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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. Can Zipf's law be adapted to normalize microarrays?

    PubMed Central

    Lu, Tim; Costello, Christine M; Croucher, Peter JP; Häsler, Robert; Deuschl, Günther; Schreiber, Stefan

    2005-01-01

    Background Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i.e. obey Zipf's law). Based on the observation that our single channel and two channel microarray data sets also followed a power-law distribution, we were motivated to develop a normalization method based on this law, and examine how it compares with existing published techniques. A computationally simple and intuitively appealing technique based on this observation is presented. Results Using pairwise comparisons using MA plots (log ratio vs. log intensity), we compared this novel method to previously published normalization techniques, namely global normalization to the mean, the quantile method, and a variation on the loess normalization method designed specifically for boutique microarrays. Results indicated that, for single channel microarrays, the quantile method was superior with regard to eliminating intensity-dependent effects (banana curves), but Zipf's law normalization does minimize this effect by rotating the data distribution such that the maximal number of data points lie on the zero of the log ratio axis. For two channel boutique microarrays, the Zipf's law normalizations performed as well as, or better than existing techniques. Conclusion Zipf's law normalization is a useful tool where the Quantile method cannot be applied, as is the case with microarrays containing functionally specific gene sets (boutique arrays). PMID:15727680

  3. A Comparative Study of Normalization Methods Used in Statistical Analysis of Oligonucleotide Microarray Data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Normalization methods used in the statistical analysis of oligonucleotide microarray data were evaluated. The oligonucleotide microarray is considered an efficient analytical tool for analyzing thousands of genes simultaneously in a single experiment. However, systematic variation in microarray, ori...

  4. Iterative normalization of cDNA microarray data.

    PubMed

    Wang, Yue; Lu, Jianping; Lee, Richard; Gu, Zhiping; Clarke, Robert

    2002-03-01

    This paper describes a new approach to normalizing microarray expression data. The novel feature is to unify the tasks of estimating normalization coefficients and identifying control gene set. Unification is realized by constructing a window function over the scatter plot defining the subset of constantly expressed genes and by affecting optimization using an iterative procedure. The structure of window function gates contributions to the control gene set used to estimate normalization coefficients. This window measures the consistency of the matched neighborhoods in the scatter plot and provides a means of rejecting control gene outliers. The recovery of normalizational regression and control gene selection are interleaved and are realized by applying coupled operations to the mean square error function. In this way, the two processes bootstrap one another. We evaluate the technique on real microarray data from breast cancer cell lines and complement the experiment with a data cluster visualization study. PMID:11936594

  5. 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

  6. Normalizing videos of anterior eye segment surgeries.

    PubMed

    Quellec, Gwénolé; Charriére, Katia; Lamard, Mathieu; Cochener, Béatrice; Cazuguel, Guy

    2014-01-01

    Anterior eye segment surgeries are usually video-recorded. If we are able to efficiently analyze surgical videos in real-time, new decision support tools will emerge. The main anatomical landmarks in these videos are the pupil boundaries and the limbus, but segmenting them is challenging due to the variety of colors and textures in the pupil, the iris, the sclera and the lids. In this paper, we present a solution to reliably normalize the center and the scale in videos, without explicitly segmenting these landmarks. First, a robust solution to track the pupil center is presented: it uses the fact that the pupil boundaries, the limbus and the sclera / lid interface are concentric. Second, a solution to estimate the zoom level is presented: it relies on the illumination pattern reflected on the cornea. The proposed solution was assessed in a dataset of 186 real-live cataract surgery videos. The distance between the true and estimated pupil centers was equal to 8.0 ± 6.9% of the limbus radius. The correlation between the estimated zoom level and the true limbus size in images was high: R = 0.834. PMID:25569912

  7. An examination of the regulatory mechanism of Pxdn mutation-induced eye disorders using microarray analysis

    PubMed Central

    YANG, YANG; XING, YIQIAO; LIANG, CHAOQUN; HU, LIYA; XU, FEI; MEI, QI

    2016-01-01

    The present study aimed to identify biomarkers for peroxidasin (Pxdn) mutation-induced eye disorders and study the underlying mechanisms involved in this process. The microarray dataset GSE49704 was used, which encompasses 4 mouse samples from embryos with Pxdn mutation and 4 samples from normal tissues. After data preprocessing, the differentially expressed genes (DEGs) between Pxdn mutation and normal tissues were identified using the t-test in the limma package, followed by functional enrichment analysis. The protein-protein interaction (PPI) network was constructed based on the STRING database, and the transcriptional regulatory (TR) network was established using the GeneCodis database. Subsequently, the overlapping DEGs with high degrees in two networks were identified, as well as the sub-network extracted from the TR network. In total, 121 (75 upregulated and 46 downregulated) DEGs were identified, and these DEGs play important roles in biological processes (BPs), including neuron development and differentiation. A PPI network containing 25 nodes such as actin, alpha 1, skeletal muscle (Acta1) and troponin C type 2 (fast) (Tnnc2), and a TR network including 120 nodes were built. By comparing the two networks, seven crucial genes which overlapped were identified, including cyclin-dependent kinase inhibitor 1B (Cdkn1b), Acta1 and troponin T type 3 (Tnnt3). In the sub-network, Cdkn1b was predicted as the target of miRNAs such as mmu-miR-24 and transcription factors (TFs) including forkhead box O4 (FOXO4) and activating enhancer binding protein 4 (AP4). Thus, we suggest that seven crucial genes, including Cdkn1b, Acta1 and Tnnt3, play important roles in the progression of eye disorders such as glaucoma. We suggest that Cdkn1b exert its effects via the inhibition of proliferation and is mediated by mmu-miR-24 and targeted by the TFs FOXO4 and AP4. PMID:27121343

  8. 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...

  9. Normalization of Affymetrix miRNA Microarrays for the Analysis of Cancer Samples.

    PubMed

    Wu, Di; Gantier, Michael P

    2016-01-01

    microRNA (miRNA) microarray normalization is a critical step for the identification of truly differentially expressed miRNAs. This is particularly important when dealing with cancer samples that have a global miRNA decrease. In this chapter, we provide a simple step-by-step procedure that can be used to normalize Affymetrix miRNA microarrays, relying on robust normal-exponential background correction with cyclic loess normalization. PMID:25971910

  10. An examination of the regulatory mechanism of Pxdn mutation-induced eye disorders using microarray analysis.

    PubMed

    Yang, Yang; Xing, Yiqiao; Liang, Chaoqun; Hu, Liya; Xu, Fei; Mei, Qi

    2016-06-01

    The present study aimed to identify biomarkers for peroxidasin (Pxdn) mutation-induced eye disorders and study the underlying mechanisms involved in this process. The microarray dataset GSE49704 was used, which encompasses 4 mouse samples from embryos with Pxdn mutation and 4 samples from normal tissues. After data preprocessing, the differentially expressed genes (DEGs) between Pxdn mutation and normal tissues were identified using the t-test in the limma package, followed by functional enrichment analysis. The protein-protein interaction (PPI) network was constructed based on the STRING database, and the transcriptional regulatory (TR) network was established using the GeneCodis database. Subsequently, the overlapping DEGs with high degrees in two networks were identified, as well as the sub-network extracted from the TR network. In total, 121 (75 upregulated and 46 downregulated) DEGs were identified, and these DEGs play important roles in biological processes (BPs), including neuron development and differentiation. A PPI network containing 25 nodes such as actin, alpha 1, skeletal muscle (Acta1) and troponin C type 2 (fast) (Tnnc2), and a TR network including 120 nodes were built. By comparing the two networks, seven crucial genes which overlapped were identified, including cyclin‑dependent kinase inhibitor 1B (Cdkn1b), Acta1 and troponin T type 3 (Tnnt3). In the sub-network, Cdkn1b was predicted as the target of miRNAs such as mmu-miR-24 and transcription factors (TFs) including forkhead box O4 (FOXO4) and activating enhancer binding protein 4 (AP4). Thus, we suggest that seven crucial genes, including Cdkn1b, Acta1 and Tnnt3, play important roles in the progression of eye disorders such as glaucoma. We suggest that Cdkn1b exert its effects via the inhibition of proliferation and is mediated by mmu-miR-24 and targeted by the TFs FOXO4 and AP4. PMID:27121343

  11. 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…

  12. Simultaneous Detection of Multiple Fish Pathogens Using a Naked-Eye Readable DNA Microarray

    PubMed Central

    Chang, Chin-I; Hung, Pei-Hsin; Wu, Chia-Che; Cheng, Ta Chih; Tsai, Jyh-Ming; Lin, King-Jung; Lin, Chung-Yen

    2012-01-01

    We coupled 16S rDNA PCR and DNA hybridization technology to construct a microarray for simultaneous detection and discrimination of eight fish pathogens (Aeromonas hydrophila, Edwardsiella tarda, Flavobacterium columnare, Lactococcus garvieae, Photobacterium damselae, Pseudomonas anguilliseptica, Streptococcus iniae and Vibrio anguillarum) commonly encountered in aquaculture. The array comprised short oligonucleotide probes (30 mer) complementary to the polymorphic regions of 16S rRNA genes for the target pathogens. Targets annealed to the microarray probes were reacted with streptavidin-conjugated alkaline phosphatase and nitro blue tetrazolium/5-bromo-4-chloro-3′-indolylphosphate, p-toluidine salt (NBT/BCIP), resulting in blue spots that are easily visualized by the naked eye. Testing was performed against a total of 168 bacterial strains, i.e., 26 representative collection strains, 81 isolates of target fish pathogens, and 61 ecologically or phylogenetically related strains. The results showed that each probe consistently identified its corresponding target strain with 100% specificity. The detection limit of the microarray was estimated to be in the range of 1 pg for genomic DNA and 103 CFU/mL for pure pathogen cultures. These high specificity and sensitivity results demonstrate the feasibility of using DNA microarrays in the diagnostic detection of fish pathogens. PMID:22736973

  13. Simultaneous detection of multiple fish pathogens using a naked-eye readable DNA microarray.

    PubMed

    Chang, Chin-I; Hung, Pei-Hsin; Wu, Chia-Che; Cheng, Ta Chih; Tsai, Jyh-Ming; Lin, King-Jung; Lin, Chung-Yen

    2012-01-01

    We coupled 16S rDNA PCR and DNA hybridization technology to construct a microarray for simultaneous detection and discrimination of eight fish pathogens (Aeromonas hydrophila, Edwardsiella tarda, Flavobacterium columnare, Lactococcus garvieae, Photobacterium damselae, Pseudomonas anguilliseptica, Streptococcus iniae and Vibrio anguillarum) commonly encountered in aquaculture. The array comprised short oligonucleotide probes (30 mer) complementary to the polymorphic regions of 16S rRNA genes for the target pathogens. Targets annealed to the microarray probes were reacted with streptavidin-conjugated alkaline phosphatase and nitro blue tetrazolium/5-bromo-4-chloro-3'-indolylphosphate, p-toluidine salt (NBT/BCIP), resulting in blue spots that are easily visualized by the naked eye. Testing was performed against a total of 168 bacterial strains, i.e., 26 representative collection strains, 81 isolates of target fish pathogens, and 61 ecologically or phylogenetically related strains. The results showed that each probe consistently identified its corresponding target strain with 100% specificity. The detection limit of the microarray was estimated to be in the range of 1 pg for genomic DNA and 10(3) CFU/mL for pure pathogen cultures. These high specificity and sensitivity results demonstrate the feasibility of using DNA microarrays in the diagnostic detection of fish pathogens. PMID:22736973

  14. 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

  15. [The retinal nerve fiber layer in normal and glaucoma eyes].

    PubMed

    Jonas, J B; Schiro, D; Naumann, G O

    1993-12-01

    Glaucoma leads to changes of the retinal nerve fiber layer (RNFL). This study was performed to evaluate glaucomatous alterations of the RNFL and to correlate them with other parameters of glaucomatous optic nerve damage. The study included red-free wide-angle fundus photographs of the RNFL of 453 normal eyes and 609 eyes with glaucoma. We evaluated the visibility of the RNFL in different fundus regions and the occurrence of localized RNFL defects. In the glaucoma eyes, including those with "early" glaucomatous optic nerve damage, the visibility of RNFL was significantly lower than in the normal eyes. The degree of RNFL visibility correlated with other morphological and perimetric parameters. Localized RNFL defects were detected in 20% of the glaucoma eyes. Their frequency increased significantly (P < 0.01) from an "early" glaucoma stage to a subgroup with medium advanced glaucomatous damage and decreased again to a stage with marked glaucomatous changes. They were significantly more common in eyes with normal pressure glaucoma, followed by eyes with primary open-angle glaucoma and finally eyes with secondary open-angle glaucoma. They were significantly associated with optic disk hemorrhages and notches of the neuroretinal rim. The results indicate that the glaucomatous changes of the RNFL are correlated with the optic disk alterations. This holds true also for eyes with "early" glaucomatous damage. It suggests that during every routine ophthalmoscopy the RNFL should be examined. Localized RNFL defects indicate optic nerve damage with a specificity of more than 90%. The contrast between localized and diffuse RNFL loss, the varying frequency of localized RNFL defects in different types of glaucoma and the association between localized RNFL defects and optic disk hemorrhages are diagnostically and pathogenetically important. PMID:8124022

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

    PubMed

    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

  17. 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

  18. 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

  19. 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

  20. Patterns of gene expression in microarrays and expressed sequence tags from normal and cataractous lenses.

    PubMed

    Sousounis, Konstantinos; Tsonis, Panagiotis A

    2012-01-01

    In this contribution, we have examined the patterns of gene expression in normal and cataractous lenses as presented in five different papers using microarrays and expressed sequence tags. The purpose was to evaluate unique and common patterns of gene expression during development, aging and cataracts. PMID:23244575

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. Dancing Eye Syndrome associated with spontaneous recovery and normal neurodevelopment.

    PubMed

    Ki Pang, K; Lynch, Bryan J; Osborne, John P; Pike, Michael G

    2010-03-01

    Five patients with spontaneously recovering Dancing Eye Syndrome/Opsoclonus Myoclonus Syndrome are described. Age at presentation ranged from 4 to 19 months. Four had symptoms of fever and a coryzal illness within days to a few weeks prior to the onset. One of the 4 also had varicella zoster 4 weeks before presentation. All had opsoclonus, myoclonus/ataxia and irritability. Associated infective agents identified were Coxsackie virus and rotavirus. Spontaneous improvement of symptoms started within 9 days of presentation and total duration of illness ranged from 10 to 24 days. Developmental progress at follow-up was normal in all cases. A range of immunomodulatory therapies have been advocated for the treatment of Dancing Eye Syndrome/Opsoclonus Myoclonus Syndrome. However, in some children, early spontaneous recovery may occur, an observation which should be borne in mind when designing therapeutic trials in this condition. PMID:19541513

  7. A Simple Method for Optimization of Reference Gene Identification and Normalization in DNA Microarray Analysis

    PubMed Central

    Casares, Federico M.

    2016-01-01

    Background Comparative DNA microarray analyses typically yield very large gene expression data sets that reflect complex patterns of change. Despite the wealth of information that is obtained, the identification of stable reference genes is required for normalization of disease- or drug-induced changes across tested groups. This is a prerequisite in quantitative real-time reverse transcription-PCR (qRT-PCR) and relative RT-PCR but rare in gene microarray analysis. The goal of the present study was to outline a simple method for identification of reliable reference genes derived from DNA microarray data sets by comparative statistical analysis of software-generated and manually calculated candidate genes. Material/Methods DNA microarray data sets derived from whole-blood samples obtained from 14 Zucker diabetic fatty (ZDF) rats (7 lean and 7 diabetic obese) were used for the method development. This involved the use of software-generated filtering parameters to accomplish the desired signal-to-noise ratios, 75th percentile signal manual normalizations, and the selection of reference genes as endogenous controls for target gene expression normalization. Results The combination of software-generated and manual normalization methods yielded a group of 5 stably expressed, suitable endogenous control genes which can be used in further target gene expression determinations in whole blood of ZDF rats. Conclusions This method can be used to correct for potentially false results and aid in the selection of suitable endogenous control genes. It is especially useful when aimed to aid the software in cases of borderline results, where the expression and/or the fold change values are just beyond the pre-established set of acceptable parameters. PMID:27122237

  8. Classification of microarrays; synergistic effects between normalization, gene selection and machine learning

    PubMed Central

    2011-01-01

    Background Machine learning is a powerful approach for describing and predicting classes in microarray data. Although several comparative studies have investigated the relative performance of various machine learning methods, these often do not account for the fact that performance (e.g. error rate) is a result of a series of analysis steps of which the most important are data normalization, gene selection and machine learning. Results In this study, we used seven previously published cancer-related microarray data sets to compare the effects on classification performance of five normalization methods, three gene selection methods with 21 different numbers of selected genes and eight machine learning methods. Performance in term of error rate was rigorously estimated by repeatedly employing a double cross validation approach. Since performance varies greatly between data sets, we devised an analysis method that first compares methods within individual data sets and then visualizes the comparisons across data sets. We discovered both well performing individual methods and synergies between different methods. Conclusion Support Vector Machines with a radial basis kernel, linear kernel or polynomial kernel of degree 2 all performed consistently well across data sets. We show that there is a synergistic relationship between these methods and gene selection based on the T-test and the selection of a relatively high number of genes. Also, we find that these methods benefit significantly from using normalized data, although it is hard to draw general conclusions about the relative performance of different normalization procedures. PMID:21982277

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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

  16. Eye Contact in Children's Social Interactions: What Is Normal Behaviour?

    ERIC Educational Resources Information Center

    Arnold, Angela; Semple, Randye J.; Beale, Ivan; Fletcher-Flinn, Claire M.

    2000-01-01

    A study of 31 typical children aged 5-10 engaged in child-to-child social interactions, found joint attention was positively related to age and activity, eye gaze was low relative to joint attention and object engagement, and eye gaze was significantly less than what has been reported for adult-child and adult-adult dyads. (Contains references.)…

  17. Longitudinal Assessment of Optical Quality and Intraocular Scattering Using the Double-Pass Instrument in Normal Eyes and Eyes with Short Tear Breakup Time

    PubMed Central

    Kobashi, Hidenaga; Kamiya, Kazutaka; Yanome, Kyohei; Igarashi, Akihito; Shimizu, Kimiya

    2013-01-01

    Purpose To assess the longitudinal changes in optical quality including intraocular scattering in normal eyes and eyes with short tear breakup time (TBUT). Methods We prospectively examined twenty eyes of 20 healthy subjects, and age-matched twenty eyes of 20 short TBUT subjects. The modulation transfer function (MTF) cutoff frequency, the Strehl ratio, and the objective scattering index (OSI) were quantitatively assessed using an Optical Quality Analysis System. We investigated the changes in these variables measured consecutively at the initial examination, 5, and 10 seconds without blinking. We also compared these variables in eyes with short TBUT with those in normal eyes. Results No significant differences in the MTF cutoff frequency, Strehl ratio, or OSI were detected over a 10-second period in normal eyes. These variables also became significantly degraded even over a 5-second period in eyes with short TBUT (p<0.01). We found significant differences in these variables at 5 and 10 seconds (p<0.05), but none immediately after the blink between normal and short TBUT eyes. Conclusions Optical quality including intraocular scattering deteriorated significantly with time in eyes with short TBUT, whereas we found significant differences over a 10-second period in normal eyes. Eyes with short TBUT showed greater deterioration in optical quality after the blink than normal eyes. The longitudinal assessment of optical quality may be effective in distinguishing eyes with short TBUT from normal eyes. PMID:24324787

  18. 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

  19. 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.

  20. Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering

    PubMed Central

    2010-01-01

    Background Cluster analysis, and in particular hierarchical clustering, is widely used to extract information from gene expression data. The aim is to discover new classes, or sub-classes, of either individuals or genes. Performing a cluster analysis commonly involve decisions on how to; handle missing values, standardize the data and select genes. In addition, pre-processing, involving various types of filtration and normalization procedures, can have an effect on the ability to discover biologically relevant classes. Here we consider cluster analysis in a broad sense and perform a comprehensive evaluation that covers several aspects of cluster analyses, including normalization. Result We evaluated 2780 cluster analysis methods on seven publicly available 2-channel microarray data sets with common reference designs. Each cluster analysis method differed in data normalization (5 normalizations were considered), missing value imputation (2), standardization of data (2), gene selection (19) or clustering method (11). The cluster analyses are evaluated using known classes, such as cancer types, and the adjusted Rand index. The performances of the different analyses vary between the data sets and it is difficult to give general recommendations. However, normalization, gene selection and clustering method are all variables that have a significant impact on the performance. In particular, gene selection is important and it is generally necessary to include a relatively large number of genes in order to get good performance. Selecting genes with high standard deviation or using principal component analysis are shown to be the preferred gene selection methods. Hierarchical clustering using Ward's method, k-means clustering and Mclust are the clustering methods considered in this paper that achieves the highest adjusted Rand. Normalization can have a significant positive impact on the ability to cluster individuals, and there are indications that background correction is

  1. Hierarchical normalized cuts: unsupervised segmentation of vascular biomarkers from ovarian cancer tissue microarrays.

    PubMed

    Janowczyk, Andrew; Chandran, Sharat; Singh, Rajendra; Sasaroli, Dimitra; Coukos, George; Feldman, Michael D; Madabhushi, Anant

    2009-01-01

    Research has shown that tumor vascular markers (TVMs) may serve as potential OCa biomarkers for prognosis prediction. One such TVM is ESM-1, which can be visualized by staining ovarian Tissue Microarrays (TMA) with an antibody to ESM-1. The ability to quickly and quantitatively estimate vascular stained regions may yield an image based metric linked to disease survival and outcome. Automated segmentation of the vascular stained regions on the TMAs, however, is hindered by the presence of spuriously stained false positive regions. In this paper, we present a general, robust and efficient unsupervised segmentation algorithm, termed Hierarchical Normalized Cuts (HNCut), and show its application in precisely quantifying the presence and extent of a TVM on OCa TMAs. The strength of HNCut is in the use of a hierarchically represented data structure that bridges the mean shift (MS) and the normalized cuts (NCut) algorithms. This allows HNCut to efficiently traverse a pyramid of the input image at various color resolutions, efficiently and accurately segmenting the object class of interest (in this case ESM-1 vascular stained regions) by simply annotating half a dozen pixels belonging to the target class. Quantitative and qualitative analysis of our results, using 100 pathologist annotated samples across multiple studies, prove the superiority of our method (sensitivity 81%, Positive predictive value (PPV), 80%) versus a popular supervised learning technique, Probabilistic Boosting Trees (sensitivity, PPV of 76% and 66%). PMID:20425992

  2. Differences in Eye Movements Control among Dyslexic, Retarded and Normal Readers in the Spanish Population.

    ERIC Educational Resources Information Center

    Martos, F. J.; Vila, J.

    1990-01-01

    Examines the relationship between dyslexia and eye movement control in Spanish-speaking children. Finds no significant differences between dyslexic and retarded readers in their eye movements during reading tasks only; no significant differences between retarded and normal readers in ocular tracking but differences between each of the groups and…

  3. 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.

  4. 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…

  5. Dissociated vertical deviation: an exaggerated normal eye movement used to damp cyclovertical latent nystagmus.

    PubMed Central

    Guyton, D L; Cheeseman, E W; Ellis, F J; Straumann, D; Zee, D S

    1998-01-01

    PURPOSE: Dissociated vertical deviation (DVD) has eluded explanation for more than a century. The purpose of this study has been to elucidate the etiology and mechanism of DVD. METHODS: Eye movement recordings of six young adults with DVD were made with dual-coil scleral search coils under various conditions of fixation, illumination, and head tilt. Horizontal, vertical, and torsional eye movements were recorded for both eyes simultaneously. Analyses of the simultaneous vertical and torsional movements occurring during the DVD response were used to separate and identify the component vergence and version eye movements involved. RESULTS: Typically, both horizontal and cyclovertical latent nystagmus developed upon occlusion of either eye. A cycloversion then occurred, with the fixing eye intorting and tending to depress, the covered eye extorting and elevating. Simultaneously, upward versions occurred for the maintenance of fixation, consisting variously of saccades and smooth eye movements, leading to further elevation of the eye behind the cover. The cyclovertical component of the latent nystagmus became partially damped as the DVD developed. CONCLUSIONS: In patients with an early-onset defect of binocular function, the occlusion of one eye, or even concentration on fixing with one eye, produces unbalanced input to the vestibular system. This results in latent nystagmus, sometimes seen only with magnification. The cyclovertical component of the latent nystagmus, when present, is similar to normal vestibular nystagmus induced by dynamic head tilting about an oblique axis. Such vestibular nystagmus characteristically produces a hyperdeviation of the eyes. In the case of cyclovertical latent nystagmus, the analogous hyperdeviation will persist unless corrected by a vertical vergence. A normal, oblique-muscle-mediated, cycloversion/vertical vergence is called into play. This occurs in the proper direction to correct the hyperdeviation, but it occurs in an exaggerated

  6. 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

  7. Central Retinal Venous Pressure in Eyes of Normal-Tension Glaucoma Patients with Optic Disc Hemorrhage

    PubMed Central

    Kim, Ko Eun; Kim, Dong Myung; Flammer, Josef; Kim, Kyoung Nam

    2015-01-01

    Objective To compare central retinal venous pressure (CRVP) among eyes with and without optic disc hemorrhage (ODH) in bilateral normal-tension glaucoma (NTG) patients and NTG eyes without an episode of ODH. Methods In this prospective study, 22 bilateral NTG patients showing a unilateral ODH and 29 bilateral NTG patients without an episode of ODH were included. Eyes were categorized into group A (n = 22, eyes with ODH), group B (n = 22, fellow eyes without ODH), and group C (n = 29, NTG eyes without an episode of ODH). A contact lens ophthalmodynamometer was used to measure CRVP and central retinal arterial pressure (CRAP). Results Intraocular pressure (IOP) measured on the day of contact lens ophthalmodynamometry showed no difference among groups. However, the mean baseline IOP in group A was significantly lower than that in group C (P = .008). The CRVP in group A (29.1 ± 10.8 mmHg) was significantly lower than that in group C (40.1 ± 8.8 mmHg, P = .001), but similar to that in group B (30.5 ± 8.7 mmHg, P = .409). A similar relationship was noted for CRAP. No significant eye-associated variable for ODH was found in group A and B by conditional logistic regression analysis (all P > 0.05). However, multivariate logistic regression analysis in groups A and C revealed that low mean baseline IOP (odds ratio [OR] = 0.69, 95% confidence interval [CI] 0.49-0.98, P = 0.043) and low CRVP (OR = 0.88, 95% CI 0.80-0.95, P = 0.003) were associated with ODH. Conclusions CRVP was lower in NTG eyes with ODH than in eyes without an episode of ODH, but similar to that of fellow eyes without ODH. These imply less likelihood of association between increased central retinal venous resistance and ODH. PMID:25996599

  8. Fundus depolarization imaging with GDx VCC scanning laser polarimeter and depolarization characteristics of normal eyes

    NASA Astrophysics Data System (ADS)

    Zhou, Qienyuan; Leder, Henry A.; Lo, Barrick P.; Reed, Geradus C.; Knighton, Robert W.; Cousins, Scott W.

    2009-02-01

    GDx VCC is a confocal scanning laser polarimeter (SLP) developed to assess the retinal nerve fiber layer (RNFL) of the eye based on measurement of the phase retardation in the backscattered light from the fundus. In addition to the phase retardation measurement, a depolarization measurement is readily available from the same image series. We hypothesize that the depolarized light in the GDx signal consists of backscattering from the retinal pigment epithelium (RPE) and the RPE-Bruch's membrane junction, and further, that subRPE deposits contribute to the depolarized backscattered light in proportion to their thickness. Therefore, a quantitative macular depolarization map will provide information about both spatial distribution and heterogeneity of the RPE structure and deposit thickness. Ultimately we predict that depolarization mapping will significantly increase the positive predictive power to identify early dry AMD eyes. In this paper, depolarization measurements in normal eyes and age related changes are reported. Data collection was performed at the Duke University Eye Center. A commercial GDx VCC system was modified with a central fixation target and, instead of depolarized light intensity images, normalized depolarization images were derived and saved in the database. Macular depolarization was observed to increase with age in normal eyes at a rate of 0.27%/yr.

  9. 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…

  10. 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

  11. Sensory eye balance in surgically corrected intermittent exotropes with normal stereopsis.

    PubMed

    Feng, Lixia; Zhou, Jiawei; Chen, Li; Hess, Robert F

    2015-01-01

    Surgery to align a deviated or strabismic eye is often done for both functional as well as cosmetic reasons. Although amblyopia is often an impediment to regaining full binocularity in strabismics in general, intermittent exotropes, because their deviation is intermittent, have no amblyopia and some degree of stereopsis. Binocular function, including a balanced ocular dominance, could be expected to be normal after surgical correction if normal levels of stereopsis and visual acuity are postsurgically achieved. Here we used a binocular phase combination paradigm to quantitatively assess the ocular dominance in a group of surgically corrected intermittent exotropes who have normal stereo and visual acuity as defined clinically. Interestingly, we found significant interocular imbalance (balance point < 0.9) in most of the surgically treated patients (8 out 10) but in none of the controls. We conclude that the two eyes may still have a residual sensory imbalance in surgically corrected strabismus even if stereopsis is within normal limits. Our study opens the possibility that a further treatment aimed at re-balancing the ocular dominance might be necessary in surgically treated intermittent exotropia to provide more efficient binocular processing in the long term. PMID:26287935

  12. Sensory eye balance in surgically corrected intermittent exotropes with normal stereopsis

    PubMed Central

    Feng, Lixia; Zhou, Jiawei; Chen, Li; Hess, Robert F.

    2015-01-01

    Surgery to align a deviated or strabismic eye is often done for both functional as well as cosmetic reasons. Although amblyopia is often an impediment to regaining full binocularity in strabismics in general, intermittent exotropes, because their deviation is intermittent, have no amblyopia and some degree of stereopsis. Binocular function, including a balanced ocular dominance, could be expected to be normal after surgical correction if normal levels of stereopsis and visual acuity are postsurgically achieved. Here we used a binocular phase combination paradigm to quantitatively assess the ocular dominance in a group of surgically corrected intermittent exotropes who have normal stereo and visual acuity as defined clinically. Interestingly, we found significant interocular imbalance (balance point < 0.9) in most of the surgically treated patients (8 out 10) but in none of the controls. We conclude that the two eyes may still have a residual sensory imbalance in surgically corrected strabismus even if stereopsis is within normal limits. Our study opens the possibility that a further treatment aimed at re-balancing the ocular dominance might be necessary in surgically treated intermittent exotropia to provide more efficient binocular processing in the long term. PMID:26287935

  13. 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.

  14. Correlation between ocular perfusion pressure and ocular pulse amplitude in glaucoma, ocular hypertension, and normal eyes

    PubMed Central

    Figueiredo, Bruno P; Cronemberger, Sebastião; Kanadani, Fabio N

    2013-01-01

    Background The purpose of this study was to investigate the correlation between ocular perfusion pressure and ocular pulse amplitude in glaucoma, ocular hypertension, and normal eyes. Methods Ninety eyes from 90 patients were included. Thirty patients had been recently diagnosed with glaucoma and had no previous history of treatment for ocular hypotension, 30 had elevated intraocular pressure (IOP) without evidence of glaucoma, and 30 had normal IOP (<21 mmHg) with no detectable glaucomatous damage. Goldmann applanation tonometry (GAT), dynamic contour tonometry (DCT), blood pressure measurement, pachymetry, Humphrey visual field, and routine ophthalmic examination was performed in each patient. Ocular perfusion pressure was calculated as the difference between mean arterial pressure and IOP. The ocular pulse amplitude was given by DCT. The Pearson correlation coefficient was used to compare the glaucomatous and ocular hypertensive groups, and comparisons with the normal IOP group were done using the Spearman’s rank correlation coefficient. Results Mean IOP by DCT was 22.7 ± 4.3 mmHg in the glaucoma group, 22.3 ± 2.8 mmHg in the ocular hypertension group, and 14.3 ± 1.6 mmHg in the control group. Mean IOP by GAT was 19.0 ± 5.1 mmHg for glaucoma, 22.4 ± 2.1 mmHg for ocular hypertension, and 12.9 ± 2.2 mmHg for controls. Mean ocular pulse amplitude was 3.4 ± 1.2 mmHg in the glaucoma group, 3.5 ± 1.2 mmHg in the ocular hypertension group, and 2.6 ± 0.9 mmHg in the control group. Mean ocular perfusion pressure was 46.3 ± 7.9 mmHg in the glaucoma group, 46.3 ± 7.9 mmHg in the ocular hypertension group, and 50.2 ± 7.0 mmHg in controls. No significant correlation between ocular perfusion pressure and ocular pulse amplitude was found in any of the groups (P = 0.865 and r = −0.032, P = 0.403 and r = −0.156, P = 0.082 and ρ = −0.307 for glaucoma, ocular hypertension, and normal eyes, respectively). Conclusion There is no significant correlation between

  15. Normal anatomy of the aqueous humour outflow system in the domestic pig eye.

    PubMed

    McMenamin, P G; Steptoe, R J

    1991-10-01

    The normal functional anatomy of the aqueous humour outflow pathways in the domestic pig is poorly documented in the literature despite its being readily available and of a similar size to the human eye. Anterior segment tissue from 12 pig eyes was appropriately fixed and investigated by light microscopy, and scanning and transmission electron microscopy. The configuration of the iridocorneal angle tissues is similar to other nonprimate mammals in several respects, i.e. it possesses a deep ciliary cleft crossed by stout pectinate ligaments and delicate uveal cords, poorly developed ciliary musculature, and an angular aqueous plexus. However, there were some noteworthy features which may make it a suitable model for specific types of glaucoma related research. These features include a shallow scleral sulcus which contains a wedge-shaped mass of corneoscleral tissue comparable in size to the human trabecular meshwork. This tissue was more trabecular than 'reticular' in arrangement, the latter being the more common in nonprimate mammalian species. The relevance of the present findings to the use and limitations of the porcine eye as a model of the human aqueous outflow pathways is discussed. PMID:1810936

  16. 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

  17. 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

  18. 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

  19. Anatomical Attributes of the Optic Nerve Head in Eyes with Parafoveal Scotoma in Normal Tension Glaucoma

    PubMed Central

    Rao, Aparna; Mukherjee, Sujoy

    2014-01-01

    Purpose To evaluate optic nerve characteristics independent of systemic factors predisposing to parafoveal scotoma in normal tension glaucoma. Methods We included 40 patients with bilateral normal tension glaucoma with parafoveal scotoma (visual field defect in one hemifield within 10° of fixation with at least one point at p<1% lying at the two innermost paracentral points) in only one eye (Parafoveal group, PF, n = 40) identified from the hospital database in this observational cross sectional study. The other eye with no parafoveal scotoma constituted the control group (n = 32). Red free fundus photographs were evaluated using Image J software analyzing parameters including vertical and horizontal disc diameter, disc haemorrhage, location and angular width of the retinal nerve fibre layer depth and displacement of the central vessel trunk, CVT (vertical and horizontal). Clinical characteristics and disc parameters were compared in the two groups. Results The PF group had lower mean deviation(MD) and visual field index (VFI) and higher pattern standard deviation (PSD) than control group (p≤0.001) for similar untreated IOP, (p = 0.9). Disc haemorrhages were more frequent in the PF group, p = 0.01. The PF group had greater width of nerve fibre layer defects, p = 0.05 and greater vertical displacement of the central vessel trunk, p = 0.001. On multivariate logistic regression, parafoveal scotoma was significantly associated with increased vertical distance of the CVT, p = 0.0001. Conclusion Increased vertical displacement of the CVT is associated with parafoveal scotoma in normal tension glaucoma. Localising the vessel trunk may help clinicians in identifying patients at risk for parafoveal involvement. PMID:24595065

  20. 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

  1. Macular thickness and macular volume measurements using spectral domain optical coherence tomography in normal Nepalese eyes

    PubMed Central

    Pokharel, Amrit; Shrestha, Gauri Shankar; Shrestha, Jyoti Baba

    2016-01-01

    Purpose To record the normative values for macular thickness and macular volume in normal Nepalese eyes. Methods In all, 126 eyes of 63 emmetropic subjects (mean age: 21.17±6.76 years; range: 10–37 years) were assessed for macular thickness and macular volume, using spectral domain-optical coherence tomography over 6×6 mm2 in the posterior pole. A fast macular thickness protocol was employed. Statistics such as the mean, median, standard deviation, percentiles, and range were used, while a P-value was set at 0.05 to test significance. Results Average macular thickness and total macular volume were larger in males compared to females. With each year of increasing age, these variables decreased by 0.556 μm and 0.0156 mm3 for average macular thickness and total macular volume, respectively. The macular thickness was greatest in the inner superior section and lowest at the center of the fovea. The volume was greatest in the outer nasal section and thinnest in the fovea. The central subfield thickness (r=−0.243, P=0.055) and foveal volume (r=0.216, P=0.09) did not correlate with age. Conclusion Males and females differ significantly with regard to macular thickness and macular volume measurements. Reports by other studies that the increase in axial length reduced thickness and volume, were negated by this study which found a positive correlation among axial length, thickness, and volume. PMID:27041990

  2. 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.

  3. 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

  4. 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

  5. Thickness Mapping of Eleven Retinal Layers Segmented Using the Diffusion Maps Method in Normal Eyes

    PubMed Central

    Kafieh, Raheleh; Rabbani, Hossein; Abramoff, Michael D.; Sonka, Milan

    2015-01-01

    This study was conducted to determine the thickness map of eleven retinal layers in normal subjects by spectral domain optical coherence tomography (SD-OCT) and evaluate their association with sex and age. Mean regional retinal thickness of 11 retinal layers was obtained by automatic three-dimensional diffusion map based method in 112 normal eyes of 76 Iranian subjects. We applied our previously reported 3D intraretinal fast layer segmentation which does not require edge-based image information but rather relies on regional image texture. The thickness maps are compared among 9 macular sectors within 3 concentric circles as defined by ETDRS. The thickness map of central foveal area in layers 1, 3, and 4 displayed the minimum thickness. Maximum thickness was observed in nasal to the fovea of layer 1 and in a circular pattern in the parafoveal retinal area of layers 2, 3, and 4 and in central foveal area of layer 6. Temporal and inferior quadrants of the total retinal thickness and most of other quadrants of layer 1 were significantly greater in the men than in the women. Surrounding eight sectors of total retinal thickness and a limited number of sectors in layers 1 and 4 significantly correlated with age. PMID:25960888

  6. 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

  7. Assessment of Schlemm’s canal in a normal human eye by swept source optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Shi, G. H.; Wang, F.; Li, X. Q.; Lu, J.; Sun, X. H.; Jiang, C. H.; Zhang, Y. D.

    2013-07-01

    We have applied custom-built anterior segment optical coherence tomography based on a 1310 nm center wavelength swept laser source to measure Schlemm’s canal (SC) area in the living human eye. A total of 50 healthy volunteers with 100 normal eyes have been measured on the nasal and temporal sides successfully. The statistical results show that there are no significant differences between females and males in respect of SC area (female: 8062.24 μm2 ± 1492.304 μm2 male: 7714.52 μm2 ± 1439.034 μm2 p = 0.095), and also no significant differences of SC area are found between the five age groups (Sig=0.253). Therefore, it would be reasonable to assume that, in normal human eyes, the SC possibly maintains the same impact on the gender- and age-related aqueous outflow facility.

  8. 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…

  9. Dual transcriptional activities of SIX proteins define their roles in normal and ectopic eye development.

    PubMed

    Anderson, Abigail M; Weasner, Bonnie M; Weasner, Brandon P; Kumar, Justin P

    2012-03-01

    The SIX family of homeodomain-containing DNA-binding proteins play crucial roles in both Drosophila and vertebrate retinal specification. In flies, three such family members exist, but only two, Sine oculis (So) and Optix, are expressed and function within the eye. In vertebrates, the homologs of Optix (Six3 and Six6) and probably So (Six1 and Six2) are also required for proper eye formation. Depending upon the individual SIX protein and the specific developmental context, transcription of target genes can either be activated or repressed. These activities are thought to occur through physical interactions with the Eyes absent (Eya) co-activator and the Groucho (Gro) co-repressor, but the relative contribution that each complex makes to overall eye development is not well understood. Here, we attempt to address this issue by investigating the role that each complex plays in the induction of ectopic eyes in Drosophila. We fused the VP16 activation and Engrailed repressor domains to both So and Optix, and attempted to generate ectopic eyes with these chimeric proteins. Surprisingly, we find that So and Optix must initially function as transcriptional repressors to trigger the formation of ectopic eyes. Both factors appear to be required to repress the expression of non-retinal selector genes. We propose that during early phases of eye development, SIX proteins function, in part, to repress the transcription of non-retinal selector genes, thereby allowing induction of the retina to proceed. This model of repression-mediated induction of developmental programs could have implications beyond the eye and might be applicable to other systems. PMID:22318629

  10. 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

  11. SNP microarray-based 24 chromosome aneuploidy screening demonstrates that cleavage-stage FISH poorly predicts aneuploidy in embryos that develop to morphologically normal blastocysts.

    PubMed

    Northrop, L E; Treff, N R; Levy, B; Scott, R T

    2010-08-01

    Although selection of chromosomally normal embryos has the potential to improve outcomes for patients undergoing IVF, the clinical impact of aneuploidy screening by fluorescence in situ hybridization (FISH) has been controversial. There are many putative explanations including sampling error due to mosaicism, negative impact of biopsy, a lack of comprehensive chromosome screening, the possibility of embryo self-correction and poor predictive value of the technology itself. Direct analysis of the negative predictive value of FISH-based aneuploidy screening for an embryo's reproductive potential has not been performed. Although previous studies have found that cleavage-stage FISH is poorly predictive of aneuploidy in morphologically normal blastocysts, putative explanations have not been investigated. The present study used a single nucleotide polymorphism (SNP) microarray-based 24 chromosome aneuploidy screening technology to re-evaluate morphologically normal blastocysts that were diagnosed as aneuploid by FISH at the cleavage stage. Mosaicism and preferential segregation of aneuploidy to the trophectoderm (TE) were evaluated by characterization of multiple sections of the blastocyst. SNP microarray technology also provided the first opportunity to evaluate self-correction mechanisms involving extrusion or duplication of aneuploid chromosomes resulting in uniparental disomy (UPD). Of all blastocysts evaluated (n = 50), 58% were euploid in all sections despite an aneuploid FISH result. Aneuploid blastocysts displayed no evidence of preferential segregation of abnormalities to the TE. In addition, extrusion or duplication of aneuploid chromosomes resulting in UPD did not occur. These findings support the conclusion that cleavage-stage FISH technology is poorly predictive of aneuploidy in morphologically normal blastocysts. PMID:20479065

  12. Comparison of Anterior Segment Biometric Measurements between Pentacam HR and IOLMaster in Normal and High Myopic Eyes

    PubMed Central

    Zhang, Yaqin; Jia, Yading; Zhang, Haining; Jia, Zhijie; Wang, Xiaogang

    2015-01-01

    Purpose To compare the anterior chamber depth (ACD), keratometry (K) and astigmatism measurements taken by IOLMaster and Pentacam HR in normal and high myopic (HM) eyes. Design A prospective observational case series. Methods Sixty-six normal eyes and 59 HM eyes underwent ACD, keratometry and astigmatism measurements with both devices. Axial length (AL) was measured on IOLMaster. The interdevice agreement was evaluated using the Bland-Altman analysis and paired t-test. The correlations between age and AL & ACD were analyzed. Vector analysis was used to compare astigmatism measurements. Results The ACD from IOLMaster and Pentacam HR was different for the normal group (P = 0.003) but not for the HM group (P = 0.280). IOLMaster demonstrated higher steep K and mean K values than Pentacam HR for both normal and HM groups (P<0.001 for all). IOLMaster also have higher flat K values for the HM groups (P<0.001) but were statistically equivalent with Pentacam HR for the normal group (P = 0.119) IOLMaster and Pentacam HR were different in astigmatism measurements for the normal group but were statistically equivalent for the HM group. For the normal group, age was negatively correlated with AL, IOLMaster ACD and Pentacam HR ACD (r = -0.395, P = 0.001; r = -0.715, P < 0.001; r = -0.643, P < 0.001). For the HM group, age was positively correlated with AL but negatively correlated with IOLMaster ACD and Pentacam HR ACD (r = 0.377, P = 0.003; r = -0.392, P = 0.002; r = -0.616, P < 0.001). Conclusions The IOLMaster and Pentacam HR have significant difference in corneal power measurements for both normal and HM groups. The two instruments also differ in ACD and astigmatism measurement for the normal group. Therefore, a single instrument is recommended for studying longitudinal changes in anterior segment biometric measurements. Age should be considered as an influencing factor for both AL and ACD values in the normal and HM group. PMID:26575265

  13. 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...

  14. Drosophila Eyes Absent Is Required for Normal Cone and Pigment Cell Development

    PubMed Central

    Karandikar, Umesh C.; Jin, Meng; Jusiak, Barbara; Kwak, SuJin; Chen, Rui; Mardon, Graeme

    2014-01-01

    In Drosophila, development of the compound eye is orchestrated by a network of highly conserved transcriptional regulators known as the retinal determination (RD) network. The retinal determination gene eyes absent (eya) is expressed in most cells within the developing eye field, from undifferentiated retinal progenitors to photoreceptor cells whose differentiation begins at the morphogenetic furrow (MF). Loss of eya expression leads to an early block in retinal development, making it impossible to study the role of eya expression during later steps of retinal differentiation. We have identified two new regulatory regions that control eya expression during retinal development. These two enhancers are necessary to maintain eya expression anterior to the MF (eya-IAM) and in photoreceptors (eya-PSE), respectively. We find that deleting these enhancers affects developmental events anterior to the MF as well as retinal differentiation posterior to the MF. In line with previous results, we find that reducing eya expression anterior to the MF affects several early steps during early retinal differentiation, including cell cycle arrest and expression of the proneural gene ato. Consistent with previous observations that suggest a role for eya in cell proliferation during early development we find that deletion of eya-IAM leads to a marked reduction in the size of the adult retinal field. On the other hand, deletion of eya-PSE leads to defects in cone and pigment cell development. In addition we find that eya expression is necessary to activate expression of the cone cell marker Cut and to regulate levels of the Hedgehog pathway effector Ci. In summary, our study uncovers novel aspects of eya-mediated regulation of eye development. The genetic tools generated in this study will allow for a detailed study of how the RD network regulates key steps in eye formation. PMID:25057928

  15. 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).

  16. 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).

  17. A comparative study of complications of cataract surgery with phacoemulsification in eyes with high and normal axial length

    PubMed Central

    Fesharaki, Hamid; Peyman, Alireza; Rowshandel, Mehdi; Peyman, Mohammadreza; Alizadeh, Pegah; Akhlaghi, Mohammadreza; Ashtari, AliReza

    2012-01-01

    Background: This study performed to assess the safety of cataract extraction with phacoemulsification and intraocular lens (IOL) implantation in patients with high axial length compared with patients with normal axial length. Materials and Methods: A total of 866 eyes were enrolled in this study; all subjects underwent phacoemulsification and IOL implantation for treatment of cataract. Seven hundred and nine eyes fell in the normal group with axial lengths ranging between 21 and 24.5 mm, and 157 eyes were considered myopic with axial length equal or greater than 26 mm. The two groups were compared regarding intraoperative surgical complications, such as vitreous loss, posterior capsular rupture, nucleolus drop, and undesirable implantation of IOL in the anterior chamber. Results: Age was a risk factor in both groups, with each year increase of age, the chance of incidence of intraoperative complications increased 1.04-folds (P = 0.03). And with 1 mm increase in axial length, the incidence of complications raised 1.22-folds (P = 0.007). There was no significant correlation between axial length and incidence of vitreous loss, although the incidence of posterior capsular rupture and nucleus fragment drops increased with increment in the axial length. Sex of the patients and side of the left or right eye were not found to be significant risk factors. Conclusions: As the results illustrate, in this survey, age and high axial length were statistically significant risk factors for incidence of intraoperative complications of cataract surgery with phacoemulsification technique. Anticipation of these complications and also preparation and prophylactic measures may decrease incidence of these complications. PMID:23326797

  18. 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

  19. 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 ...

  20. Microarrays: an overview.

    PubMed

    Lee, Norman H; Saeed, Alexander I

    2007-01-01

    Gene expression microarrays are being used widely to address a myriad of complex biological questions. To gather meaningful expression data, it is crucial to have a firm understanding of the steps involved in the application of microarrays. The available microarray platforms are discussed along with their advantages and disadvantages. Additional considerations include study design, quality control and systematic assessment of microarray performance, RNA-labeling strategies, sample allocation, signal amplification schemes, defining the number of appropriate biological replicates, data normalization, statistical approaches to identify differentially regulated genes, and clustering algorithms for data visualization. In this chapter, the underlying principles regarding microarrays are reviewed, to serve as a guide when navigating through this powerful technology. PMID:17332646

  1. 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

  2. Objective performance of a set of uncorrected 20/20 normal eyes: clinical reference

    NASA Astrophysics Data System (ADS)

    Tepichín, E.; López-Olazagasti, E.; Sánchez-de-La-Llave, D.; Cruz Félix, Angel S.; Ramírez-Zavaleta, G.; Ibarra, J.

    2011-08-01

    In recent years we have been working in the characterization of the objective average performance of a set of uncorrected human eyes with a 20/20 visual acuity, described as the resultant average wavefront aberration function (WA), point-spread function (PSF), modulation transfer function (MTF), and power refractive maps. This objective performance has been used as our clinical reference to analyze the objective pre- and post-operated performance in laser refractive surgery in different situations. We show some of our current results obtained from the application of our clinical reference.

  3. 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

  4. 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

  5. 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. ...

  6. 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

  7. 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

  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. 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

  11. Comparison of the Wave Amplitude of Visually Evoked Potential in Amblyopic Eyes between Patients with Esotropia and Anisometropia and a Normal Group

    PubMed Central

    Talebnejad, Mohammad Reza; Hosseinmenni, Saeedeh; Jafarzadehpur, Ebrahim; Mirzajani, Ali; Osroosh, Enayatollah

    2016-01-01

    Background: We compared the wave amplitude of visually evoked potential (VEP) between patients with esotropic and anisometropic amblyopic eyes and a normal group. Methods: The wave amplitude of VEP was documented in 2 groups of persons with amblyopia (15 with esotropia and 28 with anisometropia) and 1 group of individuals with normal visual acuity (n, 15). The amplitude of P100 was recorded monocularly with different spatial frequencies. Results: Our statistical analysis revealed that the wave amplitude in the 2 groups with amblyopia was significantly decreased compared to that in the normal group (P<0.001). There was a significant difference regarding the amplitude in high spatial frequencies in both high- and low-contrast conditions between the groups with esotropia and anisometropia and the normal group (P<0.001). There were also significant differences in large check-size stimuli and low-contrast condition between the amblyopic groups with esotropia and anisometropia and the normal group (P=0.013 and P=0.044, respectively). In large check-size stimuli and high-contrast condition, a significant difference was indicated only in the comparison between the esotropic amblyopic eyes and the normal eyes (P=0.036). Conclusion: The wave amplitude parameter of VEP was influenced by both types of amblyopia, but it seems that this parameter was more sensitive to esotropic amblyopia than anisometropic amblyopia. This outcome may reflect a non-parallel pattern of cortical responses in the comparison of the 2 types of amblyopia with each other and with the control group, which may be beneficial for the diagnosis and treatment of amblyopia. PMID:26989279

  12. 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…

  13. 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

  14. 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

  15. Navigating Public Microarray Databases

    PubMed Central

    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. PMID:18629145

  16. 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. PMID:18629145

  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. Eye muscle repair

    MedlinePlus

    ... Your child's eyes should look normal a few weeks after the surgery. ... Surgical Approach to the Rectus Muscles. In: Tasman W, Jaeger EA, ... Hug D, Plummer LS, Stass-Isern M. Disorders of eye movement and ...

  19. 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

  20. 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)

  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. Analysis with Support Vector Machine Shows HIV-Positive Subjects without Infectious Retinitis Have mfERG Deficiencies Compared to Normal Eyes

    PubMed Central

    Goldbaum, Michael H.; Falkenstein, Irina; Kozak, Igor; Hao, Jiucang; Bartsch, Dirk-Uwe; Sejnowski, Terrance; Freeman, William R.

    2008-01-01

    Purpose To test the following hypotheses: (1) eyes from individuals with human immunodeficiency virus (HIV) have electrophysiologic abnormalities that manifest as multifocal electroretinogram (mfERG) abnormalities; (2) the retinal effects of HIV in immune-competent HIV individuals differ from the effects in immune-incompetent HIV individuals; (3) strong machine learning classifiers (MLCs), like support vector machine (SVM), can learn to use mfERG abnormalities in the second-order kernel (SOK) to distinguish HIV from normal eyes; and (4) the mfERG abnormalities fall into patterns that can be discerned by MLCs. We applied a supervised MLC, SVM, to determine if mfERGs in eyes from patients with HIV differ from mfERGs in HIV-negative controls. Methods Ninety-nine HIV-positive patients without visible retinopathy were divided into 2 groups: (1) 59 high-CD4 individuals (H, 104 eyes), 48.5 ± 7.7 years, whose CD4 counts were never observed below 100, and (2) 40 low-CD4 individuals (L, 61 eyes), 46.2 ± 5.6 years, whose CD4 counts were below 100 for at least 6 months. The normal group (N, 82 eyes) had 41 age-matched HIV-negative individuals, 46.8 ± 6.2 years. The amplitude and latency of the first positive curve (P1, hereafter referred to as a) and the first negative curve (N1, referred to as b) in the SOK of 103 hexagon patterns of the central 28° of the retina were recorded from the eyes in each group. SVM was trained and tested with cross-validation to distinguish H from N and L from N. SOK was chosen as a presumed detector of inner retinal abnormalities. Classifier performance was measured with the area under the receiver operating characteristic (AUROC) curve to permit comparison of MLCs. Improvement in performance and identification of subsets of the most important features were sought with feature selection by backward elimination. Results In general, the SOK b-parameters separated L from N and H from N better than a-parameters, and latency separated L from N and

  3. Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots.

    PubMed

    Scholma, Jetse; Fuhler, Gwenny M; Joore, Jos; Hulsman, Marc; Schivo, Stefano; List, Alan F; Reinders, Marcel J T; Peppelenbosch, Maikel P; Post, Janine N

    2016-01-01

    Massive parallel analysis using array technology has become the mainstay for analysis of genomes and transcriptomes. Analogously, the predominance of phosphorylation as a regulator of cellular metabolism has fostered the development of peptide arrays of kinase consensus substrates that allow the charting of cellular phosphorylation events (often called kinome profiling). However, whereas the bioinformatical framework for expression array analysis is well-developed, no advanced analysis tools are yet available for kinome profiling. Especially intra-array and interarray normalization of peptide array phosphorylation remain problematic, due to the absence of "housekeeping" kinases and the obvious fallacy of the assumption that different experimental conditions should exhibit equal amounts of kinase activity. Here we describe the development of analysis tools that reliably quantify phosphorylation of peptide arrays and that allow normalization of the signals obtained. We provide a method for intraslide gradient correction and spot quality control. We describe a novel interarray normalization procedure, named repetitive signal enhancement, RSE, which provides a mathematical approach to limit the false negative results occuring with the use of other normalization procedures. Using in silico and biological experiments we show that employing such protocols yields superior insight into cellular physiology as compared to classical analysis tools for kinome profiling. PMID:27225531

  4. Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots

    PubMed Central

    Scholma, Jetse; Fuhler, Gwenny M.; Joore, Jos; Hulsman, Marc; Schivo, Stefano; List, Alan F.; Reinders, Marcel J. T.; Peppelenbosch, Maikel P.; Post, Janine N.

    2016-01-01

    Massive parallel analysis using array technology has become the mainstay for analysis of genomes and transcriptomes. Analogously, the predominance of phosphorylation as a regulator of cellular metabolism has fostered the development of peptide arrays of kinase consensus substrates that allow the charting of cellular phosphorylation events (often called kinome profiling). However, whereas the bioinformatical framework for expression array analysis is well-developed, no advanced analysis tools are yet available for kinome profiling. Especially intra-array and interarray normalization of peptide array phosphorylation remain problematic, due to the absence of “housekeeping” kinases and the obvious fallacy of the assumption that different experimental conditions should exhibit equal amounts of kinase activity. Here we describe the development of analysis tools that reliably quantify phosphorylation of peptide arrays and that allow normalization of the signals obtained. We provide a method for intraslide gradient correction and spot quality control. We describe a novel interarray normalization procedure, named repetitive signal enhancement, RSE, which provides a mathematical approach to limit the false negative results occuring with the use of other normalization procedures. Using in silico and biological experiments we show that employing such protocols yields superior insight into cellular physiology as compared to classical analysis tools for kinome profiling. PMID:27225531

  5. 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 ...

  6. 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

  7. 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.

  8. Tiling Microarray Analysis Tools

    Energy Science and Technology Software Center (ESTSC)

    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

  9. 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…

  10. Eye redness

    MedlinePlus

    Bloodshot eyes; Red eyes; Scleral infection; Conjunctival infection ... There are many causes of a red eye or eyes. Some are medical emergencies and some are a cause for concern, but not an emergency. Others are nothing to worry about. ...

  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. Eye emergencies

    MedlinePlus

    ... Trauma A black eye is usually caused by direct trauma to the eye or face. The bruise ... can cause bruising around the eyes, even without direct injury to the eye. Sometimes, serious damage to ...

  13. 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 ...

  14. 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

  15. 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. PMID:25758288

  16. 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

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

    PubMed Central

    Maurer, Michael; Molidor, Robert; Sturn, Alexander; Hartler, Juergen; Hackl, Hubert; Stocker, Gernot; Prokesch, Andreas; Scheideler, Marcel; Trajanoski, Zlatko

    2005-01-01

    Background Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. Results MARS (Microarray Analysis and Retrieval System) provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS), a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. Conclusion We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at . PMID:15836795

  18. 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

  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. Microarrays--status and prospects.

    PubMed

    Venkatasubbarao, Srivatsa

    2004-12-01

    Microarrays have become an extremely important research tool for life science researchers and are also beginning to be used in diagnostic, treatment and monitoring applications. This article provides a detailed description of microarrays prepared by in situ synthesis, deposition using microspotting methods, nonplanar bead arrays, flow-through microarrays, optical fiber bundle arrays and nanobarcodes. The problems and challenges in the development of microarrays, development of standards and diagnostic microarrays are described. Tables summarizing the vendor list of various derivatized microarray surfaces, commercially sold premade microarrays, bead arrays and unique microarray products in development are also included. PMID:15542153

  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 Emergencies

    MedlinePlus

    ... Emergencies Cardiac Emergencies Eye Emergencies Lung Emergencies Surgeries Eye Emergencies Marfan syndrome significantly increases your risk of ... light-sensitive membrane in the back of the eye (the retina) from its supporting layers. It is ...

  3. Eye Wear

    MedlinePlus

    Eye wear protects or corrects your vision. Examples are Sunglasses Safety goggles Glasses (also called eyeglasses) Contact ... jobs and some sports carry a risk of eye injury. Thousands of children and adults get eye ...

  4. 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 ...

  5. 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 ...

  6. 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 ...

  7. Eye Injuries

    MedlinePlus

    ... 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 work ...

  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. 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

  10. 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

  11. Eye Movement Disorders in Dyslexia. Final Report.

    ERIC Educational Resources Information Center

    Festinger, Leon; And Others

    Eye movements of 18 male and seven female dyslexic children and 10 normal children were evaluated to determine if eye movement disorders may be the cause of some of the symptoms associated with dyslexia. Data on eye movements were collected while Ss moved their eyes from one fixation point to another in a nonreading situation. Errors in vertical…

  12. Eye Movements, Perceptual Span, and Reading Disability.

    ERIC Educational Resources Information Center

    Rayner, Keith

    1983-01-01

    Research is reviewed on eye movements during reading, on the perceptual span and control of eye movements during normal reading, and on the nature of eye movements in dyslexia. Rather than the cause of dyslexia, eye movements are said to reflect underlying cognitive or neurological problems. (CL)

  13. 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

  14. Eye Cancer

    MedlinePlus

    ... adults are melanoma and lymphoma. The most common eye cancer in children is retinoblastoma, which starts in the cells of the retina. ... from other parts of the body. Treatment for eye cancer varies by the type and by how advanced ...

  15. 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 ...

  16. 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 ...

  17. 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…

  18. Eye Problems

    MedlinePlus

    ... Do you have diabetes, and have you noticed any changes in your vision? Yes Over time, too much glucose (sugar) in the ... eye pink, red or irritated, and are there any secretions or mucus from the eye? Yes CONJUNCTIVITIS, also called "PINK EYE," can be caused ...

  19. Eye floaters

    MedlinePlus

    ... eyes are not on the surface of your eyes, but inside them. These floaters are bits of cell debris that drift around ... is the layer in the back of the eye.) If you notice a sudden increase in floaters or if you see floaters along with flashes ...

  20. 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.

  1. Experiment K-7-31: Studies of Vestibular Primary Afferents and Eye Movements in Normal, Hypergravity and Hypogravity - Axon Cosmos Flight 2044

    NASA Technical Reports Server (NTRS)

    Correia, M. J.; Perachio, A. A.; Dickman, J. D.; Kozlovskaya, I.; Sirota, M.; Yakushin, S.; Beloozerova, I. N.

    1994-01-01

    Fourteen days of active head movements in microgravity appear to modify the gain and neural adaptation properties of the horizontal semicircular canals in the rhesus monkey. This is the first demonstration of adaptive plasticity in the sensory receptor. Reversing prisms, for example, do not modify the gain of the primary afferent response. Pulse yaw rotation, sinusoidal rotation, and sum of sinusoidal rotation testing during the first day following recovery revealed that the gain of a sample of afferents was significantly greater than the gain derived from afferent responses obtained during pre-flight and control monkey testing. There was no strong evidence of tilt sensitivity in the sample of afferents that we tested either during the pre-flight or control tests or during the first day post-flight. Two irregular afferents tested on postflight day 2 showed changes with tilt but the responses were not systematic. The spontaneous discharge did not change following flight. Mean firing rate and coefficient of variation remained constant during the post flight tests and was near the value measured during pre flight tests. The change in gain of horizontal canal afferents might be adaptive. The animals were required to look at a target for food. This required active head and eye movements. Active head movements have been shown to be hypometric and eye movements have been shown to be hypermetric during the first few days of past Cosmos flights (see introduction). It might be that the increased gain in the horizontal semicircular canals permit accurate target acquisition during hypometric head movements by driving the eyes to greater angles for smaller angles of head movement. The mechanism by which the semicircular canals recalibrate (increase their gain) is unknown. The efferent vestibular system is a logical candidate. Horizontal nystagmus during rotation about an earth vertical axis with the horizontal semicircular canals in the plane of rotation produced the same

  2. Microarrays under the microscope.

    PubMed

    Wildsmith, S E; Elcock, F J

    2001-02-01

    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

  3. 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. PMID:24784530

  4. 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

  5. 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.

  6. 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 ...

  7. Dry Eye

    MedlinePlus

    ... surgery, called punctal cautery, is recommended to permanently close the drainage holes. The procedure helps keep the limited volume of tears on the eye for a longer period of time. In some patients with dry eye, supplements or dietary sources (such as tuna fish) of omega-3 fatty ...

  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. Compressive Sensing DNA Microarrays

    PubMed Central

    2009-01-01

    Compressive sensing microarrays (CSMs) are DNA-based sensors that operate using group testing and compressive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed. PMID:19158952

  10. Hydrofluoric acid burns of the eye.

    PubMed

    McCulley, J P; Whiting, D W; Petitt, M G; Lauber, S E

    1983-06-01

    A case of hydrofluoric acid (HF) burns of the eye is reported and a review is presented of our investigation into the mechanism of HF toxicity in ocular tissues. A number of therapeutic procedures that have been successful in the treatment of HF skin burns were studied in the rabbit for use in the eye. Immediate single irrigation with water, normal saline or isotonic magnesium chloride solution is the most effective therapy for ocular HF burns. Extrapolation of other skin burn treatments to use in the eye is unacceptable due to the toxicity of these agents in normal eyes and the additive damage caused in burned eyes. PMID:6886845

  11. 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

  12. 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. PMID:26614075

  13. Healthy Eyes

    MedlinePlus

    ... Programs Training and Jobs Home > Healthy Eyes Healthy Vision Diabetes Diabetes Home How Much Do You Know? ... seeing your best. Read more. What are common vision problems? Some of the most common vision problems ...

  14. 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 ...

  15. Eye emergencies

    MedlinePlus

    ... and there is a good chance of recovery. Alkaline substances -- such as lime, lye, drain cleaners, and ... at high speed by machining, grinding, or hammering metal have the highest risk of injuring 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. 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 ...

  18. 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

  19. Aging and Your Eyes

    MedlinePlus

    ... Your Eyes Heath and Aging Aging and Your Eyes Steps to Protect Your Eyesight Common Eye Problems ... weight can also help protect your vision. Common Eye Problems The following common eye problems can be ...

  20. 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

  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. 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. PMID:23505547

  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. 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

  5. Chemistry of Natural Glycan Microarray

    PubMed Central

    Song, Xuezheng; Heimburg-Molinaro, Jamie; Cummings, Richard D.; Smith, David F.

    2014-01-01

    Glycan microarrays have become indispensable tools for studying protein-glycan interactions. Along with chemo-enzymatic synthesis, glycans isolated from natural sources have played important roles in array development and will continue to be a major source of glycans. N- and O-glycans from glycoproteins, and glycans from glycosphingolipids can be released from corresponding glycoconjugates with relatively mature methods, although isolation of large numbers and quantities of glycans are still very challenging. Glycosylphosphatidylinositol (GPI)-anchors and glycosaminoglycans (GAGs) are less represented on current glycan microarrays. Glycan microarray development has been greatly facilitated by bifunctional fluorescent linkers, which can be applied in a “Shotgun Glycomics” approach to incorporate isolated natural glycans. Glycan presentation on microarrays may affect glycan binding by GBPs, often through multivalent recognition by the GBP. PMID:24487062

  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. Eye and orbit ultrasound

    MedlinePlus

    Echography - eye orbit; Ultrasound - eye orbit; Ocular ultrasonography; Orbital ultrasonography ... ophthalmology department of a hospital or clinic. Your eye is numbed with medicine (anesthetic drops). The ultrasound ...

  8. 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

  9. Evaluating concentration estimation errors in ELISA microarray experiments

    PubMed Central

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

    2005-01-01

    Background Enzyme-linked immunosorbent assay (ELISA) is a standard immunoassay to estimate a protein's concentration in a sample. Deploying ELISA in a microarray format permits simultaneous estimation of the concentrations of numerous proteins in a small sample. These estimates, however, are uncertain due to processing error and biological variability. Evaluating estimation error is critical to interpreting biological significance and improving the ELISA microarray process. Estimation error evaluation must be automated to realize a reliable high-throughput ELISA microarray system. In this paper, we present a statistical method based on propagation of error to evaluate concentration estimation errors in the ELISA microarray process. Although propagation of error is central to this method and the focus of this paper, it is most 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 concentration estimation errors. Results We use an ELISA microarray investigation of breast cancer biomarkers to illustrate the evaluation of concentration estimation 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. We summarize the results with a simple, three-panel diagnostic visualization featuring a scatterplot of the standard data with logistic standard curve and 95% confidence intervals, an annotated histogram of sample measurements, and a plot of the 95% concentration coefficient of variation, or relative error, as a function of concentration. Conclusions This statistical method should be of value in the rapid evaluation and quality control of high-throughput ELISA microarray analyses

  10. 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.

  11. Transcriptome analysis of the planarian eye identifies ovo as a specific regulator of eye regeneration

    PubMed Central

    Lapan, Sylvain W.; Reddien, Peter W.

    2013-01-01

    Summary Among the millions of invertebrate species with visual systems, the genetic basis of eye development and function is well understood only in Drosophila melanogaster. We describe an eye transcriptome for the planarian Schmidtea mediterranea. Planarian photoreceptors expressed orthologs of genes required for phototransduction and microvillus structure in Drosophila and vertebrates, and optic pigment cells expressed solute transporters and melanin synthesis enzymes similar to those active in the vertebrate retinal pigment epithelium. Orthologs of several planarian eye genes, such as bestrophin-1 and Usher syndrome genes, cause eye defects in mammals when perturbed and were not previously described to have roles in invertebrate eyes. Five previously undescribed planarian eye transcription factors were required for normal eye formation during head regeneration. In particular, a conserved, transcription factor-encoding ovo gene was expressed from the earliest stages of eye regeneration and was required for regeneration of all cell types of the eye. PMID:22884275

  12. 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.

  13. 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) ...

  14. Eye muscle repair - discharge

    MedlinePlus

    ... Lazy eye repair - discharge; Strabismus repair - discharge; Extraocular muscle surgery - discharge ... You or your child had eye muscle repair surgery to correct eye muscle ... term for crossed eyes is strabismus. Children most often ...

  15. 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 ...

  16. 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 ...

  17. Cataracts and Other Common Eye Diseases | NIH MedlinePlus the Magazine

    MedlinePlus

    ... be viewed by a person with normal vision. Photo courtesy of National Eye Institute Tonometry: In this ... viewed by a person with diabetic eye disease. Photo courtesy of National Eye Institute People with diabetes ...

  18. The Stanford Tissue Microarray Database.

    PubMed

    Marinelli, Robert J; Montgomery, Kelli; Liu, Chih Long; Shah, Nigam H; Prapong, Wijan; Nitzberg, Michael; Zachariah, Zachariah K; Sherlock, Gavin J; Natkunam, Yasodha; West, Robert B; van de Rijn, Matt; Brown, Patrick O; Ball, Catherine A

    2008-01-01

    The Stanford Tissue Microarray Database (TMAD; http://tma.stanford.edu) is a public resource for disseminating annotated tissue images and associated expression data. Stanford University pathologists, researchers and their collaborators worldwide use TMAD for designing, viewing, scoring and analyzing their tissue microarrays. The use of tissue microarrays allows hundreds of human tissue cores to be simultaneously probed by antibodies to detect protein abundance (Immunohistochemistry; IHC), or by labeled nucleic acids (in situ hybridization; ISH) to detect transcript abundance. TMAD archives multi-wavelength fluorescence and bright-field images of tissue microarrays for scoring and analysis. As of July 2007, TMAD contained 205 161 images archiving 349 distinct probes on 1488 tissue microarray slides. Of these, 31 306 images for 68 probes on 125 slides have been released to the public. To date, 12 publications have been based on these raw public data. TMAD incorporates the NCI Thesaurus ontology for searching tissues in the cancer domain. Image processing researchers can extract images and scores for training and testing classification algorithms. The production server uses the Apache HTTP Server, Oracle Database and Perl application code. Source code is available to interested researchers under a no-cost license. PMID:17989087

  19. 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.

  20. 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.

  1. 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

  2. Characteristic attributes in cancer microarrays.

    PubMed

    Sarkar, I N; Planet, P J; Bael, T E; Stanley, S E; Siddall, M; DeSalle, R; Figurski, D H

    2002-04-01

    Rapid advances in genome sequencing and gene expression microarray technologies are providing unprecedented opportunities to identify specific genes involved in complex biological processes, such as development, signal transduction, and disease. The vast amount of data generated by these technologies has presented new challenges in bioinformatics. To help organize and interpret microarray data, new and efficient computational methods are needed to: (1) distinguish accurately between different biological or clinical categories (e.g., malignant vs. benign), and (2) identify specific genes that play a role in determining those categories. Here we present a novel and simple method that exhaustively scans microarray data for unambiguous gene expression patterns. Such patterns of data can be used as the basis for classification into biological or clinical categories. The method, termed the Characteristic Attribute Organization System (CAOS), is derived from fundamental precepts in systematic biology. In CAOS we define two types of characteristic attributes ('pure' and 'private') that may exist in gene expression microarray data. We also consider additional attributes ('compound') that are composed of expression states of more than one gene that are not characteristic on their own. CAOS was tested on three well-known cancer DNA microarray data sets for its ability to classify new microarray samples. We found CAOS to be a highly accurate and robust class prediction technique. In addition, CAOS identified specific genes, not emphasized in other analyses, that may be crucial to the biology of certain types of cancer. The success of CAOS in this study has significant implications for basic research and the future development of reliable methods for clinical diagnostic tools. PMID:12474425

  3. Microarrayed Materials for Stem Cells

    PubMed Central

    Mei, Ying

    2013-01-01

    Stem cells hold remarkable promise for applications in disease modeling, cancer therapy and regenerative medicine. Despite the significant progress made during the last decade, designing materials to control stem cell fate remains challenging. As an alternative, materials microarray technology has received great attention because it allows for high throughput materials synthesis and screening at a reasonable cost. Here, we discuss recent developments in materials microarray technology and their applications in stem cell engineering. Future opportunities in the field will also be reviewed. PMID:24311967

  4. Immunoprofiling Using NAPPA Protein Microarrays

    PubMed Central

    Sibani, Sahar; LaBaer, Joshua

    2012-01-01

    Protein microarrays provide an efficient method to immunoprofile patients in an effort to rapidly identify disease immunosignatures. The validity of using autoantibodies in diagnosis has been demonstrated in type 1 diabetes, rheumatoid arthritis, and systemic lupus, and is now being strongly considered in cancer. Several types of protein microarrays exist including antibody and antigen arrays. In this chapter, we describe the immunoprofiling application for one type of antigen array called NAPPA (nucleic acids programmable protein array). We provide a guideline for setting up the screening study and designing protein arrays to maximize the likelihood of obtaining quality data. PMID:21370064

  5. Microfluidic microarray systems and methods thereof

    DOEpatents

    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.

  6. Microarray analysis: Uses and Limitations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The use of microarray technology has exploded in resent years. All areas of biological research have found application for this powerful platform. From human disease studies to microbial detection systems, a plethora of uses for this technology are currently in place with new uses being developed ...

  7. 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

  8. Exploring the feasibility of next-generation sequencing and microarray data meta-analysis

    PubMed Central

    Wu, Po-Yen; Phan, John H.; Wang, May D.

    2016-01-01

    Emerging next-generation sequencing (NGS) technology potentially resolves many issues that prevent widespread clinical use of gene expression microarrays. However, the number of publicly available NGS datasets is still smaller than that of microarrays. This paper explores the possibilities for combining information from both microarray and NGS gene expression datasets for the discovery of differentially expressed genes (DEGs). We evaluate several existing methods in detecting DEGs using individual datasets as well as combined NGS and microarray datasets. Results indicate that analysis of combined NGS and microarray data is feasible, but successful detection of DEGs may depend on careful selection of algorithms as well as on data normalization and pre-processing. PMID:22256102

  9. 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,…

  10. Diabetes eye exams

    MedlinePlus

    ... catch problems early if you get regular eye exams. ... diabetes checks your eyes, you need an eye exam every 1 to 2 years by an eye ... problems with your vision. Many can do screening exams for damage from diabetes. Once you have eye ...

  11. Development of infrared thermal imager for dry eye diagnosis

    NASA Astrophysics Data System (ADS)

    Chiang, Huihua Kenny; Chen, Chih Yen; Cheng, Hung You; Chen, Ko-Hua; Chang, David O.

    2006-08-01

    This study aims at the development of non-contact dry eye diagnosis based on an infrared thermal imager system, which was used to measure the cooling of the ocular surface temperature of normal and dry eye patients. A total of 108 subjects were measured, including 26 normal and 82 dry eye patients. We have observed that the dry eye patients have a fast cooling of the ocular surface temperature than the normal control group. We have developed a simplified algorithm for calculating the temperature decay constant of the ocular surface for discriminating between normal and dry eye. This study shows the diagnostic of dry eye syndrome by the infrared thermal imager system has reached a sensitivity of 79.3%, a specificity of 75%, and the area under the ROC curve 0.841. The infrared thermal imager system has a great potential to be developed for dry eye screening with the advantages of non-contact, fast, and convenient implementation.

  12. Establishment of a recessive mutant small-eye rat with lens involution and retinal detachment associated with partial deletion and rearrangement of the Cryba1 gene.

    PubMed

    Yamada, Toshiyuki; Nanashima, Naoki; Shimizu, Takeshi; Nakazawa, Yosuke; Nakazawa, Mitsuru; Tsuchida, Shigeki

    2015-10-15

    From our stock of SDRs (Sprague-Dawley rats), we established a mutant strain having small opaque eyes and named it HiSER (Hirosaki small-eye rat). The HiSER phenotype is progressive and autosomal recessive. In HiSER eyes, disruption and involution of the lens, thickening of the inner nuclear layer, detachment and aggregation of the retina, rudimentary muscle in the ciliary body and cell infiltration in the vitreous humour were observed. Genetic linkage analysis using crossing with Brown Norway rat suggested that the causative gene(s) is located on chromosome 10. Microarray analysis showed that the expression level of the Cryba1 gene encoding βA3/A1-crystallin on chromosome 10 was markedly decreased in HiSER eyes. Genomic PCR revealed deletion of a 3.6-kb DNA region encompassing exons 4-6 of the gene in HiSERs. In HiSER eyes, a chimaeric transcript of the gene containing exons 1-3 and an approximately 250-bp sequence originating from the 3'-UTR of the Nufip2 gene, located downstream of the breakpoint in the opposite direction, was present. Whereas the chimaeric transcript was expressed in HiSER eyes, neither normal nor chimaeric βA3/A1-crystallin proteins were detected by Western blot analysis. Real-time RT (reverse transcription)-PCR analysis revealed that expression level of the Nufip2 gene in the HiSER eye was 40% of that in the SDR eye. These results suggest that the disappearance of the βA3/A1-crystallin protein and, in addition, down-regulation of the Nufip2 gene as a consequence of gene rearrangement causes the HiSER phenotype. PMID:26303524

  13. 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. PMID:21392280

  14. Biclustering of time series microarray data.

    PubMed

    Meng, Jia; Huang, Yufei

    2012-01-01

    Clustering is a popular data exploration technique widely used in microarray data analysis. In this chapter, we review ideas and algorithms of bicluster and its applications in time series microarray analysis. We introduce first the concept and importance of biclustering and its different variations. We then focus our discussion on the popular iterative signature algorithm (ISA) for searching biclusters in microarray dataset. Next, we discuss in detail the enrichment constraint time-dependent ISA (ECTDISA) for identifying biologically meaningful temporal transcription modules from time series microarray dataset. In the end, we provide an example of ECTDISA application to time series microarray data of Kaposi's Sarcoma-associated Herpesvirus (KSHV) infection. PMID:22130875

  15. Fractal property of eye movements in schizophrenia.

    PubMed

    Yokoyama, H; Niwa, S; Itoh, K; Mazuka, R

    1996-08-01

    On the basis of a temporal model of animal behavior we conducted temporal analysis of eye movements in schizophrenic subjects (n = 10) and normal controls (n = 10). We found a fractal property in schizophrenic subjects, the fixation time of eye movement during reading ambiguous and difficult sentences showing a clear inverse power law distribution. An exponential distribution of a nonfractal nature was found in normal controls. PMID:8855352

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

    PubMed Central

    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. PMID:26284175

  17. 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 ...

  18. Dilating Eye Drops

    MedlinePlus

    ... Frequently Asked Questions Español Condiciones Chinese Conditions Dilating Eye Drops En Español Read in Chinese What are dilating eye drops? Dilating eye drops contain medication to enlarge ( ...

  19. 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 ...

  20. The Current Status of DNA Microarrays

    NASA Astrophysics Data System (ADS)

    Shi, Leming; Perkins, Roger G.; Tong, Weida

    DNA microarray technology that allows simultaneous assay of thousands of genes in a single experiment has steadily advanced to become a mainstream method used in research, and has reached a stage that envisions its use in medical applications and personalized medicine. Many different strategies have been developed for manufacturing DNA microarrays. In this chapter, we discuss the manufacturing characteristics of seven microarray platforms that were used in a recently completed large study by the MicroArray Quality Control (MAQC) consortium, which evaluated the concordance of results across these platforms. The platforms can be grouped into three categories: (1) in situ synthesis of oligonucleotide probes on microarrays (Affymetrix GeneChip® arrays based on photolithography synthesis and Agilent's arrays based on inkjet synthesis); (2) spotting of presynthesized oligonucleotide probes on microarrays (GE Healthcare's CodeLink system, Applied Biosystems' Genome Survey Microarrays, and the custom microarrays printed with Operon's oligonucleotide set); and (3) deposition of presynthesized oligonucleotide probes on bead-based microarrays (Illumina's BeadChip microarrays). We conclude this chapter with our views on the challenges and opportunities toward acceptance of DNA microarray data in clinical and regulatory settings.

  1. The Current Status of DNA Microarrays

    NASA Astrophysics Data System (ADS)

    Shi, Leming; Perkins, Roger G.; Tong, Weida

    DNA microarray technology that allows simultaneous assay of thousands of genes in a single experiment has steadily advanced to become a mainstream method used in research, and has reached a stage that envisions its use in medical applications and personalized medicine. Many different strategies have been developed for manufacturing DNA microarrays. In this chapter, we discuss the manu facturing characteristics of seven microarray platforms that were used in a recently completed large study by the MicroArray Quality Control (MAQC) consortium, which evaluated the concordance of results across these platforms. The platforms can be grouped into three categories: (1) in situ synthesis of oligonucleotide probes on microarrays (Affymetrix GeneChip® arrays based on photolithography synthesis and Agilent's arrays based on inkjet synthesis); (2) spotting of presynthe-sized oligonucleotide probes on microarrays (GE Healthcare's CodeLink system, Applied Biosystems' Genome Survey Microarrays, and the custom microarrays printed with Operon's oligonucleotide set); and (3) deposition of presynthesized oligonucleotide probes on bead-based microarrays (Illumina's BeadChip microar-rays). We conclude this chapter with our views on the challenges and opportunities toward acceptance of DNA microarray data in clinical and regulatory settings.

  2. Tissue microarrays: applications in genomic research.

    PubMed

    Watanabe, Aprill; Cornelison, Robert; Hostetter, Galen

    2005-03-01

    The widespread application of tissue microarrays in cancer research and the clinical pathology laboratory demonstrates a versatile and portable technology. The rapid integration of tissue microarrays into biomarker discovery and validation processes reflects the forward thinking of researchers who have pioneered the high-density tissue microarray. The precise arrangement of hundreds of archival clinical tissue samples into a composite tissue microarray block is now a proven method for the efficient and standardized analysis of molecular markers. With applications in cancer research, tissue microarrays are a valuable tool in validating candidate markers discovered in highly sensitive genome-wide microarray experiments. With applications in clinical pathology, tissue microarrays are used widely in immunohistochemistry quality control and quality assurance. The timeline of a biomarker implicated in prostate neoplasia, which was identified by complementary DNA expression profiling, validated by tissue microarrays and is now used as a prognostic immunohistochemistry marker, is reviewed. The tissue microarray format provides opportunities for digital imaging acquisition, image processing and database integration. Advances in digital imaging help to alleviate previous bottlenecks in the research pipeline, permit computer image scoring and convey telepathology opportunities for remote image analysis. The tissue microarray industry now includes public and private sectors with varying degrees of research utility and offers a range of potential tissue microarray applications in basic research, prognostic oncology and drug discovery. PMID:15833047

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. Optimisation algorithms for microarray biclustering.

    PubMed

    Perrin, Dimitri; Duhamel, Christophe

    2013-01-01

    In providing simultaneous information on expression profiles for thousands of genes, microarray technologies have, in recent years, been largely used to investigate mechanisms of gene expression. Clustering and classification of such data can, indeed, highlight patterns and provide insight on biological processes. A common approach is to consider genes and samples of microarray datasets as nodes in a bipartite graphs, where edges are weighted e.g. based on the expression levels. In this paper, using a previously-evaluated weighting scheme, we focus on search algorithms and evaluate, in the context of biclustering, several variations of Genetic Algorithms. We also introduce a new heuristic "Propagate", which consists in recursively evaluating neighbour solutions with one more or one less active conditions. The results obtained on three well-known datasets show that, for a given weighting scheme, optimal or near-optimal solutions can be identified. PMID:24109756

  9. Eyeing Ganymede

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Jupiter casts a baleful eye toward the moon Ganymede in this enhanced-contrast image from NASA's Cassini spacecraft.

    Jupiter's 'eye', the Great Red Spot, was captured just before disappearing around the eastern edge of the planet. The furrowed eyebrow above and to the left of the spot is a turbulent wake region caused by westward flow that has been deflected to the north and around the Red Spot. The smallest features visible are about 240 kilometers (150 miles) across.

    Within the band south of the Red Spot are a trio of white ovals, high pressure counterclockwise-rotating regions that are dynamically similar to the Red Spot. The dark filamentary features interspersed between white ovals are probably cyclonic circulations and, unlike the ovals, are rotating clockwise.

    Jupiter's equatorial zone stretching across the planet north of the Spot appears bright white, with gigantic plume clouds spreading out from the equator both to the northeast and to the southeast in a chevron pattern. This zone looks distinctly different than it did during the Voyager flyby 21 years ago. Then, its color was predominantly brown and the only white plumes conspicuous against the darker material beneath them were oriented southwest-to-northeast.

    Ganymede is Jupiter's largest moon, about 50 percent larger than our own Moon and larger than the planet Mercury. The visible details in this image are different geological terrains. Dark areas tend to be older and heavily cratered; brighter areas are younger and less cratered. Cassini images of Ganymede and Jupiter's other large moons taken near closest approach on Dec. 30 will have resolutions about four times better than that seen here.

    This image is a color composite of ones taken with different filters by Cassini's narrow-angle camera on Nov. 18, 2000, processed to enhance contrast. Cassini is a cooperative project of NASA, the European Space Agency and the Italian Space Agency. The Jet Propulsion Laboratory, a division of

  10. 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.

  11. 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.

  12. Food Microbial Pathogen Detection and Analysis Using DNA Microarray Technologies

    PubMed Central

    Herold, Keith E.

    2008-01-01

    Abstract Culture-based methods used for microbial detection and identification are simple to use, relatively inexpensive, and sensitive. However, culture-based methods are too time-consuming for high-throughput testing and too tedious for analysis of samples with multiple organisms and provide little clinical information regarding the pathogen (e.g., antibiotic resistance genes, virulence factors, or strain subtype). DNA-based methods, such as polymerase chain reaction (PCR), overcome some these limitations since they are generally faster and can provide more information than culture-based methods. One limitation of traditional PCR-based methods is that they are normally limited to the analysis of a single pathogen, a small group of related pathogens, or a small number of relevant genes. Microarray technology enables a significant expansion of the capability of DNA-based methods in terms of the number of DNA sequences that can be analyzed simultaneously, enabling molecular identification and characterization of multiple pathogens and many genes in a single array assay. Microarray analysis of microbial pathogens has potential uses in research, food safety, medical, agricultural, regulatory, public health, and industrial settings. In this article, we describe the main technical elements of microarray technology and the application and potential use of DNA microarrays for food microbial analysis. PMID:18673074

  13. Effects of monocular viewing and eye dominance on spatial attention.

    PubMed

    Roth, Heidi L; Lora, Andrea N; Heilman, Kenneth M

    2002-09-01

    Observations in primates and patients with unilateral spatial neglect have suggested that patching of the eye ipsilateral to the injury and contralateral to the neglected space can sometimes improve attention to the neglected space. Investigators have generally attributed the effects of monocular eye patching to activation of subcortical centers that interact with cortical attentional systems. Eye patching is thought to produce preferential activation of attentional systems contralateral to the viewing eye. In this study we examined the effect of monocular eye patching on attentional biases in normal subjects. When normal subjects bisect vertical (radial) lines using both eyes, they demonstrate a far attentional bias, misbisecting lines away from their body. In a monocular viewing experiment, we found that the majority of subjects, who were right eye dominant, had relatively nearer bisections and a diminished far bias when they used their right eye (left eye covered) compared with when they used their left eye (right eye covered). The smaller group of subjects who were left eye dominant had relatively nearer bisections and a diminished far bias when they used their left eye compared with when they used their right eye. In the hemispatial placement experiment, we directly manipulated hemispheric engagement by having subjects perform the same task in right and left hemispace. We found that right eye dominant subjects had a diminished far bias in right hemispace relative to left hemispace. Left eye dominant subjects showed the opposite pattern and had a diminished far bias in left hemispace. For both groups, spatial presentation affected performance more for the non-dominant eye. The results suggest that monocular viewing is associated with preferential activation of attentional systems in the contralateral hemisphere, and that the right hemisphere (at least in right eye dominant subjects) is biased towards far space. Finally, the results suggest that the poorly

  14. Microarray dataset of Jurkat cells following miR-93 over-expression.

    PubMed

    Gioiosa, Silvia; Verduci, Lorena; Azzalin, Gianluca; Carissimi, Claudia; Fulci, Valerio; Macino, Giuseppe

    2016-09-01

    The dataset presented here represents a microarray experiment of Jurkat cell line over-expressing miR-93 after lentiviral transgenic construct transduction. Three biological replicates have been performed. We further provide normalized and processed data, log2 Fold Change based ranked list and GOterms resulting table. The raw microarray data are available in the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number ArrayExpress: E-MTAB-4588. PMID:27408928

  15. 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.

  16. Eye muscle repair - series (image)

    MedlinePlus

    ... the eyeball to the eye socket. The external muscles of the eye are found behind the conjunctiva. ... The extraocular muscles of the eye (external to the eyeball) control the positioning of the eyes. They coordinate of the eye ...

  17. 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…

  18. 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.

  19. 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...

  20. 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

  1. 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

  2. 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

  3. 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

  4. Clustering Short Time-Series Microarray

    NASA Astrophysics Data System (ADS)

    Ping, Loh Wei; Hasan, Yahya Abu

    2008-01-01

    Most microarray analyses are carried out on static gene expressions. However, the dynamical study of microarrays has lately gained more attention. Most researches on time-series microarray emphasize on the bioscience and medical aspects but few from the numerical aspect. This study attempts to analyze short time-series microarray mathematically using STEM clustering tool which formally preprocess data followed by clustering. We next introduce the Circular Mould Distance (CMD) algorithm with combinations of both preprocessing and clustering analysis. Both methods are subsequently compared in terms of efficiencies.

  5. Protein microarrays as tools for functional proteomics.

    PubMed

    LaBaer, Joshua; Ramachandran, Niroshan

    2005-02-01

    Protein microarrays present an innovative and versatile approach to study protein abundance and function at an unprecedented scale. Given the chemical and structural complexity of the proteome, the development of protein microarrays has been challenging. Despite these challenges there has been a marked increase in the use of protein microarrays to map interactions of proteins with various other molecules, and to identify potential disease biomarkers, especially in the area of cancer biology. In this review, we discuss some of the promising advances made in the development and use of protein microarrays. PMID:15701447

  6. Normal faults, normal friction?

    NASA Astrophysics Data System (ADS)

    Collettini, Cristiano; Sibson, Richard H.

    2001-10-01

    Debate continues as to whether normal faults may be seismically active at very low dips (δ < 30°) in the upper continental crust. An updated compilation of dip estimates (n = 25) has been prepared from focal mechanisms of shallow, intracontinental, normal-slip earthquakes (M > 5.5; slip vector raking 90° ± 30° in the fault plane) where the rupture plane is unambiguously discriminated. The dip distribution for these moderate-to-large normal fault ruptures extends from 65° > δ > 30°, corresponding to a range, 25° < θr < 60°, for the reactivation angle between the fault and inferred vertical σ1. In a comparable data set previously obtained for reverse fault ruptures (n = 33), the active dip distribution is 10° < δ = θr < 60°. For vertical and horizontal σ1 trajectories within extensional and compressional tectonic regimes, respectively, dip-slip reactivation is thus restricted to faults oriented at θr ≤ 60° to inferred σ1. Apparent lockup at θr ≈ 60° in each dip distribution and a dominant 30° ± 5° peak in the reverse fault dip distribution, are both consistent with a friction coefficient μs ≈ 0.6, toward the bottom of Byerlee's experimental range, though localized fluid overpressuring may be needed for reactivation of less favorably oriented faults.

  7. 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.

  8. Photoelectrochemical synthesis of DNA microarrays

    PubMed Central

    Chow, Brian Y.; Emig, Christopher J.; Jacobson, Joseph M.

    2009-01-01

    Optical addressing of semiconductor electrodes represents a powerful technology that enables the independent and parallel control of a very large number of electrical phenomena at the solid-electrolyte interface. To date, it has been used in a wide range of applications including electrophoretic manipulation, biomolecule sensing, and stimulating networks of neurons. Here, we have adapted this approach for the parallel addressing of redox reactions, and report the construction of a DNA microarray synthesis platform based on semiconductor photoelectrochemistry (PEC). An amorphous silicon photoconductor is activated by an optical projection system to create virtual electrodes capable of electrochemically generating protons; these PEC-generated protons then cleave the acid-labile dimethoxytrityl protecting groups of DNA phosphoramidite synthesis reagents with the requisite spatial selectivity to generate DNA microarrays. Furthermore, a thin-film porous glass dramatically increases the amount of DNA synthesized per chip by over an order of magnitude versus uncoated glass. This platform demonstrates that PEC can be used toward combinatorial bio-polymer and small molecule synthesis. PMID:19706433

  9. 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...

  10. 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...

  11. 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

  12. 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.

  13. 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.

  14. 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…

  15. Protein-Based Microarray for the Detection of Pathogenic Bacteria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microarrays have been used for gene expression and protein interaction studies, but recently, multianalyte diagnostic assays have employed the microarray platform. We developed a microarray immunoassay for bacteria, with biotinylated capture antibodies on streptavidin slides. To complete the fluor...

  16. The Hammer and the Eye: Beware

    PubMed Central

    Elkington, Andrew; Kanski, J. J.

    1973-01-01

    In reporting this small series of foreign-body injuries to the eye it is emphasized how normal an eye may appear and yet have a foreign body lurking in its anterior chamber. The patient's account of the injury may be very deceptive and an x-ray picture of the eye must be taken if a foreign body is even remotely suspected, particularly if a hammer is mentioned. Prompt diagnosis followed by well executed surgery leads to good results in these cases. PMID:4706811

  17. 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

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

    PubMed Central

    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

  19. 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

  20. 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

  1. Lasik eye surgery - discharge

    MedlinePlus

    ... page: //medlineplus.gov/ency/patientinstructions/000525.htm Lasik eye surgery - discharge To use the sharing features on this page, please enable JavaScript. Lasik eye surgery permanently changes the shape of the cornea ( ...

  2. 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. ...

  3. Fluorescein eye stain

    MedlinePlus

    Abnormal results may point to: Abnormal tear production (dry eye) Blocked tear duct Corneal abrasion (a scratch on ... foreign object in ) Infection Injury or trauma Severe dry eye associated with arthritis (keratoconjunctivitis sicca)

  4. 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 ...

  5. Eye Injuries (For Parents)

    MedlinePlus

    ... eye nausea or vomiting after an eye injury Think Prevention! Kids who play sports should wear protective goggles or unbreakable glasses as needed. Keep chemicals and other potentially dangerous objects out of the reach of children. Reviewed by: ...

  6. Diabetic Eye Problems

    MedlinePlus

    ... this can damage your eyes. The most common problem is diabetic retinopathy. It is a leading cause ... surgery, with follow-up care. Two other eye problems can happen to people with diabetes. A cataract ...

  7. Anatomy of the Eye

    MedlinePlus

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    MedlinePlus

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  9. Eye muscle repair

    MedlinePlus

    ... and physical exam before the procedure Orthoptic measurements (eye movement measurements) Always tell your child's doctor or nurse: ... D, Plummer LS, Stass-Isern M. Disorders of eye movement and alignment. In: Kliegman RM, Behrman RE, Jenson ...

  10. Eye Injuries (For Parents)

    MedlinePlus

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  11. Diabetes - eye care

    MedlinePlus

    ... dilated eye exam. This is called digital retinal photography. Your eye doctor may ask you to come ... doctor if: You cannot see well in dim light. You have blind spots. You have double vision ( ...

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    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 ...

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    MedlinePlus

    ... the eye (vitreous hemorrhage) Cancer of the retina ( retinoblastoma ), under the retina, or in other parts of ... Cataract removal Melanoma of the eye Retinal detachment Retinoblastoma Ultrasound Update Date 2/23/2015 Updated by: ...

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    MedlinePlus

    ... life expectancy. Do children with Down syndrome have eye problems? Individuals with Down syndrome are at increased ... When should children with Down syndrome receive an eye exam? The American Academy of Pediatrics recommends that ...

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    MedlinePlus

    ... of known infected babies. What happens to the eyes of babies born with congenital toxoplasmosis? The infection ... to further reduce the inflammation. Updated 03/2015 Eye Terms & Conditions Most Common Searches Adult Strabismus Amblyopia ...

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    MedlinePlus

    ... Glossary The Visual System Your Eyes’ Natural Defenses Eye Health and Safety First Aid Tips Healthy Vision ... More Information Optical Illusions Printables Sports and Your Eyes Gear up! If you play sports, you know ...

  17. Diabetes eye exams

    MedlinePlus

    ... are near. Sunlight can damage your eye. Wear dark glasses or shade your eyes until the effects ... to the principles of the Health on the Net Foundation (www.hon.ch). The information provided herein ...

  18. Anatomy of the Eye

    MedlinePlus

    ... it becomes red or pink. This is called conjunctivitis or “pinkeye”. Lacrimal Gland: The lacrimal gland produces tears that ... Conditions Most Common Searches Adult Strabismus Amblyopia Cataract Conjunctivitis Corneal Abrasions Dilating Eye Drops Lazy eye (defined) ...

  19. Eye - foreign object in

    MedlinePlus

    ... medlineplus.gov/ency/article/002084.htm Eye - foreign object in To use the sharing features on this ... Blinking The eye will often flush out small objects, like eyelashes and sand, through blinking and tearing. ...

  20. Get Your Eyes Tested

    MedlinePlus

    ... over age 40 Have a family history of glaucoma Have diabetes People with diabetes may need eye exams more ... or if you have a family member with diabetes or an eye disease. Eye diseases like glaucoma can lead to vision loss and blindness if ...

  1. 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…

  2. 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

  3. 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.

  4. 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

  5. Glycan profiling of endometrial cancers using lectin microarray.

    PubMed

    Nishijima, Yoshihiro; Toyoda, Masashi; Yamazaki-Inoue, Mayu; Sugiyama, Taro; Miyazawa, Masaki; Muramatsu, Toshinari; Nakamura, Kyoko; Narimatsu, Hisashi; Umezawa, Akihiro; Mikami, Mikio

    2012-10-01

    Cell surface glycans change during the process of malignant transformation. To characterize and distinguish endometrial cancer and endometrium, we performed glycan profiling using an emerging modern technology, lectin microarray analysis. The three cell lines, two from endometrial cancers [well-differentiated type (G1) and poorly differentiated type (G3)] and one from normal endometrium, were successfully categorized into three independent groups by 45 lectins. Furthermore, in cancer cells, a clear difference between G1 and G3 type was observed for the glycans recognized with six lectins, Ulex europaeus agglutinin I (UEA-I), Sambucus sieboldiana agglutinin (SSA), Sambucus nigra agglutinin (SNA), Trichosanthes japonica agglutinin I (TJA-I), Amaranthus caudatus agglutinin (ACA), and Bauhinia purpurea lectin (BPL). The lectin microarray analysis using G3 type tissues demonstrated that stage I and stage III or IV were distinguished depending on signal pattern of three lectins, Dolichos biflorus agglutinin (DBA), BPL, and ACA. In addition, the analysis of the glycans on the ovarian cancer cells showed that only anticancer drug-sensitive cell lines had almost no activities to specific three lectins. Glycan profiling by the lectin microarray may be used to assess the characteristics of tumors and potentially to predict the success of chemotherapy treatment. PMID:22957961

  6. 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

  7. Retrieving relevant experiments: The case of microRNA microarrays.

    PubMed

    Açıcı, Koray; Terzi, Yunus Kasım; Oğul, Hasan

    2015-08-01

    Content-based retrieval of biological experiments in large public repositories is a recent challenge in computational biology and bioinformatics. The task is, in general, to search in a database using a query-by-example without any experimental meta-data annotation. Here, we consider a more specific problem that seeks a solution for retrieving relevant microRNA experiments from microarray repositories. A computational framework is proposed with this objective. The framework adapts a normal-uniform mixture model for identifying differentially expressed microRNAs in microarray profiling experiments. A rank-based thresholding scheme is offered to binarize real-valued experiment fingerprints based on differential expression. An effective similarity metric is introduced to compare categorical fingerprints, which in turn infers the relevance between two experiments. Two different views of experimental relevance are evaluated, one for disease association and another for embryonic germ layer, to discern the retrieval ability of the proposed model. To the best of our knowledge, the experiment retrieval task is investigated for the first time in the context of microRNA microarrays. PMID:26116091

  8. ArrayPipe: a flexible processing pipeline for microarray data.

    PubMed

    Hokamp, Karsten; Roche, Fiona M; Acab, Michael; Rousseau, Marc-Etienne; Kuo, Byron; Goode, David; Aeschliman, Dana; Bryan, Jenny; Babiuk, Lorne A; Hancock, Robert E W; Brinkman, Fiona S L

    2004-07-01

    A number of microarray analysis software packages exist already; however, none combines the user-friendly features of a web-based interface with potential ability to analyse multiple arrays at once using flexible analysis steps. The ArrayPipe web server (freely available at www.pathogenomics.ca/arraypipe) allows the automated application of complex analyses to microarray data which can range from single slides to large data sets including replicates and dye-swaps. It handles output from most commonly used quantification software packages for dual-labelled arrays. Application features range from quality assessment of slides through various data visualizations to multi-step analyses including normalization, detection of differentially expressed genes, andcomparison and highlighting of gene lists. A highly customizable action set-up facilitates unrestricted arrangement of functions, which can be stored as action profiles. A unique combination of web-based and command-line functionality enables comfortable configuration of processes that can be repeatedly applied to large data sets in high throughput. The output consists of reports formatted as standard web pages and tab-delimited lists of calculated values that can be inserted into other analysis programs. Additional features, such as web-based spreadsheet functionality, auto-parallelization and password protection make this a powerful tool in microarray research for individuals and large groups alike. PMID:15215429

  9. 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. PMID:27190571

  10. 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

  11. 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.

  12. A cooperative polymer-DNA microarray approach to biomaterial investigation.

    PubMed

    Pernagallo, Salvatore; Diaz-Mochon, Juan Jose; Bradley, Mark

    2009-02-01

    In this study, polymer microarrays were used for the rapid identification of polymer substrates upon which a suspension cell line would both adhere and proliferate giving a detailed and rapid understanding of cell-biomaterial interactions. Analysis demonstrated that suspension K562 human erythroleukemic cells, which normally grow in suspension, adhered and proliferated on several different polymers. Phenotypic and transcriptomic analysis techniques allowed examination of the interaction between cells and polymers permitting the elucidation of putative links between phenotypic responses to cell-biomaterial interactions and global gene expression. PMID:19156288

  13. 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

  14. 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

  15. Dry Eye and Designer Ophthalmics

    PubMed Central

    Laurie, Gordon W.; Olsakovsky, Leslie A.; Conway, Brian P.; McKown, Robert L.; Kitagawa, Kazuko; Nichols, Jason J.

    2009-01-01

    EST, proteomic, and antibody capture assays are revealing a level of tear film protein complexity far greater than previously appreciated. A systems biology approach will be needed to fully appreciate function as tear protein doses fluctuate in time through different conditions. Although consensus is growing on what fully constitutes the human tear proteome, questions remain about the source and significance of the ∼256 tear proteins designated as ‘intracellular’. Many of these may derive from normal cellular turnover and could therefore be informative. A further >183 are designated as ‘extracellular’. Surprisingly, only 4 – 5% of these appear to be dysregulated in the three forms of dry eye preliminarily examined to date. Some differ and a couple overlap, suggesting that disease-specific signatures could be identified. Future dry eye treatment might include recombinant tear protein rescue as a personalized ophthalmic approach to ocular surface disease. PMID:18677231

  16. AMIC@: All MIcroarray Clusterings @ once

    PubMed Central

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

    2008-01-01

    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. PMID:18477631

  17. 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. PMID:18477631

  18. Integrating Microarray Data and GRNs.

    PubMed

    Koumakis, L; Potamias, G; Tsiknakis, M; Zervakis, M; Moustakis, V

    2016-01-01

    With the completion of the Human Genome Project and the emergence of high-throughput technologies, a vast amount of molecular and biological data are being produced. Two of the most important and significant data sources come from microarray gene-expression experiments and respective databanks (e,g., Gene Expression Omnibus-GEO (http://www.ncbi.nlm.nih.gov/geo)), and from molecular pathways and Gene Regulatory Networks (GRNs) stored and curated in public (e.g., Kyoto Encyclopedia of Genes and Genomes-KEGG (http://www.genome.jp/kegg/pathway.html), Reactome (http://www.reactome.org/ReactomeGWT/entrypoint.html)) as well as in commercial repositories (e.g., Ingenuity IPA (http://www.ingenuity.com/products/ipa)). The association of these two sources aims to give new insight in disease understanding and reveal new molecular targets in the treatment of specific phenotypes.Three major research lines and respective efforts that try to utilize and combine data from both of these sources could be identified, namely: (1) de novo reconstruction of GRNs, (2) identification of Gene-signatures, and (3) identification of differentially expressed GRN functional paths (i.e., sub-GRN paths that distinguish between different phenotypes). In this chapter, we give an overview of the existing methods that support the different types of gene-expression and GRN integration with a focus on methodologies that aim to identify phenotype-discriminant GRNs or subnetworks, and we also present our methodology. PMID:26134183

  19. DNA microarrays in prostate cancer.

    PubMed

    Ho, Shuk-Mei; Lau, Kin-Mang

    2002-02-01

    DNA microarray technology provides a means to examine large numbers of molecular changes related to a biological process in a high throughput manner. This review discusses plausible utilities of this technology in prostate cancer research, including definition of prostate cancer predisposition, global profiling of gene expression patterns associated with cancer initiation and progression, identification of new diagnostic and prognostic markers, and discovery of novel patient classification schemes. The technology, at present, has only been explored in a limited fashion in prostate cancer research. Some hurdles to be overcome are the high cost of the technology, insufficient sample size and repeated experiments, and the inadequate use of bioinformatics. With the completion of the Human Genome Project and the advance of several highly complementary technologies, such as laser capture microdissection, unbiased RNA amplification, customized functional arrays (eg, single-nucleotide polymorphism chips), and amenable bioinformatics software, this technology will become widely used by investigators in the field. The large amount of novel, unbiased hypotheses and insights generated by this technology is expected to have a significant impact on the diagnosis, treatment, and prevention of prostate cancer. Finally, this review emphasizes existing, but currently underutilized, data-mining tools, such as multivariate statistical analyses, neural networking, and machine learning techniques, to stimulate wider usage. PMID:12084220

  20. Microarray: an approach for current drug targets.

    PubMed

    Gomase, Virendra S; Tagore, Somnath; Kale, Karbhari V

    2008-03-01

    Microarrays are a powerful tool has multiple applications both in clinical and cellular and molecular biology arenas. Early assessment of the probable biological importance of drug targets, pharmacogenomics, toxicogenomics and single nucleotide polymorphisms (SNPs). A list of new drug candidates along with proposed targets for intervention is described. Recent advances in the knowledge of microarrays analysis of organisms and the availability of the genomics sequences provide a wide range of novel targets for drug design. This review gives different process of microarray technologies; methods for comparative gene expression study, applications of microarrays in medicine and pharmacogenomics and current drug targets in research, which are relevant to common diseases as they relate to clinical and future perspectives. PMID:18336225

  1. Construction of special eye models for investigation of chromatic and higher-order aberrations of eyes.

    PubMed

    Zhai, Yi; Wang, Yan; Wang, Zhaoqi; Liu, Yongji; Zhang, Lin; He, Yuanqing; Chang, Shengjiang

    2014-01-01

    An achromatic element eliminating only longitudinal chromatic aberration (LCA) while maintaining transverse chromatic aberration (TCA) is established for the eye model, which involves the angle formed by the visual and optical axis. To investigate the impacts of higher-order aberrations on vision, the actual data of higher-order aberrations of human eyes with three typical levels are introduced into the eye model along visual axis. Moreover, three kinds of individual eye models are established to investigate the impacts of higher-order aberrations, chromatic aberration (LCA+TCA), LCA and TCA on vision under the photopic condition, respectively. Results show that for most human eyes, the impact of chromatic aberration on vision is much stronger than that of higher-order aberrations, and the impact of LCA in chromatic aberration dominates. The impact of TCA is approximately equal to that of normal level higher-order aberrations and it can be ignored when LCA exists. PMID:25227016

  2. 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. PMID:16842606

  3. 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…

  4. Time Course Analysis of Gene Expression Patterns in Zebrafish Eye During Optic Nerve Regeneration

    PubMed Central

    McCurley, Amy T.

    2010-01-01

    It is well-established that neurons in the adult mammalian central nervous system (CNS) are terminally differentiated and, if injured, will be unable to regenerate their connections. In contrast to mammals, zebrafish and other teleosts display a robust neuroregenerative response. Following optic nerve crush (ONX), retinal ganglion cells (RGC) regrow their axons to synapse with topographically correct targets in the optic tectum, such that vision is restored in ∼21 days. What accounts for these differences between teleostean and mammalian responses to neural injury is not fully understood. A time course analysis of global gene expression patterns in the zebrafish eye after ONX can help to elucidate cellular and molecular mechanisms that contribute to a successful neuroregeneration. To define different phases of regeneration after ONX, alpha tubulin 1 (tuba1) and growth-associated protein 43 (gap43), markers previously shown to correspond to morphophological events, were measured by real time quantitative PCR (qPCR). Microarray analysis was then performed at defined intervals (6 hours, 1, 4, 12, and 21 days) post-ONX and compared to SHAM. Results show that optic nerve damage induces multiple, phase-related transcriptional programs, with the maximum number of genes changed and highest fold-change occurring at 4 days. Several functional groups affected by optic nerve regeneration, including cell adhesion, apoptosis, cell cycle, energy metabolism, ion channel activity, and calcium signaling, were identified. Utilizing the whole eye allowed us to identify signaling contributions from the vitreous, immune and glial cells as well as the neural cells of the retina. Comparisons between our dataset and transcriptional profiles from other models of regeneration in zebrafish retina, heart and fin revealed a subset of commonly regulated transcripts, indicating shared mechanisms in different regenerating tissues. Knowledge of gene expression patterns in all components of the

  5. Measuring eye movements during locomotion: filtering techniques for obtaining velocity signals from a video-based eye monitor

    NASA Technical Reports Server (NTRS)

    Das, V. E.; Thomas, C. W.; Zivotofsky, A. Z.; Leigh, R. J.

    1996-01-01

    Video-based eye-tracking systems are especially suited to studying eye movements during naturally occurring activities such as locomotion, but eye velocity records suffer from broad band noise that is not amenable to conventional filtering methods. We evaluated the effectiveness of combined median and moving-average filters by comparing prefiltered and postfiltered records made synchronously with a video eye-tracker and the magnetic search coil technique, which is relatively noise free. Root-mean-square noise was reduced by half, without distorting the eye velocity signal. To illustrate the practical use of this technique, we studied normal subjects and patients with deficient labyrinthine function and compared their ability to hold gaze on a visual target that moved with their heads (cancellation of the vestibulo-ocular reflex). Patients and normal subjects performed similarly during active head rotation but, during locomotion, patients held their eyes more steadily on the visual target than did subjects.

  6. 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.

  7. The Impact of Photobleaching on Microarray Analysis

    PubMed Central

    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

  8. Emmetropic eyes: objective performance and clinical reference

    NASA Astrophysics Data System (ADS)

    Tepichín-Rodríguez, Eduardo; Cruz Felix, Angel S.; López-Olazagasti, Estela; Balderas-Mata, Sandra

    2013-11-01

    The application of the wavefront sensors to measuring the monochromatic aberrations of the normal human eyes has given a new insight in the objective understanding of its performance. The resultant wavefront aberration function can be applied to evaluate the image quality on the retina, which includes the analysis of the higher-order aberrations. Among others, and due to their well-known mathematical properties for circular apertures, the wavefront aberration function is most commonly represented in terms of the Zernike polynomials. The main idea is to have a clinical reference of the objective performance of a set of normal human eyes. However, the high-order aberrations in normal human eyes are different for each persoņ that can be interpreted as that there are many possible solutions for the objective performance of emmetropic eyes. When dealing with the Zernike coefficients and excluding the spherical aberration, higher-order aberrations have a tendency to have a zero mean value. Different proposals have been suggested in the literature to deal with this feature. Moreover, it has been also shown that there is an ethnic dependency in the magnitude of the aberrations. We present in this work the objective performance of a set of uncorrected Mexican eyes, and compare them with other ethnic results published in the literature.

  9. Pipeline for macro- and microarray analyses.

    PubMed

    Vicentini, R; Menossi, M

    2007-05-01

    The pipeline for macro- and microarray analyses (PMmA) is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). It can also be used as a plugin in the BioArray Software Environment, an open-source database for array analysis, or used in a local version of the web service. All scripts in PMmA were developed in the PERL programming language and statistical analysis functions were implemented in the R statistical language. Consequently, our package is a platform-independent software. Our algorithms can correctly select almost 90% of the differentially expressed genes, showing a superior performance compared to other methods of analysis. The pipeline software has been applied to 1536 expressed sequence tags macroarray public data of sugarcane exposed to cold for 3 to 48 h. PMmA identified thirty cold-responsive genes previously unidentified in this public dataset. Fourteen genes were up-regulated, two had a variable expression and the other fourteen were down-regulated in the treatments. These new findings certainly were a consequence of using a superior statistical analysis approach, since the original study did not take into account the dependence of data variability on the average signal intensity of each gene. The web interface, supplementary information, and the package source code are available, free, to non-commercial users at http://ipe.cbmeg.unicamp.br/pub/PMmA. PMID:17464422

  10. Prevention of Eye Injuries

    PubMed Central

    Pashby, Tom

    1981-01-01

    In Canada 30,000 people are registered as blind; in one third of these, blindness might have been avoided. Prevention is the key to reducing the number of eye injuries and blind eyes. The role of the family physician in early identification of treatable conditions and in the education of patients is discussed, but responsibility for prevention belongs to all physicians. The success of prevention is seen in the great reduction in eye injuries in industry and sports since eye protectors have been commonly used. However, many dangers to the eyes are either not recognized or are not taken seriously enough. This paper discusses some of the common causes of serious eye injuries in the home, in sports and in industry. Imagesp464-aFig. 1Fig. 2Fig. 3Fig. 4 PMID:21289691

  11. Seeing the eyes in acquired prosopagnosia.

    PubMed

    Pancaroglu, Raika; Hills, Charlotte S; Sekunova, Alla; Viswanathan, Jayalakshmi; Duchaine, Brad; Barton, Jason J S

    2016-08-01

    Case reports have suggested that perception of the eye region may be impaired more than that of other facial regions in acquired prosopagnosia. However, it is unclear how frequently this occurs, whether such impairments are specific to a certain anatomic subtype of prosopagnosia, and whether these impairments are related to changes in the scanning of faces. We studied a large cohort of 11 subjects with this rare disorder, who had a variety of occipitotemporal or anterior temporal lesions, both unilateral and bilateral. Lesions were characterized by functional and structural imaging. Subjects performed a perceptual discrimination test in which they had to discriminate changes in feature position, shape, or external contour. Test conditions were manipulated to stress focused or divided attention across the whole face. In a second experiment we recorded eye movements while subjects performed a face memory task. We found that greater impairment for eye processing was more typical of subjects with occipitotemporal lesions than those with anterior temporal lesions. This eye selectivity was evident for both eye position and shape, with no evidence of an upper/lower difference for external contour. A greater impairment for eye processing was more apparent under attentionally more demanding conditions. Despite these perceptual deficits, most subjects showed a normal tendency to scan the eyes more than the mouth. We conclude that occipitotemporal lesions are associated with a partially selective processing loss for eye information and that this deficit may be linked to loss of the right fusiform face area, which has been shown to have activity patterns that emphasize the eye region. PMID:27288649

  12. 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.

  13. 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…

  14. Microarray gene expression analysis of the human airway in patients exposed to sulfur mustard.

    PubMed

    Najafi, Ali; Masoudi-Nejad, Ali; Imani Fooladi, Abbas Ali; Ghanei, Mostafa; Nourani, Mohamad Reza

    2014-08-01

    There is much data about the acute effects of sulfur mustard gas on humans, animals and cells. But less is known regarding the molecular basics of chronic complications in humans. Basically, mustard gas, as an alkylating agent, causes several chronic problems in the eyes, skin and more importantly in the pulmonary system which is the main cause of death. Although recent proteomic research has been carried out on bronchoalveolar lavage (BAL) and serum, but high-throughput transcriptomics have not yet been applied to chronic airway remodeling. This is the first cDNA-microarray report on the chronic human mustard lung disease, 25 years after exposure during the Iran-Iraq war. Microarray transcriptional profiling indicated that a total of 122 genes were significantly dysregulated in tissues located in the airway of patients. These genes are associated with the extracellular matrix components, apoptosis, stress response, inflammation and mucus secretion. PMID:24823320

  15. VisualEyes: a modular software system for oculomotor experimentation.

    PubMed

    Guo, Yi; Kim, Eun H; Kim, Eun; Alvarez, Tara; Alvarez, Tara L

    2011-01-01

    Eye movement studies have provided a strong foundation forming an understanding of how the brain acquires visual information in both the normal and dysfunctional brain.(1) However, development of a platform to stimulate and store eye movements can require substantial programming, time and costs. Many systems do not offer the flexibility to program numerous stimuli for a variety of experimental needs. However, the VisualEyes System has a flexible architecture, allowing the operator to choose any background and foreground stimulus, program one or two screens for tandem or opposing eye movements and stimulate the left and right eye independently. This system can significantly reduce the programming development time needed to conduct an oculomotor study. The VisualEyes System will be discussed in three parts: 1) the oculomotor recording device to acquire eye movement responses, 2) the VisualEyes software written in LabView, to generate an array of stimuli and store responses as text files and 3) offline data analysis. Eye movements can be recorded by several types of instrumentation such as: a limbus tracking system, a sclera search coil, or a video image system. Typical eye movement stimuli such as saccadic steps, vergent ramps and vergent steps with the corresponding responses will be shown. In this video report, we demonstrate the flexibility of a system to create numerous visual stimuli and record eye movements that can be utilized by basic scientists and clinicians to study healthy as well as clinical populations. PMID:21490568

  16. 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…

  17. Quantifying the Antibody Binding on Protein Microarrays using Microarray Nonlinear Calibration

    PubMed Central

    Yu, Xiaobo; Wallstrom, Garrick; Magee, Dewey Mitchell; Qiu, Ji; Mendoza, D. Eliseo A.; Wang, Jie; Bian, Xiaofang; Graves, Morgan; LaBaer, Joshua

    2015-01-01

    To address the issue of quantification for antibody assays with protein microarrays, we firstly developed a Microarray Nonlinear Calibration (MiNC) method that applies in the quantification of antibody binding to the surface of microarray spots. We found that MiNC significantly increased the linear dynamic range and reduced assay variations. A serological analysis of guinea pig Mycobacterium tuberculosis models showed that a larger number of putative antigen targets were identified with MiNC, which is consistent with the improved assay performance of protein microarrays. We expect that our cumulative results will provide scientists with a new appreciation of antibody assays with protein microarrays. Our MiNC method has the potential to be employed in biomedical research with multiplex antibody assays which need quantitation, including the discovery of antibody biomarkers, clinical diagnostics with multi-antibody signatures and construction of immune mathematical models. PMID:23662896

  18. Videos from the National Eye Institute: Eye Diseases

    MedlinePlus

    ... this page please turn Javascript on. Feature: Vision Videos from the National Eye Institute: Eye Diseases Past ... the early detection of eye disease. Share these videos with friends, family and colleagues. www.nei.nih. ...

  19. 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.

  20. PERFORMANCE CHARACTERISTICS OF 65-MER OLIGONUCLEOTIDE MICROARRAYS

    PubMed Central

    Lee, Myoyong; Xiang, Charlie C.; Trent, Jeffrey M.; Bittner, Michael L.

    2009-01-01

    Microarray fabrication using pre-synthesized long oligonucleotide is becoming increasingly important, but a study of large-scale array productions is not published yet. We addressed the issue of fabricating oligonucleotide microarrays by spotting commercial, pre-synthesized 65-mers with 5′ amines representing 7500 murine genes. Amine-modified oligonucleotides were immobilized on glass slides having aldehyde groups via transient Schiff base formation followed by reduction to produce a covalent conjugate. When RNA derived from the same source was used for Cy3 and Cy5 labeling and hybridized to the same array, signal intensities spanning three orders of magnitude were observed, and the coefficient of variation between the two channels for all spots was 8–10%. To ascertain the reproducibility of ratio determination of these arrays, two triplicate hybridizations (with fluorochrome reversal) comparing RNAs from a fibroblast (NIH3T3) and a breast cancer (JC) cell line were carried out. The 95% confidence interval for all spots in the six hybridizations was 0.60 – 1.66. This level of reproducibility allows use of the full range of pattern finding and discriminant analysis typically applied to cDNA microarrays. Further comparative testing was carried out with oligonucleotide microarrays, cDNA microarrays and RT-PCR assays to examine the comparability of results across these different methodologies. PMID:17617369

  1. Advancing microarray assembly with acoustic dispensing technology.

    PubMed

    Wong, E Y; Diamond, S L

    2009-01-01

    In the assembly of microarrays and microarray-based chemical assays and enzymatic bioassays, most approaches use pins for contact spotting. Acoustic dispensing is a technology capable of nanoliter transfers by using acoustic energy to eject liquid sample from an open source well. Although typically used for well plate transfers, when applied to microarraying, it avoids the drawbacks of undesired physical contact with the sample; difficulty in assembling multicomponent reactions on a chip by readdressing, a rigid mode of printing that lacks patterning capabilities; and time-consuming wash steps. We demonstrated the utility of acoustic dispensing by delivering human cathepsin L in a drop-on-drop fashion into individual 50-nanoliter, prespotted reaction volumes to activate enzyme reactions at targeted positions on a microarray. We generated variable-sized spots ranging from 200 to 750 microm (and higher) and handled the transfer of fluorescent bead suspensions with increasing source well concentrations of 0.1 to 10 x 10(8) beads/mL in a linear fashion. There are no tips that can clog, and liquid dispensing CVs are generally below 5%. This platform expands the toolbox for generating analytical arrays and meets needs associated with spatially addressed assembly of multicomponent microarrays on the nanoliter scale. PMID:19035650

  2. 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.

  3. 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…

  4. 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.

  5. 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 ...

  6. Lasik eye surgery - slideshow

    MedlinePlus

    ... this page: //medlineplus.gov/ency/presentations/100206.htm Lasik eye surgery - series To use the sharing features ... A.M. Editorial team. Related MedlinePlus Health Topics Laser Eye Surgery A.D.A.M., Inc. is accredited by ...

  7. Diabetes and eye disease

    MedlinePlus

    ... the back of the inner eye. It changes light and images that enter the eye into nerve signals, which are sent to the brain. Diabetic retinopathy is a main cause of decreased vision or blindness in Americans 20 to 74 years old. People with type 1 or type 2 ...

  8. Fluorescein eye stain

    MedlinePlus

    ... eye. The health care provider then shines a blue light at your eye. Any problems on the surface of the cornea will be stained by the dye and appear green under the blue light. The provider can determine the location and ...

  9. 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...

  10. 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…

  11. 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 ...

  12. 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

  13. 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

  14. 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

  15. Group normalization for genomic data.

    PubMed

    Ghandi, Mahmoud; Beer, Michael A

    2012-01-01

    Data normalization is a crucial preliminary step in analyzing genomic datasets. The goal of normalization is to remove global variation to make readings across different experiments comparable. In addition, most genomic loci have non-uniform sensitivity to any given assay because of variation in local sequence properties. In microarray experiments, this non-uniform sensitivity is due to different DNA hybridization and cross-hybridization efficiencies, known as the probe effect. In this paper we introduce a new scheme, called Group Normalization (GN), to remove both global and local biases in one integrated step, whereby we determine the normalized probe signal by finding a set of reference probes with similar responses. Compared to conventional normalization methods such as Quantile normalization and physically motivated probe effect models, our proposed method is general in the sense that it does not require the assumption that the underlying signal distribution be identical for the treatment and control, and is flexible enough to correct for nonlinear and higher order probe effects. The Group Normalization algorithm is computationally efficient and easy to implement. We also describe a variant of the Group Normalization algorithm, called Cross Normalization, which efficiently amplifies biologically relevant differences between any two genomic datasets. PMID:22912661

  16. 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

  17. 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 ...

  18. Long synthetic oligonucleotides for microarray expression measurement

    NASA Astrophysics Data System (ADS)

    Li, Jiong; Wang, Hong; Liu, Heping; Zhang, M.; Zhang, Chunxiu; Lu, Zu-Hong; Gao, Xiang; Kong, Dong

    2001-09-01

    There are generally two kinds of DNA microarray used for genomic-scale gene expression profiling of mRNA: cDNA and DNA chip, but both of them suffer from some drawbacks. To meet more requirements, another oligonucleotide microarray with long was produced. This type of microarray had the advantages of low cost, minimal Cross-hybridization, flexible and easy to make, which is most fit for small laboratories with special purposes. In this paper, we devised different probes with different probe lengths, GC contents and gene positions to optimization the probe design. Experiments showed 70 mer probes are suitable for both sufficient sensitivity and reasonable costs. Higher G-C content produces stronger signal intensity thus better sensitivity and probes designed at 3 untranslated region of gene within the range of 300 pb should be best for both sensitivity and specificity.

  19. 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

  20. Applications of protein microarrays for biomarker discovery

    PubMed Central

    Ramachandran, Niroshan; Srivastava, Sanjeeva; LaBaer, Joshua

    2011-01-01

    The search for new biomarkers for diagnosis, prognosis and therapeutic monitoring of diseases continues in earnest despite dwindling success at finding novel reliable markers. Some of the current markers in clinical use do not provide optimal sensitivity and specificity, with the prostate cancer antigen (PSA) being one of many such examples. The emergence of proteomic techniques and systems approaches to study disease pathophysiology has rekindled the quest for new biomarkers. In particular the use of protein microarrays has surged as a powerful tool for large scale testing of biological samples. Approximately half the reports on protein microarrays have been published in the last two years especially in the area of biomarker discovery. In this review, we will discuss the application of protein microarray technologies that offer unique opportunities to find novel biomarkers. PMID:21136793

  1. CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis.

    PubMed

    Rainer, Johannes; Sanchez-Cabo, Fatima; Stocker, Gernot; Sturn, Alexander; Trajanoski, Zlatko

    2006-07-01

    CARMAweb (Comprehensive R-based Microarray Analysis web service) is a web application designed for the analysis of microarray data. CARMAweb performs data preprocessing (background correction, quality control and normalization), detection of differentially expressed genes, cluster analysis, dimension reduction and visualization, classification, and Gene Ontology-term analysis. This web application accepts raw data from a variety of imaging software tools for the most widely used microarray platforms: Affymetrix GeneChips, spotted two-color microarrays and Applied Biosystems (ABI) microarrays. R and packages from the Bioconductor project are used as an analytical engine in combination with the R function Sweave, which allows automatic generation of analysis reports. These report files contain all R commands used to perform the analysis and guarantee therefore a maximum transparency and reproducibility for each analysis. The web application is implemented in Java based on the latest J2EE (Java 2 Enterprise Edition) software technology. CARMAweb is freely available at https://carmaweb.genome.tugraz.at. PMID:16845058

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

    PubMed Central

    Jain, Manish; Kalsi, Amanpreet Kaur

    2016-01-01

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

  3. SpotWhatR: a user-friendly microarray data analysis system.

    PubMed

    Koide, Tie; Salem-Izacc, Silvia M; Gomes, Suely L; Vêncio, Ricardo Z N

    2006-01-01

    SpotWhatR is a user-friendly microarray data analysis tool that runs under a widely and freely available R statistical language (http://www.r-project.org) for Windows and Linux operational systems. The aim of SpotWhatR is to help the researcher to analyze microarray data by providing basic tools for data visualization, normalization, determination of differentially expressed genes, summarization by Gene Ontology terms, and clustering analysis. SpotWhatR allows researchers who are not familiar with computational programming to choose the most suitable analysis for their microarray dataset. Along with well-known procedures used in microarray data analysis, we have introduced a stand-alone implementation of the HTself method, especially designed to find differentially expressed genes in low-replication contexts. This approach is more compatible with our local reality than the usual statistical methods. We provide several examples derived from the Blastocladiella emersonii and Xylella fastidiosa Microarray Projects. SpotWhatR is freely available at http://blasto.iq.usp.br/~tkoide/SpotWhatR, in English and Portuguese versions. In addition, the user can choose between "single experiment" and "batch processing" versions. PMID:16755501

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

    PubMed

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

    2016-01-01

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

  5. 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

  6. 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.

  7. Quantitative dose-response curves from subcellular lipid multilayer microarrays.

    PubMed

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

    2015-08-21

    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

  8. 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

  9. A hybrid imputation approach for microarray missing value estimation

    PubMed Central

    2015-01-01

    Background Missing data is an inevitable phenomenon in gene expression microarray experiments due to instrument failure or human error. It has a negative impact on performance of downstream analysis. Technically, most existing approaches suffer from this prevalent problem. Imputation is one of the frequently used methods for processing missing data. Actually many developments have been achieved in the research on estimating missing values. The challenging task is how to improve imputation accuracy for data with a large missing rate. Methods In this paper, induced by the thought of collaborative training, we propose a novel hybrid imputation method, called Recursive Mutual Imputation (RMI). Specifically, RMI exploits global correlation information and local structure in the data, captured by two popular methods, Bayesian Principal Component Analysis (BPCA) and Local Least Squares (LLS), respectively. Mutual strategy is implemented by sharing the estimated data sequences at each recursive process. Meanwhile, we consider the imputation sequence based on the number of missing entries in the target gene. Furthermore, a weight based integrated method is utilized in the final assembling step. Results We evaluate RMI with three state-of-art algorithms (BPCA, LLS, Iterated Local Least Squares imputation (ItrLLS)) on four publicly available microarray datasets. Experimental results clearly demonstrate that RMI significantly outperforms comparative methods in terms of Normalized Root Mean Square Error (NRMSE), especially for datasets with large missing rates and less complete genes. Conclusions It is noted that our proposed hybrid imputation approach incorporates both global and local information of microarray genes, which achieves lower NRMSE values against to any single approach only. Besides, this study highlights the need for considering the imputing sequence of missing entries for imputation methods. PMID:26330180

  10. New diagnostics for melanoma detection: from artificial intelligence to RNA microarrays.

    PubMed

    Ahlgrimm-Siess, Verena; Laimer, Martin; Arzberger, Edith; Hofmann-Wellenhof, Rainer

    2012-07-01

    Early detection of melanoma remains crucial to ensuring a favorable prognosis. Dermoscopy and total body photography are well-established noninvasive aids that increase the diagnostic accuracy of dermatologists in their daily routine, beyond that of a naked-eye examination. New noninvasive diagnostic techniques, such as reflectance confocal microscopy, multispectral digital imaging and RNA microarrays, are currently being investigated to determine their utility for melanoma detection. This review presents emerging technologies for noninvasive melanoma diagnosis, and discusses their advantages and limitations. PMID:22830402

  11. 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

  12. 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).

  13. Overview of DNA microarrays: types, applications, and their future.

    PubMed

    Bumgarner, Roger

    2013-01-01

    This unit provides an overview of DNA microarrays. Microarrays are a technology in which thousands of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. This overview first discusses the history of microarrays and the antecedent technologies that led to their development. This is followed by discussion of the methods of manufacture of microarrays and the most common biological applications. The unit ends with a brief description of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies. PMID:23288464

  14. 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

  15. Pineal function: impact of microarray analysis.

    PubMed

    Klein, David C; Bailey, Michael J; Carter, David A; Kim, Jong-so; Shi, Qiong; Ho, Anthony K; Chik, Constance L; 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

    2010-01-27

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

  16. 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

  17. 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.

  18. 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.

  19. [Treatment of eye allergies].

    PubMed

    Kari, Osmo; Saari, K Matti

    2012-01-01

    Seasonal atopic conjunctivitis is treated with antihistamines, cromoglycate and short courses of corticosteroids, in severe cases with subcutaneous or sublingual immunotherapy. Chronic conjunctivitis requires year-round treatment with mast cell stabilizers, antihistamines or topical corticosteroids. Long-term treatment of atopic blepharoconjunctivitis consists of tacrolimus or pimecrolimus cream. For atopic keratoconjunctivitis corticosteroid and, if necessary, cyclosporine eye drops are needed. First-line therapy of vernal conjunctivitis involves mast cell stabilizers and, if necessary, corticosteroid eye drops. Treatment of non-allergic eosinophilic conjunctivitis involves mast cell stabilizers, corticosteroid and, if necessary, cyclosporine eye drops. PMID:22428383

  20. 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.

  1. Autologous serum eye drops for dry eye

    PubMed Central

    Pan, Qing; Angelina, Adla; Zambrano, Andrea; Marrone, Michael; Stark, Walter J; Heflin, Thomas; Tang, Li; Akpek, Esen K

    2014-01-01

    Background Theoretically, autologous serum eye drops (AS) have a potential advantage over traditional therapies based on the assumption that AS serve not only as a lacrimal substitute to provide lubrication, but also contain other biochemical components mimicking natural tears more closely. The application of AS in dry eye treatment has gained popularity as a second-line therapy in the treatment of dry eye. Published studies on the subject indicate that autologous serum could be an effective treatment for dry eye. Objectives To evaluate the efficacy and safety of AS compared to artificial tears for treating dry eye. Search methods We searched CENTRAL (which contains the Cochrane Eyes and Vision Group Trials Register) (The Cochrane Library 2013, Issue 3), Ovid MEDLINE, Ovid MEDLINE In-Process and Other Non-Indexed Citations, Ovid MEDLINE Daily, Ovid OLD MEDLINE, (January 1950 to April 2013), EMBASE (January 1980 to April 2013), Latin American and Caribbean Literature on Health Sciences (LILACS) (January 1982 to April 2013), the meta Register of Controlled Trials (mRCT) (www.controlled-trials.com), ClinicalTrials.gov (www.clinicaltrials.gov) and the WHO International Clinical Trials Registry Platform (ICTRP) (www.who.int/ictrp/search/en). We also searched the Science Citation Index Expanded database (September 2013) and reference lists of included studies. We did not use any date or language restrictions in the electronic searches for trials. We last searched the electronic databases on 15 April 2013. Selection criteria We included randomized controlled trials (RCTs) in which AS was compared to artificial tears in the treatment of dry eye in adults. Data collection and analysis Two review authors independently screened all titles and abstracts and assessed full-text articles of potentially eligible trials. Two review authors extracted data and assessed the methodological quality and characteristics of the included trials.We contacted investigators for missing data

  2. 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

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

    PubMed Central

    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. PMID:26082788

  4. 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

  5. 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...

  6. 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...

  7. 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…

  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 classified by artificial neural networks.

    PubMed

    Linder, Roland; Richards, Tereza; Wagner, Mathias

    2007-01-01

    Systems biology has enjoyed explosive growth in both the number of people participating in this area of research and the number of publications on the topic. The field of systems biology encompasses the in silico analysis of high-throughput data as provided by DNA or protein microarrays. Along with the increasing availability of microarray data, attention is focused on methods of analyzing the expression rates. One important type of analysis is the classification task, for example, distinguishing different types of cell functions or tumors. Recently, interest has been awakened toward artificial neural networks (ANN), which have many appealing characteristics such as an exceptional degree of accuracy. Nonlinear relationships or independence from certain assumptions regarding the data distribution are also considered. The current work reviews advantages as well as disadvantages of neural networks in the context of microarray analysis. Comparisons are drawn to alternative methods. Selected solutions are discussed, and finally algorithms for the effective combination of multiple ANNs are presented. The development of approaches to use ANN-processed microarray data applicable to run cell and tissue simulations may be slated for future investigation. PMID:18220242

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Diabetic Eye Disease

    MedlinePlus

    ... Health Education Program Diabetic Eye Disease Education Program Glaucoma Education Program Low Vision Education Program Spanish-language ... FAQ Watch out for your vision! Glossary Resources Glaucoma Glaucoma Home How Much Do You Know? What ...

  15. Dry eye syndrome

    MedlinePlus

    ... of dry eyes include: Dry environment or workplace (wind, air conditioning) Sun exposure Smoking or second-hand ... NOT smoke and avoid second-hand smoke, direct wind, and air conditioning. Use a humidifier, especially in ...

  16. 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 ...

  17. 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 ...

  18. 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 ...

  19. What Is Dry Eye?

    MedlinePlus

    ... Plastic Surgery Center Laser Surgery Education Center Redmond Ethics Center Global Ophthalmology Guide Academy Publications EyeNet Ophthalmology Information for: International Ophthalmologists Media Medical Students Patients and Public Technicians and Nurses ...

  20. Down Syndrome: Eye Problems

    MedlinePlus

    American Association for Pediatric Ophthalmology and Strabismus Home About AAPOS Patient Info Resources Allied Health News & Events Meetings J AAPOS American Association for Pediatric Ophthalmology and Strabismus Eye Terms ...

  1. 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 ...

  2. 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) ...

  3. 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 ...

  4. 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 ...

  5. Melanoma of the eye

    MedlinePlus

    ... modified July 9, 2015. www.cancer.gov/types/eye/hp/intraocular-melanoma-treatment-pdq . Accessed October 7, 2015. Read ... by: Yi-Bin Chen, MD, Leukemia/Bone Marrow Transplant Program, Massachusetts General Hospital, Boston, MA. Also reviewed ...

  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. [Straight in the eyes].

    PubMed

    Diop, E; Beylot, V; Berta, C; Dugardin, C; Aigle, L

    2015-01-01

    This case report about a young French soldier hit in the eye by a spitting cobra in the Central African Republic prompts us to review the potential toxicity of this venom to the eyes and the management of this injury. The initial phase is simple to implement, but is often performed badly or not at all because unknown. It is a condition, however, for optimal recovery of the cornea. PMID:26067984

  9. 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

  10. 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

  11. 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

  12. Differential gene expression in anatomical compartments of the human eye

    PubMed Central

    Diehn, Jennifer J; Diehn, Maximilian; Marmor, Michael F; Brown, Patrick O

    2005-01-01

    Background The human eye is composed of multiple compartments, diverse in form, function, and embryologic origin, that work in concert to provide us with our sense of sight. We set out to systematically characterize the global gene expression patterns that specify the distinctive characteristics of the various eye compartments. Results We used DNA microarrays representing approximately 30,000 human genes to analyze gene expression in the cornea, lens, iris, ciliary body, retina, and optic nerve. The distinctive patterns of expression in each compartment could be interpreted in relation to the physiology and cellular composition of each tissue. Notably, the sets of genes selectively expressed in the retina and in the lens were particularly large and diverse. Genes with roles in immune defense, particularly complement components, were expressed at especially high levels in the anterior segment tissues. We also found consistent differences between the gene expression patterns of the macula and peripheral retina, paralleling the differences in cell layer densities between these regions. Based on the hypothesis that genes responsible for diseases that affect a particular eye compartment are likely to be selectively expressed in that compartment, we compared our gene expression signatures with genetic mapping studies to identify candidate genes for diseases affecting the cornea, lens, and retina. Conclusion Through genome-scale gene expression profiling, we were able to discover distinct gene expression 'signatures' for each eye compartment and identified candidate disease genes that can serve as a reference database for investigating the physiology and pathophysiology of the eye. PMID:16168081

  13. 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…

  14. Eye Safety. Mississippi Industrial Arts.

    ERIC Educational Resources Information Center

    Mississippi State Dept. of Education, Jackson. Div. of Vocational and Technical Education.

    This manual is designed to help industrial arts teachers eliminate student eye injuries within industrial arts programs. Presented first is Mississippi eye safety law. Following a discussion of eye protection equipment, illustrations of eye protection devices are provided. Guidelines are set forth for selecting shade numbers for welding filters.…

  15. 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

  16. Glycan specificity of neuraminidases determined in microarray format.

    PubMed

    McCombs, Janet E; Diaz, Jason P; Luebke, Kevin J; Kohler, Jennifer J

    2016-06-16

    Neuraminidases hydrolytically remove sialic acids from glycoconjugates. Neuraminidases are produced by both humans and their pathogens, and function in normal physiology and in pathological events. Identification of neuraminidase substrates is needed to reveal their mechanism of action, but high-throughput methods to determine glycan specificity of neuraminidases are limited. Here we use two glycan labeling reactions to monitor neuraminidase activity toward glycan substrates. While both periodate oxidation and aniline-catalyzed oxime ligation (PAL) and galactose oxidase and aniline-catalyzed oxime ligation (GAL) can be used to monitor neuraminidase activity toward glycans in microtiter plates, only GAL accurately measured neuraminidase activity toward glycans displayed on a commercial glass slide microarray. Using GAL, we confirm known linkage specificities of three pneumococcal neuraminidases and obtain new information about underlying glycan specificity. PMID:27131125

  17. 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

  18. 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

  19. Eye Motility Alterations in Retinitis Pigmentosa

    PubMed Central

    Galeoto, Giovanni; Fratipietro, Manuela

    2015-01-01

    Purpose. We evaluated a sample of individuals with retinitis pigmentosa (RP) with the aim of assessing the presence or absence of ocular motility (OM) disorders. Materials and Methods. We included 23 out of the 25 individuals from the sample (9 females and 14 males) with an average visual acuity of 6/10. Results. The cover test about the vertical deviation in near distance showed an r/l in 3.45% and an l/r in 6.9%. The assessment of OM showed that 39.1% of the sample had a severe hyperfunction of the IO of the right eye and a severe hyperfunction (34.5%) of the SO of the left eye; 21.8% had a moderate hypofunction of right SO with a moderate percentage of hypofunction of 17.5% for the SO of the left eye; 30.5%, however, showed a serious hypofunction of the SR of both eyes; 21.7% of the sample showed a hyperfunction in both eyes of the IR. Conclusion. This alteration, however, is not attributable to either a high refractive defect (medium-low myopia: −1 diopter ±3 SD) or to a severely impaired binocular vision (visual acuity, motor fusion, and stereopsis are normal or within a range of values commonly accepted). Therefore, the disorders of OM lead to a genetic origin. PMID:26124957

  20. High-performance UV-curable epoxy resin-based microarray and microfluidic immunoassay devices.

    PubMed

    Yu, Ling; Liu, Yingshuai; Gan, Ye; Li, Chang Ming

    2009-06-15

    Immunoassay devices including microarray and microfluidic systems were fabricated with an UV-curable resin by a new economic approach, which can not only simply produce a 3-dimensional (3D) patterned structure, but also simultaneously introduce functional epoxide groups for efficient protein immobilization. The performance of the epoxy resin-based microarray was improved by optimization of printing buffer, probe concentration, and immobilization time, showing a detection dynamic range of 5 orders of magnitude and a limit of detection (LOD) of 10 pg mL(-1) for immunoglobulin G (IgG). The developed microfluidic immunoassay device demonstrates a LOD of 100 pg mL(-1) for IL-5 detection. The device can also be used to colorimetrically detect proteins via naked human eyes for immunoassays. This work provides a simple and inexpensive method to fabricate a sensitive immunoassay device, especially a 3D microfluidic system, which has great potential to develop a portable immunoassay device via human eye detection for point-of-care service and/or high throughput screening of infectious diseases. PMID:19346122

  1. 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

  2. Neuroimaging in the Diagnostic Evaluation of Eye Pain.

    PubMed

    Szatmáry, Gabriella

    2016-09-01

    Ocular or eye pain is a frequent complaint encountered not only by eye care providers but neurologists. Isolated eye pain is non-specific and non-localizing; therefore, it poses significant differential diagnostic problems. A wide range of neurologic and ophthalmic disorders may cause pain in, around, or behind the eye. These include ocular and orbital diseases and primary and secondary headaches. In patients presenting with an isolated and chronic eye pain, neuroimaging is usually normal. However, at the beginning of a disease process or in low-grade disease, the eye may appear "quiet," misleading a provider lacking familiarity with underlying disorders and high index of clinical suspicion. Delayed diagnosis of some neuro-ophthalmic causes of eye pain could result in significant neurologic and ophthalmic morbidity, conceivably even mortality. This article reviews some recent advances in imaging of the eye, the orbit, and the brain, as well as research in which neuroimaging has advanced the discovery of the underlying pathophysiology and the complex differential diagnosis of eye pain. PMID:27474094

  3. 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

  4. Viral diagnosis in Indian livestock using customized microarray chips

    PubMed Central

    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. PMID:26912948

  5. 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

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

    PubMed

    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

  7. 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

  8. 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. PMID:26906778

  9. 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.

  10. 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.

  11. Immobilization Techniques for Microarray: Challenges and Applications

    PubMed Central

    Nimse, Satish Balasaheb; Song, Keumsoo; Sonawane, Mukesh Digambar; Sayyed, Danishmalik Rafiq; Kim, Taisun

    2014-01-01

    The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials) on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided. PMID:25429408

  12. Use of microarray technologies in toxicology research.

    PubMed

    Vrana, Kent E; Freeman, Willard M; Aschner, Michael

    2003-06-01

    Microarray technology provides a unique tool for the determination of gene expression at the level of messenger RNA (mRNA). The simultaneous measurement of the entire human genome (thousands of genes) will facilitate the uncovering of specific gene expression patterns that are associated with disease. One important application of microarray technology, within the context of neurotoxicological studies, is its use as a screening tool for the identification of molecular mechanisms of toxicity. Such approaches enable researchers to identify those genes and their products (either single or whole pathways) that are involved in conferring resistance or sensitivity to toxic substances. This review addresses: (1) the potential uses of array data; (2) the various array platforms, highlighting both their advantages and disadvantages; (3) insights into data analysis and presentation strategies; and (4) concrete examples of DNA array studies in neurotoxicological research. PMID:12782098

  13. 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.

  14. 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

  15. Glycan microarrays for decoding the glycome

    PubMed Central

    Rillahan, Cory D.; Paulson, James C.

    2011-01-01

    In the last decade glycan microarrays have revolutionized the analysis of the specificity of glycan binding proteins, providing information that simultaneously illuminates the biology mediated by them and decodes the information content of the glycome. Numerous methods have emerged for arraying glycans in a ‘chip’ format, and glycan libraries have been assembled that address the diversity of the human glycome. Such arrays have been successfully used for analysis of glycan binding proteins that mediate mammalian biology, host-pathogen interactions, immune recognition of glycans relevant to vaccine production and cancer antigens. This review covers the development of glycan microarrays and applications that have provided insights into the roles of mammalian and microbial glycan binding proteins. PMID:21469953

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

    PubMed Central

    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

    2015-01-01

    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. PMID:26212756

  17. 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

    2015-01-01

    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. PMID:26212756

  18. 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.

  19. 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)

  20. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses

    PubMed Central

    Stokes, Todd H; Torrance, JT; Li, Henry; Wang, May D

    2008-01-01

    Background A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only basic biological keywords linking to PubMed. As a result, it is difficult to find datasets using research context or analysis parameters information beyond a few keywords. For example, to reduce the "curse-of-dimension" problem in microarray analysis, the number of samples is often increased by merging array data from different datasets. Knowing chip data parameters such as pre-processing steps (e.g., normalization, artefact removal, etc), and knowing any previous biological validation of the dataset is essential due to the heterogeneity of the data. However, most of the microarray repositories do not have meta-data information in the first place, and do not have a a mechanism to add or insert this information. Thus, there is a critical need to create "intelligent" microarray repositories that (1) enable update of meta-data with the raw array data, and (2) provide standardized archiving protocols to minimize bias from the raw data sources. Results To address the problems discussed, we have developed a community maintained system called ArrayWiki that unites disparate meta-data of microarray meta-experiments from multiple primary sources with four key features. First, ArrayWiki provides a user-friendly knowledge management interface in addition to a programmable interface using standards developed by Wikipedia. Second, ArrayWiki includes automated quality control processes (caCORRECT) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality unavailable in other microarray repositories. Third, it provides a user-curation capability through the familiar Wiki interface. Fourth, ArrayWiki provides users with simple text-based searches across all experiment meta-data, and exposes data to search engine crawlers

  1. Artificial neural superposition eye.

    PubMed

    Brückner, Andreas; Duparré, Jacques; Dannberg, Peter; Bräuer, Andreas; Tünnermann, Andreas

    2007-09-17

    We propose an ultra-thin imaging system which is based on the neural superposition compound eye of insects. Multiple light sensitive pixels in the footprint of each lenslet of this multi-channel configuration enable the parallel imaging of the individual object points. Together with the digital superposition of related signals this multiple sampling enables advanced functionalities for artificial compound eyes. Using this technique, color imaging and a circumvention for the trade-off between resolution and sensitivity of ultra-compact camera devices have been demonstrated in this article. The optical design and layout of such a system is discussed in detail. Experimental results are shown which indicate the attractiveness of microoptical artificial compound eyes for applications in the field of machine vision, surveillance or automotive imaging. PMID:19547555

  2. Comparative Study of Anterior Eye Segment Measurements with Spectral Swept-Source and Time-Domain Optical Coherence Tomography in Eyes with Corneal Dystrophies

    PubMed Central

    Nowinska, Anna K.; Teper, Sławomir J.; Janiszewska, Dominika A.; Lyssek-Boron, Anita; Dobrowolski, Dariusz; Koprowski, Robert; Wylegala, Edward

    2015-01-01

    Purpose. To compare anterior eye segment measurements and morphology obtained with two optical coherence tomography systems (TD OCT, SS OCT) in eyes with corneal dystrophies (CDs). Methods. Fifty healthy volunteers (50 eyes) and 54 patients (96 eyes) diagnosed with CD (epithelial basement membrane dystrophy, EBMD = 12 eyes; Thiel-Behnke CD = 6 eyes; lattice CD TGFBI type = 15 eyes; granular CD type 1 = 7 eyes, granular CD type 2 = 2 eyes; macular CD = 23 eyes; and Fuchs endothelial CD = 31 eyes) were recruited for the study. Automated and manual central corneal thickness (aCCT, mCCT), anterior chamber depth (ACD), and nasal and temporal trabecular iris angle (nTIA, tTIA) were measured and compared with Bland-Altman plots. Results. Good agreement between the TD and SS OCT measurements was demonstrated for mCCT and aCCT in normal individuals and for mCCT in the CDs group. The ACD, nTIA, and tTIA measurements differed significantly in both groups. TBCD, LCD, and FECD caused increased CCT. MCD caused significant corneal thinning. FECD affected all analyzed parameters. Conclusions. Better agreement between SS OCT and TD OCT measurements was demonstrated in normal individuals compared to the CDs group. OCT provides comprehensive corneal deposits analysis and demonstrates the association of CD with CCT, ACD, and TIA measurements. PMID:26457303

  3. Metadata Management and Semantics in Microarray Repositories

    PubMed Central

    Kocabaş, F; Can, T; Baykal, N

    2011-01-01

    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

  4. 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. PMID:25821171

  5. RNAi microarray analysis in cultured mammalian cells.

    PubMed

    Mousses, Spyro; Caplen, Natasha J; Cornelison, Robert; Weaver, Don; Basik, Mark; Hautaniemi, Sampsa; Elkahloun, Abdel G; Lotufo, Roberto A; Choudary, Ashish; Dougherty, Edward R; Suh, Ed; Kallioniemi, Olli

    2003-10-01

    RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) is a powerful new tool for analyzing gene knockdown phenotypes in living mammalian cells. To facilitate large-scale, high-throughput functional genomics studies using RNAi, we have developed a microarray-based technology for highly parallel analysis. Specifically, siRNAs in a transfection matrix were first arrayed on glass slides, overlaid with a monolayer of adherent cells, incubated to allow reverse transfection, and assessed for the effects of gene silencing by digital image analysis at a single cell level. Validation experiments with HeLa cells stably expressing GFP showed spatially confined, sequence-specific, time- and dose-dependent inhibition of green fluorescence for those cells growing directly on microspots containing siRNA targeting the GFP sequence. Microarray-based siRNA transfections analyzed with a custom-made quantitative image analysis system produced results that were identical to those from traditional well-based transfection, quantified by flow cytometry. Finally, to integrate experimental details, image analysis, data display, and data archiving, we developed a prototype information management system for high-throughput cell-based analyses. In summary, this RNAi microarray platform, together with ongoing efforts to develop large-scale human siRNA libraries, should facilitate genomic-scale cell-based analyses of gene function. PMID:14525932

  6. [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

  7. 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.

  8. The trabecular meshwork in normal eyes and in exfoliation glaucoma.

    PubMed

    Rasmussen, Carol A; Kaufman, Paul L

    2014-01-01

    Trabecular meshwork (TM) and ciliary muscle contraction and relaxation function together to provide control of outflow. The active role the TM plays in the regulation of intraocular pressure (IOP) is mediated by cytoskeletal and contractility mechanisms as well as signal/transduction factors that mediate its response to stressors. This complex system is altered with age and the glaucomas, and it can be difficult to differentiate between the various etiological effects/agents. Factors such as a compromised antioxidant defense system and altered extracellular matrix metabolism are known to contribute to impaired outflow and may be common to primary open-angle glaucoma, exfoliation syndrome, and exfoliation glaucoma (XFG). Genes differentially expressed in diseased ocular tissue or in cultured HTM cell models, and thus implicated in the disease process, include SOD2, ALDH1A1, MGST1, LOX, and LOXL1, elements of the transforming growth factor-β/bone morphogenetic protein/SMAD signaling pathways, connective tissue growth factor, matrix metalloproteinase-2, a tissue inhibitor of metalloproteinases also known as TIMP-2, and endothelin-1 (ET-1). In exfoliation syndrome and XFG fibrillar, proteinaceous extracellular material is produced in excess and accumulates in both outflow pathways but does not always lead to elevated IOP. Locally produced material may accumulate in the intertrabecular spaces, juxtacanalicular (JCT) meshwork, and the inner wall of Schlemm's canal as a result of a combination of both excessive synthesis and insufficient degradation. An increase in JCT plaque and decreased cellularity in the TM are thought to contribute to decreased outflow facility in glaucoma patients, but XFG patient specimens show reduced extracellular plaque material in the JCT, and the structural integrity of trabecular endothelial cells is mostly retained and cellularity remains unchanged. The distinctions between causes/effects of structural changes leading to reduced outflow/elevated IOP are important for developing effective, individualized treatment strategies. PMID:25275898

  9. 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

  10. Real-time modulation of perceptual eye dominance in humans

    PubMed Central

    Zhou, Jiawei; Reynaud, Alexandre; Hess, Robert F.

    2014-01-01

    Ocular dominance (OD) has long served as the model for neural plasticity. The shift of OD has been demonstrated by monocular deprivation in animals only during early visual development. Here, for the first time, we show that perceptual eye dominance can be modulated in real time in normal human adults by varying the spatial image content of movies seen dichoptically by the two eyes over a period as short as 2.5 h. Unlike OD shifts seen in early visual development, this modulation in human eye dominance is not simply a consequence of reduced interocular correlation (e.g. synchronicity) or overall contrast energy, but due to the amplitude reductions of specific image components in one eye's view. The spatial properties driving this eye dominance change suggest that the underlying mechanism is binocular but not orientationally selective, therefore uniquely locating it to layer 4 B of area V1. PMID:25274364

  11. Transvection at the Eyes Absent Gene of Drosophila

    PubMed Central

    Leiserson, W. M.; Bonini, N. M.; Benzer, S.

    1994-01-01

    The Drosophila eyes absent (eya) gene is required for survival and differentiation of eye progenitor cells. Loss of gene function in the eye results in reduction or absence of the adult compound eye. Certain combinations of eya alleles undergo partial complementation, with dramatic restoration of eye size. This interaction is sensitive to the relative positions of the two alleles in the genome; rearrangements predicted to disrupt pairing of chromosomal homologs in the eya region disrupt complementation. Ten X-ray-induced rearrangements that suppress the interaction obey the same general rules as those tha disrupt transvection at the bithorax complex and the decapentaplegic gene. Moreover, like transvection in those cases, the interaction at eya depends on the presence of normal zeste function. The discovery of transvection at eya suggests that transvection interactions of this type may be more prevalent than generally thought. PMID:7896099

  12. Photorefraction of the Eye

    NASA Astrophysics Data System (ADS)

    Colicchia, Giuseppe; Wiesner, Hartmut; Zollman, Dean

    2015-02-01

    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 principles underlying the method for eccentric photorefraction and describe how students can perform it using current digital cameras. Our purpose is not to diagnose refractive errors reliably, but to use devices popular among young people that, in combination with an important ophthalmic context, may be successful in improving students' interest for learning optical concepts.

  13. 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

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

    PubMed

    Xie, Yingjun; Pei, Xiaojuan; Dong, Yu; Wu, Huiqun; Wu, Jianzhu; Shi, Huijuan; Zhuang, Xuying; Sun, Xiaofang; He, Jialing

    2016-07-01

    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

  15. 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

  16. Comparison of feature selection methods for cross-laboratory microarray analysis.

    PubMed

    Liu, Hsi-Che; Peng, Pei-Chen; Hsieh, Tzung-Chien; Yeh, Ting-Chi; Lin, Chih-Jen; Chen, Chien-Yu; Hou, Jen-Yin; Shih, Lee-Yung; Liang, Der-Cherng

    2013-01-01

    The amount of gene expression data of microarray has grown exponentially. To apply them for extensive studies, integrated analysis of cross-laboratory (cross-lab) data becomes a trend, and thus, choosing an appropriate feature selection method is an essential issue. This paper focuses on feature selection for Affymetrix (Affy) microarray studies across different labs. We investigate four feature selection methods: $(t)$-test, significance analysis of microarrays (SAM), rank products (RP), and random forest (RF). The four methods are applied to acute lymphoblastic leukemia, acute myeloid leukemia, breast cancer, and lung cancer Affy data which consist of three cross-lab data sets each. We utilize a rank-based normalization method to reduce the bias from cross-lab data sets. Training on one data set or two combined data sets to test the remaining data set(s) are both considered. Balanced accuracy is used for prediction evaluation. This study provides comprehensive comparisons of the four feature selection methods in cross-lab microarray analysis. Results show that SAM has the best classification performance. RF also gets high classification accuracy, but it is not as stable as SAM. The most naive method is $(t)$-test, but its performance is the worst among the four methods. In this study, we further discuss the influence from the number of training samples, the number of selected genes, and the issue of unbalanced data sets. PMID:24091394

  17. 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

  18. Glaucoma: Eye-to-Eye with Dr. Rachel Bishop

    MedlinePlus

    ... of this page please turn JavaScript on. Feature: Glaucoma Eye-to-Eye with Dr. Rachel Bishop Past ... nerves are pale and cupped—signs of advanced glaucoma. Yet the patient wasn't aware of any ...

  19. Eye evolution: two eyes can be better than one.

    PubMed

    Foster, Kenneth W

    2009-03-10

    The development of our eyes is owed in part to ancestral structures which functioned in phototaxis. With the origin of bilateral annelid larva, two eyes co-evolved with neurons to improve phototaxis performance. PMID:19278637

  20. 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

  1. 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

  2. [Anatomical parameters of emmetropic and varyingly myopic eyes].

    PubMed

    Deev, L A; Nivenitsyn, E L; Tret'yakov, A N; Lopashinov, P M; Volosenkova, M V

    2015-01-01

    This article summarizes the results of a study on ocular anatomy in emmetropia and different degrees of myopia conducted in the Smolensk State Medical Academy. Data of 233 patients (408 eyes) is presented. Five size parameters were measured in all cases. A mathematical model of an emmetropic eye has been developed. The results obtained allow to judge the dimensions of a normal eyeball and their changes in case of myopia progression. PMID:26845870

  3. Flexible beam shaping system using fly's eye condenser.

    PubMed

    Lindlein, Norbert; Bich, Andreas; Eisner, Martin; Harder, Irina; Lano, Maik; Voelkel, Reinhard; Weible, Ken; Zimmermann, Maik

    2010-04-20

    Normally, fly's eye condensers are used to homogenize light. However, in the case of fully coherent light, a fly's eye condenser, in connection with some simple optical elements, such as a diffractive axicon, a grating, and a telescope, can be used as a quite flexible beam shaping system, forming arrays of rings, parts of rings, or other structures with varying diameters. We present the principle, some simulation results, and some first experimental results. PMID:20411020

  4. P gene as an inherited biomarker of human eye color.

    PubMed

    Rebbeck, Timothy R; Kanetsky, Peter A; Walker, Amy H; Holmes, Robin; Halpern, Allan C; Schuchter, Lynn M; Elder, David E; Guerry, DuPont

    2002-08-01

    Human pigmentation, including eye color, has been associated with skin cancer risk. The P gene is the human homologue to the mouse pink-eye dilution locus and is responsible for oculocutaneous albinism type 2 and other phenotypes that confer eye hypopigmentation. The P gene is located on chromosome 15q11.2-q12, which is also the location of a putative eye pigmentation gene (EYCL3) inferred to exist by linkage analysis. Therefore, the P gene is a strong candidate for determination of human eye color. Using a sample of 629 normally pigmented individuals, we found that individuals were less likely to have blue or gray eyes if they had P gene variants Arg305Trp (P = 0.002), Arg419Gln (P = 0.001), or the combination of both variants (P = 0.003). These results suggest that P gene, in part, determines normal phenotypic variation in human eye color and may therefore represent an inherited biomarker of cutaneous cancer risk. PMID:12163334

  5. 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

  6. 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,…

  7. 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)

  8. The Eyes Have It

    NASA Technical Reports Server (NTRS)

    1999-01-01

    NASA'S Ames Research Center contracted with SRI international to contract a device that would be able to anticipate, track, and monitor involuntary ocular movement horizontally, vertically, and with respect to depth-of-field. This development helped research institutions to understand the eye. The Eyetracker, manufactured and distributed by Forward Optical Technologies, Inc. is now used in the clinical/medical field.

  9. 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…

  10. Administering Eye Medications.

    ERIC Educational Resources Information Center

    Morris, Sara; Michael, Nancy, Ed.

    This module on administering eye medications is intended for use in inservice or continuing education programs for persons who administer medications in long-term care facilities. Instructor information, including teaching suggestions, and a listing of recommended audiovisual materials and their sources appear first. A brief discussion follows of…

  11. Red or uncomfortable eye.

    PubMed Central

    Davey, C.; Hurwitz, B.

    1992-01-01

    1. A red, uncomfortable eye may be accompanied by other symptoms such as blurred, decreased, or double vision, haloes, photophobia, pain or discharge. 2. A careful history and brief systematic examination will sort out most problems. 3. Examine eyelids, the conjunctivae and corneas. Checking visual acuity is often important. 4. The most common underlying causes can usually be managed within general practice, though a few patients will require urgent eye assessment, or routine referral to ophthalmic outpatients. 5. The following are typical eye problems which require urgent referral: History of pain as opposed to discomfort, Trauma including foreign bodies, chemicals and suspected penetrating injury, Unexplained drop in visual acuity of two lines or more in a painful eye. Specific conditions: preseptal cellulitis, herpes simplex ulcer, scleritis, orbital cellulitis, herpes zoster, bacterial corneal ulcer, dacryocystitis. 6. The following are typical problems which may require routine referral: Persistence of the problem not relieved by simple measures, Recurrent disorders of uncertain diagnosis, Eyelid swelling such as chalazion, cysts, basal cell carcinoma, Gradual loss of vision, for example cataract, macular degeneration. PMID:1345157

  12. Diabetes - eye care

    MedlinePlus

    ... blurred vision is caused by having too much sugar and water in the lens of the eye, which is in front of the retina. Control your blood pressure . Blood pressure less than 130/80 is a ... sugar - self-care Diabetes - preventing heart attack and stroke ...

  13. 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…

  14. 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…

  15. Common eye emergencies.

    PubMed

    Gelston, Christopher D

    2013-10-15

    Ocular emergencies such as retinal detachments, mechanical globe injuries, and chemical injuries can cause permanent vision loss if they are not recognized and treated promptly. Family physicians should be familiar with the signs and symptoms associated with each condition, and be able to perform a basic eye examination to assess the situation. The assessment includes measurement of visual acuity, pupillary examination, visual field testing, slit lamp or penlight examination of the anterior segment of the eye, and direct funduscopic examination. Patients with symptomatic floaters and flashing lights require a dilated fundoscopic examination and prompt referral to an ophthalmologist for evaluation of a retinal tear or detachment. A globe laceration or rupture should be suspected in patients with a recent history of trauma from a blunt or penetrating object. Prophylactic oral antibiotics can be administered after a globe injury to prevent endophthalmitis, and the eye should be covered with a metal shield until evaluation by an ophthalmologist. Chemical injuries require immediate irrigation of the eye to neutralize the pH of the ocular surface. PMID:24364572

  16. 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.

  17. Assessing Statistical Significance in Microarray Experiments Using the Distance Between Microarrays

    PubMed Central

    Hayden, Douglas; Lazar, Peter; Schoenfeld, David

    2009-01-01

    We propose permutation tests based on the pairwise distances between microarrays to compare location, variability, or equivalence of gene expression between two populations. For these tests the entire microarray or some pre-specified subset of genes is the unit of analysis. The pairwise distances only have to be computed once so the procedure is not computationally intensive despite the high dimensionality of the data. An R software package, permtest, implementing the method is freely available from the Comprehensive R Archive Network at http://cran.r-project.org. PMID:19529777

  18. Evidence suggesting individual ocular motor control of each eye (muscle).

    PubMed

    Dell'Osso, L F

    1994-01-01

    Current models of the ocular motor system are usually presented in their most reduced form, are unilateral in architecture, and precise yoking is presumed. Although this simplifies the models, it does not accurately simulate the actual neuroanatomy and limits the models to simple, stereotyped responses. Studies of normal humans and monkeys have demonstrated striking disconjugacies in normal responses. Normal saccades may be disconjugate, or 1 eye may exhibit a dynamic overshoot. Asymmetric vergence can result in disconjugate saccades, unequal magnification spectacles cause differential saccadic gain adjustment, and saccades to unequal disparities also cause unequal saccades in the 2 eyes. In strabismus, deviated eyes typically do not mimic the movements of the fixating eye nor do their latent or congenital nystagmus waveforms duplicate those of the fixating eye. In spasmus nutans, each eye oscillates independently of the other. In achiasmatic dogs, uni-ocular saccades and uni-ocular nystagmus waveforms are seen; the same may be true in human achiasma. These data from both normals and those with abnormalities suggest that current models for ocular motor control are inadequate representations of the actual system. The inability of unilateral, yoked control (or even bilateral, yoked control) system models to duplicate the ocular motor responses of binocular mammals suggests that their ocular motor systems evolved from the bilateral, independent control systems seen in chameleons. One need only postulate a yoking overlay superimposed on two independent control systems to achieve conjugacy (bilateral, yoked, independent control) of the eyes. Abnormalities producing grossly disconjugate eye movements may then be simulated using the independent control of each eye released by a deficiency in the yoking overlay. Independent control of each eye coupled with the essential bilateral brain stem architecture implies that each individual muscle is driven by independent

  19. 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 ...

  20. Infographic on the Aging Eye

    MedlinePlus

    ... retina. Dry eye Low vision Damage to the optic nerve. Eyes do not make enough tears. Difficulty ... retina that can be seen through undilated pupil. OPTIC NERVE RAY OF LIGHT PUPIL RETINA Portion of ...

  1. 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 ...

  2. 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 ...

  3. 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

  4. 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

  5. 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.

  6. Detection of characteristic eye points in non-ideal light conditions

    NASA Astrophysics Data System (ADS)

    Wiśniewska, Joanna; Galiński, Grzegorz

    2015-09-01

    Detection of characteristic eye points under challenging light conditions is a non-trivial task. Difficulty of this task increase even more when low resolution images are used. This article introduces an adaptive solution for detection of characteristic eye points in mentioned conditions. First, light normalization algorithm is performed. Then, face and eye detection followed by determination of eye status (namely: open or closed) is done. Finally, an adaptive method for pupil and eye corners detection is developed by comparing some existing methods. Experimental results show the outperformance of the proposed method.

  7. Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment

    PubMed Central

    Konishi, Tomokazu

    2004-01-01

    Background To cancel experimental variations, microarray data must be normalized prior to analysis. Where an appropriate model for statistical data distribution is available, a parametric method can normalize a group of data sets that have common distributions. Although such models have been proposed for microarray data, they have not always fit the distribution of real data and thus have been inappropriate for normalization. Consequently, microarray data in most cases have been normalized with non-parametric methods that adjust data in a pair-wise manner. However, data analysis and the integration of resultant knowledge among experiments have been difficult, since such normalization concepts lack a universal standard. Results A three-parameter lognormal distribution model was tested on over 300 sets of microarray data. The model treats the hybridization background, which is difficult to identify from images of hybridization, as one of the parameters. A rigorous coincidence of the model to data sets was found, proving the model's appropriateness for microarray data. In fact, a closer fitting to Northern analysis was obtained. The model showed inconsistency only at very strong or weak data intensities. Measurement of z-scores as well as calculated ratios was reproducible only among data in the model-consistent intensity range; also, the ratios were independent of signal intensity at the corresponding range. Conclusion The model could provide a universal standard for data, simplifying data analysis and knowledge integration. It was deduced that the ranges of inconsistency were caused by experimental errors or additive noise in the data; therefore, excluding the data corresponding to those marginal ranges will prevent misleading analytical conclusions. PMID:14718068

  8. 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

  9. 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)

  10. How the Human Eye Focuses.

    ERIC Educational Resources Information Center

    Koretz, Jane F.; Handelman, George H.

    1988-01-01

    Describes the decline in people's ability to focus their eyes as their age increases. Discusses probable causes of this effect including changes in the eye's geometry and biochemistry. Diagrammatically illustrates age related changes in the lens of the human eye. (CW)

  11. 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)…

  12. 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

  13. 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 ...

  14. Identification of significant features in DNA microarray data

    PubMed Central

    Bair, Eric

    2013-01-01

    DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA microarray experiments is to identify genes associated with biological processes of interest. Conventional statistical tests often produce poor results when applied to microarray data owing to small sample sizes, noisy data, and correlation among the expression levels of the genes. Thus, novel statistical methods are needed to identify significant genes in DNA microarray experiments. This article discusses the challenges inherent in DNA microarray analysis and describes a series of statistical techniques that can be used to overcome these challenges. The problem of multiple hypothesis testing and its relation to microarray studies are also considered, along with several possible solutions. PMID:24244802

  15. 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.

  16. 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

  17. Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB

    PubMed Central

    Chatziioannou, Aristotelis; Moulos, Panagiotis; Kolisis, Fragiskos N

    2009-01-01

    Background The microarray data analysis realm is ever growing through the development of various tools, open source and commercial. However there is absence of predefined rational algorithmic analysis workflows or batch standardized processing to incorporate all steps, from raw data import up to the derivation of significantly differentially expressed gene lists. This absence obfuscates the analytical procedure and obstructs the massive comparative processing of genomic microarray datasets. Moreover, the solutions provided, heavily depend on the programming skills of the user, whereas in the case of GUI embedded solutions, they do not provide direct support of various raw image analysis formats or a versatile and simultaneously flexible combination of signal processing methods. Results We describe here Gene ARMADA (Automated Robust MicroArray Data Analysis), a MATLAB implemented platform with a Graphical User Interface. This suite integrates all steps of microarray data analysis including automated data import, noise correction and filtering, normalization, statistical selection of differentially expressed genes, clustering, classification and annotation. In its current version, Gene ARMADA fully supports 2 coloured cDNA and Affymetrix oligonucleotide arrays, plus custom arrays for which experimental details are given in tabular form (Excel spreadsheet, comma separated values, tab-delimited text formats). It also supports the analysis of already processed results through its versatile import editor. Besides being fully automated, Gene ARMADA incorporates numerous functionalities of the Statistics and Bioinformatics Toolboxes of MATLAB. In addition, it provides numerous visualization and exploration tools plus customizable export data formats for seamless integration by other analysis tools or MATLAB, for further processing. Gene ARMADA requires MATLAB 7.4 (R2007a) or higher and is also distributed as a stand-alone application with MATLAB Component Runtime

  18. 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.

  19. What Happens After Treatment for Eye Cancer?

    MedlinePlus

    ... having eye cancer What happens after treatment for eye cancer? For many people with eye cancer, treatment ... manage them. Follow-up after treatment of uveal (eye) melanoma Your doctor will most likely want to ...

  20. What Is a Comprehensive Dilated Eye Exam?

    MedlinePlus

    ... su oculista What is a comprehensive dilated eye exam? You may think your eyes are healthy, but ... eye care professional for a comprehensive dilated eye exam is the only way to really be sure. ...

  1. Prenatal chromosomal microarray for the Catholic physician

    PubMed Central

    Bringman, Jay J.

    2014-01-01

    Prenatal chromosomal microarray (CMA) is a test that is used to diagnose certain genetic problems in the fetus. While the test has been used in the pediatric setting for several years, it is now being introduced for use in the prenatal setting. The test offers great hope for detection of certain genetic defects in the fetus so that early intervention can be performed to improve the outcome for that individual. As with many biotechnical advances, CMA comes with certain bioethical issues that need to be addressed prior to its implementation. This paper is intended to provide guidance to all those that provide counseling regarding genetic testing options during pregnancy. PMID:24899750

  2. 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.

  3. 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.

  4. 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.

  5. Single exon-resolution targeted chromosomal microarray analysis of known and candidate intellectual disability genes.

    PubMed

    Tucker, Tracy; Zahir, Farah R; Griffith, Malachi; Delaney, Allen; Chai, David; Tsang, Erica; Lemyre, Emmanuelle; Dobrzeniecka, Sylvia; Marra, Marco; Eydoux, Patrice; Langlois, Sylvie; Hamdan, Fadi F; Michaud, Jacques L; Friedman, Jan M

    2014-06-01

    Intellectual disability affects about 3% of individuals globally, with∼50% idiopathic. We designed an exonic-resolution array targeting all known submicroscopic chromosomal intellectual disability syndrome loci, causative genes for intellectual disability, and potential candidate genes, all genes encoding glutamate receptors and epigenetic regulators. Using this platform, we performed chromosomal microarray analysis on 165 intellectual disability trios (affected child and both normal parents). We identified and independently validated 36 de novo copy-number changes in 32 trios. In all, 67% of the validated events were intragenic, involving only exon 1 (which includes the promoter sequence according to our design), exon 1 and adjacent exons, or one or more exons excluding exon 1. Seventeen of the 36 copy-number variants involve genes known to cause intellectual disability. Eleven of these, including seven intragenic variants, are clearly pathogenic (involving STXBP1, SHANK3 (3 patients), IL1RAPL1, UBE2A, NRXN1, MEF2C, CHD7, 15q24 and 9p24 microdeletion), two are likely pathogenic (PI4KA, DCX), two are unlikely to be pathogenic (GRIK2, FREM2), and two are unclear (ARID1B, 15q22 microdeletion). Twelve individuals with genomic imbalances identified by our array were tested with a clinical microarray, and six had a normal result. We identified de novo copy-number variants within genes not previously implicated in intellectual disability and uncovered pathogenic variation of known intellectual disability genes below the detection limit of standard clinical diagnostic chromosomal microarray analysis. PMID:24253858

  6. 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.

  7. 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.

  8. Auditory spatial perception dynamically realigns with changing eye position.

    PubMed

    Razavi, Babak; O'Neill, William E; Paige, Gary D

    2007-09-19

    Audition and vision both form spatial maps of the environment in the brain, and their congruency requires alignment and calibration. Because audition is referenced to the head and vision is referenced to movable eyes, the brain must accurately account for eye position to maintain alignment between the two modalities as well as perceptual space constancy. Changes in eye position are known to variably, but inconsistently, shift sound localization, suggesting subtle shortcomings in the accuracy or use of eye position signals. We systematically and directly quantified sound localization across a broad spatial range and over time after changes in eye position. A sustained fixation task addressed the spatial (steady-state) attributes of eye position-dependent effects on sound localization. Subjects continuously fixated visual reference spots straight ahead (center), to the left (20 degrees), or to the right (20 degrees) of the midline in separate sessions while localizing auditory targets using a laser pointer guided by peripheral vision. An alternating fixation task focused on the temporal (dynamic) aspects of auditory spatial shifts after changes in eye position. Localization proceeded as in sustained fixation, except that eye position alternated between the three fixation references over multiple epochs, each lasting minutes. Auditory space shifted by approximately 40% toward the new eye position and dynamically over several minutes. We propose that this spatial shift reflects an adaptation mechanism for aligning the "straight-ahead" of perceived sensory-motor maps, particularly during early childhood when normal ocular alignment is achieved, but also resolving challenges to normal spatial perception throughout life. PMID:17881531

  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. 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

  11. [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

  12. Eye movement abnormalities.

    PubMed

    Moncayo, Jorge; Bogousslavsky, Julien

    2012-01-01

    Generation and control of eye movements requires the participation of the cortex, basal ganglia, cerebellum and brainstem. The signals of this complex neural network finally converge on the ocular motoneurons of the brainstem. Infarct or hemorrhage at any level of the oculomotor system (though more frequent in the brain-stem) may give rise to a broad spectrum of eye movement abnormalities (EMAs). Consequently, neurologists and particularly stroke neurologists are routinely confronted with EMAs, some of which may be overlooked in the acute stroke setting and others that, when recognized, may have a high localizing value. The most complex EMAs are due to midbrain stroke. Horizontal gaze disorders, some of them manifesting unusual patterns, may occur in pontine stroke. Distinct varieties of nystagmus occur in cerebellar and medullary stroke. This review summarizes the most representative EMAs from the supratentorial level to the brainstem. PMID:22377853

  13. 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

  14. [The eye and cancer].

    PubMed

    Schalenbourg, Ann; Mantel, Irmela

    2015-12-16

    Cancer involves so rarely the eye that it may be recognized late. The most frequent primary intra-ocular tumours are retinoblastoma in small children and uveal melanoma in adults. Vision loss in systemic cancer has a varied differential diagnosis. Uveal metastases are most often associated with breast cancer, but can herald lung carcinoma. Masquerade syndrome looks like inflammation but represents the ocular involvement of primary CNS non-Hodgkin lymphoma. Systemic cancer drugs, as well as radiotherapy, can cause ocular toxicity, mostly at the retina. In the rare paraneoplastic syndromes, patient's cancer antibodies cross-react with retinal antigens, leading to severe vision loss. When cancer involves the eye, a fast referral into specialized care can significantly improve visual and vital prognosis. PMID:26852556

  15. 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

  16. 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

  17. Michelangelo's eye disease.

    PubMed

    Gallenga, P E; Neri, Giampiero; D'Anastasio, Ruggero; Pettorrossi, Vito Enrico; Alfieri, Emilio; Capasso, Luigi

    2012-06-01

    Charged by the Pope Julius II for painting the Cappella Sistina in Rome (between 1508 and 1512), Michelangelo worked in an elevated scaffolding, in an anomalous position with dyes (including poisoning lead salts) and solvents (such as toxic turpentine) dripping on his face and continuously inhaling, in a dim environment illuminated only with oil lamps and candles, as he described himself and sketched in a sonet addressed to Giovanni da Pistoia. In 1510 he began suffering from eye disease: the main symptom was the necessity to elevate the document he was reading up to the level of his eyes. This defect disappeared few months after he finished painting his masterpiece. We hypothesize that the Michelangelo's eyes disease was a form of acquired and transitory nystagmus induced by the many hours he spent in up gaze, with a skew deviation, a form of ocular tilt reaction resulting from the impairment of spatial sensitivity (inversion illusion) due to the persistence of the artist's head in a horizontal position, looking upward. PMID:22425178

  18. 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

  19. 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

  20. Computerized system for recognition of autism on the basis of gene expression microarray data.

    PubMed

    Latkowski, Tomasz; Osowski, Stanislaw

    2015-01-01

    The aim of this paper is to provide a means to recognize a case of autism using gene expression microarrays. The crucial task is to discover the most important genes which are strictly associated with autism. The paper presents an application of different methods of gene selection, to select the most representative input attributes for an ensemble of classifiers. The set of classifiers is responsible for distinguishing autism data from the reference class. Simultaneous application of a few gene selection methods enables analysis of the ill-conditioned gene expression matrix from different points of view. The results of selection combined with a genetic algorithm and SVM classifier have shown increased accuracy of autism recognition. Early recognition of autism is extremely important for treatment of children and increases the probability of their recovery and return to normal social communication. The results of this research can find practical application in early recognition of autism on the basis of gene expression microarray analysis. PMID:25464350

  1. Methods for gene expression profiling in dermatology research using DermArray nylon filter DNA microarrays.

    PubMed

    Davis, Richard L; DuBreuil, Rusla M; Reddy, Shanker P; Dooley, Thomas P

    2005-01-01

    Here we present methods of gene expression profiling using nylon filter deoxyribonucleic acid (DNA) microarrays and radiolabeled and nonradiolabeled hybridization probes. DermArray(R) nylon filter DNA microarrays were designed specifically for use in dermatology research. A patent-pending method was used to select approx 4400 highly informative, sequence-verified human cDNA clones for this DNA micro array. Using DermArray(R) filters, biomarkers have been discovered for normal and pathologic cells from skin, and for responses to dermatologic drugs. As an example, gene expression profiling was performed with hydroquinone-treated SKMel-28 cells, a melanoma cell line. Also included are the methods for bioinformatic analysis using Pathwaystrade mark software. PMID:15502201

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. Mining microarray expression data by literature profiling

    PubMed Central

    Chaussabel, Damien; Sher, Alan

    2002-01-01

    Background The rapidly expanding fields of genomics and proteomics have prompted the development of computational methods for managing, analyzing and visualizing expression data derived from microarray screening. Nevertheless, the lack of efficient techniques for assessing the biological implications of gene-expression data remains an important obstacle in exploiting this information. Results To address this need, we have developed a mining technique based on the analysis of literature profiles generated by extracting the frequencies of certain terms from thousands of abstracts stored in the Medline literature database. Terms are then filtered on the basis of both repetitive occurrence and co-occurrence among multiple gene entries. Finally, clustering analysis is performed on the retained frequency values, shaping a coherent picture of the functional relationship among large and heterogeneous lists of genes. Such data treatment also provides information on the nature and pertinence of the associations that were formed. Conclusions The analysis of patterns of term occurrence in abstracts constitutes a means of exploring the biological significance of large and heterogeneous lists of genes. This approach should contribute to optimizing the exploitation of microarray technologies by providing investigators with an interface between complex expression data and large literature resources. PMID:12372143

  7. Enzyme microarrays assembled by acoustic dispensing technology.

    PubMed

    Wong, E Y; Diamond, S L

    2008-10-01

    Miniaturizing bioassays to the nanoliter scale for high-throughput screening reduces the consumption of reagents that are expensive or difficult to handle. Through the use of acoustic dispensing technology, nanodroplets containing 10 microM ATP (3 microCi/microL (32)P) 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 microM substrate. The microarray was incubated at 30 degrees C (97% R(h)) for 1.5 h. The spots were then blotted to phosphocellulose membranes to capture phosphorylated substrate. With phosphor imaging to quantify the washed membranes, the assay showed that, for doses of inhibitor from 0.75 to 3 microM, Pim1 was increasingly inhibited. Signal-to-background ratios were as high as 165, and average coefficients of variation for the assay were approximately 20%. Coefficients of variation 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

  8. 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.

  9. [Regulatory proteins of vertebrate eye tissues].

    PubMed

    Krasnov, M S; Grigorian, E N; Iamskova, V P; Boguslavskiĭ, D V; Iamskov, I A

    2003-01-01

    In our work the new proteins likely belonged to the microenvironment of pigmented epithelium cells and retinal neurons in mammalian eye were studied. We attempted to understand the role of these proteins in the maintenance of normal morphological and functional state of these eye tissues. Earlier for the first time we identified the adhesion molecules with physico-chemical and biological properties much different from other known cell adhesion molecules of bovine eye. Probably, they represent one family of low molecular weigh, highly glicosylated proteins, that express biological activity in extremely low doses--10(-10) mg/ml. The homogeneity of studying proteins is confirmed by HPLC and SDS-electrophoresis in PAAG. It is shown also that these proteins are N-glycosylated, because they contain mannose and N-acetilglucosamine residues. They demonstrate as well a high calcium-binding activity, with Kd corresponded to 10(-4)-10(-6) mg/ml. For a study of the biological effect of these glycoproteins in extremely low doses, a new experimental model was proposed and developed. It was the cultivation in vitro of the posterior part of the eye obtained from the newt Pleurodeles waltl. In short-time culture system it was demonstrated that the studied glycoproteins could stabilize pigment epithelium cell differentiation and cellular interactions in the neural retina in vitro. In addition, glycoproteins, obtained from the pigmented epithelium of bovine eye could decrease the rate of bipolar cell apoptosis in the neural retina. Therefore, the novel adhesion glycoproteins, expressing their biological activity in extremely low doses, pretend to be the regulatory molecules with vivid gomeostatic effects necessary for the delicate adjustment of cell behavior action and function in sensory tissues. PMID:12881976

  10. 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.

  11. 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.

  12. The role of eye movement driven attention in functional strabismic amblyopia.

    PubMed

    Wang, Hao; Crewther, Sheila Gillard; Yin, Zheng Qin

    2015-01-01

    Strabismic amblyopia "blunt vision" is a developmental anomaly that affects binocular vision and results in lowered visual acuity. Strabismus is a term for a misalignment of the visual axes and is usually characterized by impaired ability of the strabismic eye to take up fixation. Such impaired fixation is usually a function of the temporally and spatially impaired binocular eye movements that normally underlie binocular shifts in visual attention. In this review, we discuss how abnormal eye movement function in children with misaligned eyes influences the development of normal binocular visual attention and results in deficits in visual function such as depth perception. We also discuss how eye movement function deficits in adult amblyopia patients can also lead to other abnormalities in visual perception. Finally, we examine how the nonamblyopic eye of an amblyope is also affected in strabismic amblyopia. PMID:25838941

  13. The Role of Eye Movement Driven Attention in Functional Strabismic Amblyopia

    PubMed Central

    2015-01-01

    Strabismic amblyopia “blunt vision” is a developmental anomaly that affects binocular vision and results in lowered visual acuity. Strabismus is a term for a misalignment of the visual axes and is usually characterized by impaired ability of the strabismic eye to take up fixation. Such impaired fixation is usually a function of the temporally and spatially impaired binocular eye movements that normally underlie binocular shifts in visual attention. In this review, we discuss how abnormal eye movement function in children with misaligned eyes influences the development of normal binocular visual attention and results in deficits in visual function such as depth perception. We also discuss how eye movement function deficits in adult amblyopia patients can also lead to other abnormalities in visual perception. Finally, we examine how the nonamblyopic eye of an amblyope is also affected in strabismic amblyopia. PMID:25838941

  14. 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.

  15. 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…

  16. Removal of hybridization and scanning noise from microarrays.

    PubMed

    Gopalappa, Chaitra; Das, Tapas K; Enkemann, Steven; Eschrich, Steven

    2009-09-01

    Microarray technology for measuring gene expression values has created significant opportunities for advances in disease diagnosis and individualized treatment planning. However, the random noise introduced by the sample preparation, hybridization, and scanning stages of microarray processing creates significant inaccuracies in the gene expression levels, and hence presents a major barrier in realizing the anticipated advances. Literature presents several methodologies for noise reduction, which can be broadly categorized as: 1) model based approaches for estimation and removal of hybridization noise; 2) approaches using commonly available image denoising tools; and 3) approaches involving the need for control sample(s). In this paper, we present a novel methodology for identifying and removing hybridization and scanning noise from microarray images, using a dual-tree-complex-wavelet-transform-based multiresolution analysis coupled with bivariate shrinkage thresholding. The key features of our methodology include consideration of inherent features and type of noise specific to microarray images, and the ability to work with a single microarray without needing a control. Our methodology is first benchmarked on a fabricated dataset that mimics a real microarray probe dataset. Thereafter, our methodology is tested on datasets obtained from a number of Affymetrix GeneChip human genome HG-U133 Plus 2.0 arrays, processed on HCT-116 cell line at the Microarray Core Facility of Moffitt Cancer Center and Research Institute. The results indicate an appreciable improvement in the quality of the microarray data. PMID:20051337

  17. Applications of microarray technology in breast cancer research

    PubMed Central

    Cooper, Colin S

    2001-01-01

    Microarrays provide a versatile platform for utilizing information from the Human Genome Project to benefit human health. This article reviews the ways in which microarray technology may be used in breast cancer research. Its diverse applications include monitoring chromosome gains and losses, tumour classification, drug discovery and development, DNA resequencing, mutation detection and investigating the mechanism of tumour development. PMID:11305951

  18. 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

  19. Application of Microarray Technology to Investigate Salmonella and Antimicrobial Resistance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microarrays have been developed for the study of various aspects of Salmonella, which is a model system for investigating pathogenesis. Microarrays were used to analyze the gene expression of Salmonella in various environments that mimic the host environment and these studies have helped to elucidat...

  20. [Binding capability of lidamycin apoprotein to human breast cancer detected by tissue microarrays].

    PubMed

    Cai, Lin; Gao, Rui-Juan; Guo, Xiao-Zhong; Li, Yi; Zhen, Yong-Su

    2010-05-01

    This study is to investigate the binding capability of lidamycin apoprotein (LDP), an enediyne-associated apoprotein of the chromoprotein antitumor antibiotic family, to human breast cancer and normal tissues, the correlation of LDP binding capability to human breast cancer tissues and the expression of tumor therapeutic targets such as VEGF and HER2. In this study, the binding capability of LDP to human breast cancer tissues was detected with tissue microarray. The correlation study of LDP binding capability to human breast tumor tissues and relevant therapeutic targets was performed on breast cancer tissue microarrays. Immunocytochemical examination was used to detect the binding capability of LDP to human breast carcinoma MCF-7 cells. As a result, tissue microarray showed that LDP staining of 73.2% (30/41) of breast cancer tissues was positive, whereas that of 48.3% (15/31) of the adjacent normal breast specimens was positive. The difference between the tumor and normal samples was significant (Chi2 = 4.63, P < 0.05). LDP immunoreactivity in breast cancer correlated significantly with the overexpression of VEGF and HER2 (P < 0.001 and < 0.01, r = 0.389 and 0.287, respectively). Determined with confocal immunofluorescent analysis, LDP showed the binding capability to mammary carcinoma MCF-7 cells. It is demonstrated that LDP can bind to human breast cancer tissues and there is significant difference between the breast cancer tissues and the corresponding normal tissues. Notably, the binding reactivity shows positive correlation with the expression of VEGF and HER2 in breast carcinoma tissues. The results imply that LDP may have a potential use as targeting drug carrier in the research and development of new anticancer therapeutics. This study may provide reference for drug combination of LDM and other therapeutic agents. PMID:20931759