.5 μm and −27.9 to 12.3 μm, respectively. Conclusions. Corvis ST showed excellent repeatability and interoperator reproducibility of CCT measurements in normal eyes. Corvis ST is interchangeable with Pentacam but not with ultrasound pachymetry. PMID:26697213

  17. DNA Microarrays

    NASA Astrophysics Data System (ADS)

    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.

  18. Diurnal Choroidal Thickness Changes in Normal Eyes of Turkish People Measured by Spectral Domain Optical Coherence Tomography

    PubMed Central

    Osmanbasoglu, Ozen Ayrancı; Ozkaya, Abdullah; Ozpınar, Yavuz; Yazici, Ahmet Taylan; Demirok, Ahmet

    2013-01-01

    Purpose. To analyse the diurnal variation of central choroidal thickness (CCT) in healthy emetropic patients during working hours. Methods. Fifty healthy young emmetrpic volunteers were included in this study. CCT was measured at 9 AM and 4 PM with spectral domain optical coherence tomography (Spectralis, Heidelberg Engineering) with enhanced depth imaging. Diurnal variation of CCT, the correlation between rigth and left eyes and the demographic factors affecting this variation were assessed. Findings. The mean CCT at 9 AM and 4 PM was 308.7 ± 64.5 μm and 308.7 ± 62 μm, respectively, with a mean diurnal amplitude of −0.03 ± 14.7 μm, ranging between −55 μm and 47 μm, the difference was statistically insignificant (P: 0.9). There were positive correlations between right and left eyes among CCT measurements at 9 AM, 4 PM and the mean amplitude of diurnal change (r: 0.65, P < 0.01; r: 0.60, P < 0.01; r: 0.45, P: 0.00, resp.). There was a statistically significant negative correlation between the magnitude of diurnal change and age (r: −0.27, P: 0.01). Conclusion. Although the mean CCT in the all group does not show significant variation during working hours, the pattern of diurnal variation may vary from person to person according to age, and there is a great harmony between the two eyes. PMID:23589769

  19. Tiling Microarray Analysis Tools

    SciTech Connect

    Nix, Davis Austin

    2005-05-04

    TiMAT is a package of 23 command line Java applications for use in the analysis of Affymetrix tiled genomic microarray data. TiMAT enables: 1) Rebuilding the genome annotation for entire tiled arrays (repeat filtering, chromosomal coordinate assignment). 2) Post processing of oligo intensity values (quantile normalization, median scaling, PMMM transformation), 3) Significance testing (Wilcoxon rank sum and signed rank tests, intensity difference and ratio tests) and Interval refinement (filtering based on multiple statistics, overlap comparisons), 4) Data visualization (detailed thumbnail/zoomed view with Interval Plots and data export to Affymetrix's Integrated Genome Browser) and Data reports (spreadsheet summaries and detailed profiles)

  20. Automated determination of cup-to-disc ratio for classification of glaucomatous and normal eyes on stereo retinal fundus images

    NASA Astrophysics Data System (ADS)

    Muramatsu, Chisako; Nakagawa, Toshiaki; Sawada, Akira; Hatanaka, Yuji; Yamamoto, Tetsuya; Fujita, Hiroshi

    2011-09-01

    Early diagnosis of glaucoma, which is the second leading cause of blindness in the world, can halt or slow the progression of the disease. We propose an automated method for analyzing the optic disc and measuring the cup-to-disc ratio (CDR) on stereo retinal fundus images to improve ophthalmologists' diagnostic efficiency and potentially reduce the variation on the CDR measurement. The method was developed using 80 retinal fundus image pairs, including 25 glaucomatous, and 55 nonglaucomatous eyes, obtained at our institution. A disc region was segmented using the active contour method with the brightness and edge information. The segmentation of a cup region was performed using a depth map of the optic disc, which was reconstructed on the basis of the stereo disparity. The CDRs were measured and compared with those determined using the manual segmentation results by an expert ophthalmologist. The method was applied to a new database which consisted of 98 stereo image pairs including 60 and 30 pairs with and without signs of glaucoma, respectively. Using the CDRs, an area under the receiver operating characteristic curve of 0.90 was obtained for classification of the glaucomatous and nonglaucomatous eyes. The result indicates potential usefulness of the automated determination of CDRs for the diagnosis of glaucoma.

  1. Aptamer Microarrays

    SciTech Connect

    Angel-Syrett, Heather; Collett, Jim; Ellington, Andrew D.

    2009-01-02

    In vitro selection can yield specific, high-affinity aptamers. We and others have devised methods for the automated selection of aptamers, and have begun to use these reagents for the construction of arrays. Arrayed aptamers have proven to be almost as sensitive as their solution phase counterparts, and when ganged together can provide both specific and general diagnostic signals for proteins and other analytes. We describe here technical details regarding the production and processing of aptamer microarrays, including blocking, washing, drying, and scanning. We will also discuss the challenges involved in developing standardized and reproducible methods for binding and quantitating protein targets. While signals from fluorescent analytes or sandwiches are typically captured, it has proven possible for immobilized aptamers to be uniquely coupled to amplification methods not available to protein reagents, thus allowing for protein-binding signals to be greatly amplified. Into the future, many of the biosensor methods described in this book can potentially be adapted to array formats, thus further expanding the utility of and applications for aptamer arrays.

  2. Post eye-opening maturation of visual receptive field diameters in the superior colliculus of normal- and dark-reared rats.

    PubMed

    Binns, K E; Salt, T E

    1997-04-18

    When the rat's eyes open (P14) the retino-collicular projection is largely mature but the cortico-collicular afferents are naive and mature considerably in the following week. At P14, single units in the superior colliculus' superficial grey layer (SGS) had discrete receptive fields (RFs) (diameter = 15 +/- 1.6 degrees) which expanded with age, reaching 30 +/- 2.6 degrees at P21, possibly reflecting the increasing influence of the visual cortex, whose RFs are known to be enlarged at P21. Subsequently SGS RFs retracted to 13 +/- 1.3 degrees by P23. Dark-reared (DR) rats followed a similar but delayed developmental pattern, such that RFs were still large (27 +/- 3.4 degrees) at P24. By P30 however the RFs of DR rats were the same as those of normal adults. Thus visual experience accelerates the emergence of normal RFs in the SGS.

  3. Hidden Treasures in “Ancient” Microarrays: Gene-Expression Portrays Biology and Potential Resistance Pathways of Major Lung Cancer Subtypes and Normal Tissue

    PubMed Central

    Kerkentzes, Konstantinos; Lagani, Vincenzo; Tsamardinos, Ioannis; Vyberg, Mogens; Røe, Oluf Dimitri

    2014-01-01

    Objective: Novel statistical methods and increasingly more accurate gene annotations can transform “old” biological data into a renewed source of knowledge with potential clinical relevance. Here, we provide an in silico proof-of-concept by extracting novel information from a high-quality mRNA expression dataset, originally published in 2001, using state-of-the-art bioinformatics approaches. Methods: The dataset consists of histologically defined cases of lung adenocarcinoma (AD), squamous (SQ) cell carcinoma, small-cell lung cancer, carcinoid, metastasis (breast and colon AD), and normal lung specimens (203 samples in total). A battery of statistical tests was used for identifying differential gene expressions, diagnostic and prognostic genes, enriched gene ontologies, and signaling pathways. Results: Our results showed that gene expressions faithfully recapitulate immunohistochemical subtype markers, as chromogranin A in carcinoids, cytokeratin 5, p63 in SQ, and TTF1 in non-squamous types. Moreover, biological information with putative clinical relevance was revealed as potentially novel diagnostic genes for each subtype with specificity 93–100% (AUC = 0.93–1.00). Cancer subtypes were characterized by (a) differential expression of treatment target genes as TYMS, HER2, and HER3 and (b) overrepresentation of treatment-related pathways like cell cycle, DNA repair, and ERBB pathways. The vascular smooth muscle contraction, leukocyte trans-endothelial migration, and actin cytoskeleton pathways were overexpressed in normal tissue. Conclusion: Reanalysis of this public dataset displayed the known biological features of lung cancer subtypes and revealed novel pathways of potentially clinical importance. The findings also support our hypothesis that even old omics data of high quality can be a source of significant biological information when appropriate bioinformatics methods are used. PMID:25325012

  4. Eye Infections

    MedlinePlus

    Your eyes can get infections from bacteria, fungi, or viruses. Eye infections can occur in different parts of the eye and can affect just one eye or both. Two common eye infections are Conjunctivitis - also known as pinkeye. Conjunctivitis is ...

  5. Microarrays, Integrated Analytical Systems

    NASA Astrophysics Data System (ADS)

    Combinatorial chemistry is used to find materials that form sensor microarrays. This book discusses the fundamentals, and then proceeds to the many applications of microarrays, from measuring gene expression (DNA microarrays) to protein-protein interactions, peptide chemistry, carbodhydrate chemistry, electrochemical detection, and microfluidics.

  6. Tiling Microarray Analysis Tools

    2005-05-04

    TiMAT is a package of 23 command line Java applications for use in the analysis of Affymetrix tiled genomic microarray data. TiMAT enables: 1) Rebuilding the genome annotation for entire tiled arrays (repeat filtering, chromosomal coordinate assignment). 2) Post processing of oligo intensity values (quantile normalization, median scaling, PMMM transformation), 3) Significance testing (Wilcoxon rank sum and signed rank tests, intensity difference and ratio tests) and Interval refinement (filtering based on multiple statistics, overlap comparisons),more » 4) Data visualization (detailed thumbnail/zoomed view with Interval Plots and data export to Affymetrix's Integrated Genome Browser) and Data reports (spreadsheet summaries and detailed profiles)« less

  7. Young Adults with Autism Spectrum Disorder Show Normal Attention to Eye-Gaze Information--Evidence from a New Change Blindness Paradigm

    ERIC Educational Resources Information Center

    Fletcher-Watson, Sue; Leekam, Susan R.; Findlay, John M.; Stanton, Elaine C.

    2008-01-01

    Other people's eye-gaze is a powerful social stimulus that captures and directs visual attention. There is evidence that this is not the case for children with autism spectrum disorder (ASD), although less is known about attention to eye-gaze in adults. We investigated whether young adults would detect a change to the direction of eye-gaze in…

  8. Manufacturing of microarrays.

    PubMed

    Petersen, David W; Kawasaki, Ernest S

    2007-01-01

    DNA microarray technology has become a powerful tool in the arsenal of the molecular biologist. Capitalizing on high precision robotics and the wealth of DNA sequences annotated from the genomes of a large number of organisms, the manufacture of microarrays is now possible for the average academic laboratory with the funds and motivation. Microarray production requires attention to both biological and physical resources, including DNA libraries, robotics, and qualified personnel. While the fabrication of microarrays is a very labor-intensive process, production of quality microarrays individually tailored on a project-by-project basis will help researchers shed light on future scientific questions.

  9. Eye cosmetics.

    PubMed

    Draelos, Z K

    1991-01-01

    Eye cosmetics are useful to highlight and emphasize the eyes. Currently available eye cosmetics include eye shadows, eye shadow setting creams, under-eye concealers, eye-liners, mascaras, artificial eyelashes, and eyebrow pencils. Special care must be taken when patients with sensitive skin or contact lens wearers select eye cosmetics. Eye cosmetics may also be the cause of either irritant or allergic contact dermatitis, which are two causes of the upper-eyelid dermatitis syndrome.

  10. Eye pain

    MedlinePlus

    Ophthalmalgia; Pain - eye ... Pain in the eye can be an important symptom of a health problem. Make sure you tell your health care provider if you have eye pain that does not go away. Tired eyes or ...

  11. Eye Cancer

    MedlinePlus

    ... Eye Cancer - Overview Request Permissions Print to PDF Eye Cancer - Overview Approved by the Cancer.Net Editorial Board , ... Cancer Research and Advocacy Survivorship Blog About Us Eye Cancer Guide Cancer.Net Guide Eye Cancer Overview Statistics ...

  12. A randomised controlled trial investigating the effect of nutritional supplementation on visual function in normal, and age-related macular disease affected eyes: design and methodology [ISRCTN78467674

    PubMed Central

    Bartlett, Hannah; Eperjesi, Frank

    2003-01-01

    Background Age-related macular disease is the leading cause of blind registration in the developed world. One aetiological hypothesis involves oxidation, and the intrinsic vulnerability of the retina to damage via this process. This has prompted interest in the role of antioxidants, particularly the carotenoids lutein and zeaxanthin, in the prevention and treatment of this eye disease. Methods The aim of this randomised controlled trial is to determine the effect of a nutritional supplement containing lutein, vitamins A, C and E, zinc, and copper on measures of visual function in people with and without age-related macular disease. Outcome measures are distance and near visual acuity, contrast sensitivity, colour vision, macular visual field, glare recovery, and fundus photography. Randomisation is achieved via a random number generator, and masking achieved by third party coding of the active and placebo containers. Data collection will take place at nine and 18 months, and statistical analysis will employ Student's t test. Discussion A paucity of treatment modalities for age-related macular disease has prompted research into the development of prevention strategies. A positive effect on normals may be indicative of a role of nutritional supplementation in preventing or delaying onset of the condition. An observed benefit in the age-related macular disease group may indicate a potential role of supplementation in prevention of progression, or even a degree reversal of the visual effects caused by this condition. PMID:14594455

  13. The concurrent use of three implicit measures (eye movements, pupillometry, and event-related potentials) to assess receptive vocabulary knowledge in normal adults.

    PubMed

    Ledoux, Kerry; Coderre, Emily; Bosley, Laura; Buz, Esteban; Gangopadhyay, Ishanti; Gordon, Barry

    2016-03-01

    Recent years have seen the advent and proliferation of the use of implicit techniques to study learning and cognition. One such application is the use of event-related potentials (ERPs) to assess receptive vocabulary knowledge. Other implicit assessment techniques that may be well-suited to other testing situations or to use with varied participant groups have not been used as widely to study receptive vocabulary knowledge. We sought to develop additional implicit techniques to study receptive vocabulary knowledge that could augment the knowledge gained from the use of the ERP technique. Specifically, we used a simple forced-choice paradigm to assess receptive vocabulary knowledge in normal adult participants using eye movement monitoring (EM) and pupillometry. In the same group of participants, we also used an N400 semantic incongruity ERP paradigm to assess their knowledge of two groups of words: those expected to be known to the participants (high-frequency, familiar words) and those expected to be unknown (low-frequency, unfamiliar words). All three measures showed reliable differences between the known and unknown words. EM and pupillometry thus may provide insight into receptive vocabulary knowledge similar to that from ERPs. The development of additional implicit assessment techniques may increase the feasibility of receptive vocabulary testing across a wider range of participant groups and testing situations, and may make the conduct of such testing more accessible to a wider range of researchers, clinicians, and educators.

  14. Microarrays in hematology.

    PubMed

    Walker, Josef; Flower, Darren; Rigley, Kevin

    2002-01-01

    Microarrays are fast becoming routine tools for the high-throughput analysis of gene expression in a wide range of biologic systems, including hematology. Although a number of approaches can be taken when implementing microarray-based studies, all are capable of providing important insights into biologic function. Although some technical issues have not been resolved, microarrays will continue to make a significant impact on hematologically important research. PMID:11753074

  15. Scleral Micro-RNA Signatures in Adult and Fetal Eyes

    PubMed Central

    Metlapally, Ravikanth; Gonzalez, Pedro; Hawthorne, Felicia A.; Tran-Viet, Khanh-Nhat; Wildsoet, Christine F.; Young, Terri L.

    2013-01-01

    Introduction In human eyes, ocular enlargement/growth reflects active extracellular matrix remodeling of the outer scleral shell. Micro-RNAs are small non-coding RNAs that regulate gene expression by base pairing with target sequences. They serve as nodes of signaling networks. We hypothesized that the sclera, like most tissues, expresses micro-RNAs, some of which modulate genes regulating ocular growth. In this study, the scleral micro-RNA expression profile of rapidly growing human fetal eyes was compared with that of stable adult donor eyes using high-throughput microarray and quantitative PCR analyses. Methods Scleral samples from normal human fetal (24 wk) and normal adult donor eyes were obtained (n=4 to 6, each group), and RNA extracted. Genome-wide micro-RNA profiling was performed using the Agilent micro-RNA microarray platform. Micro-RNA target predictions were obtained using Microcosm, TargetScan and PicTar algorithms. TaqMan® micro-RNA assays targeting micro-RNAs showing either highest significance, detection, or fold differences, and collagen specificity, were applied to scleral samples from posterior and peripheral ocular regions (n=7, each group). Microarray data were analyzed using R, and quantitative PCR data with 2^-deltaCt methods. Results Human sclera was found to express micro-RNAs, and comparison of microarray results for adult and fetal samples revealed many to be differentially expressed (p<0.01, min p= 6.5x1011). Specifically, fetal sclera showed increased expression of mir-214, let-7c, let-7e, mir-103, mir-107, and mir-98 (1.5 to 4 fold changes, p<0.01). However, no significant regionally specific differences .i.e., posterior vs. peripheral sclera, were observed for either adult or fetal samples. Conclusion For the first time, micro-RNA expression has been catalogued in human sclera. Some micro-RNAs show age-related differential regulation, higher in the sclera of rapidly growing fetal eyes, consistent with a role in ocular growth

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

    PubMed

    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.

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

    PubMed Central

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

    2016-01-01

    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. PMID:26813635

  18. Microarrays, antiobesity and the liver

    PubMed Central

    Castro-Chávez, Fernando

    2013-01-01

    In this review, the microarray technology and especially oligonucleotide arrays are exemplified with a practical example taken from the perilipin−/− mice and using the dChip software, available for non-lucrative purposes. It was found that the liver of perilipin−/− mice was healthy and normal, even under high-fat diet when compared with the results published for the scd1−/− mice, which under high-fat diets had a darker liver, suggestive of hepatic steatosis. Scd1 is required for the biosynthesis of monounsaturated fatty acids and plays a key role in the hepatic synthesis of triglycerides and of very-low-density lipoproteins. Both models of obesity resistance share many similar phenotypic antiobesity features, however, the perilipin−/− mice had a significant downregulation of stearoyl CoA desaturases scd1 and scd2 in its white adipose tissue, but a normal level of both genes inside the liver, even under high-fat diet. Here, different microarray methodologies are discussed, and also some of the most recent discoveries and perspectives regarding the use of microarrays, with an emphasis on obesity gene expression, and a personal remark on my findings of increased expression for hemoglobin transcripts and other hemo related genes (hemo-like), and for leukocyte like (leuko-like) genes inside the white adipose tissue of the perilipin−/− mice. In conclusion, microarrays have much to offer in comparative studies such as those in antiobesity, and also they are methodologies adequate for new astounding molecular discoveries [free full text of this article PMID:15657555

  19. Quality Visualization of Microarray Datasets Using Circos

    PubMed Central

    Koch, Martin; Wiese, Michael

    2012-01-01

    Quality control and normalization is considered the most important step in the analysis of microarray data. At present there are various methods available for quality assessments of microarray datasets. However there seems to be no standard visualization routine, which also depicts individual microarray quality. Here we present a convenient method for visualizing the results of standard quality control tests using Circos plots. In these plots various quality measurements are drawn in a circular fashion, thus allowing for visualization of the quality and all outliers of each distinct array within a microarray dataset. The proposed method is intended for use with the Affymetrix Human Genome platform (i.e., GPL 96, GPL570 and GPL571). Circos quality measurement plots are a convenient way for the initial quality estimate of Affymetrix datasets that are stored in publicly available databases.

  20. Microarray Analysis in Glioblastomas

    PubMed Central

    Bhawe, Kaumudi M.; Aghi, Manish K.

    2016-01-01

    Microarray analysis in glioblastomas is done using either cell lines or patient samples as starting material. A survey of the current literature points to transcript-based microarrays and immunohistochemistry (IHC)-based tissue microarrays as being the preferred methods of choice in cancers of neurological origin. Microarray analysis may be carried out for various purposes including the following: To correlate gene expression signatures of glioblastoma cell lines or tumors with response to chemotherapy (DeLay et al., Clin Cancer Res 18(10):2930–2942, 2012)To correlate gene expression patterns with biological features like proliferation or invasiveness of the glioblastoma cells (Jiang et al., PLoS One 8(6):e66008, 2013)To discover new tumor classificatory systems based on gene expression signature, and to correlate therapeutic response and prognosis with these signatures (Huse et al., Annu Rev Med 64(1):59–70, 2013; Verhaak et al., Cancer Cell 17(1):98–110, 2010) While investigators can sometimes use archived tumor gene expression data available from repositories such as the NCBI Gene Expression Omnibus to answer their questions, new arrays must often be run to adequately answer specific questions. Here, we provide a detailed description of microarray methodologies, how to select the appropriate methodology for a given question, and analytical strategies that can be used. Experimental methodology for protein microarrays is outside the scope of this chapter, but basic sample preparation techniques for transcript-based microarrays are included here. PMID:26113463

  1. Microarray Analysis in Glioblastomas.

    PubMed

    Bhawe, Kaumudi M; Aghi, Manish K

    2016-01-01

    Microarray analysis in glioblastomas is done using either cell lines or patient samples as starting material. A survey of the current literature points to transcript-based microarrays and immunohistochemistry (IHC)-based tissue microarrays as being the preferred methods of choice in cancers of neurological origin. Microarray analysis may be carried out for various purposes including the following: i. To correlate gene expression signatures of glioblastoma cell lines or tumors with response to chemotherapy (DeLay et al., Clin Cancer Res 18(10):2930-2942, 2012). ii. To correlate gene expression patterns with biological features like proliferation or invasiveness of the glioblastoma cells (Jiang et al., PLoS One 8(6):e66008, 2013). iii. To discover new tumor classificatory systems based on gene expression signature, and to correlate therapeutic response and prognosis with these signatures (Huse et al., Annu Rev Med 64(1):59-70, 2013; Verhaak et al., Cancer Cell 17(1):98-110, 2010). While investigators can sometimes use archived tumor gene expression data available from repositories such as the NCBI Gene Expression Omnibus to answer their questions, new arrays must often be run to adequately answer specific questions. Here, we provide a detailed description of microarray methodologies, how to select the appropriate methodology for a given question, and analytical strategies that can be used. Experimental methodology for protein microarrays is outside the scope of this chapter, but basic sample preparation techniques for transcript-based microarrays are included here. PMID:26113463

  2. Eye Injuries

    MedlinePlus

    The structure of your face helps protect your eyes from injury. Still, injuries can damage your eye, sometimes severely enough that you could lose your vision. Most eye injuries are preventable. If you play sports or ...

  3. Eye Cancer

    MedlinePlus

    Cancer of the eye is uncommon. It can affect the outer parts of the eye, such as the eyelid, which are made up ... adults are melanoma and lymphoma. The most common eye cancer in children is retinoblastoma, which starts in ...

  4. Eye Diseases

    MedlinePlus

    ... the back of the eye Macular degeneration - a disease that destroys sharp, central vision Diabetic eye problems ... defense is to have regular checkups, because eye diseases do not always have symptoms. Early detection and ...

  5. Microarrays in Glycoproteomics Research

    PubMed Central

    Yue, Tingting; Haab, Brian B.

    2009-01-01

    Microarrays have been extremely useful for investigating binding interactions among diverse types of molecular species, with the main advantage being the ability to examine many interactions using small amount of samples and reagents. Microarrays are increasingly being used to advance research in the field of glycobiology, which is the study of the nature and function and carbohydrates in health and disease. Several types of microarrays are being used in the study of glycans and proteins in glycobiology, including glycan arrays to study the recognition of carbohydrates, lectin arrays to determine carbohydrate expression on purified proteins or on cells, and antibody arrays to examine the variation in particular glycan structures on specific proteins. This review will cover the technology and applications of these types of microarrays, as well as their use for obtaining complementary information on various aspects of glycobiology. PMID:19389548

  6. Functional Protein Microarray Technology

    PubMed Central

    Hu, Shaohui; Xie, Zhi; Qian, Jiang; Blackshaw, Seth; Zhu, Heng

    2010-01-01

    Functional protein microarrays are emerging as a promising new tool for large-scale and high-throughput studies. In this article, we will review their applications in basic proteomics research, where various types of assays have been developed to probe binding activities to other biomolecules, such as proteins, DNA, RNA, small molecules, and glycans. We will also report recent progress of using functional protein microarrays in profiling protein posttranslational modifications, including phosphorylation, ubiquitylation, acetylation, and nitrosylation. Finally, we will discuss potential of functional protein microarrays in biomarker identification and clinical diagnostics. We strongly believe that functional protein microarrays will soon become an indispensible and invaluable tool in proteomics research and systems biology. PMID:20872749

  7. DNA Microarray Technology

    SciTech Connect

    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.

  8. High-throughput allogeneic antibody detection using protein microarrays.

    PubMed

    Paul, Jed; Sahaf, Bita; Perloff, Spenser; Schoenrock, Kelsi; Wu, Fang; Nakasone, Hideki; Coller, John; Miklos, David

    2016-05-01

    Enzyme-linked immunosorbent assays (ELISAs) have traditionally been used to detect alloantibodies in patient plasma samples post hematopoietic cell transplantation (HCT); however, protein microarrays have the potential to be multiplexed, more sensitive, and higher throughput than ELISAs. Here, we describe the development of a novel and sensitive microarray method for detection of allogeneic antibodies against minor histocompatibility antigens encoded on the Y chromosome, called HY antigens. Six microarray surfaces were tested for their ability to bind recombinant protein and peptide HY antigens. Significant allogeneic immune responses were determined in male patients with female donors by considering normal male donor responses as baseline. HY microarray results were also compared with our previous ELISA results. Our overall goal was to maximize antibody detection for both recombinant protein and peptide epitopes. For detection of HY antigens, the Epoxy (Schott) protein microarray surface was both most sensitive and reliable and has become the standard surface in our microarray platform. PMID:26902899

  9. DNA microarrays in neuropsychopharmacology.

    PubMed

    Marcotte, E R; Srivastava, L K; Quirion, R

    2001-08-01

    Recent advances in experimental genomics, coupled with the wealth of sequence information available for a variety of organisms, have the potential to transform the way pharmacological research is performed. At present, high-density DNA microarrays allow researchers to quickly and accurately quantify gene-expression changes in a massively parallel manner. Although now well established in other biomedical fields, such as cancer and genetics research, DNA microarrays have only recently begun to make significant inroads into pharmacology. To date, the major focus in this field has been on the general application of DNA microarrays to toxicology and drug discovery and design. This review summarizes the major microarray findings of relevance to neuropsychopharmacology, as a prelude to the design and analysis of future basic and clinical microarray experiments. The ability of DNA microarrays to monitor gene expression simultaneously in a large-scale format is helping to usher in a post-genomic age, where simple constructs about the role of nature versus nurture are being replaced by a functional understanding of gene expression in living organisms. PMID:11479006

  10. A comparison of the ocular hypotensive effect of 0.025% bromocriptine and 0.25% timolol eye drops in normal human volunteers.

    PubMed Central

    al-Sereiti, M R; Coakes, R L; O'Sullivan, D P; Turner, P

    1989-01-01

    1. The ocular hypotensive effect of 0.025% bromocriptine and 0.25% timolol eye drops was compared in nine healthy human volunteers, using non-contact tonometry. 2. Considering all post-dosing measurements compared with placebo and including the baseline values as continuous independent variables, using multiple linear regression analysis, both bromocriptine and timolol had a significant ocular hypotensive effect (P less than 0.0001) in the treated eye with a significant but lesser effect in the contralateral eye. 3. In the concentrations used, timolol was more efficacious than bromocriptine in lowering intraocular pressure (P less than 0.025). 4. Using other forms of vehicles for bromocriptine to improve efficacy and studying the ocular hypotensive effect of topical application of other dopamine-2-receptor agonists such as pergolide and lisuride was suggested. PMID:2590602

  11. Chromosomal Microarray versus Karyotyping for Prenatal Diagnosis

    PubMed Central

    Wapner, Ronald J.; Martin, Christa Lese; Levy, Brynn; Ballif, Blake C.; Eng, Christine M.; Zachary, Julia M.; Savage, Melissa; Platt, Lawrence D.; Saltzman, Daniel; Grobman, William A.; Klugman, Susan; Scholl, Thomas; Simpson, Joe Leigh; McCall, Kimberly; Aggarwal, Vimla S.; Bunke, Brian; Nahum, Odelia; Patel, Ankita; Lamb, Allen N.; Thom, Elizabeth A.; Beaudet, Arthur L.; Ledbetter, David H.; Shaffer, Lisa G.; Jackson, Laird

    2013-01-01

    Background Chromosomal microarray analysis has emerged as a primary diagnostic tool for the evaluation of developmental delay and structural malformations in children. We aimed to evaluate the accuracy, efficacy, and incremental yield of chromosomal microarray analysis as compared with karyotyping for routine prenatal diagnosis. Methods Samples from women undergoing prenatal diagnosis at 29 centers were sent to a central karyotyping laboratory. Each sample was split in two; standard karyotyping was performed on one portion and the other was sent to one of four laboratories for chromosomal microarray. Results We enrolled a total of 4406 women. Indications for prenatal diagnosis were advanced maternal age (46.6%), abnormal result on Down’s syndrome screening (18.8%), structural anomalies on ultrasonography (25.2%), and other indications (9.4%). In 4340 (98.8%) of the fetal samples, microarray analysis was successful; 87.9% of samples could be used without tissue culture. Microarray analysis of the 4282 nonmosaic samples identified all the aneuploidies and unbalanced rearrangements identified on karyotyping but did not identify balanced translocations and fetal triploidy. In samples with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 6.0% with a structural anomaly and in 1.7% of those whose indications were advanced maternal age or positive screening results. Conclusions In the context of prenatal diagnostic testing, chromosomal microarray analysis identified additional, clinically significant cytogenetic information as compared with karyotyping and was equally efficacious in identifying aneuploidies and unbalanced rearrangements but did not identify balanced translocations and triploidies. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and others; ClinicalTrials.gov number, NCT01279733.) PMID:23215555

  12. Nanotechnologies in protein microarrays.

    PubMed

    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. PMID:26039143

  13. Oligonucleotide microarrays in constitutional genetic diagnosis.

    PubMed

    Keren, Boris; Le Caignec, Cedric

    2011-06-01

    Oligonucleotide microarrays such as comparative genomic hybridization arrays and SNP microarrays enable the identification of genomic imbalances - also termed copy-number variants - with increasing resolution. This article will focus on the most significant applications of high-throughput oligonucleotide microarrays, both in genetic diagnosis and research. In genetic diagnosis, the method is becoming a standard tool for investigating patients with unexplained developmental delay/intellectual disability, autism spectrum disorders and/or with multiple congenital anomalies. Oligonucleotide microarray have also been recently applied to the detection of genomic imbalances in prenatal diagnosis either to characterize a chromosomal rearrangement that has previously been identified by standard prenatal karyotyping or to detect a cryptic genomic imbalance in a fetus with ultrasound abnormalities and a normal standard prenatal karyotype. In research, oligonucleotide microarrays have been used for a wide range of applications, such as the identification of new genes responsible for monogenic disorders and the association of a copy-number variant as a predisposing factor to a common disease. Despite its widespread use, the interpretation of results is not always straightforward. We will discuss several unexpected results and ethical issues raised by these new methods.

  14. Eye Anatomy

    MedlinePlus

    ... News About Us Donate In This Section Eye Anatomy en Español email Send this article to a ... You at Risk For Glaucoma? Childhood Glaucoma Eye Anatomy Five Common Glaucoma Tests Glaucoma Facts and Stats ...

  15. Your Eyes

    MedlinePlus

    ... the eye and keeps it healthy. previous continue Light, Lens, Action These next parts are really cool, ... the eye. previous continue Rods and Cones Process Light The retina uses special cells called rods and ...

  16. Microarrays for Undergraduate Classes

    ERIC Educational Resources Information Center

    Hancock, Dale; Nguyen, Lisa L.; Denyer, Gareth S.; Johnston, Jill M.

    2006-01-01

    A microarray experiment is presented that, in six laboratory sessions, takes undergraduate students from the tissue sample right through to data analysis. The model chosen, the murine erythroleukemia cell line, can be easily cultured in sufficient quantities for class use. Large changes in gene expression can be induced in these cells by…

  17. Green Light-emitting Diodes Light Stimuli during Incubation Enhances Posthatch Growth without Disrupting Normal Eye Development of Broiler Embryos and Hatchlings

    PubMed Central

    Zhang, L.; Zhu, X. D.; Wang, X. F.; Li, J. L.; Gao, F.; Zhou, G. H.

    2016-01-01

    Monochromatic green light-emitting diodes (LED) light stimuli influences the posthatch growth performance of chicks. This study was undertaken with the following objectives: i) to examine whether the green LED light stimuli induces an overheating effect by determining weight loss rate of fertile eggs during incubation period; ii) to look for the development of eyes and other primary organs at different ages of embryos and newly hatched chicks. Arbor Acres fertile broiler eggs (n = 480) were randomly assigned to 3 incubation groups and exposed to continuous white light, green light, or a dark environment (control) from the first day to 19 d of incubation. The light sourced from LED lamps with the intensity of 30 lx at eggshell level. The results showed that either green or white light stimuli during incubation did not significantly affect the weight loss rate of fertile eggs, hatching time, hatchability, chick embryo, or body weight (BW), the weight percentage of heart, liver, and eyes, as well as obvious systematic abnormalities in eye weight, side-to-side, back-to-front, or corneal diameter from 15 d of embryogenesis to 6 d of posthatch (p>0.05). Compared with the dark condition, green light stimuli during incubation tended to increase feed intake (p = 0.080), improved the BW gain of chicks during 0 to 6 day posthatch (p<0.05), and increased the percentage of pectoral muscle to the BW on 3- and 6-day-old chicks. In addition, embryos or chicks in green light had lower weight percentage of yolk retention on 19 d of embryogenesis and 1 d of posthatch in comparison to those in dark or white group (p<0.05). These results suggest that providing 30 lx green LED light stimuli during incubation has no detrimental effect on the development of eyes, heart and liver of embryos and hatchlings, but does have potential benefits in terms of enhancement of the chick growth during the early posthatch stages. In addition, the fertile broiler eggs stimulated with 30 lx green LED

  18. Genomic-Wide Analysis with Microarrays in Human Oncology

    PubMed Central

    Inaoka, Kenichi; Inokawa, Yoshikuni; Nomoto, Shuji

    2015-01-01

    DNA microarray technologies have advanced rapidly and had a profound impact on examining gene expression on a genomic scale in research. This review discusses the history and development of microarray and DNA chip devices, and specific microarrays are described along with their methods and applications. In particular, microarrays have detected many novel cancer-related genes by comparing cancer tissues and non-cancerous tissues in oncological research. Recently, new methods have been in development, such as the double-combination array and triple-combination array, which allow more effective analysis of gene expression and epigenetic changes. Analysis of gene expression alterations in precancerous regions compared with normal regions and array analysis in drug-resistance cancer tissues are also successfully performed. Compared with next-generation sequencing, a similar method of genome analysis, several important differences distinguish these techniques and their applications. Development of novel microarray technologies is expected to contribute to further cancer research.

  19. Eye Protection

    PubMed Central

    Pashby, Tom

    1986-01-01

    Eye injuries frequently occur in the home, at work and at play. Many result in legally blind eyes, and most are preventable. Awareness of potential hazards is essential to preventing eye injuries, particularly in children. In addition, protective devices must be used appropriately. We have developed eye protectors that have proved effective in reducing both the overall incidence and the severity of sports eye injuries. ImagesFigures 2a, bFigure 3Figures 4a, b, c, dFigure 5 PMID:21267100

  20. Microarrays under the microscope

    PubMed Central

    Wildsmith, S E; Elcock, F J

    2001-01-01

    Microarray technology is a rapidly advancing area, which is gaining popularity in many biological disciplines from drug target identification to predictive toxicology. Over the past few years, there has been a dramatic increase in the number of methods and techniques available for carrying out this form of gene expression analysis. The techniques and associated peripherals, such as slide types, deposition methods, robotics, and scanning equipment, are undergoing constant improvement, helping to drive the technology forward in terms of robustness and ease of use. These rapid developments, combined with the number of options available and the associated hyperbole, can prove daunting for the new user. This review aims to guide the researcher through the various steps of conducting microarray experiments, from initial strategy to analysing the data, with critical examination of the benefits and disadvantages along the way. PMID:11212888

  1. Undetected sex chromosome aneuploidy by chromosomal microarray.

    PubMed

    Markus-Bustani, Keren; Yaron, Yuval; Goldstein, Myriam; Orr-Urtreger, Avi; Ben-Shachar, Shay

    2012-11-01

    We report on a case of a female fetus found to be mosaic for Turner syndrome (45,X) and trisomy X (47,XXX). Chromosomal microarray analysis (CMA) failed to detect the aneuploidy because of a normal average dosage of the X chromosome. This case represents an unusual instance in which CMA may not detect chromosomal aberrations. Such a possibility should be taken into consideration in similar cases where CMA is used in a clinical setting.

  2. Eye development.

    PubMed

    Baker, Nicholas E; Li, Ke; Quiquand, Manon; Ruggiero, Robert; Wang, Lan-Hsin

    2014-06-15

    The eye has been one of the most intensively studied organs in Drosophila. The wealth of knowledge about its development, as well as the reagents that have been developed, and the fact that the eye is dispensable for survival, also make the eye suitable for genetic interaction studies and genetic screens. This article provides a brief overview of the methods developed to image and probe eye development at multiple developmental stages, including live imaging, immunostaining of fixed tissues, in situ hybridizations, and scanning electron microscopy and color photography of adult eyes. Also summarized are genetic approaches that can be performed in the eye, including mosaic analysis and conditional mutation, gene misexpression and knockdown, and forward genetic and modifier screens.

  3. EYE DEVELOPMENT

    PubMed Central

    Baker, Nicholas E.; Li, Ke; Quiquand, Manon; Ruggiero, Robert; Wang, Lan-Hsin

    2014-01-01

    The eye has been one of the most intensively studied organs in Drosophila. The wealth of knowledge about its development, as well as the reagents that have been developed, and the fact that the eye is dispensable for survival, also make the eye suitable for genetic interaction studies and genetic screens. This chapter provides a brief overview of the methods developed to image and probe eye development at multiple developmental stages, including live imaging, immunostaining of fixed tissues, in situ hybridizations, and scanning electron microscopy and color photography of adult eyes. Also summarized are genetic approaches that can be performed in the eye, including mosaic analysis and conditional mutation, gene misexpression and knockdown, and forward genetic and modifier screens. PMID:24784530

  4. Evaluating concentration estimation errors in ELISA microarray experiments

    SciTech Connect

    Daly, Don S.; White, Amanda M.; Varnum, Susan M.; Anderson, Kevin K.; Zangar, Richard C.

    2005-01-26

    Enzyme-linked immunosorbent assay (ELISA) is a standard immunoassay to predict a protein concentration in a sample. Deploying ELISA in a microarray format permits simultaneous prediction of the concentrations of numerous proteins in a small sample. These predictions, however, are uncertain due to processing error and biological variability. Evaluating prediction error is critical to interpreting biological significance and improving the ELISA microarray process. Evaluating prediction error must be automated to realize a reliable high-throughput ELISA microarray system. Methods: In this paper, we present a statistical method based on propagation of error to evaluate prediction errors in the ELISA microarray process. Although propagation of error is central to this method, it is effective only when comparable data are available. Therefore, we briefly discuss the roles of experimental design, data screening, normalization and statistical diagnostics when evaluating ELISA microarray prediction errors. We use an ELISA microarray investigation of breast cancer biomarkers to illustrate the evaluation of prediction errors. The illustration begins with a description of the design and resulting data, followed by a brief discussion of data screening and normalization. In our illustration, we fit a standard curve to the screened and normalized data, review the modeling diagnostics, and apply propagation of error.

  5. Eye Injuries at Home

    MedlinePlus

    ... Patient Stories Español Eye Health / Tips & Prevention Eye Injuries Sections Preventing Eye Injuries Recognizing and Treating Eye ... Sports Eye Injuries by the Numbers — Infographic Eye Injuries at Home Reviewed by: Brenda Pagan-Duran MD ...

  6. Surface chemistries for antibody microarrays

    SciTech Connect

    Seurynck-Servoss, Shannon L.; Baird, Cheryl L.; Rodland, Karin D.; Zangar, Richard C.

    2007-05-01

    Enzyme-linked immunosorbent assay (ELISA) microarrays promise to be a powerful tool for the detection of disease biomarkers. The original technology for printing ELISA microarray chips and capturing antibodies on slides was derived from the DNA microarray field. However, due to the need to maintain antibody structure and function when immobilized, surface chemistries used for DNA microarrays are not always appropriate for ELISA microarrays. In order to identify better surface chemistries for antibody capture, a number of commercial companies and academic research groups have developed new slide types that could improve antibody function in microarray applications. In this review we compare and contrast the commercially available slide chemistries, as well as highlight some promising recent advances in the field.

  7. The connective tissue and glial framework in the optic nerve head of the normal human eye: light and scanning electron microscopic studies.

    PubMed

    Oyama, Tokuhide; Abe, Haruki; Ushiki, Tatsuo

    2006-12-01

    The arrangement of connective tissue components (i.e., collagen, reticular, and elastic fibers) and glial elements in the optic nerve head of the human eye was investigated by the combined use of light microscopy and scanning electron microscopy (SEM). Light-microscopically, the optic nerve head could be subdivided into four parts from the different arrangements of the connective tissue framework: a surface nerve fiber layer, and prelaminar, laminar, and postlaminar regions. The surface nerve fiber layer only possessed connective tissue elements around blood vessels. In the prelaminar region, collagen fibrils, together with delicate elastic fibers, formed thin interrupted sheaths for accommodating small nerve bundles. Immunohistochemistry for the glial fibrillary acidic protein (GFAP) showed that GFAP-positive cells formed columnar structures (i.e., glial columns), with round cell bodies piled up into layers. These glial columns were located in the fibrous sheaths of collagen fibrils and elastic fibers. In the laminar region, collagen fibrils and elastic fibers ran transversely to the optic nerve axis to form a thick membranous layer - the lamina cribrosa - which had numerous round openings for accommodating optic nerve fiber bundles. GFAP-positive cellular processes also ran transversely in association with collagen and elastin components. The postlaminar region had connective tissues which linked the lamina cribrosa with fibrous sheaths for accommodating nerve bundles in the extraocular optic nerve, where GFAP-positive cells acquired characteristics typical of fibrous astrocytes. These findings indicate that collagen fibrils, as a whole, form a continuous network which serves as a skeletal framework of the optic nerve head for protecting optic nerve fibers from mechanical stress as well as for sustaining blood vessels in the optic nerve. The lamina cribrosa containing elastic fibers are considered to be plastic against the mechanical force affected by elevation

  8. Eye Complications

    MedlinePlus

    ... the cornea, which focuses light while protecting the eye. After light passes through the cornea, it travels through a ... and have them progress faster. With cataracts, the eye's clear lens clouds, blocking light. To help deal with mild cataracts, you may ...

  9. Ectopic Six3 expression in the dragon eye goldfish.

    PubMed

    Ma, Dong-Mei; Zhu, Hua-Ping; Gui, Jian-Fang

    2008-02-01

    For goldfish (Carassius auratus), there are many varieties with different eye phenotypes due to artificial selection and adaptive evolution. Dragon eye is a variant eye characterized by a large-size eyeball protruding out of the socket similar to the eye of dragon in Chinese legends. In this study, anatomical structure of the goldfish dragon eye was compared with that of the common eye, and a stretching of the retina was observed in the enlarged dragon eye. Moreover, the homeobox-containing transcription factor Six3 cDNAs were cloned from the two types of goldfish, and the expression patterns were analyzed in both normal eye and dragon eye goldfish. No amino acid sequence differences were observed between the two deduced peptides, and the expression pattern of Six3 protein in dragon eye is quite similar to common eye during embryogenesis, but from 2 days after hatching, ectopic Six3 expression began to occur in the dragon eye, especially in the outer nuclear layer cells. With eye development, more predominant Six3 distribution was detected in the outer nuclear layer cells of dragon eye than that of normal eye, and fewer cell-layers in outer nuclear layer were observed in dragon eye retina than in normal eye retina. The highlight of this study is that higher Six3 expression occurs in dragon eye goldfish than in normal eye goldfish during retinal development of larvae.

  10. Saccadic eye movements and eye-head coordination in children.

    PubMed

    Funk, C J; Anderson, M E

    1977-04-01

    The eye and head movements of nine children, ages 6 through 10, were measured in order to establish quantitative characteristics of eye movements and eye-head corrdination patterns of children with normal vision and reading levels. The relationship between saccade amplitude and duration was linear, but the slope of this relationship indicated that saccades in children may have higher velocities than they do in adults. One of three temporal patterns of head and saccadic eye movement occurred during shifts of gaze to visual targets, depending on the temporal and spatial predictability of the target. It is suggested that quantitative measurements such as these could be used to examine developmental characteristics of eye and eye-head movement control.

  11. Ecotoxicogenomics: Microarray interlaboratory comparability.

    PubMed

    Vidal-Dorsch, Doris E; Bay, Steven M; Moore, Shelly; Layton, Blythe; Mehinto, Alvine C; Vulpe, Chris D; Brown-Augustine, Marianna; Loguinov, Alex; Poynton, Helen; Garcia-Reyero, Natàlia; Perkins, Edward J; Escalon, Lynn; Denslow, Nancy D; Cristina, Colli-Dula R; Doan, Tri; Shukradas, Shweta; Bruno, Joy; Brown, Lorraine; Van Agglen, Graham; Jackman, Paula; Bauer, Megan

    2016-02-01

    Transcriptomic analysis can complement traditional ecotoxicology data by providing mechanistic insight, and by identifying sub-lethal organismal responses and contaminant classes underlying observed toxicity. Before transcriptomic information can be used in monitoring and risk assessment, it is necessary to determine its reproducibility and detect key steps impacting the reliable identification of differentially expressed genes. A custom 15K-probe microarray was used to conduct transcriptomics analyses across six laboratories with estuarine amphipods exposed to cyfluthrin-spiked or control sediments (10 days). Two sample types were generated, one consisted of total RNA extracts (Ex) from exposed and control samples (extracted by one laboratory) and the other consisted of exposed and control whole body amphipods (WB) from which each laboratory extracted RNA. Our findings indicate that gene expression microarray results are repeatable. Differentially expressed data had a higher degree of repeatability across all laboratories in samples with similar RNA quality (Ex) when compared to WB samples with more variable RNA quality. Despite such variability a subset of genes were consistently identified as differentially expressed across all laboratories and sample types. We found that the differences among the individual laboratory results can be attributed to several factors including RNA quality and technical expertise, but the overall results can be improved by following consistent protocols and with appropriate training.

  12. The Genopolis Microarray Database

    PubMed Central

    Splendiani, Andrea; Brandizi, Marco; Even, Gael; Beretta, Ottavio; Pavelka, Norman; Pelizzola, Mattia; Mayhaus, Manuel; Foti, Maria; Mauri, Giancarlo; Ricciardi-Castagnoli, Paola

    2007-01-01

    Background Gene expression databases are key resources for microarray data management and analysis and the importance of a proper annotation of their content is well understood. Public repositories as well as microarray database systems that can be implemented by single laboratories exist. However, there is not yet a tool that can easily support a collaborative environment where different users with different rights of access to data can interact to define a common highly coherent content. The scope of the Genopolis database is to provide a resource that allows different groups performing microarray experiments related to a common subject to create a common coherent knowledge base and to analyse it. The Genopolis database has been implemented as a dedicated system for the scientific community studying dendritic and macrophage cells functions and host-parasite interactions. Results The Genopolis Database system allows the community to build an object based MIAME compliant annotation of their experiments and to store images, raw and processed data from the Affymetrix GeneChip® platform. It supports dynamical definition of controlled vocabularies and provides automated and supervised steps to control the coherence of data and annotations. It allows a precise control of the visibility of the database content to different sub groups in the community and facilitates exports of its content to public repositories. It provides an interactive users interface for data analysis: this allows users to visualize data matrices based on functional lists and sample characterization, and to navigate to other data matrices defined by similarity of expression values as well as functional characterizations of genes involved. A collaborative environment is also provided for the definition and sharing of functional annotation by users. Conclusion The Genopolis Database supports a community in building a common coherent knowledge base and analyse it. This fills a gap between a local

  13. DNA Microarray-Based Diagnostics.

    PubMed

    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.

  14. Living-Cell Microarrays

    PubMed Central

    Yarmush, Martin L.; King, Kevin R.

    2011-01-01

    Living cells are remarkably complex. To unravel this complexity, living-cell assays have been developed that allow delivery of experimental stimuli and measurement of the resulting cellular responses. High-throughput adaptations of these assays, known as living-cell microarrays, which are based on microtiter plates, high-density spotting, microfabrication, and microfluidics technologies, are being developed for two general applications: (a) to screen large-scale chemical and genomic libraries and (b) to systematically investigate the local cellular microenvironment. These emerging experimental platforms offer exciting opportunities to rapidly identify genetic determinants of disease, to discover modulators of cellular function, and to probe the complex and dynamic relationships between cells and their local environment. PMID:19413510

  15. Eyes - bulging

    MedlinePlus

    ... getting worse? What other symptoms do you have? A slit-lamp examination may be done. Blood testing for thyroid disease may be done. Treatments depend on the cause. Artificial tears may be given to lubricate the eye.

  16. Eye Infections

    MedlinePlus

    ... Health Issues Conditions Abdominal ADHD Allergies & Asthma Autism Cancer Chest & Lungs Chronic Conditions Cleft & Craniofacial Developmental Disabilities Ear Nose & Throat Emotional Problems Eyes Fever From Insects or Animals Genitals and Urinary Tract Glands & Growth ...

  17. Eye emergencies

    MedlinePlus

    Supervise children carefully. Teach them how to be safe. Always wear protective eye gear when: Using power tools, hammers, or other striking tools Working with toxic chemicals Cycling or when in windy and dusty ...

  18. Eye Allergies

    MedlinePlus

    ... MD Mar. 01, 2015 Eye allergies, called allergic conjunctivitis , are a common condition that occurs when the ... with tearing and burning. Unlike bacterial or viral conjunctivitis, allergic conjunctivitis is not spread from person to ...

  19. Black Eye

    MedlinePlus

    ... Aug 30, 2016 Toddlers Most at Risk of Chemical Burns to Eyes Aug 26, 2016 Firework Blinds Teenager, Severs Hand Jun 29, ... at the Academy Financial Relationships with Industry Medical Disclaimer Privacy Policy Terms of Service For ...

  20. An imputation approach for oligonucleotide microarrays.

    PubMed

    Li, Ming; Wen, Yalu; Lu, Qing; Fu, Wenjiang J

    2013-01-01

    Oligonucleotide microarrays are commonly adopted for detecting and qualifying the abundance of molecules in biological samples. Analysis of microarray data starts with recording and interpreting hybridization signals from CEL images. However, many CEL images may be blemished by noises from various sources, observed as "bright spots", "dark clouds", and "shadowy circles", etc. It is crucial that these image defects are correctly identified and properly processed. Existing approaches mainly focus on detecting defect areas and removing affected intensities. In this article, we propose to use a mixed effect model for imputing the affected intensities. The proposed imputation procedure is a single-array-based approach which does not require any biological replicate or between-array normalization. We further examine its performance by using Affymetrix high-density SNP arrays. The results show that this imputation procedure significantly reduces genotyping error rates. We also discuss the necessary adjustments for its potential extension to other oligonucleotide microarrays, such as gene expression profiling. The R source code for the implementation of approach is freely available upon request.

  1. Integrating data from heterogeneous DNA microarray platforms.

    PubMed

    Valente, Eduardo; Rocha, Miguel

    2015-01-01

    DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination. In this work, a complete methodology for gene expression data integration and application is proposed, which comprehends a transcript-based re-annotation process and several methods for batch effect attenuation. The integrated data will be used to select the best feature set and learning algorithm for a brain tumor classification case study. The integration will consider data from heterogeneous Agilent and Affymetrix platforms, collected from public gene expression databases, such as The Cancer Genome Atlas and Gene Expression Omnibus. PMID:26673932

  2. Analysis of tear inflammatory mediators: A comparison between the microarray and Luminex methods

    PubMed Central

    Dionne, Karen; Nichols, Jason J.; Nichols, Kelly K.

    2016-01-01

    Purpose Inflammatory mediators have been shown to modulate dry eye (DE) disease and may correlate with disease severity, yet the methods used and the associated findings vary significantly in the literature. The goal of this research was to compare two methods, the quantitative microarray and the magnetic bead assay, for detecting cytokine levels in extracted tear samples across three subject groups. Methods Tears were collected from Schirmer strips of the right and left eyes of 20 soft contact lens wearers (CL), 20 normal non-contact lens wearers (NOR), and 20 DE subjects and stored at −80 °C. Tear proteins were eluted and precipitated using ammonium bicarbonate and acetone. The right and left eye samples were combined for each subject. Following the Bradford protein quantitation method, 10 µg of total protein was used for each of the two analyses, Quantibody® Human Inflammation Array 3 (RayBiotech) and High Sensitivity Human Cytokine Magnetic Bead Kit (Millipore). The assays were run using the GenePix® 4000B Scanner (Molecular Devices) or the Luminex MagPix® plate reader (Luminex), respectively. The data were then compared between the two instruments and the three subject groups Results Of the 40 proteins on the Quantibody® microarray, seven had average expression levels above the lower limit of detection: ICAM-1, MCP-1, MIG, MCSF, TIMP-1, TIMP-2, and TNF-RI. Significant differences in expression levels (p<0.05) were detected between the CL and DE groups for MCSF, TIMP-1, and TNF R1, between the NOR and DE groups for ICAM-1, and between the CL and NOR groups for ICAM-1, MCP-1, MCSF, TIMP-1, TIMP-2, and TNF-R1 when using the Student t test. Of the 13 proteins tested with Luminex, IL-1β, IL-4, IL-6, IL-7, and IL-8 had expression levels above the minimum detectable level, and these were most often detected using the Luminex assay compared to the Quantibody® microarray. Contrarily, IL-2, IL-12, IL-13, INF-g, and GM-CSF were detected more frequently using

  3. Microarray platform for omics analysis

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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 < .0035) and cardiovascular malformations (P < .0081) in subjects with abnormal microarrays. Clinicians should consider microarray analysis in individuals who have epilepsy, especially in combination with musculoskeletal malformation or cardiovascular malformation.

  5. Eye tracker.

    PubMed

    Pruehsner, W; Enderle, J D

    1999-01-01

    A device that records saccadic eye movements, the Eye Tracker, is presented in this paper. The Eye Tracker utilizes infra-red technology mounted on fully adjustable goggles to follow eye movements targeted by either a goggles mounted HUD type display or a wall mounted light bank. Output from the goggles is remotely sent to a PC type computer, which leads to device portability. The goggles can also maintain output data in an internal memory for latter download. The user interface is Windows based with the output from the goggles represented as a trace map or plotted points. This output can also be saved or printed for future reference. The user interface can be used on any PC type computer. The device is designed with reference to standard ISO design methodology. Safety in design and final product usage has also been addressed with reference to standard ISO type procedures. Device accuracy is maintained by precise construction of the IR units in the goggles and tight control of cross talk between each IR device plus filtering of ambient light signals. Also, a reset feature is included to maintain equal baseline control. An automatic switching device is included in the goggles to allow the Eye Tracker to "warm up," assuring that equal IR power is delivered for each subject tested. The IR units in the goggles are also modular in case replacement is required. PMID:11143354

  6. Microarray Analysis of Microbial Weathering

    NASA Astrophysics Data System (ADS)

    Olsson-Francis, K.; van Houdt, R.; Leys, N.; Mergeay, M.; Cockell, C. S.

    2010-04-01

    Microarray analysis of the heavy metal resistant bacterium, Cupriavidus metallidurans CH34 was used to investigate the genes involved in the weathering. The results demonstrated that large porin and membrane transporter genes were unregulated.

  7. [Protein microarrays and personalized medicine].

    PubMed

    Yu, Xiabo; Schneiderhan-Marra, Nicole; Joos, Thomas O

    2011-01-01

    Over the last 10 years, DNA microarrays have achieved a robust analytical performance, enabling their use for analyzing the whole transcriptome or for screening thousands of single-nucleotide polymorphisms in a single experiment. DNA microarrays allow scientists to correlate gene expression signatures with disease progression, to screen for disease-specific mutations, and to treat patients according to their individual genetic profiles; however, the real key is proteins and their manifold functions. It is necessary to achieve a greater understanding of not only protein function and abundance but also their role in the development of diseases. Protein concentrations have been shown to reflect the physiological and pathologic state of an organ, tissue, or cells far more directly than DNA, and proteins can be profiled effectively with protein microarrays, which require only a small amount of sample material. Protein microarrays have become wellestablished tools in basic and applied research, and the first products have already entered the in vitro diagnostics market. This review focuses on protein microarray applications for biomarker discovery and validation, disease diagnosis, and use within the area of personalized medicine. Protein microarrays have proved to be reliable research tools in screening for a multitude of parameters with only a minimal quantity of sample and have enormous potential in applications for diagnostic and personalized medicine.

  8. Teaching normal birth, normally.

    PubMed

    Hotelling, Barbara A

    2009-01-01

    Teaching normal-birth Lamaze classes normally involves considering the qualities that make birth normal and structuring classes to embrace those qualities. In this column, teaching strategies are suggested for classes that unfold naturally, free from unnecessary interventions. PMID:19436595

  9. Eye and orbit ultrasound

    MedlinePlus

    Echography - eye orbit; Ultrasound - eye orbit; Ocular ultrasonography; Orbital ultrasonography ... eye is numbed with medicine (anesthetic drops). The ultrasound wand (transducer) is placed against the front surface ...

  10. Googly Eyes

    ERIC Educational Resources Information Center

    Boss, Susan

    2009-01-01

    Beverage take-out trays are funky in their form and function. In this article, the author describes how to make googly eye masks out of discarded take-out trays and other common recycled or discarded materials. (Contains 1 online resource.)

  11. Harvesting clues from genome wide transcriptome analysis for exploring thalidomide mediated anomalies in eye development of chick embryo: Nitric oxide rectifies the thalidomide mediated anomalies by swinging back the system to normal transcriptome pattern.

    PubMed

    Kumar, Pavitra; Kasiviswanathan, Dharanibalan; Sundaresan, Lakshmikirupa; Kathirvel, Priyadarshan; Veeriah, Vimal; Dutta, Priya; Sankaranarayanan, Kavitha; Gupta, Ravi; Chatterjee, Suvro

    2016-02-01

    Thalidomide, the notorious teratogen is known to cause various developmental abnormalities, among which a range of eye deformations are very common. From the clinical point of view, it is necessary to pinpoint the mechanisms of teratogens that tune the gene expression. However, to our knowledge, the molecular basis of eye deformities under thalidomide treatmenthas not been reported so far. Present study focuses on the possible mechanism by which thalidomide affects eye development and the role of Nitric Oxide in recovering thalidomide-mediated anomalies of eye development using chick embryo and zebrafish models with transcriptome analysis. Transcriptome analysis showed that 403 genes were up-regulated and 223 genes were down-regulated significantly in thalidomide pre-treated embryos. 8% of the significantly modulated genes have been implicated in eye development including Pax6, OTX2, Dkk1 and Shh. A wide range of biological process and molecular function was affected by thalidomide exposure. Biological Processes including structural constituent of eye lens and Molecular functions such as visual perception and retinal metabolic process formed strong annotation clustersindicating the adverse effects of thalidomide on eye development and function. Here, we have discussed the whole embryo transcriptome with the expression of PAX6, SOX2, and CRYAAgenes from developing eyes. Our experimental data showing structural and functional aspects includingeye size, lens transparency and optic nerve activity and bioinformatics analyses of transcriptome suggest that NO could partially protect thalidomide treated embryos from its devastating effects on eye development and function. PMID:26717904

  12. Harvesting clues from genome wide transcriptome analysis for exploring thalidomide mediated anomalies in eye development of chick embryo: Nitric oxide rectifies the thalidomide mediated anomalies by swinging back the system to normal transcriptome pattern.

    PubMed

    Kumar, Pavitra; Kasiviswanathan, Dharanibalan; Sundaresan, Lakshmikirupa; Kathirvel, Priyadarshan; Veeriah, Vimal; Dutta, Priya; Sankaranarayanan, Kavitha; Gupta, Ravi; Chatterjee, Suvro

    2016-02-01

    Thalidomide, the notorious teratogen is known to cause various developmental abnormalities, among which a range of eye deformations are very common. From the clinical point of view, it is necessary to pinpoint the mechanisms of teratogens that tune the gene expression. However, to our knowledge, the molecular basis of eye deformities under thalidomide treatmenthas not been reported so far. Present study focuses on the possible mechanism by which thalidomide affects eye development and the role of Nitric Oxide in recovering thalidomide-mediated anomalies of eye development using chick embryo and zebrafish models with transcriptome analysis. Transcriptome analysis showed that 403 genes were up-regulated and 223 genes were down-regulated significantly in thalidomide pre-treated embryos. 8% of the significantly modulated genes have been implicated in eye development including Pax6, OTX2, Dkk1 and Shh. A wide range of biological process and molecular function was affected by thalidomide exposure. Biological Processes including structural constituent of eye lens and Molecular functions such as visual perception and retinal metabolic process formed strong annotation clustersindicating the adverse effects of thalidomide on eye development and function. Here, we have discussed the whole embryo transcriptome with the expression of PAX6, SOX2, and CRYAAgenes from developing eyes. Our experimental data showing structural and functional aspects includingeye size, lens transparency and optic nerve activity and bioinformatics analyses of transcriptome suggest that NO could partially protect thalidomide treated embryos from its devastating effects on eye development and function.

  13. Electrostatic readout of DNA microarrays with charged microspheres

    SciTech Connect

    Clack, Nathan G.; Salaita, Khalid; Groves, Jay T.

    2008-06-29

    DNA microarrays are used for gene-expression profiling, single-nucleotide polymorphism detection and disease diagnosis. A persistent challenge in this area is the lack of microarray screening technology suitable for integration into routine clinical care. In this paper, we describe a method for sensitive and label-free electrostatic readout of DNA or RNA hybridization on microarrays. The electrostatic properties of the microarray are measured from the position and motion of charged microspheres randomly dispersed over the surface. We demonstrate nondestructive electrostatic imaging with 10-μm lateral resolution over centimeter-length scales, which is four-orders of magnitude larger than that achievable with conventional scanning electrostatic force microscopy. Changes in surface charge density as a result of specific hybridization can be detected and quantified with 50-pM sensitivity, single base-pair mismatch selectivity and in the presence of complex background. Lastly, because the naked eye is sufficient to read out hybridization, this approach may facilitate broad application of multiplexed assays.

  14. Macro- and microglial responses in the fellow eyes contralateral to glaucomatous eyes.

    PubMed

    Ramírez, Ana I; Salazar, Juan J; de Hoz, Rosa; Rojas, Blanca; Gallego, Beatriz I; Salobrar-García, Elena; Valiente-Soriano, Francisco J; Triviño, Alberto; Ramirez, José M

    2015-01-01

    Most studies employing experimental models of unilateral glaucoma have used the normotensive contralateral eye as the normal control. However, some studies have recently reported the activation of the retinal macroglia and microglia in the uninjured eye, suggesting that the eye contralateral to experimental glaucoma should not be used as a control. This review analyzes the studies describing the contralateral findings and discusses some of the routes through which the signals can reach the contralateral eye to initiate the glial reactivation.

  15. Pursuit Eye Movements

    NASA Technical Reports Server (NTRS)

    Krauzlis, Rich; Stone, Leland; Null, Cynthia H. (Technical Monitor)

    1998-01-01

    When viewing objects, primates use a combination of saccadic and pursuit eye movements to stabilize the retinal image of the object of regard within the high-acuity region near the fovea. Although these movements involve widespread regions of the nervous system, they mix seamlessly in normal behavior. Saccades are discrete movements that quickly direct the eyes toward a visual target, thereby translating the image of the target from an eccentric retinal location to the fovea. In contrast, pursuit is a continuous movement that slowly rotates the eyes to compensate for the motion of the visual target, minimizing the blur that can compromise visual acuity. While other mammalian species can generate smooth optokinetic eye movements - which track the motion of the entire visual surround - only primates can smoothly pursue a single small element within a complex visual scene, regardless of the motion elsewhere on the retina. This ability likely reflects the greater ability of primates to segment the visual scene, to identify individual visual objects, and to select a target of interest.

  16. Do the eyes scan dream images during rapid eye movement sleep? Evidence from the rapid eye movement sleep behaviour disorder model.

    PubMed

    Leclair-Visonneau, Laurène; Oudiette, Delphine; Gaymard, Bertrand; Leu-Semenescu, Smaranda; Arnulf, Isabelle

    2010-06-01

    to normal rapid eye movement sleep. PMID:20478849

  17. Eye Movement Disorders

    MedlinePlus

    ... t work properly. There are many kinds of eye movement disorders. Two common ones are Strabismus - a disorder ... of the eyes, sometimes called "dancing eyes" Some eye movement disorders are present at birth. Others develop over ...

  18. Dilating Eye Drops

    MedlinePlus

    ... Conditions Most Common Searches Adult Strabismus Amblyopia Cataract Conjunctivitis Corneal Abrasions Dilating Eye Drops Lazy eye (defined) ... Loading... Most Common Searches Adult Strabismus Amblyopia Cataract Conjunctivitis Corneal Abrasions Dilating Eye Drops Lazy eye (defined) ...

  19. Why Do Eyes Water?

    MedlinePlus

    ... Help White House Lunch Recipes Why Do Eyes Water? KidsHealth > For Kids > Why Do Eyes Water? Print ... out of your nose. continue Why Do Eyes Water? Eyes water for lots of different reasons besides ...

  20. Comparing Bacterial DNA Microarray Fingerprints

    SciTech Connect

    Willse, Alan R.; Chandler, Darrell P.; White, Amanda M.; Protic, Miroslava; Daly, Don S.; Wunschel, Sharon C.

    2005-08-15

    Detecting subtle genetic differences between microorganisms is an important problem in molecular epidemiology and microbial forensics. In a typical investigation, gel electrophoresis is used to compare randomly amplified DNA fragments between microbial strains, where the patterns of DNA fragment sizes are proxies for a microbe's genotype. The limited genomic sample captured on a gel is often insufficient to discriminate nearly identical strains. This paper examines the application of microarray technology to DNA fingerprinting as a high-resolution alternative to gel-based methods. The so-called universal microarray, which uses short oligonucleotide probes that do not target specific genes or species, is intended to be applicable to all microorganisms because it does not require prior knowledge of genomic sequence. In principle, closely related strains can be distinguished if the number of probes on the microarray is sufficiently large, i.e., if the genome is sufficiently sampled. In practice, we confront noisy data, imperfectly matched hybridizations, and a high-dimensional inference problem. We describe the statistical problems of microarray fingerprinting, outline similarities with and differences from more conventional microarray applications, and illustrate the statistical fingerprinting problem for 10 closely related strains from three Bacillus species, and 3 strains from non-Bacillus species.

  1. Eye contricks

    PubMed Central

    Wade, Nicholas J

    2011-01-01

    Pictorial images are icons as well as eye-cons: they provide distillations of objects or ideas into simpler shapes. They create the impression of representing that which cannot be presented. Even at the level of the photograph, the links between icon and object are tenuous. The dimensions of depth and motion are missing from icons, and these alone introduce all manner of potential ambiguities. The history of art can be considered as exploring the missing link between icon and object. Eye-cons can also be illusions—tricks of vision so that what is seen does not necessarily correspond to what is physically presented. Pictorial images can be spatialised or stylised; spatialised images generally share some of the projective characteristics of the object represented. Written words are also icons, but they do not resemble the objects they represent—they are stylised or conventional. Icons as stylised words and spatialised images were set in delightful opposition by René Magritte in a series of pipe paintings, and this theme is here alluded to. Most of visual science is now concerned with icons—two-dimensional displays on computer monitors. Is vision now the science of eye-cons? PMID:23145240

  2. A Versatile Microarray Platform for Capturing Rare Cells

    NASA Astrophysics Data System (ADS)

    Brinkmann, Falko; Hirtz, Michael; Haller, Anna; Gorges, Tobias M.; Vellekoop, Michael J.; Riethdorf, Sabine; Müller, Volkmar; Pantel, Klaus; Fuchs, Harald

    2015-10-01

    Analyses of rare events occurring at extremely low frequencies in body fluids are still challenging. We established a versatile microarray-based platform able to capture single target cells from large background populations. As use case we chose the challenging application of detecting circulating tumor cells (CTCs) - about one cell in a billion normal blood cells. After incubation with an antibody cocktail, targeted cells are extracted on a microarray in a microfluidic chip. The accessibility of our platform allows for subsequent recovery of targets for further analysis. The microarray facilitates exclusion of false positive capture events by co-localization allowing for detection without fluorescent labelling. Analyzing blood samples from cancer patients with our platform reached and partly outreached gold standard performance, demonstrating feasibility for clinical application. Clinical researchers free choice of antibody cocktail without need for altered chip manufacturing or incubation protocol, allows virtual arbitrary targeting of capture species and therefore wide spread applications in biomedical sciences.

  3. Examination of Oral Cancer Biomarkers by Tissue Microarray Analysis

    PubMed Central

    Choi, Peter; Jordan, C. Diana; Mendez, Eduardo; Houck, John; Yueh, Bevan; Farwell, D. Gregory; Futran, Neal; Chen, Chu

    2008-01-01

    Background Oral squamous cell carcinoma (OSCC) is a major healthcare problem worldwide. Efforts in our laboratory and others focusing on the molecular characterization of OSCC tumors with the use of DNA microarrays have yielded heterogeneous results. To validate the DNA microarray results on a subset of genes from these studies that could potentially serve as biomarkers of OSCC, we elected to examine their expression by an alternate quantitative method and by assessing their protein levels. Design Based on DNA microarray data from our lab and data reported in the literature, we identified six potential biomarkers of OSCC to investigate further. We employed quantitative, real-time polymerase chain reaction (qRT-PCR) to examine expression changes of CDH11, MMP3, SPARC, POSTN, TNC, TGM3 in OSCC and normal control tissues. We further examined validated markers on the protein level by immunohistochemistry (IHC) analysis of OSCC tissue microarray (TMA) sections. Results qRT-PCR analysis revealed up-regulation of CDH11, SPARC, POSTN, and TNC gene expression, and decreased TGM3 expression in OSCC compared to normal controls. MMP3 was not found to be differentially expressed. In TMA IHC analyses, SPARC, periostin, and tenascin C exhibited increased protein expression in cancer compared to normal tissues, and their expression was primarily localized within tumor-associated stroma rather than tumor epithelium. Conversely, transglutaminase-3 protein expression was found only within keratinocytes in normal controls, and was significantly down-regulated in cancer cells. Conclusions Of six potential gene markers of OSCC, initially identified by DNA microarray analyses, differential expression of CDH11, SPARC, POSTN, TNC, and TGM3 were validated by qRT-PCR. Differential expression and localization of proteins encoded by SPARC, POSTN, TNC, and TGM3 were clearly shown by TMA IHC. PMID:18490578

  4. Temporal integration in diseased eyes.

    PubMed

    Kono, M; Yamade, S

    We examined critical duration for visual acuity in eyes with central serous retinopathy (CSR), macular edema (ME) and glaucoma. Critical duration for visual acuity is the minimum period of time to perceive the acuity chart of his best. Visual acuity was measured at several limited exposure durations and the results were then compared with that of normal eyes. The acuity target was a single Landolt ring. The size, direction, and exposure duration of the target were computer controlled. The mean critical duration for visual acuity of the CSR and ME groups was 1.78 s and 2.69 s. These were significantly longer than that of the normal group (0.62 s). The critical duration of the glaucoma group was 0.42 s, which was not significantly prolonged. Critical duration for the increment or static threshold was measured for the purpose of comparison, and no significant differences were found between the diseased eyes (the CSR and ME groups) and the normal eyes, although the thresholds were significantly higher in the diseased eyes. Next, fixation movements which occurred during visual acuity testing were observed in order to investigate their role in acuity testing. In both normal and ME eyes the frequency and amplitude of microsaccades were smaller while the visual acity chart was shown. This suggests that microsaccades play no positive role in the reading of acuity charts, and that they bear little relation to the phenomenon of critical duration for visual acuity. From these results we hypothesized that in the CSR and ME groups the X-type ganglion cells send incomplete information to the central neural system. Thus, a longer time is required to obtain complete information before responding. Furthermore, one glaucoma case suggested that in diseased eyes in which mainly the Y-cell systems are damaged, temporal specificity in visual acuity for shorter exposure duration may reveal different response patterns. PMID:9112193

  5. Temporal integration in diseased eyes.

    PubMed

    Kono, M; Yamade, S

    We examined critical duration for visual acuity in eyes with central serous retinopathy (CSR), macular edema (ME) and glaucoma. Critical duration for visual acuity is the minimum period of time to perceive the acuity chart of his best. Visual acuity was measured at several limited exposure durations and the results were then compared with that of normal eyes. The acuity target was a single Landolt ring. The size, direction, and exposure duration of the target were computer controlled. The mean critical duration for visual acuity of the CSR and ME groups was 1.78 s and 2.69 s. These were significantly longer than that of the normal group (0.62 s). The critical duration of the glaucoma group was 0.42 s, which was not significantly prolonged. Critical duration for the increment or static threshold was measured for the purpose of comparison, and no significant differences were found between the diseased eyes (the CSR and ME groups) and the normal eyes, although the thresholds were significantly higher in the diseased eyes. Next, fixation movements which occurred during visual acuity testing were observed in order to investigate their role in acuity testing. In both normal and ME eyes the frequency and amplitude of microsaccades were smaller while the visual acity chart was shown. This suggests that microsaccades play no positive role in the reading of acuity charts, and that they bear little relation to the phenomenon of critical duration for visual acuity. From these results we hypothesized that in the CSR and ME groups the X-type ganglion cells send incomplete information to the central neural system. Thus, a longer time is required to obtain complete information before responding. Furthermore, one glaucoma case suggested that in diseased eyes in which mainly the Y-cell systems are damaged, temporal specificity in visual acuity for shorter exposure duration may reveal different response patterns.

  6. Avian oncogenic virus differential diagnosis in chickens using oligonucleotide microarray.

    PubMed

    Wang, Lih-Chiann; Huang, Dean; Pu, Chang-En; Wang, Ching-Ho

    2014-12-15

    Avian oncogenic viruses include the avian leukosis virus (ALV), reticuloendotheliosis virus (REV) and Marek's disease virus (MDV). Multiple oncogenic viral infections are frequently seen, with even Marek's disease vaccines reported to be contaminated with ALV and REV. The gross lesions caused by avian oncogenic viruses often overlap, making differentiation diagnosis based on histopathology difficult. The objective of this study is to develop a rapid approach to simultaneously differentiate, subgroup and pathotype the avian oncogenic viruses. The oligonucleotide microarray was employed in this study. Particular DNA sequences were recognized using specific hybridization between the DNA target and probe on the microarray, followed with colorimetric development through enzyme reaction. With 10 designed probes, ALV-A, ALV-E, ALV-J, REV, MDV pathogenic and vaccine strains were clearly discriminated on the microarray with the naked eyes. The detection limit was 27 copy numbers, which was 10-100 times lower than multiplex PCR. Of 102 field samples screened using the oligonucleotide microarray, 32 samples were positive for ALV-E, 17 samples were positive for ALV-J, 6 samples were positive for REV, 4 samples were positive for MDV, 7 samples were positive for both ALV-A and ALV-E, 5 samples were positive for ALV-A, ALV-E and ALV-J, one sample was positive for both ALV-J and MDV, and 3 samples were positive for both REV and MDV. The oligonucleotide microarray, an easy-to-use, high-specificity, high-sensitivity and extendable assay, presents a potent technique for rapid differential diagnosis of avian oncogenic viruses and the detection of multiple avian oncogenic viral infections under field conditions.

  7. Protein microarrays: prospects and problems.

    PubMed

    Kodadek, T

    2001-02-01

    Protein microarrays are potentially powerful tools in biochemistry and molecular biology. Two types of protein microarrays are defined. One, termed a protein function array, will consist of thousands of native proteins immobilized in a defined pattern. Such arrays can be utilized for massively parallel testing of protein function, hence the name. The other type is termed a protein-detecting array. This will consist of large numbers of arrayed protein-binding agents. These arrays will allow for expression profiling to be done at the protein level. In this article, some of the major technological challenges to the development of protein arrays are discussed, along with potential solutions.

  8. Microarray Developed on Plastic Substrates.

    PubMed

    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. PMID:26614067

  9. Microfluidic microarray systems and methods thereof

    SciTech Connect

    West, Jay A. A.; Hukari, Kyle W.; Hux, Gary A.

    2009-04-28

    Disclosed are systems that include a manifold in fluid communication with a microfluidic chip having a microarray, an illuminator, and a detector in optical communication with the microarray. Methods for using these systems for biological detection are also disclosed.

  10. The Microarray Revolution: Perspectives from Educators

    ERIC Educational Resources Information Center

    Brewster, Jay L.; Beason, K. Beth; Eckdahl, Todd T.; Evans, Irene M.

    2004-01-01

    In recent years, microarray analysis has become a key experimental tool, enabling the analysis of genome-wide patterns of gene expression. This review approaches the microarray revolution with a focus upon four topics: 1) the early development of this technology and its application to cancer diagnostics; 2) a primer of microarray research,…

  11. Billie's eyes.

    PubMed

    Dunning, S E

    1993-03-01

    The author, a nurse, is personally opposed to abortion; however, her earlier encounter with a victim of an illegal abortion has prevented her from joining campaigns to reinstate bans on abortion rights. The woman, "Billie," presented to an inner-city Chicago hospital in 1970 with hemorrhaging. She had delayed going for treatment because she feared being imprisoned for having obtained an abortion. She rapidly entered septic shock, with hypotension, confusion, and hallucinations. Physicians removed her infected uterus and ovaries. Subsequent kidney failure necessitated the transfer of this young woman to another hospital where she could receive dialysis. The author was unable to obtain follow-up information on whether Billie survived. She remains haunted by the memory of Billie's wide, frightened eyes as she was placed in the ambulance. It is this memory, and the knowledge that desperate women like Billie will find someone, somewhere to perform an illegal abortion, that is behind the author's reluctant support for the right to choose.

  12. Finding an Eye Care Professional

    MedlinePlus

    ... Information > Finding an Eye Care Professional Finding an Eye Care Professional Finding an Eye Care Professional PDF* The National Eye Institute does not provide referrals or recommend specific ...

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

    PubMed

    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.

  14. Differentially expressed genes identified by cross-species microarray in the blind cavefish Astyanax.

    PubMed

    Strickler, Allen G; Jeffery, William R

    2009-03-01

    Changes in gene expression were examined by microarray analysis during development of the eyed surface dwelling (surface fish) and blind cave-dwelling (cavefish) forms of the teleost Astyanax mexicanus De Filippi, 1853. The cross-species microarray used surface and cavefish RNA hybridized to a DNA chip prepared from a closely related species, the zebrafish Danio rerio Hamilton, 1822. We identified a total of 67 differentially expressed probe sets at three days post-fertilization: six upregulated and 61 downregulated in cavefish relative to surface fish. Many of these genes function either in eye development and/or maintenance, or in programmed cell death. The upregulated probe set showing the highest mean fold change was similar to the human ubiquitin specific protease 53 gene. The downregulated probe sets showing some of the highest fold changes corresponded to genes with roles in eye development, including those encoding gamma crystallins, the guanine nucleotide binding proteins Gnat1 and Gant2, a BarH-like homeodomain transcription factor, and rhodopsin. Downregulation of gamma-crystallin and rhodopsin was confirmed by in situ hybridization and immunostaining with specific antibodies. Additional downregulated genes encode molecules that inhibit or activate programmed cell death. The results suggest that cross-species microarray can be used for identifying differentially expressed genes in cavefish, that many of these genes might be involved in eye degeneration via apoptotic processes, and that more genes are downregulated than upregulated in cavefish, consistent with the predominance of morphological losses over gains during regressive evolution.

  15. National Eye Institute

    MedlinePlus

    ... vision science and eye health fun with videos, optical illusions, and more. View the site Request for ... español NEI FAQs Eye Health Resources Studies, print materials and more. National Eye Health Education Program (NEHEP) ...

  16. Eye muscle repair - discharge

    MedlinePlus

    ... page: //medlineplus.gov/ency/patientinstructions/000111.htm Eye muscle repair - discharge To use the sharing features on ... enable JavaScript. You or your child had eye muscle repair surgery to correct eye muscle problems that ...

  17. Fluorescent eye test (image)

    MedlinePlus

    The fluorescent eye test is useful in determining if there is a scratch or other problem with the surface ... has thoroughly covered the eye a cobalt blue light is then directed on the eye. The light ...

  18. Microarray technology for use in molecular epidemiology.

    PubMed

    Vernon, Suzanne D; Whistler, Toni

    2007-01-01

    Microarrays are a powerful laboratory tool for the simultaneous assessment of the activity of thousands genes. Remarkable advances in biological sample collection, preparation and automation of hybridization have enabled the application of microarray technology to large, population-based studies. Now, microarrays have the potential to serve as screening tools for the detection of altered gene expression activity that might contribute to diseases in human populations. Reproducible and reliable microarray results depend on multiple factors. In this chapter, biological sample parameters are introduced that should be considered for any microarray experiment. Then, the microarray technology that we have successfully applied to limited biological sample from all our molecular epidemiology studies is detailed. This reproducible and reliable approach for using microarrays should be applicable to any biological questions asked.

  19. Microarray analysis in pulmonary hypertension.

    PubMed

    Hoffmann, Julia; Wilhelm, Jochen; Olschewski, Andrea; Kwapiszewska, Grazyna

    2016-07-01

    Microarrays are a powerful and effective tool that allows the detection of genome-wide gene expression differences between controls and disease conditions. They have been broadly applied to investigate the pathobiology of diverse forms of pulmonary hypertension, namely group 1, including patients with idiopathic pulmonary arterial hypertension, and group 3, including pulmonary hypertension associated with chronic lung diseases such as chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. To date, numerous human microarray studies have been conducted to analyse global (lung homogenate samples), compartment-specific (laser capture microdissection), cell type-specific (isolated primary cells) and circulating cell (peripheral blood) expression profiles. Combined, they provide important information on development, progression and the end-stage disease. In the future, system biology approaches, expression of noncoding RNAs that regulate coding RNAs, and direct comparison between animal models and human disease might be of importance. PMID:27076594

  20. Phenotypic MicroRNA Microarrays

    PubMed Central

    Kwon, Yong-Jun; Heo, Jin Yeong; Kim, Hi Chul; Kim, Jin Yeop; Liuzzi, Michel; Soloveva, Veronica

    2013-01-01

    Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the biology of selected cellular models. After reverse-transfection of microRNAs and siRNA, the cellular phenotype generated by microRNAs regulated NF-κB expression comparably to the siRNA. The ability to print microRNA molecules for reverse transfection into cells is opening up the wide horizon for the phenotypic high content screening of microRNA libraries using cellular disease models.

  1. Self-Assembling Protein Microarrays

    NASA Astrophysics Data System (ADS)

    Ramachandran, Niroshan; Hainsworth, Eugenie; Bhullar, Bhupinder; Eisenstein, Samuel; Rosen, Benjamin; Lau, Albert Y.; C. Walter, Johannes; LaBaer, Joshua

    2004-07-01

    Protein microarrays provide a powerful tool for the study of protein function. However, they are not widely used, in part because of the challenges in producing proteins to spot on the arrays. We generated protein microarrays by printing complementary DNAs onto glass slides and then translating target proteins with mammalian reticulocyte lysate. Epitope tags fused to the proteins allowed them to be immobilized in situ. This obviated the need to purify proteins, avoided protein stability problems during storage, and captured sufficient protein for functional studies. We used the technology to map pairwise interactions among 29 human DNA replication initiation proteins, recapitulate the regulation of Cdt1 binding to select replication proteins, and map its geminin-binding domain.

  2. Microarray analysis in pulmonary hypertension

    PubMed Central

    Hoffmann, Julia; Wilhelm, Jochen; Olschewski, Andrea

    2016-01-01

    Microarrays are a powerful and effective tool that allows the detection of genome-wide gene expression differences between controls and disease conditions. They have been broadly applied to investigate the pathobiology of diverse forms of pulmonary hypertension, namely group 1, including patients with idiopathic pulmonary arterial hypertension, and group 3, including pulmonary hypertension associated with chronic lung diseases such as chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. To date, numerous human microarray studies have been conducted to analyse global (lung homogenate samples), compartment-specific (laser capture microdissection), cell type-specific (isolated primary cells) and circulating cell (peripheral blood) expression profiles. Combined, they provide important information on development, progression and the end-stage disease. In the future, system biology approaches, expression of noncoding RNAs that regulate coding RNAs, and direct comparison between animal models and human disease might be of importance. PMID:27076594

  3. Lectin microarrays for glycomic analysis.

    PubMed

    Gupta, Garima; Surolia, Avadhesha; Sampathkumar, Srinivasa-Gopalan

    2010-08-01

    Glycomics is the study of comprehensive structural elucidation and characterization of all glycoforms found in nature and their dynamic spatiotemporal changes that are associated with biological processes. Glycocalyx of mammalian cells actively participate in cell-cell, cell-matrix, and cell-pathogen interactions, which impact embryogenesis, growth and development, homeostasis, infection and immunity, signaling, malignancy, and metabolic disorders. Relative to genomics and proteomics, glycomics is just growing out of infancy with great potential in biomedicine for biomarker discovery, diagnosis, and treatment. However, the immense diversity and complexity of glycan structures and their multiple modes of interactions with proteins pose great challenges for development of analytical tools for delineating structure function relationships and understanding glyco-code. Several tools are being developed for glycan profiling based on chromatography, mass spectrometry, glycan microarrays, and glyco-informatics. Lectins, which have long been used in glyco-immunology, printed on a microarray provide a versatile platform for rapid high throughput analysis of glycoforms of biological samples. Herein, we summarize technological advances in lectin microarrays and critically review their impact on glycomics analysis. Challenges remain in terms of expansion to include nonplant derived lectins, standardization for routine clinical use, development of recombinant lectins, and exploration of plant kingdom for discovery of novel lectins. PMID:20726799

  4. Lectin microarrays for glycomic analysis.

    PubMed

    Gupta, Garima; Surolia, Avadhesha; Sampathkumar, Srinivasa-Gopalan

    2010-08-01

    Glycomics is the study of comprehensive structural elucidation and characterization of all glycoforms found in nature and their dynamic spatiotemporal changes that are associated with biological processes. Glycocalyx of mammalian cells actively participate in cell-cell, cell-matrix, and cell-pathogen interactions, which impact embryogenesis, growth and development, homeostasis, infection and immunity, signaling, malignancy, and metabolic disorders. Relative to genomics and proteomics, glycomics is just growing out of infancy with great potential in biomedicine for biomarker discovery, diagnosis, and treatment. However, the immense diversity and complexity of glycan structures and their multiple modes of interactions with proteins pose great challenges for development of analytical tools for delineating structure function relationships and understanding glyco-code. Several tools are being developed for glycan profiling based on chromatography, mass spectrometry, glycan microarrays, and glyco-informatics. Lectins, which have long been used in glyco-immunology, printed on a microarray provide a versatile platform for rapid high throughput analysis of glycoforms of biological samples. Herein, we summarize technological advances in lectin microarrays and critically review their impact on glycomics analysis. Challenges remain in terms of expansion to include nonplant derived lectins, standardization for routine clinical use, development of recombinant lectins, and exploration of plant kingdom for discovery of novel lectins.

  5. Effects of PUVA on the eye

    SciTech Connect

    Backman, H.A.

    1982-01-01

    Psoriasis is a common skin disease which may be treated with 8-methoxy psoralen and long-wave ultraviolet light (PUVA). Eye protection is provided during and after treatment to prevent the development of photokeratitis and cataracts. Fifteen patients, treated with medication and ultraviolet A (UVA) had an initial complete eye examination and a repeat examination after each treatment. No patients developed cataracts but almost one-half of the patients had a mild form of photokeratoconjunctivitis. The ocular manifestations included photophobia, conjunctivitis, keratitis, and dry eyes. Tear break-up time was reduced significantly immediately after treatment for two patients but returned to normal 8 hr later. Dermatologists who employ PUVA treatments should be concerned about photokeratoconjunctivitis and the dry-eye ocular manifestations included photophobia, conjunctivitis, keratitis, and dry eyes. Tear break-up time was reduced significantly immediately after treatment for two patients but returned to normal 8 hr later. Dermatologists who employ PUVA treatments should be concerned about photokeratoconjunctivitis and the dry-eye ocular manifestations included photophobia, conjunctivitis, keratitis, and dry eyes. Tear break-up time was reduced significantly immediately after treatment for two patients but returned to normal 8 hr later. Dermatologists who employ PUVA treatments should be concerned about photokeratoconjunctivitis and the dry-eye syndrome.

  6. Current Protocols in Chemical Biology Construction and Use of Glycan Microarrays

    PubMed Central

    Campbell, Christopher T.; Zhang, Yalong; Gildersleeve, Jeffrey C.

    2011-01-01

    Glycosylation is an important post-translational modification that influences many biological processes critical for development, normal physiologic function, and diseases. Unfortunately, progress towards understanding the roles of glycans in biology has been slow due to the challenges of studying glycans and the proteins that interact with them. Glycan microarrays provide a high-throughput approach for the rapid analysis of carbohydrate-macromolecule interactions. Protocols detailed here are intended to help laboratories with basic familiarity of DNA or protein microarrays to begin printing and performing assays using glycan microarrays. Basic and advanced data processing are also detailed, along with strategies for improving reproducibility of data collected with glycan arrays. PMID:23836542

  7. Saccadic eye movement during spaceflight

    NASA Technical Reports Server (NTRS)

    Uri, John J.; Linder, Barry J.; Moore, Thomas P.; Pool, Sam L.; Thornton, William E.

    1989-01-01

    Saccadic eye movements were studied in six subjects during two Space Shuttle missions. Reaction time, peak velocity and accuracy of horizontal, visually-guided saccades were examined preflight, inflight and postflight. Conventional electro-oculography was used to record eye position, with the subjects responding to pseudo-randomly illuminated targets at 0 deg and + or - 10 deg and 20 deg visual angles. In all subjects, preflight measurements were within normal limits. Reaction time was significantly increased inflight, while peak velocity was significantly decreased. A tendency toward a greater proportion of hypometric saccades inflight was also noted. Possible explanations for these changes and possible correlations with space motion sickness are discussed.

  8. Assessing Agreement between miRNA Microarray Platforms

    PubMed Central

    Bassani, Niccolò P.; Ambrogi, Federico; Biganzoli, Elia M.

    2014-01-01

    Over the last few years, miRNA microarray platforms have provided great insights into the biological mechanisms underlying the onset and development of several diseases. However, only a few studies have evaluated the concordance between different microarray platforms using methods that took into account measurement error in the data. In this work, we propose the use of a modified version of the Bland–Altman plot to assess agreement between microarray platforms. To this aim, two samples, one renal tumor cell line and a pool of 20 different human normal tissues, were profiled using three different miRNA platforms (Affymetrix, Agilent, Illumina) on triplicate arrays. Intra-platform reliability was assessed by calculating pair-wise concordance correlation coefficients (CCC) between technical replicates and overall concordance correlation coefficient (OCCC) with bootstrap percentile confidence intervals, which revealed moderate-to-good repeatability of all platforms for both samples. Modified Bland–Altman analysis revealed good patterns of concordance for Agilent and Illumina, whereas Affymetrix showed poor-to-moderate agreement for both samples considered. The proposed method is useful to assess agreement between array platforms by modifying the original Bland–Altman plot to let it account for measurement error and bias correction and can be used to assess patterns of concordance between other kinds of arrays other than miRNA microarrays.

  9. SAMMD: Staphylococcus aureus Microarray Meta-Database

    PubMed Central

    Nagarajan, Vijayaraj; Elasri, Mohamed O

    2007-01-01

    Background Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation system to comprehensively examine them. We report the development of the Staphylococcus aureus Microarray meta-database (SAMMD) which includes data from all the published transcriptional profiles. SAMMD is a web-accessible database that helps users to perform a variety of analysis against and within the existing transcriptional profiles. Description SAMMD is a relational database that uses MySQL as the back end and PHP/JavaScript/DHTML as the front end. The database is normalized and consists of five tables, which holds information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from the peer-reviewed published articles. Data extraction and conversion was done using perl scripts while data entry was done through phpMyAdmin tool. The database is accessible via a web interface that contains several features such as a simple search by ORF ID, gene name, gene product name, advanced search using gene lists, comparing among datasets, browsing, downloading, statistics, and help. The database is licensed under General Public License (GPL). Conclusion SAMMD is hosted and available at . Currently there are over 9500 entries for regulated genes, from 67 microarray experiments. SAMMD will help staphylococcal scientists to analyze their

  10. Feature-based eye corner detection from static images

    NASA Astrophysics Data System (ADS)

    Xia, Haiying; Yan, Guoping; You, Chao

    2009-10-01

    Eye corner detection is important for eye extraction, face normalization, other facial landmark extraction and so on. We present a feature-based method for eye corner detection from static images in this paper. This method is capable of locating eye corners automatically. The process of eye corner detection is divided into two stages: classifier training and classifier application. For training, two classifiers trained by AdaBoost with Haar-like features, are skillfully designed to detect inner eye corners and outer eye corners. Then, two classifiers are applied to input images to search targets. Eye corners are finally located according to two eye models from targets. Experimental results tested on BioID face database and our own database demonstrate that our method obtains a high accuracy under clutter conditions.

  11. Eating for Your Eyes

    ERIC Educational Resources Information Center

    Stastny, Sherri Nordstrom; Garden-Robinson, Julie

    2011-01-01

    An educational program targeting older adults was developed to increase knowledge regarding nutrition and eye health. With age, the chance for eye disease increases, so prevention is critical. The Eating for Your Eyes program has promoted behavior changes regarding eye health among the participants. This program is easily replicated and use is…

  12. Integrated Amplification Microarrays for Infectious Disease Diagnostics

    PubMed Central

    Chandler, Darrell P.; Bryant, Lexi; Griesemer, Sara B.; Gu, Rui; Knickerbocker, Christopher; Kukhtin, Alexander; Parker, Jennifer; Zimmerman, Cynthia; George, Kirsten St.; Cooney, Christopher G.

    2012-01-01

    This overview describes microarray-based tests that combine solution-phase amplification chemistry and microarray hybridization within a single microfluidic chamber. The integrated biochemical approach improves microarray workflow for diagnostic applications by reducing the number of steps and minimizing the potential for sample or amplicon cross-contamination. Examples described herein illustrate a basic, integrated approach for DNA and RNA genomes, and a simple consumable architecture for incorporating wash steps while retaining an entirely closed system. It is anticipated that integrated microarray biochemistry will provide an opportunity to significantly reduce the complexity and cost of microarray consumables, equipment, and workflow, which in turn will enable a broader spectrum of users to exploit the intrinsic multiplexing power of microarrays for infectious disease diagnostics.

  13. Microarray data analysis and mining approaches.

    PubMed

    Cordero, Francesca; Botta, Marco; Calogero, Raffaele A

    2007-12-01

    Microarray based transcription profiling is now a consolidated methodology and has widespread use in areas such as pharmacogenomics, diagnostics and drug target identification. Large-scale microarray studies are also becoming crucial to a new way of conceiving experimental biology. A main issue in microarray transcription profiling is data analysis and mining. When microarrays became a methodology of general use, considerable effort was made to produce algorithms and methods for the identification of differentially expressed genes. More recently, the focus has switched to algorithms and database development for microarray data mining. Furthermore, the evolution of microarray technology is allowing researchers to grasp the regulative nature of transcription, integrating basic expression analysis with mRNA characteristics, i.e. exon-based arrays, and with DNA characteristics, i.e. comparative genomic hybridization, single nucleotide polymorphism, tiling and promoter structure. In this article, we will review approaches used to detect differentially expressed genes and to link differential expression to specific biological functions.

  14. Automated Microarray Image Analysis Toolbox for MATLAB

    SciTech Connect

    White, Amanda M.; Daly, Don S.; Willse, Alan R.; Protic, Miroslava; Chandler, Darrell P.

    2005-09-01

    The Automated Microarray Image Analysis (AMIA) Toolbox for MATLAB is a flexible, open-source microarray image analysis tool that allows the user to customize analysis of sets of microarray images. This tool provides several methods of identifying and quantify spot statistics, as well as extensive diagnostic statistics and images to identify poor data quality or processing. The open nature of this software allows researchers to understand the algorithms used to provide intensity estimates and to modify them easily if desired.

  15. Surface free energy and microarray deposition technology.

    PubMed

    McHale, Glen

    2007-03-01

    Microarray techniques use a combinatorial approach to assess complex biochemical interactions. The fundamental goal is simultaneous, large-scale experimentation analogous to the automation achieved in the semiconductor industry. However, microarray deposition inherently involves liquids contacting solid substrates. Liquid droplet shapes are determined by surface and interfacial tension forces, and flows during drying. This article looks at how surface free energy and wetting considerations may influence the accuracy and reliability of spotted microarray experiments.

  16. THE ABRF MARG MICROARRAY SURVEY 2005: TAKING THE PULSE ON THE MICROARRAY FIELD

    EPA Science Inventory

    Over the past several years microarray technology has evolved into a critical component of any discovery based program. Since 1999, the Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) has conducted biennial surveys designed to generate a pr...

  17. Living Cell Microarrays: An Overview of Concepts.

    PubMed

    Jonczyk, Rebecca; Kurth, Tracy; Lavrentieva, Antonina; Walter, Johanna-Gabriela; Scheper, Thomas; Stahl, Frank

    2016-01-01

    Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays. PMID:27600077

  18. Living Cell Microarrays: An Overview of Concepts

    PubMed Central

    Jonczyk, Rebecca; Kurth, Tracy; Lavrentieva, Antonina; Walter, Johanna-Gabriela; Scheper, Thomas; Stahl, Frank

    2016-01-01

    Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays. PMID:27600077

  19. Living Cell Microarrays: An Overview of Concepts

    PubMed Central

    Jonczyk, Rebecca; Kurth, Tracy; Lavrentieva, Antonina; Walter, Johanna-Gabriela; Scheper, Thomas; Stahl, Frank

    2016-01-01

    Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays.

  20. Highly parallel microbial diagnostics using oligonucleotide microarrays.

    PubMed

    Loy, Alexander; Bodrossy, Levente

    2006-01-01

    Oligonucleotide microarrays are highly parallel hybridization platforms, allowing rapid and simultaneous identification of many different microorganisms and viruses in a single assay. In the past few years, researchers have been confronted with a dramatic increase in the number of studies reporting development and/or improvement of oligonucleotide microarrays for microbial diagnostics, but use of the technology in routine diagnostics is still constrained by a variety of factors. Careful development of microarray essentials (such as oligonucleotide probes, protocols for target preparation and hybridization, etc.) combined with extensive performance testing are thus mandatory requirements for the maturation of diagnostic microarrays from fancy technological gimmicks to robust and routinely applicable tools.

  1. Maxwellian Eye Fixation during Natural Scene Perception

    PubMed Central

    Duchesne, Jean; Bouvier, Vincent; Guillemé, Julien; Coubard, Olivier A.

    2012-01-01

    When we explore a visual scene, our eyes make saccades to jump rapidly from one area to another and fixate regions of interest to extract useful information. While the role of fixation eye movements in vision has been widely studied, their random nature has been a hitherto neglected issue. Here we conducted two experiments to examine the Maxwellian nature of eye movements during fixation. In Experiment 1, eight participants were asked to perform free viewing of natural scenes displayed on a computer screen while their eye movements were recorded. For each participant, the probability density function (PDF) of eye movement amplitude during fixation obeyed the law established by Maxwell for describing molecule velocity in gas. Only the mean amplitude of eye movements varied with expertise, which was lower in experts than novice participants. In Experiment 2, two participants underwent fixed time, free viewing of natural scenes and of their scrambled version while their eye movements were recorded. Again, the PDF of eye movement amplitude during fixation obeyed Maxwell's law for each participant and for each scene condition (normal or scrambled). The results suggest that eye fixation during natural scene perception describes a random motion regardless of top-down or of bottom-up processes. PMID:23226987

  2. Maxwellian eye fixation during natural scene perception.

    PubMed

    Duchesne, Jean; Bouvier, Vincent; Guillemé, Julien; Coubard, Olivier A

    2012-01-01

    When we explore a visual scene, our eyes make saccades to jump rapidly from one area to another and fixate regions of interest to extract useful information. While the role of fixation eye movements in vision has been widely studied, their random nature has been a hitherto neglected issue. Here we conducted two experiments to examine the Maxwellian nature of eye movements during fixation. In Experiment 1, eight participants were asked to perform free viewing of natural scenes displayed on a computer screen while their eye movements were recorded. For each participant, the probability density function (PDF) of eye movement amplitude during fixation obeyed the law established by Maxwell for describing molecule velocity in gas. Only the mean amplitude of eye movements varied with expertise, which was lower in experts than novice participants. In Experiment 2, two participants underwent fixed time, free viewing of natural scenes and of their scrambled version while their eye movements were recorded. Again, the PDF of eye movement amplitude during fixation obeyed Maxwell's law for each participant and for each scene condition (normal or scrambled). The results suggest that eye fixation during natural scene perception describes a random motion regardless of top-down or of bottom-up processes. PMID:23226987

  3. Groundtruth approach to accurate quantitation of fluorescence microarrays

    SciTech Connect

    Mascio-Kegelmeyer, L; Tomascik-Cheeseman, L; Burnett, M S; van Hummelen, P; Wyrobek, A J

    2000-12-01

    To more accurately measure fluorescent signals from microarrays, we calibrated our acquisition and analysis systems by using groundtruth samples comprised of known quantities of red and green gene-specific DNA probes hybridized to cDNA targets. We imaged the slides with a full-field, white light CCD imager and analyzed them with our custom analysis software. Here we compare, for multiple genes, results obtained with and without preprocessing (alignment, color crosstalk compensation, dark field subtraction, and integration time). We also evaluate the accuracy of various image processing and analysis techniques (background subtraction, segmentation, quantitation and normalization). This methodology calibrates and validates our system for accurate quantitative measurement of microarrays. Specifically, we show that preprocessing the images produces results significantly closer to the known ground-truth for these samples.

  4. MatArray: a Matlab toolbox for microarray data.

    PubMed

    Venet, David

    2003-03-22

    The microarray technology allows the high-throughput quantification of the mRNA level of thousands of genes under dozens of conditions, generating a wealth of data which must be analyzed using some form of computational means. A popular framework for such analysis is Matlab, a powerful computing language for which many functions have been written. However, although complex topics like neural networks or principal component analysis are freely available in Matlab, functions to perform more basic tasks like data normalization or hierarchical clustering in an efficient manner are not. The MatArray toolbox aims at filling this gap by offering efficient implementations of the most needed functions for microarray analysis. The functions in the toolbox are command-line only, since it is geared toward seasoned Matlab users.

  5. 2008 Microarray Research Group (MARG Survey): Sensing the State of Microarray Technology

    EPA Science Inventory

    Over the past several years, the field of microarrays has grown and evolved drastically. In its continued efforts to track this evolution and transformation, the ABRF-MARG has once again conducted a survey of international microarray facilities and individual microarray users. Th...

  6. THE ABRF-MARG MICROARRAY SURVEY 2004: TAKING THE PULSE OF THE MICROARRAY FIELD

    EPA Science Inventory

    Over the past several years, the field of microarrays has grown and evolved drastically. In its continued efforts to track this evolution, the ABRF-MARG has once again conducted a survey of international microarray facilities and individual microarray users. The goal of the surve...

  7. Ageing changes in the eye

    PubMed Central

    Salvi, S M; Akhtar, S; Currie, Z

    2006-01-01

    Ageing changes occur in all the structures of the eye causing varied effects. This article attempts to review the parameters of what is considered within the “normal limits” of ageing so as to be able to distinguish those conditions from true disease processes. Improving understanding of the ageing changes will help understand some of the problems that the ageing population faces. PMID:16954455

  8. Genetic regulation of vertebrate eye development.

    PubMed

    Zagozewski, J L; Zhang, Q; Eisenstat, D D

    2014-11-01

    Eye development is a complex and highly regulated process that consists of several overlapping stages: (i) specification then splitting of the eye field from the developing forebrain; (ii) genesis and patterning of the optic vesicle; (iii) regionalization of the optic cup into neural retina and retina pigment epithelium; and (iv) specification and differentiation of all seven retinal cell types that develop from a pool of retinal progenitor cells in a precise temporal and spatial manner: retinal ganglion cells, horizontal cells, cone photoreceptors, amacrine cells, bipolar cells, rod photoreceptors and Müller glia. Genetic regulation of the stages of eye development includes both extrinsic (such as morphogens, growth factors) and intrinsic factors (primarily transcription factors of the homeobox and basic helix-loop helix families). In the following review, we will provide an overview of the stages of eye development highlighting the role of several important transcription factors in both normal developmental processes and in inherited human eye diseases.

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

    PubMed

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

    2013-04-01

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

  10. Imaging of mouse embryonic eye development using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Syed, Saba H.; Kasiraj, Alyssa; Larina, Irina V.; Dickinson, Mary E.; Larin, Kirill V.

    2010-02-01

    Congenital abnormalities are often caused by genetic disorders which alter the normal development of the eye. Embryonic eye imaging in mouse model is important for understanding of normal and abnormal eye development and can contribute to prevention and treatment of eye defects in humans. In this study, we used Swept Source Optical Coherence Tomography (SS-OCT) to image eye structure in mouse embryos at 12.5 to 17.5 days post coitus (dpc). The imaging depth of the OCT allowed us to visualize the whole eye globe at these stages. Different ocular tissues including lens, cornea, eyelids, and hyaloid vasculature were visualized. These results suggest that OCT imaging is a useful tool to study embryonic eye development in the mouse model.

  11. Studying bovine early embryo transcriptome by microarray.

    PubMed

    Dufort, Isabelle; Robert, Claude; Sirard, Marc-André

    2015-01-01

    Microarrays represent a significant advantage when studying gene expression in early embryo because they allow for a speedy study of a large number of genes even if the sample of interest contains small quantities of genetic material. Here we describe the protocols developed by the EmbryoGENE Network to study the bovine transcriptome in early embryo using a microarray experimental design.

  12. Microarrays Made Simple: "DNA Chips" Paper Activity

    ERIC Educational Resources Information Center

    Barnard, Betsy

    2006-01-01

    DNA microarray technology is revolutionizing biological science. DNA microarrays (also called DNA chips) allow simultaneous screening of many genes for changes in expression between different cells. Now researchers can obtain information about genes in days or weeks that used to take months or years. The paper activity described in this article…

  13. Application of microarray technology in pulmonary diseases

    PubMed Central

    Tzouvelekis, Argyris; Patlakas, George; Bouros, Demosthenes

    2004-01-01

    Microarrays are a powerful tool that have multiple applications both in clinical and cell biology arenas of common lung diseases. To exemplify how this tool can be useful, in this review, we will provide an overview of the application of microarray technology in research relevant to common lung diseases and present some of the future perspectives. PMID:15585067

  14. Sensing immune responses with customized peptide microarrays.

    PubMed

    Schirwitz, Christopher; Loeffler, Felix F; Felgenhauer, Thomas; Stadler, Volker; Breitling, Frank; Bischoff, F Ralf

    2012-12-01

    The intent to solve biological and biomedical questions in high-throughput led to an immense interest in microarray technologies. Nowadays, DNA microarrays are routinely used to screen for oligonucleotide interactions within a large variety of potential interaction partners. To study interactions on the protein level with the same efficiency, protein and peptide microarrays offer similar advantages, but their production is more demanding. A new technology to produce peptide microarrays with a laser printer provides access to affordable and highly complex peptide microarrays. Such a peptide microarray can contain up to 775 peptide spots per cm², whereby the position of each peptide spot and, thus, the amino acid sequence of the corresponding peptide, is exactly known. Compared to other techniques, such as the SPOT synthesis, more features per cm² at lower costs can be synthesized which paves the way for laser printed peptide microarrays to take on roles as efficient and affordable biomedical sensors. Here, we describe the laser printer-based synthesis of peptide microarrays and focus on an application involving the blood sera of tetanus immunized individuals, indicating the potential of peptide arrays to sense immune responses.

  15. Eye Movements of Flatfish for Different Gravity Condition

    NASA Astrophysics Data System (ADS)

    Iwata, Kaori; Takabayashi, Akira; Imada, Hideki; Miyachi, Ei-Ichi

    On Earth, gravity sensation plays a basic role for all of physiological phenomena in every creature. In microgravity, loss of gravity input causes many functional disorders in animals and humans. During adaptation to microgravity, otolith-mediated response such as eye movements would alter. Flatfish provide a natural model for the study of adaptive changes in the vestibuloocular reflex. During metamorphosis, vestibular and oculomotor coordinate of flatfish displaced 90 degrees about the longitudinal body axis. Therefore, it is expected that microgravity induce the sensory mismatch in adult flatfish. In this study, we analyzed the eye movements of normal and otolith removed flatfish for body tilting and the eye movements of normal flatfish during microgravity produced by parabolic aircraft flight. The fish was fixed on the tilting table controlled by computer. The eye movements for body tilting along the different body axis were video-recorded. The vertical and torsional eye rotations were analyzed frame by frame. In normal flatfish, torsional eye movements were larger for head up or head down tilting than leftward or rightward tilting. On the other hand, vertical eye movements were larger for leftward or rightward tilting than head up or head down tilting. After removal of left side utlicular otolith, the vertical eye movement for 180 degrees body tilting disappeared. For the changes of gravity, vertical eye movements were observed. These results suggested that eye movements of flatfish adapted to Earth's gravity condition and sacculus and lagena might play important role for otolith-ocular eye movements.

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

    PubMed

    Liang, Lifeng; Wang, Cassie T; Sun, Xiaofang; Liu, Lian; Li, Man; Witz, Craig; Williams, Daniel; Griffith, Jason; Skorupski, Josh; Haddad, Ghassan; Gill, Jimmy; Wang, Wei-Hua

    2013-01-01

    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 embryos.

  17. Microarray Applications in Microbial Ecology Research.

    SciTech Connect

    Gentry, T.; Schadt, C.; Zhou, J.

    2006-04-06

    Microarray technology has the unparalleled potential tosimultaneously determine the dynamics and/or activities of most, if notall, of the microbial populations in complex environments such as soilsand sediments. Researchers have developed several types of arrays thatcharacterize the microbial populations in these samples based on theirphylogenetic relatedness or functional genomic content. Several recentstudies have used these microarrays to investigate ecological issues;however, most have only analyzed a limited number of samples withrelatively few experiments utilizing the full high-throughput potentialof microarray analysis. This is due in part to the unique analyticalchallenges that these samples present with regard to sensitivity,specificity, quantitation, and data analysis. This review discussesspecific applications of microarrays to microbial ecology research alongwith some of the latest studies addressing the difficulties encounteredduring analysis of complex microbial communities within environmentalsamples. With continued development, microarray technology may ultimatelyachieve its potential for comprehensive, high-throughput characterizationof microbial populations in near real-time.

  18. Real-time DNA microarray analysis

    PubMed Central

    Hassibi, Arjang; Vikalo, Haris; Riechmann, José Luis; Hassibi, Babak

    2009-01-01

    We present a quantification method for affinity-based DNA microarrays which is based on the real-time measurements of hybridization kinetics. This method, i.e. real-time DNA microarrays, enhances the detection dynamic range of conventional systems by being impervious to probe saturation in the capturing spots, washing artifacts, microarray spot-to-spot variations, and other signal amplitude-affecting non-idealities. We demonstrate in both theory and practice that the time-constant of target capturing in microarrays, similar to all affinity-based biosensors, is inversely proportional to the concentration of the target analyte, which we subsequently use as the fundamental parameter to estimate the concentration of the analytes. Furthermore, to empirically validate the capabilities of this method in practical applications, we present a FRET-based assay which enables the real-time detection in gene expression DNA microarrays. PMID:19723688

  19. Real-time DNA microarray analysis.

    PubMed

    Hassibi, Arjang; Vikalo, Haris; Riechmann, José Luis; Hassibi, Babak

    2009-11-01

    We present a quantification method for affinity-based DNA microarrays which is based on the real-time measurements of hybridization kinetics. This method, i.e. real-time DNA microarrays, enhances the detection dynamic range of conventional systems by being impervious to probe saturation in the capturing spots, washing artifacts, microarray spot-to-spot variations, and other signal amplitude-affecting non-idealities. We demonstrate in both theory and practice that the time-constant of target capturing in microarrays, similar to all affinity-based biosensors, is inversely proportional to the concentration of the target analyte, which we subsequently use as the fundamental parameter to estimate the concentration of the analytes. Furthermore, to empirically validate the capabilities of this method in practical applications, we present a FRET-based assay which enables the real-time detection in gene expression DNA microarrays. PMID:19723688

  20. Tissue Microarrays in Clinical Oncology

    PubMed Central

    Voduc, David; Kenney, Challayne; Nielsen, Torsten O.

    2008-01-01

    The tissue microarray is a recently-implemented, high-throughput technology for the analysis of molecular markers in oncology. This research tool permits the rapid assessment of a biomarker in thousands of tumor samples, using commonly available laboratory assays such as immunohistochemistry and in-situ hybridization. Although introduced less than a decade ago, the TMA has proven to be invaluable in the study of tumor biology, the development of diagnostic tests, and the investigation of oncological biomarkers. This review describes the impact of TMA-based research in clinical oncology and its potential future applications. Technical aspects of TMA construction, and the advantages and disadvantages inherent to this technology are also discussed. PMID:18314063

  1. DNA Microarrays for Identifying Fishes

    PubMed Central

    Nölte, M.; Weber, H.; Silkenbeumer, N.; Hjörleifsdottir, S.; Hreggvidsson, G. O.; Marteinsson, V.; Kappel, K.; Planes, S.; Tinti, F.; Magoulas, A.; Garcia Vazquez, E.; Turan, C.; Hervet, C.; Campo Falgueras, D.; Antoniou, A.; Landi, M.; Blohm, D.

    2008-01-01

    In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a “Fish Chip” for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products. PMID:18270778

  2. Ultrasonography of the eye and orbit.

    PubMed

    Dudea, Sorin M

    2011-06-01

    Ultrasonography (US) is, quite often, the first imaging modality used in eye and orbit assessment. The indications of ophthalmic US cover a wide range of disease where direct clinical assessment is impossible or of little value. Doppler US enhances the ability to assess blood flow in the main arteries and veins. In order to take full advantage of all the possibilities US has to offer the examiner thorough knowledge of the examination technique and normal US anatomy of the eye and orbit is required. This paper reviews the basics of the examination technique and ultrasound anatomy of the eye and orbit.

  3. Distinct Biochemical Activities of Eyes absent During Drosophila Eye Development.

    PubMed

    Jin, Meng; Mardon, Graeme

    2016-01-01

    Eyes absent (Eya) is a highly conserved transcriptional coactivator and protein phosphatase that plays vital roles in multiple developmental processes from Drosophila to humans. Eya proteins contain a PST (Proline-Serine-Threonine)-rich transactivation domain, a threonine phosphatase motif (TPM), and a tyrosine protein phosphatase domain. Using a genomic rescue system, we find that the PST domain is essential for Eya activity and Dac expression, and the TPM is required for full Eya function. We also find that the threonine phosphatase activity plays only a minor role during Drosophila eye development and the primary function of the PST and TPM domains is transactivation that can be largely substituted by the heterologous activation domain VP16. Along with our previous results that the tyrosine phosphatase activity of Eya is dispensable for normal Eya function in eye formation, we demonstrate that a primary function of Eya during Drosophila eye development is as a transcriptional coactivator. Moreover, the PST/TPM and the threonine phosphatase activity are not required for in vitro interaction between retinal determination factors. Finally, this work is the first report of an Eya-Ey physical interaction. These findings are particularly important because they highlight the need for an in vivo approach that accurately dissects protein function. PMID:26980695

  4. Diabetic Eye Problems

    MedlinePlus

    ... too high. Over time, this can damage your eyes. The most common problem is diabetic retinopathy. It ... light-sensitive tissue at the back of your eye. You need a healthy retina to see clearly. ...

  5. Diabetes - eye care

    MedlinePlus

    Diabetic retinopathy - care ... until the problem is very bad. Your health care provider can catch problems early if you get ... doctor (ophthalmologist). Choose an eye doctor who takes care of people with diabetes. Your eye exam may ...

  6. Diabetes and eye disease

    MedlinePlus

    ... the eye that can lead to blindness Macular edema: blurry vision due to fluid leaking into the ... in your retina (neovascularization) or you develop macular edema, treatment is usually needed. Eye surgery is the ...

  7. Eye Injuries (For Parents)

    MedlinePlus

    ... and comfortable as possible until help arrives. continue Chemical Exposure Many chemicals, even those found around the house, can damage an eye. If your child gets a chemical in the eye and you know what it ...

  8. Eye Injuries at Work

    MedlinePlus

    ... Bureau of Labor Statistics, more than 20,000 workplace eye injuries happen each year. Injuries on the job often ... Occupational Safety and Health Administration (OSHA) reports that workplace eye injuries cost an estimated $300 million a year in ...

  9. What Is Dry Eye?

    MedlinePlus

    ... Our Sites EyeWiki International Society of Refractive Surgery Museum of Vision Subspecialties Cataract/Anterior Segment Comprehensive Ophthalmology ... Our Sites EyeWiki International Society of Refractive Surgery Museum of Vision Subspecialties Cataract/Anterior Segment Comprehensive Ophthalmology ...

  10. New technologies for fabricating biological microarrays

    NASA Astrophysics Data System (ADS)

    Larson, Bradley James

    This dissertation contains the description of two technologies that we have developed to reduce the cost and improve the quality of spotted biological microarrays. The first is a device, called a fluid microplotter, that uses ultrasonics to deposit spots with diameters of less than 5 microns. It consists of a dispenser, composed of a micropipette fastened to a piece of PZT piezoelectric, attached to a precision positioning system. A gentle pumping of fluid to the surface occurs when the micropipette is driven at specific frequencies. Spots or continuous lines can be deposited in this manner. The small fluid features conserve expensive and limited-quantity biological reagents. We characterize the performance of the microplotter in depositing fluid and examine the theoretical underpinnings of its operation. We present an analytical expression for the diameter of a deposited spot as a function of droplet volume and wettability of a surface and compare it with experimental results. We also examine the resonant properties of the piezoelectric element used to drive the dispenser and relate that to the frequencies at which pumping occurs. Finally, we propose a mechanism to explain the pumping behavior within the microplotter dispenser. The second technology we present is a process that uses a cold plasma and a subsequent in vacuo vapor-phase reaction to terminate a variety of oxide surfaces with epoxide chemical groups. These epoxide groups can react with amine-containing biomolecules to form strong covalent linkages between the biomolecules and the treated surface. The use of a plasma activation step followed by an in vacuo vapor-phase reaction allows for the precise control of surface functional groups, rather than the mixture of functionalities normally produced. This process modifies a range of different oxide surfaces, is fast, consumes a minimal amount of reagents, and produces attachment densities for bound biomolecules that are comparable to or better than

  11. Relevant and significant supervised gene clusters for microarray cancer classification.

    PubMed

    Maji, Pradipta; Das, Chandra

    2012-06-01

    An important application of microarray data in functional genomics is to classify samples according to their gene expression profiles such as to classify cancer versus normal samples or to classify different types or subtypes of cancer. One of the major tasks with gene expression data is to find co-regulated gene groups whose collective expression is strongly associated with sample categories. In this regard, a gene clustering algorithm is proposed to group genes from microarray data. It directly incorporates the information of sample categories in the grouping process for finding groups of co-regulated genes with strong association to the sample categories, yielding a supervised gene clustering algorithm. The average expression of the genes from each cluster acts as its representative. Some significant representatives are taken to form the reduced feature set to build the classifiers for cancer classification. The mutual information is used to compute both gene-gene redundancy and gene-class relevance. The performance of the proposed method, along with a comparison with existing methods, is studied on six cancer microarray data sets using the predictive accuracy of naive Bayes classifier, K-nearest neighbor rule, and support vector machine. An important finding is that the proposed algorithm is shown to be effective for identifying biologically significant gene clusters with excellent predictive capability. PMID:22552589

  12. Chromatin immunoprecipitation and microarray-based analysis of protein location

    PubMed Central

    Lee, Tong Ihn; Johnstone, Sarah E; Young, Richard A

    2010-01-01

    Genome-wide location analysis, also known as ChIP-Chip, combines chromatin immunoprecipitation and DNA microarray analysis to identify protein-DNA interactions that occur in living cells. Protein-DNA interactions are captured in vivo by chemical crosslinking. Cell lysis, DNA fragmentation and immunoaffinity purification of the desired protein will co-purify DNA fragments that are associated with that protein. The enriched DNA population is then labeled, combined with a differentially labeled reference sample and applied to DNA microarrays to detect enriched signals. Various computational and bioinformatic approaches are then applied to normalize the enriched and reference channels, to connect signals to the portions of the genome that are represented on the DNA microarrays, to provide confidence metrics and to generate maps of protein-genome occupancy. Here, we describe the experimental protocols that we use from crosslinking of cells to hybridization of labeled material, together with insights into the aspects of these protocols that influence the results. These protocols require approximately 1 week to complete once sufficient numbers of cells have been obtained, and have been used to produce robust, high-quality ChIP-chip results in many different cell and tissue types. PMID:17406303

  13. A Versatile Microarray Platform for Capturing Rare Cells

    PubMed Central

    Brinkmann, Falko; Hirtz, Michael; Haller, Anna; Gorges, Tobias M.; Vellekoop, Michael J.; Riethdorf, Sabine; Müller, Volkmar; Pantel, Klaus; Fuchs, Harald

    2015-01-01

    Analyses of rare events occurring at extremely low frequencies in body fluids are still challenging. We established a versatile microarray-based platform able to capture single target cells from large background populations. As use case we chose the challenging application of detecting circulating tumor cells (CTCs) – about one cell in a billion normal blood cells. After incubation with an antibody cocktail, targeted cells are extracted on a microarray in a microfluidic chip. The accessibility of our platform allows for subsequent recovery of targets for further analysis. The microarray facilitates exclusion of false positive capture events by co-localization allowing for detection without fluorescent labelling. Analyzing blood samples from cancer patients with our platform reached and partly outreached gold standard performance, demonstrating feasibility for clinical application. Clinical researchers free choice of antibody cocktail without need for altered chip manufacturing or incubation protocol, allows virtual arbitrary targeting of capture species and therefore wide spread applications in biomedical sciences. PMID:26493176

  14. MAGMA: analysis of two-channel microarrays made easy.

    PubMed

    Rehrauer, Hubert; Zoller, Stefan; Schlapbach, Ralph

    2007-07-01

    The web application MAGMA provides a simple and intuitive interface to identify differentially expressed genes from two-channel microarray data. While the underlying algorithms are not superior to those of similar web applications, MAGMA is particularly user friendly and can be used without prior training. The user interface guides the novice user through the most typical microarray analysis workflow consisting of data upload, annotation, normalization and statistical analysis. It automatically generates R-scripts that document MAGMA's entire data processing steps, thereby allowing the user to regenerate all results in his local R installation. The implementation of MAGMA follows the model-view-controller design pattern that strictly separates the R-based statistical data processing, the web-representation and the application logic. This modular design makes the application flexible and easily extendible by experts in one of the fields: statistical microarray analysis, web design or software development. State-of-the-art Java Server Faces technology was used to generate the web interface and to perform user input processing. MAGMA's object-oriented modular framework makes it easily extendible and applicable to other fields and demonstrates that modern Java technology is also suitable for rather small and concise academic projects. MAGMA is freely available at www.magma-fgcz.uzh.ch. PMID:17517778

  15. Fecal source tracking in water using a mitochondrial DNA microarray.

    PubMed

    Vuong, Nguyet-Minh; Villemur, Richard; Payment, Pierre; Brousseau, Roland; Topp, Edward; Masson, Luke

    2013-01-01

    A mitochondrial-based microarray (mitoArray) was developed for rapid identification of the presence of 28 animals and one family (cervidae) potentially implicated in fecal pollution in mixed activity watersheds. Oligonucleotide probes for genus or subfamily-level identification were targeted within the 12S rRNA - Val tRNA - 16S rRNA region in the mitochondrial genome. This region, called MI-50, was selected based on three criteria: 1) the ability to be amplified by universal primers 2) these universal primer sequences are present in most commercial and domestic animals of interest in source tracking, and 3) that sufficient sequence variation exists within this region to meet the minimal requirements for microarray probe discrimination. To quantify the overall level of mitochondrial DNA (mtDNA) in samples, a quantitative-PCR (Q-PCR) universal primer pair was also developed. Probe validation was performed using DNA extracted from animal tissues and, for many cases, animal-specific fecal samples. To reduce the amplification of potentially interfering fish mtDNA sequences during the MI-50 enrichment step, a clamping PCR method was designed using a fish-specific peptide nucleic acid. DNA extracted from 19 water samples were subjected to both array and independent PCR analyses. Our results confirm that the mitochondrial microarray approach method could accurately detect the dominant animals present in water samples emphasizing the potential for this methodology in the parallel scanning of a large variety of animals normally monitored in fecal source tracking.

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

    SciTech Connect

    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.

  17. Dwarf Eye Disorder

    ERIC Educational Resources Information Center

    Science Teacher, 2005

    2005-01-01

    Johns Hopkins researchers at the Wilmer Eye Institute have discovered what appears to be the first human gene mutation that causes extreme farsightedness. The researchers report that nanophthalmos, Greek for "dwarf eye," is a rare, potentially blinding disorder caused by an alteration in a gene called MFRP that helps control eye growth and…

  18. Eye - foreign object in

    MedlinePlus

    ... to gently flush it out with water or eye drops. If that does not work, try touching a second cotton-tipped swab to the object to remove it. If the object is on the white of the eye, try gently rinsing the eye with water or ...

  19. Microarray-integrated optoelectrofluidic immunoassay system.

    PubMed

    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.

  20. Chromosome microarrays in diagnostic testing: interpreting the genomic data.

    PubMed

    Peters, Greg B; Pertile, Mark D

    2014-01-01

    DNA-based Chromosome MicroArrays (CMAs) are now well established as diagnostic tools in clinical genetics laboratories. Over the last decade, the primary application of CMAs has been the genome-wide detection of a particular class of mutation known as copy number variants (CNVs). Since 2010, CMA testing has been recommended as a first-tier test for detection of CNVs associated with intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies…in the post-natal setting. CNVs are now regarded as pathogenic in 14-18 % of patients referred for these (and related) disorders.Through consideration of clinical examples, and several microarray platforms, we attempt to provide an appreciation of microarray diagnostics, from the initial inspection of the microarray data, to the composing of the patient report. In CMA data interpretation, a major challenge comes from the high frequency of clinically irrelevant CNVs observed within "patient" and "normal" populations. As might be predicted, the more common and clinically insignificant CNVs tend to be the smaller ones <100 kb in length, involving few or no known genes. However, this relationship is not at all straightforward: CNV length and gene content are only very imperfect indicators of CNV pathogenicity. Presently, there are no reliable means of separating, a priori, the benign from the pathological CNV classes.This chapter also considers sources of technical "noise" within CMA data sets. Some level of noise is inevitable in diagnostic genomics, given the very large number of data points generated in any one test. Noise further limits CMA resolution, and some miscalling of CNVs is unavoidable. In this, there is no ideal solution, but various strategies for handling noise are available. Even without solutions, consideration of these diagnostic problems per se is informative, as they afford critical insights into the biological and technical underpinnings of CNV discovery. These are indispensable

  1. Progress in the application of DNA microarrays.

    PubMed Central

    Lobenhofer, E K; Bushel, P R; Afshari, C A; Hamadeh, H K

    2001-01-01

    Microarray technology has been applied to a variety of different fields to address fundamental research questions. The use of microarrays, or DNA chips, to study the gene expression profiles of biologic samples began in 1995. Since that time, the fundamental concepts behind the chip, the technology required for making and using these chips, and the multitude of statistical tools for analyzing the data have been extensively reviewed. For this reason, the focus of this review will be not on the technology itself but on the application of microarrays as a research tool and the future challenges of the field. PMID:11673116

  2. DNA Microarrays in Herbal Drug Research

    PubMed Central

    Chavan, Preeti; Joshi, Kalpana; Patwardhan, Bhushan

    2006-01-01

    Natural products are gaining increased applications in drug discovery and development. Being chemically diverse they are able to modulate several targets simultaneously in a complex system. Analysis of gene expression becomes necessary for better understanding of molecular mechanisms. Conventional strategies for expression profiling are optimized for single gene analysis. DNA microarrays serve as suitable high throughput tool for simultaneous analysis of multiple genes. Major practical applicability of DNA microarrays remains in DNA mutation and polymorphism analysis. This review highlights applications of DNA microarrays in pharmacodynamics, pharmacogenomics, toxicogenomics and quality control of herbal drugs and extracts. PMID:17173108

  3. Eyes open versus eyes closed - Effect on human rotational responses

    NASA Technical Reports Server (NTRS)

    Wall, Conrad, III; Furman, Joseph M. R.

    1989-01-01

    The effect of eyelid closure on the response to rotational vestibular stimulation was assessed by evaluating 16 normal human subjects with both earth vertical axis (EVA) and earth horizontal axis (EHA) yaw rotations with either eyes closed (EC) or eyes open in the dark (EOD). Results indicated that for EVA rotation, the subjects' responses were of larger magnitude and less variable with EOD than with EC. However, for EHA rotation, responses were of larger magnitude and equally variable with EC as compared to EOD. Data also indicated that the quality of the EHA response with EC was altered because eyelid closure influenced the amount of periodic gaze. It is concluded that eyelid closure has an effect upon both canalocular and otolithocular reflexes and it is suggested that both EVA and EHA rotational testing be performed with EOD rather than with EC.

  4. Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays.

    PubMed

    Wu, Xiaogang; Huang, Hui; Wei, Tao; Pandey, Ragini; Reinhard, Christoph; Li, Shuyu D; Chen, Jake Y

    2012-01-01

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

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

    PubMed

    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.

  6. Restriction site tagged (RST) microarrays: a novel technique to study the species composition of complex microbial systems

    PubMed Central

    Zabarovsky, Eugene R.; Petrenko, Lev; Protopopov, Alexei; Vorontsova, Olga; Kutsenko, Alexey S.; Zhao, Yanyan; Kilosanidze, Gelena; Zabarovska, Veronika; Rakhmanaliev, Elian; Pettersson, Bertil; Kashuba, Vladimir I.; Ljungqvist, Olle; Norin, Elisabeth; Midtvedt, Tore; Möllby, Roland; Winberg, Gösta; Ernberg, Ingemar

    2003-01-01

    We have developed a new type of microarray, restriction site tagged (RST), for example NotI, microarrays. In this approach only sequences surrounding specific restriction sites (i.e. NotI linking clones) were used for generating microarrays. DNA was labeled using a new procedure, NotI representation, where only sequences surrounding NotI sites were labeled. Due to these modifications, the sensitivity of RST microarrays increases several hundred-fold compared to that of ordinary genomic microarrays. In a pilot experiment we have produced NotI microarrays from Gram-positive and Gram-negative bacteria and have shown that even closely related Escherichia coli strains can be easily discriminated using this technique. For example, two E.coli strains, K12 and R2, differ by less than 0.1% in their 16S rRNA sequences and thus the 16S rRNA sequence would not easily discriminate between these strains. However, these strains showed distinctly different hybridization patterns with NotI microarrays. The same technique can be adapted to other restriction enzymes as well. This type of microarray opens the possibility not only for studies of the normal flora of the gut but also for any problem where quantitative and qualitative analysis of microbial (or large viral) genomes is needed. PMID:12907747

  7. Comparison of microarray preprocessing methods.

    PubMed

    Shakya, K; Ruskin, H J; Kerr, G; Crane, M; Becker, J

    2010-01-01

    Data preprocessing in microarray technology is a crucial initial step before data analysis is performed. Many preprocessing methods have been proposed but none has proved to be ideal to date. Frequently, datasets are limited by laboratory constraints so that the need is for guidelines on quality and robustness, to inform further experimentation while data are yet restricted. In this paper, we compared the performance of four popular methods, namely MAS5, Li & Wong pmonly (LWPM), Li & Wong subtractMM (LWMM), and Robust Multichip Average (RMA). The comparison is based on the analysis carried out on sets of laboratory-generated data from the Bioinformatics Lab, National Institute of Cellular Biotechnology (NICB), Dublin City University, Ireland. These experiments were designed to examine the effect of Bromodeoxyuridine (5-bromo-2-deoxyuridine, BrdU) treatment in deep lamellar keratoplasty (DLKP) cells. The methodology employed is to assess dispersion across the replicates and analyze the false discovery rate. From the dispersion analysis, we found that variability is reduced more effectively by LWPM and RMA methods. From the false positive analysis, and for both parametric and nonparametric approaches, LWMM is found to perform best. Based on a complementary q-value analysis, LWMM approach again is the strongest candidate. The indications are that, while LWMM is marginally less effective than LWPM and RMA in terms of variance reduction, it has considerably improved discrimination overall.

  8. AMIC@: All MIcroarray Clusterings @ once.

    PubMed

    Geraci, Filippo; Pellegrini, Marco; Renda, M Elena

    2008-07-01

    The AMIC@ Web Server offers a light-weight multi-method clustering engine for microarray gene-expression data. AMIC@ is a highly interactive tool that stresses user-friendliness and robustness by adopting AJAX technology, thus allowing an effective interleaved execution of different clustering algorithms and inspection of results. Among the salient features AMIC@ offers, there are: (i) automatic file format detection, (ii) suggestions on the number of clusters using a variant of the stability-based method of Tibshirani et al. (iii) intuitive visual inspection of the data via heatmaps and (iv) measurements of the clustering quality using cluster homogeneity. Large data sets can be processed efficiently by selecting algorithms (such as FPF-SB and k-Boost), specifically designed for this purpose. In case of very large data sets, the user can opt for a batch-mode use of the system by means of the Clustering wizard that runs all algorithms at once and delivers the results via email. AMIC@ is freely available and open to all users with no login requirement at the following URL http://bioalgo.iit.cnr.it/amica.

  9. Protein Microarrays: Novel Developments and Applications

    PubMed Central

    Berrade, Luis; Garcia, Angie E.

    2011-01-01

    Protein microarray technology possesses some of the greatest potential for providing direct information on protein function and potential drug targets. For example, functional protein microarrays are ideal tools suited for the mapping of biological pathways. They can be used to study most major types of interactions and enzymatic activities that take place in biochemical pathways and have been used for the analysis of simultaneous multiple biomolecular interactions involving protein-protein, protein-lipid, protein-DNA and protein-small molecule interactions. Because of this unique ability to analyze many kinds of molecular interactions en masse, the requirement of very small sample amount and the potential to be miniaturized and automated, protein microarrays are extremely well suited for protein profiling, drug discovery, drug target identification and clinical prognosis and diagnosis. The aim of this review is to summarize the most recent developments in the production, applications and analysis of protein microarrays. PMID:21116694

  10. [Studies of dibekacin eye-drops. Intraocular penetration (author's transl)].

    PubMed

    Tomono, N; Nakayoshi, T; Fujita, M; Kikai, S; Oishi, M

    1980-06-01

    Ocular tissue levels of dibekacin (DKB) were studied in rabbits after instillation of 0.3% DKB eye-drops five times every 5 minutes. (1) In normal eyes, DKB levels were determined in all of the outer parts of eye and some of inner parts such as aqueous humor and vitreous body. Such levels were relatively higher than those of gentamicin. (2) In cauterized eyes by NaOH tissue levels were several times higher than those obtained in normal eyes. (3) Considering these results and MIC levels against both Gram-positive and Gram-negative bacteria such as Pseudomonas aeruginosa or Staphylococcus aureus, it is suggested that 0.3% DKB eye-drops will show effectiveness in clinical use. PMID:7452907

  11. Contributions to Statistical Problems Related to Microarray Data

    ERIC Educational Resources Information Center

    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…

  12. The Impact of Photobleaching on Microarray Analysis.

    PubMed

    von der Haar, Marcel; Preuß, John-Alexander; von der Haar, Kathrin; Lindner, Patrick; Scheper, Thomas; Stahl, Frank

    2015-01-01

    DNA-Microarrays have become a potent technology for high-throughput analysis of genetic regulation. However, the wide dynamic range of signal intensities of fluorophore-based microarrays exceeds the dynamic range of a single array scan by far, thus limiting the key benefit of microarray technology: parallelization. The implementation of multi-scan techniques represents a promising approach to overcome these limitations. These techniques are, in turn, limited by the fluorophores' susceptibility to photobleaching when exposed to the scanner's laser light. In this paper the photobleaching characteristics of cyanine-3 and cyanine-5 as part of solid state DNA microarrays are studied. The effects of initial fluorophore intensity as well as laser scanner dependent variables such as the photomultiplier tube's voltage on bleaching and imaging are investigated. The resulting data is used to develop a model capable of simulating the expected degree of signal intensity reduction caused by photobleaching for each fluorophore individually, allowing for the removal of photobleaching-induced, systematic bias in multi-scan procedures. Single-scan applications also benefit as they rely on pre-scans to determine the optimal scanner settings. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the lab-to-lab comparability of microarray experiment results. PMID:26378589

  13. Automated analytical microarrays: a critical review.

    PubMed

    Seidel, Michael; Niessner, Reinhard

    2008-07-01

    Microarrays provide a powerful analytical tool for the simultaneous detection of multiple analytes in a single experiment. The specific affinity reaction of nucleic acids (hybridization) and antibodies towards antigens is the most common bioanalytical method for generating multiplexed quantitative results. Nucleic acid-based analysis is restricted to the detection of cells and viruses. Antibodies are more universal biomolecular receptors that selectively bind small molecules such as pesticides, small toxins, and pharmaceuticals and to biopolymers (e.g. toxins, allergens) and complex biological structures like bacterial cells and viruses. By producing an appropriate antibody, the corresponding antigenic analyte can be detected on a multiplexed immunoanalytical microarray. Food and water analysis along with clinical diagnostics constitute potential application fields for multiplexed analysis. Diverse fluorescence, chemiluminescence, electrochemical, and label-free microarray readout systems have been developed in the last decade. Some of them are constructed as flow-through microarrays by combination with a fluidic system. Microarrays have the potential to become widely accepted as a system for analytical applications, provided that robust and validated results on fully automated platforms are successfully generated. This review gives an overview of the current research on microarrays with the focus on automated systems and quantitative multiplexed applications.

  14. Evaluation of Surface Chemistries for Antibody Microarrays

    SciTech Connect

    Seurynck-Servoss, Shannon L.; White, Amanda M.; Baird, Cheryl L.; Rodland, Karin D.; Zangar, Richard C.

    2007-12-01

    Antibody microarrays are an emerging technology that promises to be a powerful tool for the detection of disease biomarkers. The current technology for protein microarrays has been primarily derived from DNA microarrays and is not fully characterized for use with proteins. For example, there are a myriad of surface chemistries that are commercially available for antibody microarrays, but no rigorous studies that compare these different surfaces. Therefore, we have used an enzyme-linked immunosorbent assay (ELISA) microarray platform to analyze 16 different commercially available slide types. Full standard curves were generated for 24 different assays. We found that this approach provides a rigorous and quantitative system for comparing the different slide types based on spot size and morphology, slide noise, spot background, lower limit of detection, and reproducibility. These studies demonstrate that the properties of the slide surface affect the activity of immobilized antibodies and the quality of data produced. Although many slide types can produce useful data, glass slides coated with poly-L-lysine or aminosilane, with or without activation with a crosslinker, consistently produce superior results in the ELISA microarray analyses we performed.

  15. Sex hormones and the dry eye.

    PubMed

    Truong, Susan; Cole, Nerida; Stapleton, Fiona; Golebiowski, Blanka

    2014-07-01

    The greater prevalence of dry eye in women compared to men suggests that sex hormones may have a role in this condition. This review aims to present evidence for how sex hormones may affect the ocular structures involved in the production, regulation and maintenance of the normal tear film. It is hypothesised that hormone changes alter the homeostasis of the ocular surface and contribute to dry eye. Androgens impact on the structure and function of the meibomian and lacrimal glands and therefore androgen deficiency is, at least in part, associated with the aetiology of dry eye. In contrast, reports of the effects of oestrogen and progesterone on these ocular structures and on the conjunctiva are contradictory and the mechanisms of action of these female-specific sex hormones in the eye are not well understood. The uncertainty of the effects of oestrogen and progesterone on dry eye symptoms is reflected in the controversial relationship between hormone replacement therapy and the signs and symptoms of dry eye. Current understanding of sex hormone influences on the immune system suggests that oestrogen may modulate a cascade of inflammatory events, which underlie dry eye.

  16. [Protection of the eyes in racket sports].

    PubMed

    Prince, P; Laurencelle, L

    1988-06-01

    A survey was conducted on 1032 racket sport players from 10 randomly selected racket sport centers in Quebec during the month of October 1985. The use of protective eye glasses was found to be higher in racketball (70.2%) and squash (45.8%) than in badminton (8.8%) or tennis (3.5%). While a little less than 60% of protective eye glasses were equipped with unbreakable lenses, 40% of protective glasses were simple eye guards, containing no lens at all. Hence a large number of players assumed that they had adequate protection while wearing simple eye guards or their everyday normal glasses. Gender differences did not seem to affect the use of protective eye glasses. A general observation was that the older the player the better the eye protection, whereas novice players tended to be less prepared to use the protective glasses. The use of protective eye glasses was found to be compulsory in close to 46% of racketball centers and in 25% of squash clubs.

  17. Binocular coordination of the eyes during reading.

    PubMed

    Liversedge, Simon P; Rayner, Keith; White, Sarah J; Findlay, John M; McSorley, Eugene

    2006-09-01

    Saccadic eye movements and fixations are the behavioral means by which we visually sample text during reading. Human oculomotor control is governed by a complex neurophysiological system involving the brain stem, superior colliculus, and several cortical areas. A very widely held belief among researchers investigating primate vision is that the oculomotor system serves to orient the visual axes of both eyes to fixate the same target point in space. It is argued that such precise positioning of the eyes is necessary to place images on corresponding retinal locations, such that on each fixation a single, nondiplopic, visual representation is perceived. Vision works actively through a continual sampling process involving saccades and fixations. Here we report that during normal reading, the eyes do not always fixate the same letter within a word. We also demonstrate that saccadic targeting is yoked and based on a unified cyclopean percept of a whole word since it is unaffected if different word parts are delivered exclusively to each eye via a dichoptic presentation technique. These two findings together suggest that the visual signal from each eye is fused at a very early stage in the visual pathway, even when the fixation disparity is greater than one character (0.29 deg), and that saccade metrics for each eye are computed on the basis of that fused signal.

  18. The modern office environment desiccates the eyes?

    PubMed

    Wolkoff, P; Nøjgaard, J K; Franck, C; Skov, P

    2006-08-01

    Eye irritation is a common complaint in the office environment. The purpose of this overview is to merge knowledge within indoor air science, ophthalmology, and occupational health to promote understanding eye irritation symptomatology, the cause of which is still partly unknown. High periocular relative humidity appears to protect the pre-corneal tear film against desiccation and sensory irritating pollutants and reduces the development of eye irritation symptoms. This is particularly relevant for intensive computer work, where the pre-corneal tear film is altered resulting in dry spot formation and eye dryness, in addition to enhanced susceptibility towards sensory irritating pollutants. The workplace, thermal conditions, and work schedule (including breaks) should be planned in such a way to help maintain a normal eye blink frequency to minimize alterations of the pre-corneal tear film. The role of relative humidity on eye irritation symptoms should not be underestimated. Multiple short breaks are justified by the beneficial effect on the pre-corneal tear film. In addition, longer breaks in tasks, which require demanding visual work, should be considered. In addition, air temperature as well as certain alkene oxidation products by ozone may worsen eye irritation symptoms, but the latter factor may be smaller at higher relative humidity.

  19. Control and Functions of Fixational Eye Movements

    PubMed Central

    Rucci, Michele; Poletti, Martina

    2016-01-01

    Humans and other species explore a visual scene by rapidly shifting their gaze 2-3 times every second. Although the eyes may appear immobile in the brief intervals in between saccades, microscopic (fixational) eye movements are always present, even when attending to a single point. These movements occur during the very periods in which visual information is acquired and processed and their functions have long been debated. Recent technical advances in controlling retinal stimulation during normal oculomotor activity have shed new light on the visual contributions of fixational eye movements and their degree of control. The emerging body of evidence, reviewed in this article, indicates that fixational eye movements are important components of the strategy by which the visual system processes fine spatial details, enabling both precise positioning of the stimulus on the retina and encoding of spatial information into the joint space-time domain.

  20. The eyes of a tiny 'Orsten' crustacean - a compound eye at receptor level?

    PubMed

    Schoenemann, Brigitte

    2013-01-14

    Among the oldest fossil crustaceans are those of the Late Cambrian (Furongian 499 ± 0.3-488.3 ± 1.7 Ma) of Västergötland, central Sweden and the lower Ordovician (Tremadocian 488.3 and 478.6 Ma) of the island of Őland. These are three-dimensionally preserved in nodules from the so called 'stinkstone' ('Orsten') limestone. 'Orsten'-like fossils represent tiny, often meiobenthic organsisms (Haug, Maas, & Waloszek, 2009) smaller than 2mm, which mainly were arthropods, especially crustaceans close to the stemline. As a result of phosphatisation, hairs, bristles and even cellular structures up to 0.3 μm are preserved (Walossek, 1993), especially compound eyes, as typical for all visually orientated crustaceans (Schoenemann et al., 2011). We show a miniscule prototype of a compound eye (∼40 μm) in a small crustacean, which lived almost half a billion years ago. The eye is close to but comfortably established above being limited in its resolving power by diffraction, but it is too small to be an apposition eye, normally regarded as the basal form of all compound eyes, as is found in bees, dragonflies, crustaceans and many other arthropods still living today. The facets of this compound eye are ∼8 μm in size, the surface structure indicates the relicts of a tiny lens covering each facet. In order to work functionally and to ensure that that diffraction and waveguide problems were avoided, it seems reasonable to suppose that the compound eye consisted of visual units, each with a single photoreceptor cell directly below a weak lens for capturing and slightly focusing the light. The entire unit has a diameter similar to that of a normal sensory cell as found in compound eyes. Thus, the early compound eye analysed here may be interpreted as a prototype representing the earliest stages of the evolution of crustacean compound eyes.

  1. Eyeing the eyes in social scenes: Evidence for top-down control of stimulus selection in simultanagnosia.

    PubMed

    Dalrymple, Kirsten A; Gray, Alexander K; Perler, Brielle L; Birmingham, Elina; Bischof, Walter F; Barton, Jason J S; Kingstone, Alan

    2013-01-01

    Simultanagnosia is a disorder of visual attention resulting from bilateral parieto-occipital lesions. Healthy individuals look at eyes to infer people's attentional states, but simultanagnosics allocate abnormally few fixations to eyes in scenes. It is unclear why simultanagnosics fail to fixate eyes, but it might reflect that they are (a) unable to locate and fixate them, or (b) do not prioritize attentional states. We compared eye movements of simultanagnosic G.B. to those of healthy subjects viewing scenes normally or through a restricted window of vision. They described scenes and explicitly inferred attentional states of people in scenes. G.B. and subjects viewing scenes through a restricted window made few fixations on eyes when describing scenes, yet increased fixations on eyes when inferring attention. Thus G.B. understands that eyes are important for inferring attentional states and can exert top-down control to seek out and process the gaze of others when attentional states are of interest.

  2. Eye injuries in childhood.

    PubMed

    Grin, T R; Nelson, L B; Jeffers, J B

    1987-07-01

    A 3-year survey was conducted of all children with eye injuries admitted to Wills Eye Hospital to determine demographic, etiologic, and prophylactic factors. There were 278 cases, representing 22% of all ocular injuries in children requiring admission. The frequency of childhood ocular injuries is high, often resulting in serious visual impairment. Many of these injuries are preventable. The causes of pediatric eye injuries and preventive measures are discussed.

  3. LASIK and dry eye.

    PubMed

    Toda, Ikuko

    2007-01-01

    Dry eye is one of the most common complications after laser-assisted in situ keratomileusis (LASIK). The clinical signs of post-LASIK dry eye include positive vital staining of ocular surface, decreased tear film breakup time and Schirmer test, reduced corneal sensitivity, and decreased functional visual acuity. The symptoms and signs last at least 1 month after LASIK. Although the mechanisms for developing post-LASIK dry eye are not completely understood, loss of corneal innervation by flap-making may affect the reflex loops of the corneal-lacrimal gland, corneal-blinking, and blinking-meibomian gland, and blinking-meibomian gland, resulting in decreased aqueous and lipid tear secretion and mucin expression. As LASIK enhancement by flap-lifting induces less dry eye symptoms and signs than first surgery, it is suggested that other factors rather than loss of neurotrophic effect may be involved in the mechanisms of post-LASIK dry eye. The treatments of dry eye include artificial tears, topical cyclosporine, hot compress, punctal plugs, and autologous serum eye drops. For patients with severe preoperative dry eye, a combination of punctal plugs and serum eye drops is required to be used before surgery.

  4. Eye development and the appearance and maintenance of corneal transparency

    NASA Technical Reports Server (NTRS)

    Conrad, G. W.; Funderburgh, J. L.; Spooner, B. S. (Principal Investigator)

    1992-01-01

    Embryonic development of the eye, including the cornea, depends on the appearance and steady maintenance of intraocular pressure. The eye is a gravity-sensitive organ, as evidence by changes in pupil diameter during parabolic flight. The cornea is largely a paracrystal of extracellular matrix. The extent to which it will polymerize normally in microgravity has yet to be determined.

  5. The Role of Eye Movements in Subitizing and Counting

    ERIC Educational Resources Information Center

    Watson, Derrick G.; Maylor, Elizabeth A.; Bruce, Lucy A. M.

    2007-01-01

    Previous work has suggested that eye movements may be necessary for accurate enumeration beyond the subitization range of about 4 items. This study determined the frequency of eye movements normally made during enumeration, their relationship to response times, and whether they are required for accurate performance. This was achieved by monitoring…

  6. Emotion Words Affect Eye Fixations during Reading

    ERIC Educational Resources Information Center

    Scott, Graham G.; O'Donnell, Patrick J.; Sereno, Sara C.

    2012-01-01

    Emotion words are generally characterized as possessing high arousal and extreme valence and have typically been investigated in paradigms in which they are presented and measured as single words. This study examined whether a word's emotional qualities influenced the time spent viewing that word in the context of normal reading. Eye movements…

  7. DNA microarray analyses in higher plants.

    PubMed

    Galbraith, David W

    2006-01-01

    DNA microarrays were originally devised and described as a convenient technology for the global analysis of plant gene expression. Over the past decade, their use has expanded enormously to cover all kingdoms of living organisms. At the same time, the scope of applications of microarrays has increased beyond expression analyses, with plant genomics playing a leadership role in the on-going development of this technology. As the field has matured, the rate-limiting step has moved from that of the technical process of data generation to that of data analysis. We currently face major problems in dealing with the accumulating datasets, not simply with respect to how to archive, access, and process the huge amounts of data that have been and are being produced, but also in determining the relative quality of the different datasets. A major recognized concern is the appropriate use of statistical design in microarray experiments, without which the datasets are rendered useless. A vigorous area of current research involves the development of novel statistical tools specifically for microarray experiments. This article describes, in a necessarily selective manner, the types of platforms currently employed in microarray research and provides an overview of recent activities using these platforms in plant biology.

  8. Advancing Microarray Assembly with Acoustic Dispensing Technology

    PubMed Central

    Wong, E. Y.; Diamond, S. L.

    2011-01-01

    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 drawbacks of undesired physical contact with 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, pre-spotted reaction volumes to activate enzyme reactions at targeted positions on a microarray. We generated variable-sized spots ranging from 200 to 750 μm (and higher), and handled the transfer of fluorescent bead suspensions with increasing source well concentrations of 0.1 to 10 ×108 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. PMID:19035650

  9. A Synthetic Kinome Microarray Data Generator

    PubMed Central

    Maleki, Farhad; Kusalik, Anthony

    2015-01-01

    Cellular pathways involve the phosphorylation and dephosphorylation of proteins. Peptide microarrays called kinome arrays facilitate the measurement of the phosphorylation activity of hundreds of proteins in a single experiment. Analyzing the data from kinome microarrays is a multi-step process. Typically, various techniques are possible for a particular step, and it is necessary to compare and evaluate them. Such evaluations require data for which correct analysis results are known. Unfortunately, such kinome data is not readily available in the community. Further, there are no established techniques for creating artificial kinome datasets with known results and with the same characteristics as real kinome datasets. In this paper, a methodology for generating synthetic kinome array data is proposed. The methodology relies on actual intensity measurements from kinome microarray experiments and preserves their subtle characteristics. The utility of the methodology is demonstrated by evaluating methods for eliminating heterogeneous variance in kinome microarray data. Phosphorylation intensities from kinome microarrays often exhibit such heterogeneous variance and its presence can negatively impact downstream statistical techniques that rely on homogeneity of variance. It is shown that using the output from the proposed synthetic data generator, it is possible to critically compare two variance stabilization methods. PMID:27600233

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

    PubMed Central

    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 (S3VM) 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 S3VM 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. PMID:27170887

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

    PubMed

    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.

  12. An Eye for Learning.

    ERIC Educational Resources Information Center

    Ostwald, Thomas

    1995-01-01

    Presents a hands-on activity as an excellent starting point for investigations related to the eye. Involves making a simple model of the vertebrate eye to illustrate the formation of an upside-down image on the retina by the lens. Links to investigations in numerous science disciplines including astronomy, genetics, biology, earth science, and…

  13. Photorefraction of the Eye

    ERIC Educational Resources Information Center

    Colicchia, Giuseppe; Wiesner, Hartmut; Zollman, Dean

    2015-01-01

    Photorefraction is a method to easily estimate the refractive state of the eye. The principle of photorefraction involves projecting light into the eye during flash photography and then examining the paths of light that emerge from the pupil after scattering on the back portion of the interior of the eyeball (fundus). We will explain the optical…

  14. Eye tissues study

    NASA Astrophysics Data System (ADS)

    Tuchin, Valery V.; Bashkatov, Alexey N.; Maksimova, Irina L.; Sinichkin, Yurii P.; Simonenko, Georgy V.; Genina, Elina A.; Lakodina, Nina A.

    2001-08-01

    Theoretical and in vitro and in vivo experimental study of spectral and polarization characteristics of the human and rabbit eye tissues are presented. The possibility of control of optical properties of eye cornea, lens and sclera is discussed and realized experimentally for glucose solution as the refractive index matching factor.

  15. Preventing Eye Injuries

    MedlinePlus

    ... Eye Injuries Reviewed by: Brenda Pagan-Duran MD Mar. 01, 2016 Protecting your eyes from injury is one of the most basic things you can do to keep your vision healthy throughout your life. You may be somewhat aware of the possible ...

  16. Smoking and Eye Health

    MedlinePlus

    ... Eye Health Apr. 14, 2014 Avoiding smoking and second hand smoke — or quitting if you are a smoker — are ... influence your eyes’ health. And tobacco smoke, including second-hand smoke, is an irritant that worsens dry eye , a ...

  17. Understanding pink eye

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pink eye (PE) is a physiological tuber disorder that can result in serious processing complications and storage losses. The earliest external symptoms consist of an ephemeral pinkish discoloration around tuber eyes, predominately at the bud end of the tuber. These pinkish areas can then develop into...

  18. Computer Analysis of Eye Blood-Vessel Images

    NASA Technical Reports Server (NTRS)

    Wall, R. J.; White, B. S.

    1984-01-01

    Technique rapidly diagnoses diabetes mellitus. Photographs of "whites" of patients' eyes scanned by computerized image analyzer programmed to quantify density of small blood vessels in conjuctiva. Comparison with data base of known normal and diabetic patients facilitates rapid diagnosis.

  19. Optimised laser microdissection of the human ocular surface epithelial regions for microarray studies

    PubMed Central

    2013-01-01

    Background The most important challenge of performing insitu transcriptional profiling of the human ocular surface epithelial regions is obtaining samples in sufficient amounts, without contamination from adjacent tissue, as the region of interest is microscopic and closely apposed to other tissues regions. We have effectively collected ocular surface (OS) epithelial tissue samples from the Limbal Epithelial Crypt (LEC), limbus, cornea and conjunctiva of post-mortem cadaver eyes with laser microdissection (LMD) technique for gene expression studies with spotted oligonucleotide microarrays and Gene 1.0 ST arrays. Methods Human donor eyes (4 pairs for spotted oligonucleotide microarrays, 3 pairs for Gene 1.0 ST arrays) consented for research were included in this study with due ethical approval of the Nottingham Research Ethics Committee. Eye retrieval was performed within 36 hours of post-mortem period. The dissected corneoscleral buttons were immersed in OCT media and frozen in liquid nitrogen and stored at −80°C till further use. Microscopic tissue sections of interest were taken on PALM slides and stained with Toluidine Blue for laser microdissection with PALM microbeam systems. Optimisation of the laser microdissection technique was crucial for efficient and cost effective sample collection. Results The starting concentration of RNA as stipulated by the protocol of microarray platforms was taken as the cut-off concentration of RNA samples in our studies. The area of LMD tissue processed for spotted oligonucleotide microarray study ranged from 86,253 μm2 in LEC to 392,887 μm2 in LEC stroma. The RNA concentration of the LMD samples ranged from 22 to 92 pg/μl. The recommended starting concentration of the RNA samples used for Gene 1.0 ST arrays was 6 ng/5 μl. To achieve the desired RNA concentration the area of ocular surface epithelial tissue sample processed for the Gene 1.0 ST array experiments was approximately 100,0000 μm2 to 130,0000 μm2. RNA

  20. How Were Eye Movements Recorded Before Yarbus?

    PubMed

    Wade, Nicholas J

    2015-01-01

    Alfred Yarbus introduced a new dimension of precision in recording how the eyes moved, either when attempts were made to keep them stationary or when scanning pictures. Movements of the eyes had been remarked upon for millennia, but recording how they move is a more recent preoccupation. Emphasis was initially placed on abnormalities of oculomotor function (like strabismus) before normal features were considered. The interest was in where the eyes moved to rather than determining how they got there. The most venerable technique for examining ocular stability involved comparing the relative motion between an afterimage and a real image. In the late 18th century, Wells compared afterimages generated before body rotation with real images observed following it when dizzy; he described both lateral and torsional nystagmus, thereby demonstrating the directional discontinuities in eye velocities. At around the same time Erasmus Darwin used afterimages as a means of demonstrating ocular instability when attempting to fixate steadily. However, the overriding concern in the 19th century was with eye position rather than eye movements. Thus, the characteristics of nystagmus were recorded before those of saccades and fixations. Eye movements during reading were described by Hering and by Lamare (working in Javal's laboratory) in 1879; both used similar techniques of listening (with tubes placed over the eyelids) to the sounds made during contractions of the extraocular muscles. Photographic records of eye movements during reading were made by Dodge early in the 20th century, and this stimulated research using a wider array of patterns. Eye movements over pictures were examined by Stratton and later by Buswell, who drew attention to the effects of instructions on the pattern of eye movements. In midcentury, attention shifted back to the stability of the eyes during fixation, with the emphasis on involuntary movements. The suction cap methods developed by Yarbus were applied

  1. How Were Eye Movements Recorded Before Yarbus?

    PubMed

    Wade, Nicholas J

    2015-01-01

    Alfred Yarbus introduced a new dimension of precision in recording how the eyes moved, either when attempts were made to keep them stationary or when scanning pictures. Movements of the eyes had been remarked upon for millennia, but recording how they move is a more recent preoccupation. Emphasis was initially placed on abnormalities of oculomotor function (like strabismus) before normal features were considered. The interest was in where the eyes moved to rather than determining how they got there. The most venerable technique for examining ocular stability involved comparing the relative motion between an afterimage and a real image. In the late 18th century, Wells compared afterimages generated before body rotation with real images observed following it when dizzy; he described both lateral and torsional nystagmus, thereby demonstrating the directional discontinuities in eye velocities. At around the same time Erasmus Darwin used afterimages as a means of demonstrating ocular instability when attempting to fixate steadily. However, the overriding concern in the 19th century was with eye position rather than eye movements. Thus, the characteristics of nystagmus were recorded before those of saccades and fixations. Eye movements during reading were described by Hering and by Lamare (working in Javal's laboratory) in 1879; both used similar techniques of listening (with tubes placed over the eyelids) to the sounds made during contractions of the extraocular muscles. Photographic records of eye movements during reading were made by Dodge early in the 20th century, and this stimulated research using a wider array of patterns. Eye movements over pictures were examined by Stratton and later by Buswell, who drew attention to the effects of instructions on the pattern of eye movements. In midcentury, attention shifted back to the stability of the eyes during fixation, with the emphasis on involuntary movements. The suction cap methods developed by Yarbus were applied

  2. Protein microarrays for parasite antigen discovery.

    PubMed

    Driguez, Patrick; Doolan, Denise L; Molina, Douglas M; Loukas, Alex; Trieu, Angela; Felgner, Phil L; McManus, Donald P

    2015-01-01

    The host serological profile to a parasitic infection, such as schistosomiasis, can be used to define potential vaccine and diagnostic targets. Determining the host antibody response using traditional approaches is hindered by the large number of putative antigens in any parasite proteome. Parasite protein microarrays offer the potential for a high-throughput host antibody screen to simplify this task. In order to construct the array, parasite proteins are selected from available genomic sequence and protein databases using bioinformatic tools. Selected open reading frames are PCR amplified, incorporated into a vector for cell-free protein expression, and printed robotically onto glass slides. The protein microarrays can be probed with antisera from infected/immune animals or humans and the antibody reactivity measured with fluorophore labeled antibodies on a confocal laser microarray scanner to identify potential targets for diagnosis or therapeutic or prophylactic intervention. PMID:25388117

  3. Quantitative Dose-Response Curves from Subcellular Lipid Multilayer Microarrays

    PubMed Central

    Kusi-Appiah, A. E.; Lowry, T. W.; Darrow, E. M.; Wilson, K.; Chadwick, B. P.; Davidson, M. W.; Lenhert, S.

    2015-01-01

    The dose-dependent bioactivity of small molecules on cells is a crucial factor in drug discovery and personalized medicine. Although small-molecule microarrays are a promising platform for miniaturized screening, it has been a challenge to use them to obtain quantitative dose-response curves in vitro, especially for lipophilic compounds. Here we establish a small-molecule microarray assay capable of controlling the dosage of small lipophilic molecules delivered to cells by varying the sub-cellular volumes of surface supported lipid micro- and nanostructure arrays fabricated with nanointaglio. Features with sub-cellular lateral dimensions were found necessary to obtain normal cell adhesion with HeLa cells. The volumes of the lipophilic drug-containing nanostructures were determined using a fluorescence microscope calibrated by atomic-force microscopy. We used the surface supported lipid volume information to obtain EC-50 values for the response of HeLa cells to three FDA-approved lipophilic anticancer drugs, docetaxel, imiquimod and triethylenemelamine, which were found to be significantly different from neat lipid controls. No significant toxicity was observed on the control cells surrounding the drug/lipid patterns, indicating lack of interference or leakage from the arrays. Comparison of the microarray data to dose-response curves for the same drugs delivered liposomally from solution revealed quantitative differences in the efficacy values, which we explain in terms of cell-adhesion playing a more important role in the surface-based assay. The assay should be scalable to a density of at least 10,000 dose response curves on the area of a standard microtiter plate. PMID:26167949

  4. Design issues in toxicogenomics using DNA microarray experiment

    SciTech Connect

    Lee, Kyoung-Mu; Kim, Ju-Han; Kang, Daehee . E-mail: dhkang@snu.ac.kr

    2005-09-01

    The methods of toxicogenomics might be classified into omics study (e.g., genomics, proteomics, and metabolomics) and population study focusing on risk assessment and gene-environment interaction. In omics study, microarray is the most popular approach. Genes falling into several categories (e.g., xenobiotics metabolism, cell cycle control, DNA repair etc.) can be selected up to 20,000 according to a priori hypothesis. The appropriate type of samples and species should be selected in advance. Multiple doses and varied exposure durations are suggested to identify those genes clearly linked to toxic response. Microarray experiments can be affected by numerous nuisance variables including experimental designs, sample extraction, type of scanners, etc. The number of slides might be determined from the magnitude and variance of expression change, false-positive rate, and desired power. Instead, pooling samples is an alternative. Online databases on chemicals with known exposure-disease outcomes and genetic information can aid the interpretation of the normalized results. Gene function can be inferred from microarray data analyzed by bioinformatics methods such as cluster analysis. The population study often adopts hospital-based or nested case-control design. Biases in subject selection and exposure assessment should be minimized, and confounding bias should also be controlled for in stratified or multiple regression analysis. Optimal sample sizes are dependent on the statistical test for gene-to-environment or gene-to-gene interaction. The design issues addressed in this mini-review are crucial in conducting toxicogenomics study. In addition, integrative approach of exposure assessment, epidemiology, and clinical trial is required.

  5. Eye formation in the absence of retina

    PubMed Central

    Swindell, Eric C.; Liu, Chaomei; Shah, Rina; Smith, April N.; Lang, Richard A.; Jamrich, Milan

    2008-01-01

    Eye development is a complex process that involves the formation of the retina and the lens, collectively called the eyeball, as well as the formation of auxiliary eye structures such as the eyelid, lacrimal gland, cornea and conjunctiva. The developmental requirements for the formation of each individual structure are only partially understood. We have shown previously that the homeobox-containing gene Rx is a key component in eye formation, as retinal structures do not develop and retina-specific gene expression is not observed in Rx-deficient mice. In addition, Rx−/− embryos do not develop any lens structure, despite the fact that Rx is not expressed in the lens. This demonstrates that during normal mammalian development, retina-specific gene expression is necessary for lens formation. In this paper we show that lens formation can be restored in Rx-deficient embryos experimentally, by the elimination of β-catenin expression in the head surface ectoderm. This suggests that β-catenin is involved in lens specification either through Wnt signaling or through its function in cell adhesion. In contrast to lens formation, we demonstrate that the development of auxiliary eye structures does not depend on retina-specific gene expression or retinal morphogenesis. These results point to the existence of two separate developmental processes involved in the formation of the eye and its associated structures. One involved in the formation of the eyeball and the second involved in the formation of the auxiliary eye structures. PMID:18675797

  6. Enhancing Interdisciplinary Mathematics and Biology Education: A Microarray Data Analysis Course Bridging These Disciplines

    PubMed Central

    Evans, Irene M.

    2010-01-01

    BIO2010 put forth the goal of improving the mathematical educational background of biology students. The analysis and interpretation of microarray high-dimensional data can be very challenging and is best done by a statistician and a biologist working and teaching in a collaborative manner. We set up such a collaboration and designed a course on microarray data analysis. We started using Genome Consortium for Active Teaching (GCAT) materials and Microarray Genome and Clustering Tool software and added R statistical software along with Bioconductor packages. In response to student feedback, one microarray data set was fully analyzed in class, starting from preprocessing to gene discovery to pathway analysis using the latter software. A class project was to conduct a similar analysis where students analyzed their own data or data from a published journal paper. This exercise showed the impact that filtering, preprocessing, and different normalization methods had on gene inclusion in the final data set. We conclude that this course achieved its goals to equip students with skills to analyze data from a microarray experiment. We offer our insight about collaborative teaching as well as how other faculty might design and implement a similar interdisciplinary course. PMID:20810954

  7. Eye burning - itching and discharge

    MedlinePlus

    ... allergies or hay fever Infections, bacterial or viral ( conjunctivitis or pink eye) Chemical irritants (such as chlorine ... to help with allergies. Pink eye or viral conjunctivitis causes a red or bloodshot eye and excessive ...

  8. Hybridization and Selective Release of DNA Microarrays

    SciTech Connect

    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 to

  9. Analysis of High-Throughput ELISA Microarray Data

    SciTech Connect

    White, Amanda M.; Daly, Don S.; Zangar, Richard C.

    2011-02-23

    Our research group develops analytical methods and software for the high-throughput analysis of quantitative enzyme-linked immunosorbent assay (ELISA) microarrays. ELISA microarrays differ from DNA microarrays in several fundamental aspects and most algorithms for analysis of DNA microarray data are not applicable to ELISA microarrays. In this review, we provide an overview of the steps involved in ELISA microarray data analysis and how the statistically sound algorithms we have developed provide an integrated software suite to address the needs of each data-processing step. The algorithms discussed are available in a set of open-source software tools (http://www.pnl.gov/statistics/ProMAT).

  10. Photo-Generation of Carbohydrate Microarrays

    NASA Astrophysics Data System (ADS)

    Carroll, Gregory T.; Wang, Denong; Turro, Nicholas J.; Koberstein, Jeffrey T.

    The unparalleled structural diversity of carbohydrates among biological molecules has been recognized for decades. Recent studies have highlighted carbohydrate signaling roles in many important biological processes, such as fertilization, embryonic development, cell differentiation and cellȁ4cell communication, blood coagulation, inflammation, chemotaxis, as well as host recognition and immune responses to microbial pathogens. In this chapter, we summarize recent progress in the establishment of carbohydrate-based microarrays and the application of these technologies in exploring the biological information content in carbohydrates. A newly established photochemical platform of carbohydrate microarrays serves as a model for a focused discussion.

  11. Protein Microarrays for the Detection of Biothreats

    NASA Astrophysics Data System (ADS)

    Herr, Amy E.

    Although protein microarrays have proven to be an important tool in proteomics research, the technology is emerging as useful for public health and defense applications. Recent progress in the measurement and characterization of biothreat agents is reviewed in this chapter. Details concerning validation of various protein microarray formats, from contact-printed sandwich assays to supported lipid bilayers, are presented. The reviewed technologies have important implications for in vitro characterization of toxin-ligand interactions, serotyping of bacteria, screening of potential biothreat inhibitors, and as core components of biosensors, among others, research and engineering applications.

  12. Pineal Function: Impact of Microarray Analysis

    PubMed Central

    Klein, David C.; Bailey, Michael J.; Carter, David A.; Kim, Jong-so; Shi, Qiong; Ho, Anthony; Chik, Constance; Gaildrat, Pascaline; Morin, Fabrice; Ganguly, Surajit; Rath, Martin F.; Møller, Morten; Sugden, David; Rangel, Zoila G.; Munson, Peter J.; Weller, Joan L.; Coon, Steven L.

    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-hour schedule. This effort has highlighted surprising similarity to the retina and has provided reason to explore new avenues of study including intracellular signaling, signal transduction, transcriptional cascades, thyroid/retinoic acid hormone signaling, metal biology, RNA splicing, and the role the pineal gland plays in the immune/inflammation response. The new foundation that microarray analysis has provided will broadly support future research on pineal function. PMID:19622385

  13. The use of microarrays in microbial ecology

    SciTech Connect

    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

  14. MicroRNA expression profiling using microarrays.

    PubMed

    Love, Cassandra; Dave, Sandeep

    2013-01-01

    MicroRNAs are small noncoding RNAs which are able to regulate gene expression at both the transcriptional and translational levels. There is a growing recognition of the role of microRNAs in nearly every tissue type and cellular process. Thus there is an increasing need for accurate quantitation of microRNA expression in a variety of tissues. Microarrays provide a robust method for the examination of microRNA expression. In this chapter, we describe detailed methods for the use of microarrays to measure microRNA expression and discuss methods for the analysis of microRNA expression data. PMID:23666707

  15. Eye development in the Cape dune mole rat.

    PubMed

    Nikitina, Natalya V; Kidson, Susan H

    2014-03-01

    Studies on mammalian species with naturally reduced eyes can provide valuable insights into the evolutionary developmental mechanisms underlying the reduction of the eye structures. Because few naturally microphthalmic animals have been studied and eye reduction must have evolved independently in many of the modern groups, novel evolutionary developmental models for eye research have to be sought. Here, we present a first report on embryonic eye development in the Cape dune mole rat, Bathyergus suillus. The eyes of these animals contain all the internal structures characteristic of the normal eye but exhibit abnormalities in the anterior chamber structures. The lens is small but develops normally and exhibits a normal expression of α- and γ-crystallins. One of the interesting features of these animals is an extremely enlarged and highly pigmented ciliary body. In order to understand the molecular basis of this unusual feature, the expression pattern of an early marker of the ciliary zone, Ptmb4, was investigated in this animal. Surprisingly, in situ hybridization results revealed that Ptmb4 expression was absent from the ciliary body zone of the developing Bathyergus eye.

  16. Advocacy for eye care

    PubMed Central

    Ravilla, Thulasiraj D; Ramasamy, Dhivya

    2012-01-01

    The effectiveness of eye care service delivery is often dependant on how the different stakeholders are aligned. These stakeholders range from the ministries of health who have the capacity to grant government subsidies for eye care, down to the primary healthcare workers who can be enrolled to screen for basic eye diseases. Advocacy is a tool that can help service providers draw the attention of key stakeholders to a particular area of concern. By enlisting the support, endorsement and participation of a wider circle of players, advocacy can help to improve the penetration and effectiveness of the services provided. There are several factors in the external environmental that influence the eye care services – such as the availability of trained manpower, supply of eye care consumables, government rules and regulations. There are several instances where successful advocacy has helped to create an enabling environment for eye care service delivery. Providing eye care services in developing countries requires the support – either for direct patient care or for support services such as producing trained manpower or for research and dissemination. Such support, in the form of financial or other resources, can be garnered through advocacy. PMID:22944745

  17. Perceived visual motion as effective stimulus to pursuit eye movement system

    NASA Technical Reports Server (NTRS)

    Yasui, S.; Young, L. R.

    1975-01-01

    Human eye tracking of a foveal afterimage during angular head oscillation in the dark produced smooth eye movements exceeding those for normal vestibular nystagmus, and a reduction in the frequency of the fast phase component of nystagmus eye movements. These results may support a closed loop extension of the corollary discharge theory, with oculomotor commands based on perceived object velocity.

  18. Eye-Safe Lidar

    NASA Technical Reports Server (NTRS)

    Byer, Robert L.

    1989-01-01

    Laser infrared radar (lidar) undergoing development harmless to human eyes, consists almost entirely of solid-state components, and offers high range resolution. Operates at wavelength of about 2 micrometers. If radiation from such device strikes eye, almost completely absorbed by cornea without causing damage, even if aimed directly at eye. Continuous-wave light from laser oscillator amplified and modulated for transmission from telescope. Small portion of output of oscillator fed to single-mode fiber coupler, where mixed with return pulses. Intended for remote Doppler measurements of winds and differential-absorption measurements of concentrations of gases in atmosphere.

  19. Eye-wall resection.

    PubMed Central

    Char, D H; Miller, T; Crawford, J B

    2000-01-01

    PURPOSE: To review the ocular retention rates, visual results, and metastases in uveal tumors managed with eye-wall resection techniques. METHODS: This was a retrospective analysis of uveal tumors selected for eye-wall resection with the surgical procedures performed by a single surgeon. All enucleation specimens were reviewed by one author. Both parametric and non-parametric analysis of data was performed. RESULTS: A total of 132 eyes were scheduled for eye-wall resection surgery. Mean patient age was 52 years (range, 11 to 86 years). Tumors involved the iris alone in 17 cases, the iris-ciliary body in 53, the ciliary body alone in 16, and the choroid (ciliochoroidal, iris-ciliary body-choroid, or choroid) in 46 cases. A total of 114 eyes harbored melanomas; tumors located more posteriorly were more likely to have epithelioid cells (P < .05). Mean follow-up was 6 years. Mean number of clock hours in iris and iris-ciliary body tumors was 3.5. In tumors that involved the choroid, the mean largest diameter was 12.6 mm and the mean thickness was 8.2 mm. Ninety-three (70%) of 132 eyes were retained. Histologic assessment of surgical margins did not correlate with either evidence of tumor in enucleated eyes or metastatic disease. Surgical margins of tumors located more anteriorly were more likely to be clear on histologic evaluation (P < .05). Approximately 56% of retained eyes had a final visual acuity of 20/40 or better; visual results were significantly better in tumors located more anteriorly (P < .05). All retained eyes with iris tumors had a final visual acuity of 20/40 or better. In tumors that involved the choroid, 8 of 25 retained eyes kept visual acuity of 20/40 or better. Metastases developed in 8 patients; all metastatic events developed in patients with tumors that involved the choroid, and 7 of 8 were mixed cell melanomas. CONCLUSIONS: Seventy percent of eyes were retained, and 56% of these had a final visual acuity of 20/40 or better. Only 7% of patients

  20. Eye movements in ataxia-telangiectasia.

    PubMed

    Baloh, R W; Yee, R D; Boder, E

    1978-11-01

    The spectrum of eye movement disorders in six patients with ataxia-telangiectasia at different stages of progression was assessed quantitatively by electrooculography. All patients demonstrated abnormalities of voluntary and involuntary saccades. The youngest and least involved patient had significantly increased reaction times of voluntary saccades, but normal accuracy and velocity. The other patients demonstrated increased reaction times and marked hypometria of horizontal and vertical voluntary saccades. Saccade velocity remained normal. Vestibular and optokinetic fast components (involuntary saccades) had normal amplitude and velocity but the eyes deviated tonically in the direction of the slow component. We conclude that patients with ataxia-telangiectasia have a defect in the initiation of voluntary and involuntary saccades in the earliest stages. These findings are distinctly different from those in other familial cerebellar atrophy syndromes.

  1. High quality epoxysilane substrate for clinical multiplex serodiagnostic proteomic microarrays

    NASA Astrophysics Data System (ADS)

    Ewart, Tom; Carmichael, Stuart; Lea, Peter

    2005-09-01

    Polylysine and aminopropylsilane treated glass comprised the majority of substrates employed in first generation genetic microarray substrates. Second generation single stranded long oligo libraries with amino termini provided for controlled terminal specific attachment, and rationally designed unique sequence libraries with normalized melting temperatures. These libraries benefit from active covalent coupling surfaces such as Epoxysilane. The latter's oxime ring shows versatile reactivity with amino-, thiol- and hydroxyl- groups thus encompassing small molecule, oligo and proteomic microarray applications. Batch-to-batch production uniformity supports entry of the Epoxysilane process into clinical diagnostics. We carried out multiple print runs of 21 clinically relevant bacterial and viral antigens at optimized concentrations, plus human IgG and IgM standards in triplicate on multiple batches of Epoxysilane substrates. A set of 45 patient sera were assayed in a 35 minute protocol using 10 microliters per array in a capillary-fill format (15 minute serum incubation, wash, 15 minute incubation with Cy3-labeled anti-hIgG plus Dy647-labeled anti-hIgM, final wash). The LOD (3 SD above background) was better than 1 microgram/ml for IgG, and standard curves were regular and monotonically increasing over the range 0 to 1000 micrograms/ml. Ninety-five percent of the CVs for the standards were under 10%, and 90% percent of CVs for antigen responses were under 10% across all batches of Epoxysilane and print runs. In addition, where SDs are larger than expected, microarray images may be readily reviewed for quality control purposes and pin misprints quickly identified. In order to determine the influence of stirring on sensitivity and speed of the microarray assay, we printed 10 common ToRCH antigens (H. pylori, T. gondii, Rubella, Rubeola, C. trachomatis, Herpes 1 and 2, CMV, C. jejuni, and EBV) in Epoxysilane-activated slide-wells. Anti-IgG-Cy3 direct binding to printed Ig

  2. A new method for gridding DNA microarrays.

    PubMed

    Charalambous, Christoforos C; Matsopoulos, George K

    2013-10-01

    In this paper, a new methodological scheme for the gridding of DNA microarrays is proposed. The scheme composes of a series of processes applied sequentially. Each DNA microarray image is pre-processed to remove any noise and the center of each spot is detected using a template matching algorithm. Then, an initial gridding is automatically placed on the DNA microarray image by 'building' rectangular pyramids around the detected spots' centers. The gridlines "move" between the pyramids, horizontally and vertically, forming this initial grid. Furthermore, a refinement process is applied composing of a five-step approach in order to correct gridding imperfections caused by its initial placement, both in non-spot cases and in more than one spot enclosure cases. The proposed gridding scheme is applied on DNA microarray images under known transformations and on real-world DNA data. Its performance is compared against the projection pursuit method, which is often used due to its speed and simplicity, as well as against a state-of-the-art method, the Optimal Multi-level Thresholding Gridding (OMTG). According to the obtained results, the proposed gridding scheme outperforms both methods, qualitatively and quantitatively.

  3. Diagnostic Oligonucleotide Microarray Fingerprinting of Bacillus Isolates

    SciTech Connect

    Chandler, Darrell P.; Alferov, Oleg; Chernov, Boris; Daly, Don S.; Golova, Julia; Perov, Alexander N.; Protic, Miroslava; Robison, Richard; Shipma, Matthew; White, Amanda M.; Willse, Alan R.

    2006-01-01

    A diagnostic, genome-independent microbial fingerprinting method using DNA oligonucleotide microarrays was used for high-resolution differentiation between closely related Bacillus strains, including two strains of Bacillus anthracis that are monomorphic (indistinguishable) via amplified fragment length polymorphism fingerprinting techniques. Replicated hybridizations on 391-probe nonamer arrays were used to construct a prototype fingerprint library for quantitative comparisons. Descriptive analysis of the fingerprints, including phylogenetic reconstruction, is consistent with previous taxonomic organization of the genus. Newly developed statistical analysis methods were used to quantitatively compare and objectively confirm apparent differences in microarray fingerprints with the statistical rigor required for microbial forensics and clinical diagnostics. These data suggest that a relatively simple fingerprinting microarray and statistical analysis method can differentiate between species in the Bacillus cereus complex, and between strains of B. anthracis. A synthetic DNA standard was used to understand underlying microarray and process-level variability, leading to specific recommendations for the development of a standard operating procedure and/or continued technology enhancements for microbial forensics and diagnostics.

  4. Data Analysis Strategies for Protein Microarrays

    PubMed Central

    Díez, Paula; Dasilva, Noelia; González-González, María; Matarraz, Sergio; Casado-Vela, Juan; Orfao, Alberto; Fuentes, Manuel

    2012-01-01

    Microarrays constitute a new platform which allows the discovery and characterization of proteins. According to different features, such as content, surface or detection system, there are many types of protein microarrays which can be applied for the identification of disease biomarkers and the characterization of protein expression patterns. However, the analysis and interpretation of the amount of information generated by microarrays remain a challenge. Further data analysis strategies are essential to obtain representative and reproducible results. Therefore, the experimental design is key, since the number of samples and dyes, among others aspects, would define the appropriate analysis method to be used. In this sense, several algorithms have been proposed so far to overcome analytical difficulties derived from fluorescence overlapping and/or background noise. Each kind of microarray is developed to fulfill a specific purpose. Therefore, the selection of appropriate analytical and data analysis strategies is crucial to achieve successful biological conclusions. In the present review, we focus on current algorithms and main strategies for data interpretation.

  5. Shrinkage covariance matrix approach for microarray data

    NASA Astrophysics Data System (ADS)

    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 < p. This leads to a biased estimate of the covariance matrix. In this study, the 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.

  6. Microarrays (DNA Chips) for the Classroom Laboratory

    ERIC Educational Resources Information Center

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

    2006-01-01

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

  7. Data Analysis Strategies for Protein Microarrays

    PubMed Central

    Díez, Paula; Dasilva, Noelia; González-González, María; Matarraz, Sergio; Casado-Vela, Juan; Orfao, Alberto; Fuentes, Manuel

    2012-01-01

    Microarrays constitute a new platform which allows the discovery and characterization of proteins. According to different features, such as content, surface or detection system, there are many types of protein microarrays which can be applied for the identification of disease biomarkers and the characterization of protein expression patterns. However, the analysis and interpretation of the amount of information generated by microarrays remain a challenge. Further data analysis strategies are essential to obtain representative and reproducible results. Therefore, the experimental design is key, since the number of samples and dyes, among others aspects, would define the appropriate analysis method to be used. In this sense, several algorithms have been proposed so far to overcome analytical difficulties derived from fluorescence overlapping and/or background noise. Each kind of microarray is developed to fulfill a specific purpose. Therefore, the selection of appropriate analytical and data analysis strategies is crucial to achieve successful biological conclusions. In the present review, we focus on current algorithms and main strategies for data interpretation. PMID:27605336

  8. DISC-BASED IMMUNOASSAY MICROARRAYS. (R825433)

    EPA Science Inventory

    Microarray technology as applied to areas that include genomics, diagnostics, environmental, and drug discovery, is an interesting research topic for which different chip-based devices have been developed. As an alternative, we have explored the principle of compact disc-based...

  9. MICROARRAY DATA ANALYSIS USING MULTIPLE STATISTICAL MODELS

    EPA Science Inventory

    Microarray Data Analysis Using Multiple Statistical Models

    Wenjun Bao1, Judith E. Schmid1, Amber K. Goetz1, Ming Ouyang2, William J. Welsh2,Andrew I. Brooks3,4, ChiYi Chu3,Mitsunori Ogihara3,4, Yinhe Cheng5, David J. Dix1. 1National Health and Environmental Effects Researc...

  10. Raman-based microarray readout: a review.

    PubMed

    Haisch, Christoph

    2016-07-01

    For a quarter of a century, microarrays have been part of the routine analytical toolbox. Label-based fluorescence detection is still the commonest optical readout strategy. Since the 1990s, a continuously increasing number of label-based as well as label-free experiments on Raman-based microarray readout concepts have been reported. This review summarizes the possible concepts and methods and their advantages and challenges. A common label-based strategy is based on the binding of selective receptors as well as Raman reporter molecules to plasmonic nanoparticles in a sandwich immunoassay, which results in surface-enhanced Raman scattering signals of the reporter molecule. Alternatively, capture of the analytes can be performed by receptors on a microarray surface. Addition of plasmonic nanoparticles again leads to a surface-enhanced Raman scattering signal, not of a label but directly of the analyte. This approach is mostly proposed for bacteria and cell detection. However, although many promising readout strategies have been discussed in numerous publications, rarely have any of them made the step from proof of concept to a practical application, let alone routine use. Graphical Abstract Possible realization of a SERS (Surface-Enhanced Raman Scattering) system for microarray readout. PMID:26973235

  11. PRACTICAL STRATEGIES FOR PROCESSING AND ANALYZING SPOTTED OLIGONUCLEOTIDE MICROARRAY DATA

    EPA Science Inventory

    Thoughtful data analysis is as important as experimental design, biological sample quality, and appropriate experimental procedures for making microarrays a useful supplement to traditional toxicology. In the present study, spotted oligonucleotide microarrays were used to profile...

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

    PubMed

    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

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

    PubMed

    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

  14. Measuring information flow in cellular networks by the systems biology method through microarray data.

    PubMed

    Chen, Bor-Sen; Li, Cheng-Wei

    2015-01-01

    In general, it is very difficult to measure the information flow in a cellular network directly. In this study, based on an information flow model and microarray data, we measured the information flow in cellular networks indirectly by using a systems biology method. First, we used a recursive least square parameter estimation algorithm to identify the system parameters of coupling signal transduction pathways and the cellular gene regulatory network (GRN). Then, based on the identified parameters and systems theory, we estimated the signal transductivities of the coupling signal transduction pathways from the extracellular signals to each downstream protein and the information transductivities of the GRN between transcription factors in response to environmental events. According to the proposed method, the information flow, which is characterized by signal transductivity in coupling signaling pathways and information transductivity in the GRN, can be estimated by microarray temporal data or microarray sample data. It can also be estimated by other high-throughput data such as next-generation sequencing or proteomic data. Finally, the information flows of the signal transduction pathways and the GRN in leukemia cancer cells and non-leukemia normal cells were also measured to analyze the systematic dysfunction in this cancer from microarray sample data. The results show that the signal transductivities of signal transduction pathways change substantially from normal cells to leukemia cancer cells.

  15. Rehabilitation of Partially Eviscerated Eye with Custom Made Ocular Prosthesis—A Case Report

    PubMed Central

    Thirunavukkarasu, Ilango; Rai, Rathika; R., Prabhu; Deshpande, Varun A.; S., Arun Kumar

    2014-01-01

    Human eyes are the most precious gift from nature; presence of a pair of eye not only gives expression to life but also adds dignity to the face. The loss of an eye causes disfigurement of the face and causes anxiety, stress and depression in their life. The rehabilitation of patients with congenital or acquired defects of the eye is a challenging job. The aim of the rehabilitation is to restore the patient’s normal appearance, comfort along with reasonable functional eye movements. This case report describes the rehabilitation of partially eviscerated eye of the patient with custom made ocular prosthesis. PMID:24596798

  16. LASIK eye surgery

    MedlinePlus

    Laser-Assisted In Situ Keratomileusis; Laser vision correction; Nearsightedness - Lasik; Myopia - Lasik ... For clear vision, the eye's cornea and lens must bend (refract) light rays properly. This allows images to be focused on ...

  17. Anatomy of the Eye

    MedlinePlus

    ... Conditions Frequently Asked Questions Español Condiciones Chinese Conditions Anatomy of the Eye En Español Read in Chinese External (Extraocular) Anatomy Extraocular Muscles: There are six muscles that are ...

  18. Multimodal eye recognition

    NASA Astrophysics Data System (ADS)

    Zhou, Zhi; Du, Yingzi; Thomas, N. L.; Delp, Edward J., III

    2010-04-01

    Multimodal biometrics use more than one means of biometric identification to achieve higher recognition accuracy, since sometimes a unimodal biometric is not good enough used to do identification and classification. In this paper, we proposed a multimodal eye recognition system, which can obtain both iris and sclera patterns from one color eye image. Gabor filter and 1-D Log-Gabor filter algorithms have been applied as the iris recognition algorithms. In sclera recognition, we introduced automatic sclera segmentation, sclera pattern enhancement, sclera pattern template generation, and sclera pattern matching. We applied kernelbased matching score fusion to improve the performance of the eye recognition system. The experimental results show that the proposed eye recognition method can achieve better performance compared to unimodal biometric identification, and the accuracy of our proposed kernel-based matching score fusion method is higher than two classic linear matching score fusion methods: Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA).

  19. Diabetes eye exams

    MedlinePlus

    ... Once you have eye disease caused by diabetes, you need to see an ophthalmologist. ... feel stinging when the drops are first placed. You may have a ... using a bright light. The doctor can then see areas that may ...

  20. Using Eye Makeup

    MedlinePlus

    ... in a moving vehicle. Do not separate your mascara-clumped lashes with sharp items. If you tend ... all eye makeup at night before sleeping, especially mascara that can stick to the lashes. Brush a ...

  1. Amblyopia: Lazy Eye Treatment

    MedlinePlus

    ... Choosing Safe Toys this Holiday Dec 02, 2015 Digital Glasses For Lazy Eye Nov 19, 2015 Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About ...

  2. Amblyopia: Lazy Eye Symptoms

    MedlinePlus

    ... Choosing Safe Toys this Holiday Dec 02, 2015 Digital Glasses For Lazy Eye Nov 19, 2015 Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About ...

  3. Amblyopia: Lazy Eye Diagnosis

    MedlinePlus

    ... Choosing Safe Toys this Holiday Dec 02, 2015 Digital Glasses For Lazy Eye Nov 19, 2015 Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About ...

  4. Fungal Eye Infections

    MedlinePlus

    ... Zoonotic Infectious Disease Division of Foodborne, Waterborne, and Environmental Diseases Mycotic Diseases Branch Fungal Eye Infections Recommend on ... Zoonotic Infectious Disease Division of Foodborne, Waterborne, and Environmental Diseases Mycotic Diseases Branch File Formats Help: How do ...

  5. Dry eye syndrome

    MedlinePlus

    ... particles that have gotten in. A healthy tear film on the eye is necessary for good vision. ... exam Diagnostic staining of the cornea and tear film Measurement of tear film break-up time (TBUT) ...

  6. Eye Injuries in Sports

    MedlinePlus

    ... these injuries can be prevented. Overall, basketball and baseball cause the most eye injuries, followed by water ... involve body contact. Some high-risk sports are baseball, basketball, hockey, football, lacrosse, tennis and other racquet ...

  7. Examining microarray slide quality for the EPA using SNL's hyperspectral microarray scanner.

    SciTech Connect

    Rohde, Rachel M.; Timlin, Jerilyn Ann

    2005-11-01

    This report summarizes research performed at Sandia National Laboratories (SNL) in collaboration with the Environmental Protection Agency (EPA) to assess microarray quality on arrays from two platforms of interest to the EPA. Custom microarrays from two novel, commercially produced array platforms were imaged with SNL's unique hyperspectral imaging technology and multivariate data analysis was performed to investigate sources of emission on the arrays. No extraneous sources of emission were evident in any of the array areas scanned. This led to the conclusions that either of these array platforms could produce high quality, reliable microarray data for the EPA toxicology programs. Hyperspectral imaging results are presented and recommendations for microarray analyses using these platforms are detailed within the report.

  8. Identifying Fishes through DNA Barcodes and Microarrays

    PubMed Central

    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

    2010-01-01

    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. PMID

  9. Facilitating functional annotation of chicken microarray data

    PubMed Central

    2009-01-01

    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 will be updated on regular

  10. Microarray analysis at single molecule resolution

    PubMed Central

    Mureşan, Leila; Jacak, Jarosław; Klement, Erich Peter; Hesse, Jan; Schütz, Gerhard J.

    2010-01-01

    Bioanalytical chip-based assays have been enormously improved in sensitivity in the recent years; detection of trace amounts of substances down to the level of individual fluorescent molecules has become state of the art technology. The impact of such detection methods, however, has yet not fully been exploited, mainly due to a lack in appropriate mathematical tools for robust data analysis. One particular example relates to the analysis of microarray data. While classical microarray analysis works at resolutions of two to 20 micrometers and quantifies the abundance of target molecules by determining average pixel intensities, a novel high resolution approach [1] directly visualizes individual bound molecules as diffraction limited peaks. The now possible quantification via counting is less susceptible to labeling artifacts and background noise. We have developed an approach for the analysis of high-resolution microarray images. It consists first of a single molecule detection step, based on undecimated wavelet transforms, and second, of a spot identification step via spatial statistics approach (corresponding to the segmentation step in the classical microarray analysis). The detection method was tested on simulated images with a concentration range of 0.001 to 0.5 molecules per square micron and signal-to-noise ratio (SNR) between 0.9 and 31.6. For SNR above 15 the false negatives relative error was below 15%. Separation of foreground/background proved reliable, in case foreground density exceeds background by a factor of 2. The method has also been applied to real data from high-resolution microarray measurements. PMID:20123580

  11. The eyes of trilobites: The oldest preserved visual system.

    PubMed

    Clarkson, Euan; Levi-Setti, Riccardo; Horváth, Gabor

    2006-12-01

    The oldest preserved visual systems are to be found in the extinct trilobites, marine euarthropods which existed between about 520 and 250 million years ago. Because they possessed a calcified cuticle, they have a good fossil record, and commonly the lens-bearing surfaces of their paired compound eyes are well preserved. The sublensar structures, however, remain unknown. Three kinds of eyes have been distinguished. Holochroal eyes, apomorphic for trilobites, typically have many contiguous small lenses, set on a kidney-shaped visual surface. Lens optics, angular range of vision, and ontogeny have been established for many compound eyes. Some pelagic trilobites have enormous eyes, subtending a panoramic field of view. Schizochroal eyes are found only in one group, the phacopids (Ordovician to Devonian). These have large lenses, separated from each other by cuticular material, and the lenses have a complex doublet or triplet internal structure, which could focus light sharply. The optics of phacopid eyes are becoming increasingly well known despite the fact that there are no direct counterparts in any living arthropods today. Schizochroal eyes are apomorphic for phacopids and were derived by paedomorphosis from a holochroal precursor. Abathochroal eyes are confined to a short-lived Cambrian group, the eodiscids (of which most representatives were blind). Less is known about them than other trilobite eyes and their origins remain obscure. Some trilobite groups had no eyes, but had other kinds of sensory organs. In Upper Devonian times several groups of trilobites independently underwent progressive eye-reduction leading to blindness, related to prevailing environmental conditions of the time. The last trilobites (of Carboniferous and Permian age), however, had normal holochroal eyes, which persisted until the final extinction of trilobites at the end of the Permian. PMID:18089074

  12. High throughput screening of starch structures using carbohydrate microarrays.

    PubMed

    Tanackovic, Vanja; Rydahl, Maja Gro; Pedersen, Henriette Lodberg; Motawia, Mohammed Saddik; Shaik, Shahnoor Sultana; Mikkelsen, Maria Dalgaard; Krunic, Susanne Langgaard; Fangel, Jonatan Ulrik; Willats, William George Tycho; Blennow, Andreas

    2016-01-01

    In this study we introduce the starch-recognising carbohydrate binding module family 20 (CBM20) from Aspergillus niger for screening biological variations in starch molecular structure using high throughput carbohydrate microarray technology. Defined linear, branched and phosphorylated maltooligosaccharides, pure starch samples including a variety of different structures with variations in the amylopectin branching pattern, amylose content and phosphate content, enzymatically modified starches and glycogen were included. Using this technique, different important structures, including amylose content and branching degrees could be differentiated in a high throughput fashion. The screening method was validated using transgenic barley grain analysed during development and subjected to germination. Typically, extreme branching or linearity were detected less than normal starch structures. The method offers the potential for rapidly analysing resistant and slowly digested dietary starches. PMID:27468930

  13. High throughput screening of starch structures using carbohydrate microarrays

    PubMed Central

    Tanackovic, Vanja; Rydahl, Maja Gro; Pedersen, Henriette Lodberg; Motawia, Mohammed Saddik; Shaik, Shahnoor Sultana; Mikkelsen, Maria Dalgaard; Krunic, Susanne Langgaard; Fangel, Jonatan Ulrik; Willats, William George Tycho; Blennow, Andreas

    2016-01-01

    In this study we introduce the starch-recognising carbohydrate binding module family 20 (CBM20) from Aspergillus niger for screening biological variations in starch molecular structure using high throughput carbohydrate microarray technology. Defined linear, branched and phosphorylated maltooligosaccharides, pure starch samples including a variety of different structures with variations in the amylopectin branching pattern, amylose content and phosphate content, enzymatically modified starches and glycogen were included. Using this technique, different important structures, including amylose content and branching degrees could be differentiated in a high throughput fashion. The screening method was validated using transgenic barley grain analysed during development and subjected to germination. Typically, extreme branching or linearity were detected less than normal starch structures. The method offers the potential for rapidly analysing resistant and slowly digested dietary starches. PMID:27468930

  14. Eye Protection in Educational Institutions.

    ERIC Educational Resources Information Center

    New Jersey State Dept. of Education, Trenton. Div. of Vocational Education.

    Intended to help reduce the number of school eye injuries in New Jersey, this document begins with a brief review of existing legislation regarding eye protection in educational institutions and a list of elements essential in an eye safety program. Second, eye protection equipment is examined in terms of: the advantages of safety spectacles over…

  15. Development of a gold nanoparticle-based oligonucleotide microarray for simultaneous detection of seven swine viruses.

    PubMed

    Wang, Xiaoqiang; Dang, Erle; Gao, Jinzhuai; Guo, Sen; Li, Zheng

    2013-07-01

    A gold nanoparticle (GNP) based oligonucleotide microarray assay (GNMA) that combined GNP-based multiplex asymmetric PCR with silver enhancement detection, was developed for simultaneous detection of seven important swine viruses in intensive swine production. Multiplex PCR was first performed to enable the target fragments of seven viruses containing a universal sequence, which were labeled simultaneously with GNPs by multiplex asymmetric PCR in the presence of excess GNP-conjugated primer. Target labeled products were captured by virus-specific oligonucleotide probes immobilized on microarrays, followed by silver staining for signal enhancement. Black image of microarray spots was easily detected by the naked eye or a simple flatbed scanner and quantified. The results for purified plasmid constructs indicated that the assay was highly specific for detecting the seven viruses in single or multiple infections, and as few as 6-80 copies/μl of specific viral target fragments were detected successfully. Fifty-seven archived samples were tested by this assay, and the results were 100% consistent with previous results based on real-time PCR and those obtained by conventional PCR/RT-PCR and sequencing. The assay is appropriate for the routine diagnosis of viral infections in pigs due to its simplicity, low-cost, high specificity and sensitivity.

  16. Reading without saccadic eye movements.

    PubMed

    Rubin, G S; Turano, K

    1992-05-01

    To assess the limitation on reading speed imposed by saccadic eye movements, we measured reading speed in 13 normally-sighted observers using two modes of text presentations: PAGE text which presents an entire passage conventionally in static, paragraph format, and rapid serial visual presentation (RSVP) which presents text sequentially, one word at a time at the same location in the visual field. In Expt 1, subjects read PAGE and RSVP text orally across a wide range of letter sizes (2X to 32X single-letter acuity) and reading speed was computed from the number of correct words read per minute. Reading speeds were consistently faster for RSVP compared to PAGE text at all letter sizes tested. The average speeds for text of an intermediate letter size (8X acuity) were 1171 words/min for RSVP and 303 words/min for PAGE text. In Expt 2 subjects read PAGE and RSVP text silently and a multiple-choice comprehension test was administered after each passage. All subjects continued to read RSVP text faster, and 6 subjects read at the maximum testable rate (1652 words/min) with at least 75% correct on the comprehension tests. Experiment 3 assessed the minimum word exposure time required for decoding text using RSVP to minimize potential delays due to saccadic eye movement control. Successive words were presented for a fixed duration (word duration) with a blank interval (ISI) between words. The minimum word duration required for accurate oral reading averaged 69.4 msec and was not reduced by increasing ISI. We interpret these results as an indication that the programming and execution of saccadic eye movements impose an upper limit on conventional reading speed.

  17. Vergence Eye Movements in Patients with Schizophrenia

    PubMed Central

    Bolding, MS; Lahti, AC; White, D; Moore, C; Gurler, D; Gawne, TJ; Gamlin, PD

    2014-01-01

    Previous studies have shown that smooth pursuit eye movements are impaired in patients with schizophrenia. However, under normal viewing conditions, targets move not only in the frontoparallel plane but also in depth, and tracking them requires both smooth pursuit and vergence eye movements. Although previous studies in humans and non-human primates suggest that these two eye movement subsystems are relatively independent of one another, to our knowledge, there have been no prior studies of vergence tracking behavior in patients with schizophrenia. Therefore, we have investigated these eye movements in patients with schizophrenia and in healthy controls. We found that patients with schizophrenia exhibited substantially lower gains compared to healthy controls during vergence tracking at all tested speeds (e.g. 0.25 Hz vergence tracking mean gain of 0.59 vs. 0.86). Further, consistent with previous reports, patients with schizophrenia exhibited significantly lower gains than healthy controls during smooth pursuit at higher target speeds (e.g. 0.5 Hz smooth pursuit mean gain of 0.64 vs. 0.73). In addition, there was a modest (r≈0.5), but significant, correlation between smooth pursuit and vergence tracking performance in patients with schizophrenia. Our observations clearly demonstrate substantial vergence tracking deficits in patients with schizophrenia. In these patients, deficits for smooth pursuit and vergence tracking are partially correlated suggesting overlap in the central control of smooth pursuit and vergence eye movements. PMID:25088242

  18. Adaptive Optics for the Human Eye

    NASA Astrophysics Data System (ADS)

    Williams, D. R.

    2000-05-01

    Adaptive optics can extend not only the resolution of ground-based telescopes, but also the human eye. Both static and dynamic aberrations in the cornea and lens of the normal eye limit its optical quality. Though it is possible to correct defocus and astigmatism with spectacle lenses, higher order aberrations remain. These aberrations blur vision and prevent us from seeing at the fundamental limits set by the retina and brain. They also limit the resolution of cameras to image the living retina, cameras that are a critical for the diagnosis and treatment of retinal disease. I will describe an adaptive optics system that measures the wave aberration of the eye in real time and compensates for it with a deformable mirror, endowing the human eye with unprecedented optical quality. This instrument provides fresh insight into the ultimate limits on human visual acuity, reveals for the first time images of the retinal cone mosaic responsible for color vision, and points the way to contact lenses and laser surgical methods that could enhance vision beyond what is currently possible today. Supported by the NSF Science and Technology Center for Adaptive Optics, the National Eye Institute, and Bausch and Lomb, Inc.

  19. Aging effects upon pursuit eye movements.

    PubMed

    Kato, I; Sakuma, A; Ogino, S; Takahashi, K; Okada, T

    1995-01-01

    Quantitative assessment of aging effects upon pursuit eye movements was done in step-ramp stimulus conditions using 32 normal individuals. Eye movements were recorded with infrared reflection oculography. The target was a spot of 0.5 degree red lazar light. The light spot was blanked for 5 ms while the mirror galvanometer moved to a new position. Eye and target position were sampled at 250 Hz and analysed by a personal computer. In onward stimulation in which 2 degrees, 4 degrees, 6 degrees and 8 degrees position steps were followed by fixed ramp speed (10 degrees/s), and also in backward stimulation in which 2 degrees, 4 degrees, 6 degrees step positions were followed by 9 degrees, 17 degrees and 27 degrees/s, eye acceleration increased depending upon increase of retinal slip velocity in the younger group below 49 years. Among the factors effecting aging effects, the cerebrum might be important because visual recognition and eye acceleration are performed in the parietal lobe. PMID:8749143

  20. The injured eye

    PubMed Central

    Scott, Robert

    2011-01-01

    Eye injuries come at a high cost to society and are avoidable. Ocular blast injuries can be primary, from the blast wave itself; secondary, from fragments carried by the blast wind; tertiary; due to structural collapse or being thrown against a fixed object; or quaternary, from burns and indirect injuries. Ballistic eye protection significantly reduces the incidence of eye injuries and should be encouraged from an early stage in Military training. Management of an injured eye requires meticulous history taking, evaluation of vision that measures the acuity and if there is a relative pupillary defect as well as careful inspection of the eyes, under anaesthetic if necessary. A lateral canthotomy with cantholysis should be performed immediately if there is a sight-threatening retrobulbar haemorrhage. Systemic antibiotics should be prescribed if there is a suspected penetrating or perforating injury. A ruptured globe should be protected by an eye shield. Primary repair of ruptured globes should be performed in a timely fashion. Secondary procedures will often be required at a later date to achieve sight preservation. A poor initial visual acuity is not a guarantee of a poor final result. The final result can be predicted after approximately 3–4 weeks. Future research in eye injuries attempts to reduce scarring and neuronal damage as well as to promote photoreceptor rescue, using post-transcriptional inhibition of cell death pathways and vaccination to promote neural recovery. Where the sight has been lost sensory substitution of a picture from a spectacle mounted video camera to the touch receptors of the tongue can be used to achieve appreciation of the outside world. PMID:21149360

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

    PubMed

    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.

  2. Advancing translational research with next-generation protein microarrays.

    PubMed

    Yu, Xiaobo; Petritis, Brianne; LaBaer, Joshua

    2016-04-01

    Protein microarrays are a high-throughput technology used increasingly in translational research, seeking to apply basic science findings to enhance human health. In addition to assessing protein levels, posttranslational modifications, and signaling pathways in patient samples, protein microarrays have aided in the identification of potential protein biomarkers of disease and infection. In this perspective, the different types of full-length protein microarrays that are used in translational research are reviewed. Specific studies employing these microarrays are presented to highlight their potential in finding solutions to real clinical problems. Finally, the criteria that should be considered when developing next-generation protein microarrays are provided. PMID:26749402

  3. Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts.

    PubMed

    Trost, Brett; Moir, Catherine A; Gillespie, Zoe E; Kusalik, Anthony; Mitchell, Jennifer A; Eskiw, Christopher H

    2015-09-01

    DNA microarrays and RNA sequencing (RNA-seq) are major technologies for performing high-throughput analysis of transcript abundance. Recently, concerns have been raised regarding the concordance of data derived from the two techniques. Using cDNA libraries derived from normal human foreskin fibroblasts, we measured changes in transcript abundance as cells transitioned from proliferative growth to quiescence using both DNA microarrays and RNA-seq. The internal reproducibility of the RNA-seq data was greater than that of the microarray data. Correlations between the RNA-seq data and the individual microarrays were low, but correlations between the RNA-seq values and the geometric mean of the microarray values were moderate. The two technologies had good agreement when considering probes with the largest (both positive and negative) fold change (FC) values. An independent technique, quantitative reverse-transcription PCR (qRT-PCR), was used to measure the FC of 76 genes between proliferative and quiescent samples, and a higher correlation was observed between the qRT-PCR data and the RNA-seq data than between the qRT-PCR data and the microarray data.

  4. Iron homeostasis and eye disease

    PubMed Central

    Loh, Allison; Hadziahmetovic, Majda; Dunaief, Joshua L.

    2009-01-01

    Summary Iron is necessary for life, but excess iron can be toxic to tissues. Iron is thought to damage tissues primarily by generating oxygen free radicals through the Fenton reaction. We present an overview of the evidence supporting iron's potential contribution to a broad range of eye disease using an anatomical approach. Firstly, iron can be visualized in the cornea as iron lines in the normal aging cornea as well as in diseases like keratoconus and pterygium. In the lens, we present the evidence for the role of oxidative damage in cataractogenesis. Also, we review the evidence that iron may play a role in the pathogenesis of the retinal disease age-related macular degeneration. Although currently there is no direct link between excess iron and development of optic neuropathies, ferrous iron's ability to form highly reactive oxygen species may play a role in optic nerve pathology. Lastly, we discuss recent advances in prevention and therapeutics for eye disease with antioxidants and iron chelators,. PMID:19059309

  5. Statistical Considerations for Analysis of Microarray Experiments

    PubMed Central

    Owzar, Kouros; Barry, William T.; Jung, Sin-Ho

    2014-01-01

    Microarray technologies enable the simultaneous interrogation of expressions from thousands of genes from a biospecimen sample taken from a patient. This large set of expressions generate a genetic profile of the patient that may be used to identify potential prognostic or predictive genes or genetic models for clinical outcomes. The aim of this article is to provide a broad overview of some of the major statistical considerations for the design and analysis of microarrays experiments conducted as correlative science studies to clinical trials. An emphasis will be placed on how the lack of understanding and improper use of statistical concepts and methods will lead to noise discovery and misinterpretation of experimental results. PMID:22212230

  6. Plasmonically amplified fluorescence bioassay with microarray format

    NASA Astrophysics Data System (ADS)

    Gogalic, S.; Hageneder, S.; Ctortecka, C.; Bauch, M.; Khan, I.; Preininger, Claudia; Sauer, U.; Dostalek, J.

    2015-05-01

    Plasmonic amplification of fluorescence signal in bioassays with microarray detection format is reported. A crossed relief diffraction grating was designed to couple an excitation laser beam to surface plasmons at the wavelength overlapping with the absorption and emission bands of fluorophore Dy647 that was used as a label. The surface of periodically corrugated sensor chip was coated with surface plasmon-supporting gold layer and a thin SU8 polymer film carrying epoxy groups. These groups were employed for the covalent immobilization of capture antibodies at arrays of spots. The plasmonic amplification of fluorescence signal on the developed microarray chip was tested by using interleukin 8 sandwich immunoassay. The readout was performed ex situ after drying the chip by using a commercial scanner with high numerical aperture collecting lens. Obtained results reveal the enhancement of fluorescence signal by a factor of 5 when compared to a regular glass chip.

  7. Microarrays: how many do you need?

    PubMed

    Zien, Alexander; Fluck, Juliane; Zimmer, Ralf; Lengauer, Thomas

    2003-01-01

    We estimate the number of microarrays that is required in order to gain reliable results from a common type of study: the pairwise comparison of different classes of samples. We show that current knowledge allows for the construction of models that look realistic with respect to searches for individual differentially expressed genes and derive prototypical parameters from real data sets. Such models allow investigation of the dependence of the required number of samples on the relevant parameters: the biological variability of the samples within each class, the fold changes in expression that are desired to be detected, the detection sensitivity of the microarrays, and the acceptable error rates of the results. We supply experimentalists with general conclusions as well as a freely accessible Java applet at www.scai.fhg.de/special/bio/howmanyarrays/ for fine tuning simulations to their particular settings. PMID:12935350

  8. A Flexible Microarray Data Simulation Model

    PubMed Central

    Dembélé, Doulaye

    2013-01-01

    Microarray technology allows monitoring of gene expression profiling at the genome level. This is useful in order to search for genes involved in a disease. The performances of the methods used to select interesting genes are most often judged after other analyzes (qPCR validation, search in databases...), which are also subject to error. A good evaluation of gene selection methods is possible with data whose characteristics are known, that is to say, synthetic data. We propose a model to simulate microarray data with similar characteristics to the data commonly produced by current platforms. The parameters used in this model are described to allow the user to generate data with varying characteristics. In order to show the flexibility of the proposed model, a commented example is given and illustrated. An R package is available for immediate use.

  9. Profiling protein function with small molecule microarrays

    PubMed Central

    Winssinger, Nicolas; Ficarro, Scott; Schultz, Peter G.; Harris, Jennifer L.

    2002-01-01

    The regulation of protein function through posttranslational modification, local environment, and protein–protein interaction is critical to cellular function. The ability to analyze on a genome-wide scale protein functional activity rather than changes in protein abundance or structure would provide important new insights into complex biological processes. Herein, we report the application of a spatially addressable small molecule microarray to an activity-based profile of proteases in crude cell lysates. The potential of this small molecule-based profiling technology is demonstrated by the detection of caspase activation upon induction of apoptosis, characterization of the activated caspase, and inhibition of the caspase-executed apoptotic phenotype using the small molecule inhibitor identified in the microarray-based profile. PMID:12167675

  10. Application of DNA Microarray to Clinical Diagnostics.

    PubMed

    Patel, Ankita; Cheung, Sau W

    2016-01-01

    Microarray-based technology to conduct array comparative genomic hybridization (aCGH) has made a significant impact on the diagnosis of human genetic diseases. Such diagnoses, previously undetectable by traditional G-banding chromosome analysis, are now achieved by identifying genomic copy number variants (CNVs) using the microarray. Not only can hundreds of well-characterized genetic syndromes be detected in a single assay, but new genomic disorders and disease-causing genes can also be discovered through the utilization of aCGH technology. Although other platforms such as single nucleotide polymorphism (SNP) arrays can be used for detecting CNVs, in this chapter we focus on describing the methods for performing aCGH using Agilent oligonucleotide arrays for both prenatal (e.g., amniotic fluid and chorionic villus sample) and postnatal samples (e.g., blood).

  11. Don't it make my blue eyes brown: heterochromia and other abnormalities of the iris

    PubMed Central

    Rennie, I G

    2012-01-01

    Eye colour is one of the most important characteristics in determining facial appearance. In this paper I shall discuss the anatomy and genetics of normal eye colour, together with a wide and diverse range of conditions that may produce an alteration in normal iris pigmentation or form. PMID:21979861

  12. COMPU-EYE: a high resolution computational compound eye.

    PubMed

    Lee, Woong-Bi; Jang, Hwanchol; Park, Sangjun; Song, Young Min; Lee, Heung-No

    2016-02-01

    In nature, the compound eyes of arthropods have evolved towards a wide field of view (FOV), infinite depth of field and fast motion detection. However, compound eyes have inferior resolution when compared with the camera-type eyes of vertebrates, owing to inherent structural constraints such as the optical performance and the number of ommatidia. For resolution improvements, in this paper, we propose COMPUtational compound EYE (COMPU-EYE), a new design that increases acceptance angles and uses a modern digital signal processing (DSP) technique. We demonstrate that the proposed COMPU-EYE provides at least a four-fold improvement in resolution.

  13. Anti-CD antibody microarray for human leukocyte morphology examination allows analyzing rare cell populations and suggesting preliminary diagnosis in leukemia.

    PubMed

    Khvastunova, Alina N; Kuznetsova, Sofya A; Al-Radi, Liubov S; Vylegzhanina, Alexandra V; Zakirova, Anna O; Fedyanina, Olga S; Filatov, Alexander V; Vorobjev, Ivan A; Ataullakhanov, Fazly

    2015-07-27

    We describe a method for leukocyte sorting by a microarray of anti-cluster-of-differentiation (anti-CD) antibodies and for preparation of the bound cells for morphological or cytochemical examination. The procedure results in a "sorted" smear with cells positive for certain surface antigens localised in predefined areas. The morphology and cytochemistry of the microarray-captured normal and neoplastic peripheral blood mononuclear cells are identical to the same characteristics in a smear. The microarray permits to determine the proportions of cells positive for the CD antigens on the microarray panel with high correlation with flow cytometry. Using the anti-CD microarray we show that normal granular lymphocytes and lymphocytes with radial segmentation of the nuclei are positive for CD3, CD8, CD16 or CD56 but not for CD4 or CD19. We also show that the described technique permits to obtain a pure leukemic cell population or to separate two leukemic cell populations on different antibody spots and to study their morphology or cytochemistry directly on the microarray. In cases of leukemias/lymphomas when circulating neoplastic cells are morphologically distinct, preliminary diagnosis can be suggested from full analysis of cell morphology, cytochemistry and their binding pattern on the microarray.

  14. Weighted analysis of general microarray experiments

    PubMed Central

    Sjögren, Anders; Kristiansson, Erik; Rudemo, Mats; Nerman, Olle

    2007-01-01

    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. PMID:17937807

  15. Multivariate normality

    NASA Technical Reports Server (NTRS)

    Crutcher, H. L.; Falls, L. W.

    1976-01-01

    Sets of experimentally determined or routinely observed data provide information about the past, present and, hopefully, future sets of similarly produced data. An infinite set of statistical models exists which may be used to describe the data sets. The normal distribution is one model. If it serves at all, it serves well. If a data set, or a transformation of the set, representative of a larger population can be described by the normal distribution, then valid statistical inferences can be drawn. There are several tests which may be applied to a data set to determine whether the univariate normal model adequately describes the set. The chi-square test based on Pearson's work in the late nineteenth and early twentieth centuries is often used. Like all tests, it has some weaknesses which are discussed in elementary texts. Extension of the chi-square test to the multivariate normal model is provided. Tables and graphs permit easier application of the test in the higher dimensions. Several examples, using recorded data, illustrate the procedures. Tests of maximum absolute differences, mean sum of squares of residuals, runs and changes of sign are included in these tests. Dimensions one through five with selected sample sizes 11 to 101 are used to illustrate the statistical tests developed.

  16. Compound eye formation in the termite Incisitermes minor (Isoptera: Kalotermitidae).

    PubMed

    Rose, Taylor C; Ediger, Emily F; Lehman-Schletewitz, Joy; McClane, Nathan W; Schweigert, Kristen C; Alzweideh, Saif; Wadsworth, Lauren; Husseneder, Claudia; Morris, Joshua W; Ziesmann, Jurgen

    2015-07-01

    The postembryonic development and caste differentiation patterns of lower termites have been described multiple times in a variety of different species. However, most of these studies focused on gross ontogeny, without carefully describing the maturation of any particular organ or organ system. The few studies that have attempted to correlate caste development and organ differentiation have produced somewhat inconsistent results, especially in the area of eye formation. Therefore, in order to help further elucidate the relationship between eye formation and postembryonic differentiation in lower termites, we studied eye development in the termite, Incisitermes minor (Hagen). Eye formation in I. minor began in the earliest larvae, with only an eye primordium. However, in all later larval stages, characteristic eye structures were observed and were shown to progressively differentiate through larval and nymphal stages. Curiously, pigmentation began with three to eight groups of cells in early larvae and the number of these pigmented groups increased along the developmental time course. Ultimately, a uniformly pigmented eye area was formed by the early nymphal stage. The overall eye area also gradually increased along with normal caste development, but the characteristic lenses seen in a prototypical insect compound eye did not completely form until after the final nymphal stage. Electrophysiological measurements provided clear evidence that eyes were indeed functional at all stages of development where pigment was present. Based upon this data, the eye development pattern in I. minor appeared to follow a divergent pathway from holometabolous insects and an intermediate pathway between typical hemimetabolous eye development and the heterochronic shift observed in other termite species.

  17. Microarray analysis in gastric cancer: A review

    PubMed Central

    D’Angelo, Giovanna; Di Rienzo, Teresa; Ojetti, Veronica

    2014-01-01

    Gastric cancer is one of the most common tumors worldwide. Although several treatment options have been developed, the mortality rate is increasing. Lymph node involvement is considered the most reliable prognostic indicator in gastric cancer. Early diagnosis improves the survival rate of patients and increases the likelihood of successful treatment. The most reliable diagnostic method is endoscopic examination, however, it is expensive and not feasible in poorer countries. Therefore, many innovative techniques have been studied to develop a new non-invasive screening test and to identify specific serum biomarkers. DNA microarray analysis is one of the new technologies able to measure the expression levels of a large number of genes simultaneously. It is possible to define the gene expression profile of the tumor and to correlate it with the prognosis and metastasis formation. Several studies in the literature have been published on the role of microarray analysis in gastric cancer and the mechanisms of proliferation and metastasis formation. The aim of this review is to analyze the importance of microarray analysis and its clinical applications to better define the genetic characteristics of gastric cancer and its possible implications in a more decisive treatment. PMID:25232233

  18. Repeatability of published microarray gene expression analyses.

    PubMed

    Ioannidis, John P A; Allison, David B; Ball, Catherine A; Coulibaly, Issa; Cui, Xiangqin; Culhane, Aedín C; Falchi, Mario; Furlanello, Cesare; Game, Laurence; Jurman, Giuseppe; Mangion, Jon; Mehta, Tapan; Nitzberg, Michael; Page, Grier P; Petretto, Enrico; van Noort, Vera

    2009-02-01

    Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005-2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered.

  19. High-Throughput Enzyme Kinetics Using Microarrays

    SciTech Connect

    Guoxin Lu; Edward S. Yeung

    2007-11-01

    We report a microanalytical method to study enzyme kinetics. The technique involves immobilizing horseradish peroxidase on a poly-L-lysine (PLL)- coated glass slide in a microarray format, followed by applying substrate solution onto the enzyme microarray. Enzyme molecules are immobilized on the PLL-coated glass slide through electrostatic interactions, and no further modification of the enzyme or glass slide is needed. In situ detection of the products generated on the enzyme spots is made possible by monitoring the light intensity of each spot using a scientific-grade charged-coupled device (CCD). Reactions of substrate solutions of various types and concentrations can be carried out sequentially on one enzyme microarray. To account for the loss of enzyme from washing in between runs, a standard substrate solution is used for calibration. Substantially reduced amounts of substrate solution are consumed for each reaction on each enzyme spot. The Michaelis constant K{sub m} obtained by using this method is comparable to the result for homogeneous solutions. Absorbance detection allows universal monitoring, and no chemical modification of the substrate is needed. High-throughput studies of native enzyme kinetics for multiple enzymes are therefore possible in a simple, rapid, and low-cost manner.

  20. Development and Applications of the Lectin Microarray.

    PubMed

    Hirabayashi, Jun; Kuno, Atsushi; Tateno, Hiroaki

    2015-01-01

    The lectin microarray is an emerging technology for glycomics. It has already found maximum use in diverse fields of glycobiology by providing simple procedures for differential glycan profiling in a rapid and high-throughput manner. Since its first appearance in the literature in 2005, many application methods have been developed essentially on the same platform, comprising a series of glycan-binding proteins immobilized on an appropriate substrate such as a glass slide. Because the lectin microarray strategy does not require prior liberation of glycans from the core protein in glycoprotein analysis, it should encourage researchers not familiar with glycotechnology to use glycan analysis in future work. This feasibility should provide a broader range of experimental scientists with good opportunities to investigate novel aspects of glycoscience. Applications of the technology include not only basic sciences but also the growing fields of bio-industry. This chapter describes first the essence of glycan profiling and the basic fabrication of the lectin microarray for this purpose. In the latter part the focus is on diverse applications to both structural and functional glycomics, with emphasis on the wide applicability now available with this new technology. Finally, the importance of developing advanced lectin engineering is discussed.

  1. Metadata management and semantics in microarray repositories.

    PubMed

    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. PMID:24052712

  2. Chicken sperm transcriptome profiling by microarray analysis.

    PubMed

    Singh, R P; Shafeeque, C M; Sharma, S K; Singh, R; Mohan, J; Sastry, K V H; Saxena, V K; Azeez, P A

    2016-03-01

    It has been confirmed that mammalian sperm contain thousands of functional RNAs, and some of them have vital roles in fertilization and early embryonic development. Therefore, we attempted to characterize transcriptome of the sperm of fertile chickens using microarray analysis. Spermatozoal RNA was pooled from 10 fertile males and used for RNA preparation. Prior to performing the microarray, RNA quality was assessed using a bioanalyzer, and gDNA and somatic cell RNA contamination was assessed by CD4 and PTPRC gene amplification. The chicken sperm transcriptome was cross-examined by analysing sperm and testes RNA on a 4 × 44K chicken array, and results were verified by RT-PCR. Microarray analysis identified 21,639 predominantly nuclear-encoded transcripts in chicken sperm. The majority (66.55%) of the sperm transcripts were shared with the testes, while surprisingly, 33.45% transcripts were detected (raw signal intensity greater than 50) only in the sperm and not in the testes. The greatest proportion of up-regulated transcripts were responsible for signal transduction (63.20%) followed by embryonic development (56.76%) and cell structure (56.25%). Of the 20 most abundant transcripts, 18 remain uncharacterized, whereas the least abundant genes were mostly associated with the ribosome. These findings lay a foundation for more detailed investigations on sperm RNAs in chickens to identify sperm-based biomarkers for fertility.

  3. [Genomic medicine. Polymorphisms and microarray applications].

    PubMed

    Spalvieri, Mónica P; Rotenberg, Rosa G

    2004-01-01

    This update shows new concepts related to the significance of DNA variations among individuals, as well as to their detection by using a new technology. The sequencing of the human genome is only the beginning of what will enable us to understand genetic diversity. The unit of DNA variability is the polymorphism of a single nucleotide (SNP). At present, studies on SNPs are restricted to basic research but the large number of papers on this subject makes feasible their entrance into clinical practice. We illustrate here the use of SNPs as molecular markers in ethnical genotyping, gene expression in some diseases and as potential targets in pharmacological response, and also introduce the technology of arrays. Microarrays experiments allow the quantification and comparison of gene expression on a large scale, at the same time, by using special chips and array designs. Conventional methods provide data from up to 20 genes, while a single microarray may provide information about thousands of them simultaneously, leading to a more rapid and accurate genotyping. Biotechnology improvements will facilitate our knowledge of each gene sequence, the frequency and exact location of SNPs and their influence on cellular behavior. Although experimental efficiency and validity of results from microarrays are still controversial, the knowledge and characterization of a patient's genetic profile will lead, undoubtedly, to advances in prevention, diagnosis, prognosis and treatment of human diseases. PMID:15637833

  4. Penetrating eye injuries.

    PubMed Central

    Patel, B C

    1989-01-01

    A review of all penetrating eye injuries treated at the Manchester Royal Eye Hospital over four years (1 January 1982-31 December 1985) was undertaken. A total of 202 penetrating eye injuries were seen of which 68 (34%) were in children under the age of 15 years. Airgun, dart, and knife injuries accounted for 28 (41%) of the injuries. Thirty seven patients (54%) achieved a good visual result (6/12 or better) and eight (12%) had enucleations. The period of inpatient treatment ranged from two to 18 days. From the analysis of the activities at the time of the injury, many of the injuries can be considered to be preventable. PMID:2705791

  5. Influences of reference plane and direction of measurement on eye aberration measurement

    NASA Astrophysics Data System (ADS)

    Atchison, David A.; Charman, W. Neil

    2005-12-01

    We explored effects of measurement conditions on wave aberration estimates for uncorrected, axially myopic model eyes. Wave aberrations were initially referenced to either the anterior corneal pole or the natural entrance pupil of symmetrical eye models, with rays traced into the eye from infinity (into the eye) to simulate normal vision, into the eye from infinity and then back out of the eye from the retinal intercepts (into/out of the eye), or out of the eye from the retinal fovea (out of the eye). The into-the-eye and out-of-the-eye ray traces gave increases in spherical aberration as myopia increased, but the into/out-of-the-eye ray trace showed little variation in spherical aberration. Reference plane choice also affected spherical aberration. Corresponding residual aberrations were calculated after the models had been optically corrected, either by placing the object or image plane at the paraxial far point or by modifying corneas to simulate laser ablation corrections. Correcting aberrations by ablation was more complete if the original aberrations were referenced to the cornea rather than to the entrance pupil. For eyes corrected by spectacle lenses, failure to allow for effects of pupil magnification on apparent entrance pupil diameter produced larger changes in measured aberrations. The general findings regarding choice of reference plane and direction of measurement were found to be equally applicable to eyes that lacked rotational symmetry.

  6. Aetiological Factors in Dyslexia: I. Saccadic Eye Movement Control.

    ERIC Educational Resources Information Center

    Leisman, Gerald; Schwartz, Joddy

    1978-01-01

    A study examined the character of saccadic eye movement (as reflected by duration/amplitude and velocity/amplitude functions) in 20 dyslexic and 20 normal children (mean age 8.2 years) and 28 normal adults (mean age 26.2 years). (Author/PHR)

  7. Comparison of postoperative corneal changes between dry eye and non-dry eye in a murine cataract surgery model

    PubMed Central

    Kwon, Jin Woo; Chung, Yeon Woong; Choi, Jin A; La, Tae Yoon; Jee, Dong Hyun; Cho, Yang Kyung

    2016-01-01

    AIM To compare the effects of the surgical insult of cataract surgery on corneal inflammatory infiltration, neovascularization (NV) and lymphangiogenesis (LY) between the dry eye and non-dry eye in murine cataract surgery models. METHODS We established two groups of animals, one with normal eyes (non-dry eye) and the second with induced dry eyes. In both groups, we used surgical insults to mimic human cataract surgery, which consisted of lens extraction, corneal incision and suture. After harvesting of corneas on the 9th postoperative day and immunohistochemical staining, we compared NV, LY and CD11b+ cell infiltration in the corneas. RESULTS Dry eye group had significantly more inflammatory infiltration (21.75%±7.17% vs 3.65%±1.49%; P=0.049). The dry eye group showed significantly more NV (48.21%±4.02% vs 26.24%±6.01%; P=0.016) and greater levels of LY (9.27%±0.48% vs 4.84%±1.15%; P=0.007). In corneas on which no surgery was performed, there was no induction of NV in both the dry and non-dry group, but dry eye group demonstrated more CD11b+ cells infiltration than the non-dry eye group (0.360%±0.160% vs 0.023%±0.006%; P=0.068). Dry eye group showed more NV than non-dry eye group in both topical PBS application and subconjunctival PBS injection (P=0.020 and 0.000, respectively). CONCLUSION In a murine cataract surgery model, preexisting dry eye can induce more postoperative NV, LY, and inflammation in corneal tissue. PMID:26949638

  8. Single nucleotide polymorphism-based microarray analysis for the diagnosis of hydatidiform moles

    PubMed Central

    XIE, YINGJUN; PEI, XIAOJUAN; DONG, YU; WU, HUIQUN; WU, JIANZHU; SHI, HUIJUAN; ZHUANG, XUYING; SUN, XIAOFANG; HE, JIALING

    2016-01-01

    In clinical diagnostics, single nucleotide polymorphism (SNP)-based microarray analysis enables the detection of copy number variations (CNVs), as well as copy number neutral regions, that are absent of heterozygosity throughout the genome. The aim of the present study was to evaluate the effectiveness and sensitivity of SNP-based microarray analysis in the diagnosis of hydatidiform mole (HM). By using whole-genome SNP microarray analysis, villous genotypes were detected, and the ploidy of villous tissue was determined to identify HMs. A total of 66 villous tissues and two twin tissues were assessed in the present study. Among these samples, 11 were triploid, one was tetraploid, 23 were abnormal aneuploidy, three were complete genome homozygosity, and the remaining ones were normal ploidy. The most noteworthy finding of the present study was the identification of six partial HMs and three complete HMs from those samples that were not identified as being HMs on the basis of the initial diagnosis of experienced obstetricians. This study has demonstrated that the application of an SNP-based microarray analysis was able to increase the sensitivity of diagnosis for HMs with partial and complete HMs, which makes the identification of these diseases at an early gestational age possible. PMID:27151252

  9. GPR-Analyzer: a simple tool for quantitative analysis of hierarchical multispecies microarrays.

    PubMed

    Dittami, Simon M; Edvardsen, Bente

    2013-10-01

    Monitoring of marine microalgae is important to predict and manage harmful algae blooms. It currently relies mainly on light-microscopic identification and enumeration of algal cells, yet several molecular tools are currently being developed to complement traditional methods. MIcroarray Detection of Toxic ALgae (MIDTAL) is an FP7-funded EU project aiming to establish a hierarchical multispecies microarray as one of these tools. Prototype arrays are currently being tested with field samples, yet the analysis of the large quantities of data generated by these arrays presents a challenge as suitable analysis tools or protocols are scarce. This paper proposes a two-part protocol for the analysis of the MIDTAL and other hierarchical multispecies arrays: Signal-to-noise ratios can be used to determine the presence or absence of signals and to identify potential false-positives considering parallel and hierarchical probes. In addition, normalized total signal intensities are recommended for comparisons between microarrays and in order to relate signals for specific probes to cell concentrations using external calibration curves. Hybridization- and probe-specific detection limits can be calculated to help evaluate negative results. The suggested analyses were implemented in "GPR-Analyzer", a platform-independent and graphical user interface-based application, enabling non-specialist users to quickly and quantitatively analyze hierarchical multispecies microarrays. It is available online at http://folk.uio.no/edvardse/gpranalyzer . PMID:22767354

  10. DNA Microarray for Detection of Gastrointestinal Viruses

    PubMed Central

    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

  11. DNA microarray for detection of gastrointestinal viruses.

    PubMed

    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; Isa, Pavel

    2015-01-01

    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 × 10(3) 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

  12. Statistically designing microarrays and microarray experiments to enhance sensitivity and specificity.

    PubMed

    Hsu, Jason C; Chang, Jane; Wang, Tao; Steingrímsson, Eiríkur; Magnússon, Magnús Karl; Bergsteinsdottir, Kristin

    2007-01-01

    Gene expression signatures from microarray experiments promise to provide important prognostic tools for predicting disease outcome or response to treatment. A number of microarray studies in various cancers have reported such gene signatures. However, the overlap of gene signatures in the same disease has been limited so far, and some reported signatures have not been reproduced in other populations. Clearly, the methods used for verifying novel gene signatures need improvement. In this article, we describe an experiment in which microarrays and sample hybridization are designed according to the statistical principles of randomization, replication and blocking. Our results show that such designs provide unbiased estimation of differential expression levels as well as powerful tests for them.

  13. Comments on selected fundamental aspects of microarray analysis.

    PubMed

    Riva, Alessandra; Carpentier, Anne-Sophie; Torrésani, Bruno; Hénaut, Alain

    2005-10-01

    Microarrays are becoming a ubiquitous tool of research in life sciences. However, the working principles of microarray-based methodologies are often misunderstood or apparently ignored by the researchers who actually perform and interpret experiments. This in turn seems to lead to a common over-expectation regarding the explanatory and/or knowledge-generating power of microarray analyses. In this note we intend to explain basic principles of five (5) major groups of analytical techniques used in studies of microarray data and their interpretation: the principal component analysis (PCA), the independent component analysis (ICA), the t-test, the analysis of variance (ANOVA), and self organizing maps (SOM). We discuss answers to selected practical questions related to the analysis of microarray data. We also take a closer look at the experimental setup and the rules, which have to be observed in order to exploit microarrays efficiently. Finally, we discuss in detail the scope and limitations of microarray-based methods. We emphasize the fact that no amount of statistical analysis can compensate for (or replace) a well thought through experimental setup. We conclude that microarrays are indeed useful tools in life sciences but by no means should they be expected to generate complete answers to complex biological questions. We argue that even well posed questions, formulated within a microarray-specific terminology, cannot be completely answered with the use of microarray analyses alone.

  14. Inter-eye comparison of retinal oximetry and vessel caliber between eyes with asymmetrical glaucoma severity in different glaucoma subtypes

    PubMed Central

    Cheng, Clarissa Shu Ming; Lee, Yi Fang; Ong, Charles; Yap, Zhu Li; Tsai, Andrew; Mohla, Aditi; Nongpiur, Monisha E; Aung, Tin; Perera, Shamira A

    2016-01-01

    Background To compare retinal vessel oxygenation and vessel caliber in primary angle-closure glaucoma (PACG), primary open-angle glaucoma (POAG), normal-tension glaucoma (NTG), and normal controls, as well as between eyes of asymmetrical glaucoma severity. Methods This was a prospective, cross-sectional study. The 159 subjects (PACG, n=39; POAG, n=41; NTG, n=41; normal controls, n=38) underwent retinal oxygen saturation measurements using the Oxymap T1 Retinal Oximeter, optical coherence tomography, and Humphrey visual field testing. Retinal oxygen saturation and vessel diameter were compared between the glaucoma groups and normal controls, as well as between eyes of asymmetrical glaucoma severity. Kruskal–Wallis test was performed for comparison among different subtypes of glaucoma. Wilcoxon signed-rank test was used to compare the inter-eye differences. Results Compared to normal controls, arteriolar oxygen saturation was increased in PACG eyes (P=0.048) but not in POAG or NTG eyes. There were no significant differences in oxygen saturation in venules or arteriovenous (AV) difference in all three glaucoma groups. Venular diameter was significantly reduced in all glaucoma groups compared to normal controls (P<0.001), but no such change was observed in arteriolar diameter (P=0.10). When comparing between eyes of asymmetrical glaucoma severity, arteriolar oxygen saturation (P=0.03) and AV difference (P=0.04) were significantly higher, while arteriolar diameter was significantly lower (P=0.001) in the worse eye in PACG group. There were no significant differences in oximetric parameters or vessel calibers between the worse and the better eyes in POAG and NTG groups. Conclusion Eyes with PACG showed increased arteriolar oxygen saturation and increased AV difference. This was not observed in POAG and NTG eyes. Arteriolar diameter in PACG and venular diameter in all three glaucoma groups were reduced. The difference observed in PACG eyes may be due to an increased

  15. Child readers' eye movements in reading Thai.

    PubMed

    Kasisopa, Benjawan; Reilly, Ronan G; Luksaneeyanawin, Sudaporn; Burnham, Denis

    2016-06-01

    It has recently been found that adult native readers of Thai, an alphabetic scriptio continua language, engage similar oculomotor patterns as readers of languages written with spaces between words; despite the lack of inter-word spaces, first and last characters of a word appear to guide optimal placement of Thai readers' eye movements, just to the left of word-centre. The issue addressed by the research described here is whether eye movements of Thai children also show these oculomotor patterns. Here the effect of first and last character frequency and word frequency on the eye movements of 18 Thai children when silently reading normal unspaced and spaced text was investigated. Linear mixed-effects model analyses of viewing time measures (first fixation duration, single fixation duration, and gaze duration) and of landing site location revealed that Thai children's eye movement patterns were similar to their adult counterparts. Both first character frequency and word frequency played important roles in Thai children's landing sites; children tended to land their eyes further into words, close to the word centre, if the word began with higher frequency first characters, and this effect was facilitated in higher frequency words. Spacing also facilitated more effective use of first character frequency and it also assisted in decreasing children's viewing time. The use of last-character frequency appeared to be a later development, affecting mainly single fixation duration and gaze duration. In general, Thai children use the same oculomotor control mechanisms in reading spaced and unspaced texts as Thai adults, who in turn have similar oculomotor control as readers of spaced texts. Thus, it appears that eye movements in reading converge on the optimal landing site using whatever cues are available to guide such placement. PMID:27137836

  16. Saccadic eye movements of dyslexic adult subjects.

    PubMed

    Fischer, B; Biscaldi, M; Otto, P

    1993-09-01

    The characteristics of visually guided saccadic eye movements were compared in 12 normal adult subjects and 12 test subjects of normal intelligence, but with problems in reading and writing. All subjects were examined psychometrically for different cognitive abilities, and for their reading and writing capabilities. The anamnestic reports about their reading and writing problems earlier in their lives were analysed. Based on scores of the writing and reading tests, the test group was subdivided into two subgroups: A and B (group A reached medium, group B very low scores in both tests). Five different non-cognitive eye movement tasks were applied: two single tasks (gap and overlap) requiring single saccades from a fixation point to a peripherally appearing target and three sequential tasks (overlap, synchronous, and simultaneous) requiring sequences of saccades to four equally spaced targets presented sequentially to the right side from an initial fixation point. Many parameters of the subjects' eye movement performance were determined and their mean values were calculated for each subject. The Student t-test revealed that the eye movement data of the two test groups deviated differently from the data of the control group. Group B had the largest deviation of the eye movement parameter from the control group. The differentiating parameters were the consistency of target acquisition, the saccadic reaction time, and the number of anticipatory responses in the single target tasks. In the sequential tasks these differences were in the amplitude, the number of saccades, and the fixation durations. The incidence of regressive saccades did not discriminate between test subjects and controls. The possible underlying deficits in the attentional control over the saccadic system and their implications for reading are discussed.

  17. Eye-Tracking Data

    PubMed Central

    Galesic, Mirta; Tourangeau, Roger; Couper, Mick P.; Conrad, Frederick G.

    2008-01-01

    Survey researchers since Cannell have worried that respondents may take various shortcuts to reduce the effort needed to complete a survey. The evidence for such shortcuts is often indirect. For instance, preferences for earlier versus later response options have been interpreted as evidence that respondents do not read beyond the first few options. This is really only a hypothesis, however, that is not supported by direct evidence regarding the allocation of respondent attention. In the current study, we used a new method to more directly observe what respondents do and do not look at by recording their eye movements while they answered questions in a Web survey. The eye-tracking data indicate that respondents do in fact spend more time looking at the first few options in a list of response options than those at the end of the list; this helps explain their tendency to select the options presented first regardless of their content. In addition, the eye-tracking data reveal that respondents are reluctant to invest effort in reading definitions of survey concepts that are only a mouse click away or paying attention to initially hidden response options. It is clear from the eye-tracking data that some respondents are more prone to these and other cognitive shortcuts than others, providing relatively direct evidence for what had been suspected based on more conventional measures. PMID:21253437

  18. Eye Movements and Perception.

    ERIC Educational Resources Information Center

    Gaarder, Kenneth

    An explanation of visual perception is presented using physiological facts, analogies to digital computers, and analogies to the structure of written languages. According to the explanation, visual input is discontinuous, with the discontinuities mediated by and correlated with the jumps of the eye. This is analogous to the gated and buffer-stored…

  19. Through Students' Eyes.

    ERIC Educational Resources Information Center

    McLean-Donaldson, Karen B.

    1994-01-01

    Identifies how students perceive racism and its effects on student learning and whether antiracist/multicultural arts (ARMA) curricula can empower students to address racism in schools. Results show racism, through students' eyes, damages learning, attitudes, and behavior. ARMA positively effected students' ability to confront racism within their…

  20. Through Our Eyes

    ERIC Educational Resources Information Center

    Narva, Sara

    2009-01-01

    Through Our Eyes was a multimedia performance created in collaboration with the author's five modern dance students. Through video, sound, and dance, the piece shows some ways race has affected their lives. The author did not set out at the beginning of the semester to make this project in her dance class. It was born out of a hard conversation,…

  1. Dynamic Eye Model.

    ERIC Educational Resources Information Center

    Journal of Science and Mathematics Education in Southeast Asia, 1981

    1981-01-01

    Instructions (with diagrams and parts list) are provided for constructing an eye model with a pliable lens made from a plastic bottle which can vary its convexity to accommodate changing positions of an object being viewed. Also discusses concepts which the model can assist in developing. (Author/SK)

  2. [Eye and the pregnacy].

    PubMed

    Dima, Anne Marie

    2012-01-01

    Pregnancy is associated with changes in many organs and systems including the eyes. Sometimes in pregnancy may appear physiological and pathological ocular changes that may be associated with pre-existing problems. In such cases it is very important interdisciplinary collaboration gynecologist, ophthalmologist.

  3. Eye of the Beholder

    ERIC Educational Resources Information Center

    Rogers, Michael

    2010-01-01

    Art, like beauty, as the adage goes, is in the eye of the beholder. Art also is a living, breathing thing that evolves over time, so what is considered "art" is ever changing--how many of the great artists whose works today sell for fortunes were failures during their lifetime? The 20th century unknowingly gave birth to new variations of art that…

  4. Eyes for Learning

    ERIC Educational Resources Information Center

    Orfield, Antonia

    2008-01-01

    Vision is the dominant sense, and the eyes are connected with almost every other part of the brain. If the vision system is poorly developed, children trying to learn suffer. Without good up close vision, students are handicapped even if no one knows or suspects it--they may not even know it themselves. Students do not know that the way they see…

  5. An eye for inspiration

    NASA Astrophysics Data System (ADS)

    2009-11-01

    The discovery that the eye of a particular mantis shrimp has an achromatic quarter-waveplate that is superior to modern-day devices could be a source of inspiration to those designing optical components. Nature Photonics spoke to Nicholas Roberts, one of the researchers involved in the study.

  6. The Eyes Have It.

    ERIC Educational Resources Information Center

    Walsh, Janet

    1982-01-01

    Discusses the health hazards of working with the visual display systems of computers, in particular the eye problems associated with long-term use of video display terminals. Excerpts from and ordering information for the National Institute for Occupational Safety and Health report on such hazards are included. (JJD)

  7. Microarray analysis of thioacetamide-treated type 1 diabetic rats

    SciTech Connect

    Devi, Sachin S.; Mehendale, Harihara M. . E-mail: mehendale@ulm.edu

    2006-04-01

    It is well known that diabetes imparts high sensitivity to numerous hepatotoxicants. Previously, we have shown that a normally non-lethal dose of thioacetamide (TA, 300 mg/kg) causes 90% mortality in type 1 diabetic (DB) rats due to inhibited tissue repair allowing progression of liver injury. On the other hand, DB rats exposed to 30 mg TA/kg exhibit delayed tissue repair and delayed recovery from injury. The objective of this study was to investigate the mechanism of impaired tissue repair and progression of liver injury in TA-treated DB rats by using cDNA microarray. Gene expression pattern was examined at 0, 6, and 12 h after TA challenge, and selected mechanistic leads from microarray experiments were confirmed by real-time RT-PCR and further investigated at protein level over the time course of 0 to 36 h after TA treatment. Diabetic condition itself increased gene expression of proteases and decreased gene expression of protease inhibitors. Administration of 300 mg TA/kg to DB rats further elevated gene expression of proteases and suppressed gene expression of protease inhibitors, explaining progression of liver injury in DB rats after TA treatment. Inhibited expression of genes involved in cell division cycle (cyclin D1, IGFBP-1, ras, E2F) was observed after exposure of DB rats to 300 mg TA/kg, explaining inhibited tissue repair in these rats. On the other hand, DB rats receiving 30 mg TA/kg exhibit delayed expression of genes involved in cell division cycle, explaining delayed tissue repair in these rats. In conclusion, impaired cyclin D1 signaling along with increased proteases and decreased protease inhibitors may explain impaired tissue repair that leads to progression of liver injury initiated by TA in DB rats.

  8. [The genetic background for the eye malformations anophthalmia and microphthalmia].

    PubMed

    Roos, Laura Sønderberg; Grønskov, Karen; Jensen, Hanne; Tümer, Zeynep

    2012-03-12

    Anophthalmia and microphthalmia (AO/MO) are rare congenital eye malformations, in which the eyeball is apparently absent or smaller than normal, which causes various degrees of visual impairment. Over 200 different AO/MO-related syndromes have been described, but the genetic background is unknown in many cases. The aim of this article is to give an overview of AO/MO, focusing on the genetic background. It is illustrated that the future identification of new AO/MO related genes will benefit in the genetic counseling of AO/MO patients, and in the understanding of eye development and congenital eye malformations.

  9. Pseudomonas corneal ulcer. The causative role of contaminated eye cosmetics.

    PubMed

    Reid, F R; Wood, T O

    1979-09-01

    The clinical significance of contaminated ocular cosmetics is illustrated by the case of a 47-year-old woman in whom a Pseudomonas corneal ulcer developed immediately after she sustained minor corneal trauma with a mascara applicator. Pseudomonas aeruginosa was cultured from the corneal ulcer and the mascara. In addition to the causative role in acute corneal ulcers, contaminated eye cosmetics contribute to chronic external eye infections. Retail eye cosmetics are typically free of contamination when purchased. The inoculation of the cosmetic occurs during normal use. PMID:112953

  10. Eye movements during reading: a theory of saccade initiation times.

    PubMed

    Yang, S N; McConkie, G W

    2001-01-01

    As people read continuous text, on occasional single eye fixations the text was replaced by one of six alternate stimulus patterns. Frequency distributions of the durations of these fixations were used to test predictions from four types of theories of saccadic eye movement control. Contrary to current cognitive theories, cognitive influences appeared to delay saccades rather than trigger them. Two saccade disruption times were identified, suggesting the existence of three distributions of saccades, labeled early, normal and late. The Competition-inhibition theory, an enhanced version of Findlay and Walker's (1999) theory, is proposed to account for eye movement control during reading.

  11. Simple Solutions for Dry Eye

    MedlinePlus

    ... are more concentrated in the tear film of dry eye patients. In hot weather, sleep with the windows shut and keep cool with air conditioning. • Dry eye patients often develop or aggravate allergies. An ...

  12. Recognizing and Treating Eye Injuries

    MedlinePlus

    ... and seek medical attention. In case of a chemical burn to the eye: Immediately flush the eye ... Academy Jobs at the Academy Financial Relationships with Industry Medical Disclaimer Privacy Policy Terms of Service For ...

  13. Medicare Benefits and Your Eyes

    MedlinePlus

    ... Eye Health Report Reports and External Resources The Cost of Vision Problems The Future of Vision Vision Problems in the U.S. Healthy Eyes Education Series Online Training and Certification Patient Education Materials ...

  14. Normalizing Rejection.

    PubMed

    Conn, Vicki S; Zerwic, Julie; Jefferson, Urmeka; Anderson, Cindy M; Killion, Cheryl M; Smith, Carol E; Cohen, Marlene Z; Fahrenwald, Nancy L; Herrick, Linda; Topp, Robert; Benefield, Lazelle E; Loya, Julio

    2016-02-01

    Getting turned down for grant funding or having a manuscript rejected is an uncomfortable but not unusual occurrence during the course of a nurse researcher's professional life. Rejection can evoke an emotional response akin to the grieving process that can slow or even undermine productivity. Only by "normalizing" rejection, that is, by accepting it as an integral part of the scientific process, can researchers more quickly overcome negative emotions and instead use rejection to refine and advance their scientific programs. This article provides practical advice for coming to emotional terms with rejection and delineates methods for working constructively to address reviewer comments. PMID:26041785

  15. Model-based dose calculations for COMS eye plaque brachytherapy using an anatomically realistic eye phantom

    SciTech Connect

    Lesperance, Marielle; Inglis-Whalen, M.; Thomson, R. M.

    2014-02-15

    simulation by up to 16%. In the full eye model simulations, the average dose to the lens is larger by 7%–9% than the dose to the center of the lens, and the maximum dose to the optic nerve is 17%–22% higher than the dose to the optic disk for all radionuclides. In general, when normalized to the same prescription dose at the tumor apex, doses delivered to all structures of interest in the full eye model are lowest for{sup 103}Pd and highest for {sup 131}Cs, except for the tumor where the average dose is highest for {sup 103}Pd and lowest for {sup 131}Cs. Conclusions : The eye is not radiologically water-equivalent, as doses from simulations of the plaque in the full eye model differ considerably from doses for the plaque in a water phantom and from simulated TG-43 calculated doses. This demonstrates the importance of model-based dose calculations for eye plaque brachytherapy, for which accurate elemental compositions of ocular media are necessary.

  16. Shrimps that pay attention: saccadic eye movements in stomatopod crustaceans.

    PubMed

    Marshall, N J; Land, M F; Cronin, T W

    2014-01-01

    Discovering that a shrimp can flick its eyes over to a fish and follow up by tracking it or flicking back to observe something else implies a 'primate-like' awareness of the immediate environment that we do not normally associate with crustaceans. For several reasons, stomatopods (mantis shrimp) do not fit the general mould of their subphylum, and here we add saccadic, acquisitional eye movements to their repertoire of unusual visual capabilities. Optically, their apposition compound eyes contain an area of heightened acuity, in some ways similar to the fovea of vertebrate eyes. Using rapid eye movements of up to several hundred degrees per second, objects of interest are placed under the scrutiny of this area. While other arthropod species, including insects and spiders, are known to possess and use acute zones in similar saccadic gaze relocations, stomatopods are the only crustacean known with such abilities. Differences among species exist, generally reflecting both the eye size and lifestyle of the animal, with the larger-eyed more sedentary species producing slower saccades than the smaller-eyed, more active species. Possessing the ability to rapidly look at and assess objects is ecologically important for mantis shrimps, as their lifestyle is, by any standards, fast, furious and deadly. PMID:24395969

  17. Shrimps that pay attention: saccadic eye movements in stomatopod crustaceans

    PubMed Central

    Marshall, N. J.; Land, M. F.; Cronin, T. W.

    2014-01-01

    Discovering that a shrimp can flick its eyes over to a fish and follow up by tracking it or flicking back to observe something else implies a ‘primate-like’ awareness of the immediate environment that we do not normally associate with crustaceans. For several reasons, stomatopods (mantis shrimp) do not fit the general mould of their subphylum, and here we add saccadic, acquisitional eye movements to their repertoire of unusual visual capabilities. Optically, their apposition compound eyes contain an area of heightened acuity, in some ways similar to the fovea of vertebrate eyes. Using rapid eye movements of up to several hundred degrees per second, objects of interest are placed under the scrutiny of this area. While other arthropod species, including insects and spiders, are known to possess and use acute zones in similar saccadic gaze relocations, stomatopods are the only crustacean known with such abilities. Differences among species exist, generally reflecting both the eye size and lifestyle of the animal, with the larger-eyed more sedentary species producing slower saccades than the smaller-eyed, more active species. Possessing the ability to rapidly look at and assess objects is ecologically important for mantis shrimps, as their lifestyle is, by any standards, fast, furious and deadly. PMID:24395969

  18. Formation and characterization of DNA microarrays at silicon nitride substrates.

    PubMed

    Manning, Mary; Redmond, Gareth

    2005-01-01

    A versatile method for direct, covalent attachment of DNA microarrays at silicon nitride layers, previously deposited by chemical vapor deposition at silicon wafer substrates, is reported. Each microarray fabrication process step, from silicon nitride substrate deposition, surface cleaning, amino-silanation, and attachment of a homobifunctional cross-linking molecule to covalent immobilization of probe oligonucleotides, is defined, characterized, and optimized to yield consistent probe microarray quality, homogeneity, and probe-target hybridization performance. The developed microarray fabrication methodology provides excellent (high signal-to-background ratio) and reproducible responsivity to target oligonucleotide hybridization with a rugged chemical stability that permits exposure of arrays to stringent pre- and posthybridization wash conditions through many sustained cycles of reuse. Overall, the achieved performance features compare very favorably with those of more mature glass based microarrays. It is proposed that this DNA microarray fabrication strategy has the potential to provide a viable route toward the successful realization of future integrated DNA biochips.

  19. Experiments on a Model Eye

    ERIC Educational Resources Information Center

    Arell, Antti; Kolari, Samuli

    1978-01-01

    Explains a laboratory experiment dealing with the optical features of the human eye. Shows how to measure the magnification of the retina and the refractive anomaly of the eye could be used to measure the refractive power of the observer's eye. (GA)

  20. ADAPTIVE EYE MODEL - Poster Paper

    NASA Astrophysics Data System (ADS)

    Galetskiy, Sergey O.; Kudryashov, Alexey V.

    2008-01-01

    We propose experimental adaptive eye model based on flexible 18-electrode bimorph mirror reproducing human eye aberrations up to 4th radial order of Zernike polynomials at frequency of 10Hz. The accuracy of aberrations reproduction in most cases is better than λ/10 RMS. The model is introduced to aberrometer for human eye aberrations compensation to improve visual acuity test.

  1. Eye Protection in Kansas Schools.

    ERIC Educational Resources Information Center

    Hay, Kenneth M.; And Others

    A law passed by a state legislature requires that students in industrial arts shops and science laboratories must wear eye protective devices. Explanatory material presents the text of the bill and guidelines for implementation, including--(1) types of eye hazards, (2) types of protective devices, (3) administrating eye safety equipment, (4)…

  2. LIMNOLOGICAL OPTOMETRY: EXAMINING EARTH'S EYE

    EPA Science Inventory

    In Thoreau's Walden, a lake is described as the landscape's most expressive feature and the earth's eye. Collectively, scientists are charged by society to assess, monitor, and remedy maladies of earth's eye in the same way optometrists maintain the health of the human eye. This ...

  3. Reconstructing the eyes of Urbilateria.

    PubMed Central

    Arendt, D; Wittbrodt, J

    2001-01-01

    The shared roles of Pax6 and Six homologues in the eye development of various bilaterians suggest that Urbilateria, the common ancestors of all Bilateria, already possessed some simple form of eyes. Here, we re-address the homology of bilaterian cerebral eyes at the level of eye anatomy, of eye-constituting cell types and of phototransductory molecules. The most widespread eye type found in Bilateria are the larval pigment-cup eyes located to the left and right of the apical organ in primary, ciliary larvae of Protostomia and Deuterostomia. They can be as simple as comprising a single pigment cell and a single photoreceptor cell in inverse orientation. Another more elaborate type of cerebral pigment-cup eyes with an everse arrangement of photoreceptor cells is found in adult Protostomia. Both inverse larval and everse adult eyes employ rhabdomeric photoreceptor cells and thus differ from the chordate cerebral eyes with ciliary photoreceptors. This is highly significant because on the molecular level we find that for phototransduction rhabdomeric versus ciliary photoreceptor cells employ divergent rhodopsins and non-orthologous G-proteins, rhodopsin kinases and arrestins. Our comparison supports homology of cerebral eyes in Protostomia; it challenges, however, homology of chordate and non-chordate cerebral eyes that employ photoreceptor cells with non-orthologous phototransductory cascades. PMID:11604122

  4. DNA methylation analysis using CpG microarrays is impaired in benzopyrene exposed cells

    SciTech Connect

    Sadikovic, Bekim; Andrews, Joseph; Rodenhiser, David I.

    2007-12-15

    Epigenetic alterations have emerged as a key mechanism involved in tumorigenesis. These disruptions are partly due to environmental factors that change normal DNA methylation patterns necessary for transcriptional regulation and chromatin compaction. Microarray technologies are allowing environmentally susceptible epigenetic patterns to be mapped and the precise targets of environmentally induced alterations to be identified. Previously, we observed BaP-induced epigenetic events and cell cycle disruptions in breast cancer cell lines that included time- and concentration-dependent loss of proliferation as well as sequence-specific hypo- and hypermethylation events. In this present report, we further characterized epigenetic changes in BaP-exposed MCF-7 cells. We analyzed DNA methylation on a CpG island microarray platform with over 5400 unique genomic regions. Depleted and enriched microarray targets, representative of putative DNA methylation changes, were identified across the genome; however, subsequent sodium bisulfite analyses revealed no changes in DNA methylation at a number of these loci. Instead, we found that the identification of DNA methylation changes using this restriction enzyme-based microarray approach corresponded with the regions of DNA bound by the BaP derived DNA adducts. This DNA adduct formation occurs at both methylated and unmethylated CpG dinucleotides and affects PCR amplification during sample preparation. Our data suggest that caution should be exercised when interpreting data from comparative microarray experiments that rely on enzymatic reactions. These results are relevant to genome screening approaches involving environmental exposures in which DNA adduct formation at specific nucleotide sites may bias target acquisition and compromise the correct identification of epigenetically responsive genes.

  5. ProMAT: protein microarray analysis tool

    SciTech Connect

    White, Amanda M.; Daly, Don S.; Varnum, Susan M.; Anderson, Kevin K.; Bollinger, Nikki; Zangar, Richard C.

    2006-04-04

    Summary: ProMAT is a software tool for statistically analyzing data from ELISA microarray experiments. The software estimates standard curves, sample protein concentrations and their uncertainties for multiple assays. ProMAT generates a set of comprehensive figures for assessing results and diagnosing process quality. The tool is available for Windows or Mac, and is distributed as open-source Java and R code. Availability: ProMAT is available at http://www.pnl.gov/statistics/ProMAT. ProMAT requires Java version 1.5.0 and R version 1.9.1 (or more recent versions) which are distributed with the tool.

  6. Protein Microarrays--Without a Trace

    SciTech Connect

    Camarero, J A

    2007-04-05

    Many experimental approaches in biology and biophysics, as well as applications in diagnosis and drug discovery, require proteins to be immobilized on solid supports. Protein microarrays, for example, provide a high-throughput format to study biomolecular interactions. The technique employed for protein immobilization is a key to the success of these applications. Recent biochemical developments are allowing, for the first time, the selective and traceless immobilization of proteins generated by cell-free systems without the need for purification and/or reconcentration prior to the immobilization step.

  7. Scan of the back of human eye

    NASA Technical Reports Server (NTRS)

    2003-01-01

    ProVision Technologies, a NASA commercial space center at Sternis Space Center in Mississippi, has developed a new hyperspectral imaging (HSI) system that is much smaller than the original large units used aboard remote sensing aircraft and satellites. The new apparatus is about the size of a breadbox. HSI may be useful to ophthalmologists to study and diagnose eye health, both on Earth and in space, by examining the back of the eye to determine oxygen and blood flow quickly and without any invasion. ProVision's hyperspectral imaging system can scan the human eye and produce a graph showing optical density or light absorption, which can then be compared to a graph from a normal eye. Scans of the macula, optic disk or optic nerve head, and blood vessels can be used to detect anomalies and identify diseases in this delicate and important organ. ProVision has already developed a relationship with the University of Alabama at Birmingham, but is still on the lookout for a commercial partner in this application.

  8. Unidirectional abnormal eye movement without gaze nystagmus - Report of a case.

    PubMed

    Mizuno, Masahiro; Shibasaki, Osamu; Shindo, Susumu; Ito, Akinori; Kase, Yasuhiro

    2016-06-01

    We report here a case with unidirectional abnormalities of smooth eye movements without gaze nystagmus. Abnormalities of eye movements were confined to unidirectional (leftward) horizontal pursuit and slow phase of OKN; however, horizontal VOR (slow phase of caloric nystagmus) and saccade were normal, and vertical eye movements were also normal. No lesions were detected in the central nervous system, and any history of drug intake was denied. Although the cause of the unidirectional abnormality in eye movement of this case is still not clear, a congenital origin seems to be the most probable. PMID:26386498

  9. Normal development.

    PubMed

    Girard, Nadine; Koob, Meriam; Brunel, Herv

    2016-01-01

    Numerous events are involved in brain development, some of which are detected by neuroimaging. Major changes in brain morphology are depicted by brain imaging during the fetal period while changes in brain composition can be demonstrated in both pre- and postnatal periods. Although ultrasonography and computed tomography can show changes in brain morphology, these techniques are insensitive to myelination that is one of the most important events occurring during brain maturation. Magnetic resonance imaging (MRI) is therefore the method of choice to evaluate brain maturation. MRI also gives insight into the microstructure of brain tissue through diffusion-weighted imaging and diffusion tensor imaging. Metabolic changes are also part of brain maturation and are assessed by proton magnetic resonance spectroscopy. Understanding and knowledge of the different steps in brain development are required to be able to detect morphologic and structural changes on neuroimaging. Consequently alterations in normal development can be depicted. PMID:27430460

  10. Applications of Functional Protein Microarrays in Basic and Clinical Research

    PubMed Central

    Zhu, Heng; Qian, Jiang

    2013-01-01

    The protein microarray technology provides a versatile platform for characterization of hundreds of thousands of proteins in a highly parallel and high-throughput manner. It is viewed as a new tool that overcomes the limitation of DNA microarrays. On the basis of its application, protein microarrays fall into two major classes: analytical and functional protein microarrays. In addition, tissue or cell lysates can also be directly spotted on a slide to form the so-called “reverse-phase” protein microarray. In the last decade, applications of functional protein microarrays in particular have flourished in studying protein function and construction of networks and pathways. In this chapter, we will review the recent advancements in the protein microarray technology, followed by presenting a series of examples to illustrate the power and versatility of protein microarrays in both basic and clinical research. As a powerful technology platform, it would not be surprising if protein microarrays will become one of the leading technologies in proteomic and diagnostic fields in the next decade. PMID:22989767

  11. Refractive index change detection based on porous silicon microarray

    NASA Astrophysics Data System (ADS)

    Chen, Weirong; Jia, Zhenhong; Li, Peng; Lv, Guodong; Lv, Xiaoyi

    2016-05-01

    By combining photolithography with the electrochemical anodization method, a microarray device of porous silicon (PS) photonic crystal was fabricated on the crystalline silicon substrate. The optical properties of the microarray were analyzed with the transfer matrix method. The relationship between refractive index and reflectivity of each array element of the microarray at 633 nm was also studied, and the array surface reflectivity changes were observed through digital imaging. By means of the reflectivity measurement method, reflectivity changes below 10-3 can be observed based on PS microarray. The results of this study can be applied to the detection of biosensor arrays.

  12. Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.

    PubMed

    Arloth, Janine; Bader, Daniel M; Röh, Simone; Altmann, Andre

    2015-01-01

    Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. An accurate mapping of the array probes is essential to generate reliable biological findings. However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases. Here, we present the Re-Annotator, a re-annotation pipeline for microarray probe sequences. It is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays. The Re-Annotator uses a custom-built mRNA reference database to identify the positions of gene expression array probe sequences. We applied Re-Annotator to the Illumina Human-HT12 v4 microarray platform and found that about one quarter (25%) of the probes differed from the manufacturer's annotation. In further computational experiments on experimental gene expression data, we compared Re-Annotator to another probe re-annotation tool, ReMOAT, and found that Re-Annotator provided an improved re-annotation of microarray probes. A thorough re-annotation of probe information is crucial to any microarray analysis. The Re-Annotator pipeline is freely available at http://sourceforge.net/projects/reannotator along with re-annotated files for Illumina microarrays HumanHT-12 v3/v4 and MouseRef-8 v2.

  13. Chemiluminescence microarrays in analytical chemistry: a critical review.

    PubMed

    Seidel, Michael; Niessner, Reinhard

    2014-09-01

    Multi-analyte immunoassays on microarrays and on multiplex DNA microarrays have been described for quantitative analysis of small organic molecules (e.g., antibiotics, drugs of abuse, small molecule toxins), proteins (e.g., antibodies or protein toxins), and microorganisms, viruses, and eukaryotic cells. In analytical chemistry, multi-analyte detection by use of analytical microarrays has become an innovative research topic because of the possibility of generating several sets of quantitative data for different analyte classes in a short time. Chemiluminescence (CL) microarrays are powerful tools for rapid multiplex analysis of complex matrices. A wide range of applications for CL microarrays is described in the literature dealing with analytical microarrays. The motivation for this review is to summarize the current state of CL-based analytical microarrays. Combining analysis of different compound classes on CL microarrays reduces analysis time, cost of reagents, and use of laboratory space. Applications are discussed, with examples from food safety, water safety, environmental monitoring, diagnostics, forensics, toxicology, and biosecurity. The potential and limitations of research on multiplex analysis by use of CL microarrays are discussed in this review.

  14. Studying cellular processes and detecting disease with protein microarrays

    SciTech Connect

    Zangar, Richard C.; Varnum, Susan M.; Bollinger, Nikki

    2005-10-31

    Protein microarrays are a rapidly developing analytic tool with diverse applications in biomedical research. These applications include profiling of disease markers or autoimmune responses, understanding molecular pathways, protein modifications and protein activities. One factor that is driving this expanding usage is the wide variety of experimental formats that protein microarrays can take. In this review, we provide a short, conceptual overview of the different approaches for protein microarray. We then examine some of the most significant applications of these microarrays to date, with an emphasis on how global protein analyses can be used to facilitate biomedical research.

  15. The use of antigen microarrays in antibody profiling.

    PubMed

    Papp, Krisztián; Prechl, József

    2012-01-01

    Technological advances in the field of microarray production and analysis lead to the development of protein microarrays. Of these, antigen microarrays are one particular format that allows the study of antigen-antibody interactions in a miniaturized and highly multiplexed fashion. Here, we describe the parallel detection of antibodies with different specificities in human serum, a procedure also called antibody profiling. Autoantigens printed on microarray slides are reacted with test sera and the bound antibodies are identified by fluorescently labeled secondary reagents. Reactivity patterns generated this way characterize individuals and can help design novel diagnostic tools.

  16. Novel R pipeline for analyzing Biolog Phenotypic MicroArray data.

    PubMed

    Vehkala, Minna; Shubin, Mikhail; Connor, Thomas R; Thomson, Nicholas R; Corander, Jukka

    2015-01-01

    Data produced by Biolog Phenotype MicroArrays are longitudinal measurements of cells' respiration on distinct substrates. We introduce a three-step pipeline to analyze phenotypic microarray data with novel procedures for grouping, normalization and effect identification. Grouping and normalization are standard problems in the analysis of phenotype microarrays defined as categorizing bacterial responses into active and non-active, and removing systematic errors from the experimental data, respectively. We expand existing solutions by introducing an important assumption that active and non-active bacteria manifest completely different metabolism and thus should be treated separately. Effect identification, in turn, provides new insights into detecting differing respiration patterns between experimental conditions, e.g. between different combinations of strains and temperatures, as not only the main effects but also their interactions can be evaluated. In the effect identification, the multilevel data are effectively processed by a hierarchical model in the Bayesian framework. The pipeline is tested on a data set of 12 phenotypic plates with bacterium Yersinia enterocolitica. Our pipeline is implemented in R language on the top of opm R package and is freely available for research purposes. PMID:25786143

  17. Eye and head motion during head turns in spaceflight

    NASA Technical Reports Server (NTRS)

    Thornton, William E.; Uri, John J.; Moore, Thomas P.; Pool, Sam L.

    1988-01-01

    Eye-head motion was studied pre-, in- and postflight during single voluntary head turns. A transient increase in vestibulo-ocular reflex (VOR) gain occurred early in the flight, but later trended toward normal. This increased gain was produced by a relative increase in eye counterrotation velocity. Asymmetries in gain with right and left turns also occurred, caused by asymmetries in eye counterrotation velocities. These findings were remarkably similar to those from Soviet primate studies using gaze fixation targets, except the human study trended more rapidly toward normal. These findings differ substantially from those measuring VOR gain by head oscillation, in which no significant changes were found inflight. No visual disturbances were noted in either test condition or in normal activities. These head turn studies are the only ones to date documenting any functional change in VOR in weightlessness.

  18. An Eye on Trafficking Genes: Identification of Four Eye Color Mutations in Drosophila

    PubMed Central

    Grant, Paaqua; Maga, Tara; Loshakov, Anna; Singhal, Rishi; Wali, Aminah; Nwankwo, Jennifer; Baron, Kaitlin; Johnson, Diana

    2016-01-01

    Genes that code for proteins involved in organelle biogenesis and intracellular trafficking produce products that are critical in normal cell function . Conserved orthologs of these are present in most or all eukaryotes, including Drosophila melanogaster. Some of these genes were originally identified as eye color mutants with decreases in both types of pigments found in the fly eye. These criteria were used for identification of such genes, four eye color mutations that are not annotated in the genome sequence: chocolate, maroon, mahogany, and red Malpighian tubules were molecularly mapped and their genome sequences have been evaluated. Mapping was performed using deletion analysis and complementation tests. chocolate is an allele of the VhaAC39-1 gene, which is an ortholog of the Vacuolar H+ ATPase AC39 subunit 1. maroon corresponds to the Vps16A gene and its product is part of the HOPS complex, which participates in transport and organelle fusion. red Malpighian tubule is the CG12207 gene, which encodes a protein of unknown function that includes a LysM domain. mahogany is the CG13646 gene, which is predicted to be an amino acid transporter. The strategy of identifying eye color genes based on perturbations in quantities of both types of eye color pigments has proven useful in identifying proteins involved in trafficking and biogenesis of lysosome-related organelles. Mutants of these genes can form the basis of valuable in vivo models to understand these processes. PMID:27558665

  19. Nutrition and the eye.

    PubMed

    Congdon, N G; West, K P

    1999-12-01

    The topic "nutrition and the eye" cannot adequately be covered in a single review article; indeed, dozens of books and hundreds of articles have been written on the subject. This review concentrates on three areas in which specific nutrients are known or theorized to have a major impact on vision and the visual system: vitamin A deficiency; antioxidants and their proposed role in the prevention of age-related cataract and macular degeneration; and nutritional optic neuropathies, including those of the recent Cuban epidemic. In addition, this article touches on nutritional treatments that have been suggested for several less common eye diseases and, finally, considers several less prevalent conditions in which deficiency of or excess exposure to a particular nutrient has been associated with ocular pathology. PMID:10662253

  20. [STD in the eye].

    PubMed

    Usui, Masahiko; Minoda, Hirosi

    2009-01-01

    In this paper, we review sexually transmitted diseases (STD) involving the eye. Recently conjunctivitis due to Chlamydia trachomatis in children and adults is increasing, and that of Neisseria gonorrhoeae resistant to multiple antibiotics has attracted special attention in our country. Syphilis has many ocular manifestations such as keratitis, iridocyclitis, retinochorioiditis, and neuritis, etc. Ocular complications related to HIV infection, including HIV retinopathy, cytomegalovirus retinitis, zoster ophthalmics, and Kaposi s sarcoma in conjunctiva are increasing in Japan. Phthirus pubis infection of the eye lid, and human T-cell lymphotropic virus type 1 (HTLV-1)-associated uveitis are occasionally reported. Furthermore conjunctival tumor associated with human papilloma virus (HPV) infection, acute retinal necrosis(ARN) due to herpes simplex virus type 2 (HSV-2), as well as hepatitis B virus (HVB) and hepatitis C virus (HVC) retinopathy are also mentioned in this review. PMID:19177759

  1. Eye movements during transcendental meditation.

    PubMed

    Tebēcis, A K

    1976-01-01

    Characteristic changes in eye movements occurred during meditation with closed eyes in a proportion of subjects experienced in TM. The most common changes were an increase in slow, large-amplitude, 'rolling' eye movements and a concomitant decrease in rapid, low-amplitude, 'jerky' eye movements. Much variation occurred between individuals, however, some subjects showing no differences between TM and non-meditation. Any changes that occurred were not necessarily constant for the whole recording period nor consistent between sessions. The physiological effects of TM are far more variable than previously publicized. In general, the main changes in eye movements during TM are similar to those during passive hypnosis.

  2. [Conservative treatment of dry eye].

    PubMed

    Hefner, J; Reinshagen, H

    2014-11-01

    The use of topic anti-inflammatory drugs has become very important in the treatment of dry eye disease. Besides the basic therapy including tear replacement, use of serum eye drops and mucolytic eye drops, the topical application of corticosteroids and cyclosporin A is more commonly used in moderate to severe forms of dry eye disease. The consistent treatment of Meibomian gland dysfunction as a frequent reason for evaporative dry eye is also of particular importance. Understanding the chronicity of the disease and long-term compliance are the essential for successful therapy of this widespread disease.

  3. [Conservative treatment of dry eye].

    PubMed

    Hefner, J; Reinshagen, H

    2014-11-01

    The use of topic anti-inflammatory drugs has become very important in the treatment of dry eye disease. Besides the basic therapy including tear replacement, use of serum eye drops and mucolytic eye drops, the topical application of corticosteroids and cyclosporin A is more commonly used in moderate to severe forms of dry eye disease. The consistent treatment of Meibomian gland dysfunction as a frequent reason for evaporative dry eye is also of particular importance. Understanding the chronicity of the disease and long-term compliance are the essential for successful therapy of this widespread disease. PMID:25275793

  4. Dry eye syndrome.

    PubMed

    Javadi, Mohammad-Ali; Feizi, Sepehr

    2011-07-01

    Our understanding of keratoconjunctivitis sicca (KCS), also known as dry eye syndrome, has been changed over recent years. Until lately, the condition was thought to be merely due to aqueous tear insufficiency. Today, it is understood that KCS is a multifactorial disorder due to inflammation of the ocular surface and lacrimal gland, neurotrophic deficiency and meibomian gland dysfunction. This change in paradigm has led to the development of new and more effective medications.

  5. Assessment of Corneal Epithelial Thickness in Dry Eye Patients

    PubMed Central

    Cui, Xinhan; Hong, Jiaxu; Wang, Fei; Deng, Sophie X.; Yang, Yujing; Zhu, Xiaoyu; Wu, Dan; Zhao, Yujin; Xu, Jianjiang

    2014-01-01

    Purpose To investigate the features of corneal epithelial thickness topography with Fourier-domain optical coherence tomography (OCT) in dry eye patients. Methods In this cross-sectional study, 100 symptomatic dry eye patients and 35 normal subjects were enrolled. All participants answered the ocular surface disease index questionnaire and were subjected to OCT, corneal fluorescein staining, tear breakup time, Schirmer 1 test without anesthetic (S1t), and meibomian morphology. Several epithelium statistics for each eye, including central, superior, inferior, minimum, maximum, minimum – maximum, and map standard deviation, were averaged. Correlations of epithelial thickness with the symptoms of dry eye were calculated. Results The mean (±SD) central, superior, and inferior corneal epithelial thickness was 53.57 (±3.31) μm, 52.00 (±3.39) μm, and 53.03 (±3.67) μm in normal eyes and 52.71 (±2.83) μm, 50.58 (±3.44) μm, and 52.53 (±3.36) μm in dry eyes, respectively. The superior corneal epithelium was thinner in dry eye patients compared with normal subjects (p=0.037),whereas central and inferior epithelium were not statistically different. In the dry eye group, patients with higher severity grades had thinner superior (p = 0.017) and minimum (p < 0.001) epithelial thickness, more wide range (p = 0.032), and greater deviation (p = 0.003). The average central epithelial thickness had no correlation with tear breakup time, S1t, or the severity of meibomian glands, whereas average superior epithelial thickness positively correlated with S1t (r = 0.238, p = 0.017). Conclusions Fourier-domain OCT demonstrated that the thickness map of the dry eye corneal epithelium was thinner than normal eyes in the superior region. In more severe dry eye disease patients, the superior and minimum epithelium was much thinner, with a greater range of map standard deviation. PMID:25279779

  6. Segmentation of prostate cancer tissue microarray images

    NASA Astrophysics Data System (ADS)

    Cline, Harvey E.; Can, Ali; Padfield, Dirk

    2006-02-01

    Prostate cancer is diagnosed by histopathology interpretation of hematoxylin and eosin (H and E)-stained tissue sections. Gland and nuclei distributions vary with the disease grade. The morphological features vary with the advance of cancer where the epithelial regions grow into the stroma. An efficient pathology slide image analysis method involved using a tissue microarray with known disease stages. Digital 24-bit RGB images were acquired for each tissue element on the slide with both 10X and 40X objectives. Initial segmentation at low magnification was accomplished using prior spectral characteristics from a training tissue set composed of four tissue clusters; namely, glands, epithelia, stroma and nuclei. The segmentation method was automated by using the training RGB values as an initial guess and iterating the averaging process 10 times to find the four cluster centers. Labels were assigned to the nearest cluster center in red-blue spectral feature space. An automatic threshold algorithm separated the glands from the tissue. A visual pseudo color representation of 60 segmented tissue microarray image was generated where white, pink, red, blue colors represent glands, epithelia, stroma and nuclei, respectively. The higher magnification images provided refined nuclei morphology. The nuclei were detected with a RGB color space principle component analysis that resulted in a grey scale image. The shape metrics such as compactness, elongation, minimum and maximum diameters were calculated based on the eigenvalues of the best-fitting ellipses to the nuclei.

  7. Inferring genetic networks from microarray data.

    SciTech Connect

    May, Elebeoba Eni; Davidson, George S.; Martin, Shawn Bryan; Werner-Washburne, Margaret C.; Faulon, Jean-Loup Michel

    2004-06-01

    In theory, it should be possible to infer realistic genetic networks from time series microarray data. In practice, however, network discovery has proved problematic. The three major challenges are: (1) inferring the network; (2) estimating the stability of the inferred network; and (3) making the network visually accessible to the user. Here we describe a method, tested on publicly available time series microarray data, which addresses these concerns. The inference of genetic networks from genome-wide experimental data is an important biological problem which has received much attention. Approaches to this problem have typically included application of clustering algorithms [6]; the use of Boolean networks [12, 1, 10]; the use of Bayesian networks [8, 11]; and the use of continuous models [21, 14, 19]. Overviews of the problem and general approaches to network inference can be found in [4, 3]. Our approach to network inference is similar to earlier methods in that we use both clustering and Boolean network inference. However, we have attempted to extend the process to better serve the end-user, the biologist. In particular, we have incorporated a system to assess the reliability of our network, and we have developed tools which allow interactive visualization of the proposed network.

  8. Intensity-based segmentation of microarray images.

    PubMed

    Nagarajan, Radhakrishnan

    2003-07-01

    The underlying principle in microarray image analysis is that the spot intensity is a measure of the gene expression. This implicitly assumes the gene expression of a spot to be governed entirely by the distribution of the pixel intensities. Thus, a segmentation technique based on the distribution of the pixel intensities is appropriate for the current problem. In this paper, clustering-based segmentation is described to extract the target intensity of the spots. The approximate boundaries of the spots in the microarray are determined by manual adjustment of rectilinear grids. The distribution of the pixel intensity in a grid containing a spot is assumed to be the superposition of the foreground and the local background. The k-means clustering technique and the partitioning around medoids (PAM) were used to generate a binary partition of the pixel intensity distribution. The median (k-means) and the medoid (PAM) of the cluster members are chosen as the cluster representatives. The effectiveness of the clustering-based segmentation techniques was tested on publicly available arrays generated in a lipid metabolism experiment (Callow et al., 2000). The results are compared against those obtained using the region-growing approach (SPOT) (Yang et al., 2001). The effect of additive white Gaussian noise is also investigated. PMID:12906242

  9. Microarray analysis of the developing cortex.

    PubMed

    Semeralul, Mawahib O; Boutros, Paul C; Likhodi, Olga; Okey, Allan B; Van Tol, Hubert H M; Wong, Albert H C

    2006-12-01

    Abnormal development of the prefrontal cortex (PFC) is associated with a number of neuropsychiatric disorders that have an onset in childhood or adolescence. Although the basic laminar structure of the PFC is established in utero, extensive remodeling continues into adolescence. To map the overall pattern of changes in cortical gene transcripts during postnatal development, we made serial measurements of mRNA levels in mouse PFC using oligonucleotide microarrays. We observed changes in mRNA transcripts consistent with known postnatal morphological and biochemical events. Overall, most transcripts that changed significantly showed a progressive decrease in abundance after birth, with the majority of change between postnatal weeks 2 and 4. Genes with cell proliferative, cytoskeletal, extracellular matrix, plasma membrane lipid/transport, protein folding, and regulatory functions had decreases in mRNA levels. Quantitative PCR verified the microarray results for six selected genes: DNA methyltransferase 3A (Dnmt3a), procollagen, type III, alpha 1 (Col3a1), solute carrier family 16 (monocarboxylic acid transporters), member 1 (Slc16a1), MARCKS-like 1 (Marcksl1), nidogen 1 (Nid1) and 3-hydroxybutyrate dehydrogenase (heart, mitochondrial) (Bdh).

  10. Enzyme Microarrays Assembled by Acoustic Dispensing Technology

    PubMed Central

    Wong, E. Y.; Diamond, S. L.

    2008-01-01

    Miniaturizing bioassays to the nanoliter scale for high-throughput screening reduces the consumption of reagents that are expensive or difficult to handle. Utilizing acoustic dispensing technology, nanodroplets containing 10 µM ATP (3 µCi/µL 32P) and reaction buffer in 10% glycerol were positionally dispensed to the surface of glass slides to form 40 nL compartments (100 droplets/slide) for Pim1 (Proviral integration site 1) kinase reactions. The reactions were activated by dispensing 4 nL of various levels of a pyridocarbazolo-cyclopentadienyl ruthenium-complex Pim1 inhibitor, followed by dispensing 4 nL of a Pim1 kinase and peptide substrate solution to achieve final concentrations of 150 nM enzyme and 10 µM substrate. The microarray was incubated at 30°C (97% Rh) for 1.5 hr. The spots were then blotted to phosphocellulose membranes to capture phosphorylated substrate. Using phosphor imaging to quantify the washed membranes, the assay showed that, for doses of inhibitor from 0.75 µM to 3 µM, Pim1 was increasingly inhibited. Signal-to-background ratios were as high as 165 and average coefficients of variation (CVs) for the assay were ~20%. CVs for dispensing typical working buffers were under 5%. Thus, microarrays assembled by acoustic dispensing are promising as cost-effective tools that can be used in protein assay development. PMID:18616925

  11. Laser direct writing of biomolecule microarrays

    NASA Astrophysics Data System (ADS)

    Serra, P.; Fernández-Pradas, J. M.; Berthet, F. X.; Colina, M.; Elvira, J.; Morenza, J. L.

    Protein-based biosensors are highly efficient tools for protein detection and identification. The production of these devices requires the manipulation of tiny amounts of protein solutions in conditions preserving their biological properties. In this work, laser induced forward transfer (LIFT) was used for spotting an array of a purified bacterial antigen in order to check the viability of this technique for the production of protein microarrays. A pulsed Nd:YAG laser beam (355 nm wavelength, 10 ns pulse duration) was used to transfer droplets of a solution containing the Treponema pallidum 17 kDa protein antigen on a glass slide. Optical microscopy showed that a regular array of micrometric droplets could be precisely and uniformly spotted onto a solid substrate. Subsequently, it was proved that LIFT deposition of a T. pallidum 17 kDa antigen onto nylon-coated glass slides preserves its antigenic reactivity and diagnostic properties. These results support that LIFT is suitable for the production of protein microarrays and pave the way for future diagnostics applications.

  12. Christoph Scheiner's eye studies.

    PubMed

    Daxecker, F

    1992-01-01

    Christoph Scheiner was born in 1573 or 1575. In 1595 he entered into the Order of the Jesuits; he died in 1650. In 1619 his book Oculus, dealing with the optics of the eye, appeared in Innsbruck. The invention of the telescope was of utmost importance for progress in astronomical and physical research. Scheiner himself built telescopes and discovered the sunspots. As a result, an unpleasant priority dispute with Galilei ensued. From 1624 onwards, Scheiner was in Rome, where his main work Rosa Ursina was published in 1630. A part of this book deals with the physiological optics of the eye as well. Some of his discoveries and experiments are taken from these two books: determination of the radius of curvature of the cornea, discovery of the nasal exit of the optic nerve, increase in the radius of curvature of the lens in case of accommodation, Scheiner's procedure (double images with ametropia), refractive indices of various parts of the eye, Scheiner's experiment. Without any doubt, Christoph Scheiner belongs to the foremost scientists of the first half of the 17th century. PMID:1473465

  13. Christoph Scheiner's eye studies.

    PubMed

    Daxecker, F

    1992-01-01

    Christoph Scheiner was born in 1573 or 1575. In 1595 he entered into the Order of the Jesuits; he died in 1650. In 1619 his book Oculus, dealing with the optics of the eye, appeared in Innsbruck. The invention of the telescope was of utmost importance for progress in astronomical and physical research. Scheiner himself built telescopes and discovered the sunspots. As a result, an unpleasant priority dispute with Galilei ensued. From 1624 onwards, Scheiner was in Rome, where his main work Rosa Ursina was published in 1630. A part of this book deals with the physiological optics of the eye as well. Some of his discoveries and experiments are taken from these two books: determination of the radius of curvature of the cornea, discovery of the nasal exit of the optic nerve, increase in the radius of curvature of the lens in case of accommodation, Scheiner's procedure (double images with ametropia), refractive indices of various parts of the eye, Scheiner's experiment. Without any doubt, Christoph Scheiner belongs to the foremost scientists of the first half of the 17th century.

  14. Comprehensive eye evaluation algorithm

    NASA Astrophysics Data System (ADS)

    Agurto, C.; Nemeth, S.; Zamora, G.; Vahtel, M.; Soliz, P.; Barriga, S.

    2016-03-01

    In recent years, several research groups have developed automatic algorithms to detect diabetic retinopathy (DR) in individuals with diabetes (DM), using digital retinal images. Studies have indicated that diabetics have 1.5 times the annual risk of developing primary open angle glaucoma (POAG) as do people without DM. Moreover, DM patients have 1.8 times the risk for age-related macular degeneration (AMD). Although numerous investigators are developing automatic DR detection algorithms, there have been few successful efforts to create an automatic algorithm that can detect other ocular diseases, such as POAG and AMD. Consequently, our aim in the current study was to develop a comprehensive eye evaluation algorithm that not only detects DR in retinal images, but also automatically identifies glaucoma suspects and AMD by integrating other personal medical information with the retinal features. The proposed system is fully automatic and provides the likelihood of each of the three eye disease. The system was evaluated in two datasets of 104 and 88 diabetic cases. For each eye, we used two non-mydriatic digital color fundus photographs (macula and optic disc centered) and, when available, information about age, duration of diabetes, cataracts, hypertension, gender, and laboratory data. Our results show that the combination of multimodal features can increase the AUC by up to 5%, 7%, and 8% in the detection of AMD, DR, and glaucoma respectively. Marked improvement was achieved when laboratory results were combined with retinal image features.

  15. Pediatric Eye Screening Instrumentation

    NASA Astrophysics Data System (ADS)

    Chen, Ying-Ling; Lewis, J. W. L.

    2001-11-01

    Computational evaluations are presented for binocular eye screening using the off-axis digital retinascope. The retinascope, such as the iScreen digital screening system, has been employed to perform pediatric binocular screening using a flash lamp and single-shot camera recording. The digital images are transferred electronically to a reading center for analysis. The method has been shown to detect refractive error, amblyopia, anisocoria, and ptosis. This computational work improves the performance of the system and forms the basis for automated data analysis. For this purpose, variouis published eye models are evaluated with simulated retinascope images. Two to ten million rays are traced in each image calculation. The poster will present the simulation results for a range of eye conditions of refractive error of -20 to +20 diopters with 0.5- to-1 diopter resolution, pupil size of 3 to 8 mm diameter (1-mm increment), and staring angle of 2 to 12 degree (2-degree increment). The variation of the results with the system conditions such as the off-axis distance of light source and the shutter size of camera are also evaluated. The quantitative analysis for each eye’s and system’s condition is then performed to obtain parameters for automatic reading. The summary of the system performance is given and performance-enhancement design modifications are presented.

  16. Schizophrenia and the eye

    PubMed Central

    Silverstein, Steven M.; Rosen, Richard

    2015-01-01

    Although visual processing impairments are common in schizophrenia, it is not clear to what extent these originate in the eye vs. the brain. This review highlights potential contributions, from the retina and other structures of the eye, tovisual processing impairments in schizophrenia and high-risk states. A second goal is to evaluate the status of retinal abnormalities as biomarkers for schizophrenia. The review was motivated by known retinal changes in other disorders (e.g., Parkinson's disease, multiple sclerosis), and their relationships to perceptual and cognitive impairments, and disease progression therein. The evidence reviewed suggests two major conclusions. One is that there are multiple structural and functional disturbances of the eye in schizophrenia, all of which could be factors in the visual disturbances of patients. These include retinal venule widening, retinal nerve fiber layer thinning, dopaminergic abnormalities, abnormal ouput of retinal cells as measured by electroretinography (ERG), maculopathies and retinopathies, cataracts, poor acuity, and strabismus. Some of these are likely to be illness-related, whereas others may be due to medication or comorbid conditions. The second conclusion is that certain retinal findings can serve as biomarkers of neural pathology, and disease progression, in schizophrenia. The strongest evidence for this to date involves findings of widened retinal venules, thinning of the retinal nerve fiber layer, and abnormal ERG amplitudes. These data suggest that a greater understanding of the contribution of retinal and other ocular pathology to the visual and cognitive disturbances of schizophrenia is warranted, and that retinal changes have untapped clinical utility. PMID:26345525

  17. Eye preferences in captive chimpanzees.

    PubMed

    Braccini, Stephanie N; Lambeth, Susan P; Schapiro, Steven J; Fitch, W Tecumseh

    2012-09-01

    Over the last century, the issue of brain lateralization in primates has been extensively investigated and debated, yet no previous study has reported eye preference in great apes. This study examined eye preference in 45 captive chimpanzees (Pan troglodytes) in response to various stimuli. Eye preference was assessed when animals looked through a hole that only accommodated one eye at an empty box, a mirror, a picture of a dog, a rubber snake, food biscuits, bananas, a rubber duck, and a video camera. Main effects of stimulus type were found for direction of eye preference, number of looks, and looking duration, but not for strength of eye preference. A left-eye bias was found for viewing the rubber snake and a right-eye bias was found for viewing the bananas, supporting theories that emotional valence may affect lateralized behaviors. In addition, a significant shift in eye preference took place from the initial look to subsequent looks when viewing the snake. These results are not consistent with previous reports of human eye preference and may reflect lateralization differences for emotional processing. No relationship between eye preference and previously recorded hand preference was found. PMID:22733385

  18. Pioneers of eye movement research.

    PubMed

    Wade, Nicholas J

    2010-01-01

    Recent advances in the technology affording eye movement recordings carry the risk of neglecting past achievements. Without the assistance of this modern armoury, great strides were made in describing the ways the eyes move. For Aristotle the fundamental features of eye movements were binocular, and he described the combined functions of the eyes. This was later given support using simple procedures like placing a finger over the eyelid of the closed eye and culminated in Hering's law of equal innervation. However, the overriding concern in the 19th century was with eye position rather than eye movements. Appreciating discontinuities of eye movements arose from studies of vertigo. The characteristics of nystagmus were recorded before those of saccades and fixations. Eye movements during reading were described by Hering and by Lamare in 1879; both used similar techniques of listening to sounds made during contractions of the extraocular muscles. Photographic records of eye movements during reading were made by Dodge early in the 20th century, and this stimulated research using a wider array of patterns. In the mid-20th century attention shifted to the stability of the eyes during fixation, with the emphasis on involuntary movements. The contributions of pioneers from Aristotle to Yarbus are outlined.

  19. Pioneers of eye movement research

    PubMed Central

    Wade, Nicholas J

    2010-01-01

    Recent advances in the technology affording eye movement recordings carry the risk of neglecting past achievements. Without the assistance of this modern armoury, great strides were made in describing the ways the eyes move. For Aristotle the fundamental features of eye movements were binocular, and he described the combined functions of the eyes. This was later given support using simple procedures like placing a finger over the eyelid of the closed eye and culminated in Hering's law of equal innervation. However, the overriding concern in the 19th century was with eye position rather than eye movements. Appreciating discontinuities of eye movements arose from studies of vertigo. The characteristics of nystagmus were recorded before those of saccades and fixations. Eye movements during reading were described by Hering and by Lamare in 1879; both used similar techniques of listening to sounds made during contractions of the extraocular muscles. Photographic records of eye movements during reading were made by Dodge early in the 20th century, and this stimulated research using a wider array of patterns. In the mid-20th century attention shifted to the stability of the eyes during fixation, with the emphasis on involuntary movements. The contributions of pioneers from Aristotle to Yarbus are outlined. PMID:23396982

  20. Label-free detection repeatability of protein microarrays by oblique-incidence reflectivity difference method

    NASA Astrophysics Data System (ADS)

    Dai, Jun; Li, Lin; Wang, JingYi; He, LiPing; Lu, HuiBin; Ruan, KangCheng; Jin, KuiJuan; Yang, GuoZhen

    2012-12-01

    We examine the repeatabilities of oblique-incidence reflectivity difference (OIRD) method for label-free detecting biological molecular interaction using protein microarrays. The experimental results show that the repeatabilities are the same in a given microarray or microarray-microarray and are consistent, indicating that OIRD is a promising label-free detection technique for biological microarrays.

  1. Dry eye, blepharitis and chronic eye irritation: divide and conquer.

    PubMed

    Gilbard, J P

    1999-01-01

    Dry eye and posterior blepharitis are the two most common causes for chronic eye irritation. Dry eye is caused by loss of water from the tear film resulting from either decreased tear production or increased tear film evaporation. The resultant increase in tear film osmolarity causes the changes on the eye surface responsible for the symptoms of dry eye. Posterior blepharitis causes eye irritation from inflammation, and leads to the development of meibomian gland dysfunction. The patient history is a powerful tool in narrowing the differential diagnosis of chronic eye irritation or even establishing the diagnosis. The exam adds power to the history, and sorts out the mechanisms causing dry eye symptoms. The primary goal of dry eye treatment is to lower elevated tear film osmolarity. This can be achieved with TheraTears treatment, either with or without punctal plugs. The primary goal of meibomitis treatment is to reduce inflammation. This can be achieved by hot compresses and lid massage and, when necessary, systemic treatment with low dose doxycycline. By determining the cause or causes of chronic eye irritation, effective treatments can be employed.

  2. Changes of vertical eye movements of goldfish for different otolith stimulation by linear acceleration

    NASA Astrophysics Data System (ADS)

    Takabayashi, A.; Ohmura-Iwasaki, T.; Mori, S.

    2003-10-01

    Eye movements serves to hold the gaze steady or to shift the gaze to an object of interest. On Earth, signals from otoliths can be interpreted either as linear motion or as tilt with respect to gravity. In microgravity, static tilt will no longer give rise to changes in otolith activity. However, linear acceleration as well as angular acceleration stimulate the otolith organ. Therefore, during adaptation to microgravity, otolith-mediated response such as eye movements alter. In this study, we analyzed the eye movements of goldfish during linear acceleration. The eye movements during rectangular linear acceleration along the different body axis were video-recorded. The vertical eye rotations were analyzed frame by frame. In normal fish, leftward lateral acceleration induced downward eye rotation in the left eye and upward eye rotation in the right eye. Acceleration from caudal to rostral evoked downward eye rotation in both eyes. When the direction of acceleration was shifted 15 degrees left, the responses in the left eye disappeared. These results suggested that otolith organs in each side were stimulated differently.

  3. Changes of vertical eye movements of goldfish for different otolith stimulation by linear acceleration

    NASA Astrophysics Data System (ADS)

    Takabayashi, A.; Ohmura, T.; Mori, S.

    Eye movements serve to hold the gaze steady or to shift the gaze to an object of interest. On Earth, signals from otoliths can be interpreted either as linear motion or as tilt with respect to gravity. In microgravity, static tilt will no longer give rise to change in otolith activity. However, linear acceleration as well as angular acceleration stimulate otolith organ. Therefore, during adaptation to microgravity, otolith-mediated response such as eye movements would alter. In this study, we analyzed the eye movements of goldfish during linear acceleration. The eye movements during rectangular linear acceleration along the different body axis were video-recorded. The vertical eye rotations were analyzed frame by frame. In normal fish, acceleration from caudal to rostral evoked downward eye rotation in both eyes. Leftward lateral acceleration induced downward eye rotation in left eye and upward eye rotation in right eye. When the direction of acceleration was shifted to left about 15 degrees, the responses in left eye was disappeared. These results suggested that otolith organs in each side were stimulated in different way.

  4. Autofluorescence spectroscopy for early diagnosis of cancer eye

    NASA Astrophysics Data System (ADS)

    Majumder, Shovan K.; Ghosh, Nirmalya; Rathod, Sopan M.; Gupta, Pradeep K.

    2007-02-01

    We report an in-vitro autofluorescence spectroscopic study of cow eye tissue to explore the applicability of the approach in discriminating early stage "cancer eye" from normal squamous eye tissues. Significant differences were observed in the autofluorescence signatures between the "cancer eye" and normal eye tissues. The spectral differences were quantified by employing a probability-based diagnostic algorithm developed based on recently formulated theory of Relevance Vector Machine (RVM), a Bayesian machine-learning framework of statistical pattern recognition. The algorithm provided sensitivity and specificity values of 97 +/- 2% towards cancer for the training set data based on leave-one-out cross validation and a sensitivity of 97 +/- 2% and a specificity of 99 +/- 1% towards cancer for the independent validation set data. These results suggest that autofluorescence spectroscopy might prove to be a quantitative in-vivo diagnostic modality for early and accurate diagnosis of "cancer eye" in veterinary clinical setting, which would help improve ranch management from both economic and animal care standpoint.

  5. Eye Movements of Patients with Tunnel Vision while Walking

    PubMed Central

    Vargas-Martín, Fernando; Peli, Eli

    2006-01-01

    Purpose To determine how severe peripheral field loss (PFL) affects the dispersion of eye movements relative to the head, while walking in real environments. This information should help to better define the visual field and clearance requirements for head-mounted mobility visual aids. Methods Eye positions relative to the head were recorded in five retinitis pigmentosa patients with less than 15° of visual field and three normally-sighted people, each walking in varied environments for more than 30 minutes. The eye position recorder was made portable by modifying a head-mounted ISCAN system. Custom data processing was implemented to reject unreliable data. Sample standard deviations of eye position (dispersion) were compared across subject groups and environments. Results PFL patients exhibited narrower horizontal eye position dispersions than normally-sighted subjects (9.4° vs. 14.2°, p < 0.0001) and PFL patients’ vertical dispersions were smaller when walking indoors than outdoors (8.2° vs. 10.3°, p = 0.048). Conclusions When walking, the PFL patients did not increase their scanning eye movements to compensate for missing peripheral vision information. Their horizontal scanning was actually reduced, possibly because saccadic amplitude is limited by a lack of peripheral stimulation. The results suggest that a field-of-view as wide as 40° may be needed for closed (immersive) head-mounted mobility aids, while a much narrower display, perhaps as narrow as 20°, might be sufficient with an open design. PMID:17122116

  6. Experimental Approaches to Microarray Analysis of Tumor Samples

    ERIC Educational Resources Information Center

    Furge, Laura Lowe; Winter, Michael B.; Meyers, Jacob I.; Furge, Kyle A.

    2008-01-01

    Comprehensive measurement of gene expression using high-density nucleic acid arrays (i.e. microarrays) has become an important tool for investigating the molecular differences in clinical and research samples. Consequently, inclusion of discussion in biochemistry, molecular biology, or other appropriate courses of microarray technologies has…

  7. Demonstrating a Multi-drug Resistant Mycobacterium tuberculosis Amplification Microarray

    PubMed Central

    Linger, Yvonne; Kukhtin, Alexander; Golova, Julia; Perov, Alexander; Qu, Peter; Knickerbocker, Christopher; Cooney, Christopher G.; Chandler, Darrell P.

    2014-01-01

    Simplifying microarray workflow is a necessary first step for creating MDR-TB microarray-based diagnostics that can be routinely used in lower-resource environments. An amplification microarray combines asymmetric PCR amplification, target size selection, target labeling, and microarray hybridization within a single solution and into a single microfluidic chamber. A batch processing method is demonstrated with a 9-plex asymmetric master mix and low-density gel element microarray for genotyping multi-drug resistant Mycobacterium tuberculosis (MDR-TB). The protocol described here can be completed in 6 hr and provide correct genotyping with at least 1,000 cell equivalents of genomic DNA. Incorporating on-chip wash steps is feasible, which will result in an entirely closed amplicon method and system. The extent of multiplexing with an amplification microarray is ultimately constrained by the number of primer pairs that can be combined into a single master mix and still achieve desired sensitivity and specificity performance metrics, rather than the number of probes that are immobilized on the array. Likewise, the total analysis time can be shortened or lengthened depending on the specific intended use, research question, and desired limits of detection. Nevertheless, the general approach significantly streamlines microarray workflow for the end user by reducing the number of manually intensive and time-consuming processing steps, and provides a simplified biochemical and microfluidic path for translating microarray-based diagnostics into routine clinical practice. PMID:24796567

  8. Demonstrating a multi-drug resistant Mycobacterium tuberculosis amplification microarray.

    PubMed

    Linger, Yvonne; Kukhtin, Alexander; Golova, Julia; Perov, Alexander; Qu, Peter; Knickerbocker, Christopher; Cooney, Christopher G; Chandler, Darrell P

    2014-04-25

    Simplifying microarray workflow is a necessary first step for creating MDR-TB microarray-based diagnostics that can be routinely used in lower-resource environments. An amplification microarray combines asymmetric PCR amplification, target size selection, target labeling, and microarray hybridization within a single solution and into a single microfluidic chamber. A batch processing method is demonstrated with a 9-plex asymmetric master mix and low-density gel element microarray for genotyping multi-drug resistant Mycobacterium tuberculosis (MDR-TB). The protocol described here can be completed in 6 hr and provide correct genotyping with at least 1,000 cell equivalents of genomic DNA. Incorporating on-chip wash steps is feasible, which will result in an entirely closed amplicon method and system. The extent of multiplexing with an amplification microarray is ultimately constrained by the number of primer pairs that can be combined into a single master mix and still achieve desired sensitivity and specificity performance metrics, rather than the number of probes that are immobilized on the array. Likewise, the total analysis time can be shortened or lengthened depending on the specific intended use, research question, and desired limits of detection. Nevertheless, the general approach significantly streamlines microarray workflow for the end user by reducing the number of manually intensive and time-consuming processing steps, and provides a simplified biochemical and microfluidic path for translating microarray-based diagnostics into routine clinical practice.

  9. Flap Thickness in Eyes with Ectasia after LASIK

    PubMed Central

    Randleman, J. Bradley; Hebson, Carolyn B.; Larson, Paul M.

    2015-01-01

    Purpose To measure central flap thickness in eyes with ectasia after LASIK and to compare these values with estimated anticipated flap thickness based on average published values for each device used for flap creation. Setting Emory Vision at Emory University, Atlanta GA, USA Methods Confocal microscopic analysis using the Confoscan 3 (Nidek technologies) to measure central flap thickness in eyes with ectasia after LASIK, and evaluation of pre-LASIK records, including basic patient demographics, preoperative corneal topographies, estimated anticipated flap thickness based on published average thickness values, and residual stromal bed thickness (RSB) calculations using both measured and estimated flap thicknesses. Results Fifty eyes from 29 patients were evaluated. Average measured flap thickness was (138 ± 26 μ, range 90 to 220 μ). There were no significant differences between measured and estimated flap thicknesses (138 vs. 135 μ, p = 0.5) or RSB (329 vs. 332 μ, p = 0.7), nor were there any differences in flap thickness between eyes with normal or abnormal corneal topographies. Only one eye had a measured flap resulting in unintended RSB < 250 microns; this occurred in an eye with abnormal topography. Conclusions Measured central flap thickness was not thicker than estimated for the vast majority of eyes developing ectasia after LASIK. Thus, excessively thick flaps do not appear to be a major contributing factor to the pathogenesis of ectasia after LASIK. PMID:22424807

  10. In vivo laser-induced breakdown in the rabbit eye

    NASA Astrophysics Data System (ADS)

    Cain, Clarence P.; DiCarlo, Cheryl D.; Kennedy, Paul K.; Noojin, Gary D.; Amnotte, Rodney E.; Roach, William P.

    1995-05-01

    Threshold measurements for femtosecond laser pulsewidths have been made for retinal minimum visible lesions (MVLs) in Dutch Belted rabbit and rhesus monkey eyes. Laser-induced breakdown (LIB) thresholds in biological materials including vitreous, normal saline, tap water, and ultrapure water have been measured and reported using an artificial eye. We have recorded on video the first LIB causing bubble formation in any eye in vivo using albino rabbit eyes (New Zealand white) with 120- femtosecond (fs) pulses and pulse energies as low as 5 microjoules ((mu) J). These bubbles were clearly formed anterior to the retina within the vitreous humor and, with 60 (mu) J of energy, they lasted for several seconds before disappearing and leaving no apparent damage to the retina. We believe this to be true LIB because of the lack of pigmentation or melanin granules within the albino rabbit eye (thus no absorptive elements) and because of the extremely high peak powers within the 5-(mu) J, 120-fs laser pulse. These high peak powers produce self-focusing of the pulse within the vitreous. The bubble formation at the breakdown site acts as a limiting mechanism for energy transmission and may explain why high-energy femotsecond pulses at energies up to 100 (mu) J sometimes do not cause severe damage in the pigmented rabbit eye. This fact may also explain why it is so difficult to produce hemorrhagic lesions in either the rabbit or primate eye with 100-fs laser pulses.

  11. Identification of novel pancreatic adenocarcinoma cell-surface targets by gene expression profiling and tissue microarray.

    PubMed

    Morse, David L; Balagurunathan, Yoga; Hostetter, Galen; Trissal, Maria; Tafreshi, Narges K; Burke, Nancy; Lloyd, Mark; Enkemann, Steven; Coppola, Domenico; Hruby, Victor J; Gillies, Robert J; Han, Haiyong

    2010-09-01

    Pancreatic cancer has a high mortality rate, which is generally related to the initial diagnosis coming at late stage disease combined with a lack of effective treatment options. Novel agents that selectively detect pancreatic cancer have potential for use in the molecular imaging of cancer, allowing for non-invasive determination of tumor therapeutic response and molecular characterization of the disease. Such agents may also be used for the targeted delivery of therapy to tumor cells while decreasing systemic effects. Using complementary assays of mRNA expression profiling to determine elevated expression in pancreatic cancer tissues relative to normal pancreas tissues, and validation of protein expression by immunohistochemistry on tissue microarray, we have identified cell-surface targets with potential for imaging and therapeutic agent development. Expression profiles of 2177 cell-surface genes for 28 pancreatic tumor specimens and 4 normal pancreas tissue samples were evaluated. Expression in normal tissues was evaluated using array data from 103 samples representing 28 organ sites as well as mining published data. One-hundred seventy unique targets were highly expressed in 2 or more of the pancreatic tumor specimens and were not expressed in the normal pancreas samples. Two targets (TLR2 and ABCC3) were further validated for protein expression by tissue microarray (TMA) based immunohistochemistry. These validated targets have potential for the development of diagnostic imaging and therapeutic agents for pancreatic cancer.

  12. An ultralow background substrate for protein microarray technology.

    PubMed

    Feng, Hui; Zhang, Qingyang; Ma, Hongwei; Zheng, Bo

    2015-08-21

    We herein report an ultralow background substrate for protein microarrays. Conventional protein microarray substrates often suffer from non-specific protein adsorption and inhomogeneous spot morphology. Consequently, surface treatment and a suitable printing solution are required to improve the microarray performance. In the current work, we improved the situation by developing a new microarray substrate based on a fluorinated ethylene propylene (FEP) membrane. A polydopamine microspot array was fabricated on the FEP membrane, with proteins conjugated to the FEP surface through polydopamine. Uniform microspots were obtained on FEP without the application of a special printing solution. The modified FEP membrane demonstrated ultralow background signal and was applied in protein and peptide microarray analysis. PMID:26134063

  13. cDNA microarray screening in food safety.

    PubMed

    Roy, Sashwati; Sen, Chandan K

    2006-04-01

    The cDNA microarray technology and related bioinformatics tools presents a wide range of novel application opportunities. The technology may be productively applied to address food safety. In this mini-review article, we present an update highlighting the late breaking discoveries that demonstrate the vitality of cDNA microarray technology as a tool to analyze food safety with reference to microbial pathogens and genetically modified foods. In order to bring the microarray technology to mainstream food safety, it is important to develop robust user-friendly tools that may be applied in a field setting. In addition, there needs to be a standardized process for regulatory agencies to interpret and act upon microarray-based data. The cDNA microarray approach is an emergent technology in diagnostics. Its values lie in being able to provide complimentary molecular insight when employed in addition to traditional tests for food safety, as part of a more comprehensive battery of tests.

  14. Finding dominant sets in microarray data.

    PubMed

    Fu, Xuping; Teng, Li; Li, Yao; Chen, Wenbin; Mao, Yumin; Shen, I-Fan; Xie, Yi

    2005-01-01

    Clustering allows us to extract groups of genes that are tightly coexpressed from Microarray data. In this paper, a new method DSF_Clust is developed to find dominant sets (clusters). We have preformed DSF_Clust on several gene expression datasets and given the evaluation with some criteria. The results showed that this approach could cluster dominant sets of good quality compared to kmeans method. DSF_Clust deals with three issues that have bedeviled clustering, some dominant sets being statistically determined in a significance level, predefining cluster structure being not required, and the quality of a dominant set being ensured. We have also applied this approach to analyze published data of yeast cell cycle gene expression and found some biologically meaningful gene groups to be dug out. Furthermore, DSF_Clust is a potentially good tool to search for putative regulatory signals.

  15. Digital microarray analysis for digital artifact genomics

    NASA Astrophysics Data System (ADS)

    Jaenisch, Holger; Handley, James; Williams, Deborah

    2013-06-01

    We implement a Spatial Voting (SV) based analogy of microarray analysis for digital gene marker identification in malware code sections. We examine a famous set of malware formally analyzed by Mandiant and code named Advanced Persistent Threat (APT1). APT1 is a Chinese organization formed with specific intent to infiltrate and exploit US resources. Manidant provided a detailed behavior and sting analysis report for the 288 malware samples available. We performed an independent analysis using a new alternative to the traditional dynamic analysis and static analysis we call Spatial Analysis (SA). We perform unsupervised SA on the APT1 originating malware code sections and report our findings. We also show the results of SA performed on some members of the families associated by Manidant. We conclude that SV based SA is a practical fast alternative to dynamics analysis and static analysis.

  16. Ritonavir and bull’s eye maculopathy: case report

    PubMed Central

    Pinto, Rita; Vila-Franca, Marta; Oliveira Afonso, Cláudia; Ornelas, Conceição; Santos, Luisa

    2013-01-01

    Objective: To report on a case of retinal pigment epithelium (RPE) toxicity apparently associated with ritonavir. Methods: We describe a case of gradual-onset blurry vision in both eyes in a 30-year-old HIV-positive male on Highly-Active Antiretroviral Therapy (HAART) including ritonavir Results: The patient presented with a visual acuity of 3/10 in each eye, and fundoscopy revealed paracentral pigment mottling. Computerized perimetry showed a ring-scotoma in both eyes. Fluorescein angiography revealed an anular RPE defect in both eyes, congruent with hyperautofluorescent changes on autofluorescence imaging. Full-field ERG was normal. Conclusions: Since ritonavir has previously been linked with toxicity to the RPE, we consider this report as further evidence of this association.

  17. Eye Position Changes during Reading Fixations are Spatially Selective

    PubMed Central

    Inhoff, Albrecht W.; Solomon, Matthew S.; Seymour, Bradley A.; Radach, Ralph

    2008-01-01

    Intra-fixation location changes were measured when one-line sentences written in lower or aLtErNaTiNg case were read. Intra-fixation location changes were common and their size was normally distributed except for a relatively high proportion of fixations without a discernible location change. Location changes that did occur were systematically biased toward the right when alternating case was read. Irrespective of case type, changes of the right eye were biased toward the right at the onset of sentence reading, and this spatial bias decreased as sentence reading progressed from left to right. The left eye showed a relatively stable right-directed bias. These results show that processing demands can pull the two fixated eyes in the same direction and that the response to this pull can differ for the right and left eye. PMID:18313717

  18. Bilateral Glaucomatous Optic Neuropathy Caused by Eye Rubbing.

    PubMed

    Savastano, Alfonso; Savastano, Maria Cristina; Carlomusto, Laura; Savastano, Silvio

    2015-01-01

    In this report, we describe a particular condition of a 52-year-old man who showed advanced bilateral glaucomatous-like optic disc damage, even though the intraocular pressure resulted normal during all examinations performed. Visual field test, steady-state pattern electroretinogram, retinal nerve fiber layer and retinal tomographic evaluations were performed to evaluate the optic disc damage. Over a 4-year observational period, his visual acuity decreased to 12/20 in the right eye and counting fingers in the left eye. Visual fields were severely compromised, and intraocular pressure values were not superior to 14 mm Hg during routine examinations. An accurate anamnesis and the suspicion of this disease represent a crucial aspect to establish the correct diagnosis. In fact, our patient strongly rubbed his eyes for more than 10 h per day. Recurrent and continuous eye rubbing can induce progressive optic neuropathy, causing severe visual field damage similar to the pathology of advanced glaucoma.

  19. Eye position changes during reading fixations are spatially selective.

    PubMed

    Inhoff, Albrecht W; Solomon, Matthew S; Seymour, Bradley A; Radach, Ralph

    2008-03-01

    Intra-fixation location changes were measured when one-line sentences written in lower or aLtErNaTiNg case were read. Intra-fixation location changes were common and their size was normally distributed except for a relatively high proportion of fixations without a discernible location change. Location changes that did occur were systematically biased toward the right when alternating case was read. Irrespective of case type, changes of the right eye were biased toward the right at the onset of sentence reading, and this spatial bias decreased as sentence reading progressed from left to right. The left eye showed a relatively stable right-directed bias. These results show that processing demands can pull the two fixated eyes in the same direction and that the response to this pull can differ for the right and left eye.

  20. Lens of Eye Dosimetry

    SciTech Connect

    Mallett, Michael Wesley

    2015-03-23

    An analysis of LANL occupational dose measurements was made with respect to lens of eye dose (LOE), in particular, for plutonium workers. Table 1 shows the reported LOE as a ratio of the “deep” (photon only) and “deep+neutron” dose for routine monitored workers at LANL for the past ten years. The data compares the mean and range of these values for plutonium workers* and non-routine plutonium workers. All doses were reported based on measurements with the LANL Model 8823 TLD.

  1. Analysis of environmental transcriptomes by DNA microarrays.

    PubMed

    Parro, Víctor; Moreno-Paz, Mercedes; González-Toril, Elena

    2007-02-01

    In this work we investigated the correlations between global gene expression patterns and environmental parameters in natural ecosystems. We studied the preferential gene expression of the iron oxidizer bacterium Leptospirillum ferrooxidans to adapt its physiology to changes in the physicochemical parameters in its natural medium. Transcriptome analysis by DNA microarrays can proportionate an instant picture about the preferential gene expression between two different environmental samples. However, this type of analysis is very difficult and complex in natural ecosystems, mainly because of the broad biodiversity and multiple environmental parameters that may affect gene expression. The necessity of high-quality RNA preparations as well as complicated data analysis are also technological limitations. The low prokaryotic diversity of the extremely acidic and iron-rich waters of the Tinto River (Spain) ecosystem, where L. ferrooxidans is abundant, allows the opportunity to achieve global gene expression studies and to associate gene function with environmental parameters. We applied a total RNA amplification protocol validated previously for the amplification of the environmental transcriptome (meta-transcriptome). The meta-transcriptome of two sites from the Tinto River mainly differing in the salt and oxygen contents were amplified and analysed by a L. ferrooxidans DNA microarray. The results showed a clear preferential induction of genes involved in certain physicochemical parameters like: high salinity (ectAB, otsAB), low oxygen concentration (cydAB), iron uptake (fecA-exbBD-tonB), oxidative stress (carotenoid synthesis, oxyR, recG), potassium (kdpBAC) or phosphate concentrations (pstSCAB), etc. We conclude that specific gene expression patterns can be useful indicators for the physiological conditions in a defined ecosystem. Also, the upregulation of certain genes and operons reveals information about the environmental conditions (nutrient limitations, stresses

  2. Lipid Microarray Biosensor for Biotoxin Detection.

    SciTech Connect

    Singh, Anup K.; Throckmorton, Daniel J.; Moran-Mirabal, Jose C.; Edel, Joshua B.; Meyer, Grant D.; Craighead, Harold G.

    2006-05-01

    We present the use of micron-sized lipid domains, patterned onto planar substrates and within microfluidic channels, to assay the binding of bacterial toxins via total internal reflection fluorescence microscopy (TIRFM). The lipid domains were patterned using a polymer lift-off technique and consisted of ganglioside-populated DSPC:cholesterol supported lipid bilayers (SLBs). Lipid patterns were formed on the substrates by vesicle fusion followed by polymer lift-off, which revealed micron-sized SLBs containing either ganglioside GT1b or GM1. The ganglioside-populated SLB arrays were then exposed to either Cholera toxin subunit B (CTB) or Tetanus toxin fragment C (TTC). Binding was assayed on planar substrates by TIRFM down to 1 nM concentration for CTB and 100 nM for TTC. Apparent binding constants extracted from three different models applied to the binding curves suggest that binding of a protein to a lipid-based receptor is strongly affected by the lipid composition of the SLB and by the substrate on which the bilayer is formed. Patterning of SLBs inside microfluidic channels also allowed the preparation of lipid domains with different compositions on a single device. Arrays within microfluidic channels were used to achieve segregation and selective binding from a binary mixture of the toxin fragments in one device. The binding and segregation within the microfluidic channels was assayed with epifluorescence as proof of concept. We propose that the method used for patterning the lipid microarrays on planar substrates and within microfluidic channels can be easily adapted to proteins or nucleic acids and can be used for biosensor applications and cell stimulation assays under different flow conditions. KEYWORDS. Microarray, ganglioside, polymer lift-off, cholera toxin, tetanus toxin, TIRFM, binding constant.4

  3. Development of a magnetic nanoparticles microarray for simultaneous and simple detection of foodborne pathogens.

    PubMed

    Li, Song; Liu, Hongna; Deng, Yan; Lin, Lin; He, Nongyue

    2013-07-01

    Foodborne diseases are a widespread and growing public health problem affecting both developed and developing countries, microbiologically contaminated food and water are the major causes of diarrhoeal diseases. Methods based on polymerase chain reaction (PCR) and microarrays are rapid and sensitive enough to detect very small quantities of microorganisms, however, the requirement for expensive equipments limits their application. In the present paper, we describe a method based on multiplex PCR and magnetic nanoparticles labelling for simultaneous detection of four major foodborne pathogens, including Escherichia coli O157:H7, Salmonella enterica, Vibrio cholera and Campylobacter jejuni. The process utilizes an oligonucleotide array onto which 5' biotinylated single strand PCR products were hybridized and visualized with streptavidin-coated magnetic nanoparticles (SA-MNPs), the signal from which could be detected by the naked eye, microscope or CCD camera. By employing SA-MNPs as visible labels, the microarray unambiguously distinguished all 4 pathogens with detection sensitivity up to 316 CFU/mL. Due to its high sensitivity, specificity and simple detection procedure, the magnetic bead assay provides a powerful tool for the detection and identification of foodborne pathogens in a modestly equipped laboratory. PMID:23909141

  4. Application of Phenotype Microarray technology to soil microbiology

    NASA Astrophysics Data System (ADS)

    Mocali, Stefano

    2016-04-01

    It is well established that soil microorganisms are extremely diverse and only a small fraction has been successfully cultured in the laboratory. Furthermore, addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of interest in the reconstruction and biotechnological manipulation of metabolic pathways. High-throughput culture in micro wells provides a method for rapid screening of a wide variety of growth conditions and commercially available plates contain a large number of substrates, nutrient sources, and inhibitors, which can provide an assessment of the phenotype of an organism. Thus, over the last years, Phenotype Microarray (PM) technology has been used to address many specific issues related to the metabolic functionality of microorganisms. However, computational tools that could directly link PM data with the gene(s) of interest followed by the extraction of information on gene-phenotype correlation are still missing. Here potential applications of phenotype arrays to soil microorganisms, use of the plates in stress response studies and for assessment of phenotype of environmental communities are described. Considerations and challenges in data interpretation and visualization, including data normalization, statistics, and curve fitting are also discussed. In particular, here we present DuctApe, a suite that allows the analysis of both genomic sequences and PM data, to find metabolic differences among PM experiments and to correlate them with KEGG pathways and gene presence/absence patterns.

  5. Eye Tracking Detects Disconjugate Eye Movements Associated with Structural Traumatic Brain Injury and Concussion

    PubMed Central

    Ritlop, Robert; Reyes, Marleen; Nehrbass, Elena; Li, Meng; Lamm, Elizabeth; Schneider, Julia; Shimunov, David; Sava, Maria; Kolecki, Radek; Burris, Paige; Altomare, Lindsey; Mehmood, Talha; Smith, Theodore; Huang, Jason H.; McStay, Christopher; Todd, S. Rob; Qian, Meng; Kondziolka, Douglas; Wall, Stephen; Huang, Paul

    2015-01-01

    Abstract Disconjugate eye movements have been associated with traumatic brain injury since ancient times. Ocular motility dysfunction may be present in up to 90% of patients with concussion or blast injury. We developed an algorithm for eye tracking in which the Cartesian coordinates of the right and left pupils are tracked over 200 sec and compared to each other as a subject watches a short film clip moving inside an aperture on a computer screen. We prospectively eye tracked 64 normal healthy noninjured control subjects and compared findings to 75 trauma subjects with either a positive head computed tomography (CT) scan (n=13), negative head CT (n=39), or nonhead injury (n=23) to determine whether eye tracking would reveal the disconjugate gaze associated with both structural brain injury and concussion. Tracking metrics were then correlated to the clinical concussion measure Sport Concussion Assessment Tool 3 (SCAT3) in trauma patients. Five out of five measures of horizontal disconjugacy were increased in positive and negative head CT patients relative to noninjured control subjects. Only one of five vertical disconjugacy measures was significantly increased in brain-injured patients relative to controls. Linear regression analysis of all 75 trauma patients demonstrated that three metrics for horizontal disconjugacy negatively correlated with SCAT3 symptom severity score and positively correlated with total Standardized Assessment of Concussion score. Abnormal eye-tracking metrics improved over time toward baseline in brain-injured subjects observed in follow-up. Eye tracking may help quantify the severity of ocular motility disruption associated with concussion and structural brain injury. PMID:25582436

  6. Eye tracking detects disconjugate eye movements associated with structural traumatic brain injury and concussion.

    PubMed

    Samadani, Uzma; Ritlop, Robert; Reyes, Marleen; Nehrbass, Elena; Li, Meng; Lamm, Elizabeth; Schneider, Julia; Shimunov, David; Sava, Maria; Kolecki, Radek; Burris, Paige; Altomare, Lindsey; Mehmood, Talha; Smith, Theodore; Huang, Jason H; McStay, Christopher; Todd, S Rob; Qian, Meng; Kondziolka, Douglas; Wall, Stephen; Huang, Paul

    2015-04-15

    Disconjugate eye movements have been associated with traumatic brain injury since ancient times. Ocular motility dysfunction may be present in up to 90% of patients with concussion or blast injury. We developed an algorithm for eye tracking in which the Cartesian coordinates of the right and left pupils are tracked over 200 sec and compared to each other as a subject watches a short film clip moving inside an aperture on a computer screen. We prospectively eye tracked 64 normal healthy noninjured control subjects and compared findings to 75 trauma subjects with either a positive head computed tomography (CT) scan (n=13), negative head CT (n=39), or nonhead injury (n=23) to determine whether eye tracking would reveal the disconjugate gaze associated with both structural brain injury and concussion. Tracking metrics were then correlated to the clinical concussion measure Sport Concussion Assessment Tool 3 (SCAT3) in trauma patients. Five out of five measures of horizontal disconjugacy were increased in positive and negative head CT patients relative to noninjured control subjects. Only one of five vertical disconjugacy measures was significantly increased in brain-injured patients relative to controls. Linear regression analysis of all 75 trauma patients demonstrated that three metrics for horizontal disconjugacy negatively correlated with SCAT3 symptom severity score and positively correlated with total Standardized Assessment of Concussion score. Abnormal eye-tracking metrics improved over time toward baseline in brain-injured subjects observed in follow-up. Eye tracking may help quantify the severity of ocular motility disruption associated with concussion and structural brain injury.

  7. Optics of arthropod compound eye.

    PubMed

    Shaw, S R

    1969-07-01

    The extent to which light can escape from one ommatidium into its neighbors in the compound eye has been examined by recording from single receptors during stimulation of single facets. In the "apposition" eye of the drone honeybee and locust, optical interaction is extremely small. In the "superposition" eye of the crayfish, more than half the light captured by the average cell gets in through neighboring facets, even when screening pigments are in the fully lightadapted position.

  8. Image analysis and statistical evaluation of two-dimensional human eye retina images of healthy and glaucomatous eyes

    NASA Astrophysics Data System (ADS)

    Pluhacek, Frantisek; Pospisil, Jaroslav

    2003-11-01

    In this paper, a new automatic glaucoma diagnostics method which enables to determine the probability of glaucoma occurrence in a studied eye is described. This method is based on the computer image analysis of two-dimensional images of the blind spot of the human eye retina and on the successive statistical evaluation of the obtained data. First, the characteristic symptoms of glaucoma are shortly described. Next, a suitable numerical parameter of the retina blind spot is defined. The computer image analysis method of the automatic determination of the mentioned parameter is described and it is applied to a set of normal healthy eye images and to a set of glaucomatous eye images. The probability of glaucoma occurrence for each value of the introduced parameter is suitably defined and computed by virtue of the statistical evaluation of the obtained results.

  9. Automatic dry eye detection.

    PubMed

    Yedidya, Tamir; Hartley, Richard; Guillon, Jean-Pierre; Kanagasingam, Yogesan

    2007-01-01

    Dry Eye Syndrome is a common disease in the western world, with effects from uncomfortable itchiness to permanent damage to the ocular surface. Nevertheless, there is still no objective test that provides reliable results. We have developed a new method for the automated detection of dry areas in videos taken after instilling fluorescein in the tear film. The method consists of a multi-step algorithm to first locate the iris in each image, then align the images and finally analyze the aligned sequence in order to find the regions of interest. Since the fluorescein spreads on the ocular surface of the eye the edges of the iris are fuzzy making the detection of the iris challenging. We use RANSAC to first detect the upper and lower eyelids and then the iris. Then we align the images by finding differences in intensities at different scales and using a least squares optimization method (Levenberg-Marquardt), to overcome the movement of the iris and the camera. The method has been tested on videos taken from different patients. It is demonstrated to find the dry areas accurately and to provide a measure of the extent of the disease. PMID:18051131

  10. Laser eye injuries.

    PubMed

    Barkana, Y; Belkin, M

    2000-01-01

    Laser instruments are used in many spheres of human activity, including medicine, industry, laboratory research, entertainment, and, notably, the military. This widespread use of lasers has resulted in many accidental injuries. Injuries are almost always retinal, because of the concentration of visible and near-infrared radiation on the retina. The retina is therefore the body tissue most vulnerable to laser radiation. The nature and severity of this type of retinal injury is determined by multiple laser-related and eye-related factors, the most important being the duration and amount of energy delivered and the retinal location of the lesion. The clinical course of significant retinal laser injuries is characterized by sudden loss of vision, often followed by marked improvement over a few weeks, and occasionally severe late complications. Medical and surgical treatment is limited. Laser devices hazardous to the human eye are currently in widespread use by armed forces. Furthermore, lasers may be employed specifically for visual incapacitation on future battlefields. Adherence to safety practices effectively prevents accidental laser-induced ocular injuries. However, there is no practical way to prevent injuries that are maliciously inflicted, as expected from laser weapons.

  11. Eye Surgery Light

    NASA Technical Reports Server (NTRS)

    1978-01-01

    During eye surgery, the surgeon uses an illuminating instrument called an opthalmoscope for close examination of the retina or the interior of the eye. Ordinarily, electric power for the head-mounted light is supplied through a cord from an overhead swivel arm or a floor pedestal. Within limits of cord length and swivel arm movement, the surgeon has considerable freedom of motion. But when more than one opthalmoscope is involved, tangling and interference of the power cords becomes a problem. St. Luke's Hospital, Cleveland, Ohio asked Lewis Research Center for assistance in finding a solution. Lewis responded with a battery-powered system that totally frees the surgeon of attached cords and swivels. Borrowing from space technology, Lewis used small, lightweight nickel-cadmium batteries that can deliver high intensity light for an hour and can be recharged overnight. The Opthalmoscope Powerpack consists of eight batteries in three containers affixed to a webbed belt, and a novel on-off switch equipped with a springloaded plexiglass "flapper." The belt pack is worn underneath the surgical gown and the flapper permits the doctor to activate the switch by elbow pressure. Lewis built five units and they have been in service at St. Luke's Hospital for a year. Used for routine examinations as well as for surgery, they have demonstrated excellent reliability.

  12. Eye Surgery Light

    NASA Technical Reports Server (NTRS)

    1978-01-01

    During eye surgery, the surgeon uses an illuminating instrument called an opthalmoscope for close examination of the retina or the interior of the eye. Ordinarily, electric power for the head-mounted light is supplied through a cord from an overhead swivel arm or a floor pedestal. Within limits of cord length and swivel arm movement, the surgeon has considerable freedom of motion. But when more than one opthalmoscope is involved, tangling and interference of the power cords becomes a problem. St. Luke's Hospital, Cleveland, Ohio asked Lewis Research Center for assistance in finding a solution. Lewis responded with a battery-powered system that totally frees the surgeon of attached cords and swivels. Borrowing from space technology, Lewis used small, lightweight nickel-cadmium batteries that can deliver high intensity light for an hour and can be recharged overnight. The Opthalmoscope Powerpack consists of eight batteries in three containers affixed to a webbed belt, and a novel on-off switch equipped with a spring-loaded plexiglass 'flapper.' The belt pack is worn underneath the surgical gown and the flapper permits the doctor to activate the switch by elbow pressure. Lewis built five units and they have been in service at St. Luke's Hospital for a year. Used for routine examinations as well as for surgery, they have demonstrated excellent reliability.

  13. Aging and dry eye disease.

    PubMed

    Ding, Juan; Sullivan, David A

    2012-07-01

    Dry eye disease is a prevalent eye disorder that in particular affects the elderly population. One of the major causes of dry eye, meibomian gland dysfunction (MGD), shows increased prevalence with aging. MGD is caused by hyperkeratinization of the ductal epithelium of meibomian gland and reduced quantity and/or quality of meibum, the holocrine product that stabilizes and prevents the evaporation of the tear film. Of note, retinoids which are used in current anti-aging cosmetics may promote the development of MGD and dry eye disease. In this review, we will discuss the possible mechanisms of age-related MGD.

  14. Aging and dry eye disease

    PubMed Central

    Ding, Juan; Sullivan, David A.

    2012-01-01

    Dry eye disease is a prevalent eye disorder that in particular affects the elderly population. One of the major causes of dry eye, meibomian gland dysfunction (MGD), shows increased prevalence with aging. MGD is caused by hyperkeratinization of the ductal epithelium of meibomian gland and reduced quantity and/or quality of meibum, the holocrine product that stabilizes and prevents the evaporation of the tear film. Of note, retinoids which are used in current anti-aging cosmetics may promote the development of MGD and dry eye disease. In this review, we will discuss the possible mechanisms of age-related MGD. PMID:22569356

  15. Developmental palaeobiology of trilobite eyes and its evolutionary significance

    NASA Astrophysics Data System (ADS)

    Thomas, A. T.

    2005-06-01

    Understanding of the calcified composite eyes of trilobites, the oldest preserved visual system, has advanced greatly in recent decades. Three types of trilobite eye occur, the more derived abathochroal and schizochroal types having evolved neotenically from holochroal eyes. Comparative morphology and phylogenetic considerations suggest that all three eye-types were underlain by common developmental systems. So far, understanding of these systems has been based entirely on morphological data from fossils, particularly the way the visual surface grew and the patterning of lens emplacement. Lenses characteristically form a hexagonal array comprising horizontal rows and, conspicuously in schizochroal eyes, dorso-ventral files. Because individual trilobites sometimes have eyes with different numbers of files, file number must reflect the operation of a developmental programme rather than being under immediate genetic control. An empirical developmental model has been devised to describe trilobite eye development, with separate rules dealing with the initiation of lens emplacement, growth and differentiation of the visual surface, and the termination of lens emplacement. Rarely, trilobites may have visual surfaces of normal size, but which lack lenses. This confirms that visual surface growth must have been regulated separately from lens emplacement, and is a feature that cannot be accounted for by the existing developmental model. Such a developmental separation is one of a number of similarities shared with Drosophila, the modern arthropod in which eye development is best understood. Many aspects of eye development are conserved in the Euarthropoda, and in bilaterian metazoans in general. A revised model for trilobite eye development is proposed using extant phylogenetic bracketing, interpreting morphological data from the fossils in the context of the hierarchy of developmental controls now becoming known from living animals. This new model suggests that overall eye

  16. Deconstructing Interocular Suppression: Attention and Divisive Normalization.

    PubMed

    Li, Hsin-Hung; Carrasco, Marisa; Heeger, David J

    2015-10-01

    In interocular suppression, a suprathreshold monocular target can be rendered invisible by a salient competitor stimulus presented in the other eye. Despite decades of research on interocular suppression and related phenomena (e.g., binocular rivalry, flash suppression, continuous flash suppression), the neural processing underlying interocular suppression is still unknown. We developed and tested a computational model of interocular suppression. The model included two processes that contributed to the strength of interocular suppression: divisive normalization and attentional modulation. According to the model, the salient competitor induced a stimulus-driven attentional modulation selective for the location and orientation of the competitor, thereby increasing the gain of neural responses to the competitor and reducing the gain of neural responses to the target. Additional suppression was induced by divisive normalization in the model, similar to other forms of visual masking. To test the model, we conducted psychophysics experiments in which both the size and the eye-of-origin of the competitor were manipulated. For small and medium competitors, behavioral performance was consonant with a change in the response gain of neurons that responded to the target. But large competitors induced a contrast-gain change, even when the competitor was split between the two eyes. The model correctly predicted these results and outperformed an alternative model in which the attentional modulation was eye specific. We conclude that both stimulus-driven attention (selective for location and feature) and divisive normalization contribute to interocular suppression.

  17. Identification of different subtypes of breast cancer using tissue microarray.

    PubMed

    Munirah, M A; Siti-Aishah, M A; Reena, M Z; Sharifah, N A; Rohaizak, M; Norlia, A; Rafie, M K M; Asmiati, A; Hisham, A; Fuad, I; Shahrun, N S; Das, S

    2011-01-01

    Breast cancer may be classified into luminal A, luminal B, HER2+/ER-, basal-like and normal-like subtypes based on gene expression profiling or immunohistochemical (IHC) characteristics. The main aim of the present study was to classify breast cancer into molecular subtypes based on immunohistochemistry findings and correlate the subtypes with clinicopathological factors. Two hundred and seventeen primary breast carcinomas tumor tissues were immunostained for ER, PR, HER2, CK5/6, EGFR, CK8/18, p53 and Ki67 using tissue microarray technique. All subtypes were significantly associated with Malay ethnic background (p=0.035) compared to other racial origins. The most common subtypes of breast cancers were luminal A and was significantly associated with low histological grade (p<0.000) and p53 negativity (p=0.003) compared to HER2+/ER-, basal-like and normal-like subtypes with high histological grade (p<0.000) and p53 positivity (p=0.003). Luminal B subtype had the smallest mean tumor size (p=0.009) and also the highest mean number of lymph nodes positive (p=0.032) compared to other subtypes. All markers except EGFR and Ki67 were significantly associated with the subtypes. The most common histological type was infiltrating ductal carcinoma, NOS. Majority of basal-like subtype showed comedo-type necrosis (68.8%) and infiltrative margin (81.3%). Our studies suggest that IHC can be used to identify the different subtypes of breast cancer and all subtypes were significantly associated with race, mean tumor size, mean number of lymph node positive, histological grade and all immunohistochemical markers except EGFR and Ki67.

  18. Variability of eye movements when viewing dynamic natural scenes.

    PubMed

    Dorr, Michael; Martinetz, Thomas; Gegenfurtner, Karl R; Barth, Erhardt

    2010-01-01

    How similar are the eye movement patterns of different subjects when free viewing dynamic natural scenes? We collected a large database of eye movements from 54 subjects on 18 high-resolution videos of outdoor scenes and measured their variability using the Normalized Scanpath Saliency, which we extended to the temporal domain. Even though up to about 80% of subjects looked at the same image region in some video parts, variability usually was much greater. Eye movements on natural movies were then compared with eye movements in several control conditions. "Stop-motion" movies had almost identical semantic content as the original videos but lacked continuous motion. Hollywood action movie trailers were used to probe the upper limit of eye movement coherence that can be achieved by deliberate camera work, scene cuts, etc. In a "repetitive" condition, subjects viewed the same movies ten times each over the course of 2 days. Results show several systematic differences between conditions both for general eye movement parameters such as saccade amplitude and fixation duration and for eye movement variability. Most importantly, eye movements on static images are initially driven by stimulus onset effects and later, more so than on continuous videos, by subject-specific idiosyncrasies; eye movements on Hollywood movies are significantly more coherent than those on natural movies. We conclude that the stimuli types often used in laboratory experiments, static images and professionally cut material, are not very representative of natural viewing behavior. All stimuli and gaze data are publicly available at http://www.inb.uni-luebeck.de/tools-demos/gaze. PMID:20884493

  19. AMDA 2.13: A major update for automated cross-platform microarray data analysis.

    PubMed

    Kapetis, Dimos; Clarelli, Ferdinando; Vitulli, Federico; de Rosbo, Nicole Kerlero; Beretta, Ottavio; Foti, Maria; Ricciardi-Castagnoli, Paola; Zolezzi, Francesca

    2012-07-01

    Microarray platforms require analytical pipelines with modules for data pre-processing including data normalization, statistical analysis for identification of differentially expressed genes, cluster analysis, and functional annotation. We previously developed the Automated Microarray Data Analysis (AMDA, version 2.3.5) pipeline to process Affymetrix 3' IVT GeneChips. The availability of newer technologies that demand open-source tools for microarray data analysis has impelled us to develop an updated multi-platform version, AMDA 2.13. It includes additional quality control metrics, annotation-driven (annotation grade of Affymetrix NetAffx) and signal-driven (Inter-Quartile Range) gene filtering, and approaches to experimental design. To enhance understanding of biological data, differentially expressed genes have been mapped into KEGG pathways. Finally, a more stable and user-friendly interface was designed to integrate the requirements for different platforms. AMDA 2.13 allows the analysis of Affymetrix (cartridges and plates) and whole transcript probe design (Gene 1.0/1.1 ST and Exon 1.0 ST GeneChips), Illumina Bead Arrays, and one-channel Agilent 4×44 arrays. Relative to early versions, it supports various experimental designs and delivers more insightful biological understanding and up-to-date annotations.

  20. Microarray analysis reveals altered circulating microRNA expression in mice infected with Coxsackievirus B3

    PubMed Central

    Sun, Chaoyu; Tong, Lei; Zhao, Wenran; Wang, Yan; Meng, Yuan; Lin, Lexun; Liu, Bingchen; Zhai, Yujia; Zhong, Zhaohua; Li, Xueqi

    2016-01-01

    Coxsackievirus B3 (CVB3) is a common causative agent in the development of inflammatory cardiomyopathy. However, whether the expression of peripheral blood microRNAs (miRNAs) is altered in this process is unknown. The present study investigated changes to miRNA expression in the peripheral blood of CVB3-infected mice. Utilizing miRNA microarray technology, differential miRNA expression was examined between normal and CVB3-infected mice. The present results suggest that specific miRNAs were differentially expressed in the peripheral blood of mice infected with CVB3, varying with infection duration. Using miRNA microarray analysis, a total of 96 and 89 differentially expressed miRNAs were identified in the peripheral blood of mice infected with CVB3 for 3 and 6 days, respectively. Quantitative polymerase chain reaction was used to validate differentially expressed miRNAs, revealing a consistency of these results with the miRNA microarray analysis results. The biological functions of the differentially expressed miRNAs were then predicted by bioinformatics analysis. The potential biological roles of differentially expressed miRNAs included hypertrophic cardiomyopathy, dilated cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy. These results may provide important insights into the mechanisms responsible for the progression of CVB3 infection. PMID:27698715