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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. Optimized LOWESS normalization parameter selection for DNA microarray data

    PubMed Central

    Berger, John A; Hautaniemi, Sampsa; Järvinen, Anna-Kaarina; Edgren, Henrik; Mitra, Sanjit K; Astola, Jaakko

    2004-01-01

    Background Microarray data normalization is an important step for obtaining data that are reliable and usable for subsequent analysis. One of the most commonly utilized normalization techniques is the locally weighted scatterplot smoothing (LOWESS) algorithm. However, a much overlooked concern with the LOWESS normalization strategy deals with choosing the appropriate parameters. Parameters are usually chosen arbitrarily, which may reduce the efficiency of the normalization and result in non-optimally normalized data. Thus, there is a need to explore LOWESS parameter selection in greater detail. Results and discussion In this work, we discuss how to choose parameters for the LOWESS method. Moreover, we present an optimization approach for obtaining the fraction of data points utilized in the local regression and analyze results for local print-tip normalization. The optimization procedure determines the bandwidth parameter for the local regression by minimizing a cost function that represents the mean-squared difference between the LOWESS estimates and the normalization reference level. We demonstrate the utility of the systematic parameter selection using two publicly available data sets. The first data set consists of three self versus self hybridizations, which allow for a quantitative study of the optimization method. The second data set contains a collection of DNA microarray data from a breast cancer study utilizing four breast cancer cell lines. Our results show that different parameter choices for the bandwidth window yield dramatically different calibration results in both studies. Conclusions Results derived from the self versus self experiment indicate that the proposed optimization approach is a plausible solution for estimating the LOWESS parameters, while results from the breast cancer experiment show that the optimization procedure is readily applicable to real-life microarray data normalization. In summary, the systematic approach to obtain critical

  3. Immunohistochemical characteristics of normal canine eyes.

    PubMed

    Labelle, P; Reilly, C M; Naydan, D K; Labelle, A L

    2012-09-01

    Immunohistochemistry is widely utilized in diagnostic laboratories to study neoplastic and nonneoplastic diseases. Knowledge of the immunohistochemical characteristics of normal tissue is essential for interpretation of immunoreactivity in pathologic conditions. In this study, immunohistochemistry was performed with a broad panel of diagnostically relevant antibodies on 4 normal canine globes--namely, vimentin, pan-cytokeratin (AE1/AE3), cytokeratin 7, cytokeratin 8/18, cytokeratin 20, α-smooth muscle actin, muscle specific actin, desmin, Melan-A, microphthalmia transcription factor, S-100, glial fibrillary acidic protein, triple neurofilaments, neuron-specific enolase, chromogranin A, synaptophysin, laminin and CD31. Results include cytokeratin immunoreactivity limited to the conjunctival epithelium, corneal epithelium, and retinal pigment epithelium; distinct patterns of immunopositivity of muscle markers; and widespread immunoreactivity for vimentin and most neural/neuroendocrine markers. These findings in normal eyes provide the basis for interpretation of ocular immunohistochemistry in dogs. Published immunophenotypes of primary ocular neoplasms are also reviewed.

  4. 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...

  5. 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

  6. 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…

  7. 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

  8. Better performance through amblyopic than through normal eyes.

    PubMed

    Fahle, M; Bachmann, G

    1996-07-01

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

  9. Eye-specific retinogeniculate segregation independent of normal neuronal activity.

    PubMed

    Huberman, Andrew D; Wang, Guo-Yong; Liets, Lauren C; Collins, Odell A; Chapman, Barbara; Chalupa, Leo M

    2003-05-09

    The segregation of initially intermingled left and right eye inputs to the dorsal lateral geniculate nucleus (DLGN) during development is thought to be in response to precise spatial and temporal patterns of spontaneous ganglion cell activity. To test this hypothesis, we disrupted the correlated activity of neighboring ganglion cells in the developing ferret retina through immunotoxin depletion of starburst amacrine cells. Despite the absence of this type of correlated activity, left and right eye inputs segregated normally in the DLGN. By contrast, when all spontaneous activity was blocked, the projections from the two eyes remained intermingled. Thus, certain features of normal neural activity patterns are not required for the formation of eye-specific projections to the DLGN.

  10. 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

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

    PubMed

    Astola, Laura; Molenaar, Jaap

    2014-07-01

    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.

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

    PubMed Central

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

    2015-01-01

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

  13. Nonspecific hybridization scaling of microarray expression estimates: a physicochemical approach for chip-to-chip normalization.

    PubMed

    Binder, Hans; Brücker, Jan; Burden, Conrad J

    2009-03-05

    The problem of inferring accurate quantitative estimates of transcript abundances from gene expression microarray data is addressed. Particular attention is paid to correcting chip-to-chip variations arising mainly as a result of unwanted nonspecific background hybridization to give transcript abundances measured in a common scale. This study verifies and generalizes a model of the mutual dependence between nonspecific background hybridization and the sensitivity of the specific signal using an approach based on the physical chemistry of surface hybridization. We have analyzed GeneChip oligonucleotide microarray data taken from a set of five benchmark experiments including dilution, Latin Square, and "Golden spike" designs. Our analysis concentrates on the important effect of changes in the unwanted nonspecific background inherent in the technology due to changes in total RNA target concentration and/or composition. We find that incremental changes in nonspecific background entail opposite sign incremental changes in the effective specific binding constant. This effect, which we refer to as the "up-down" effect, results from the subtle interplay of competing interactions between the probes and specific and nonspecific targets at the chip surface and in bulk solution. We propose special rules for proper normalization of expression values considering the specifics of the up-down effect. Particularly for normalization one has to level the expression values of invariant expressed probes. Existing heuristic normalization techniques which do not exclude absent probes, level intensities instead of expression values, and/or use low variance criteria for identifying invariant sets of probes lead to biased results. Strengths and pitfalls of selected normalization methods are discussed. We also find that the extent of the up-down effect is modified if RNA targets are replaced by DNA targets, in that microarray sensitivity and specificity are improved via a decrease in

  14. 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.

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

    PubMed

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

    2011-06-01

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

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

    PubMed

    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 201TI 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 201TI 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 201TI images requires gender-matched normal files.

  17. 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

  18. 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

  19. 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.

  20. 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

  1. Comparisons of robustness and sensitivity between cancer and normal cells by microarray data.

    PubMed

    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.

  2. 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.

  3. 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

  4. 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.

  5. Eye and head movements in reading-disabled and normal children.

    PubMed

    Petri, J L; Anderson, M E

    1980-12-01

    Coordination of eye and head movements on nonreading tasks was investigated in 16 reading-disabled and 18 normal children aged 6 to 11 years. Types of eye movements are described and mechanisms controlling eye and head movement are reviewed. Significant differences were found between the two groups in sequencing of eye and head movements that were made in response to the appearance of visual stimuli at unexpected times and positions. Some reading-disabled children also were found to require more eye movements to achieve fixation on targets at known positions. It is suggested that the vestibular system may be implicated as a factor in the results obtained from the reading-disabled children and that the atypical eye-head movement patterns observed may did in stabilizing their visual world.

  6. 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

  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. Unilateral optic disc pit and orbital cyst in an eye with normal axial length.

    PubMed

    Dhir, Luna; Thaller, Vladimir T

    2010-01-01

    Orbital cyst and optic disc pits are both congenital embryological anomalies. Orbital cysts occurring in association with optic disc colobomata and microphthalmic eyes have been widely reported in literature. The authors describe the case of a 69-year-old man with an asymptomatic orbital mass, who was investigated and found to have a coexistent optic disc pit and orbital cyst. The axial length was normal. Visual acuity was reduced due to epiretinal membrane at the macula as a consequence of serous maculopathy secondary to the optic disc pit. No active intervention was offered due to poor visual potential, and no changes in the cyst occurred over time. This is an unusual case of coexistent orbital cyst and optic disc pit in an eye with normal axial length, although the dual pathology has previously been described in a microphthalmic eye.

  9. The anatomy at the lamina cribrosa in the normal cat eye.

    PubMed

    Radius, R L; Bade, B

    1982-10-01

    In normal cat eyes, the mean cross-sectional area of the nerve fiber bundles is greater in the temporal than in the nasal lamina cribrosa. The area occupied by the interbundle trabeculae is less in the temporal sectors than in the nasal sectors of the nerve. The number and the shape of the laminar pores are similar in all nerve sectors.

  10. 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…

  11. A microarray gene analysis of peripheral whole blood in normal adult male rats after long-term GH gene therapy.

    PubMed

    Qin, Ying; Tian, Ya-Ping

    2010-06-01

    The main aims of this study were to determine the effects of GH gene abuse/misuse in normal animals and to discover genes that could be used as candidate biomarkers for the detection of GH gene therapy abuse/misuse in humans. We determined the global gene expression profile of peripheral whole blood from normal adult male rats after long-term GH gene therapy using CapitalBio 27 K Rat Genome Oligo Arrays. Sixty one genes were found to be differentially expressed in GH gene-treated rats 24 weeks after receiving GH gene therapy, at a two-fold higher or lower level compared to the empty vector group (p < 0.05). These genes were mainly associated with angiogenesis, oncogenesis, apoptosis, immune networks, signaling pathways, general metabolism, type I diabetes mellitus, carbon fixation, cell adhesion molecules, and cytokine-cytokine receptor interaction. The results imply that exogenous GH gene expression in normal subjects is likely to induce cellular changes in the metabolism, signal pathways and immunity. A real-time qRT-PCR analysis of a selection of the genes confirmed the microarray data. Eight differently expressed genes were selected as candidate biomarkers from among these 61 genes. These 8 showed five-fold higher or lower expression levels after the GH gene transduction (p < 0.05). They were then validated in real-time PCR experiments using 15 single-treated blood samples and 10 control blood samples. In summary, we detected the gene expression profiles of rat peripheral whole blood after long-term GH gene therapy and screened eight genes as candidate biomarkers based on the microarray data. This will contribute to an increased mechanistic understanding of the effects of chronic GH gene therapy abuse/misuse in normal subjects.

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

    PubMed Central

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

    2016-01-01

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

  13. Protein serine/threonine phosphotase-1 is essential in governing normal development of vertebrate eye.

    PubMed

    Liu, W-B; Yan, Q; Liu, F-Y; Tang, X-C; Chen, H-G; Liu, J; Nie, L; Zhang, X-W; Ji, W-K; Hu, X-H; Hu, W-F; Woodward, Z; Wu, K-L; Wu, M-X; Liu, X-L; Luo, L-X; Yu, M-B; Liu, Y-Z; Liu, S-J; Li, D W-C

    2012-12-01

    Protein serine/threonine phosphatase-1 (PP-1) is one of the key enzymes responsible for dephosphorylation in vertebrates. Protein dephosphorylation via PP-1 is implicated in many different biological processes including gene expression, cell cycle control, transformation, neuronal transmission, apoptosis, autophage and senescence. However, whether PP-1 directly controls animal development remains to be investigated. Here, we present direct evidence to show that PP-1 plays an essential role in regulating eye development of vertebrates. Using goldfish as a model system, we have shown the following novel results. First, inhibition of PP-1 activity leads to death of a majority of the treated embryos, and the survived embryos displayed severe phenotype in the eye. Second, knockdown of each catalytic subunit of PP-1 with morpholino oligomers leads to partial (PP-lα knockdown) or complete (PP-lβ or PP-lγ knockdown) death of the injected embryos. The survived embryos from PP-1α knockdown displayed clear retardation in lens differentiation. Finally, overexpression of each subunit of PP-1 also causes death of majority of the injected embryos and leads to abnormal development of goldfish eye. Mechanistically, Pax-6 is one of the major downstream targets mediating the effects of PP-1 function since the eye phenotype in Pax-6 knockdown fish is similar to that derived from overexpression of PP-1. Together, our results for the first time provide direct evidence that protein phosphatase-1 plays a key role in governing normal eye formation during goldfish development.

  14. Normal and diseased personal eye modeling using age-appropriate lens parameters

    PubMed Central

    Chen, Ying-Ling; Shi, L.; Lewis, J. W. L.; Wang, M.

    2012-01-01

    Personalized eye modeling of normal and diseased eye conditions is attractive due to the recent availability of detailed ocular measurements in clinic environments and the promise of its medical and industrial applications. In the customized modeling, the optical properties of the crystalline lens including the gradient refractive index, the lens bio-geometry and orientation are typically assigned with average lens parameters from literature since typically they are not clinically available. Although, through the optical optimization by assigning lens parameters as variables, the clinical measured wavefront aberration can be achieved, the optimized lens biometry and orientation often end up at edges of the statistical distribution. Without an effective validation of these models today, the fidelity of the final lens (and therefore the model) remains questionable. To develop a more reliable customized model without detailed lens information, we incorporate age-appropriate lens parameters as the initial condition of optical optimization. A biconic lens optimization was first performed to provide a correct lens profile for accurate lower order aberration and then followed by the wavefront optimization. Clinical subjects were selected from all ages with both normal and diseased corneal and refractive conditions. 19 ammetropic eyes ( + 4D to −11D), and 16 keratoconus eyes (mild to moderate with cylinder 0.25 to 6D) were modeled. Age- and gender-corrected refractive index was evaluated. Final models attained the lens shapes comparable to the statistical distribution in their age. PMID:22714237

  15. 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

  16. Distribution of albumin in the normal monkey eye as revealed by Evans blue fluorescence microscopy.

    PubMed

    Radius, R L; Anderson, D R

    1980-03-01

    Since intravenously injected Evans blue binds irreversibly to serum albumin, its distribution reflects albumin exchange between the intravascular and extravascular tissue compartments. In histologic specimens examined by fluorescence, microscopy, extravasated Evans blue--albumin complex was identified within the ciliary body and trabecular meshwork of normal monkey eyes. In eyes fixed by intra-arterial perfusion of fixative, no dye was identified in the choroid, retina, or optic nerve. With immersion fixation, however, some extravasation was seen in the choroid and adjacent optic nerve. In some specimens, the optic nerve was stained not only with material apparently leaking from the choroid but also from a breakdown of the blood-brain barrier in the major disc vasculature during the interval before fixative penetrates into the tissue. Perfusion fixation must be used to avoid this artifact, and freezing techniques would be even better.

  17. 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.

  18. Immunolocalization of CYP1B1 in normal, human, fetal and adult eyes.

    PubMed

    Doshi, Manali; Marcus, Craig; Bejjani, Bassem A; Edward, Deepak P

    2006-01-01

    CYP1B1 is a cytochrome P450 enzyme implicated in autosomal recessive primary congenital glaucoma (PCG). The mechanism and function of CYP1B1 in the development of the PCG phenotype is unknown. Previously, investigators have reported detection of Cyp1b1 mRNA in the ciliary body and epithelium and neuroepithelium in the developing mouse eye, employing in situ hybridization techniques. Similarly, additional investigators have detected CYP1B1 mRNA in the iris, ciliary body, non-pigmented ciliary epithelial line, cornea, retinal-pigment epithelium, and retina in the human adult eye, using Northern blotting. This study was designed to immunolocalize CYP1B1 protein in the various ocular structures of normal, human fetal and adult eyes. Normal fetal and adult eyes were immunolabeled with a polyclonal antibody against human CYP1B1 using indirect immunofluorescence, and then compared with appropriate controls. The intensity of immunolabeling of the various ocular structures was assessed by qualitative and semi-quantitative techniques. In the anterior segment anti-CYP1B1 immunoreactivity (IR) was detected early in fetal development in the primitive ciliary epithelium. As well, the most intense CYP1B1 IR was in the non-pigmented ciliary epithelium. In addition, CYP1B1 IR was also present in the corneal epithelium and keratocytes, both layers of the iris pigmented epithelium, and retina. However, CYP1B1 IR was absent in the trabecular meshwork in all of the samples. In general, CYP1B1 immunolabeling in the human fetal eyes was more intense when compared to adult eyes. CYP1B1 IR was primarily immunolocalized to the non-pigmented ciliary epithelium and early in fetal development. In addition, CYP1B1 IR was not detected in the trabecular meshwork. These findings suggest that the abnormalities in the development of the trabecular meshwork in PCG may result from diminished or absent metabolism of important endogenous substrates in the ciliary epithelium due to non-functional CYP1B1

  19. Analysis of normal human eye with different age groups using infrared images.

    PubMed

    Acharya, U Rajendra; Ng, E Y K; Yee, Gerk Chang; Hua, Tan Jian; Kagathi, Manjunath

    2009-06-01

    The human body temperature is a good health indicator. All objects emit thermal radiation as a function temperature and wavelength for all wavelengths. The wavelength of infrared rays lies between visible and microwave radiations ranging between 700 nm to 0.1 mm. Infrared (IR) imaging is relatively inexpensive, noninvasive and harmless. Nowadays, it is widely used in the medical field for diagnosis. In this work, we have applied image processing techniques on the IR images of the eye for the analysis of the ocular surface temperature (OST) of the normal subjects of three categories (young, middle and old ages). In our study, 67 IR normal images were analyzed. Two parameters, average ocular temperature and the temperature deviation were proposed to study the variability of OST in different normal category subjects. Our study shows that, the two parameters proposed, show distinct ranges for different groups with 'p' values less than 0.05.

  20. 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

  1. Effects of Exercise on the Structure and Circulation of Choroid in Normal Eyes

    PubMed Central

    Mori, Junya; Okuda, Natsuki; Imaizumi, Hiroko; Iwasaki, Masanori; Shimizu, Miho; Miyamoto, Hirotomo; Akaiwa, Kei; Semba, Kentaro; Sonoda, Shozo; Sakamoto, Taiji; Mitamura, Yoshinori

    2016-01-01

    Aims To determine the effects of dynamic exercise on the circulation and the luminal and stromal areas of the choroid in normal eyes. Methods This was a prospective interventional study of 38 eyes of 38 normal subjects enrolled by invitation. The systolic and diastolic blood pressures, heart rate, intraocularpressure, mean ocular perfusion pressure (MOPP), choroidal blood velocity, and enhanced depth imaging optical coherence tomographic (EDI-OCT) images were recorded before, and immediately after mild dynamic exercise. The same measurements were recorded after 10 min of rest. The choroidal blood velocity was measured bylaser speckle flowgraphy, and the mean blur rate was used for the evaluations. The horizontal EDI-OCT images of the subfoveal choroid were converted to binary images. The central choroidal thickness (CCT), total cross sectional choroidal area, luminal areas, stromal areas, and the ratio of luminal area to total choroidal area (L/C ratio) were determined from these images. Results The systolic and diastolic blood pressures, heart rate, MOPP, and the mean blur rate were significantly increased immediately after the exercise and significantly decreased 10 minutes after the exercise. There wereno significant changes in the mean CCT, the mean total choroidal area, the mean luminal and stromal areas, and the mean L/C ratio after the exercise. Conclusions Our results suggest that a rest period is needed before measurements of blood flow velocity but not necessary for the EDI-OCT imaging to determine the choroidal thickness and area. PMID:27973598

  2. Glucose transporter Glut-1 is detectable in peri-necrotic regions in many human tumor types but not normal tissues: Study using tissue microarrays.

    PubMed

    Airley, Rachel; Evans, Andrew; Mobasheri, Ali; Hewitt, Stephen M

    2010-05-20

    The hypoxic tumor microenvironment is associated with malignant progression and poor treatment response. The glucose transporter Glut-1 is a prognostic factor and putative hypoxia marker. So far, studies of Glut-1 in cancer have utilized conventional immunohistochemical analysis in a series of individual biopsy or surgical specimens. Tissue microarrays, however, provide a rapid, inexpensive means of profiling biomarker expression. To evaluate hypoxia markers, tissue cores must show the architectural features of hypoxia; i.e. viable tissue surrounding necrotic regions. Glut-1 may be a useful biomarker to validate tissue microarrays for use in studies of hypoxia-regulated genes in cancer. In this study, we carried out immunohistochemical detection of Glut-1 protein in many tumor and normal tissue types in a range of tissue microarrays. Glut-1 was frequently found in peri-necrotic regions, occurring in 9/34 lymphomas, 6/12 melanomas, and 5/16 glioblastomas; and in 43/54 lung, 22/84 colon, and 23/60 ovarian tumors. Expression was rare in breast (6/40) and prostate (1/57) tumors, and in normal tissue, was restricted to spleen, tongue, and CNS endothelium. In conclusion, tissue microarrays enable the observation of Glut-1 expression in peri-necrotic regions, which may be linked to hypoxia, and reflect previous studies showing differential Glut-1 expression across tumor types and non-malignant tissue.

  3. Anterior segment angiography of the normal canine eye: a comparison between indocyanine green and sodium fluorescein.

    PubMed

    Pirie, C G; Alario, A

    2014-03-01

    The objective of this study was to assess and compare indocyanine green (IG) and sodium fluorescein (SF) angiographic findings in the normal canine anterior segment using a digital single lens reflex (dSLR) camera adaptor. Images were obtained from 10 brown-eyed Beagles, free of ocular and systemic disease. All animals received butorphanol (0.2 mg/kg IM), maropitant citrate (1.0 mg/kg SC) and diphenhydramine (2.0 mg/kg SC) 20 min prior to propofol (4 mg/kg IV bolus, 0.2 mg/kg/min continuous rate infusion). Standard color imaging was performed prior to the administration of 0.25% IG (1 mg/kg IV). Imaging was performed using a full spectrum dSLR camera, dSLR camera adaptor, camera lens (Canon 60 mm f/2.8 Macro) and an accessory flash. Images were obtained at a rate of 1/s immediately following IG bolus for 30 s, then at 1, 2, 3, 4 and 5 min. Ten minutes later, 10% SF (20 mg/kg IV) was administered. Imaging was repeated using the same adaptor system and imaging sequence protocol. Arterial, capillary and venous phases were identified during anterior segment IG angiography (ASIGA) and their time sequences were recorded. ASIGA offered improved visualization of the iris vasculature in heavily pigmented eyes compared to anterior segment SF angiography (ASSFA), since visualization of the vascular pattern during ASSFA was not possible due to pigment masking. Leakage of SF was noted in a total of six eyes. The use of IG and SF was not associated with any observed adverse events. The adaptor described here provides a cost-effective alternative to existing imaging systems.

  4. 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

  5. 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

  6. 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.

  7. Effect of age and sex on retinal layer thickness and volume in normal eyes

    PubMed Central

    Won, Jae Yon; Kim, Sung Eun; Park, Young-Hoon

    2016-01-01

    Abstract The aim of the study was to evaluate the effect of sex and age on the thickness of the retinal layer in normal eyes using spectral-domain optical coherence tomography (SD-OCT). Fifty healthy subjects between the ages of 20 and 80 had their retinal layers measured using SD-OCT at Seoul St. Mary's Hospital. Mean thickness and volume were measured for 9 retinal layers in the fovea, the pericentral ring, and the peripheral ring. The differences of sex- and age-related thickness and volume in each retinal layer were analyzed. The retinal nerve fiber layer (RNFL), ganglion cell layer (GCL), inner plexiform layer (IPL), inner nuclear layer (INL), and outer plexiform layer (OPL) were thinnest in the fovea area, whereas the outer nuclear layer (ONL), photoreceptor layer (PHL), and retinal pigment epithelium (RPE) were thickest at similar locations. Mean thickness of the RNFL, GCL, IPL, and OPL was significantly greater in men than women. However, mean thickness of the ONL was greater in women than in men. When compared between patients < 30 years and > 60 years of age, the thickness and volume of peripheral RNFL, GCL, and pericentral and peripheral IPL were significantly larger in the younger group than the older group. Conversely, the thickness and volume of foveal INL and IR were larger in the older group than in the younger group. The thickness and volume of the retinal layer in normal eyes significantly vary depending on age and sex. These results should be considered when evaluating layer analysis in retinal disease. PMID:27861391

  8. Diurnal variations in luminal and stromal areas of choroid in normal eyes

    PubMed Central

    Kinoshita, Takamasa; Mitamura, Yoshinori; Shinomiya, Kayo; Egawa, Mariko; Iwata, Akiko; Fujihara, Akiko; Ogushi, Yoko; Semba, Kentaro; Akaiwa, Kei; Uchino, Eisuke; Sonoda, Shozo; Sakamoto, Taiji

    2017-01-01

    Aims To determine the diurnal variations of the luminal and stromal areas of the choroid in normal eyes. Methods This was a prospective observational study of 38 eyes of 38 normal subjects. The blood pressure, heart rate, intraocular pressure and enhanced depth imaging optical coherence tomographic (EDI-OCT) images were recorded every 3 hours between 6:00 and 21:00 hours. The horizontal EDI-OCT images of the subfoveal choroid were converted to binary images. The central choroidal thickness (CCT), total cross-sectional choroidal area, the luminal areas, stromal areas and the ratio of luminal area to total choroidal area (L/C ratio) were determined. Results There were significant diurnal variations in the CCT, total choroidal area, luminal area and L/C ratio with the maximum values at 6:00 hours and the minimum values at 15:00 hours (p<0.001 for the CCT, p=0.011 for the total choroidal area, p<0.001 for the luminal area and p=0.014 for the L/C ratio). There was no significant variation in the stromal area (p=0.216). The range of fluctuation in the CCT was significantly correlated with that in the luminal area and the total choroidal area (p<0.001). However, there was no significant correlation between the fluctuation range in the CCT and that in the stromal area (p=0.095). There was no statistical relationship between the systemic parameters and the choroidal parameters. Conclusions The changes in the luminal area are most likely responsible for the diurnal change in the CCT and subfoveal choroidal area. Trial registration number UMIN000019060, Pre-results. PMID:27297216

  9. 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

  10. Peripapillary Choroidal Thickness Variation With Age and Race in Normal Eyes

    PubMed Central

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

    2015-01-01

    Purpose. This study examined the association between peripapillary choroidal thickness (PCT) with age and race in a group of African descent (AD) and European descent (ED) subjects with normal eyes. Methods. Optic nerve head images from enhanced depth imaging spectral-domain optical coherence tomography of 166 normal eyes from 84 subjects of AD and ED were manually delineated to identify the principal surfaces of Bruch's membrane (BM), Bruch's membrane opening (BMO), and anterior sclera (AS). Peripapillary choroidal thickness was measured between BM and AS at increasing distance away from BMO. The mean PCT was compared between AD and ED subjects and generalized estimating equation (GEE) regression analysis was used to examine the association between race and PCT overall, in each quadrant, and by distance from BMO. Models were adjusted for age, BMO area, and axial length in the regression analysis. Results. Overall, the mean PCT increased from 63.9 μm ± 18.1 at 0 to 250 μm to 170.3 μm ± 56.7 at 1500 to 2000 μm from BMO. Individuals of AD had a greater mean PCT than those of ED at all distances from BMO (P < 0.05 at each distance) and in each quadrant (P < 0.05 in each quadrant). Results from multivariate regression indicate that ED subjects had significantly lower PCT compared to AD overall and in all quadrants and distances from BMO. Increasing age was also significantly associated with a lower PCT in both ED and AD participants. Conclusions. Peripapillary choroidal thickness varies with race and age, as individuals of AD have a thicker peripapillary choroid than those of ED. (ClinicalTrials.gov number, NCT00221923.) PMID:25711640

  11. Gaze position corrective eye movements in normal subjects and in patients with vestibular deficits.

    PubMed

    Peng, Grace C Y; Minor, Lloyd B; Zee, David S

    2005-04-01

    Eye movements in response to high-acceleration head rotations (thrusts) in the horizontal plane from patients with unilateral (UVD) or bilateral vestibular loss (BVD) were recorded. The rapid, gaze-position corrections (GPCs) that appeared when vestibulo-ocular reflex (VOR) slow phases were undercompensatory were characterized. For comparison, eye movements from normal subjects who were asked to generate saccades in the direction opposite head rotation (in the same direction as slow phases) were recorded. This normal-subject model produced responses with spatial and temporal characteristics similar to those from GPCs in patients as follows: When head rotations were generated actively, compared with passively, gaze-position errors and corresponding GPCs were smaller and occurred earlier. During passively generated head thrusts, GPCs still occurred when head rotations were made in total darkness, though their accuracy decreased as the requirement for maintaining gaze on a specific location in space was relaxed. Time of onset of GPCs was not rigidly tied to head kinematics (peak velocity or peak acceleration). Speeds of GPCs, however, were lower than speeds of similar-sized, head-fixed saccades. Finally, during passive and active head thrusts in patients, sustained, high-frequency (20 to 30 Hz) oscillations that appeared as tiny saccades were occasionally observed, one immediately following the other, resembling a compensatory slow-phase response. Taken together, the results suggest that one strategy for overcoming a VOR deficit is to enlist the saccadic system to produce an oculomotor response that is required to compensate for head rotation. This response may come in the form of high-velocity GPCs or smaller-amplitude oscillations.

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

    PubMed Central

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

    2001-01-01

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

  13. Optical Coherence Tomography Measurement of Macular and Nerve Fiber Layer Thickness in Normal and Glaucomatous Human Eyes

    PubMed Central

    Guedes, Viviane; Schuman, Joel S.; Hertzmark, Ellen; Wollstein, Gadi; Correnti, Anthony; Mancini, Ronald; Lederer, David; Voskanian, Serineh; Velazquez, Leonardo; Pakter, Helena M.; Pedut-Kloizman, Tamar; Fujimoto, James G.; Mattox, Cynthia

    2007-01-01

    Purpose To evaluate the hypothesis that macular thickness correlates with the diagnosis of glaucoma. Design Cross-sectional study. Participants We studied 367 subjects (534 eyes), including 166 eyes of 109 normal subjects, 83 eyes of 58 glaucoma suspects, 196 eyes of 132 early glaucoma patients, and 89 eyes of 68 advanced glaucoma patients. Methods We used optical coherence tomography (OCT) to measure macular and nerve fiber layer (NFL) thickness and to analyze their correlation with each other and with glaucoma status. We used both the commercial and prototype OCT units and evaluated correspondence between measurements performed on the same eyes on the same days. Main Outcome Measure Macular and NFL thickness as measured by OCT. Results All NFL parameters both in prototype and commercial OCT units were statistically significantly different comparing normal subjects and either early or advanced glaucoma (P < 0.001). Inner ring, outer ring, and mean macular thickness both in prototype and commercial OCT devices were found to be significantly different between normal subjects and advanced glaucomatous eyes (P < 0.001). The outer ring was the only macular parameter that could significantly differentiate between normal and early glaucoma with either the prototype or commercial OCT unit (P = 0.003, P = 0.008, respectively). The area under the receiver operator characteristic (AROC) curves comparing mean NFL thickness between normal and advanced glaucomatous eyes was 1.00 for both the prototype and commercial OCT devices for eyes scanned on both machines on the same day. The AROC comparing mean macular thickness in normal and advanced glaucomatous eyes scanned on both machines on the same day was 0.88 for the prototype OCT device and 0.80 for the commercial OCT. Conclusions Both macular and NFL thickness as measured by OCT showed statistically significant correlations with glaucoma, although NFL thickness showed a stronger association than macular thickness. There was

  14. 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

  15. Retinal vessel density from optical coherence tomography angiography to differentiate early glaucoma, pre-perimetric glaucoma and normal eyes

    PubMed Central

    Akil, Handan; Huang, Alex S.; Francis, Brian A.; Sadda, Sirinivas R.; Chopra, Vikas

    2017-01-01

    Purpose To evaluate optic nerve vascular density using swept source optical coherence tomography angiography (OCTA) in patients with early primary open angle glaucoma (POAG), pre-perimetric glaucoma and normal eyes. Methods This is a prospective, observational study including 56 eyes in total and divided into 3 groups; 20 eyes with mild POAG, 20 pre-perimetric glaucoma eyes, and 16 age-matched normal eyes as controls. The optic disc region was imaged by a 1050-nm-wavelength swept-source OCT system (DRI OCT Triton, TOPCON). Vessel density was assessed as the ratio of the area occupied by the vessels in 3 distinct regions: 1) within the optic nerve head; 2) in the 3 mm papillary region around the optic disc; and 3) in the peripapillary region, defined as a 700-μm-wide elliptical annulus around the disc. The potential associations between vessel density and structural, functional measures were analyzed. Results There was a statistically significant difference for the peripapillary vessel density, optic nerve head vessel density, and papillary vessel density among all the groups (p<0.001). Control eyes showed a significant difference for all measured vessel densities compared to glaucomatous eyes (p values from 0.001 to 0.024). There was a statistically significant difference between control and pre-perimetric glaucoma eyes for peripapillary, optic nerve head and papillary vessel density values (p values from 0.001 to 0.007). The optic nerve head vessel density, superior and inferior papillary area vessel density (Pearson r = 0.512, 0.436, 0.523 respectively) were highly correlated with mean overall, superior and inferior RNFL thickness in POAG eyes (p = 0.04, p = 0.02 and p = 0.04 respectively). Multiple linear regression analysis of POAG group showed that optic nerve head vessel density in POAG group was more strongly linked to RNFL thickness than to any other variables. Conclusions Eyes with mild POAG could be differentiated from pre-perimetric glaucoma eyes, which

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

    PubMed Central

    Johnstone, Murray; Martin, Elizabeth; Jamil, Annisa

    2015-01-01

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

  17. 3D modeling to characterize lamina cribrosa surface and pore geometries using in vivo images from normal and glaucomatous eyes.

    PubMed

    Sredar, Nripun; Ivers, Kevin M; Queener, Hope M; Zouridakis, George; Porter, Jason

    2013-07-01

    En face adaptive optics scanning laser ophthalmoscope (AOSLO) images of the anterior lamina cribrosa surface (ALCS) represent a 2D projected view of a 3D laminar surface. Using spectral domain optical coherence tomography images acquired in living monkey eyes, a thin plate spline was used to model the ALCS in 3D. The 2D AOSLO images were registered and projected onto the 3D surface that was then tessellated into a triangular mesh to characterize differences in pore geometry between 2D and 3D images. Following 3D transformation of the anterior laminar surface in 11 normal eyes, mean pore area increased by 5.1 ± 2.0% with a minimal change in pore elongation (mean change = 0.0 ± 0.2%). These small changes were due to the relatively flat laminar surfaces inherent in normal eyes (mean radius of curvature = 3.0 ± 0.5 mm). The mean increase in pore area was larger following 3D transformation in 4 glaucomatous eyes (16.2 ± 6.0%) due to their more steeply curved laminar surfaces (mean radius of curvature = 1.3 ± 0.1 mm), while the change in pore elongation was comparable to that in normal eyes (-0.2 ± 2.0%). This 3D transformation and tessellation method can be used to better characterize and track 3D changes in laminar pore and surface geometries in glaucoma.

  18. 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…

  19. MarC-V: a spreadsheet-based tool for analysis, normalization, and visualization of single cDNA microarray experiments.

    PubMed

    Schageman, J J; Basit, M; Gallardo, T D; Garner, H R; Shohet, R V

    2002-02-01

    The comprehensive analysis and visualization of data extracted from cDNA microarrays can be a time-consuming and error-prone process that becomes increasingly tedious with increased number of gene elements on a particular microarray. With the increasingly large number of gene elements on today's microarrays, analysis tools must be developed to meet this challenge. Here, we present MarC-V, a Microsoft Excel spreadsheet tool with Visual Basic macros to automate much of the visualization and calculation involved in the analysis process while providing the familiarity and flexibility of Excel. Automated features of this tool include (i) lower-bound thresholding, (ii) data normalization, (iii) generation of ratio frequency distribution plots, (iv) generation of scatter plots color-coded by expression level, (v) ratio scoring based on intensity measurements, (vi) filtering of data based on expression level or specific gene interests, and (vii) exporting data for subsequent multi-array analysis. MarC-V also has an importing function included for GenePix results (GPR) raw data files.

  20. Relative contributions of the two eyes to perceived egocentric visual direction in normal binocular vision.

    PubMed

    Sridhar, Deepika; Bedell, Harold E

    2011-05-11

    Perceived egocentric direction (EVD) is based on the sensed position of the eyes in the orbit and the oculocentric visual direction (eye-centered, OVD). Previous reports indicate that in some subjects eye-position information from the two eyes contributes unequally to the perceived EVD. Findings from other studies indicate that the retinal information from the two eyes may not always contribute equally to perceived OVD. The goal of this study was to assess whether these two sources of information covary similarly within the same individuals. Open-loop pointing responses to an isolated target presented randomly at several horizontal locations were collected from 13 subjects during different magnitudes of asymmetric vergence to estimate the contribution of the position information from each eye to perceived EVD. For the same subjects, the direction at which a horizontally or vertically disparate target with different interocular contrast or luminance ratios appeared aligned with a non-disparate target estimated the relative contribution of each eye's retinal information. The results show that the eye-position and retinal information vary similarly in most subjects, which is consistent with a modified version of Hering's law of visual direction.

  1. Expression profile of the matricellular protein osteopontin in primary open-angle glaucoma and the normal human eye.

    PubMed

    Chowdhury, Uttio Roy; Jea, Seung-Youn; Oh, Dong-Jin; Rhee, Douglas J; Fautsch, Michael P

    2011-08-16

    PURPOSE. To characterize the role of osteopontin (OPN) in primary open-angle glaucoma (POAG) and normal eyes. METHODS. OPN quantification was performed by enzyme-linked immunosorbent assay in aqueous humor (AH) obtained from human donor eyes (POAG and normal) and surgical samples (POAG and elective cataract removal). OPN expression and localization in whole eye tissue sections and primary normal human trabecular meshwork (NTM) cells were studied by Western blot and immunohistochemistry. Latanoprost-free acid (LFA)-treated NTM cells were analyzed for OPN gene and protein expression. Intraocular pressure was measured by tonometry, and central corneal thickness was measured by optical coherence tomography in young OPN(-/-) and wild-type mice. RESULTS. OPN levels were significantly reduced in donor POAG AH compared with normal AH (0.54 ± 0.18 ng/μg [n = 8] vs. 0.77 ± 0.23 ng/μg [n = 9]; P = 0.039). A similar trend was observed in surgical AH (1.05 ± 0.31 ng/μg [n = 20] vs. 1.43 ± 0.88 ng/μg [n = 20]; P = 0.083). OPN was present in the trabecular meshwork, corneal epithelium and endothelium, iris, ciliary body, retina, vitreous humor, and optic nerve. LFA increased OPN gene expression, but minimal change in OPN protein expression was observed. No difference in intraocular pressure (17.5 ± 2.0 mm Hg [n = 56] vs. 17.3 ± 1.9 mm Hg [n = 68]) but thinner central corneal thickness (91.7 ± 3.6 μm [n = 50] vs. 99.2 ± 5.5 μm [n = 70]) was noted between OPN(-/-) and wild-type mice. CONCLUSIONS. OPN is widely distributed in the human eye and was found in lower concentrations in POAG AH. Reduction of OPN in young mice does not affect IOP.

  2. 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

  3. 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...

  4. Comparison of Ethnic-specific Databases in Heidelberg Retina Tomography-3 to Discriminate Between Early Glaucoma and Normal Chinese Eyes

    PubMed Central

    Tan, Xiu Ling; Yap, Sae Cheong; Li, Xiang; Yip, Leonard W.

    2017-01-01

    Purpose: To compare the diagnostic accuracy of the 3 race-specific normative databases in Heidelberg Retina Tomography (HRT)-3, in differentiating between early glaucomatous and healthy normal Chinese eyes. Method: 52 healthy volunteers and 25 glaucoma patients were recruited for this prospective cross-sectional study. All underwent standardized interviews, ophthalmic examination, perimetry and HRT optic disc imaging. Area under the curve (AUC) receiver operating characteristics, sensitivity and specificity were derived to assess the discriminating abilities of the 3 normative databases, for both Moorfields Regression Analysis (MRA) and Glaucoma Probability Score (GPS). Results: A significantly higher percentage (65%) of patients were classified as “within normal limits” using the MRA-Indian database, as compared to the MRA-Caucasian and MRA-African-American databases. However, for GPS, this was observed using the African-American database. For MRA, the highest sensitivity was obtained with both Caucasian and African-American databases (68%), while the highest specificity was from the Indian database (94%). The AUC for discrimination between glaucomatous and normal eyes by MRA-Caucasian, MRA-African-American and MRA-Indian databases were 0.77 (95% CI, 0.67-0.88), 0.79 (0.69-0.89) and 0.73 (0.63-0.84) respectively. For GPS, the highest sensitivity was obtained using either Caucasian or Indian databases (68%). The highest specificity was seen with the African-American database (98%). The AUC for GPS-Caucasian, GPS-African-American and GPS-Indian databases were 0.76 (95% CI, 0.66-0.87), 0.77 (0.67-0.87) and 0.76 (0.66-0.87) respectively. Conclusion: Comparison of the 3 ethnic databases did not reveal significant differences to differentiate early glaucomatous from normal Chinese eyes.

  5. 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).

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

    PubMed

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

    2015-10-01

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

  7. 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

  8. Dendritic cells and macrophages in the uveal tract of the normal mouse eye

    PubMed Central

    McMenamin, P.

    1999-01-01

    BACKGROUND/AIMS—Dendritic cells (DC) and macrophages are components of the immune cell populations in the uveal tract whose density, distribution, turnover, and function may play a role in the maintenance of immunological homeostasis in the eye. Little is known of these cells in the mouse eye despite this being the predominant experimental model in many studies of ocular immune responses and immunoinflammatory mediated eye diseases. The aim of the present study was to obtain further immunophenotypic data on resident tissue macrophages and DC populations in the mouse uveal tract.
METHODS—Pieces of iris, ciliary body, and choroid dissected from perfusion fixed BALB/c mice were incubated whole in a variety of anti-macrophage and DC monoclonal antibodies (mAbs). Labelled cells were visualised using either single or double immunoperoxidase techniques.
RESULTS—Quantitative analysis and double immunolabelling revealed that 80% of F4/80+ cells (a mAb that recognises both DC and macrophages) in the iris are macrophages (SER4+). The iris contained a network of Ia+ cells (412 (SD 130) cells/mm2) of which two thirds appear to be DC. A similar pattern was observed in the ciliary body and choroid. Only a few DC in the uveal tract were very weakly reactive for mAbs which recognise B7-1 (CD80), B7-2 (CD86), β2 integrin (mAb N418), and multivesicular bodies associated with antigen presentation (mAb M342).
CONCLUSIONS—The present study reveals that the mouse uveal tract, like the rat, contains rich networks of DC and resident tissue macrophages. The networks of resident tissue macrophages in the mouse uveal tract closely resemble similar networks in non-ocular tissues. The phenotype of uveal tract DC suggests they are in the "immature" phase of their life cycle, similar to Langerhans cells of the skin, thus implying their role in situ within the eye is antigen capture and not antigen presentation.

 PMID:10216062

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

    SciTech Connect

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

    1995-08-01

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

  10. Comparison of choroidal thickness measurements between spectral-domain OCT and swept-source OCT in normal and diseased eyes

    PubMed Central

    Zafar, Sidra; Siddiqui, MA Rehman; Shahzad, Rida

    2016-01-01

    Purpose Sub-foveal choroidal thickness (SFCT) is affected in many ocular diseases. The aim of this study was to compare SFCT measurements between Topcon 3D 2000 spectral-domain optical coherence tomography (SD-OCT) and Topcon swept-source OCT (SS-OCT), with different laser wavelengths, in normal and diseased populations. Materials and methods This was a prospective, cross-sectional, noninterventional study including 27 normal volunteers and 27 participants with retinal disease. OCT scans were performed sequentially and under standardized conditions using both SD-OCT and SS-OCT. The OCT scans were evaluated by two independent graders. Paired t-tests and intraclass correlation coefficients (ICCs) were used to assess the statistically significant difference between SFCT measurements as measured by the two devices. Results Mean SFCT measurements for all 54 participants were 264.9±103.1 μm using SD-OCT (range: 47–470 μm) and 278.5±110.5 μm using SS-OCT (range: 56–502 μm), with an inter-device ICC of 0.850. Greater variability was noted in the diseased eyes. Inter-device ICCs were 0.870 (95% CI; 0.760–0.924) and 0.840 (95% CI; 0.654–0.930) for normal and diseased eyes, respectively. However, the difference was not statistically significant (P=0.132). Conclusion Both machines reliably measure SFCT. Larger studies are needed to confirm these findings. PMID:27881909

  11. Light scattering study of the normal human eye lens: Elastic properties and age dependence

    PubMed Central

    Bailey, Sheldon T.; Twa, Michael D.; Gump, Jared C.; Venkiteshwar, Manoj; Bullimore, Mark A.

    2015-01-01

    The human ocular lens is a tissue capable of changing its shape to dynamically adjust the optical power of the eye, a function known as accommodation, which gradually declines with age. This capability is the response of the lens tissue to external forces which, in turn, is modulated by the biomechanical characteristics of lens tissues. In order to investigate the contributions of lens sclerosis to loss of accommodation, we report on in vitro confocal Brillouin light scattering studies of human ocular lenses spanning over a 30-70 year age range. Using this non-destructive measurement method, we determined that the longitudinal bulk modulus (average ± SD) of the lens nucleus (2.79±0.14 GPa) was consistently greater than the bulk modulus of the lens cortex (2.36±0.09 GPa). Moreover, our results showed that these differences were not age dependent over the 40 year age range that we evaluated using healthy lens tissues. Our results are consistent with the hypothesis that an age-dependent change in the bulk modulus of lens tissues does not fully account for the natural decline of accommodation. PMID:20529725

  12. 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

  13. 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. ...

  14. Comparison of central corneal thickness measurements using ultrasound pachymetry, ultrasound biomicroscopy, and the Artemis-2 VHF scanner in normal eyes

    PubMed Central

    Al-Farhan, Haya M; Al-Otaibi, Wafa’a Majed

    2012-01-01

    Purpose To compare the precision of central corneal thickness (CCT) measurements taken with the handheld ultrasound pachymeter (USP), ultrasound biomicroscopy (UBM), and the Artemis-2 very high frequency ultrasound scanner (VHFUS) on normal subjects. Design Prospective study. Methods One eye from each of 61 normal subjects was randomly selected for this study. The measurements of the CCT were taken with the USP, VHFUS, and UBM. Results were compared statistically using repeated-measures analysis of variance (ANOVA), Pearson’s correlation coefficient, and limits of agreement. Results The average CCT (± standard deviation) was 530.1 ± 30.5 μm, 554.9 ± 31.7 μm, and 559.5 ± 30.7 μm for UBM, VHFUS, and USP respectively. The intraobserver repeatability analyses of variance are not significant for USP, UBM, and VHFUS. P-values were 0.17, 0.19, and 0.37 respectively. Repeated-measures ANOVA showed a significant difference between the three different methods of measuring CCT (P = 0.0001). The ANOVA test revealed no statistically significant difference between USP and VHFUS (P > 0.05), yet statistical significant differences with UBM versus USP and UBM versus VHFUS (P < 0.001). There were high correlations between the three instruments (P < 0.0001). The mean differences (and upper/lower limits of agreement) for CCT measurements were 29.4 ± 14.3 (2.7/56), 4.6 ± 8.6 (−14.7/23.8), and −24.8 ± 13.1 (−50.4/0.8) for USP versus UBM, USP versus VHFUS, and UBM versus VHFUS, respectively. Conclusion The UBM produces CCT measurements that vary significantly from those returned by the USP and the VHFUS, suggesting that the UBM may not be used interchangeably with either equipment for monitoring the CCT in the clinical setting. PMID:22848145

  15. 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.

  16. Analyzing Microarray Data.

    PubMed

    Hung, Jui-Hung; Weng, Zhiping

    2017-03-01

    Because there is no widely used software for analyzing RNA-seq data that has a graphical user interface, this protocol provides an example of analyzing microarray data using Babelomics. This analysis entails performing quantile normalization and then detecting differentially expressed genes associated with the transgenesis of a human oncogene c-Myc in mice. Finally, hierarchical clustering is performed on the differentially expressed genes using the Cluster program, and the results are visualized using TreeView.

  17. CD25+CD127+Foxp3- Cells Represent a Major Subpopulation of CD8+ T Cells in the Eye Chambers of Normal Mice

    PubMed Central

    Ziółkowska, Natalia; Ziółkowski, Hubert; Małaczewska, Joanna

    2017-01-01

    The aim of this study has been to determine whether eye chambers constitute part of the normal migratory pathway of naive CD4+ and CD8+ T cells in mouse and if natural CD4+CD25+Foxp3+ and CD8+CD25+Foxp3+ regulatory T cells are present within these eye compartments. To this aim, the cells obtained from aqueous humor (AH) of normal mice were phenotyped in terms of the expression CD4, CD8, CD25, CD127 and transcription factor Foxp3. The mean percentage of CD8+ T cells in the total AH lymphocyte population was as high as 28.69%; the mean percentage of CD8high and CD8low cells in this population was 34.09% and 65.91%, respectively. The presence of cells with the regulatory phenotype, i.e. CD25+Foxp3+ cells, constituted only 0.32% of CD8+ T cell subset. Regarding the expression of CD25, AH CD8+ T cells were an exceptional population in that nearly 85% of these cells expressed this molecule without concomitant Foxp3 expression. Despite having this phenotype, they should not be viewed as activated cells because most of them co-expressed CD127, which indicates that they are naive lymphocytes. With regard to the markers applied in the present research, CD8+CD25+CD127+Foxp3- T cells represent the most numerous subset of AH CD8+ cells. The results suggest that eye chambers in mice are an element in the normal migratory pathway of naive CD8+ T cells. The study presented herein demonstrated only trace presence of CD4+ cells in the eye chambers, as the mean percentage of these cells was just 0.56. Such selective and specific homing of CD8+ and CD4+ cells to the eye chambers is most clearly engaged in the induction and maintenance of ocular immune privilege. PMID:28081241

  18. 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

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

    PubMed Central

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

    2015-01-01

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

  20. 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…

  1. 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

  2. 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.

  3. Computational fluid dynamics assisted characterization of parafoveal hemodynamics in normal and diabetic eyes using adaptive optics scanning laser ophthalmoscopy.

    PubMed

    Lu, Yang; Bernabeu, Miguel O; Lammer, Jan; Cai, Charles C; Jones, Martin L; Franco, Claudio A; Aiello, Lloyd Paul; Sun, Jennifer K

    2016-12-01

    Diabetic retinopathy (DR) is the leading cause of visual loss in working-age adults worldwide. Previous studies have found hemodynamic changes in the diabetic eyes, which precede clinically evident pathological alterations of the retinal microvasculature. There is a pressing need for new methods to allow greater understanding of these early hemodynamic changes that occur in DR. In this study, we propose a noninvasive method for the assessment of hemodynamics around the fovea (a region of the eye of paramount importance for vision). The proposed methodology combines adaptive optics scanning laser ophthalmoscopy and computational fluid dynamics modeling. We compare results obtained with this technique with in vivo measurements of blood flow based on blood cell aggregation tracking. Our results suggest that parafoveal hemodynamics, such as capillary velocity, wall shear stress, and capillary perfusion pressure can be noninvasively and reliably characterized with this method in both healthy and diabetic retinopathy patients.

  4. Computational fluid dynamics assisted characterization of parafoveal hemodynamics in normal and diabetic eyes using adaptive optics scanning laser ophthalmoscopy

    PubMed Central

    Lu, Yang; Bernabeu, Miguel O.; Lammer, Jan; Cai, Charles C.; Jones, Martin L.; Franco, Claudio A.; Aiello, Lloyd Paul; Sun, Jennifer K.

    2016-01-01

    Diabetic retinopathy (DR) is the leading cause of visual loss in working-age adults worldwide. Previous studies have found hemodynamic changes in the diabetic eyes, which precede clinically evident pathological alterations of the retinal microvasculature. There is a pressing need for new methods to allow greater understanding of these early hemodynamic changes that occur in DR. In this study, we propose a noninvasive method for the assessment of hemodynamics around the fovea (a region of the eye of paramount importance for vision). The proposed methodology combines adaptive optics scanning laser ophthalmoscopy and computational fluid dynamics modeling. We compare results obtained with this technique with in vivo measurements of blood flow based on blood cell aggregation tracking. Our results suggest that parafoveal hemodynamics, such as capillary velocity, wall shear stress, and capillary perfusion pressure can be noninvasively and reliably characterized with this method in both healthy and diabetic retinopathy patients. PMID:28078170

  5. Eye-voice span during rapid automatized naming of digits and dice in Chinese normal and dyslexic children.

    PubMed

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

    2013-11-01

    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 digits for both groups, but group differences in eye-movement measures and in the eye-voice span (i.e. the distance between the currently fixated item and the voiced item) were generally larger in digit-RAN than in dice-RAN. In addition, dyslexics were less efficient in parafoveal processing in these RAN tasks. Since the two RAN tasks required the same phonological output and on the assumption that naming dice is less practiced than naming digits in general, the results suggest that the translation of alphanumeric visual symbols into phonological codes is less efficient in dyslexic children. The dissociation of the print-to-sound conversion and phonological representation suggests that the degree of automaticity in translation from visual symbols to phonological codes in addition to phonological processing per se is also critical to understanding dyslexia.

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  7. Eye Cancer

    MedlinePlus

    ... Cancer > Eye Cancer > Eye Cancer: Overview Request Permissions Eye Cancer: Overview Approved by the Cancer.Net Editorial ... trained to treat intraocular cancer. Parts of the eye The eye is the organ that collects light ...

  8. Eye redness

    MedlinePlus

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

  9. Microarrays in cancer research.

    PubMed

    Grant, Geraldine M; Fortney, Amanda; Gorreta, Francesco; Estep, Michael; Del Giacco, Luca; Van Meter, Amy; Christensen, Alan; Appalla, Lakshmi; Naouar, Chahla; Jamison, Curtis; Al-Timimi, Ali; Donovan, Jean; Cooper, James; Garrett, Carleton; Chandhoke, Vikas

    2004-01-01

    Microarray technology has presented the scientific community with a compelling approach that allows for simultaneous evaluation of all cellular processes at once. Cancer, being one of the most challenging diseases due to its polygenic nature, presents itself as a perfect candidate for evaluation by this approach. Several recent articles have provided significant insight into the strengths and limitations of microarrays. Nevertheless, there are strong indications that this approach will provide new molecular markers that could be used in diagnosis and prognosis of cancers. To achieve these goals it is essential that there is a seamless integration of clinical and molecular biological data that allows us to elucidate genes and pathways involved in various cancers. To this effect we are currently evaluating gene expression profiles in human brain, ovarian, breast and hematopoetic, lung, colorectal, head and neck and biliary tract cancers. To address the issues we have a joint team of scientists, doctors and computer scientists from two Virginia Universities and a major healthcare provider. The study has been divided into several focus groups that include; Tissue Bank Clinical & Pathology Laboratory Data, Chip Fabrication, QA/QC, Tissue Devitalization, Database Design and Data Analysis, using multiple microarray platforms. Currently over 300 consenting patients have been enrolled in the study with the largest number being that of breast cancer patients. Clinical data on each patient is being compiled into a secure and interactive relational database and integration of these data elements will be accomplished by a common programming interface. This clinical database contains several key parameters on each patient including demographic (risk factors, nutrition, co-morbidity, familial history), histopathology (non genetic predictors), tumor, treatment and follow-up information. Gene expression data derived from the tissue samples will be linked to this database, which

  10. Overview of Protein Microarrays

    PubMed Central

    Reymond Sutandy, FX; Qian, Jiang; Chen, Chien-Sheng; Zhu, Heng

    2013-01-01

    Protein microarray is an emerging technology that provides a versatile platform for characterization of hundreds of thousands of proteins in a highly parallel and high-throughput way. Two major classes of protein microarrays are defined to describe their applications: analytical and functional protein microarrays. In addition, tissue or cell lysates can also be fractionated and spotted on a slide to form a reverse-phase protein microarray. While the fabrication technology is maturing, applications of protein microarrays, especially functional protein microarrays, have flourished during the past decade. Here, we will first review recent advances in the protein microarray technologies, and then present a series of examples to illustrate the applications of analytical and functional protein microarrays in both basic and clinical research. The research areas will include detection of various binding properties of proteins, study of protein posttranslational modifications, analysis of host-microbe interactions, profiling antibody specificity, and identification of biomarkers in autoimmune diseases. As a powerful technology platform, it would not be surprising if protein microarrays will become one of the leading technologies in proteomic and diagnostic fields in the next decade. PMID:23546620

  11. 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 ...

  12. Healthy Eyes

    MedlinePlus

    ... of this page please turn Javascript on. Healthy Eyes Maintaining Your Vision Click for more information Taking ... have a comprehensive dilated eye exam. Who Performs Eye Exams? An eye care professional is either an ...

  13. 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

  14. 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

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

    PubMed

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

    2016-01-27

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

  16. Microarrays, antiobesity and the liver

    PubMed Central

    Castro-Chávez, Fernando

    2013-01-01

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

  17. Microarray in parasitic infections

    PubMed Central

    Sehgal, Rakesh; Misra, Shubham; Anand, Namrata; Sharma, Monika

    2012-01-01

    Modern biology and genomic sciences are rooted in parasitic disease research. Genome sequencing efforts have provided a wealth of new biological information that promises to have a major impact on our understanding of parasites. Microarrays provide one of the major high-throughput platforms by which this information can be exploited in the laboratory. Many excellent reviews and technique articles have recently been published on applying microarrays to organisms for which fully annotated genomes are at hand. However, many parasitologists work on organisms whose genomes have been only partially sequenced. This review is mainly focused on how to use microarray in these situations. PMID:23508469

  18. 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 ...

  19. 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 ...

  20. 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 ...

  1. Watery eyes

    MedlinePlus

    ... the most common causes of excess tearing is dry eyes . Drying causes the eyes to become uncomfortable, which stimulates the body to produce too many tears. One of the main tests for tearing is to check whether the eyes ...

  2. A 14-year-old girl who regained normal vision after bilateral visual impairment following hot water injury to the eyes

    PubMed Central

    Monsudi, Kehinde F.; Ayanniyi, Abdulkabir A.

    2010-01-01

    A 14-year-old girl presented with bilateral visual impairment following hot water injury to the eyes. The patient was admitted for a week and managed with guttae tropicamide 0.5% 8 h, diclofenac sodium 0.1% 4 h, and fluoroquinolone 0.3% 6 h and ointment chloramphenicol 8 h. Also, the patient was managed with capsule doxycycline 100 mg 12 h for 10 days, tablet cataflam 50 mg 12 h for 7 days and intramuscular tetanus toxoid 0.5 mg stat and dermacine cream for facial scald. The visual acuities improved from 3/60 (right eye) and 6/24 (left eye) to 6/6 in both eyes. There were resolutions of facial/eye pain, tearing, photophobia, lid edema, blepharospasm, and conjunctival hyperemia. There was complete healing of facial wounds and corneal ulcers. She was discharged from hospital on the 7th day of admission. Prompt presentation, degree of scald sustained, and appropriate medical intervention enhanced visual recovery and wound healing in the patient. PMID:23960925

  3. Eye movement tics.

    PubMed Central

    Shawkat, F; Harris, C M; Jacobs, M; Taylor, D; Brett, E M

    1992-01-01

    An 8-year-old girl presented with opsoclonus-like eye movement and an 18 month history of intermittent facial tics. Investigations were all normal. Electro-oculography showed the eye movements to be of variable amplitude (10-40 degrees), with no intersaccadic interval, and with a frequency of 3-4 Hz. Saccades, smooth pursuit, optokinetic, and vestibular reflexes were all normal. These abnormal eye movements eventually disappeared. It is thought that they were a form of ocular tics. PMID:1477052

  4. A New Distribution Family for Microarray Data.

    PubMed

    Kelmansky, Diana Mabel; Ricci, Lila

    2017-02-10

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

  5. [Tear osmolarity and dry eye].

    PubMed

    Pan, Shi-yin; Xiao, Xiang-hua; Wang, Yang-zheng; Liu, Xian-ning; Zhu, Xiu-ping

    2011-05-01

    Dry eye is a common eye disease, and its incidence rate has been escalating. The increased tear osmolarity is one of the main reasons for complaint, damage and inflammation of dry eye patients. With the breakthrough of testing technology for tear osmolarity, more research and application of tear osmolarity was reported, and papers on tear osmolarity of normal eye and dry eye in different regions were also published. In this article, the progress of the tear osmolarity research, the range of tear osmolarity and its application in diagnosis and therapy of dry eye was introduced, and the prospect for the clinical application of hypotonic artificial tears was also discussed.

  6. 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

  7. Multievidence microarray mining.

    PubMed

    Seifert, Martin; Scherf, Matthias; Epple, Anton; Werner, Thomas

    2005-10-01

    Microarray mining is a challenging task because of the superposition of several processes in the data. We believe that the combination of microarray data-based analyses (statistical significance analysis of gene expression) with array-independent analyses (literature-mining and promoter analysis) enables some of the problems of traditional array analysis to be overcome. As a proof-of-principle, we revisited publicly available microarray data derived from an experiment with platelet-derived growth factor (PDGF)-stimulated fibroblasts. Our strategy revealed results beyond the detection of the major metabolic pathway known to be linked to the PDGF response: we were able to identify the crosstalking regulatory networks underlying the metabolic pathway without using a priori knowledge about the experiment.

  8. DNA microarray technology. Introduction.

    PubMed

    Pollack, Jonathan R

    2009-01-01

    DNA microarray technology has revolutionized biological research by enabling genome-scale explorations. This chapter provides an overview of DNA microarray technology and its application to characterizing the physical genome, with a focus on cancer genomes. Specific areas discussed include investigations of DNA copy number alteration (and loss of heterozygosity), DNA methylation, DNA-protein (i.e., chromatin and transcription factor) interactions, DNA replication, and the integration of diverse genome-scale data types. Also provided is a perspective on recent advances and future directions in characterizing the physical genome.

  9. The questionably dry eye.

    PubMed Central

    Mackie, I. A.; Seal, D. V.

    1981-01-01

    This paper is concerned with the recognition of the dry eye when the clinical diagnosis is in doubt and other external eye diseases may be present. Papillary conjunctivitis is common to the dry eye as well as other pathological conditions and confuses the diagnosis. We have correlated the factors involved in the assessment for dryness. We have shown that particulate matter in the unstained tear film is associated with low tear lysozyme concentration. Tear flow and tear lysozyme are not necessarily interrelated, but a low lysozyme concentration (tear lysozyme ratio < 1.0) is associated with keratoconjunctivitis sicca. The Schirmer I test can produce false positive results, and we have suggested a modification to overcome this. This modified test will detect the eye with severely depleted lysozyme secretion, but it is unreliable for detecting the eye with moderately depleted secretion. We find that its lowest normal limit should be considered as 6 mm. Images PMID:7448154

  10. 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…

  11. Protein Microarray Technology

    PubMed Central

    Hall, David A.; Ptacek, Jason

    2007-01-01

    Protein chips have emerged as a promising approach for a wide variety of applications including the identification of protein-protein interactions, protein-phospholipid interactions, small molecule targets, and substrates of proteins kinases. They can also be used for clinical diagnostics and monitoring disease states. This article reviews current methods in the generation and applications of protein microarrays. PMID:17126887

  12. 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…

  13. Distribution of the AQP4 water channel in normal human tissues: protein and tissue microarrays reveal expression in several new anatomical locations, including the prostate gland and seminal vesicles.

    PubMed

    Mobasheri, Ali; Marples, David; Young, Iain S; Floyd, Rachel V; Moskaluk, Christopher A; Frigeri, Antonio

    2007-01-01

    Aquaporins facilitate osmotically driven water movement across cell membranes. Aquaporin 4 (AQP4) is a major water channel in the central nervous system where it participates in cerebral water balance. AQP4 is also present in basolateral membranes of lower respiratory tract airway and renal collecting duct epithelial cells, gastric parietal cells and skeletal muscle cells. However, the distribution of AQP4 in many other tissues is still unknown. The aim of this study was to determine the expression and relative abundance of AQP4 in human Tissue MicroArrays (TMAs) and human protein microarrays by immunohistochemistry and chemiluminescence. In the central nervous system AQP4 was abundantly expressed in the cerebral cortex, cerebellar cortex (purkinje/granular layer), ependymal cell layer, hippocampus and spinal cord. Lower levels were detected in choroid plexus, white matter and meninges. In the musculoskeletal system AQP4 was highly expressed in the sarcolemma of skeletal muscle from the chest and neck. In the male genital system AQP4 was moderately expressed in seminiferous tubules, seminal vesicles, prostate and epidiymis. In the respiratory system AQP4 was moderately expressed in lung and bronchus. AQP expression was abundant in the kidney. In the gastrointestinal system AQP4 was moderately present in basolateral membranes of parietal cells at the base of gastric glands. AQP4 was also detected in salivary glands, adrenals, anterior pituitary, prostate and seminal vesicles. Human protein microarrays verified the TMA data. Our findings suggest that AQP4 is expressed more widely than previously thought in human organs and may be involved in prostatic and seminal fluid formation.

  14. 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 ...

  15. Eye emergencies

    MedlinePlus

    ... tissue covering the front of the eye. Dust, sand, and other debris can easily enter the eye. ... clear itself of tiny objects, like eyelashes and sand, through blinking and tearing. If not, don't ...

  16. Eye Emergencies

    MedlinePlus

    ... Fight for victory. Marfan & Related Disorders What is Marfan Syndrome? What are Related Disorders? What are the Signs? ... Emergencies Eye Emergencies Lung Emergencies Surgeries Eye Emergencies Marfan syndrome significantly increases your risk of retinal detachment, a ...

  17. 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 ...

  18. Relationship Between Visual Field Sensitivity and Retinal Nerve Fiber Layer Thickness Measured by Scanning Laser Polarimetry and Optical Coherence Tomography in Normal, Ocular Hypertensive and Glaucomatous Eyes

    PubMed Central

    Lleó-Pérez, Antonio; Ortuño-Soto, Amparo; Rahhal, M.S.; Sanchis-Gimeno, Juan A.

    2010-01-01

    Purpose To evaluate the correlation between automated achromatic perimetry (AAP) and the output of two retinal nerve fiber layer (RNFL) analysers: scanning laser polarimetry (GDx-VCC) and optical coherence tomography (OCT). Methods Quantitative RNFL measurements with GDx-VCC and Stratus-OCT were obtained in one eye from 52 healthy subjects, 38 ocular hypertensive (OHT) patients and 94 glaucomatous patients. All patients underwent a complete examination, including AAP using the Swedish interactive threshold algorithm (SITA). The relationship between RNFL measurements and SITA visual field global indices were assessed by means of the following methods: analysis of variance, bivariate Pearson's correlation coefficient, multivariate linear regression techniques and nonlinear regression models, and the coefficient of determination (r2) was calculated. Results RNFL thickness values were significantly lower in glaucomatous eyes than in healthy and ocular hypertensive eyes for both nerve fiber analysers (P≤0.001), except for the inferior 120° average thickness in GDx-VCC. Linear regression models constructed for GDx-VCC measurements and OCT-derived RNFL thickness with SITA visual field global indices demonstrated that, for the mean deviation, the only predictor in the model was the nerve fiber indicator for GDx-VCC (r2=0.255), and for the pattern standard deviation, the predictors in the model were the nerve fiber indicator for GDx-VCC (r2=0.246) and the maximum thickness in the superior quadrant for Stratus-OCT (r2=0.196). The best curvilinear fit was obtained with the cubic model. Conclusions Quantitative measurements of RNFL thickness using either GDx-VCC or OCT correlate moderately with visual field global indices in moderate glaucoma patients. We did not find a correlation between visual field global indices and RNFL thickness in early glaucoma patients. Further study is needed to develop new analytical methods that will increase RNFL analyser's sensitivity in

  19. Eye Allergies

    MedlinePlus

    ... It is usually a temporary condition associated with seasonal allergies. You can get eye allergies from pet dander, ... Privacy Policy Related Is El Niño Making Your Allergies Worse? May 16, 2016 The link between seasonal allergens and dry eye Apr 27, 2015 Eye ...

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

    PubMed

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

    2016-11-01

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

  1. Unilateral Amblyopia Affects Two Eyes: Fellow Eye Deficits in Amblyopia.

    PubMed

    Meier, Kimberly; Giaschi, Deborah

    2017-03-01

    Unilateral amblyopia is a visual disorder that arises after selective disruption of visual input to one eye during critical periods of development. In the clinic, amblyopia is understood as poor visual acuity in an eye that was deprived of pattern vision early in life. By its nature, however, amblyopia has an adverse effect on the development of a binocular visual system and the interactions between signals from two eyes. Visual functions aside from visual acuity are impacted, and many studies have indicated compromised sensitivity in the fellow eye even though it demonstrates normal visual acuity. While these fellow eye deficits have been noted, no overarching theory has been proposed to describe why and under what conditions the fellow eye is impacted by amblyopia. Here, we consider four explanations that may account for decreased fellow eye sensitivity: the fellow eye is adversely impacted by treatment for amblyopia; the maturation of the fellow eye is delayed by amblyopia; fellow eye sensitivity is impacted for visual functions that rely on binocular cortex; and fellow eye deficits reflect an adaptive mechanism that works to equalize the sensitivity of the two eyes. To evaluate these ideas, we describe five visual functions that are commonly reported to be deficient in the amblyopic eye (hyperacuity, contrast sensitivity, spatial integration, global motion, and motion-defined form), and unify the current evidence for fellow eye deficits. Further research targeted at exploring fellow eye deficits in amblyopia will provide us with a broader understanding of normal visual development and how amblyopia impacts the developing visual system.

  2. Membrane-based microarrays

    NASA Astrophysics Data System (ADS)

    Dawson, Elliott P.; Hudson, James; Steward, John; Donnell, Philip A.; Chan, Wing W.; Taylor, Richard F.

    1999-11-01

    Microarrays represent a new approach to the rapid detection and identification of analytes. Studies to date have shown that the immobilization of receptor molecules (such as DNA, oligonucleotides, antibodies, enzymes and binding proteins) onto silicon and polymeric substrates can result in arrays able to detect hundreds of analytes in a single step. The formation of the receptor/analyte complex can, itself, lead to detection, or the complex can be interrogated through the use of fluorescent, chemiluminescent or radioactive probes and ligands.

  3. 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

  4. Annotating nonspecific SAGE tags with microarray data.

    PubMed

    Ge, Xijin; Jung, Yong-Chul; Wu, Qingfa; Kibbe, Warren A; Wang, San Ming

    2006-01-01

    SAGE (serial analysis of gene expression) detects transcripts by extracting short tags from the transcripts. Because of the limited length, many SAGE tags are shared by transcripts from different genes. Relying on sequence information in the general gene expression database has limited power to solve this problem due to the highly heterogeneous nature of the deposited sequences. Considering that the complexity of gene expression at a single tissue level should be much simpler than that in the general expression database, we reasoned that by restricting gene expression to tissue level, the accuracy of gene annotation for the nonspecific SAGE tags should be significantly improved. To test the idea, we developed a tissue-specific SAGE annotation database based on microarray data (). This database contains microarray expression information represented as UniGene clusters for 73 normal human tissues and 18 cancer tissues and cell lines. The nonspecific SAGE tag is first matched to the database by the same tissue type used by both SAGE and microarray analysis; then the multiple UniGene clusters assigned to the nonspecific SAGE tag are searched in the database under the matched tissue type. The UniGene cluster presented solely or at higher expression levels in the database is annotated to represent the specific gene for the nonspecific SAGE tags. The accuracy of gene annotation by this database was largely confirmed by experimental data. Our study shows that microarray data provide a useful source for annotating the nonspecific SAGE tags.

  5. Analysis of Microarray and RNA-seq Expression Profiling Data.

    PubMed

    Hung, Jui-Hung; Weng, Zhiping

    2017-03-01

    Gene expression profiling refers to the simultaneous measurement of the expression levels of a large number of genes (often all genes in a genome), typically in multiple experiments spanning a variety of cell types, treatments, or environmental conditions. Expression profiling is accomplished by assaying mRNA levels with microarrays or next-generation sequencing technologies (RNA-seq). This introduction describes normalization and analysis of data generated from microarray or RNA-seq experiments.

  6. 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.

  7. 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.

  8. Surface chemistries for antibody microarrays

    SciTech Connect

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

    2007-05-01

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

  9. Design of a covalently bonded glycosphingolipid microarray.

    PubMed

    Arigi, Emma; Blixt, Ola; Buschard, Karsten; Clausen, Henrik; Levery, Steven B

    2012-01-01

    Glycosphingolipids (GSLs) are well known ubiquitous constituents of all eukaryotic cell membranes, yet their normal biological functions are not fully understood. As with other glycoconjugates and saccharides, solid phase display on microarrays potentially provides an effective platform for in vitro study of their functional interactions. However, with few exceptions, the most widely used microarray platforms display only the glycan moiety of GSLs, which not only ignores potential modulating effects of the lipid aglycone, but inherently limits the scope of application, excluding, for example, the major classes of plant and fungal GSLs. In this work, a prototype "universal" GSL-based covalent microarray has been designed, and preliminary evaluation of its potential utility in assaying protein-GSL binding interactions investigated. An essential step in development involved the enzymatic release of the fatty acyl moiety of the ceramide aglycone of selected mammalian GSLs with sphingolipid N-deacylase (SCDase). Derivatization of the free amino group of a typical lyso-GSL, lyso-G(M1), with a prototype linker assembled from succinimidyl-[(N-maleimidopropionamido)-diethyleneglycol] ester and 2-mercaptoethylamine, was also tested. Underivatized or linker-derivatized lyso-GSL were then immobilized on N-hydroxysuccinimide- or epoxide-activated glass microarray slides and probed with carbohydrate binding proteins of known or partially known specificities (i.e., cholera toxin B-chain; peanut agglutinin, a monoclonal antibody to sulfatide, Sulph 1; and a polyclonal antiserum reactive to asialo-G(M2)). Preliminary evaluation of the method indicated successful immobilization of the GSLs, and selective binding of test probes. The potential utility of this methodology for designing covalent microarrays that incorporate GSLs for serodiagnosis is discussed.

  10. Diabetes eye exams

    MedlinePlus

    Diabetic retinopathy - eye exams; Diabetes - eye exams; Glaucoma - diabetic eye exam; Macular edema - diabetic eye exam ... if the doctor who takes care of your diabetes checks your eyes, you need an eye exam ...

  11. Fluorescein eye stain

    MedlinePlus

    ... Blinking spreads the dye and coats the tear film covering the surface of the cornea. The tear film contains water, oil, and mucus to protect and ... is normal, the dye remains in the tear film on the surface of the eye and does ...

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

    PubMed

    Oyama, Tokuhide; Abe, Haruki; Ushiki, Tatsuo

    2006-12-01

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

  13. Eye Health

    PubMed Central

    Connell, A. M. S.

    1988-01-01

    The status of eye care in the Caribbean is discussed. Methods of primary eye care providers at all levels from primary to tertiary in the region are presented against a background of the major causes of blindness, cataract, glaucoma, and diabetic retinopathy. Epidemiological surveys examining prevalence, risk factors, and intervention programs are being undertaken. PMID:3404562

  14. Eye Infections

    MedlinePlus

    ... Issues Listen Español Text Size Email Print Share Eye Infections in Infants & Children Page Content ​​​If the ... must be treated early to prevent serious complications. Eye infections that occur after the newborn period: These ...

  15. Your Eyes

    MedlinePlus

    ... sense combinations of light waves that enable our eyes to see millions of colors. Helping You See It All Rods and cones ... the great messenger in the back of your eye. The rods and cones of the retina change the colors and shapes you see into millions of nerve ...

  16. Eyes - bulging

    MedlinePlus

    ... emotional support is important. When to Contact a Medical Professional Call your health care provider if: You have bulging eyes and the cause has not yet been diagnosed. Bulging eyes are accompanied by other symptoms. ... The provider will ask about your medical history and do a physical exam. Some questions ...

  17. Ectopic Six3 expression in the dragon eye goldfish.

    PubMed

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

    2008-02-01

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

  18. 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

  19. 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.

  20. Living-cell microarrays.

    PubMed

    Yarmush, Martin L; King, Kevin R

    2009-01-01

    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.

  1. Black 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 ...

  2. Eye Symptoms

    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 ...

  3. Dry Eye

    MedlinePlus

    ... Courier services use: Rockville, MD 20852) 301-451-2020 Research at NEI Office of the Scientific Director ... Eye Disease Education Program Glaucoma Education Program Low Vision Education Program Hispanic/Latino Program Vision and Aging ...

  4. Healthy Eyes

    MedlinePlus

    ... openings visit HHS USAJobs 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 ...

  5. Preventing Eye Injuries

    MedlinePlus

    ... Stories Español Eye Health / Eye Health A-Z Eye Injuries Sections Preventing Eye Injuries Recognizing and Treating ... Infographic Five Steps to Safer Champagne Celebrations Preventing Eye Injuries Reviewed by: Brenda Pagan-Duran MD Mar. ...

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

    PubMed

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

    2015-11-01

    Microarray testing has revolutionized clinical cytogenetics, as it provides a significantly higher resolution and greater clinical yield than karyotype analysis. This study assessed the clinical utility of single-nucleotide polymorphism microarray in patients with epilepsy. Study subjects were patients between the ages of birth to 23 years who were diagnosed with epilepsy and had a microarray performed at Cincinnati Children's Hospital Medical Center. Statistical analysis explored the association of microarray results and brain magnetic resonance imaging (MRI), seizure type, and structural malformations. Approximately 17.7% (26/147) of participants had an abnormal microarray as defined by laboratory guidelines. There were no differences in frequency of abnormal brain MRI or seizure type between the abnormal and normal microarray groups. There was a higher prevalence of musculoskeletal malformations (P < .0035) and cardiovascular malformations (P < .0081) in subjects with abnormal microarrays. Clinicians should consider microarray analysis in individuals who have epilepsy, especially in combination with musculoskeletal malformation or cardiovascular malformation.

  7. Microarray simulator as educational tool.

    PubMed

    Ruusuvuori, Pekka; Nykter, Matti; Mäkiraatikka, Eeva; Lehmussola, Antti; Korpelainen, Tomi; Erkkilä, Timo; Yli-Harja, Olli

    2007-01-01

    As many real-world applications, microarray measurements are inapplicable for large-scale teaching purposes due to their laborious preparation process and expense. Fortunately, many phases of the array preparation process can be efficiently demonstrated by using a software simulator tool. Here we propose the use of microarray simulator as an aiding tool in teaching of computational biology. Three case studies on educational use of the simulator are presented, which demonstrate the effect of gene knock-out, synthetic time series, and effect of noise sources. We conclude that the simulator, used for teaching the principles of microarray measurement technology, proved to be a useful tool in education.

  8. 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

  9. WebArray: an online platform for microarray data analysis

    PubMed Central

    Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

    2005-01-01

    Background Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments. Results The currently implemented functions were based on limma and affy package from Bioconductor, the spacings LOESS histogram (SPLOSH) method, PCA-assisted normalization method and genome mapping method. WebArray incorporates these packages and provides a user-friendly interface for accessing a wide range of key functions of limma and others, such as spot quality weight, background correction, graphical plotting, normalization, linear modeling, empirical bayes statistical analysis, false discovery rate (FDR) estimation, chromosomal mapping for genome comparison. Conclusion WebArray offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. The website is freely available at . It runs on a Linux server with Apache and MySQL. PMID:16371165

  10. Optimization of Cyanine Dye Stability and Analysis of FRET Interaction on DNA Microarrays

    PubMed Central

    von der Haar, Marcel; Heuer, Christopher; Pähler, Martin; von der Haar, Kathrin; Lindner, Patrick; Scheper, Thomas; Stahl, Frank

    2016-01-01

    The application of DNA microarrays for high throughput analysis of genetic regulation is often limited by the fluorophores used as markers. The implementation of multi-scan techniques is limited by the fluorophores’ susceptibility to photobleaching when exposed to the scanner laser light. This paper presents combined mechanical and chemical strategies which enhance the photostability of cyanine 3 and cyanine 5 as part of solid state DNA microarrays. These strategies are based on scanning the microarrays while the hybridized DNA is still in an aqueous solution with the presence of a reductive/oxidative system (ROXS). Furthermore, the experimental setup allows for the analysis and eventual normalization of Förster-resonance-energy-transfer (FRET) interaction of cyanine-3/cyanine-5 dye combinations on the microarray. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the comparability of microarray experiment results between labs. PMID:27916881

  11. Electrostatic readout of DNA microarrays with charged microspheres

    PubMed Central

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

    2014-01-01

    DNA microarrays are used for gene-expression profiling, single-nucleotide polymorphism detection and disease diagnosis1–3. A persistent challenge in this area is the lack of microarray screening technology suitable for integration into routine clinical care4,5. Here, 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. Because the naked eye is sufficient to read out hybridization, this approach may facilitate broad application of multiplexed assays. PMID:18587384

  12. 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.

  13. A New Distribution Family for Microarray Data †

    PubMed Central

    Kelmansky, Diana Mabel; Ricci, Lila

    2017-01-01

    The traditional approach with microarray data has been to apply transformations that approximately normalize them, with the drawback of losing the original scale. The alternative standpoint taken here is to search for models that fit the data, characterized by the presence of negative values, preserving their scale; one advantage of this strategy is that it facilitates a direct interpretation of the results. A new family of distributions named gpower-normal indexed by p∈R is introduced and it is proven that these variables become normal or truncated normal when a suitable gpower transformation is applied. Expressions are given for moments and quantiles, in terms of the truncated normal density. This new family can be used to model asymmetric data that include non-positive values, as required for microarray analysis. Moreover, it has been proven that the gpower-normal family is a special case of pseudo-dispersion models, inheriting all the good properties of these models, such as asymptotic normality for small variances. A combined maximum likelihood method is proposed to estimate the model parameters, and it is applied to microarray and contamination data. R codes are available from the authors upon request. PMID:28208652

  14. Genomics of hybrid poplar (Populus trichocarpax deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences in poplar.

    PubMed

    Ralph, Steven; Oddy, Claire; Cooper, Dawn; Yueh, Hesther; Jancsik, Sharon; Kolosova, Natalia; Philippe, Ryan N; Aeschliman, Dana; White, Rick; Huber, Dezene; Ritland, Carol E; Benoit, François; Rigby, Tracey; Nantel, André; Butterfield, Yaron S N; Kirkpatrick, Robert; Chun, Elizabeth; Liu, Jerry; Palmquist, Diana; Wynhoven, Brian; Stott, Jeffrey; Yang, George; Barber, Sarah; Holt, Robert A; Siddiqui, Asim; Jones, Steven J M; Marra, Marco A; Ellis, Brian E; Douglas, Carl J; Ritland, Kermit; Bohlmann, Jörg

    2006-04-01

    As part of a genomics strategy to characterize inducible defences against insect herbivory in poplar, we developed a comprehensive suite of functional genomics resources including cDNA libraries, expressed sequence tags (ESTs) and a cDNA microarray platform. These resources are designed to complement the existing poplar genome sequence and poplar (Populus spp.) ESTs by focusing on herbivore- and elicitor-treated tissues and incorporating normalization methods to capture rare transcripts. From a set of 15 standard, normalized or full-length cDNA libraries, we generated 139,007 3'- or 5'-end sequenced ESTs, representing more than one-third of the c. 385,000 publicly available Populus ESTs. Clustering and assembly of 107,519 3'-end ESTs resulted in 14,451 contigs and 20,560 singletons, altogether representing 35,011 putative unique transcripts, or potentially more than three-quarters of the predicted c. 45,000 genes in the poplar genome. Using this EST resource, we developed a cDNA microarray containing 15,496 unique genes, which was utilized to monitor gene expression in poplar leaves in response to herbivory by forest tent caterpillars (Malacosoma disstria). After 24 h of feeding, 1191 genes were classified as up-regulated, compared to only 537 down-regulated. Functional classification of this induced gene set revealed genes with roles in plant defence (e.g. endochitinases, Kunitz protease inhibitors), octadecanoid and ethylene signalling (e.g. lipoxygenase, allene oxide synthase, 1-aminocyclopropane-1-carboxylate oxidase), transport (e.g. ABC proteins, calreticulin), secondary metabolism [e.g. polyphenol oxidase, isoflavone reductase, (-)-germacrene D synthase] and transcriptional regulation [e.g. leucine-rich repeat transmembrane kinase, several transcription factor classes (zinc finger C3H type, AP2/EREBP, WRKY, bHLH)]. This study provides the first genome-scale approach to characterize insect-induced defences in a woody perennial providing a solid platform for

  15. 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 ...

  16. 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.

  17. The bioinformatics of microarrays to study cancer: Advantages and disadvantages

    NASA Astrophysics Data System (ADS)

    Rodríguez-Segura, M. A.; Godina-Nava, J. J.; Villa-Treviño, S.

    2012-10-01

    Microarrays are devices designed to analyze simultaneous expression of thousands of genes. However, the process will adds noise into the information at each stage of the study. To analyze these thousands of data is necessary to use bioinformatics tools. The traditional analysis begins by normalizing data, but the obtained results are highly dependent on how it is conducted the study. It is shown the need to develop new strategies to analyze microarray. Liver tissue taken from an animal model in which is chemically induced cancer is used as an example.

  18. Microarray Technologies in Fungal Diagnostics.

    PubMed

    Rupp, Steffen

    2017-01-01

    Microarray technologies have been a major research tool in the last decades. In addition they have been introduced into several fields of diagnostics including diagnostics of infectious diseases. Microarrays are highly parallelized assay systems that initially were developed for multiparametric nucleic acid detection. From there on they rapidly developed towards a tool for the detection of all kind of biological compounds (DNA, RNA, proteins, cells, nucleic acids, carbohydrates, etc.) or their modifications (methylation, phosphorylation, etc.). The combination of closed-tube systems and lab on chip devices with microarrays further enabled a higher automation degree with a reduced contamination risk. Microarray-based diagnostic applications currently complement and may in the future replace classical methods in clinical microbiology like blood cultures, resistance determination, microscopic and metabolic analyses as well as biochemical or immunohistochemical assays. In addition, novel diagnostic markers appear, like noncoding RNAs and miRNAs providing additional room for novel nucleic acid based biomarkers. Here I focus an microarray technologies in diagnostics and as research tools, based on nucleic acid-based arrays.

  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. Assessing differential expression in two-color microarrays: a resampling-based empirical Bayes approach.

    PubMed

    Li, Dongmei; Le Pape, Marc A; Parikh, Nisha I; Chen, Will X; Dye, Timothy D

    2013-01-01

    Microarrays are widely used for examining differential gene expression, identifying single nucleotide polymorphisms, and detecting methylation loci. Multiple testing methods in microarray data analysis aim at controlling both Type I and Type II error rates; however, real microarray data do not always fit their distribution assumptions. Smyth's ubiquitous parametric method, for example, inadequately accommodates violations of normality assumptions, resulting in inflated Type I error rates. The Significance Analysis of Microarrays, another widely used microarray data analysis method, is based on a permutation test and is robust to non-normally distributed data; however, the Significance Analysis of Microarrays method fold change criteria are problematic, and can critically alter the conclusion of a study, as a result of compositional changes of the control data set in the analysis. We propose a novel approach, combining resampling with empirical Bayes methods: the Resampling-based empirical Bayes Methods. This approach not only reduces false discovery rates for non-normally distributed microarray data, but it is also impervious to fold change threshold since no control data set selection is needed. Through simulation studies, sensitivities, specificities, total rejections, and false discovery rates are compared across the Smyth's parametric method, the Significance Analysis of Microarrays, and the Resampling-based empirical Bayes Methods. Differences in false discovery rates controls between each approach are illustrated through a preterm delivery methylation study. The results show that the Resampling-based empirical Bayes Methods offer significantly higher specificity and lower false discovery rates compared to Smyth's parametric method when data are not normally distributed. The Resampling-based empirical Bayes Methods also offers higher statistical power than the Significance Analysis of Microarrays method when the proportion of significantly differentially

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

    PubMed

    Lapan, Sylvain W; Reddien, Peter W

    2012-08-30

    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.

  2. 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.

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

    PubMed

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

    2010-06-01

    to normal rapid eye movement sleep.

  4. 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.

  5. Eye Complications in IBD

    MedlinePlus

    ... Home > Resources > Eye Complications in IBD Go Back Eye Complications in IBD Email Print + Share Approximately 10% ... doctor’s attention sooner rather than later. TYPES OF EYE DISORDERS UVEITIS One of the most common eye ...

  6. Eye Injuries at Work

    MedlinePlus

    ... Ophthalmologist Patient Stories Español Eye Health / Tips & Prevention Eye Injuries Sections Preventing Eye Injuries Recognizing and Treating ... Numbers — Infographic Five Steps to Safer Champagne Celebrations Eye Injuries at Work Edited by: Shirley Dang Feb. ...

  7. Conjunctivitis (Pink Eye)

    MedlinePlus

    ... can be embedded on web pages. Conjunctivitis (Pink Eye) One-Page Overview Pink, itchy eyes? Conjunctivitis – or ... yourself from getting and spreading pink eye . Pink Eye: What To Do Discusses causes and treatment, when ...

  8. Conjunctivitis or pink eye

    MedlinePlus

    Inflammation - conjunctiva; Pink eye; Chemical conjunctivitis, Pinkeye; Pink-eye ... Tears most often protect the eyes by washing away the germs and irritants. Tears contain proteins and antibodies that kill germs. Pink eye is most often caused ...

  9. Eye Injuries at Home

    MedlinePlus

    ... Ophthalmologist Patient Stories Español Eye Health / Tips & Prevention Eye Injuries Sections Preventing Eye Injuries Recognizing and Treating ... Numbers — Infographic Five Steps to Safer Champagne Celebrations Eye Injuries at Home Reviewed by: Brenda Pagan-Duran ...

  10. Eye Involvement in TSC

    MedlinePlus

    ... Privacy Policy Sitemap Learn Engage Donate About TSC Eyes Campbell (1905) first described the eye involvement in ... some form of eye involvement. Nonretinal and Retinal Eye Findings Facial angiofibromas may involve the eyelids of ...

  11. 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 ...

  12. 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 ...

  13. Why Do Eyes Water?

    MedlinePlus

    ... Happens in the Operating Room? Why Do Eyes Water? KidsHealth > For Kids > Why Do Eyes Water? A ... out of your nose. continue Why Do Eyes Water? Eyes water for lots of different reasons besides ...

  14. About the Eye

    MedlinePlus

    ... NEI for Kids > About the Eye All About Vision About the Eye Ask a Scientist Video Series ... Eye Health and Safety First Aid Tips Healthy Vision Tips Protective Eyewear Sports and Your Eyes Fun ...

  15. Sports and Your Eyes

    MedlinePlus

    ... for Kids > Sports and Your Eyes All About Vision About the Eye Ask a Scientist Video Series ... Eye Health and Safety First Aid Tips Healthy Vision Tips Protective Eyewear Sports and Your Eyes Fun ...

  16. Strabismus and eye muscle function.

    PubMed

    Lennerstrand, Gunnar

    2007-11-01

    Studies of external eye muscle morphology and physiology are reviewed, with respect to both motor and sensory functions in concomitant strabismus. The eye muscles have a more complex fibre composition than other striated muscle, and they are among the fastest and most fatigue-resistant muscles in the body. However, it is not generally believed that concomitant strabismus is due to a primary abnormality of the eye muscles or the ocular motor system. The gross anatomy of eye muscles, including the shape and position of the eye muscle pulleys, was not changed in strabismus. The histology of the eye muscle fibres was also basically the same, but changes have been observed in the cellular and biochemical machinery of the fibres, most notably in the singly innervated orbital fibres. Functionally, this was seen as slower contractions and reduced fatigue resistance of eye muscles in animals with strabismus and defects of binocular vision. Most likely the changes represented an adaptation to modified visual demands on the ocular motor control, because of the defects of binocular vision in strabismus from an early age. Adaptation of eye muscle function to visual demands could be seen also in the adult human ocular motor system, but here the effects could be reversed with treatment in some conditions. External eye muscles in the human have sensory organs, muscle spindles and tendon organs, responding to changes in muscle force and length. It is not known how these proprioceptors are used more specifically in ocular motor control, and there is no stretch reflex in the external eye muscles. However, a clear influence on space localization and eye position can be demonstrated with vibratory stimulation of the eye muscles, presumably activating muscle spindles. Different effects were observed in normal subjects and in adult patients with strabismus, which would indicate that the proprioceptive input from one eye of strabismic patients could be suppressed by the other eye, similar

  17. Eye contricks

    PubMed Central

    Wade, Nicholas J

    2011-01-01

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

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

    PubMed

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

    2014-12-15

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

  19. Microfluidic microarray systems and methods thereof

    SciTech Connect

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

    2009-04-28

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

  20. Imaging systems of human eye: a review.

    PubMed

    Acharya, Rajendra U; Yun, Wong Li; Ng, E Y K; Yu, Wenwei; Suri, Jasjit S

    2008-08-01

    The eyes are complex sensory organs and are designed to optimize vision under conditions of varying light. There are a number of eye disorders that can influence vision. Eye disorders among the elderly are a major health problem. With advancing age, the normal function of eye tissues decreases and there is an increased incidence of ocular pathology. The most common causes of age related eye disorder and visual impairment in the elderly are cataracts and primary open angle glaucoma. Different imaging systems are available to visualize the different parts of the eye non-invasively with higher accuracy. This paper discusses the various techniques available namely, computed tomography, confocal laser scanning microscopy, magnetic resonance imaging, optical coherence tomography, ultrasound imaging, infrared thermography for the imaging of the different eye abnormalities.

  1. 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,…

  2. Software and tools for microarray data analysis.

    PubMed

    Mehta, Jai Prakash; Rani, Sweta

    2011-01-01

    A typical microarray experiment results in series of images, depending on the experimental design and number of samples. Software analyses the images to obtain the intensity at each spot and quantify the expression for each transcript. This is followed by normalization, and then various data analysis techniques are applied on the data. The whole analysis pipeline requires a large number of software to accurately handle the massive amount of data. Fortunately, there are large number of freely available and commercial software to churn the massive amount of data to manageable sets of differentially expressed genes, functions, and pathways. This chapter describes the software and tools which can be used to analyze the gene expression data right from the image analysis to gene list, ontology, and pathways.

  3. Automation of cDNA microarray hybridization and washing yields improved data quality.

    PubMed

    Yauk, Carole; Berndt, Lynn; Williams, Andrew; Douglas, George R

    2005-07-29

    Microarray technology allows the analysis of whole-genome transcription within a single hybridization, and has become a standard research tool. It is extremely important to minimize variation in order to obtain high quality microarray data that can be compared among experiments and laboratories. The majority of facilities implement manual hybridization approaches for microarray studies. We developed an automated method for cDNA microarray hybridization that uses equivalent pre-hybridization, hybridization and washing conditions to the suggested manual protocol. The automated method significantly decreased variability across microarray slides compared to manual hybridization. Although normalized signal intensities for buffer-only spots across the chips were identical, significantly reduced variation and inter-quartile ranges were obtained using the automated workstation. This decreased variation led to improved correlation among technical replicates across slides in both the Cy3 and Cy5 channels.

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

    PubMed

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

    2015-01-01

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

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. DNA microarray technology in dermatology.

    PubMed

    Kunz, Manfred

    2008-03-01

    In recent years, DNA microarray technology has been used for the analysis of gene expression patterns in a variety of skin diseases, including malignant melanoma, psoriasis, lupus erythematosus, and systemic sclerosis. Many of the studies described herein confirmed earlier results on individual genes or functional groups of genes. However, a plethora of new candidate genes, gene patterns, and regulatory pathways have been identified. Major progresses were reached by the identification of a prognostic gene pattern in malignant melanoma, an immune signaling cluster in psoriasis, and a so-called interferon signature in systemic lupus erythematosus. In future, interference with genes or regulatory pathways with the use of different RNA interference technologies or targeted therapy may not only underscore the functional significance of microarray data but also may open interesting therapeutic perspectives. Large-scale gene expression analyses may also help to design more individualized treatment approaches of cutaneous diseases.

  10. 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.

  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. Fellow Eye in Unilateral Primary Congenital Glaucoma

    PubMed Central

    2017-01-01

    ABSTRACT Aim This is a report of the incidence of bilateral cases in a cohort of primary congenital glaucoma (PCG) cases and a study of the biometric characteristics of the fellow normal eyes in unilateral cases. Materials and methods The charts of 134 PCG children were reviewed, of which 78 cases (58.2%) were found to have bilateral disease. The remaining 56 patients (41.8%) with unilateral disease had their fellow normal eyes compared with an age-matched cohort of ophthalmologically free children. Results There were no differences between the normal fellow eyes of PCG cases and the control eyes in the corneal diameter and central corneal thickness (CCT), whereas the normal fellow eyes of PCG cases had higher intraocular pressure (IOP) and cup/disc (C/D) ratios. Conclusion The fellow eyes of apparently unilateral PCG cases are not typically normal anatomically like other children unaffected by PCG. Clinical significance A very high index of suspicion has to be kept for PCG cases that present apparently unilaterally, and meticulous prolonged follow-up is mandatory. How to cite this article Bayoumi NHL. Fellow Eye in Unilateral Primary Congenital Glaucoma. J Curr Glaucoma Pract 2017;11(1):28-30. PMID:28138215

  13. 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.

  14. Twisted story of eye migration in flatfish.

    PubMed

    Saele, Oystein; Smáradóttir, Heiddís; Pittman, Karin

    2006-06-01

    Early molecular markers for flatfish metamorphosis and eye migration must be linked to the ethmoid region, the earliest part of the flatfish cranium to change, as well as chondral and dermal ossification processes. Serial sections, morphological landmarks, and stereology were used to determine where and when the remodeling of tissues and asymmetry occurs in the head region of metamorphosing Atlantic halibut, Hippoglossus hippoglossus. Not all parts of the head remodel or migrate, and those that do may be asynchronous. Normal metamorphosis limits the torsion of the Atlantic halibut head to the anterior part of the neurocranium and excludes the tip of the snout and the general jaw area. The first cranial structure displaying eye migration-related asymmetric development is the paraethmoid part of the ethmoid cartilage. In early eye migration the medial frontal process moves apace with the eyes, whereas near completion the migrating eye moves significantly closer to the frontal process. Structures of the jaw remain mostly symmetrical, with the exception of the adductor mandibulae muscle and the bone maxillare, which are larger on the abocular than on the ocular side, the muscle occupying the space vacated by the migration of the eye. Thus, normal eye migration involves a series of temperospatially linked events. In juveniles lacking eye migration (arrested metamorphosis), the dermal bone, the prefrontal, does not develop. The two abnormal paraethmoids develop symmetrically as two plate-like structures curving anteriorly, whereas normal elongate fused paraethmoids curve at their posterior. The abocular side retrorbital vesicles are largest in volume only after the completion of normal eye migration. Factors involved in completion of normal metamorphosis and eye migration in flatfish affect chondral and dermal ossification signals in the ethmoid group, as well as remodeling of the mineralized frontal, a series of linked events not involving the entire neurocranium.

  15. Molecular genetic analysis of Drosophila eyes absent mutants reveals an eye enhancer element.

    PubMed Central

    Zimmerman, J E; Bui, Q T; Liu, H; Bonini, N M

    2000-01-01

    The eyes absent (eya) gene is critical for normal eye development in Drosophila and is highly conserved to vertebrates. To define regions of the gene critical for eye function, we have defined the mutations in the four viable eya alleles. Two of these mutations are eye specific and undergo transvection with other mutations in the gene. These were found to be deletion mutations that remove regulatory sequence critical for eye cell expression of the gene. Two other viable alleles cause a reduced eye phenotype and affect the function of the gene in additional tissues, such as the ocelli. These mutations were found to be insertion mutations of different transposable elements within the 5' UTR of the transcript. Detailed analysis of one of these revealed that the transposable element has become subject to regulation by eye enhancer sequences of the eya gene, disrupting normal expression of EYA in the eye. More extended analysis of the deletion region in the eye-specific alleles indicated that the deleted region defines an enhancer that activates gene expression in eye progenitor cells. This enhancer is responsive to ectopic expression of the eyeless gene. This analysis has defined a critical regulatory region required for proper eye expression of the eya gene. PMID:10628984

  16. National Eye Institute

    MedlinePlus

    ... around the world. Learn more Video: Next-Generation Eye Imaging Tools Learn about how the NEI Audacious ... eyeGENE® International Research 3-D Retina Organoid Challenge Eye and Vision Research The latest on NEI research. ...

  17. Eye Injuries (For Parents)

    MedlinePlus

    ... Old Feeding Your 1- to 2-Year-Old Eye Injuries KidsHealth > For Parents > Eye Injuries Print A ... sand, dirt, and other foreign bodies on the eye surface) Wash your hands thoroughly before touching the ...

  18. Pink Eye (Conjunctivitis)

    MedlinePlus

    ... have allergic conjunctivitis. Preventing the spread of pink eye Practice good hygiene to control the spread of ... return to school or child care. Preventing pink eye in newborns Newborns' eyes are susceptible to bacteria ...

  19. Diabetes - eye care

    MedlinePlus

    ... page: //medlineplus.gov/ency/patientinstructions/000078.htm Diabetes - eye care To use the sharing features on this ... prevent them from getting worse. You Need Regular eye Exams Every year, you should have an eye ...

  20. 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 ( ...

  1. Eye Cosmetic Safety

    MedlinePlus

    ... when they are new. FDA has an Import Alert in effect for cosmetics -- including eye cosmetics -- contaminated ... in the area of the eye. An import alert for cosmetics containing illegal colors lists several eye ...

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

    PubMed

    Dehghan Khalilabad, Nastaran; Hassanpour, Hamid

    2017-02-01

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

  3. A Customized DNA Microarray for Microbial Source Tracking ...

    EPA Pesticide Factsheets

    It is estimated that more than 160, 000 miles of rivers and streams in the United States are impaired due to the presence of waterborne pathogens. These pathogens typically originate from human and other animal fecal pollution sources; therefore, a rapid microbial source tracking (MST) method is needed to facilitate water quality assessment and impaired water remediation. We report a novel qualitative DNA microarray technology consisting of 453 probes for the detection of general fecal and host-associated bacteria, viruses, antibiotic resistance, and other environmentally relevant genetic indicators. A novel data normalization and reduction approach is also presented to help alleviate false positives often associated with high-density microarray applications. To evaluate the performance of the approach, DNA and cDNA was isolated from swine, cattle, duck, goose and gull fecal reference samples, as well as soiled poultry liter and raw municipal sewage. Based on nonmetric multidimensional scaling analysis of results, findings suggest that the novel microarray approach may be useful for pathogen detection and identification of fecal contamination in recreational waters. The ability to simultaneously detect a large collection of environmentally important genetic indicators in a single test has the potential to provide water quality managers with a wide range of information in a short period of time. Future research is warranted to measure microarray performance i

  4. 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.

  5. 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

  6. 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.

  7. Altered aquaporin expression in glaucoma eyes.

    PubMed

    Tran, Thuy Linh; Bek, Toke; la Cour, Morten; Nielsen, Søren; Prause, Jan Ulrik; Hamann, Steffen; Heegaard, Steffen

    2014-09-01

    Aquaporins (AQP) are channels in the cell membrane that mainly facilitate a passive transport of water. In the eye, AQPs are expressed in the ciliary body and retina and may contribute to the pathogenesis of glaucoma and optic neuropathy. We investigated the expression of AQP1, AQP3, AQP4, AQP5, AQP7 and AQP9 in human glaucoma eyes compared with normal eyes. Nine glaucoma eyes were examined. Of these, three eyes were diagnosed with primary open angle glaucoma; three eyes had neovascular glaucoma; and three eyes had chronic angle-closure glaucoma. Six eyes with normal intraocular pressure and without glaucoma were used as control. Immunohistochemistry was performed using antibodies against AQP1, AQP3, AQP4, AQP5, AQP7 and AQP9. For each specimen, optical densities of immunoprecipitates were measured using Photoshop and the staining intensities were calculated. Immunostaining showed labelling of AQP7 and AQP9 in the nonpigmented ciliary epithelium and the staining intensities were significantly decreased in glaucoma eyes (p = 0.003; p = 0.018). AQP7 expression in the Müller cell endfeet was increased (p = 0.046), and AQP9 labelling of the retinal ganglion cells (RGC) showed decreased intensity (p = 0.037). No difference in AQP1, AQP4 and AQP9 expression was found in the optic nerve fibres. This study is the first investigating AQPs in human glaucoma eyes. We found a reduced expression of AQP9 in the retinal ganglion cells of glaucoma eyes. Glaucoma also induced increased AQP7 expression in the Müller cell endfeet. In the ciliary body of glaucoma eyes, the expression of AQP7 and AQP9 was reduced. Therefore, the expression of AQPs seems to play a role in glaucoma.

  8. Surface characterization of carbohydrate microarrays.

    PubMed

    Scurr, David J; Horlacher, Tim; Oberli, Matthias A; Werz, Daniel B; Kroeck, Lenz; Bufali, Simone; Seeberger, Peter H; Shard, Alexander G; Alexander, Morgan R

    2010-11-16

    Carbohydrate microarrays are essential tools to determine the biological function of glycans. Here, we analyze a glycan array by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to gain a better understanding of the physicochemical properties of the individual spots and to improve carbohydrate microarray quality. The carbohydrate microarray is prepared by piezo printing of thiol-terminated sugars onto a maleimide functionalized glass slide. The hyperspectral ToF-SIMS imaging data are analyzed by multivariate curve resolution (MCR) to discern secondary ions from regions of the array containing saccharide, linker, salts from the printing buffer, and the background linker chemistry. Analysis of secondary ions from the linker common to all of the sugar molecules employed reveals a relatively uniform distribution of the sugars within the spots formed from solutions with saccharide concentration of 0.4 mM and less, whereas a doughnut shape is often formed at higher-concentration solutions. A detailed analysis of individual spots reveals that in the larger spots the phosphate buffered saline (PBS) salts are heterogeneously distributed, apparently resulting in saccharide concentrated at the rim of the spots. A model of spot formation from the evaporating sessile drop is proposed to explain these observations. Saccharide spot diameters increase with saccharide concentration due to a reduction in surface tension of the saccharide solution compared to PBS. The multivariate analytical partial least squares (PLS) technique identifies ions from the sugars that in the complex ToF-SIMS spectra correlate with the binding of galectin proteins.

  9. Diagnostic challenges for multiplexed protein microarrays.

    PubMed

    Master, Stephen R; Bierl, Charlene; Kricka, Larry J

    2006-11-01

    Multiplexed protein analysis using planar microarrays or microbeads is growing in popularity for simultaneous assays of antibodies, cytokines, allergens, drugs and hormones. However, this new assay format presents several new operational issues for the clinical laboratory, such as the quality control of protein-microarray-based assays, the release of unrequested test data and the use of diagnostic algorithms to transform microarray data into diagnostic results.

  10. Automated Microarray Image Analysis Toolbox for MATLAB

    SciTech Connect

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

    2005-09-01

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

  11. 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...

  12. 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

  13. 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.

  14. 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…

  15. 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.

  16. Rapid eye movement latency in children and adolescents.

    PubMed

    Mason, Thornton B A; Teoh, Laurel; Calabro, Kristen; Traylor, Joel; Karamessinis, Laurie; Schultz, Brian; Samuel, John; Gallagher, Paul R; Marcus, Carole L

    2008-09-01

    Rapid eye movement sleep distribution changes during development, but little is known about rapid eye movement latency variation in childhood by age, sex, or pathologic sleep states. We hypothesized that: (1) rapid eye movement latency would differ in normal children by age, with a younger cohort (1-10 years) demonstrating shorter rapid eye movement latency than an older group (>10-18 years); (2) rapid eye movement latency in children would differ from typical adult rapid eye movement latency; and (3) intrinsic sleep disorders (narcolepsy, pediatric obstructive sleep apnea syndrome) would disrupt normal developmental patterns of rapid eye movement latency. A retrospective chart review included data from clinic visits and of rapid eye movement latency and other parameters measured by overnight polysomnography. Participants included 98 control children, 90 children with obstructive sleep apnea syndrome, and 13 children with narcolepsy. There were no statistically significant main effects of age category or sex on rapid eye movement latency. Rapid eye movement latency, however, exhibited a significant inverse correlation with age within the older control children. Healthy children exhibited rapid eye movement latencies significantly longer than adults. Normal control patients demonstrated significantly longer rapid eye movement latency than obstructive sleep apnea syndrome and narcolepsy patients.

  17. Eyeless initiates the expression of both sine oculis and eyes absent during Drosophila compound eye development.

    PubMed

    Halder, G; Callaerts, P; Flister, S; Walldorf, U; Kloter, U; Gehring, W J

    1998-06-01

    The Drosophila Pax-6 gene eyeless acts high up in the genetic hierarchy involved in compound eye development and can direct the formation of extra eyes in ectopic locations. Here we identify sine oculis and eyes absent as two mediators of the eye-inducing activity of eyeless. We show that eyeless induces and requires the expression of both genes independently during extra eye development. During normal eye development, eyeless is expressed earlier than and is required for the expression of sine oculis and eyes absent, but not vice versa. Based on the results presented here and those of others, we propose a model in which eyeless induces the initial expression of both sine oculis and eyes absent in the eye disc. sine oculis and eyes absent then appear to participate in a positive feedback loop that regulates the expression of all three genes. In contrast to the regulatory interactions that occur in the developing eye disc, we also show that in the embryonic head, sine oculis acts in parallel to eyeless and twin of eyeless, a second Pax-6 gene from Drosophila. Recent studies in vertebrate systems indicate that the epistatic relationships among the corresponding vertebrate homologs are very similar to those observed in Drosophila.

  18. 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...

  19. 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...

  20. 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.

  1. The Effect of an Eye Movement Recorder on Head Movements,

    DTIC Science & Technology

    1982-07-01

    in several research settings. For example, the NAC Eye Mark (e Recorder system (an eye movement recorder that utilizes the cor- neal reflection...reported that the NAC system could be used with a large number of subjects and that normal eye movement patterns were not altered by the use of’ this...equipment (2,4); however, no mention has been made of the extent to which the NAC system alters normal head movement patterns. It has been shown that head

  2. Microarray analysis of p-anisaldehyde-induced transcriptome of Saccharomyces cerevisiae.

    PubMed

    Yu, Lu; Guo, Na; Yang, Yi; Wu, Xiuping; Meng, Rizeng; Fan, Junwen; Ge, Fa; Wang, Xuelin; Liu, Jingbo; Deng, Xuming

    2010-03-01

    p-Anisaldehyde (4-methoxybenzaldehyde), an extract from Pimpinella anisum L. seeds, is a potential novel preservative. To reveal the possible action mechanism of p-anisaldehyde against microorganisms, yeast-based commercial oligonucleotide microarrays were used to analyze the genome-wide transcriptional changes in response to p-anisaldehyde. Quantitative real-time RT-PCR was performed for selected genes to verify the microarray results. We interpreted our microarray data with the clustering tool, T-profiler. Analysis of microarray data revealed that p-anisaldehyde induced the expression of genes related to sulphur assimilation, aromatic aldehydes metabolism, and secondary metabolism, which demonstrated that the addition of p-anisaldehyde may influence the normal metabolism of aromatic aldehydes. This genome-wide transcriptomics approach revealed first insights into the response of Saccharomyces cerevisiae (S. cerevisiae) to p-anisaldehyde challenge.

  3. 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…

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

    PubMed

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

    2013-04-01

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

  5. 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

  6. Analysis of DNA microarray expression data.

    PubMed

    Simon, Richard

    2009-06-01

    DNA microarrays are powerful tools for studying biological mechanisms and for developing prognostic and predictive classifiers for identifying the patients who require treatment and are best candidates for specific treatments. Because microarrays produce so much data from each specimen, they offer great opportunities for discovery and great dangers or producing misleading claims. Microarray based studies require clear objectives for selecting cases and appropriate analysis methods. Effective analysis of microarray data, where the number of measured variables is orders of magnitude greater than the number of cases, requires specialized statistical methods which have recently been developed. Recent literature reviews indicate that serious problems of analysis exist a substantial proportion of publications. This manuscript attempts to provide a non-technical summary of the key principles of statistical design and analysis for studies that utilize microarray expression profiling.

  7. Microarray Applications in Microbial Ecology Research.

    SciTech Connect

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

    2006-04-06

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

  8. In control: systematic assessment of microarray performance.

    PubMed

    van Bakel, Harm; Holstege, Frank C P

    2004-10-01

    Expression profiling using DNA microarrays is a powerful technique that is widely used in the life sciences. How reliable are microarray-derived measurements? The assessment of performance is challenging because of the complicated nature of microarray experiments and the many different technology platforms. There is a mounting call for standards to be introduced, and this review addresses some of the issues that are involved. Two important characteristics of performance are accuracy and precision. The assessment of these factors can be either for the purpose of technology optimization or for the evaluation of individual microarray hybridizations. Microarray performance has been evaluated by at least four approaches in the past. Here, we argue that external RNA controls offer the most versatile system for determining performance and describe how such standards could be implemented. Other uses of external controls are discussed, along with the importance of probe sequence availability and the quantification of labelled material.

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

    PubMed

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

    2013-01-01

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

  10. Chaotic mixer improves microarray hybridization.

    PubMed

    McQuain, Mark K; Seale, Kevin; Peek, Joel; Fisher, Timothy S; Levy, Shawn; Stremler, Mark A; Haselton, Frederick R

    2004-02-15

    Hybridization is an important aspect of microarray experimental design which influences array signal levels and the repeatability of data within an array and across different arrays. Current methods typically require 24h and use target inefficiently. In these studies, we compare hybridization signals obtained in conventional static hybridization, which depends on diffusional target delivery, with signals obtained in a dynamic hybridization chamber, which employs a fluid mixer based on chaotic advection theory to deliver targets across a conventional glass slide array. Microarrays were printed with a pattern of 102 identical probe spots containing a 65-mer oligonucleotide capture probe. Hybridization of a 725-bp fluorescently labeled target was used to measure average target hybridization levels, local signal-to-noise ratios, and array hybridization uniformity. Dynamic hybridization for 1h with 1 or 10ng of target DNA increased hybridization signal intensities approximately threefold over a 24-h static hybridization. Similarly, a 10- or 60-min dynamic hybridization of 10ng of target DNA increased hybridization signal intensities fourfold over a 24h static hybridization. In time course studies, static hybridization reached a maximum within 8 to 12h using either 1 or 10ng of target. In time course studies using the dynamic hybridization chamber, hybridization using 1ng of target increased to a maximum at 4h and that using 10ng of target did not vary over the time points tested. In comparison to static hybridization, dynamic hybridization reduced the signal-to-noise ratios threefold and reduced spot-to-spot variation twofold. Therefore, we conclude that dynamic hybridization based on a chaotic mixer design improves both the speed of hybridization and the maximum level of hybridization while increasing signal-to-noise ratios and reducing spot-to-spot variation.

  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. Genetic regulation of vertebrate eye development.

    PubMed

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

    2014-11-01

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

  13. Functional eye movement disorders.

    PubMed

    Kaski, D; Bronstein, A M

    2017-01-01

    Functional (psychogenic) eye movement disorders are perhaps less established in the medical literature than other types of functional movement disorders. Patients may present with ocular symptoms (e.g., blurred vision or oscillopsia) or functional eye movements may be identified during the formal examination of the eyes in patients with other functional disorders. Convergence spasm is the most common functional eye movement disorder, but functional gaze limitation, functional eye oscillations (also termed "voluntary nystagmus"), and functional convergence paralysis may be underreported. This chapter reviews the different types of functional eye movement abnormalities and provides a practical framework for their diagnosis and management.

  14. 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.

  15. Eye Movements of Flatfish for Different Gravity Condition

    NASA Astrophysics Data System (ADS)

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

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

  16. Fixations to the eyes aids in facial encoding; covertly attending to the eyes does not.

    PubMed

    Laidlaw, Kaitlin E W; Kingstone, Alan

    2017-02-01

    When looking at images of faces, people will often focus their fixations on the eyes. It has previously been demonstrated that the eyes convey important information that may improve later facial recognition. Whether this advantage requires that the eyes be fixated, or merely attended to covertly (i.e. while looking elsewhere), is unclear from previous work. While attending to the eyes covertly without fixating them may be sufficient, the act of using overt attention to fixate the eyes may improve the processing of important details used for later recognition. In the present study, participants were shown a series of faces and, in Experiment 1, asked to attend to them normally while avoiding looking at either the eyes or, as a control, the mouth (overt attentional avoidance condition); or in Experiment 2 fixate the center of the face while covertly attending to either the eyes or the mouth (covert attention condition). After the first phase, participants were asked to perform an old/new face recognition task. We demonstrate that a) when fixations to the eyes are avoided during initial viewing then subsequent face discrimination suffers, and b) covert attention to the eyes alone is insufficient to improve face discrimination performance. Together, these findings demonstrate that fixating the eyes provides an encoding advantage that is not availed by covert attention alone.

  17. A note on oligonucleotide expression values not being normally distributed.

    PubMed

    Hardin, Johanna; Wilson, Jason

    2009-07-01

    Novel techniques for analyzing microarray data are constantly being developed. Though many of the methods contribute to biological discoveries, inability to properly evaluate the novel techniques limits their ability to advance science. Because the underlying distribution of microarray data is unknown, novel methods are typically tested against the assumed normal distribution. However, microarray data are not, in fact, normally distributed, and assuming so can have misleading consequences. Using an Affymetrix technical replicate spike-in data set, we show that oligonucleotide expression values are not normally distributed for any of the standard methods for calculating expression values. The resulting data tend to have a large proportion of skew and heavy tailed genes. Additionally, we show that standard methods can give unexpected and misleading results when the data are not well approximated by the normal distribution. Robust methods are therefore recommended when analyzing microarray data. Additionally, new techniques should be evaluated with skewed and/or heavy-tailed data distributions.

  18. ExpressYourself: a modular platform for processing and visualizing microarray data

    PubMed Central

    Luscombe, Nicholas M.; Royce, Thomas E.; Bertone, Paul; Echols, Nathaniel; Horak, Christine E.; Chang, Joseph T.; Snyder, Michael; Gerstein, Mark

    2003-01-01

    DNA microarrays are widely used in biological research; by analyzing differential hybridization on a single microarray slide, one can detect changes in mRNA expression levels, increases in DNA copy numbers and the location of transcription factor binding sites on a genomic scale. Having performed the experiments, the major challenge is to process large, noisy datasets in order to identify the specific array elements that are significantly differentially hybridized. This normally requires aggregating different, often incompatible programs into a multi-step pipeline. Here we present ExpressYourself, a fully integrated platform for processing microarray data. In completely automated fashion, it will correct the background array signal, normalize the Cy5 and Cy3 signals, score levels of differential hybridization, combine the results of replicate experiments, filter problematic regions of the array and assess the quality of individual and replicate experiments. ExpressYourself is designed with a highly modular architecture so various types of microarray analysis algorithms can readily be incorporated as they are developed; for example, the system currently implements several normalization methods, including those that simultaneously consider signal intensity and slide location. The processed data are presented using a web-based graphical interface to facilitate comparison with the original images of the array slides. In particular, Express Yourself is able to regenerate images of the original microarray after applying various steps of processing, which greatly facilities identification of position-specific artifacts. The program is freely available for use at http://bioinfo.mbb.yale.edu/expressyourself. PMID:12824348

  19. Eye movements of flatfish for the changes of gravity (II).

    PubMed

    Iwata, Kaori; Takabayashi, Akira; Miyachi, Ei-ichi

    2007-07-01

    In this study, we analysed the eye movements of flatfish for body tilting and compared with that of goldfish. 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 analysed frame by frame. In normal flatfish, vertical eye movement of left eye to leftward tilting was larger than that to rightward tilting. For head up or head down tilting, clear vertical eye movements were observed. On the other hand, torsional eye movements showed similar characteristics as goldfish. These results suggested that sacculus and lagena were important for otolith-ocular eye movements in flatfish.

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

    PubMed

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

    2013-01-01

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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. Cytogenetic investigation of cat-eye syndrome.

    PubMed

    Walknowska, J; Peakman, D; Weleber, R G

    1977-10-01

    Using multiple chromosomal banding techniques, we studied a child with typical cat-eye syndrome and ocular retraction syndrome. Although the mother was was chromosomally normal, other maternal relatives showed features of the cat-eye syndrome, suggesting the basic abnormality is heritable. The abnormal chromosome in our case was most likely the product of reciprocal translocation where short arm plus centromeric chromatin from two separate acrocentric chromosomes fused together. The chromosomes involved were probably No. 22 and either Nos. 13 or 14. The basic underlying defect in cat-eye syndrome may be a heritable fragile site or some other predisposition leading to complex chromosomal interchange.

  6. Ultrasonography of the eye and orbit.

    PubMed

    Dudea, Sorin M

    2011-06-01

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

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

    PubMed

    Jin, Meng; Mardon, Graeme

    2016-03-16

    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.

  8. Eye Injuries in Sports

    MedlinePlus

    ... eye protectors. Some very-high-risk sports are boxing, wrestling and contact martial arts.What are the ... eye problems or if you have a family history of retinal problems. If so, you should be ...

  9. Eye Injuries (For Parents)

    MedlinePlus

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

  10. What Is Dry Eye?

    MedlinePlus Videos and Cool Tools

    ... Kierstan Boyd Reviewed by: Brenda Pagan-Duran MD Mar. 01, 2017 Our eyes need tears to stay ... Ask an Ophthalmologist Answers Is stopping Restasis dangerous? Mar 06, 2017 Why are my eyes bloodshot when ...

  11. Diabetes and eye disease

    MedlinePlus

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

  12. Eye muscle repair

    MedlinePlus

    ... and physical exam before the procedure Orthoptic measurements (eye movement measurements) Always tell your child's health care provider: ... D, Plummer LS, Stass-Isern M. Disorders of eye movement and alignment. In: Kliegman RM, Stanton BF, St. ...

  13. Eye Drop Tips

    MedlinePlus

    ... Involved News About Us Donate In This Section Eye Drop Tips en Español email Send this article ... the reach of children. Steps For Putting In Eye Drops: Start by tilting your head backward while ...

  14. Down Syndrome: Eye Problems

    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 ...

  15. 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. ...

  16. Eye Safety at Home

    MedlinePlus

    ... Eye Emergencies How to Jump Start a Car Battery Safely Electronic Screens and Your Eyes Nutrition and ... External Resources The Cost of Vision Problems The Future of Vision Vision Problems in the U.S. Healthy ...

  17. Recommended Sports Eye Protectors

    MedlinePlus

    ... Eye Emergencies How to Jump Start a Car Battery Safely Electronic Screens and Your Eyes Nutrition and ... External Resources The Cost of Vision Problems The Future of Vision Vision Problems in the U.S. Healthy ...

  18. Eye Safety at Work

    MedlinePlus

    ... Eye Emergencies How to Jump Start a Car Battery Safely Electronic Screens and Your Eyes Nutrition and ... External Resources The Cost of Vision Problems The Future of Vision Vision Problems in the U.S. Healthy ...

  19. Bags Under Eyes

    MedlinePlus

    ... Home and lifestyle treatments may help reduce or eliminate puffy eyes. Medical and surgical treatments are available ... The following tips can help you reduce or eliminate bags under eyes: Use a cool compress. Wet ...

  20. Eyes, Bulging (Proptosis)

    MedlinePlus

    ... Article Medical Dictionary Also of Interest (Quiz) Allergic Conjunctivitis (Video) Overview of the Eyes (News) Stem Cells ... and covers the white of the eye. Allergic conjunctivitis is inflammation of the conjunctiva caused by an ...

  1. LASIK Eye Surgery

    MedlinePlus

    ... of your cornea, which could lead to inaccurate measurements and a poor surgical outcome. Your doctor will ... of your eye. Theoretically, the more detailed the measurements, the more accurate your eye doctor can be ...

  2. Diabetic Eye Disease

    MedlinePlus

    ... visit HHS USAJobs Home > Diabetic Eye Disease Healthy Vision Diabetes Diabetes Home How Much Do You Know? What You Should Know Protecting Against Vision Loss Staying on TRACK Diabetic Eye Disease FAQ ...

  3. 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.

  4. Infrared Eye: Prototype 2

    DTIC Science & Technology

    2016-06-07

    The Infrared (IR) Eye was developed with support from the National Search and Rescue Secretariat (NSS), in view of improving the efficiency of...airborne search-and rescue operations. The IR Eye concept is based on the human eye and uses simultaneously two fields of view to optimize area coverage and...within the wide field and slaved to the operator’s line of sight by means of an eye -tracking system. The images from both cameras are fused and shown

  5. Identification of candidate genes in osteoporosis by integrated microarray analysis

    PubMed Central

    Li, J. J.; Wang, B. Q.; Yang, Y.; Li, D.

    2016-01-01

    Objectives In order to screen the altered gene expression profile in peripheral blood mononuclear cells of patients with osteoporosis, we performed an integrated analysis of the online microarray studies of osteoporosis. Methods We searched the Gene Expression Omnibus (GEO) database for microarray studies of peripheral blood mononuclear cells in patients with osteoporosis. Subsequently, we integrated gene expression data sets from multiple microarray studies to obtain differentially expressed genes (DEGs) between patients with osteoporosis and normal controls. Gene function analysis was performed to uncover the functions of identified DEGs. Results A total of three microarray studies were selected for integrated analysis. In all, 1125 genes were found to be significantly differentially expressed between osteoporosis patients and normal controls, with 373 upregulated and 752 downregulated genes. Positive regulation of the cellular amino metabolic process (gene ontology (GO): 0033240, false discovery rate (FDR) = 1.00E + 00) was significantly enriched under the GO category for biological processes, while for molecular functions, flavin adenine dinucleotide binding (GO: 0050660, FDR = 3.66E-01) and androgen receptor binding (GO: 0050681, FDR = 6.35E-01) were significantly enriched. DEGs were enriched in many osteoporosis-related signalling pathways, including those of mitogen-activated protein kinase (MAPK) and calcium. Protein-protein interaction (PPI) network analysis showed that the significant hub proteins contained ubiquitin specific peptidase 9, X-linked (Degree = 99), ubiquitin specific peptidase 19 (Degree = 57) and ubiquitin conjugating enzyme E2 B (Degree = 57). Conclusion Analysis of gene function of identified differentially expressed genes may expand our understanding of fundamental mechanisms leading to osteoporosis. Moreover, significantly enriched pathways, such as MAPK and calcium, may involve in osteoporosis through osteoblastic differentiation and

  6. 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…

  7. Eye Movements and Learning.

    ERIC Educational Resources Information Center

    Nesbit, Larry L.

    Research on the use of eye movement indices (such as number of fixations, the average fixation duration, and saccadic movements) as a measure of cognitive processing is reviewed in this paper. Information is provided on the physiology of the eye, computer applications to eye movement study, the influence of stimulus materials and intelligence on…

  8. 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

  9. 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

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

    PubMed

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

    2014-10-31

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

  11. Mutational analysis using oligonucleotide microarrays

    PubMed Central

    Hacia, J.; Collins, F.

    1999-01-01

    The development of inexpensive high throughput methods to identify individual DNA sequence differences is important to the future growth of medical genetics. This has become increasingly apparent as epidemiologists, pathologists, and clinical geneticists focus more attention on the molecular basis of complex multifactorial diseases. Such undertakings will rely upon genetic maps based upon newly discovered, common, single nucleotide polymorphisms. Furthermore, candidate gene approaches used in identifying disease associated genes necessitate screening large sequence blocks for changes tracking with the disease state. Even after such genes are isolated, large scale mutational analyses will often be needed for risk assessment studies to define the likely medical consequences of carrying a mutated gene.
This review concentrates on the use of oligonucleotide arrays for hybridisation based comparative sequence analysis. Technological advances within the past decade have made it possible to apply this technology to many different aspects of medical genetics. These applications range from the detection and scoring of single nucleotide polymorphisms to mutational analysis of large genes. Although we discuss published scientific reports, unpublished work from the private sector12 could also significantly affect the future of this technology.


Keywords: mutational analysis; oligonucleotide microarrays; DNA chips PMID:10528850

  12. 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.

  13. Gaze aversion in autistic and normal children.

    PubMed

    Richer, J M; Coss, R G

    1976-03-01

    Autistic children rarely engage in eye contact, and whilst observation suggests this is due to a specific avoidance of eye contact, some experimental studies have challenged this. In this study the effects on autistic and normal children of an adult looking at them with both eyes, with one eye covered, or apparently not looking at them (both eyes covered) were investigated. As expected, autistic children looked more at the adult with his eyes covered, and also engaged in less flight behaviour. They looked less when two eyes were exposed than one, confirming the potency of the two-eye pattern in provoking gaze aversion. Normal children engaged in much more eye contact than the autistic children, with fewer flight behaviours and stereotypies, supporting the hypothesis that autistic children are predominatly flight motivated. Other, sometimes conflicting, results of previous studies are discussed. Teachers and nurses are recommened not to make efforts to engage autistic children even in friendly eye contact as this provokes more flight behaviour.

  14. 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.

  15. Protein Microarrays: Novel Developments and Applications

    PubMed Central

    Berrade, Luis; Garcia, Angie E.

    2011-01-01

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

  16. Training the Eyes for Competition: Fighting Eyes.

    ERIC Educational Resources Information Center

    Williams, Darrell; Bradford, Vincent

    1989-01-01

    Fencers should be taught to discipline their eyes to focus on the opponent's hand. The rationale for this strategy as well as drills to develop "hand watching" skills are presented in this article. (IAH)

  17. 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…

  18. PATMA: parser of archival tissue microarray.

    PubMed

    Roszkowiak, Lukasz; Lopez, Carlos

    2016-01-01

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

  19. PATMA: parser of archival tissue microarray

    PubMed Central

    2016-01-01

    Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images. PMID:27920955

  20. 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

  1. 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

  2. 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.

  3. 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

  4. Control and Functions of Fixational Eye Movements

    PubMed Central

    Rucci, Michele; Poletti, Martina

    2016-01-01

    Humans and other species explore a visual scene by rapidly shifting their gaze 2-3 times every second. Although the eyes may appear immobile in the brief intervals in between saccades, microscopic (fixational) eye movements are always present, even when attending to a single point. These movements occur during the very periods in which visual information is acquired and processed and their functions have long been debated. Recent technical advances in controlling retinal stimulation during normal oculomotor activity have shed new light on the visual contributions of fixational eye movements and their degree of control. The emerging body of evidence, reviewed in this article, indicates that fixational eye movements are important components of the strategy by which the visual system processes fine spatial details, enabling both precise positioning of the stimulus on the retina and encoding of spatial information into the joint space-time domain. PMID:27795997

  5. Computer-Assisted Eye Examination: Background and Prospects.

    DTIC Science & Technology

    1982-05-01

    potential resolution. Squares represent normal eyes; triangles represent those with some chronic pathological process such as glaucoma, macular a...of the major generic questions are: Are you troubled in any way with blurred vision? Hlave you headaches, eye pain or eye strain, or fatigue ? Do your...cannot resolve the pattern and thus does not contribute to the response. Furthermore, the central macular area is far more extensively represented in

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

    PubMed

    Schoenemann, Brigitte

    2013-01-14

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

  7. 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.

  8. Corneal thickness in dry eyes in an Iraqi population

    PubMed Central

    Ali, Noora Mauwafak; Hamied, Furkaan M; Farhood, Qasim K

    2017-01-01

    Background Dry eye disorder is a multifactorial disease of the tears and ocular surface that results in discomfort and visual disturbance. Corneal pachymetry becomes increasingly important in refractive surgery, for the accurate assessment of intraocular pressure, and in the preoperative assessment of other ocular surgeries. Purpose To assess the effect of dry eye disorder on the central corneal thickness (CCT) by comparing with CCT of normal eyes of age-matched individuals. Patients and methods The total number of eyes examined was 280 (140 dry eyes from 70 patients and 140 normal eyes from 70 individuals). Pentacam (Scheimpflug imaging system) was used for measuring the CCT of all eyes. Results Patients with dry eye syndrome had significantly lower CCT compared to the control group (P<0.01). Its mean was 536.5 versus 561.3, respectively. Conclusion CCT of dry eyes was significantly reduced when compared with age- and gender-matched population. This result can be attributed to chronic desiccation by the inflammatory mediators in dry eyes, leading to corneal thinning. PMID:28260857

  9. Validation of affinity reagents using antigen microarrays.

    PubMed

    Sjöberg, Ronald; Sundberg, Mårten; Gundberg, Anna; Sivertsson, Asa; Schwenk, Jochen M; Uhlén, Mathias; Nilsson, Peter

    2012-06-15

    There is a need for standardised validation of affinity reagents to determine their binding selectivity and specificity. This is of particular importance for systematic efforts that aim to cover the human proteome with different types of binding reagents. One such international program is the SH2-consortium, which was formed to generate a complete set of renewable affinity reagents to the SH2-domain containing human proteins. Here, we describe a microarray strategy to validate various affinity reagents, such as recombinant single-chain antibodies, mouse monoclonal antibodies and antigen-purified polyclonal antibodies using a highly multiplexed approach. An SH2-specific antigen microarray was designed and generated, containing more than 6000 spots displayed by 14 identical subarrays each with 406 antigens, where 105 of them represented SH2-domain containing proteins. Approximately 400 different affinity reagents of various types were analysed on these antigen microarrays carrying antigens of different types. The microarrays revealed not only very detailed specificity profiles for all the binders, but also showed that overlapping target sequences of spotted antigens were detected by off-target interactions. The presented study illustrates the feasibility of using antigen microarrays for integrative, high-throughput validation of various types of binders and antigens.

  10. 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.

  11. 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…

  12. A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets

    PubMed Central

    Izadi, Fereshteh; Zarrini, Hamid Najafi; Kiani, Ghaffar; Jelodar, Nadali Babaeian

    2016-01-01

    A Gene Regulatory Network (GRN) is a collection of interactions between molecular regulators and their targets in cells governing gene expression level. Omics data explosion generated from high-throughput genomic assays such as microarray and RNA-Seq technologies and the emergence of a number of pre-processing methods demands suitable guidelines to determine the impact of transcript data platforms and normalization procedures on describing associations in GRNs. In this study exploiting publically available microarray and RNA-Seq datasets and a gold standard of transcriptional interactions in Arabidopsis, we performed a comparison between six GRNs derived by RNA-Seq and microarray data and different normalization procedures. As a result we observed that compared algorithms were highly data-specific and Networks reconstructed by RNA-Seq data revealed a considerable accuracy against corresponding networks captured by microarrays. Topological analysis showed that GRNs inferred from two platforms were similar in several of topological features although we observed more connectivity in RNA-Seq derived genes network. Taken together transcriptional regulatory networks obtained by Robust Multiarray Averaging (RMA) and Variance-Stabilizing Transformed (VST) normalized data demonstrated predicting higher rate of true edges over the rest of methods used in this comparison. PMID:28293077

  13. 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

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

    PubMed

    Chakraborty, Debasis; Maulik, Ujjwal

    2014-01-01

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

  15. Posttranslational Modification Assays on Functional Protein Microarrays.

    PubMed

    Neiswinger, Johnathan; Uzoma, Ijeoma; Cox, Eric; Rho, HeeSool; Jeong, Jun Seop; Zhu, Heng

    2016-10-03

    Protein microarray technology provides a straightforward yet powerful strategy for identifying substrates of posttranslational modifications (PTMs) and studying the specificity of the enzymes that catalyze these reactions. Protein microarray assays can be designed for individual enzymes or a mixture to establish connections between enzymes and substrates. Assays for four well-known PTMs-phosphorylation, acetylation, ubiquitylation, and SUMOylation-have been developed and are described here for use on functional protein microarrays. Phosphorylation and acetylation require a single enzyme and are easily adapted for use on an array. The ubiquitylation and SUMOylation cascades are very similar, and the combination of the E1, E2, and E3 enzymes plus ubiquitin or SUMO protein and ATP is sufficient for in vitro modification of many substrates.

  16. Eye proprioception may provide real time eye position information.

    PubMed

    Wang, Jing; Pan, Yujun

    2013-03-01

    Because of the frequency of eye movements, online knowledge of eye position is crucial for the accurate spatial perception and behavioral navigation. Both the internal monitoring signal (corollary discharge) of eye movements and the eye proprioception signal are thought to contribute to the localization of the eye position in the orbit. However, the functional role of these two eye position signals in spatial cognition has been disputed for more than a century. The predominant view proposes that the online analysis of eye position is exclusively provided by the corollary discharge signal, while the eye proprioception signal only plays a role in the long-term calibration of the oculomotor system. However, increasing evidence from recent behavioral and physiological studies suggests that the eye proprioception signal may play a role in the online monitoring of eye position. The purpose of this review is to discuss the feasibility and possible function of the eye proprioceptive signal for online monitoring of eye position.

  17. Etiological yield of SNP microarrays in idiopathic intellectual disability.

    PubMed

    Utine, G Eda; Haliloğlu, Göknur; Volkan-Salancı, Bilge; Çetinkaya, Arda; Kiper, Pelin Ö; Alanay, Yasemin; Aktaş, Dilek; Anlar, Banu; Topçu, Meral; Boduroğlu, Koray; Alikaşifoğlu, Mehmet

    2014-05-01

    Intellectual disability (ID) has a prevalence of 3% and is classified according to its severity. An underlying etiology cannot be determined in 75-80% in mild ID, and in 20-50% of severe ID. After it has been shown that copy number variations involving short DNA segments may cause ID, genome-wide SNP microarrays are being used as a tool for detecting submicroscopic copy number changes and uniparental disomy. This study was performed to investigate the presence of copy number changes in patients with ID of unidentified etiology. Affymetrix(®) 6.0 SNP microarray platform was used for analysis of 100 patients and their healthy parents, and data were evaluated using various databases and literature. Etiological diagnoses were made in 12 patients (12%). Homozygous deletion in NRXN1 gene and duplication in IL1RAPL1 gene were detected for the first time. Two separate patients had deletions in FOXP2 and UBE2A genes, respectively, for which only few patients have recently been reported. Interstitial and subtelomeric copy number changes were described in 6 patients, in whom routine cytogenetic tools revealed normal results. In one patient uniparental disomy type of Angelman syndrome was diagnosed. SNP microarrays constitute a screening test able to detect very small genomic changes, with a high etiological yield even in patients already evaluated using traditional cytogenetic tools, offer analysis for uniparental disomy and homozygosity, and thereby are helpful in finding novel disease-causing genes: for these reasons they should be considered as a first-tier genetic screening test in the evaluation of patients with ID and autism.

  18. 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.

  19. 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

  20. 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…

  1. Common Eye Disorders

    MedlinePlus

    ... eye,” is the most common cause of vision impairment in children. Amblyopia is the medical term used ... the most common cause of permanent one-eye vision impairment among children and young and middle-aged adults. ...

  2. Why Do Eyes Water?

    MedlinePlus

    ... A Movies & More Quizzes Kids' Dictionary of Medical Words En Español What Other Kids Are Reading Taking Care of Your Ears Taking Care of Your Skin Taking Care of Your Teeth El cuidado de los dientes Video: Getting an X-ray Why Do Eyes Water? KidsHealth > For Kids > Why Do Eyes Water? Print ...

  3. 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…

  4. 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...

  5. Enhancing interdisciplinary mathematics and biology education: a microarray data analysis course bridging these disciplines.

    PubMed

    Tra, Yolande V; 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.

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

    PubMed Central

    Evans, Irene M.

    2010-01-01

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

  7. Profiling of differentially expressed genes in human gingival epithelial cells and fibroblasts by DNA microarray.

    PubMed

    Abiko, Yoshimitsu; Hiratsuka, Koichi; Kiyama-Kishikawa, Michiko; Tsushima, Katsumasa; Ohta, Mitsuhiro; Sasahara, Hiroshige

    2004-03-01

    Gingival epithelial cells and fibroblasts play important roles and have a harmonious relationship under normal and disease conditions, but the precise differences between theses cells remain unknown. To study the differences in gene expression between human gingival epithelial cells (HGE) and human gingival fibroblasts (HGF), mRNA was recovered from primary cultured cells and analyzed using cDNA microarray technology. The cDNA retro-transcribed from equal quantities of mRNA was labeled with the fluorescent dyes Cy5 and Cy3. The mixed probes were then hybridized with 7276 genes on the DNA microarray, after which fluorescence signals were scanned and further analyzed using GeneSpring software. Of the 7276 genes screened, 469 showed expression levels that were more than 2-fold greater in HGE than in HGF, while 293 showed expression levels that were more than 2-fold greater in HGF than in HGE. To confirm the reliability of the microarray results, keratin K5 and desmocolin, and vimentin and gp130, which showed higher mRNA levels in HGE and HGF, respectively, were selected and their mRNA levels were further analyzed by RT-PCR. The results of RT-PCR correlated well with those of microarray analysis. The present findings using a DNA microarray to detect differences in the gene expression profiles of HGE and HGF may be beneficial for genetic diagnosis of periodontal tissue metabolism and periodontal diseases.

  8. 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.

  9. Analysis of High-Throughput ELISA Microarray Data

    SciTech Connect

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

    2011-02-23

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

  10. 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

  11. 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.

  12. Are 3-D Movies Bad for Your Eyes?

    MedlinePlus

    ... the viewer has a problem with focusing or depth perception. Also, the techniques used to create the 3- ... eyes), or other conditions that persistently inhibit focusing, depth perception or normal 3-D vision, would have difficulty ...

  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. [Dynamic posturography in normal subjects].

    PubMed

    Salami, A; Guglielmetti, G; Bindi, G F; Dellepiane, M

    1990-01-01

    The relative lack of data on the dynamic posturography led us to start a study in order to give our contributions to the standardization of M1, M2, M3, response parameters in normal subjects. Our research was carried out on 35 normal subjects aged 21 to 50. All of them were standing in Romberg's position on a Tönnies model board in a normally lit and ventilated room. We performed two tests: the first one open-eyed staring at no point, the second, 5 minutes later, closed-eyed. The EMG signals were obtained by surface electrodes on triceps sural and front tibial muscles. The EMG recording was determined by a "tilt" movement of the board at a steady speed of 50 per sec. and 4 wide. We use a XT 286 IBM computer with "T POST" software for checking and testing the data. Our results showed a significant variation in the value of the duration parameter in open-eyed and closed-eyed tests. Latency and area values were inferior to those obtained by other authors, except for Diener and Dichgans (3) whose results differ in latency value only.

  15. Recognizing and Treating Eye Injuries

    MedlinePlus

    ... Eye Injuries Reviewed by: Brenda Pagan-Duran MD Mar. 01, 2016 When an eye injury does occur, ... Fireworks Eye Safety Jun 10, 2016 Protective Eyewear Mar 01, 2016 Scleritis Symptoms Mar 01, 2015 What ...

  16. 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 ...

  17. Mycoplasma and associated bacteria isolated from ovine pink-eye.

    PubMed

    Langford, E V

    1971-01-01

    A mycoplasma was recovered from the untreated conjunctival membranes of nine sheep affected by Pink-eye. It was neither isolated from the conjunctiva of treated animals which were affected nor from the conjunctiva of normal animals either in contact or not in contact with affected animals. Bacteria found on normal conjunctival membranes were Neisseria ovis, Escherichia coli, Staphylococcus epidermididis, Streptococcus and Bacillus spp. Bacteria found in clinical cases of Pink-eye were N. ovis, E. coli, a Streptococcus and Pseudomonas spp.

  18. 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

  19. Eye development in the Cape dune mole rat.

    PubMed

    Nikitina, Natalya V; Kidson, Susan H

    2014-03-01

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

  20. Cyanoacrylate Adhesives in Eye Wounds.

    DTIC Science & Technology

    EYE, *WOUNDS AND INJURIES), (*ADHESIVES, EYE), (*ACRYLIC RESINS, ADHESIVES), CORNEA , HEALING, TISSUES(BIOLOGY), TOLERANCES(PHYSIOLOGY), NECROSIS, SURGICAL SUPPLIES, STRENGTH(PHYSIOLOGY), SURGERY, THERAPY

  1. Advocacy for eye care.

    PubMed

    Ravilla, Thulasiraj D; Ramasamy, Dhivya

    2012-01-01

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

  2. 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...

  3. 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.

  4. Analytical Protein Microarrays: Advancements Towards Clinical Applications

    PubMed Central

    Sauer, Ursula

    2017-01-01

    Protein microarrays represent a powerful technology with the potential to serve as tools for the detection of a broad range of analytes in numerous applications such as diagnostics, drug development, food safety, and environmental monitoring. Key features of analytical protein microarrays include high throughput and relatively low costs due to minimal reagent consumption, multiplexing, fast kinetics and hence measurements, and the possibility of functional integration. So far, especially fundamental studies in molecular and cell biology have been conducted using protein microarrays, while the potential for clinical, notably point-of-care applications is not yet fully utilized. The question arises what features have to be implemented and what improvements have to be made in order to fully exploit the technology. In the past we have identified various obstacles that have to be overcome in order to promote protein microarray technology in the diagnostic field. Issues that need significant improvement to make the technology more attractive for the diagnostic market are for instance: too low sensitivity and deficiency in reproducibility, inadequate analysis time, lack of high-quality antibodies and validated reagents, lack of automation and portable instruments, and cost of instruments necessary for chip production and read-out. The scope of the paper at hand is to review approaches to solve these problems. PMID:28146048

  5. Analytical Protein Microarrays: Advancements Towards Clinical Applications.

    PubMed

    Sauer, Ursula

    2017-01-29

    Protein microarrays represent a powerful technology with the potential to serve as tools for the detection of a broad range of analytes in numerous applications such as diagnostics, drug development, food safety, and environmental monitoring. Key features of analytical protein microarrays include high throughput and relatively low costs due to minimal reagent consumption, multiplexing, fast kinetics and hence measurements, and the possibility of functional integration. So far, especially fundamental studies in molecular and cell biology have been conducted using protein microarrays, while the potential for clinical, notably point-of-care applications is not yet fully utilized. The question arises what features have to be implemented and what improvements have to be made in order to fully exploit the technology. In the past we have identified various obstacles that have to be overcome in order to promote protein microarray technology in the diagnostic field. Issues that need significant improvement to make the technology more attractive for the diagnostic market are for instance: too low sensitivity and deficiency in reproducibility, inadequate analysis time, lack of high-quality antibodies and validated reagents, lack of automation and portable instruments, and cost of instruments necessary for chip production and read-out. The scope of the paper at hand is to review approaches to solve these problems.

  6. Microarrays (DNA Chips) for the Classroom Laboratory

    ERIC Educational Resources Information Center

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

    2006-01-01

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

  7. 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.

  8. 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...

  9. 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.

  10. A Method of Microarray Data Storage Using Array Data Type

    PubMed Central

    Tsoi, Lam C.; Zheng, W. Jim

    2009-01-01

    A well-designed microarray database can provide valuable information on gene expression levels. However, designing an efficient microarray database with minimum space usage is not an easy task since designers need to integrate the microarray data with the information of genes, probe annotation, and the descriptions of each microarray experiment. Developing better methods to store microarray data can greatly improve the efficiency and usefulness of such data. A new schema is proposed to store microarray data by using array data type in an object-relational database management system – PostgreSQL. The implemented database can store all the microarray data from the same chip in an array data structure. The variable length array data type in PostgreSQL can store microarray data from same chip. The implementation of our schema can help to increase the data retrieval and space efficiency. PMID:17392028

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

    EPA Science Inventory

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

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

    PubMed

    Guzzi, Pietro Hiram; Cannataro, Mario

    2013-08-01

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

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

    PubMed

    Chen, Bor-Sen; Li, Cheng-Wei

    2015-01-01

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

  14. 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

  15. 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.

  16. Personal identification by eyes.

    PubMed

    Marinović, Dunja; Njirić, Sanja; Coklo, Miran; Muzić, Vedrana

    2011-09-01

    Identification of persons through the eyes is in the field of biometrical science. Many security systems are based on biometric methods of personal identification, to determine whether a person is presenting itself truly. The human eye contains an extremely large number of individual characteristics that make it particularly suitable for the process of identifying a person. Today, the eye is considered to be one of the most reliable body parts for human identification. Systems using iris recognition are among the most secure biometric systems.

  17. An eye movement technique for correlating fixational target eye movements with location on the retinal image.

    PubMed

    Barrett, S F; Zwick, H

    2000-01-01

    Recent investigation demonstrate that ocular motility in eyes with retinal pathology may show a lower propensity to visit such areas of the retina as compared to non-pathological retinal sites. While current ophthalmic instruments with the ability to image both the retina and visual function test target placement on the retina have provided this observation, the ability to quantify in real time these images as an eye movement measurement is presently lacking and the objective of this paper. A Rodenstock confocal scanning ophthalmoscope (CSLO) was used to image the retina during the performance of a visual fixation task. Direct observation of acuity target placement at the retina under continuous viewing conditions was possible with this apparatus. Target fixation eye movement images of the retina were rapidly digitized from video tape records and registered using a specialized rapid retinal image tracking algorithm. Fixational eye movement pattern densities at the retina were derived from these data. Preliminary data obtained demonstrate the utility of this technique in quantifying fixation eye movement patterns observed in three human patients with vocation-related laser retinal injury. In all patients, areas of severe retinal damage was generally avoided. The density of ocular eye movement tends to reflect regions of retinal normality and avoidance of retinal regions with severe pathology. Variation in eye movement density may exist where pathology is less severe.

  18. 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

  19. Choroidal thickness evaluation of healthy eyes, central serous chorioretinopathy, and fellow eyes using spectral domain optical coherence tomography in Indian population

    PubMed Central

    Arora, Supriya; Pyare, Richa; Sridharan, Preethi; Arora, Tarun; Thakar, Meenakshi; Ghosh, Basudeb

    2016-01-01

    Aim: The purpose of this study is to establish a normative database of subfoveal choroidal thickness (CT) in healthy young Indians using spectral domain optical coherence tomography (SD OCT). Evaluation and comparison of CT of central serous chorioretinopathy (CSC) and fellow eyes were also performed. Materials and Methods: This was a prospective, cross-sectional, and observational study. It included 112 normal eyes of 112 healthy volunteers who had no evidence of ocular or systemic disease, 84 CSC eyes with acute, treatment-naïve CSC, and 69 fellow eyes with no evidence of neurosensory detachment or pigment epithelium detachment on SD OCT. Complete history, examination, and SD OCT were performed in all eyes. Results: The mean age of 81 patients (84 eyes) with CSC was 35.04 ± 8.86 years, 69 fellow eyes was 34.61 ± 8.71 years, and 112 healthy volunteers (112 eyes) was 33.16 ± 9.4 years (P < 0.05). The mean subfoveal CT of CSC eyes was 429 ± 74.18 μ, fellow eyes was 360 ± 57.99 μ, and normal eyes was 301.80 ± 46.59 μ (P < 0.001). Conclusion: CT varies not only with age, axial length, and refractive error but also with races. Therefore, it is important to establish a normative database in a particular population before carrying out further research in diseased states. CT in CSC eyes is significantly thicker than fellow eyes, and CT of fellow eyes is significantly thicker than normal eyes. This reinforces the fact that choroidal permeability is increased in both eyes of patients with CSC. PMID:27905337

  20. 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

  1. LASIK eye surgery

    MedlinePlus

    Laser-Assisted In Situ Keratomileusis; Laser vision correction; Nearsightedness - Lasik; Myopia - Lasik ... length of the eye. LASIK uses an excimer laser (an ultraviolet laser) to remove a thin layer ...

  2. Anatomy of the Eye

    MedlinePlus

    ... the eye. It is disc shaped with a hole in the middle (the pupil). Muscles in the ... of photoreceptors are rods and cones. Rods perceive black and white and serve night vision primarily. Cones ...

  3. Eye Injuries (For Parents)

    MedlinePlus

    ... if the foreign body has been flushed out. Seek Medical Care If Your Child Has: been struck ... eyelid an eye that's very sensitive to light Seek Emergency Care Immediately If Your Child Has: trouble ...

  4. What Is Eye Cancer?

    MedlinePlus

    ... of cancers, see our documents on them. Intraocular melanoma (melanoma of the eye) Intraocular melanoma is the most ... the rest of this document focuses on intraocular melanomas and lymphomas. Written by References The American Cancer ...

  5. Laser photocoagulation - eye

    MedlinePlus

    ... the retina that provides sharp central vision (macular edema) This surgery also treats the following eye problems: ... in time. If your treatment was for macular edema, your vision may seem worse for a few ...

  6. Multimodal eye recognition

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

  7. 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 ...

  8. Amblyopia: Lazy Eye Symptoms

    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 ...

  9. Using Eye Makeup

    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 ...

  10. Amblyopia: Lazy Eye Diagnosis

    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 ...

  11. Smoking and Eye Health

    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 ...

  12. LASIK - Laser Eye Surgery

    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 ...

  13. Amblyopia: Lazy Eye Treatment

    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 ...

  14. Melanoma of the eye

    MedlinePlus

    Small melanomas may be treated with: Surgery Laser Radiation therapy (such as Gamma Knife , CyberKnife , brachytherapy) Surgery to remove the eye (enucleation) may be needed. Other treatments that may be used ...

  15. Facts About Pink Eye

    MedlinePlus

    ... Courier services use: Rockville, MD 20852) 301-451-2020 Research at NEI Office of the Scientific Director ... Eye Disease Education Program Glaucoma Education Program Low Vision Education Program Hispanic/Latino Program Vision and Aging ...

  16. Diagram of the Eye

    MedlinePlus

    ... Courier services use: Rockville, MD 20852) 301-451-2020 Research at NEI Office of the Scientific Director ... Eye Disease Education Program Glaucoma Education Program Low Vision Education Program Hispanic/Latino Program Vision and Aging ...

  17. Eye Disease Simulations

    MedlinePlus

    ... Courier services use: Rockville, MD 20852) 301-451-2020 Research at NEI Office of the Scientific Director ... Eye Disease Education Program Glaucoma Education Program Low Vision Education Program Hispanic/Latino Program Vision and Aging ...

  18. Eye Injuries (For Parents)

    MedlinePlus

    ... the eyelid. Others, like those that happen during sports activities, can be serious and require medical attention. Signs and Symptoms redness stinging or burning watering sensitivity to light blurred vision swelling of the eyelids discoloration around the eye ...

  19. Eye pigments in wild-type and eye-color mutant strains of the African malaria vector Anopheles gambiae.

    PubMed

    Beard, C B; Benedict, M Q; Primus, J P; Finnerty, V; Collins, F H

    1995-01-01

    Chromatographic analysis of pigments extracted from wild-type eyes of the mosquito Anopheles gambiae reveals the presence of the ommatin precursor 3-hydroxykynurenine, its transamination derivative xanthurenic acid, and a dark, red-brown pigment spot that probably is composed of two or more low mobility xanthommatins. No colored or fluorescent pteridines are evident. Mosquitoes homozygous for an autosomal recessive mutation at the red-eye (r) locus have a brick-red eye color in larvae, pupae, and young adults, in contrast to the almost black color of the wild eye. Mosquitoes homozygous for this mutant allele have levels of ommochrome precursors that are indistinguishable from the wild-type, but the low-mobility xanthommatin spot is ochre-brown in color rather than red-brown as in the wild-type. Mosquitoes with two different mutant alleles at the X-linked pink-eye locus (p, which confers a pink eye color, and pw, which confers a white eye phenotype in homozygotes or hemizygous males) have normal levels of ommochrome precursors but no detectable xanthommatins. Mosquitoes homozygous for both the r and p mutant alleles have apricot-colored eyes and show no detectable xanthommatins. Both the pink-eye and red-eye mutations appear to involve defects in the transport into or assembly of pigments in the membrane-bound pigment granules rather then defects in ommochrome synthesis.

  20. Corneal temperature in patients with dry eye evaluated by infrared radiation thermometry.

    PubMed Central

    Fujishima, H; Toda, I; Yamada, M; Sato, N; Tsubota, K

    1996-01-01

    AIMS: The corneal temperature change following each blink was investigated in patients with dry eye using an infrared radiation thermometer. METHODS: Twenty patients with dry eye and 20 normal controls were enrolled in this study. Subjects kept their eyes open for 10 seconds without blinking and corneal temperature was measured every second with a recently improved infrared radiation thermometer. RESULTS: In the 20 patients with dry eye, corneal temperature change after keeping the eye open for 10 seconds was 0.21 (SD 0.06) degree C while it was 0.61 (0.28) degree C in the 20 normal patients (p = 0.0001). In an exponential equation, the inclination of the slope of a patient with dry eye was smaller than the normal. The correlation coefficient was r = 0.79 (0.16) in patients with dry eye and r = 0.90 (0.07) in normal patients. The mean K value of patients with dry eye was 0.20 (0.13)/second and that of normal subjects was 0.31 (0.19)/second (p = 0.03). CONCLUSION: Findings demonstrate the usefulness of this thermometer for measuring corneal temperature in the evaluation of dry eye. Decrease in corneal temperature with each blink in patients with dry eye was smaller than in normal subjects. Images PMID:8664227

  1. Modern sports eye injuries

    PubMed Central

    Capão Filipe, J A; Rocha-Sousa, A; Falcão-Reis, F; Castro-Correia, J

    2003-01-01

    Aims: To determine the severity and long term sequelae of eye injuries caused by modern sports that could be responsible for significant ocular trauma in the future. Methods: Prospective observational study of 24 (25 eyes) athletes with sports related ocular injuries from health clubs, war games, adventure, radical and new types of soccer, presenting to an eye emergency department between 1992 and 2002 (10 years). Results: Modern sports were responsible for 8.3% of the 288 total sports eye injuries reported. Squash (29.2%) was the most common cause, followed by paintball (20.8%) and motocross (16.6%). The most common diagnosis during the follow up period was retinal breaks (20%). 18 (75%) patients sustained a severe injury. The final visual acuity remained <20/100 in two paintball players. Conclusions: Ocular injuries resulting from modern sports are often severe. Adequate instruction of the participants in the games, proper use of eye protectors, and a routine complete ophthalmological examination after an eye trauma should be mandatory. PMID:14609827

  2. 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

  3. 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…

  4. Integrated analysis of microarray data and gene function information.

    PubMed

    Cui, Yan; Zhou, Mi; Wong, Wing Hung

    2004-01-01

    Microarray data should be interpreted in the context of existing biological knowledge. Here we present integrated analysis of microarray data and gene function classification data using homogeneity analysis. Homogeneity analysis is a graphical multivariate statistical method for analyzing categorical data. It converts categorical data into graphical display. By simultaneously quantifying the microarray-derived gene groups and gene function categories, it captures the complex relations between biological information derived from microarray data and the existing knowledge about the gene function. Thus, homogeneity analysis provides a mathematical framework for integrating the analysis of microarray data and the existing biological knowledge.

  5. 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

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

    PubMed

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

    2015-01-01

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

  7. Development of an oligonucleotide-based DNA microarray for transcriptional analysis of Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) genes.

    PubMed

    Yang, Dan-Hui; Barari, Mehrnoosh; Arif, Basil M; Krell, Peter J

    2007-08-01

    A modified oligonucleotide-based two-channel DNA microarray was developed for characterization of temporal expression profiles of select Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) ORFs including its 7 unique ORFs. The microarray chip contained oligonucleotide probes for 23 CfMNPV ORFs and their complements as well as five host genes. Total RNA was isolated at different times post infection from Cf203 insect cells infected with CfMNPV. The cDNA was synthesized, fluorescent labelled with Cy3, and co-hybridized to the microarray chips along with Cy5-labelled viral genomic DNA, which served as equimolar reference standards for each probe. Transcription of the 7 CfMNPV unique ORFs was detected using DNA microarray analysis and their temporal expression profiles suggest that they are functional genes. The expression levels of three host genes varied throughout virus infection and therefore were unsuitable for normalization between microarrays. The DNA microarray results were compared to quantitative RT-PCR (qRT-PCR). Transcription of the non-coding (antisense) strands of some of the CfMNPV select genes including the polyhedrin gene, was also detected by array analysis and confirmed by qRT-PCR. The polyhedrin antisense transcript, based on long-range RT-PCR analysis, appeared to be a read-through product of an adjacent ORF in the same orientation as the antisense transcript.

  8. Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

    PubMed Central

    Ranjbar, Reza; Behzadi, Payam; Mammina, Caterina

    2016-01-01

    Background: Francisella tularensis (F. tularensis) is the etiological microorganism for tularemia. There are different forms of tularemia such as respiratory tularemia. Respiratory tularemia is the most severe form of tularemia with a high rate of mortality; if not treated. Therefore, traditional microbiological tools and Polymerase Chain Reaction (PCR) are not useful for a rapid, reliable, accurate, sensitive and specific diagnosis. But, DNA microarray technology does. DNA microarray technology needs to appropriate microarray probe designing. Objective: The main goal of this original article was to design suitable long oligo microarray probes for detection and identification of F. tularensis. Method: For performing this research, the complete genomes of F. tularensis subsp. tularensis FSC198, F. tularensis subsp. holarctica LVS, F. tularensis subsp. mediasiatica, F. tularensis subsp. novicida (F. novicida U112), and F. philomiragia subsp. philomiragia ATCC 25017 were studied via NCBI BLAST tool, GView and PanSeq Servers and finally the microarray probes were produced and processed via AlleleID 7.7 software and Oligoanalyzer tool, respectively. Results: In this in silico investigation, a number of long oligo microarray probes were designed for detecting and identifying F. tularensis. Among these probes, 15 probes were recognized as the best candidates for microarray chip designing. Conclusion: Calibrated microarray probes reduce the biasis of DNA microarray technology as an advanced, rapid, accurate and cost-effective molecular diagnostic tool with high specificity and sensitivity. Professional microarray probe designing provides us with much more facility and flexibility regarding preparation of a microarray diagnostic chip. PMID:28077973

  9. Detecting outlier samples in microarray data.

    PubMed

    Shieh, Albert D; Hung, Yeung Sam

    2009-01-01

    In this paper, we address the problem of detecting outlier samples with highly different expression patterns in microarray data. Although outliers are not common, they appear even in widely used benchmark data sets and can negatively affect microarray data analysis. It is important to identify outliers in order to explore underlying experimental or biological problems and remove erroneous data. We propose an outlier detection method based on principal component analysis (PCA) and robust estimation of Mahalanobis distances that is fully automatic. We demonstrate that our outlier detection method identifies biologically significant outliers with high accuracy and that outlier removal improves the prediction accuracy of classifiers. Our outlier detection method is closely related to existing robust PCA methods, so we compare our outlier detection method to a prominent robust PCA method.

  10. Molecular diagnosis and prognosis with DNA microarrays.

    PubMed

    Wiltgen, Marco; Tilz, Gernot P

    2011-05-01

    Microarray analysis makes it possible to determine thousands of gene expression values simultaneously. Changes in gene expression, as a response to diseases, can be detected allowing a better understanding and differentiation of diseases at a molecular level. By comparing different kinds of tissue, for example healthy tissue and cancer tissue, the microarray analysis indicates induced gene activity, repressed gene activity or when there is no change in the gene activity level. Fundamental patterns in gene expression are extracted by several clustering and machine learning algorithms. Certain kinds of cancer can be divided into subtypes, with different clinical outcomes, by their specific gene expression patterns. This enables a better diagnosis and tailoring of individual patient treatments.

  11. 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.

  12. 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

  13. Eye Motility Alterations in Retinitis Pigmentosa.

    PubMed

    Migliorini, Raffaele; Comberiati, Anna Maria; Galeoto, Giovanni; Fratipietro, Manuela; Arrico, Loredana

    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.

  14. Vergence Eye Movements in Patients with Schizophrenia

    PubMed Central

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

    2014-01-01

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

  15. Ultrahigh density microarrays of solid samples.

    PubMed

    LeBaron, Matthew J; Crismon, Heidi R; Utama, Fransiscus E; Neilson, Lynn M; Sultan, Ahmed S; Johnson, Kevin J; Andersson, Eva C; Rui, Hallgeir

    2005-07-01

    We present a sectioning and bonding technology to make ultrahigh density microarrays of solid samples, cutting edge matrix assembly (CEMA). Maximized array density is achieved by a scaffold-free, self-supporting construction with rectangular array features that are incrementally scalable. This platform technology facilitates arrays of >10,000 tissue features on a standard glass slide, inclusion of unique sample identifiers for improved manual or automated tracking, and oriented arraying of stratified or polarized samples.

  16. Metadata management and semantics in microarray repositories.

    PubMed

    Kocabaş, F; Can, T; Baykal, N

    2011-12-01

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

  17. Methods for fabricating microarrays of motile bacteria.

    PubMed

    Rozhok, Sergey; Shen, Clifton K-F; Littler, Pey-Lih H; Fan, Zhifang; Liu, Chang; Mirkin, Chad A; Holz, Richard C

    2005-04-01

    Motile bacterial cell microarrays were fabricated by attaching Escherichia coli K-12 cells onto predesigned 16-mercaptohexadecanoic acid patterned microarrays, which were covalently functionalized with E. coli antibodies or poly-L-lysine. By utilizing 11-mercaptoundecyl-penta(ethylene glycol) or 11-mercapto-1-undecanol as passivating molecules, nonspecific binding of E. coli was significantly reduced. Microcontact printing and dip-pen nanolithography were used to prepare microarrays for bacterial adhesion, which was studied by optical fluorescence and atomic force microscopy. These data indicate that single motile E. coli can be attached to predesigned line or dot features and binding can occur via the cell body or the flagella of bacteria. Adherent bacteria are viable (remain alive and motile after adhesion to patterned surface features) for more than four hours. Individual motile bacterial cells can be placed onto predesigned surface features that are at least 1.3 microm in diameter or larger. The importance of controlling the adhesion of single bacterial cell to a surface is discussed with regard to biomotor design.

  18. 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.

  19. 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

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

    PubMed

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

    2015-07-27

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

  1. Laser eye protection

    NASA Astrophysics Data System (ADS)

    Allen, Ralph G.; Labo, Jack A.; Mayo, Michael W.

    1990-07-01

    Laser applications have proliferated in recent years and as to be expected their presence is no longer confined to the laboratory or places where access to their radiation can be easily controlled. One obvious application where this is so is in military operations where various devices such as laser range finders target designators and secure communications equipment elevate the risk of exposure specifically eye exposure to unacceptable levels. Although the need for eye protection in the laboratory and other controlled areas has been appreciated since the invention of the laser the use of lasers in circumstances where safety or the risk of temporary loss of vision which can not always be ensured by administrative procedures has made adequate eye protection essential. It is the critical nature of many military operations that has driven the search for eye protection against both nuclear and laser radiation. At the same time the requirement to maintain useful vision during irradiation as well as advances in laser technology have complicated the problem enormously. Pertinent aspects of the problem such as laser characteristics- -pulse width repetition rate laser wavelength tunability or agility as well as laser power or energy have been placed in perspective. In addition possible effects on vision for various exposures have been estimated as have the characteristics required of eye protective devices. Various classes of devices are discussed and advantages and disadvantages noted. 1.

  2. Simultaneous detection and differentiation of Newcastle disease and avian influenza viruses using oligonucleotide microarrays.

    PubMed

    Wang, Lih-Chiann; Pan, Chu-Hsiang; Severinghaus, Lucia Liu; Liu, Lu-Yuan; Chen, Chi-Tsong; Pu, Chang-En; Huang, Dean; Lir, Jihn-Tsair; Chin, Shih-Chien; Cheng, Ming-Chu; Lee, Shu-Hwae; Wang, Ching-Ho

    2008-03-18

    Newcastle disease (ND) and avian influenza (AI) are two of the most important zoonotic viral diseases of birds throughout the world. These two viruses often have a great impact upon the poultry industry. Both viruses are associated with transmission from wild to domestic birds, and often display similar signs that need to be differentiated. A rapid surveillance among wild and domestic birds is important for early disease detection and intervention, and is the basis for what measures should be taken. The surveillance, thus, should be able to differentiate the diseases and provide a detailed analysis of the virus strains. Here, we described a fast, simultaneous and inexpensive approach to the detection of Newcastle disease virus (NDV) and avian influenza virus (AIV) using oligonucleotide microarrays. The NDV pathotypes and the AIV haemagglutinin subtypes H5 and H7 were determined at the same time. Different probes on a microarray targeting the same gene were implemented in order to encompass the diversified virus strains or provide multiple confirmations of the genotype. This ensures good sensitivity and specificity among divergent viruses. Twenty-four virus isolates and twenty-four various combinations of the viruses were tested in this study. All viruses were successfully detected and typed. The hybridization results on microarrays were clearly identified with the naked eyes, with no further imaging equipment needed. The results demonstrate that the detection and typing of multiple viruses can be performed simultaneously and easily using oligonucleotide microarrays. The proposed method may provide potential for rapid surveillance and differential diagnosis of these two important zoonoses in both wild and domestic birds.

  3. 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

  4. DNA microarray for detection of gastrointestinal viruses.

    PubMed

    Martínez, Miguel A; Soto-Del Río, María de Los Dolores; Gutiérrez, Rosa María; Chiu, Charles Y; Greninger, Alexander L; Contreras, Juan Francisco; López, Susana; Arias, Carlos F; Isa, Pavel

    2015-01-01

    Gastroenteritis is a clinical illness of humans and other animals that is characterized by vomiting and diarrhea and caused by a variety of pathogens, including viruses. An increasing number of viral species have been associated with gastroenteritis or have been found in stool samples as new molecular tools have been developed. In this work, a DNA microarray capable in theory of parallel detection of more than 100 viral species was developed and tested. Initial validation was done with 10 different virus species, and an additional 5 species were validated using clinical samples. Detection limits of 1 × 10(3) virus particles of Human adenovirus C (HAdV), Human astrovirus (HAstV), and group A Rotavirus (RV-A) were established. Furthermore, when exogenous RNA was added, the limit for RV-A detection decreased by one log. In a small group of clinical samples from children with gastroenteritis (n = 76), the microarray detected at least one viral species in 92% of the samples. Single infection was identified in 63 samples (83%), and coinfection with more than one virus was identified in 7 samples (9%). The most abundant virus species were RV-A (58%), followed by Anellovirus (15.8%), HAstV (6.6%), HAdV (5.3%), Norwalk virus (6.6%), Human enterovirus (HEV) (9.2%), Human parechovirus (1.3%), Sapporo virus (1.3%), and Human bocavirus (1.3%). To further test the specificity and sensitivity of the microarray, the results were verified by reverse transcription-PCR (RT-PCR) detection of 5 gastrointestinal viruses. The RT-PCR assay detected a virus in 59 samples (78%). The microarray showed good performance for detection of RV-A, HAstV, and calicivirus, while the sensitivity for HAdV and HEV was low. Furthermore, some discrepancies in detection of mixed infections were observed and were addressed by reverse transcription-quantitative PCR (RT-qPCR) of the viruses involved. It was observed that differences in the amount of genetic material favored the detection of the most abundant

  5. 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.

  6. 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

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

    PubMed

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

    2015-07-01

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

  8. Eye screening in the elderly.

    PubMed

    Keane, E M; O'Connor, M; Coakley, D; Walsh, J B

    1997-01-01

    Poor vision is considered to be a common unreported illness in the elderly population. To determine its prevalence we carried out an eye screen on 150 randomly selected co-operative elderly subjects attending St James's Hospital. A database [mean age 78.2 years (range 65 to 97)], medical history, mini-mental test score [mean score 9.1 (range 2 to 10)], mobility assessment and history of eye problems was gathered. A visual test of both eyes together (standard N6 and N8), inspection of the eyes, tonometry (Perkin's handheld tonometer) and fundoscopy were performed on each subject and the need and reason for referral to an optician or an ophthalmologist was documented. Results show that 64% of subjects could read N6 or N8. Tonometry revealed no subject with raised intraocular pressure, including 4 subjects who were currently on treatment for glaucoma. Fundoscopy showed that 57.3% of subjects had some evidence of cataracts, 16.6% moderate and 3% severe. The retina appeared normal in 58.6% of subjects, 20.6% of the population had hypertensive changes, 4.6% had diabetic changes, 3% had optic atrophy, 1.3% had macular degeneration and a further 10% could not be clearly visualised due to cataracts. 90% of subjects wore glasses and the average duration since the glasses were last changed was 3.7 years (range 2 weeks to 20 years). No glasses examined were in need of cleaning or repair. 36% of subjects could not read N8 (28 of these had forgotten their glasses and were advised to visit their optician if they could not read newsprint). 7.3% of subjects were referred to an optician for new glasses, 1.3% were referred to an ophthalmologist for newly diagnosed cataracts and 6.6% were regular attenders to an ophthalmologist. We conclude that the rate of new referrals for the occurrence of correctable undetected visual acuity deficit was lower than expected at 8.6% of subjects screened.

  9. 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.

  10. 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)

  11. 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.

  12. Eye pathologies in neonates

    PubMed Central

    Mansoor, Nyaish; Mansoor, Tihami; Ahmed, Mansoor

    2016-01-01

    In the United Kingdom, newborn assessment incorporates a screening eye examination for any structural abnormalities, observation of neonate's visual behaviour and direct ophthalmoscopy examination looking for red reflex. Early identification and immediate management of eye related pathologies should commence soon after birth as early diagnosis and prompt intervention may have significant impact on the prognosis for many potentially blinding but treatable disorders such as congenital cataracts and retinoblastoma. If left undetected and untreated, such problems may potentially lead to irreversible damage to the vision which persists into adulthood resulting in lack of self-confidence together with difficulties in educational attainment and job opportunities. PMID:28003988

  13. 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

  14. Multimodal Regulation Orchestrates Normal and Complex Disease States in the Retina.

    PubMed

    Olivares, A M; Jelcick, A S; Reinecke, J; Leehy, B; Haider, A; Morrison, M A; Cheng, L; Chen, D F; DeAngelis, M M; Haider, N B

    2017-04-06

    Regulation of biological processes occurs through complex, synergistic mechanisms. In this study, we discovered the synergistic orchestration of multiple mechanisms regulating the normal and diseased state (age related macular degeneration, AMD) in the retina. We uncovered gene networks with overlapping feedback loops that are modulated by nuclear hormone receptors (NHR), miRNAs, and epigenetic factors. We utilized a comprehensive filtering and pathway analysis strategy comparing miRNA and microarray data between three mouse models and human donor eyes (normal and AMD). The mouse models lack key NHRS (Nr2e3, RORA) or epigenetic (Ezh2) factors. Fifty-four total miRNAs were differentially expressed, potentially targeting over 150 genes in 18 major representative networks including angiogenesis, metabolism, and immunity. We identified sixty-eight genes and 5 miRNAS directly regulated by NR2E3 and/or RORA. After a comprehensive analysis, we discovered multimodal regulation by miRNA, NHRs, and epigenetic factors of three miRNAs (miR-466, miR1187, and miR-710) and two genes (Ell2 and Entpd1) that are also associated with AMD. These studies provide insight into the complex, dynamic modulation of gene networks as well as their impact on human disease, and provide novel data for the development of innovative and more effective therapeutics.

  15. 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.

  16. 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.

  17. Indian Soldiers Need Eye Protection

    PubMed Central

    2017-01-01

    Combat-related eye injuries entail enormous financial, social and psychological cost. Military Combat Eye Protection (MCEP) decreases both the incidence and severity of eye injuries. Experts have recognised the need for MCEP for Indian soldiers. We aim to review the combat-related eye injuries and combat eye protection among the Indian soldiers. Global practices of MCEP are also reviewed. We also aim to offer our recommendations for Indian soldiers. We carried out Medline search for combat-related eye injuries and MCEP and separately searched for eye injuries among Indian soldiers during war and other operations. We present the findings as results. Recommendations are based on the opinions of the experts. Combat-related eye injuries increased from 3% of injured in the 1965 Indo-Pakistan War to 4.8% in 1971 war. During peace-keeping operations in Sri Lanka (1987-89) eye injuries increased to 10.5% of the injured. Statistics on eye injuries during counterinsurgency operations are not available. MCEP have shown reduction in eye injuries, and thus MCEP forms a part of personal equipment of the soldiers in developed countries. Indian soldiers do not have provision of MCEP. Combat-related eye injuries among Indian Army soldiers have been increasing. Data on eye injuries during counterinsurgency operations are not available. Indian soldiers do not have provision of MCEP. Provision of MCEP is therefore desirable. Awareness program among the commanders and the soldiers shall result in attitudinal changes and increased compliance. PMID:28384904

  18. 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

  19. The eye of Vesalius.

    PubMed

    De Laey, Jean J

    2011-05-01

    In the time of Vesalius, knowledge of ocular anatomy was limited. The first description of the anatomy of the eye comes from Democrites, for whom the eye was surrounded by two 'coats', filled with a homogenous fluid. The optic nerve was hollow and the lens was considered to be a postmortem artefact. Until the 15th century AD, medicine was influenced by the writings of Galenus and the model of the eye he proposed was still considered valid, even after Vesalius. According to the Alexandrian tradition, the lens was considered as the seat of visual perception. Although Vesalius rightly deserves the title of father of modern anatomy, his description of ocular anatomy was rudimentary and often incorrect. He described a musculus retractorius bulbi, which is found only in lower mammals, not in primates. The lens, the role of which as an optical device he recognized correctly, was placed too centrally in the eye. The optic nerve was not correctly placed and, following Galenus, Vesalius described only seven cranial nerves. The Galenian concept of ocular anatomy was to endure until the development of the microscope by Anthony van Leeuwenhoek. Modern ocular anatomy, in fact, can be dated from the works of Zinn.

  20. 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…

  1. 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…

  2. 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.

  3. 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…

  4. Eye-controlled ''teletypewriter''

    NASA Technical Reports Server (NTRS)

    Holt, J. D.; Leavitt, L. D.; Bowen, H. D.

    1974-01-01

    Oculometer provides dynamic measurement of subject's look direction, and its outputs can be used to generate visual display of his look pattern and/or to cause equipment operation associated with his lookpoint at given times. Measured eye-direction information could be used as control input at man/machine interface.

  5. Dynamic Eye Model.

    ERIC Educational Resources Information Center

    Journal of Science and Mathematics Education in Southeast Asia, 1981

    1981-01-01

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

  6. The blind beautiful eye.

    PubMed

    Feinsod, M

    2000-03-01

    Master Jehan Yperman, a medieval surgeon, observed that when the optic nerve is injured, the eye becomes blind and beautiful. This is an attempt to trace the footsteps of this forgotten surgeon and to track the history of the cosmetic use of the belladonna herb, as well as the concept of amaurotic mydriasis.

  7. 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…

  8. 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,…

  9. Microarray Technology Applied to Human Allergic Disease

    PubMed Central

    Hamilton, Robert G.

    2017-01-01

    IgE antibodies serve as the gatekeeper for the release of mediators from sensitized (IgE positive) mast cells and basophils following a relevant allergen exposure which can lead to an immediate-type hypersensitivity (allergic) reaction. Purified recombinant and native allergens were combined in the 1990s with state of the art chip technology to establish the first microarray-based IgE antibody assay. Triplicate spots to over 100 allergenic molecules are immobilized on an amine-activated glass slide to form a single panel multi-allergosorbent assay. Human antibodies, typically of the IgE and IgG isotypes, specific for one or many allergens bind to their respective allergen(s) on the chip. Following removal of unbound serum proteins, bound IgE antibody is detected with a fluorophore-labeled anti-human IgE reagent. The fluorescent profile from the completed slide provides a sensitization profile of an allergic patient which can identify IgE antibodies that bind to structurally similar (cross-reactive) allergen families versus molecules that are unique to a single allergen specificity. Despite its ability to rapidly analyze many IgE antibody specificities in a single simple assay format, the chip-based microarray remains less analytically sensitive and quantitative than its singleplex assay counterpart (ImmunoCAP, Immulite). Microgram per mL quantities of allergen-specific IgG antibody can also complete with nanogram per mL quantities of specific IgE for limited allergen binding sites on the chip. Microarray assays, while not used in clinical immunology laboratories for routine patient IgE antibody testing, will remain an excellent research tool for defining sensitization profiles of populations in epidemiological studies. PMID:28134842

  10. Development of a microarray for identification of pathogenic Clostridium species

    PubMed Central

    Janvilisri, Tavan; Scaria, Joy; Gleed, Robin; Fubini, Susan; Bonkosky, Michelle M.; Gröhn, Yrjö T.; Chang, Yung-Fu

    2009-01-01

    In recent years, Clostridium species have rapidly reemerged as human and animal pathogens. The detection and identification of pathogenic Clostridium species is therefore critical for clinical diagnosis and antimicrobial therapy. Traditional diagnostic techniques for clostridia are laborious, time-consuming and may adversely affect the therapeutic outcome. In this study, we developed an oligonucleotide diagnostic microarray for pathogenic Clostridium species. The microarray specificity was tested against 65 Clostridium isolates. The applicability of this microarray in a clinical setting was assessed with the use of mock stool samples. The microarray was successful in discriminating at least four species with the limit of detection as low as 104 CFU/ml. In addition, the pattern of virulence and antibiotic resistance genes of tested strains were determined through the microarrays. This approach demonstrates the high-throughput detection and identification of Clostridium species and provides advantages over traditional methods. Microarray-based techniques are promising applications for clinical diagnosis and epidemiological investigations. PMID:19879710

  11. Application of DNA microarray technology to gerontological studies.

    PubMed

    Masuda, Kiyoshi; Kuwano, Yuki; Nishida, Kensei; Rokutan, Kazuhito

    2013-01-01

    Gene expression patterns change dramatically in aging and age-related events. The DNA microarray is now recognized as a useful device in molecular biology and widely used to identify the molecular mechanisms of aging and the biological effects of drugs for therapeutic purpose in age-related diseases. Recently, numerous technological advantages have led to the evolution of DNA microarrays and microarray-based techniques, revealing the genomic modification and all transcriptional activity. Here, we show the step-by-step methods currently used in our lab to handling the oligonucleotide microarray and miRNA microarray. Moreover, we introduce the protocols of ribonucleoprotein [RNP] immunoprecipitation followed by microarray analysis (RIP-chip) which reveal the target mRNA of age-related RNA-binding proteins.

  12. 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.

  13. Tissue microarrays for early target evaluation.

    PubMed

    Simon, Ronald; Mirlacher, Martina; Sauter, Guido

    2004-09-01

    Early assessment of the probable biological importance of drug targets, the potential market size of a successful new drug, and possible treatment side effects are critical for risk management in drug development. A comprehensive molecular epidemiology analysis involving thousands of well-characterized human tissues will thus provide vital information for strategic decision-making. Tissue microarray (TMA) technology is ideally suited for such projects. The simultaneous analysis of thousands of tissues enables highly standardized, fast and affordable translational research studies of unprecedented scale.:

  14. 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.

  15. 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.

  16. Corneal trauma from projection of metallic mercury into the eyes.

    PubMed

    Weber, F L; Babel, J

    1979-06-01

    A 24-year-old woman sustained bilateral ocular lesions due to projection of mercury into the eyes during an explosion in a chemical laboratory. A lamellar keratectomy was performed on the right eye four hours after the accident, and 12 days later, the same procedure was performed of the left eye. Studies by light and electron microscopy were done on both specimens. The essential findings were total loss of epithelium, necrosis of keratocytes, absence of inflammatory reaction, and absence of superficial stromal repair in the specimen that was obtained 12 days after the accident. These findings indirectly confirm the importance of epithelium and normally vascularized conjunctiva in healing wounds of the cornea.

  17. Acute Reversible Charles Bonnet Syndrome Following Eye Patch Placement.

    PubMed

    Nan, Lian; Yanbin, Hou; Jingping, Zhao

    2013-01-01

    Charles Bonnet syndrome (CBS) is characterised by recurrent vivid visual hallucinations in the presence of normal cognition. We present a case of CBS secondary to eye patching following Pars Plana Vitrectomy with an unusually acute onset in a 48-year-old woman. She presented with formed visual hallucinations that started less than 30 min after patching of her left eye. The patch was removed after 2 d, and these hallucinations persisted 2 d following eye patch removal. It is important that the ophthalmic surgeon be aware of the potential for development of CBS and offer appropriate referral and reassurance should it occur.

  18. 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 ...

  19. Medicare Benefits and Your Eyes

    MedlinePlus

    ... Eye Emergencies How to Jump Start a Car Battery Safely Electronic Screens and Your Eyes Nutrition and ... External Resources The Cost of Vision Problems The Future of Vision Vision Problems in the U.S. Healthy ...

  20. Prevent Eye Injuries from Fireworks

    MedlinePlus

    ... Eye Emergencies How to Jump Start a Car Battery Safely Electronic Screens and Your Eyes Nutrition and ... External Resources The Cost of Vision Problems The Future of Vision Vision Problems in the U.S. Healthy ...

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. Normal and abnormal lid function.

    PubMed

    Rucker, Janet C

    2011-01-01

    This chapter on lid function is comprised of two primary sections, the first on normal eyelid anatomy, neurological innervation, and physiology, and the second on abnormal eyelid function in disease states. The eyelids serve several important ocular functions, the primary objectives of which are protection of the anterior globe from injury and maintenance of the ocular tear film. Typical eyelid behaviors to perform these functions include blinking (voluntary, spontaneous, or reflexive), voluntary eye closure (gentle or forced), partial lid lowering during squinting, normal lid retraction during emotional states such as surprise or fear (startle reflex), and coordination of lid movements with vertical eye movements for maximal eye protection. Detailed description of the neurological innervation patterns and neurophysiology of each of these lid behaviors is provided. Abnormal lid function is divided by conditions resulting in excessive lid closure (cerebral ptosis, apraxia of lid opening, blepharospasm, oculomotor palsy, Horner's syndrome, myasthenia gravis, and mechanical) and those resulting in excessive lid opening (midbrain lid retraction, facial nerve palsy, and lid retraction due to orbital disease).

  7. 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.

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

    PubMed

    Seidel, Michael; Niessner, Reinhard

    2014-09-01

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

  9. 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.

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

    PubMed

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

    2015-01-01

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

  11. Application of DNA microarrays in occupational health research.

    PubMed

    Koizumi, Shinji

    2004-01-01

    The profiling of gene expression patterns with DNA microarrays is recently being widely used not only in basic molecular biological studies but also in the practical fields. In clinical application, for example, this technique is expected to be quite useful in making a correct diagnosis. In the pharmacological area, the microarray analysis can be applied to drug discovery and individualized drug treatment. Although not so popular as these examples, DNA microarrays could also be a powerful tool in studies relevant to occupational health. This review will describe the outline of gene expression profiling with DNA microarrays and prospects in occupational health research.

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

    PubMed Central

    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

    2014-01-01

    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

  13. 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.

  14. On-chip lectin microarray for glycoprofiling of different gastritis types and gastric cancer

    PubMed Central

    Roy, Bibhas; Chattopadhyay, Gautam; Mishra, Debasish; Das, Tamal; Chakraborty, Suman; Maiti, Tapas K.

    2014-01-01

    An on-chip lectin microarray based glycomic approach is employed to identify glyco markers for different gastritis and gastric cancer. Changes in protein glycosylation have impact on biological function and carcinogenesis. These altered glycosylation patterns in serum proteins and membrane proteins of tumor cells can be unique markers of cancer progression and hence have been exploited to diagnose various stages of cancer through lectin microarray technology. In the present work, we aimed to study the alteration of glycan structure itself in different stages of gastritis and gastric cancer thoroughly. In order to perform the study from both serum and tissue glycoproteins in an efficient and high-throughput manner, we indigenously developed and employed lectin microarray integrated on a microfluidic lab-on-a-chip platform. We analyzed serum and gastric biopsy samples from 8 normal, 15 chronic Type-B gastritis, 10 chronic Type-C gastritis, and 6 gastric adenocarcinoma patients and found that the glycoprofile obtained from tissue samples was more distinctive than that of the sera samples. We were able to establish signature glycoprofile for the three disease groups, that were absent in healthy normal individuals. In addition, our findings elucidated certain novel signature glycan expression in chronic gastritis and gastric cancer. In silico analysis showed that glycoprofile of chronic gastritis and gastric adenocarcinoma formed close clusters, confirming the previously hypothesized linkage between them. This signature can be explored further as gastric cancer marker to develop novel analytical tools and obtain in-depth understanding of the disease prognosis. PMID:24959308

  15. 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)

  16. 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 ...

  17. 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)

  18. 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

  19. ADAPTIVE EYE MODEL - Poster Paper

    NASA Astrophysics Data System (ADS)

    Galetskiy, Sergey O.; Kudryashov, Alexey V.

    2008-01-01

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

  20. Zeptosens' protein microarrays: a novel high performance microarray platform for low abundance protein analysis.

    PubMed

    Pawlak, Michael; Schick, Eginhard; Bopp, Martin A; Schneider, Michael J; Oroszlan, Peter; Ehrat, Markus

    2002-04-01

    Protein microarrays are considered an enabling technology, which will significantly expand the scope of current protein expression and protein interaction analysis. Current technologies, such as two-dimensional gel electrophoresis (2-DE) in combination with mass spectrometry, allowing the identification of biologically relevant proteins, have a high resolving power, but also considerable limitations. As was demonstrated by Gygi et al. (Proc. Nat. Acad. Sci. USA 2000,97, 9390-9395), most spots in 2-DE, observed from whole cell extracts, are from high abundance proteins, whereas low abundance proteins, such as signaling molecules or kinases, are only poorly represented. Protein microarrays are expected to significantly expedite the discovery of new markers and targets of pharmaceutical interest, and to have the potential for high-throughput applications. Key factors to reach this goal are: high read-out sensitivity for quantification also of low abundance proteins, functional analysis of proteins, short assay analysis times, ease of handling and the ability to integrate a variety of different targets and new assays. Zeptosens has developed a revolutionary new bioanalytical system based on the proprietary planar waveguide technology which allows us to perform multiplexed, quantitative biomolecular interaction analysis with highest sensitivity in a microarray format upon utilizing the specific advantages of the evanescent field fluorescence detection. The analytical system, comprising an ultrasensitive fluorescence reader and microarray chips with integrated microfluidics, enables the user to generate a multitude of high fidelity data in applications such as protein expression profiling or investigating protein-protein interactions. In this paper, the important factors for developing high performance protein microarray systems, especially for targeting low abundant messengers of relevant biological information, will be discussed and the performance of the system will

  1. Manufacturing DNA microarrays from unpurified PCR products

    PubMed Central

    Diehl, Frank; Beckmann, Boris; Kellner, Nadine; Hauser, Nicole C.; Diehl, Susanne; Hoheisel, Jörg D.

    2002-01-01

    For the production of DNA microarrays from PCR products, purification of the the DNA fragments prior to spotting is a major expense in cost and time. Also, a considerable amount of material is lost during this process and contamination might occur. Here, a protocol is presented that permits the manufacture of microarrays from unpurified PCR products on aminated surfaces such as glass slides coated with the widely used poly(l-lysine) or aminosilane. The presence of primer molecules in the PCR sample does not increase the non-specific signal upon hybridisation. Overall, signal intensity on arrays made of unpurified PCR products is 94% of the intensity obtained with the respective purified molecules. This slight loss in signal, however, is offset by a reduced variation in the amount of DNA present at the individual spot positions across an array, apart from the considerable savings in time and cost. In addition, a larger number of arrays can be made from one batch of amplification products. PMID:12177307

  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. Solution processed organic microarray with inverted structure

    NASA Astrophysics Data System (ADS)

    Toglia, Patrick; Lewis, Jason; Lafalce, Evan; Jiang, Xiaomei

    2011-03-01

    We have fabricated inverted organic microarray using a novel solution-based technique. The array consists of 60 small (1 square mm) solar cells on a one inch by one inch glass substrate. The device utilizes photoactive materials such as a blend of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). Manipulation of active layer nanomorphology has been done by choice of solvents and annealing conditions. Detailed analysis of device physics including current voltage characteristics, external quantum efficiency and carrier recombinations will be presented and complimented by AFM images and glazing angle XRD of the active layer under different processing conditions. The procedure described here has the full potential for use in future fabrication of microarrays with single cell as small as 0.01 square mm for application in DC power supplies for electrostatic Microelectromechanical systems (MEMS) devices. This work was supported by New Energy Technology Inc. and Florida High Tech Corridor Matching Fund (FHT 09-18).

  4. Clickable Polymeric Coating for Glycan Microarrays.

    PubMed

    Zilio, Caterina; Sola, Laura; Cretich, Marina; Bernardi, Anna; Chiari, Marcella

    2017-01-01

    The interaction of carbohydrates with a variety of biological targets, including antibodies, proteins, viruses, and cells are of utmost importance in many aspects of biology. Glycan microarrays are increasingly used to determine the binding specificity of glycan-binding proteins. In this study, a novel microarray support is reported for the fabrication of glycan arrays that combines the higher sensitivity of a layered Si-SiO2 surface with a novel polymeric coating easily modifiable by subsequent click reaction. The alkyne-containing copolymer, adsorbed from an aqueous solution, produces a coating by a single step procedure and serves as a soft, tridimensional support for the oriented immobilization of carbohydrates via azide/alkyne Cu (I) catalyzed "click" reaction. The advantages of a functional 3D polymer coating making use of a click chemistry immobilization are combined with the high fluorescence sensitivity and superior signal-to-noise ratio of a Si-SiO2 substrate. The proposed approach enables the attachment of complex sugars on a silicon oxide surface by a method that does not require skilled personnel and chemistry laboratories.

  5. 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.

  6. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression

    PubMed Central

    Rhodes, Daniel R.; Yu, Jianjun; Shanker, K.; Deshpande, Nandan; Varambally, Radhika; Ghosh, Debashis; Barrette, Terrence; Pandey, Akhilesh; Chinnaiyan, Arul M.

    2004-01-01

    Many studies have used DNA microarrays to identify the gene expression signatures of human cancer, yet the critical features of these often unmanageably large signatures remain elusive. To address this, we developed a statistical method, comparative metaprofiling, which identifies and assesses the intersection of multiple gene expression signatures from a diverse collection of microarray data sets. We collected and analyzed 40 published cancer microarray data sets, comprising 38 million gene expression measurements from >3,700 cancer samples. From this, we characterized a common transcriptional profile that is universally activated in most cancer types relative to the normal tissues from which they arose, likely reflecting essential transcriptional features of neoplastic transformation. In addition, we characterized a transcriptional profile that is commonly activated in various types of undifferentiated cancer, suggesting common molecular mechanisms by which cancer cells progress and avoid differentiation. Finally, we validated these transcriptional profiles on independent data sets. PMID:15184677

  7. Lens coloboma in one eye and ectopia lentis in the other eye of a patient with Marfan syndrome.

    PubMed

    Thapa, Bikram Bahadur; Singh, Ramandeep; Ram, Jagat; Kumar, Abiraj

    2014-12-09

    We present a case of Marfan syndrome with lens coloboma in one eye and ectopia lentis in the other. A 14-year-old girl reported decreased vision in the left eye. Her visual acuity was 6/24 and counting fingers at 1 m in the right and left eyes, respectively. Her intraocular pressure was 15 mm Hg in both eyes. Evaluation of the right eye on slit lamp biomicroscopy under mydriasis revealed an inferiorly visible flattened and concave crystalline lens equator from 4 to 8 o'clock position along with notching and absence of zonules, suggestive of lens coloboma. Left eye examination revealed a superiorly subluxated lens from 3 to 9 o'clock position and posterior subcapsular cataract. The posterior segment evaluation of both eyes was normal. Her father, aunt and grandfather were of tall stature, characteristic of Marfan syndrome. On systemic evaluation, the patient was diagnosed as Marfan syndrome. After surgical correction she achieved vision of 6/6 in both eyes.

  8. 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.

  9. Comparative study of p63 and p53 expression in tissue microarrays of malignant melanomas.

    PubMed

    Brinck, Ulrich; Ruschenburg, Ilka; Di Como, Charles J; Buschmann, Nadine; Betke, Herbert; Stachura, Jerzy; Cordon-Cardo, Carlos; Korabiowska, Monika

    2002-12-01

    p63 is a known homologue of p53. In contrast to p53, however, p63 mutations are rarely seen in tumours. There have been several reports that p63 plays a regulatory role in the normal differentiation of cells, whereas its role in tumour biology must still be elucidated. The main aim of this study was to compare p63 and p53 expression in tissue microarrays of malignant melanomas and to establish any prognostic significance. p63 expression was found in 2 out of 59 tumours, both pT4. The p63 index did not exceed 30%. p53 expression was found in 27 out of 59 melanomas, with maximal expression in up to 80% of tumour cells. There were no correlations observed between the two markers. Multivariate analysis confirmed the prognostically independent role of p53. This study also confirmed that tissue microarrays can be used effectively for evaluation of the expression of certain tumour markers.

  10. Estimating equation–based causality analysis with application to microarray time series data

    PubMed Central

    Hu, Jianhua; Hu, Feifang

    2009-01-01

    Microarray time-course data can be used to explore interactions among genes and infer gene network. The crucial step in constructing gene network is to develop an appropriate causality test. In this regard, the expression profile of each gene can be treated as a time series. A typical existing method establishes the Granger causality based on Wald type of test, which relies on the homoscedastic normality assumption of the data distribution. However, this assumption can be seriously violated in real microarray experiments and thus may lead to inconsistent test results and false scientific conclusions. To overcome the drawback, we propose an estimating equation–based method which is robust to both heteroscedasticity and nonnormality of the gene expression data. In fact, it only requires the residuals to be uncorrelated. We will use simulation studies and a real-data example to demonstrate the applicability of the proposed method. PMID:19329818

  11. Assessing Differential Expression Measurements by Highly Parallel Pyrosequencing and DNA Microarrays: A Comparative Study

    PubMed Central

    Ariño, Joaquín; Casamayor, Antonio; Pérez, Julián Perez; Pedrola, Laia; Álvarez-Tejado, Miguel; Marbà, Martina; Santoyo, Javier

    2013-01-01

    Abstract To explore the feasibility of pyrosequencing for quantitative differential gene expression analysis we have performed a comparative study of the results of the sequencing experiments to those obtained by a conventional DNA microarray platform. A conclusion from our analysis is that, over a threshold of 35 normalized reads per gene, the measurements of gene expression display a good correlation with the references. The observed concordance between pyrosequencing and DNA microarray platforms beyond the threshold was of 0.8, measured as a Pearson's correlation coefficient. In differential gene expression the initial aim is the quantification the differences among transcripts when comparing experimental conditions. Thus, even in a scenario of low coverage the concordance in the measurements is quite acceptable. On the other hand, the comparatively longer read size obtained by pyrosequencing allows detecting unconventional splicing forms. PMID:21919703

  12. Eye lens dosimetry in anesthesiology: a prospective study.

    PubMed

    Vaes, Bart; Van Keer, Karel; Struelens, Lara; Schoonjans, Werner; Nijs, Ivo; Vandevenne, Jan; Van Poucke, Sven

    2017-04-01

    The eye lens is one of the most sensitive organs for radiation injury and exposure might lead to radiation induced cataract. Eye lens dosimetry in anesthesiology has been published in few clinical trials and an active debate about the causality of radiation induced cataract is still ongoing. Recently, the International Commission on Radiological Protection (ICRP) recommended a reduction in the annual dose limit for occupational exposure for the lens of the eye from 150 to 20 mSv, averaged over a period of 5 years, with the dose in a single year not exceeding 50 mSv. This prospective study investigated eye lens dosimetry in anesthesiology practice during a routine year of professional activity. The radiation exposure measured represented the exposure in a normal working schedule of a random anesthesiologist during 1 month and this cumulative eye lens dose was extrapolated to 1 year. Next, eye lens doses were measured in anesthesiology during neuro-embolisation procedures, radiofrequency ablations or vertebroplasty/kyphoplasty procedures. The eye lens doses are measured in terms of the dose equivalent H p(3) with the Eye-D dosimeter (Radcard, Poland) close to the right eye (on the temple). In 16 anesthesiologists, the estimated annual eye lens doses range from a minimum of 0.4 mSv to a maximum of 3.5 mSv with an average dose of 1.33 mSv. Next, eye lens doses were measured for nine neuro-embolisation procedures, ten radiofrequency ablations and six vertebroplasty/kyphoplasty procedures. Average eye lens doses of 77 ± 76 µSv for neuro-embolisations, 38 ± 34 µSv for cardiac ablations and 40 ± 44 µSv for vertebro-/kyphoplasty procedures were recorded. The maximum doses were respectively 264, 97 and 122 µSv. This study demonstrated that the estimated annual eye lens dose is well below the revised ICRP's limit of 20 mSv/year. However, we demonstrated high maximum and average doses during neuro-embolisation, cardiac ablation and vertebro

  13. 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.

  14. An Eye on Trafficking Genes: Identification of Four Eye Color Mutations in Drosophila

    PubMed Central

    Grant, Paaqua; Maga, Tara; Loshakov, Anna; Singhal, Rishi; Wali, Aminah; Nwankwo, Jennifer; Baron, Kaitlin; Johnson, Diana

    2016-01-01

    Genes that code for proteins involved in organelle biogenesis and intracellular trafficking produce products that are critical in normal cell function . Conserved orthologs of these are present in most or all eukaryotes, including Drosophila melanogaster. Some of these genes were originally identified as eye color mutants with decreases in both types of pigments found in the fly eye. These criteria were used for identification of such genes, four eye color mutations that are not annotated in the genome sequence: chocolate, maroon, mahogany, and red Malpighian tubules were molecularly mapped and their genome sequences have been evaluated. Mapping was performed using deletion analysis and complementation tests. chocolate is an allele of the VhaAC39-1 gene, which is an ortholog of the Vacuolar H+ ATPase AC39 subunit 1. maroon corresponds to the Vps16A gene and its product is part of the HOPS complex, which participates in transport and organelle fusion. red Malpighian tubule is the CG12207 gene, which encodes a protein of unknown function that includes a LysM domain. mahogany is the CG13646 gene, which is predicted to be an amino acid transporter. The strategy of identifying eye color genes based on perturbations in quantities of both types of eye color pigments has proven useful in identifying proteins involved in trafficking and biogenesis of lysosome-related organelles. Mutants of these genes can form the basis of valuable in vivo models to understand these processes. PMID:27558665

  15. An Eye on Trafficking Genes: Identification of Four Eye Color Mutations in Drosophila.

    PubMed

    Grant, Paaqua; Maga, Tara; Loshakov, Anna; Singhal, Rishi; Wali, Aminah; Nwankwo, Jennifer; Baron, Kaitlin; Johnson, Diana

    2016-10-13

    Genes that code for proteins involved in organelle biogenesis and intracellular trafficking produce products that are critical in normal cell function . Conserved orthologs of these are present in most or all eukaryotes, including Drosophila melanogaster Some of these genes were originally identified as eye color mutants with decreases in both types of pigments found in the fly eye. These criteria were used for identification of such genes, four eye color mutations that are not annotated in the genome sequence: chocolate, maroon, mahogany, and red Malpighian tubules were molecularly mapped and their genome sequences have been evaluated. Mapping was performed using deletion analysis and complementation tests. chocolate is an allele of the VhaAC39-1 gene, which is an ortholog of the Vacuolar H(+) ATPase AC39 subunit 1. maroon corresponds to the Vps16A gene and its product is part of the HOPS complex, which participates in transport and organelle fusion. red Malpighian tubule is the CG12207 gene, which encodes a protein of unknown function that includes a LysM domain. mahogany is the CG13646 gene, which is predicted to be an amino acid transporter. The strategy of identifying eye color genes based on perturbations in quantities of both types of eye color pigments has proven useful in identifying proteins involved in trafficking and biogenesis of lysosome-related organelles. Mutants of these genes can form the basis of valuable in vivo models to understand these processes.

  16. 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.

  17. Ultrasonographic anatomy of the bovine eye.

    PubMed

    Potter, Timothy J; Hallowell, Gayle D; Bowen, I Mark

    2008-01-01

    The purposes of the study were to describe the ultrasonographic appearance and measurements of the normal bovine eye, to compare the measurements to those reported previously for cadaveric eyes and to describe differences between ocular dimensions of Holstein Friesian and Jersey cattle. Sixty transpalpebral ocular ultrasonographic examinations were performed on 30 adult Holstein Friesian cows, and 16 examinations were performed on 8 adult Jersey cows. Transpalpebral ultrasonographic images were obtained with a 10 MHz linear transducer in both horizontal and vertical imaging planes. The ultrasonographic appearance of structures within the bovine eye is similar to that in other species, although the ciliary artery was frequently identified, appearing as a 0.33 +/- 0.04 cm diameter hypoechoic area. The axial length of the globe was significantly greater in Holstein Friesian cattle (3.46 +/- 0.09 cm) compared with Jersey cattle (3.27 +/- 0.19 cm; P = 0.001), although the vitreous depth was smaller in Holstein Friesian cattle (1.46 +/- 0.09 cm) (P = 0.0009). The anterioposterior depth of the lens was significantly greater in Jersey cattle (1.92 +/- 0.11 cm) and the cornea was thinner in Jersey cattle (0.17 +/- 0.02 cm). The appearance and ocular distances for live animals were similar to those reported previously for cadaveric specimens. The knowledge of normal ocular dimensions facilitates the use of ultrasonography in the evaluation of ocular disease in cattle.

  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. Comprehensive eye evaluation algorithm

    NASA Astrophysics Data System (ADS)

    Agurto, C.; Nemeth, S.; Zamora, G.; Vahtel, M.; Soliz, P.; Barriga, S.

    2016-03-01

    In recent years, several research groups have developed automatic algorithms to detect diabetic retinopathy (DR) in individuals with diabetes (DM), using digital retinal images. Studies have indicated that diabetics have 1.5 times the annual risk of developing primary open angle glaucoma (POAG) as do people without DM. Moreover, DM patients have 1.8 times the risk for age-related macular degeneration (AMD). Although numerous investigators are developing automatic DR detection algorithms, there have been few successful efforts to create an automatic algorithm that can detect other ocular diseases, such as POAG and AMD. Consequently, our aim in the current study was to develop a comprehensive eye evaluation algorithm that not only detects DR in retinal images, but also automatically identifies glaucoma suspects and AMD by integrating other personal medical information with the retinal features. The proposed system is fully automatic and provides the likelihood of each of the three eye disease. The system was evaluated in two datasets of 104 and 88 diabetic cases. For each eye, we used two non-mydriatic digital color fundus photographs (macula and optic disc centered) and, when available, information about age, duration of diabetes, cataracts, hypertension, gender, and laboratory data. Our results show that the combination of multimodal features can increase the AUC by up to 5%, 7%, and 8% in the detection of AMD, DR, and glaucoma respectively. Marked improvement was achieved when laboratory results were combined with retinal image features.

  20. Perspectives on eye development.

    PubMed

    Fini, M E; Strissel, K J; West-Mays, J A

    1997-01-01

    The lens of the vertebrate eye was the classic model used to demonstrate the concepts of inductive interactions controlling development. However, it is in the Drosophila model that the greatest progress in understanding molecular mechanisms of eye development have most recently been mode. This progress can be attributed to the power of molecular genetics, an approach that was once confined to simpler systems like worms and flies, but is now becoming possible in vertebrates. Thus, the use of transgenic and knock-out gene technology, coupled with the availability of new positional cloning methods, has recently initiated a surge of progress in the mouse genetic model and has also led to the identification of genes involved in human inherited disorders. In addition, gene transfer techniques have opened up opportunities for progress using chick, Xenopus, and other classic developmental systems. Finally, a new vertebrate genetic model, zebrafish, appears very promising for molecular studies. As a result of the opportunities presented by these new approaches, eye development has come into the limelight, hence the timeliness of this focus issue of Developmental Genetics. In this introductory review, we discuss three areas of current work arising through the use of these newer genetic approaches, and pertinent to research articles presented herein. We also touch on related studies reported at the first Keystone Meeting on Ocular Cell and Molecular Biology, recently held in Tamarron Springs, Colorado, January 7-12, 1997.

  1. 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

  2. Intraocular eyelashes and iris cyst in anterior chamber following penetrating eye injury: a case report

    PubMed Central

    Sahu, Sabin; Puri, Lila Raj; Singh, Sanjay Kumar

    2017-01-01

    Background The presence of intraocular eyelashes following penetrating eye injury or ocular surgery is relatively uncommon. The response of the eye to intraocular eyelashes is variable. The eyelash may be symptomatic or may remain asymptomatic for long periods. Objective We report a case with two intraocular eyelashes and an iris cyst after 2 years of asymptomatic period following penetrating eye injury. Case presentation A 24-year-old male presented with decreased vision in the left eye which he had noticed for the previous 2 weeks. His visual acuity was 6/6 in the right eye and 6/18 in the left eye, improving to 6/9 with -2.5 DC × 140° correction. The intraocular pressure was 12 mmHg in both eyes. On slit-lamp examination, the left eye showed 8 mm linear peripheral corneal opacity nasally, two eyelashes in the superior anterior chamber, and an iris cyst measuring 4 mm × 4 mm in the superior iris. The right eye was normal. Dilated fundus examination of both eyes was normal. The eyelashes and cyst were removed surgically. There were no complications during the 3-month follow-up period. Conclusion Intraocular implantation of eyelashes following penetrating eye injury can remain asymptomatic for long periods; however, late development of iris cyst may occur. PMID:28356777

  3. 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…

  4. 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

  5. Demonstrating a multi-drug resistant Mycobacterium tuberculosis amplification microarray.

    PubMed

    Linger, Yvonne; Kukhtin, Alexander; Golova, Julia; Perov, Alexander; Qu, Peter; Knickerbocker, Christopher; Cooney, Christopher G; Chandler, Darrell P

    2014-04-25

    Simplifying microarray workflow is a necessary first step for creating MDR-TB microarray-based diagnostics that can be routinely used in lower-resource environments. An amplification microarray combines asymmetric PCR amplification, target size selection, target labeling, and microarray hybridization within a single solution and into a single microfluidic chamber. A batch processing method is demonstrated with a 9-plex asymmetric master mix and low-density gel element microarray for genotyping multi-drug resistant Mycobacterium tuberculosis (MDR-TB). The protocol described here can be completed in 6 hr and provide correct genotyping with at least 1,000 cell equivalents of genomic DNA. Incorporating on-chip wash steps is feasible, which will result in an entirely closed amplicon method and system. The extent of multiplexing with an amplification microarray is ultimately constrained by the number of primer pairs that can be combined into a single master mix and still achieve desired sensitivity and specificity performance metrics, rather than the number of probes that are immobilized on the array. Likewise, the total analysis time can be shortened or lengthened depending on the specific intended use, research question, and desired limits of detection. Nevertheless, the general approach significantly streamlines microarray workflow for the end user by reducing the number of manually intensive and time-consuming processing steps, and provides a simplified biochemical and microfluidic path for translating microarray-based diagnostics into routine clinical practice.

  6. Discordant Dry Eye Disease (An American Ophthalmological Society Thesis)

    PubMed Central

    Shtein, Roni M.; Harper, Daniel E.; Pallazola, Vincent; Harte, Steven E.; Hussain, Munira; Sugar, Alan; Williams, David A.; Clauw, Daniel J.

    2016-01-01

    Purpose To improve understanding of dry eye disease and highlight a subgroup of patients who have a component of central sensitization and neuropathic pain contributing to their condition. Methods Prospective, cross-sectional, IRB-approved study comparing isolated dry eye disease (n=48) to fibromyalgia (positive control; n=23) and healthy (negative control; n=26) individuals with ocular surface examination, corneal confocal microscopy, quantitative sensory testing, and self-reported ocular symptoms and systemic associations. A subset of patients also underwent skin biopsy and/or brain neuroimaging. Dry eye patients were split into concordant (ie, those with dry eyes on examination) and discordant (ie, those with dry eye symptoms but normal examination) subgroups for further analysis. We hypothesized that on the systemic measures included, concordant patients would resemble healthy controls, whereas discordant patients would show evidence of centralized mechanisms similar to fibromyalgia. Results Schirmer test and Ocular Surface Disease Index (OSDI) scores indicated significant decreases in tear production (Schirmer: healthy, 18.5±8.2 mm; dry, 11.2±5.4 mm; fibromyalgia, 14.4±7.5; P<.001) and increases in self-reported dry eye symptoms (OSDI: healthy, 1.9±3.0; dry, 20.3±17.7; fibromyalgia, 20.3±17.1; P<.001) in the dry eye and fibromyalgia patients, compared to controls. The discordant subgroup had decreased corneal nerve density and decreased visual quality-of-life scores, similar to patients with fibromyalgia. Concordant patients were more similar to healthy controls on these measures. Conclusions Individuals with discordant dry eye may have a central pathophysiologic mechanism leading to their eye pain symptoms, which could be an important factor to consider in treatment of chronic idiopathic dry eye. PMID:28050051

  7. Dry Eye as a Mucosal Autoimmune Disease

    PubMed Central

    Stern, Michael E.; Schaumburg, Chris S.; Pflugfelder, Stephen C.

    2013-01-01

    Dry eye is a common ocular surface inflammatory disease that significantly affects quality of life. Dysfunction of the lacrimal function unit (LFU) alters tear composition and breaks ocular surface homeostasis, facilitating chronic inflammation and tissue damage. Accordingly, the most effective treatments to date are geared towards reducing inflammation and restoring normal tear film. The pathogenic role of CD4+ T cells is well known, and the field is rapidly realizing the complexity of other innate and adaptive immune factors involved in the development and progression of disease. The data support the hypothesis that dry eye is a localized autoimmune disease originating from an imbalance in the protective immunoregulatory and proinflammatory pathways of the ocular surface. PMID:23360156

  8. Eye Movements Reveal Hierarchical Motion Processing

    NASA Technical Reports Server (NTRS)

    Mulligan, Jeffrey B.; Null, Cynthia H. (Technical Monitor)

    1996-01-01

    Purpose: In the analysis of visual motion, local features such as orientation are analyzed early in the cortical processing stream (V1), while integration across orientation and space is thought to occur in higher cortical areas such as MT, MST, etc. If all areas provide inputs to eye movement control centers, we would expect that local properties would drive eye movements with relatively short latencies, while global properties would require longer latencies. When such latencies are observed, they can provide information about when (and where?) various stimulus properties are analyzed. Methods: The stimulus employed was an elliptical Gabor patch with a drifting carrier, in which the orientations of the carrier grating and the contrast window were varied independently. We have previously demonstrated that the directional percepts evoked by this stimulus vary between the "grating direction" (the normal to the grating's orientation) and the "window direction", and that similar effects can be observed in reflexive eye movements. Subjects viewed such a stimulus while attempting to maintain steady fixation on the center of the pattern, and the small reflexive eye movements ("stare OKN") were recorded. In the middle of the trial, the orientation of either the grating or the window was rotated smoothly by 30 degrees. Results: Responses to the shift of both grating orientation and window orientation are seen in the average OKN slow phase velocity. Grating rotations produce a rapid OKN rotation to the grating direction (100 ms latency, 300 ms time constant), followed by a slower rebound to the steady state perceived direction midway between the grating and window directions. Window rotations, on the other hand, evoke a slower response (200 ms latency, 500 ms time constant). Conclusions: The results demonstrate multiple cortical inputs to eye movement control: a fast, early input driven by orientation, and a slower input from higher areas sensitive to global stimulus

  9. Digital microarray analysis for digital artifact genomics

    NASA Astrophysics Data System (ADS)

    Jaenisch, Holger; Handley, James; Williams, Deborah

    2013-06-01

    We implement a Spatial Voting (SV) based analogy of microarray analysis for digital gene marker identification in malware code sections. We examine a famous set of malware formally analyzed by Mandiant and code named Advanced Persistent Threat (APT1). APT1 is a Chinese organization formed with specific intent to infiltrate and exploit US resources. Manidant provided a detailed behavior and sting analysis report for the 288 malware samples available. We performed an independent analysis using a new alternative to the traditional dynamic analysis and static analysis we call Spatial Analysis (SA). We perform unsupervised SA on the APT1 originating malware code sections and report our findings. We also show the results of SA performed on some members of the families associated by Manidant. We conclude that SV based SA is a practical fast alternative to dynamics analysis and static analysis.

  10. Giant Magnetoresistive Sensors for DNA Microarray

    PubMed Central

    Xu, Liang; Yu, Heng; Han, Shu-Jen; Osterfeld, Sebastian; White, Robert L.; Pourmand, Nader; Wang, Shan X.

    2009-01-01

    Giant magnetoresistive (GMR) sensors are developed for a DNA microarray. Compared with the conventional fluorescent sensors, GMR sensors are cheaper, more sensitive, can generate fully electronic signals, and can be easily integrated with electronics and microfluidics. The GMR sensor used in this work has a bottom spin valve structure with an MR ratio of 12%. The single-strand target DNA detected has a length of 20 bases. Assays with DNA concentrations down to 10 pM were performed, with a dynamic range of 3 logs. A double modulation technique was used in signal detection to reduce the 1/f noise in the sensor while circumventing electromagnetic interference. The logarithmic relationship between the magnetic signal and the target DNA concentration can be described by the Temkin isotherm. Furthermore, GMR sensors integrated with microfluidics has great potential of improving the sensitivity to 1 pM or below, and the total assay time can be reduced to less than 1 hour. PMID:20824116

  11. Uses of Dendrimers for DNA Microarrays

    PubMed Central

    Caminade, Anne-Marie; Padié, Clément; Laurent, Régis; Maraval, Alexandrine; Majoral, Jean-Pierre

    2006-01-01

    Biosensors such as DNA microarrays and microchips are gaining an increasing importance in medicinal, forensic, and environmental analyses. Such devices are based on the detection of supramolecular interactions called hybridizations that occur between complementary oligonucleotides, one linked to a solid surface (the probe), and the other one to be analyzed (the target). This paper focuses on the improvements that hyperbranched and perfectly defined nanomolecules called dendrimers can provide to this methodology. Two main uses of dendrimers for such purpose have been described up to now; either the dendrimer is used as linker between the solid surface and the probe oligonucleotide, or the dendrimer is used as a multilabeled entity linked to the target oligonucleotide. In the first case the dendrimer generally induces a higher loading of probes and an easier hybridization, due to moving away the solid phase. In the second case the high number of localized labels (generally fluorescent) induces an increased sensitivity, allowing the detection of small quantities of biological entities.

  12. Meta-analysis of incomplete microarray studies.

    PubMed

    Zollinger, Alix; Davison, Anthony C; Goldstein, Darlene R

    2015-10-01

    Meta-analysis of microarray studies to produce an overall gene list is relatively straightforward when complete data are available. When some studies lack information-providing only a ranked list of genes, for example-it is common to reduce all studies to ranked lists prior to combining them. Since this entails a loss of information, we consider a hierarchical Bayes approach to meta-analysis using different types of information from different studies: the full data matrix, summary statistics, or ranks. The model uses an informative prior for the parameter of interest to aid the detection of differentially expressed genes. Simulations show that the new approach can give substantial power gains compared with classical meta-analysis and list aggregation methods. A meta-analysis of 11 published studies with different data types identifies genes known to be involved in ovarian cancer and shows significant enrichment.

  13. Protein microarray applications: Autoantibody detection and posttranslational modification.

    PubMed

    Atak, Apurva; Mukherjee, Shuvolina; Jain, Rekha; Gupta, Shabarni; Singh, Vedita Anand; Gahoi, Nikita; K P, Manubhai; Srivastava, Sanjeeva

    2016-10-01

    The discovery of DNA microarrays was a major milestone in genomics; however, it could not adequately predict the structure or dynamics of underlying protein entities, which are the ultimate effector molecules in a cell. Protein microarrays allow simultaneous study of thousands of proteins/peptides, and various advancements in array technologies have made this platform suitable for several diagnostic and functional studies. Antibody arrays enable researchers to quantify the abundance of target proteins in biological fluids and assess PTMs by using the antibodies. Protein microarrays have been used to assess protein-protein interactions, protein-ligand interactions, and autoantibody profiling in various disease conditions. Here, we summarize different microarray platforms with focus on its biological and clinical applications in autoantibody profiling and PTM studies. We also enumerate the potential of tissue microarrays to validate findings from protein arrays as well as other approaches, highlighting their significance in proteomics.

  14. DNA microarray-based mutation discovery and genotyping.

    PubMed

    Gresham, David

    2011-01-01

    DNA microarrays provide an efficient means of identifying single-nucleotide polymorphisms (SNPs) in DNA samples and characterizing their frequencies in individual and mixed samples. We have studied the parameters that determine the sensitivity of DNA probes to SNPs and found that the melting temperature (T (m)) of the probe is the primary determinant of probe sensitivity. An isothermal-melting temperature DNA microarray design, in which the T (m) of all probes is tightly distributed, can be implemented by varying the length of DNA probes within a single DNA microarray. I describe guidelines for designing isothermal-melting temperature DNA microarrays and protocols for labeling and hybridizing DNA samples to DNA microarrays for SNP discovery, genotyping, and quantitative determination of allele frequencies in mixed samples.

  15. Identification of novel pancreatic adenocarcinoma cell-surface targets by gene expression profiling and tissue microarray

    PubMed Central

    Morse, David L.; Balagurunathan, Yoga; Hostetter, Galen; Trissal, Maria; Tafreshi, Narges K.; Burke, Nancy; Lloyd, Mark; Enkemann, Steven; Coppola, Domenico; Hruby, Victor; Gillies, Robert J.; Han, Haiyong

    2010-01-01

    Pancreatic cancer has a high mortality rate, which is generally related to the initial diagnosis coming at late stage disease combined with a lack of effective treatment options. Novel agents that selectively detect pancreatic cancer have potential for use in the molecular imaging of cancer, allowing for non-invasive determination of tumor therapeutic response and molecular characterization of the disease. Such agents may also be used for the targeted delivery of therapy to tumor cells while decreasing systemic effects. Using complementary assays of mRNA expression profiling to determine elevated expression in pancreatic cancer tissues relative to normal pancreas tissues, and validation of protein expression by immunohistochemistry on tissue microarray, we have identified cell-surface targets with potential for imaging and therapeutic agent development. Expression profiles of 2177 cell-surface genes for 28 pancreatic tumor specimens and 4 normal pancreas tissue samples were evaluated. Expression in normal tissues was evaluated using array data from 103 samples representing 28 organ sites as well as mining published data. One-hundred seventy unique targets were highly expressed in 2 or more of the pancreatic tumor specimens and were not expressed in the normal pancreas samples. Two targets (TLR2 and ABCC3) were further validated for protein expression by tissue microarray (TMA) based immunohistochemistry. These validated targets have potential for the development of diagnostic imaging and therapeutic agents for pancreatic cancer. PMID:20510208

  16. Image microarrays (IMA): Digital pathology's missing tool

    PubMed Central

    Hipp, Jason; Cheng, Jerome; Pantanowitz, Liron; Hewitt, Stephen; Yagi, Yukako; Monaco, James; Madabhushi, Anant; Rodriguez-canales, Jaime; Hanson, Jeffrey; Roy-Chowdhuri, Sinchita; Filie, Armando C.; Feldman, Michael D.; Tomaszewski, John E.; Shih, Natalie NC.; Brodsky, Victor; Giaccone, Giuseppe; Emmert-Buck, Michael R.; Balis, Ulysses J.

    2011-01-01

    Introduction: The increasing availability of whole slide imaging (WSI) data sets (digital slides) from glass slides offers new opportunities for the development of computer-aided diagnostic (CAD) algorithms. With the all-digital pathology workflow that these data sets will enable in the near future, literally millions of digital slides will be generated and stored. Consequently, the field in general and pathologists, specifically, will need tools to help extract actionable information from this new and vast collective repository. Methods: To address this limitation, we designed and implemented a tool (dCORE) to enable the systematic capture of image tiles with constrained size and resolution that contain desired histopathologic features. Results: In this communication, we describe a user-friendly tool that will enable pathologists to mine digital slides archives to create image microarrays (IMAs). IMAs are to digital slides as tissue microarrays (TMAs) are to cell blocks. Thus, a single digital slide could be transformed into an array of hundreds to thousands of high quality digital images, with each containing key diagnostic morphologies and appropriate controls. Current manual digital image cut-and-paste methods that allow for the creation of a grid of images (such as an IMA) of matching resolutions are tedious. Conclusion: The ability to create IMAs representing hundreds to thousands of vetted morphologic features has numerous applications in education, proficiency testing, consensus case review, and research. Lastly, in a manner analogous to the way conventional TMA technology has significantly accelerated in situ studies of tissue specimens use of IMAs has similar potential to significantly accelerate CAD algorithm development. PMID:22200030

  17. Fluorescence detection in (sub-)nanoliter microarrays

    NASA Astrophysics Data System (ADS)

    van den Doel, L. Richard; Vellekoop, Michael J.; Sarro, Pasqualina M.; Picioreanu, S.; Moerman, R.; Frank, J.; van Dedem, G. W. K.; Hjelt, Kari H.; van Vliet, Lucas J.; Young, Ian T.

    1999-06-01

    The goal of our TU Delft interfaculty research program is to develop intelligent molecular diagnostic systems (IMDS) that can analyze liquid samples that contain a variety of biochemical compounds such as those associated with fermentation processes. One specific project within the IMDS program focuses on photon sensors. In order to analyze the liquid samples we use dedicated microarrays. At this stage, these are basically miniaturized micro titre plates. Typical dimensions of a vial are 200 X 200 X 20 micrometer3. These dimensions may be varied and the shape of the vials can be modified with a result that the volume of the vials varies from 0.5 to 1.6 nl. For all experiments, we have used vials with the shape of a truncated pyramid. These vials are fabricated in silicon by a wet etching process. For testing purposes the vials are filled with rhodamine solutions of various concentrations. To avoid evaporation glycerol-water (1:1, v/v) with a viscosity of 8.3 times the viscosity of water is used as solvent. We aim at wide field-of-view imaging at the expense of absolute sensitivity: the field-of-view increases quadratically with decreasing magnification. Small magnification, however, implies low Numerical Aperture (NA). The ability of a microscope objective to collect photons is proportional to the square of the NA. To image the entire microarray we have used an epi-illumination fluorescence microscope equipped with a low magnification (2.5 X/0.075) objective and a scientific CCD camera to integrate the photons emitted from the fluorescing particles in the solutions in the vials. From these experiments we found that for this setup the detection limit is on the order of micromolar concentrations of fluorescing particles. This translates to 108 molecules per vial.

  18. Lipid Microarray Biosensor for Biotoxin Detection.

    SciTech Connect

    Singh, Anup K.; Throckmorton, Daniel J.; Moran-Mirabal, Jose C.; Edel, Joshua B.; Meyer, Grant D.; Craighead, Harold G.

    2006-05-01

    We present the use of micron-sized lipid domains, patterned onto planar substrates and within microfluidic channels, to assay the binding of bacterial toxins via total internal reflection fluorescence microscopy (TIRFM). The lipid domains were patterned using a polymer lift-off technique and consisted of ganglioside-populated DSPC:cholesterol supported lipid bilayers (SLBs). Lipid patterns were formed on the substrates by vesicle fusion followed by polymer lift-off, which revealed micron-sized SLBs containing either ganglioside GT1b or GM1. The ganglioside-populated SLB arrays were then exposed to either Cholera toxin subunit B (CTB) or Tetanus toxin fragment C (TTC). Binding was assayed on planar substrates by TIRFM down to 1 nM concentration for CTB and 100 nM for TTC. Apparent binding constants extracted from three different models applied to the binding curves suggest that binding of a protein to a lipid-based receptor is strongly affected by the lipid composition of the SLB and by the substrate on which the bilayer is formed. Patterning of SLBs inside microfluidic channels also allowed the preparation of lipid domains with different compositions on a single device. Arrays within microfluidic channels were used to achieve segregation and selective binding from a binary mixture of the toxin fragments in one device. The binding and segregation within the microfluidic channels was assayed with epifluorescence as proof of concept. We propose that the method used for patterning the lipid microarrays on planar substrates and within microfluidic channels can be easily adapted to proteins or nucleic acids and can be used for biosensor applications and cell stimulation assays under different flow conditions. KEYWORDS. Microarray, ganglioside, polymer lift-off, cholera toxin, tetanus toxin, TIRFM, binding constant.4

  19. Early sensitivity for eyes within faces: a new neuronal account of holistic and featural processing.

    PubMed

    Nemrodov, Dan; Anderson, Thomas; Preston, Frank F; Itier, Roxane J

    2014-08-15

    Eyes are central to face processing however their role in early face encoding as reflected by the N170 ERP component is unclear. Using eye tracking to enforce fixation on specific facial features, we found that the N170 was larger for fixation on the eyes compared to fixation on the forehead, nasion, nose or mouth, which all yielded similar amplitudes. This eye sensitivity was seen in both upright and inverted faces and was lost in eyeless faces, demonstrating it was due to the presence of eyes at fovea. Upright eyeless faces elicited largest N170 at nose fixation. Importantly, the N170 face inversion effect (FIE) was strongly attenuated in eyeless faces when fixation was on the eyes but was less attenuated for nose fixation and was normal when fixation was on the mouth. These results suggest the impact of eye removal on the N170 FIE is a function of the angular distance between the fixated feature and the eye location. We propose the Lateral Inhibition, Face Template and Eye Detector based (LIFTED) model which accounts for all the present N170 results including the FIE and its interaction with eye removal. Although eyes elicit the largest N170 response, reflecting the activity of an eye detector, the processing of upright faces is holistic and entails an inhibitory mechanism from neurons coding parafoveal information onto neurons coding foveal information. The LIFTED model provides a neuronal account of holistic and featural processing involved in upright and inverted faces and offers precise predictions for further testing.

  20. Autofluorescence spectroscopy for early diagnosis of cancer eye

    NASA Astrophysics Data System (ADS)

    Majumder, Shovan K.; Ghosh, Nirmalya; Rathod, Sopan M.; Gupta, Pradeep K.

    2007-02-01

    We report an in-vitro autofluorescence spectroscopic study of cow eye tissue to explore the applicability of the approach in discriminating early stage "cancer eye" from normal squamous eye tissues. Significant differences were observed in the autofluorescence signatures between the "cancer eye" and normal eye tissues. The spectral differences were quantified by employing a probability-based diagnostic algorithm developed based on recently formulated theory of Relevance Vector Machine (RVM), a Bayesian machine-learning framework of statistical pattern recognition. The algorithm provided sensitivity and specificity values of 97 +/- 2% towards cancer for the training set data based on leave-one-out cross validation and a sensitivity of 97 +/- 2% and a specificity of 99 +/- 1% towards cancer for the independent validation set data. These results suggest that autofluorescence spectroscopy might prove to be a quantitative in-vivo diagnostic modality for early and accurate diagnosis of "cancer eye" in veterinary clinical setting, which would help improve ranch management from both economic and animal care standpoint.

  1. Intensive Care Nurses' Views and Practices for Eye Care: An International Comparison.

    PubMed

    Güler, Elem Kocaçal; Eşer, İsmet; Fashafsheh, Imad Hussein Deeb

    2016-02-18

    Eye care is an important area of critical care. However, lack of eye care studies is a common issue across the globe. The aim of this study is to determine the views and practices of intensive care unit (ICU) nurses on eye care in Turkey and Palestine. This descriptive study was conducted using a self-administrated questionnaire. The data were collected from 111 nurses in nine kinds of ICUs in two education hospital. Normal saline (75.9%) was the most commonly reported solution for eye hygiene among the Palestinian nurses, and gauze soaked in normal saline or sterile water (64.3%) were the most frequently used supplies by the Turkish nurses. Although both Palestinian and Turkish ICU nurses took some precautions to prevent eye complications in critical patients, there were some gaps and insufficiencies in the eye care of ICU patients. There is a need for continuing training in this area.

  2. Application of Phenotype Microarray technology to soil microbiology

    NASA Astrophysics Data System (ADS)

    Mocali, Stefano

    2016-04-01

    It is well established that soil microorganisms are extremely diverse and only a small fraction has been successfully cultured in the laboratory. Furthermore, addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of interest in the reconstruction and biotechnological manipulation of metabolic pathways. High-throughput culture in micro wells provides a method for rapid screening of a wide variety of growth conditions and commercially available plates contain a large number of substrates, nutrient sources, and inhibitors, which can provide an assessment of the phenotype of an organism. Thus, over the last years, Phenotype Microarray (PM) technology has been used to address many specific issues related to the metabolic functionality of microorganisms. However, computational tools that could directly link PM data with the gene(s) of interest followed by the extraction of information on gene-phenotype correlation are still missing. Here potential applications of phenotype arrays to soil microorganisms, use of the plates in stress response studies and for assessment of phenotype of environmental communities are described. Considerations and challenges in data interpretation and visualization, including data normalization, statistics, and curve fitting are also discussed. In particular, here we present DuctApe, a suite that allows the analysis of both genomic sequences and PM data, to find metabolic differences among PM experiments and to correlate them with KEGG pathways and gene presence/absence patterns.

  3. Unscaled Bayes factors for multiple hypothesis testing in microarray experiments.

    PubMed

    Bertolino, Francesco; Cabras, Stefano; Castellanos, Maria Eugenia; Racugno, Walter

    2015-12-01

    Multiple hypothesis testing collects a series of techniques usually based on p-values as a summary of the available evidence from many statistical tests. In hypothesis testing, under a Bayesian perspective, the evidence for a specified hypothesis against an alternative, conditionally on data, is given by the Bayes factor. In this study, we approach multiple hypothesis testing based on both Bayes factors and p-values, regarding multiple hypothesis testing as a multiple model selection problem. To obtain the Bayes factors we assume default priors that are typically improper. In this case, the Bayes factor is usually undetermined due to the ratio of prior pseudo-constants. We show that ignoring prior pseudo-constants leads to unscaled Bayes factor which do not invalidate the inferential procedure in multiple hypothesis testing, because they are used within a comparative scheme. In fact, using partial information from the p-values, we are able to approximate the sampling null distribution of the unscaled Bayes factor and use it within Efron's multiple testing procedure. The simulation study suggests that under normal sampling model and even with small sample sizes, our approach provides false positive and false negative proportions that are less than other common multiple hypothesis testing approaches based only on p-values. The proposed procedure is illustrated in two simulation studies, and the advantages of its use are showed in the analysis of two microarray experiments.

  4. Comparison of optical coherence tomography findings in a patient with central retinal artery occlusion in one eye and end-stage glaucoma in the fellow eye.

    PubMed

    Greene, Daniel P; Richards, Charles P; Ghazi, Nicola G

    2012-01-01

    This case describes a patient with chronic central retinal artery occlusion in one eye and end-stage traumatic glaucoma in the fellow eye. Optical coherence tomography (OCT) of the macula of the chronic phase of central retinal artery occlusion of the right eye indicated loss of the normal foveal depression, extensive inner retinal atrophy, and marked retinal thinning. In contrast, scans of the left eye with end-stage glaucoma demonstrated an intact foveal depression and limited retinal thinning. The pattern of macular OCT findings in this patient illustrates distinguishing features between chronic central retinal artery occlusion and chronic optic neuropathy due to end-stage glaucoma.

  5. Highly sensitive detection of multiple tumor markers for lung cancer using gold nanoparticle probes and microarrays.

    PubMed

    Gao, Wanlei; Wang, Wentao; Yao, Shihua; Wu, Shan; Zhang, Honglian; Zhang, Jishen; Jing, Fengxiang; Mao, Hongju; Jin, Qinghui; Cong, Hui; Jia, Chunping; Zhang, Guojun; Zhao, Jianlong

    2017-03-15

    Assay of multiple serum tumor markers such as carcinoembryonic antigen (CEA), cytokeratin 19 fragment antigen (CYFRA21-1), and neuron specific enolase (NSE), is important for the early diagnosis of lung cancer. Dickkopf-1 (DKK1), a novel serological and histochemical biomarker, was recently reported to be preferentially expressed in lung cancer. Four target proteins were sandwiched by capture antibodies attached to microarrays and detection antibodies carried on modified gold nanoparticles. Optical signals generated by the sandwich structures were amplified by gold deposition with HAuCl4 and H2O2, and were observable by microscopy or the naked eye. The four tumor markers were subsequently measured in 106 lung cancer patients and 42 healthy persons. The assay was capable of detecting multiple biomarkers in serum sample at concentration of <1 ng mL(-1) in 1 h. Combined detection of the four tumor markers highly improved the sensitivity (to 87.74%) for diagnosis of lung cancer compared with sensitivity of single markers. A rapid, highly sensitive co-detection method for multiple biomarkers based on gold nanoparticles and microarrays was developed. In clinical use, it would be expected to improve the early diagnosis of lung cancer.

  6. Occupational cow horn eye injuries in ibadan, Nigeria.

    PubMed

    Ibrahim, Oa; Olusanya, Ba

    2014-11-01

    This case series aims to describe the clinical features, management, and outcome of occupational eye injuries caused by cow horns and to recommend possible preventive measures. A review of patients with cow horn inflicted eye injuries seen at the University College Hospital, Ibadan between January 2006, and December 2011 was conducted. Three patients were identified, and their charts were reviewed for demographic information, mechanism of injury, initial and final visual acuity, surgeries performed, as well as anatomic and visual outcome. The three patients were males and were aged 45, 22, and 49 years, respectively. They were all involved in cattle-related jobs, and they all had unilateral open-globe injuries with corneoscleral lacerations. Presenting visual acuity was nil light perception in the injured eyes. The contralateral eyes were all normal. Two of the patients required evisceration of the eye, while the third patient underwent repair of lacerations. Visual improvement was not achieved in any of the patients. Cow horn eye injuries may be quite severe and could result in loss of the eye with monocular blindness. Careful attention must be paid to prevent such injuries. Cattle rearers and dealers should wear safety goggles, and proper restraint of the animals is advocated.

  7. FRACTIONATION OF THE EYE PIGMENTS OF DROSOPHILA MELANOGASTER.

    PubMed

    Wald, G; Allen, G

    1946-09-20

    Eye pigments of normal and mutant types of D. melanogaster have been extracted with water and fractionated by chromatographic adsorption on powdered talc. Spectra of all the fractions obtainable in solution have been measured and the general chemical behavior of the pigments is described. Two chemically distinct groups of pigments are found, to be identified with the earlier designated red and brown components. The red component in the wild-type eye contains three well defined pigments, two of them capable of further subdivision so that the total number of fractions obtained is five. There is also present a brown component pigment which could not be treated quantitatively by the methods employed. All members of the wild-type red component are found in cinnabar eyes, unaccompanied by the brown component. Conversely, brown eyes contain a pigment indistinguishable from the wild-type brown component, virtually alone. In sepia eyes, one red component and two brown component pigments can be distinguished, all three pigments differing from those of wild-type eyes. Pigments apparently identical with those found in wild-type melanogaster eyes have also been found in D. virilis.

  8. The potential role of neuropathic mechanisms in dry eye syndromes.

    PubMed

    Mcmonnies, Charles W

    Dry eye syndromes can involve both nociceptive and neuropathic symptoms. Nociceptive symptoms are the normal physiological responses to noxious stimuli. Neuropathic symptoms are caused by a lesion or disease of the somatosensory nervous system and can be the result of hypersensitisation of peripheral or central corneal and conjunctival somatosensory nerves. For example, inflammation could induce neuroplastic peripheral sensitisation of the ocular surface or lid wiper and exacerbate nociceptive symptoms. Neuropathic symptoms may explain the incommensurate relation between signs and symptoms in some dry eye syndromes although absence of signs of a dry eye syndrome may also be a consequence of inappropriate methods used when examining for them. Involvement of neuropathic mechanisms may also help explain dry eye symptoms which occur in association with reduced corneal sensitivity. This review includes a discussion of the potential for ocular symptoms involving neuropathic mechanisms to contribute to psychosocial problems such as depression, stress, anxiety and sleep disorders as well as for these types of psychosocial problems to contribute to neuropathic mechanisms and dry eye syndromes. Failure to consider the possibility that neuropathic mechanisms can contribute to dry eye syndromes may reduce accuracy of diagnosis and the suitability of treatment provided. Dry eye symptoms in the absence of commensurate evidence of tear dysfunction, and unsatisfactory response to tear dysfunction therapies should prompt consideration of neuropathic mechanisms being involved. Symptoms which persist after local anaesthetic instillation are more likely to be neuropathic in origin. Reducing inflammation may help limit any associated neuroplastic hypersensitivity.

  9. 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.

  10. Live Speech Driven Head-and-Eye Motion Generators.

    PubMed

    Le, Binh H; Ma, Xiaohan; Deng, Zhigang

    2012-11-01

    This paper describes a fully automated framework to generate realistic head motion, eye gaze, and eyelid motion simultaneously based on live (or recorded) speech input. Its central idea is to learn separate yet interrelated statistical models for each component (head motion, gaze, or eyelid motion) from a prerecorded facial motion data set: 1) Gaussian Mixture Models and gradient descent optimization algorithm are employed to generate head motion from speech features; 2) Nonlinear Dynamic Canonical Correlation Analysis model is used to synthesize eye gaze from head motion and speech features, and 3) nonnegative linear regression is used to model voluntary eye lid motion and log-normal distribution is used to describe involuntary eye blinks. Several user studies are conducted to evaluate the effectiveness of the proposed speech-driven head and eye motion generator using the well-established paired comparison methodology. Our evaluation results clearly show that this approach can significantly outperform the state-of-the-art head and eye motion generation algorithms. In addition, a novel mocap+video hybrid data acquisition technique is introduced to record high-fidelity head movement, eye gaze, and eyelid motion simultaneously.

  11. How to administer eye drops and eye ointment.

    PubMed

    Shaw, Mary

    2016-05-25

    Rationale and key points Eye drops and eye ointment are the mainstay of treatment of ocular conditions. Failure to prioritise administration of these medicines can prolong the condition and may present a risk to the patient's vision. ▶ Eye drops and eye ointments are used to treat acute and chronic conditions of the eye and surrounding structures. Eye drops must be instilled before applying eye ointment, since the ointment will affect the absorption of the eye drop. ▶ Nurses require knowledge of the technique, side effects and potential interactions associated with systemically or topically applied medicines to the eye to ensure patient safety and optimum outcomes. Reflective activity Clinical skills articles can help update your practice and ensure it remains evidence based. Apply this article to your practice. Reflect on and write a short account of: 1. How this article will change your practice. 2. How you intend to develop your knowledge and skills regarding treatment of ocular conditions. Subscribers can update their reflective accounts at rcni.com/portfolio.

  12. Bilateral Glaucomatous Optic Neuropathy Caused by Eye Rubbing.

    PubMed

    Savastano, Alfonso; Savastano, Maria Cristina; Carlomusto, Laura; Savastano, Silvio

    2015-01-01

    In this report, we describe a particular condition of a 52-year-old man who showed advanced bilateral glaucomatous-like optic disc damage, even though the intraocular pressure resulted normal during all examinations performed. Visual field test, steady-state pattern electroretinogram, retinal nerve fiber layer and retinal tomographic evaluations were performed to evaluate the optic disc damage. Over a 4-year observational period, his visual acuity decreased to 12/20 in the right eye and counting fingers in the left eye. Visual fields were severely compromised, and intraocular pressure values were not superior to 14 mm Hg during routine examinations. An accurate anamnesis and the suspicion of this disease represent a crucial aspect to establish the correct diagnosis. In fact, our patient strongly rubbed his eyes for more than 10 h per day. Recurrent and continuous eye rubbing can induce progressive optic neuropathy, causing severe visual field damage similar to the pathology of advanced glaucoma.

  13. Directional eye fixation sensor using birefringence-based foveal detection

    NASA Astrophysics Data System (ADS)

    Gramatikov, Boris I.; Zalloum, Othman H. Y.; Wu, Yi Kai; Hunter, David G.; Guyton, David L.

    2007-04-01

    We recently developed and reported an eye fixation monitor that detects the fovea by its radial orientation of birefringent nerve fibers. The instrument used a four-quadrant photodetector and a normalized difference function to check for a best match between the detector quadrants and the arms of the bow-tie pattern of polarization states surrounding the fovea. This function had a maximum during central fixation but could not tell where the subject was looking relative to the center. We propose a linear transformation to obtain horizontal and vertical eye position coordinates from the four photodetector signals, followed by correction based on a priori calibration information. The method was verified on both a computer model and on human eyes. The major advantage of this new eye-tracking method is that it uses true information coming from the fovea, rather than reflections from other structures, to identify the direction of foveal gaze.

  14. Loiasis: African eye worm.

    PubMed

    Padgett, Jeannie J; Jacobsen, Kathryn H

    2008-10-01

    The filarial parasite Loa loa is transmitted by Chrysops fly bites. Loiasis is endemic in rainforest areas of West and Central Africa, and sporadic cases have also been diagnosed in travellers and migrants. Whilst many infected persons are asymptomatic, microfilariae may be detected in the blood or adult worms may be seen under the skin or the sclera of the eye. Mass treatment programmes for onchocerciasis have raised concern about the risk of severe adverse effects when ivermectin is distributed in areas co-endemic for onchocerciasis and loiasis.

  15. [Eye and lymph drainage].

    PubMed

    Grüntzig, J; Schicha, H; Huth, F

    1979-06-01

    Up to now lymphatics in the eye could not be pointed out. An ocular lymph drainage is denied. Földi succeeded in producing experimentally the syndrome of "lymphostatic encephalopathy and ophthalmopathy" by operative blockade of the cervical lymphatics in animals. In the first part of the present paper a historical view considering the subject "Eye and lymphatic system" is given. In the second part it is entered into the particulars of own experimental studies. As to our own investigations, rabbits have been injected 99mTc-sulfur-colloid, 99mTc-microcolloid, 99mTc-Albumin and 198Au-colloid into the retrobulbar space, anterior chamber, vitreous body and subconjuctival space of one eye. Measurements of the activity's distribution have been made in vivo with an Anger type camera (pho-Gamma-IV Hp, Searle Nuclear Chicago) and in vitro after section with a sodium iodine crystal well counter (Clinimat-200, Picker). In some animals the investigation has been combined with a bilateral dissection of the cervical lymph nodes. After injection in the retrobulbar space a significant concentration of the activity could be observed for the most part in the equilateral Lymphonodulus cervicalis profundus. By the cervical lymph blockade the removal of lymphoctopic substances from the retrobulbar space was largely inhibited. After injection in the anterior chamber a significant concentration could be observed for the most part in the equilateral Lymphonodulus cervicalis superficialis. After intravitreal injection a drainage to the bilateral deep cervical lymph nodes could be observed. After injection into the subconjunctival space a significant accumulation of activity could be registered in the equilateral Lymphonoduli mandibulares and cervicales superficiales. The data substantiate a segmental lymph drainage from the eye: vitreous body and retrobulbar space for the most part into the Lymphonoduli cervicales profundi, anterior chamber and subconjunctival space for the most part into

  16. Lens of Eye Dosimetry

    SciTech Connect

    Mallett, Michael Wesley

    2015-03-23

    An analysis of LANL occupational dose measurements was made with respect to lens of eye dose (LOE), in particular, for plutonium workers. Table 1 shows the reported LOE as a ratio of the “deep” (photon only) and “deep+neutron” dose for routine monitored workers at LANL for the past ten years. The data compares the mean and range of these values for plutonium workers* and non-routine plutonium workers. All doses were reported based on measurements with the LANL Model 8823 TLD.

  17. On biometrics with eye movements.

    PubMed

    Zhang, Youming; Juhola, Martti

    2016-04-07

    Eye movements are a relatively novel data source for biometric identification. When video cameras applied to eye tracking become smaller and more efficient, this data source could offer interesting opportunities for the development of eye movement biometrics. In the present article, we study primarily biometric identification as seen as a classification task of multiple classes, and secondarily biometric verification considered as binary classification. Our research is based on the saccadic eye movement signal measurements from 109 young subjects. In order to test the data measured, we use a procedure of biometric identification according to the one-versus-one (subject) principle. In a development from our previous research, which also involved biometric verification based on saccadic eye movements, we now apply another eye movement tracker device with a higher sampling frequency of 250 Hz. The results obtained are good, with correct identification rates at 80-90% at their best.

  18. Eye tracking detects disconjugate eye movements associated with structural traumatic brain injury and concussion.

    PubMed

    Samadani, Uzma; Ritlop, Robert; Reyes, Marleen; Nehrbass, Elena; Li, Meng; Lamm, Elizabeth; Schneider, Julia; Shimunov, David; Sava, Maria; Kolecki, Radek; Burris, Paige; Altomare, Lindsey; Mehmood, Talha; Smith, Theodore; Huang, Jason H; McStay, Christopher; Todd, S Rob; Qian, Meng; Kondziolka, Douglas; Wall, Stephen; Huang, Paul

    2015-04-15

    Disconjugate eye movements have been associated with traumatic brain injury since ancient times. Ocular motility dysfunction may be present in up to 90% of patients with concussion or blast injury. We developed an algorithm for eye tracking in which the Cartesian coordinates of the right and left pupils are tracked over 200 sec and compared to each other as a subject watches a short film clip moving inside an aperture on a computer screen. We prospectively eye tracked 64 normal healthy noninjured control subjects and compared findings to 75 trauma subjects with either a positive head computed tomography (CT) scan (n=13), negative head CT (n=39), or nonhead injury (n=23) to determine whether eye tracking would reveal the disconjugate gaze associated with both structural brain injury and concussion. Tracking metrics were then correlated to the clinical concussion measure Sport Concussion Assessment Tool 3 (SCAT3) in trauma patients. Five out of five measures of horizontal disconjugacy were increased in positive and negative head CT patients relative to noninjured control subjects. Only one of five vertical disconjugacy measures was significantly increased in brain-injured patients relative to controls. Linear regression analysis of all 75 trauma patients demonstrated that three metrics for horizontal disconjugacy negatively correlated with SCAT3 symptom severity score and positively correlated with total Standardized Assessment of Concussion score. Abnormal eye-tracking metrics improved over time toward baseline in brain-injured subjects observed in follow-up. Eye tracking may help quantify the severity of ocular motility disruption associated with concussion and structural brain injury.

  19. Eye Tracking Detects Disconjugate Eye Movements Associated with Structural Traumatic Brain Injury and Concussion

    PubMed Central

    Ritlop, Robert; Reyes, Marleen; Nehrbass, Elena; Li, Meng; Lamm, Elizabeth; Schneider, Julia; Shimunov, David; Sava, Maria; Kolecki, Radek; Burris, Paige; Altomare, Lindsey; Mehmood, Talha; Smith, Theodore; Huang, Jason H.; McStay, Christopher; Todd, S. Rob; Qian, Meng; Kondziolka, Douglas; Wall, Stephen; Huang, Paul

    2015-01-01

    Abstract Disconjugate eye movements have been associated with traumatic brain injury since ancient times. Ocular motility dysfunction may be present in up to 90% of patients with concussion or blast injury. We developed an algorithm for eye tracking in which the Cartesian coordinates of the right and left pupils are tracked over 200 sec and compared to each other as a subject watches a short film clip moving inside an aperture on a computer screen. We prospectively eye tracked 64 normal healthy noninjured control subjects and compared findings to 75 trauma subjects with either a positive head computed tomography (CT) scan (n=13), negative head CT (n=39), or nonhead injury (n=23) to determine whether eye tracking would reveal the disconjugate gaze associated with both structural brain injury and concussion. Tracking metrics were then correlated to the clinical concussion measure Sport Concussion Assessment Tool 3 (SCAT3) in trauma patients. Five out of five measures of horizontal disconjugacy were increased in positive and negative head CT patients relative to noninjured control subjects. Only one of five vertical disconjugacy measures was significantly increased in brain-injured patients relative to controls. Linear regression analysis of all 75 trauma patients demonstrated that three metrics for horizontal disconjugacy negatively correlated with SCAT3 symptom severity score and positively correlated with total Standardized Assessment of Concussion score. Abnormal eye-tracking metrics improved over time toward baseline in brain-injured subjects observed in follow-up. Eye tracking may help quantify the severity of ocular motility disruption associated with concussion and structural brain injury. PMID:25582436

  20. Construction of a robust microarray from a non-model species (largemouth bass) using pyrosequencing technology

    PubMed Central

    Garcia-Reyero, Natàlia; Griffitt, Robert J.; Liu, Li; Kroll, Kevin J.; Farmerie, William G.; Barber, David S.; Denslow, Nancy D.

    2009-01-01

    A novel custom microarray for largemouth bass (Micropterus salmoides) was designed with sequences obtained from a normalized cDNA library using the 454 Life Sciences GS-20 pyrosequencer. This approach yielded in excess of 58 million bases of high-quality sequence. The sequence information was combined with 2,616 reads obtained by traditional suppressive subtractive hybridizations to derive a total of 31,391 unique sequences. Annotation and coding sequences were predicted for these transcripts where possible. 16,350 annotated transcripts were selected as target sequences for the design of the custom largemouth bass oligonucleotide microarray. The microarray was validated by examining the transcriptomic response in male largemouth bass exposed to 17β-œstradiol. Transcriptomic responses were assessed in liver and gonad, and indicated gene expression profiles typical of exposure to œstradiol. The results demonstrate the potential to rapidly create the tools necessary to assess large scale transcriptional responses in non-model species, paving the way for expanded impact of toxicogenomics in ecotoxicology. PMID:19936325