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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. Transformation and normalization of oligonucleotide microarray data.

    PubMed

    Geller, Sue C; Gregg, Jeff P; Hagerman, Paul; Rocke, David M

    2003-09-22

    Most methods of analyzing microarray data or doing power calculations have an underlying assumption of constant variance across all levels of gene expression. The most common transformation, the logarithm, results in data that have constant variance at high levels but not at low levels. Rocke and Durbin showed that data from spotted arrays fit a two-component model and Durbin, Hardin, Hawkins, and Rocke, Huber et al. and Munson provided a transformation that stabilizes the variance as well as symmetrizes and normalizes the error structure. We wish to evaluate the applicability of this transformation to the error structure of GeneChip microarrays. We demonstrate in an example study a simple way to use the two-component model of Rocke and Durbin and the data transformation of Durbin, Hardin, Hawkins and Rocke, Huber et al. and Munson on Affymetrix GeneChip data. In addition we provide a method for normalization of Affymetrix GeneChips simultaneous with the determination of the transformation, producing a data set without chip or slide effects but with constant variance and with symmetric errors. This transformation/normalization process can be thought of as a machine calibration in that it requires a few biologically constant replicates of one sample to determine the constant needed to specify the transformation and normalize. It is hypothesized that this constant needs to be found only once for a given technology in a lab, perhaps with periodic updates. It does not require extensive replication in each study. Furthermore, the variance of the transformed pilot data can be used to do power calculations using standard power analysis programs. SPLUS code for the transformation/normalization for four replicates is available from the first author upon request. A program written in C is available from the last author.

  3. Statistical eye model for normal eyes.

    PubMed

    Rozema, Jos J; Atchison, David A; Tassignon, Marie-José

    2011-06-23

    To create a binocular statistical eye model based on previously measured ocular biometric data. Thirty-nine parameters were determined for a group of 127 healthy subjects (37 male, 90 female; 96.8% Caucasian) with an average age of 39.9 ± 12.2 years and spherical equivalent refraction of -0.98 ± 1.77 D. These parameters described the biometry of both eyes and the subjects' age. Missing parameters were complemented by data from a previously published study. After confirmation of the Gaussian shape of their distributions, these parameters were used to calculate their mean and covariance matrices. These matrices were then used to calculate a multivariate Gaussian distribution. From this, an amount of random biometric data could be generated, which were then randomly selected to create a realistic population of random eyes. All parameters had Gaussian distributions, with the exception of the parameters that describe total refraction (i.e., three parameters per eye). After these non-Gaussian parameters were omitted from the model, the generated data were found to be statistically indistinguishable from the original data for the remaining 33 parameters (TOST [two one-sided t tests]; P < 0.01). Parameters derived from the generated data were also significantly indistinguishable from those calculated with the original data (P > 0.05). The only exception to this was the lens refractive index, for which the generated data had a significantly larger SD. A statistical eye model can describe the biometric variations found in a population and is a useful addition to the classic eye models.

  4. 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

  5. Microarray expression profiling in adhesion and normal peritoneal tissues.

    PubMed

    Ambler, Dana R; Golden, Alicia M; Gell, Jennifer S; Saed, Ghassan M; Carey, David J; Diamond, Michael P

    2012-05-01

    To identify molecular markers associated with adhesion and normal peritoneal tissue using microarray expression profiling. Comparative study. University hospital. Five premenopausal women. Adhesion and normal peritoneal tissue samples were obtained from premenopausal women. Ribonucleic acid was extracted using standard protocols and processed for hybridization to Affymetrix Whole Transcript Human Gene Expression Chips. Microarray data were obtained from five different patients, each with adhesion tissue and normal peritoneal samples. Real-time polymerase chain reaction was performed for confirmation using standard protocols. Gene expression in postoperative adhesion and normal peritoneal tissues. A total of 1,263 genes were differentially expressed between adhesion and normal tissues. One hundred seventy-three genes were found to be up-regulated and 56 genes were down-regulated in the adhesion tissues compared with normal peritoneal tissues. The genes were sorted into functional categories according to Gene Ontology annotations. Twenty-six up-regulated genes and 11 down-regulated genes were identified with functions potentially relevant to the pathophysiology of postoperative adhesions. We evaluated and confirmed expression of 12 of these specific genes via polymerase chain reaction. The pathogenesis, natural history, and optimal treatment of postoperative adhesive disease remains unanswered. Microarray analysis of adhesions identified specific genes with increased and decreased expression when compared with normal peritoneum. Knowledge of these genes and ontologic pathways with altered expression provide targets for new therapies to treat patients who have or are at risk for postoperative adhesions. Copyright © 2012 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  6. 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.

  7. 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...

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

    EPA Science Inventory

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

  9. Model selection and efficiency testing for normalization of cDNA microarray data

    PubMed Central

    Futschik, Matthias; Crompton, Toni

    2004-01-01

    In this study we present two novel normalization schemes for cDNA microarrays. They are based on iterative local regression and optimization of model parameters by generalized cross-validation. Permutation tests assessing the efficiency of normalization demonstrated that the proposed schemes have an improved ability to remove systematic errors and to reduce variability in microarray data. The analysis also reveals that without parameter optimization local regression is frequently insufficient to remove systematic errors in microarray data. PMID:15287982

  10. 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

  11. Tonometry of normal eyes in raptors.

    PubMed

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

    1994-04-01

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

  12. 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…

  13. 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…

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

    PubMed

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

    2012-01-01

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

  15. 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

  16. Eye size in retinoblastoma: MR imaging measurements in normal and affected eyes.

    PubMed

    de Graaf, Pim; Knol, Dirk L; Moll, Annette C; Imhof, Saskia M; Schouten-van Meeteren, Antoinette Y N; Castelijns, Jonas A

    2007-07-01

    To evaluate eye size retrospectively by using magnetic resonance (MR) imaging to measure axial length (AL), equatorial diameter (ED), and eye volume (EV) in patients with retinoblastoma and to evaluate the possible effect of retinoblastoma on eye size. Local ethics committee approval was obtained with waiver of informed consent. MR images of 100 patients with retinoblastoma (50 girls, 50 boys; mean age, 19 months; age range, 9 days to 68 months) were scored by one observer (AL, ED, EV, and tumor volume measurements), with a second observer reviewing all measurements. Normal eyes of patients with unilateral retinoblastoma served as controls. Interobserver measurement agreement was evaluated in a random subset of 50 eyes with use of intraclass correlation coefficients. Linear mixed model analysis was used with adjustments for age, laterality, and sex. Interobserver agreement was good (intraclass correlation coefficients >or= 0.89). Eyes with retinoblastoma had significantly shorter ALs (95% confidence interval [CI]: -0.57 mm, -0.16 mm; P=.001) and EDs (95% CI: -1.01 mm, -0.66 mm; P<.001) and significantly smaller EVs (95% CI: -336 mm(3), -151 mm(3); P<.001) than normal eyes. Within patients, a significant negative relationship was found between tumor volume and EV (P<.001). MR imaging measurements of AL, ED, and EV were significantly smaller in eyes with retinoblastoma than in normal eyes. In addition, in patients with retinoblastoma, the larger the tumor volume, the smaller the eye. (c) RSNA, 2007.

  17. 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.

  18. A Novel scoring system for distinguishing keratoconus from normal eyes.

    PubMed

    Oruçoğlu, Faik; Toker, Ebru

    2016-10-01

    To evaluate the accuracy of a novel scoring system in differentiation of keratoconus (KC) eyes from normal eyes using a Scheimpflug camera system tomography. Marmara University Hospital, Istanbul, Turkey and Birinci Eye Hospital, Istanbul, Turkey. Retrospective case-control study. The study included 624 keratoconus eyes and 512 healthy eyes. Thirty nine significant parameters obtained from the Scheimpflug imaging system (Pentacam-Oculus Optikgeräte GmbH, Wetzlar, Germany) were studied. The cut-off value and area under receiver operating characteristic (AUROC) curve analysis for each studied parameter were established in the previous study. Minus three and plus three standard deviations of the cut-off value were scored after multiplication of AUROC for each parameter. The sum of all scores (TKS; Total Keratoconus Score) was compared between keratoconus and normal eyes. Average TKS value was -29.57±5.65 (Range from -43.11 to -7.09) in normal eyes and 36.23±24.3 (Range from -16.82 to 97.45) in keratoconus eyes (p<0.001). Receiver operating characteristic curve analyses showed perfect predictive accuracy for TKS (ROC 1.0 (95% CI: 0.999-1.0)). The TKS distinguished the keratoconus group from the normal group with 99% sensitivity and 99% specificity at the best cut-off point of -12.45. The new scoring system measured by the Scheimpflug imaging system provides perfect discrimination of keratoconus from normal corneas. Copyright © 2016 British Contact Lens Association. Published by Elsevier Ltd. All rights reserved.

  19. 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.

  20. 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

  1. Assessing quality and normalization of microarrays: case studies using neurological genomic data.

    PubMed

    Hershey, A D; Burdine, D; Liu, C; Nick, T G; Gilbert, D L; Glauser, T A

    2008-07-01

    Genomic analysis using microarray tools has the potential benefit of enhancing our understanding of neurological diseases. The analysis of these data is complex due to the large amount of data generated. Many tools have been developed to assist with this, but standard methods of analysis of these tools have not been established. This study analyzed the sensitivity and specificity of different analytical methods for gene identification and presents a standardized approach. Affymetrix HG-U133 plus 2.0 microarray datasets from two neurological diseases - chronic migraine and new-onset epilepsy - were used as source data and methods of analysis for normalization of data and identification of gene changes were compared. Housekeeping genes were used to identify non-specific changes and gender related genes were used to identify specific changes. Initial normalization of data revealed that 5-10% of the microarray were potential outliers due to technical errors. Two separate methods of analysis (dChip and Bioconductor) identified the same microarray chips as outliers. For specificity and sensitivity testing, performing a per-gene normalization was found to be inferior to standard preprocessing procedures using robust multichip average analysis. Technical variation in microarray preprocessing may account for chip-to-chip and batch-to-batch variations and outliers need to be removed prior to analysis. Specificity and sensitivity of the final results are best achieved following this identification and removal with standard genomic analysis techniques. Future tools may benefit from the use of standard tools of measurement.

  2. [Modified method of constructing tissue microarray which contains keloid and normal skin].

    PubMed

    Zhang, Zhenyu; Chen, Junjie; Cen, Ying; Zhao, Sha; Liao, Dianying; Gong, Jing

    2010-08-01

    To seek for a method of constructing the tissue microarray which contains keloid, skin around keloid, and normal skin. The specimens were gained from patients of voluntary donation between March and May 2009, including the tissues of keloid (27 cases), skin around keloid (13 cases), and normal skin (27 cases). The specimens were imbedded by paraffin as donor blocks. The traditional method of constructing the tissue microarray and section were modified according to the histological characteristics of the keloid and skin tissue and the experimental requirement. The tissue cores were drilled from donor blocks and attached securely on the adhesive platform which was prepared. The adhesive platform with tissue cores in situ was placed into an imbedding mold, which then was preheated briefly. Paraffin at approximately 70 degrees C was injected to fill the mold and then cooled to room temperature. Then HE staining, immunohistochemistry staining were performed and the results were observed by microscope. The constructed tissue microarray block contained 67 cores as designed and displayed smooth surface with no crack. All the cores distributed regularly, had no disintegration or manifest shift. HE staining of tissue microarray section showed that all cores had equal thickness, distinct layer, manifest contradistinction, well-defined edge, and consistent with original pathological diagnosis. Immunohistochemistry staining results demonstrated that all cores contained enough tissue dose to apply group comparison. However, in tissue microarray which was made as traditional method, many cores missed and a few cores shifted obviously. Applying modified method can successfully construct tissue microarray which is composed of keloid, skin around keloid, and normal skin. This tissue microarray will become an effective tool of researching the pathogenesis of keloid.

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

    PubMed Central

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

    2006-01-01

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

  4. Smooth pursuit eye movements in normal and dyslexic children.

    PubMed

    Black, J L; Collins, D W; De Roach, J N; Zubrick, S R

    1984-08-01

    This paper describes a detailed study of horizontal eye movements associated with visual tracking of a smoothly moving target. Essentially all children, even at target velocities as low as 5 degrees/sec., show some saccadic eye movements superimposed on smooth tracking movements. Detailed analysis of pursuit eye-movements from a group of 26 poor readers and 34 normal controls (8 to 13 yr.) showed that about 25% of poor readers have an abnormally raised saccadic component in smooth pursuit. This suggests that studies of eye movements during tracking of smoothly moving targets at low velocity, combined with a quantitative approach to data analysis, may be useful for early detection of a significant proportion of poor-reading children.

  5. 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.

  6. Bigaussian Wavefront Model for Normal and Keratoconic Eyes.

    PubMed

    Rozema, Jos J; Rodríguez, Pablo; Navarro, Rafael; Koppen, Carina

    2017-06-01

    To report bigaussian multivariate wavefront models capable of stochastically generating an unlimited amount of plausible wavefront data for either normal or keratoconic eyes. The models use centroid wavefront data measured previously with an iTrace in 330 healthy right eyes and 122 keratoconic right eyes. These centroids were fitted to an 11th-order Zernike series, followed by principal component analysis to reduce dimensionality and remove correlations. The remaining parameters were then fitted to a sum of two multivariate Gaussian distributions. This fit then forms the core of the stochastic model, which may be used to generate synthetic data. Finally, the agreement between the original and synthetic data was tested using two one-sided t tests. For normal eyes, the first eigenvectors mostly represent pure Zernike polynomials, with a decreasing degree of purity with increasing order. For keratoconic eyes, eigenvector purity was considerably lower than for normal eyes. Depending on the data set, series of 22 to 29 eigenvectors were found sufficient for accurate wavefront reconstruction (i.e., root-mean-square errors below 0.05 μm). These eigenvectors were then used as a base for the stochastic models. In all models and all Zernike coefficients, the mean of the synthetic data was significantly equal to that of the original data (two one-sided t test, P > .05/75), but the variability of the synthetic data is often significantly lower (F test, P < .05/75). This synthetic wavefront model may be safely used in calculations as an alternative to actual measurements should such data not be available.

  7. 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

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

    PubMed

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

    2015-08-21

    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.

  9. Influence of axial length of normal eyes on PERG.

    PubMed

    Hidajat, Rudy; Mclay, Jan; Burley, Celeste; Elder, Mark; Morton, Jason; Goode, David

    2003-09-01

    The influence of the axial length (AL) of the eye on flash electroretinogram (ERG) responses has been well established in the literature, suggesting an association between ERG abnormalities with myopia (AL > 25 mm). The aim of our present study was to determine whether the AL of normal eyes can also influence the pattern electroretinogram (PERG) on normal subjects. Thirty-nine normal volunteers were subjected to PERG measurements following the standard set by the International Society for Clinical Electrophysiology of Vision (ISCEV). The AL of the eyeball was measured using a TOMEY ultrasonic A scanner. Each volunteer had a complete ophthalmic examination including visual acuity, refraction, intraocular pressure, visual field, colour vision, orthoptic assessment and retinal photographs and had a best corrected visual acuity of 6/9 or better. Only one eye from each of the 39 normal volunteers was included in the statistical analysis of the results. The normal volunteer group had a mean P50 amplitude of 3.8 +/- 1.1 SD microV. The range of AL was between 21.8 and 25.7 mm (mean = 23.8 +/- 1.0 SD mm). Overall findings obtained from this investigation indicate a significant correlation between the AL of normal eyes and the PERG P50 amplitude (Spearman rank correlation coefficient r = -0.413, p < 0.01). The correlation accounts for 17% of the variance observed in the 39 amplitude values. This confirms the current hypothesis that the PERG amplitude is inversely related to axial length and means that AL should be considered when interpreting PERG amplitudes.

  10. 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

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

    PubMed

    Adriaens, Michiel E; Jaillard, Magali; Eijssen, Lars M T; Mayer, Claus-Dieter; Evelo, Chris T A

    2012-01-25

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

  12. Pupil size and retinal straylight in the normal eye.

    PubMed

    Franssen, Luuk; Tabernero, Juan; Coppens, Joris E; van den Berg, Thomas J T P

    2007-05-01

    Glare problems originating from bright lights are generally experienced more strongly at night. The typical disability glare is known to result from retinal straylight. In this study, the effects of pupil diameter and, especially in the case of small pupils, of eye wall translucency on the amount of retinal straylight were investigated. Straylight was measured as a function of pupil diameter ranging from 1.3 to >8 mm in five normal subjects by using a white-light, CRT-based system for scattering angles of 3.5 degrees , 7 degrees , and 14 degrees . In the study of red-free light, a yellow-LED based system was used with the same five subjects for scattering angles of 3.5 degrees , 10 degrees , and 28 degrees . Data were analyzed to assess effects of (1) inhomogeneity of light-scattering over the pupil plane, (2) translucency of the eye wall, and (3) effects of the periphery of the lens. To estimate the order of magnitude of pupil contraction in the typical glare situation, pupil reflexes resulting from the sudden appearance of headlight-equivalent bright lights were recorded in three subjects in a laboratory environment. For natural pupils (between 2 and 7 mm diameter), straylight weakly depends on pupil diameter (within 0.2 log units). For large scatter angles and small pupil diameters, eye wall translucency contributes significantly to straylight in a wavelength- and pigmentation-dependent manner. Pupil diameters decreased to photopic values under typical night-driving glare conditions. In normal eyes, straylight values measured with photopic pupils are by approximation also valid for mesopic and scotopic pupils, such as in night driving. Measurement of straylight under large angle and small pupil conditions can be used for quantitative assessment of eye wall translucency.

  13. 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.

  14. 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.

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

    PubMed Central

    2011-01-01

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

  16. Algorithm for correcting the keratometric estimation error in normal eyes..

    PubMed

    Camps, Vicente J; Pinero Llorens, David P; de Fez, Dolores; Coloma, Pilar; Caballero, Maria Teresa; Garcia, Celia; Miret, Juan J

    2012-02-01

    To obtain an accurate algorithm for calculating the keratometric index that minimizes the errors in the calculation of corneal power assuming only a single corneal surface in the range of corneal curvatures of the normal population. Corneal power was calculated by using the classical keratometric index and also by using the Gaussian equation. Differences between types of calculation of corneal power were determined and modeled by regression analysis. We proposed two options for the selection of the most appropriate keratometric index (n(k)) value for each specific case. First was the use of specific linear equations (depending on the ratio of the anterior to the posterior curvature, k ratio) according to the value of the central radius of curvature of the anterior corneal surface (r(1c)) in 0.1 mm steps and the theoretical eye model considered. The second was the use of a general simplified equation only requiring r(1c) (Gullstrand eye model, n(k) = -0.0064286r(1c) + 1.37688; Le Grand eye model, n(k) = -0.0063804r(1c) + 1.37806). The generalization of the keratometric index (n(k)) value is not an appropriate approximation for the estimation of the corneal power and it can lead to significant errors. We proposed a new algorithm depending on r(1c), with a maximal associated error in the calculation of the corneal power of 0.5 D and without requiring knowledge of the posterior corneal curvature.

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

    PubMed Central

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

    2013-01-01

    While Illumina microarrays can be used successfully for detecting small gene expression changes due to their high degree of technical replicability, there is little information on how different normalization and differential expression analysis strategies affect outcomes. To evaluate this, we assessed concordance across gene lists generated by applying different combinations of normalization strategy and analytical approach to two Illumina datasets with modest expression changes. In addition to using traditional statistical approaches, we also tested an approach based on combinatorial optimization. We found that the choice of both normalization strategy and analytical approach considerably affected outcomes, in some cases leading to substantial differences in gene lists and subsequent pathway analysis results. Our findings suggest that important biological phenomena may be overlooked when there is a routine practice of using only one approach to investigate all microarray datasets. Analytical artefacts of this kind are likely to be especially relevant for datasets involving small fold changes, where inherent technical variation—if not adequately minimized by effective normalization—may overshadow true biological variation. This report provides some basic guidelines for optimizing outcomes when working with Illumina datasets involving small expression changes. PMID:27605185

  18. 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

  19. Diode laser endoscopic cyclophotocoagulation in the normal equine eye.

    PubMed

    Harrington, Jay T; McMullen, Richard J; Cullen, John M; Campbell, Nigel B; Gilger, Brian C

    2013-03-01

    To determine the clinical and histologic effects of diode endoscopic cyclophotocoagulation (ECP) in the phakic equine eye. Phase I: 10 equine cadaver eyes. Phase II: four normal adult horses. Phase I: ECP probe angle of reach (AR) was determined. Multiple ECP energy levels: 0.75, 0.90, 1.05, 1.20, 1.35, 1.50 J, and the resulting visible and histologic ciliary process changes were evaluated. Phase II: Ocular quadrants were treated with ECP at 0.90, 1.14, 1.38 J, and a control. The contralateral eye underwent a sham operation. Tissue changes (clinical and histologic) were evaluated. Phase I: Mean combined AR was 162 ± 29 degrees. Mean visible tissue scores: 2.60 ± 0.58 (0.75 J) to 5.04 ± 0.30 (1.50 J) from possible total of 6. Tissue 'popping' was observed at 1.50 J. Histologic ciliary tissue damage was present at all settings. Phase II: Mean visible tissue scores: 2.90 ± 0.48 (0.90 J), 3.61 ± 0.57 (1.14 J), and 4.52 ± 0.56 (1.38 J). Tissue 'popping' was observed at 1.38 J. Histologic ciliary tissue damage was present at all settings. Clinical effects included acute inflammation, intraocular pressure reduction, cataract formation, corneal edema, corneal ulceration, and postoperative ocular hypertension. Diode ECP between 0.90 and 1.14 J is a potential treatment option for glaucoma in horses based on visible tissue effects and target ciliary epithelium damage. Iatrogenic cataract development may limit the use of an anterior chamber approach in phakic horses. Supported in part by an ACVO VAF grant. © 2012 American College of Veterinary Ophthalmologists.

  20. Microarray analysis of differentially expressed genes in preeclamptic and normal placental tissues.

    PubMed

    Ma, K; Lian, Y; Zhou, S; Hu, R; Xiong, Y; Ting, P; Xiong, Y; Li, X; Wang, X

    2014-01-01

    To detect the candidate genes for preeclampsia (PE). The gene expression profiles in preeclamptic and normal placental tissues were analyzed using cDNA microarray approach and the altered expression of important genes were further confirmed by real-time RT-PCR (reverse transcription polymerase chain reaction) technique. Total RNA was extracted from placental tissues of three cases with severe PE and from three cases with normal pregnancy. After scanning, differentially expressed genes were detected by software. In two experiments (the fluorescent labels were exchanged), a total of 111 differentially expressed genes were detected. In placental tissue ofpreeclamptic pregnancy, 68 differentially expressed genes were up-regulated, and 44 differentially expressed genes were down-regulated. Of these genes, 16 highly differentially expressed genes were confirmed by real-time fluorescent quantitative RT-PCR, and the result showed that the ratio of gene expression differences was comparable to that detected by cDNA microarray. The results of bioinformatic analysis showed that encoding products of differentially expressed genes were correlated to infiltration of placenta trophoblastic cells, immunomodulatory factors, pregnancy-associated plasma protein, signal transduction pathway, and cell adhesion. Further studies on the biological function and regulating mechanism of these genes will provide new clues for better understanding of etiology and pathogenesis of PE.

  1. 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.

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

    SciTech Connect

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

    1988-12-01

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

  3. 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.

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

    PubMed Central

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

    2015-01-01

    New minimal invasive diagnostic methods for early detection of lung cancer are urgently needed. It is known that the immune system responds to tumors with production of tumor-autoantibodies. Protein microarrays are a suitable highly multiplexed platform for identification of autoantibody signatures against tumor-associated antigens (TAA). These microarrays can be probed using 0.1 mg immunoglobulin G (IgG), purified from 10 µL of plasma. We used a microarray comprising recombinant proteins derived from 15,417 cDNA clones for the screening of 100 lung cancer samples, including 25 samples of each main histological entity of lung cancer, and 100 controls. Since this number of samples cannot be processed at once, the resulting data showed non-biological variances due to “batch effects”. Our aim was to evaluate quantile normalization, “distance-weighted discrimination” (DWD), and “ComBat” for their effectiveness in data pre-processing for elucidating diagnostic immune-signatures. “ComBat” data adjustment outperformed the other methods and allowed us to identify classifiers for all lung cancer cases versus controls and small-cell, squamous cell, large-cell, and adenocarcinoma of the lung with an accuracy of 85%, 94%, 96%, 92%, and 83% (sensitivity of 0.85, 0.92, 0.96, 0.88, 0.83; specificity of 0.85, 0.96, 0.96, 0.96, 0.83), respectively. These promising data would be the basis for further validation using targeted autoantibody tests. PMID:27600218

  5. 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.

  6. 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

  7. High-throughput biomarker segmentation on ovarian cancer tissue microarrays via hierarchical normalized cuts.

    PubMed

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

    2012-05-01

    We present a system for accurately quantifying the presence and extent of stain on account of a vascular biomarker on tissue microarrays. We demonstrate our flexible, robust, accurate, and high-throughput minimally supervised segmentation algorithm, termed hierarchical normalized cuts (HNCuts) for the specific problem of quantifying extent of vascular staining on ovarian cancer tissue microarrays. The high-throughput aspect of HNCut is driven by the use of a hierarchically represented data structure that allows us to merge two powerful image segmentation algorithms-a frequency weighted mean shift and the normalized cuts algorithm. HNCuts rapidly traverses a hierarchical pyramid, generated from the input image at various color resolutions, enabling the rapid analysis of large images (e.g., a 1500 × 1500 sized image under 6 s on a standard 2.8-GHz desktop PC). HNCut is easily generalizable to other problem domains and only requires specification of a few representative pixels (swatch) from the object of interest in order to segment the target class. Across ten runs, the HNCut algorithm was found to have average true positive, false positive, and false negative rates (on a per pixel basis) of 82%, 34%, and 18%, in terms of overlap, when evaluated with respect to a pathologist annotated ground truth of the target region of interest. By comparison, a popular supervised classifier (probabilistic boosting trees) was only able to marginally improve on the true positive and false negative rates (84% and 14%) at the expense of a higher false positive rate (73%), with an additional computation time of 62% compared to HNCut. We also compared our scheme against a k-means clustering approach, which both the HNCut and PBT schemes were able to outperform. Our success in accurately quantifying the extent of vascular stain on ovarian cancer TMAs suggests that HNCut could be a very powerful tool in digital pathology and bioinformatics applications where it could be used to

  8. 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.

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

    PubMed Central

    2010-01-01

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

  10. The cut-off value for normal nuchal translucency evaluated by chromosomal microarray analysis.

    PubMed

    Maya, Idit; Yacobson, Shiri; Kahana, Sarit; Yeshaya, Josepha; Tenne, Tamar; Agmon-Fishman, Ifaat; Cohen-Vig, Lital; Shohat, Mordechai; Basel-Vanagaite, Lina; Sharony, Reuven

    2017-01-30

    An association between isolated, increased nuchal translucency thickness and pathogenic chromosomal microarray analysis (CMA) has been reported. A recent meta-analysis reported that most studies used a 3.5 mm cut-off value. Considering nuchal translucency distribution and the commonly accepted 5% false positive rate in maternal serum screening, nuchal translucency cut-off levels should be reconsidered. This study evaluated the unique contribution of CMA to the investigation of foetuses with mildly increased nuchal translucency (NT) thickness of 3.0-3.4 mm. This was a retrospective, multicenter study. A single laboratory performed all genetic analyses. Comparative Genomic Hybridization Microarray analysis or Single Nucleotide Polymorphism Array technology was used for CMA. NT was divided into three groups (≤2.9; 3.0-3.4; ≥3.5 mm) and the results were compared, focusing on pregnancies with NT as the only medical indication for CMA at the time of the invasive procedure. If combined first trimester screening (NT and biochemistry) indicated increased risk for common aneuploidies, the case was excluded. CMA results were recorded in 1,588 pregnancies, of which 770 foetuses had NT as a normal or an isolated abnormal finding. Of these, 462 had NT ≤2.9 mm, 170 had NT 3.0-3.4 mm and 138 had NT ≥3.5 mm. Pathogenic copy number variations were found in 1.7%, 7.1%, and 13.0%, respectively. The results suggest that CMA should be part of the investigation in foetuses with isolated, mildly increased NT (3.0-3.4 mm). This article is protected by copyright. All rights reserved.

  11. 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

  12. Detection of Keratoconus in Clinically and Algorithmically Topographically Normal Fellow Eyes Using Epithelial Thickness Analysis

    PubMed Central

    Reinstein, Dan Z.; Archer, Timothy J.; Urs, Raksha; Gobbe, Marine; RoyChoudhury, Arindam; Silverman, Ronald H.

    2017-01-01

    PURPOSE To assess the effectiveness of a keratoconus-detection algorithm derived from Artemis very high-frequency (VHF) digital ultrasound (ArcScan Inc., Morrison, CO) epithelial thickness maps in the fellow eye from a series of patients with unilateral keratoconus. METHODS The study included 10 patients with moderate to advanced keratoconus in one eye but a clinically and algorithmically topographically normal fellow eye. VHF digital ultrasound epithelial thickness data were acquired and a previously developed classification model was applied for identification of keratoconus to the clinically normal fellow eyes. Pentacam (Oculus Optikgeräte, Wetzlar, Germany) Belin-Ambrósio Display (BAD) data (5 of 10 eyes), and Orbscan (Bausch & Lomb, Rochester, NY) SCORE data (9 of 10 eyes) were also evaluated. RESULTS Five of the 10 fellow eyes were classified as keratoconic by the VHF digital ultrasound epithelium model. Five of 9 fellow eyes were classified as keratoconic by the SCORE model. For the 5 fellow eyes with Pentacam and VHF digital ultrasound data, one was classified as keratoconic by the VHF digital ultrasound model, one (different) eye by a combined VHF digital ultrasound and Pentacam model, and none by BAD-D alone. CONCLUSIONS Under the assumption that keratoconus is a bilateral but asymmetric disease, half of the ‘normal’ fellow eyes could be found to have keratoconus using epithelial thickness maps. The Orbscan SCORE or the combination of topographic BAD criteria with epithelial maps did not perform better. PMID:26544561

  13. Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection.

    PubMed

    Borel, Nicole; Mukhopadhyay, Sanghamitra; Kaiser, Carmen; Sullivan, Erin D; Miller, Richard D; Timms, Peter; Summersgill, James T; Ramirez, Julio A; Pospischil, Andreas

    2006-10-19

    Chlamydophila pneumoniae infection has been implicated as a potential risk factor for atherosclerosis, however the mechanism leading to persistent infection and its role in the disease process remains to be elucidated. We validated the use of tissue microarray (TMA) technology, in combination with immunohistochemistry (IHC), to test antibodies (GroEL, GroES, GspD, Ndk and Pyk) raised against differentially expressed proteins under an interferon-gamma (IFN-gamma) induced model of chlamydial persistence. In the cell pellet array, we were able to identify differences in protein expression patterns between untreated and IFN-gamma treated samples. Typical, large chlamydial inclusions could be observed in the untreated samples with all antibodies, whereas the number of inclusions were decreased and were smaller and atypical in shape in the IFN-gamma treated samples. The staining results obtained with the TMA method were generally similar to the changes observed between normal and IFN-gamma persistence using proteomic analysis. Subsequently, it was shown in a second TMA including archival atheromatous heart tissues from 12 patients undergoing heart transplantation, that GroEL, GroES, GspD and Pyk were expressed in atheromatous heart tissue specimens as well, and were detectable morphologically within lesions by IHC. TMA technology proved useful in documenting functional proteomics data with the morphologic distribution of GroEL, GroES, GspD, Ndk and Pyk within formalin-fixed, paraffin-embedded cell pellets and tissues from patients with severe coronary atherosclerosis. The antibodies GroEL and GroES, which were upregulated under persistence in proteomic analysis, displayed positive reaction in atheromatous heart tissue from 10 out of 12 patients. These may be useful markers for the detection of persistent infection in vitro and in vivo.

  14. Comparison between eyelid indices of ptotic eye and normal fellow eye in patients with unilateral congenital ptosis.

    PubMed

    Bagheri, Abbas; Tavakoli, Mehdi; Najmi, Hadi; Erfanian Salim, Reza; Yazdani, Shahin

    2016-01-01

    To evaluate the relationship between levator muscle function (LMF) and other eyelid parameters in the normal and affected eyes of patients with unilateral congenital ptosis. This study includes subjects with unilateral congenital upper lid ptosis who were referred for operation over a 2-year period. Patients with other eyelid abnormalities and previous eyelid surgery were excluded. Eyelid parameters including LMF, lid fissure height (LFH) and margin reflex distance (MRD) were measured in both eyes and analyzed. A total of 77 patients with mean age of 26.4 ± 16.4 years were enrolled in the study. Mean LMF was 8.3 ± 4.6 mm in the ptotic and 13.1 ± 3.6 mm in the normal fellow eyes. Each millimeter of difference in LMF was associated with 0.30 mm of difference in LFH (95% CI: 0.25-0.35, P < 0.001) and 0.11 mm of difference in MRD of the ptotic eyes (95% CI: 0.08-0.12, P < 0.001) in the same direction. In addition, each millimeter of difference in LMF of ptotic eyes was associated with 0.48 mm of difference (95% CI: 0.33-0.62, P < 0.001) in LMF of non-ptotic eyes in the same direction. A direct correlation was observed between LMF, and LFH and MRD in ptotic eyes which confirms the role of levator muscle dysfunction in the development of congenital ptosis and its severity. Furthermore, a direct correlation was also present between LMF of ptotic and non-ptotic eyes suggesting possible bilateral involvement in apparently unilateral congenital ptosis. Copyright © 2015 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

  15. Enhanced Depth Imaging of Central Laminar Thickness in Optic Neuropathy: Comparison with Normal Eyes.

    PubMed

    Thitiwichienlert, Suntaree; Ishikawa, Hitoshi; Asakawa, Ken; Ikeda, Tetsuya; Shimizu, Kimiya

    2015-08-01

    The purpose of this study was to compare central laminar thickness (LT) among patients with glaucomatous optic neuropathy (GON), patients with non-GON, and normal subjects using enhanced-depth imaging optical coherence tomography (EDI-OCT). Enrolled were 57 patients (n = 64 eyes), including 30 women and 27 men. Three groups were identified: GON (n = 18 eyes), non-GON (n = 16 eyes), and control (n = 30 eyes). The GON group comprised eyes with primary open-angle glaucoma (POAG) (n = 9) and normal-tension glaucoma (NTG) (n = 9). The non-GON group comprised eyes with demyelinating optic neuritis (n = 9), anterior ischemic optic neuropathy (AION) (n = 2), compressive ON (n = 2), Leber hereditary ON (n = 2), and traumatic ON (n = 1). GON and non-GON groups were further divided into mild, moderate, and severe subgroups. Inclusion in the GON group was based on mean deviations (MDs) of visual fields; inclusion in the non-GON group was based on critical flicker frequency (CFF) responses. Intraclass correlation coefficients (ICCs) were used to verify reproducibility of measurements. LTs of GON and non-GON group eyes were thinner than those of control group eyes (p < 0.01); LTs of GON group eyes were thinner than those of non-GON group eyes (p = 0.01). LTs of severe GON subgroup eyes were thinner than those of moderate and mild GON subgroup eyes (p < 0.001; p = 0.024, respectively). LTs of severe non-GON subgroup eyes were thinner than those of mild non-GON subgroup eyes (p = 0.002). These results show that EDI-OCT is valuable for documenting structural abnormalities in optic neuropathy (ON).

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

    ERIC Educational Resources Information Center

    Martos, F. J.; Vila, J.

    1990-01-01

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

  17. Genomic microarray in fetuses with increased nuchal translucency and normal karyotype: a systematic review and meta-analysis.

    PubMed

    Grande, M; Jansen, F A R; Blumenfeld, Y J; Fisher, A; Odibo, A O; Haak, M C; Borrell, A

    2015-12-01

    To estimate the incremental yield of detecting copy number variants (CNVs) by genomic microarray over karyotyping in fetuses with increased nuchal translucency (NT) diagnosed by first-trimester ultrasound. This was a systematic review conducted in accordance with PRISMA criteria. We searched PubMed, Ovid MEDLINE and Web of Science for studies published between January 2009 and January 2015 that described CNVs in fetuses with increased NT, usually defined as ≥  3.5 mm, and normal karyotype. Search terms included: fetal or prenatal, nuchal translucency or cystic hygroma or ultrasound anomaly, array comparative genomic hybridization or copy number variants, with related search terms. Risk differences were pooled to estimate the overall and stratified microarray incremental yield using RevMan. Quality assessment of included studies was performed using the Quality Assessment tool for Diagnostic Accuracy Studies (QUADAS-2) checklist. Seventeen studies met the inclusion criteria for analysis. Meta-analysis indicated an incremental yield of 5.0% (95% CI, 2.0-8.0%) for the detection of CNVs using microarray when pooling results. Stratified analysis of microarray results demonstrated a 4.0% (95% CI, 2.0-7.0%) incremental yield in cases of isolated NT and 7.0% (95% CI, 2.0-12.0%) when other malformations were present. The most common pathogenic CNVs reported were 22q11.2 deletion, 22q11.2 duplication, 10q26.12q26.3 deletion and 12q21q22 deletion. The pooled prevalence for variants of uncertain significance was 1%. The use of genomic microarray provides a 5.0% incremental yield of detecting CNVs in fetuses with increased NT and normal karyotype. Copyright © 2015 ISUOG. Published by John Wiley & Sons Ltd.

  18. Choroidal thickness predicts ocular growth in normal chicks but not in eyes with experimentally altered growth

    PubMed Central

    Nickla, Debora L; Totonelly, Kristen

    2017-01-01

    Background In hatchling chicks, the thickness of the choroid is quite variable. It has been postulated that thickness per se or the changes occurring during early life might play a causal role in the regulation of ocular growth. We tested this notion by measuring ocular dimensions in several experimental conditions that alter ocular growth and in the fellow eyes. Methods Chicks aged 12 to 14 days wore monocular lenses or diffusers (+10 D, n = 23; −10 D, n = 16; diffusers, n = 16) for four to five days. Fellow untreated eyes served as controls. A separate group of completely untreated birds aged eight days were also tested (n = 12). We tested two drugs known to alter ocular growth. The dopaminergic agonist quinpirole was injected daily for five days into eyes wearing negative lenses (n = 47). The muscarinic agonist oxotremorine was injected one time into normal eyes (n = 27). All eyes were measured using high-frequency A-scan ultrasonography at the start and end of the experiment. Spearman’s correlation coefficient was used in all analyses. Results Choroidal thickness predicted ocular growth rates in normal eyes: eyes with thinner choroids grew faster than those with thicker choroids (p = 0.0001). Furthermore, there was a negative correlation between initial thickness and the change in thickness (p = 0.0353). By contrast, eyes wearing lenses or diffusers did not show a correlation between initial thickness and growth rate. For lens-wearing eyes injected with quinpirole, which slowed growth, initial choroidal thickness predicted subsequent growth rate (p = 0.0126), similar to normal eyes. This was not so for oxotremorine, which stimulated growth. Conclusions The loss of the association between choroidal thickness and subsequent growth rate in eyes with experimentally altered growth implies an uncoupling of the choroidal response from the visual regulation of ocular growth. The negative correlation between initial thickness and ocular growth in eyes injected with

  19. 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.

  20. 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.

  1. Results of the Schirmer tear test performed with open and closed eyes in clinically normal horses.

    PubMed

    Trbolova, Alexandra; Ghaffari, Masoud Selk

    2017-05-31

    The Schirmer tear test (STT) is widely used in both human and veterinary ophthalmology. Two types of STTs have been developed: STT I and SST II. The STT I measures the basal and reflex tear production and is the most widely used STT. However, several factors influence the STT results such as the person performing the test and the location of the strip placement within the conjunctival sac. The aim of this study was to measure the basal and reflex tear production (STT I) in clinically normal horses with open versus closed eyes. Forty clinically healthy horses without any ocular diseases were included. On day 1, the STT I was first performed on all the horses with the eyes open followed by an STT I with closed eyes performed 30 min later. On day 2, all horses had their eyes closed during the first STT and the eyes open during the second test performed 30 min later. The mean value of the STTs performed on open eye was significantly less than the STT performed on closed eye on both days of examination. This study showed a small but statistically significant difference between STT values obtained with open versus closed eyes in clinically normal horses.

  2. Frequency Domain Electroretinography in Retinitis Pigmentosa versus Normal Eyes.

    PubMed

    Hassan-Karimi, Homa; Jafarzadehpur, Ebrahim; Blouri, Bahram; Hashemi, Hassan; Sadeghi, Arash Zare; Mirzajani, Ali

    2012-01-01

    To compare electroretinogram (ERG) characteristics in patients with retinitis pigmentosa (RP) and normal subjects using frequency domain analysis. Five basic ERG recordings were performed in normal subjects and patients with a clinical diagnosis of RP according to the ISCEV (International Society of Clinical Electrophysiology of Vision) protocol. Frequency domain analysis was performed by MATLAB software. Different frequency domain parameters were compared between the study groups. Peak frequency (Fmod) of flicker and oscillatory responses in RP patients showed significant (P<0.0001) high pass response as compared to normal controls. Peak frequency (Fmod) of the other responses was not significantly different between the two groups. In addition to conventional ERG using time domain methods, frequency domain analysis may be useful for diagnosis of RP. Oscillatory and flicker responses may be analyzed in frequency domain. Fast Fourier transform may reveal two distinct high pass responses (shift to higher frequencies) in Fmod. Time and frequency domain analyses may be performed simultaneously with many modern ERG machines and may therefore be recommended in RP patients.

  3. 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

  4. Choroidal thickness predicts ocular growth in normal chicks but not in eyes with experimentally altered growth.

    PubMed

    Nickla, Debora L; Totonelly, Kristen

    2015-11-01

    In hatchling chicks, the thickness of the choroid is quite variable. It has been postulated that thickness per se or the changes occurring during early life might play a causal role in the regulation of ocular growth. We tested this notion by measuring ocular dimensions in several experimental conditions that alter ocular growth and in the fellow eyes. Chicks aged 12 to 14 days wore monocular lenses or diffusers (+10 D, n = 23; -10 D, n = 16; diffusers, n = 16) for four to five days. Fellow untreated eyes served as controls. A separate group of completely untreated birds aged eight days were also tested (n = 12). We tested two drugs known to alter ocular growth. The dopaminergic agonist quinpirole was injected daily for five days into eyes wearing negative lenses (n = 47). The muscarinic agonist oxotremorine was injected one time into normal eyes (n = 27). All eyes were measured using high-frequency A-scan ultrasonography at the start and end of the experiment. Spearman's correlation coefficient was used in all analyses. Choroidal thickness predicted ocular growth rates in normal eyes: eyes with thinner choroids grew faster than those with thicker choroids (p = 0.0001). Furthermore, there was a negative correlation between initial thickness and the change in thickness (p = 0.0353). By contrast, eyes wearing lenses or diffusers did not show a correlation between initial thickness and growth rate. For lens-wearing eyes injected with quinpirole, which slowed growth, initial choroidal thickness predicted subsequent growth rate (p = 0.0126), similar to normal eyes. This was not so for oxotremorine, which stimulated growth. The loss of the association between choroidal thickness and subsequent growth rate in eyes with experimentally altered growth implies an uncoupling of the choroidal response from the visual regulation of ocular growth. The negative correlation between initial thickness and ocular growth in eyes injected with

  5. Eye-specific retinogeniculate segregation proceeds normally following disruption of patterned spontaneous retinal activity.

    PubMed

    Speer, Colenso M; Sun, Chao; Liets, Lauren C; Stafford, Ben K; Chapman, Barbara; Cheng, Hwai-Jong

    2014-11-07

    Spontaneous retinal activity (SRA) is important during eye-specific segregation within the dorsal lateral geniculate nucleus (dLGN), but the feature(s) of activity critical for retinogeniculate refinement are controversial. Pharmacologically or genetically manipulating cholinergic signaling during SRA perturbs correlated retinal ganglion cell (RGC) spiking and disrupts eye-specific retinofugal refinement in vivo, consistent with an instructive role for SRA during visual system development. Paradoxically, ablating the starburst amacrine cells (SACs) that generate cholinergic spontaneous activity disrupts correlated RGC firing without impacting retinal activity levels or eye-specific segregation in the dLGN. Such experiments suggest that patterned SRA during retinal waves is not critical for eye-specific refinement and instead, normal activity levels are permissive for retinogeniculate development. Here we revisit the effects of ablating the cholinergic network during eye-specific segregation and show that SAC ablation disrupts, but does not eliminate, retinal waves with no concomitant impact on normal eye-specific segregation in the dLGN. We induced SAC ablation in postnatal ferret pups beginning at birth by intraocular injection of a novel immunotoxin selective for the ferret vesicular acetylcholine transporter (Ferret VAChT-Sap). Through dual-patch whole-cell and multi-electrode array recording we found that SAC ablation altered SRA patterns and led to significantly smaller retinal waves compared with controls. Despite these defects, eye-specific segregation was normal. Further, interocular competition for target territory in the dLGN proceeded in cases where SAC ablation was asymmetric in the two eyes. Our data demonstrate normal eye-specific retinogeniculate development despite significant abnormalities in patterned SRA. Comparing our current results with earlier studies suggests that defects in retinal wave size, absolute levels of SRA, correlations between RGC

  6. 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

  7. 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.

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

    PubMed Central

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

    2016-01-01

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

  12. Central and peripheral corneal thickness measurement in normal and keratoconic eyes using three corneal pachymeters.

    PubMed

    Feizi, Sepehr; Jafarinasab, Mohammad Reza; Karimian, Farid; Hasanpour, Hosein; Masudi, Ali

    2014-01-01

    To assess the agreement among ultrasonic pachymetry, the Galilei dual Scheimpflug analyzer, and Orbscan II for central and peripheral (Galilei vs. Orbscan) corneal thickness (CCT and PCT) measurement in normal and keratoconic eyes. In this prospective study, CCT and PCT were measured in 88 eyes of 88 refractive surgery candidates and 128 eyes of 69 keratoconic patients with ultrasonic pachymetry, the Galilei, and Orbscan II. The readings by the three instruments were compared using one-way analysis of normal variance. Agreement among the three devices was assessed using Pearson and intraclass correlation coefficients, and Bland-Altman plots. The same analyses were employed to evaluate agreement between Galilei and Orbscan II for PCT measurement. In the normal group, mean CCT was 551.0±39.4, 566.9±33.5, and 565.5±40.9 μm measured by ultrasonic pachymetry, the Galilei, and Orbscan II, respectively (P<0.001). The corresponding figures in the keratoconus group were 492.0±61.7, 502.0±42.1, and 470.6±56.9 μm, respectively (P<0.001). Mean PCT was 612.5±35.3 and 640.9±38.0 μm in the normal group (P<0.001) and 567.6±35.2 and 595.1±41.4 μm in the keratoconus group (P<0.001) by the Galilei and Orbscan II, respectively. CCT and PCT measurements obtained by different devices were significantly correlated in both groups. To measure CCT, the Galilei and Orbscan II can be used interchangeably in normal eyes, but not in keratoconic eyes. For PCT, there is a systematic error between measurements obtained by the Galilei and Orbscan II. However, it is possible to change optical pachymeter readings into those obtained by ultrasonic pachymetry using a constant.

  13. Differential eye movements in mild traumatic brain injury versus normal controls.

    PubMed

    Cifu, David X; Wares, Joanna R; Hoke, Kathy W; Wetzel, Paul A; Gitchel, George; Carne, William

    2015-01-01

    Objective measures to diagnose and to monitor improvement of symptoms following mild traumatic brain injury (mTBI) are lacking. Computerized eye tracking has been advocated as a rapid, user friendly, and field-ready technique to meet this need. Eye-tracking data collected via a head-mounted, video-based binocular eye tracker was used to examine saccades, fixations, and smooth pursuit movement in military Service Members with postconcussive syndrome (PCS) and asymptomatic control subjects in an effort to determine if eye movement differences could be found and quantified. Sixty Military Service Members with PCS and 26 asymptomatic controls. The diagnosis of mTBI was confirmed by the study physiatrist's history, physical examination, and a review of any medical records. Various features of saccades, fixation and smooth pursuit eye movements were analyzed. Subjects with symptomatic mTBI had statistically larger position errors, smaller saccadic amplitudes, smaller predicted peak velocities, smaller peak accelerations, and longer durations. Subjects with symptomatic mTBI were also less likely to follow a target movement (less primary saccades). In general, symptomatic mTBI tracked the stepwise moving targets less accurately, revealing possible brain dysfunction. A reliable, standardized protocol that appears to differentiate mTBI from normals was developed for use in future research. This investigation represents a step toward objective identification of those with PCS. Future studies focused on increasing the specificity of eye movement differences in those with PCS are needed.

  14. Vessel Caliber in Normal Tension and Primary Open Angle Glaucoma Eyes With Hemifield Damage.

    PubMed

    Rao, Aparna; Agarwal, Komal; Mudunuri, Harika; Padhy, Debananda; Roy, Avik K; Mukherjee, Sujoy

    2017-01-01

    The purpose of the study was to evaluate retinal vessel diameter in age-matched normal tension glaucoma (NTG) and primary open angle glaucoma (POAG) eyes with hemifield involvement. Fundus photographs of patients with hemifield defect, good visibility of retinal nerve fiber layer defect, and vessels were compared with 30 controls. One eye of each patient (28 NTG and 30 POAG) was randomly chosen for analysis using Image J software by different clinicians at 2 levels. The structural parameters analyzed included retinal nerve fiber layer defect width, diameter of vessels (superotemporal or inferotemporal artery and superotemporal or inferotemporal vein). The average superotemporal artery diameter was similar in NTG (71±16.8 µm), POAG (79±26.6 µm), and controls (82±14.1 µm), P=0.2 with similar pattern seen for other vessels. The affected quadrant in all eyes and those with disc hemorrhage (n=8) did not have significantly different arteries and veins diameter as compared with the unaffected quadrant in that eye. No relation of artery or vein diameter with retinal nerve fiber layer defect width or clinical variables in NTG or POAG eyes was seen on multivariate regression analysis. The vessel diameter was not significantly different in the affected and unaffected quadrants of age and severity-matched NTG and POAG eyes with hemifield structural and functional defect as reported in earlier studies. These results point toward the possibility that vascular diameter changes may not be the cause for glaucomatous changes.

  15. Intereye asymmetry in bilateral keratoconus, keratoconus suspect and normal eyes and its relationship with disease severity.

    PubMed

    Naderan, Mohammad; Rajabi, Mohammad Taher; Zarrinbakhsh, Parviz

    2017-04-21

    To describe the intereye asymmetry in patients with keratoconus (KC), keratoconus suspect (KCS) and normal participants, and to evaluate the relationship between asymmetry and disease severity. In this prospective observational comparative study, 446 patients with bilateral KC, 68 patients with bilateral KCS and 306 normal participants underwent topographic, keratometric and pachymetric evaluations by Pentacam as well as refractive and visual acuity examinations. The intereye asymmetry in each parameter was calculated and compared between the groups. All parameters were significantly different between the worse and better eyes in the KC group (p<0.05), but not in the KCS and normal groups. No significant differences were observed in the measurements of the worse and better eyes of the normal group (p>0.05). There was a statistically significant greater intereye asymmetry in all parameters in the KC group compared with the KCS and normal groups (p<0.05). The intraclass correlations were poor in patients with KC, moderate to good in patients suspected with KC and strong in normal participants. There were statistically significant relationships between the intereye asymmetry in all parameters and KC severity in the worse eye in which intereye asymmetry significantly increased with an increase in disease severity, based on Keratoconus Severity Score classification (p<0.05). According to receiver operating characteristic analysis, the intereye asymmetry would effectively discriminate KC and KCS from normal eyes. KC is an asymmetric disease, and the degree of asymmetry is associated with disease severity. The analysis of intereye asymmetry should be performed along with unilateral evaluation in the screening of KC. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  16. 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

  17. 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.

  18. 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

  19. Normal macular thickness measurements using optical coherence tomography in healthy eyes of adult Chinese persons: the Handan Eye Study.

    PubMed

    Duan, Xin Rong; Liang, Yuan Bo; Friedman, David S; Sun, Lan Ping; Wong, Tien Yin; Tao, Qiu Shan; Bao, Lingzhi; Wang, Ning Li; Wang, Jie Jin

    2010-08-01

    To describe macular thickness measured by optical coherence tomography (OCT) in healthy eyes of adult Chinese persons. Population-based cross-sectional study. Chinese adults aged 30+ years who were residents of Handan, North China. The Handan Eye Study is a population-based study of eye disease in Chinese persons. Eligible residents underwent a comprehensive ophthalmic examination including OCT (Stratus OCT, Carl Zeiss Meditec Inc., Jena, Germany). Fast macular thickness scans were performed over maculae within 6 mm in diameter, divided into 3 regions (central, inner, and outer, with a diameter of 1, 3, and 6 mm, respectively) and 9 quadrants (1 in the central region and 4 each in the inner and outer regions). Retinal thickness (means and standard deviations) was calculated by OCT mapping software, presented for foveal minimum, central macula (within 1 mm diameter), and inner and outer regions divided by 8 quadrants. Macular thickness measured by OCT. Of the 6830 participants (90.4% response rate) examined, 2230 eyes of healthy subjects with high-quality OCT scans were selected (32.7% of participants; mean age, 46.4+/-9.9 years, 58.4% were women). The mean foveal minimum, central, inner, and outer macular thicknesses were 150.3 (18.1) microm, 176.4 (17.5) microm, 255.3 (14.9) microm, and 237.7 (12.4) microm, respectively (overall differences, P<0.001). The mean foveal volume was 0.139 (0.014) mm(3), and the mean total macular volume was 6.761 (0.516) mm(3). In the inner region, the nasal quadrant was thinner than the superior and inferior quadrants, and in the outer region, the nasal quadrant was the thickest (P<0.001). Age was positively correlated with foveal (beta coefficient = 3.582) and central macular (beta coefficient = 2.422) thicknesses. The foveal minimum, central, inner, and outer macular thicknesses were significantly greater in men than in women. Fasting plasma glucose was negatively correlated with central macular thickness (2.416 mm reduction per

  20. CHOROIDAL MORPHOLOGY IN EYES WITH POLYPOIDAL CHOROIDAL VASCULOPATHY AND NORMAL OR SUBNORMAL SUBFOVEAL CHOROIDAL THICKNESS.

    PubMed

    Lee, Won Ki; Baek, Jiwon; Dansingani, Kunal K; Lee, Jae Hyung; Freund, K Bailey

    2016-12-01

    To subsegment the choroid in patients with polypoidal choroidal vasculopathy and to determine whether the ratio of choriocapillaris/Sattler layer thickness to total choroidal thickness is decreased at sites of polypoidal pathology. Retrospective, observational, cross-sectional study. A total of 320 eyes of 305 patients with polypoidal choroidal vasculopathy were studied with optical coherence tomography and dye angiography. The ratio of choriocapillaris/Sattler layer thickness to total choroidal thickness was calculated at polypoidal lesion sites in eyes with subfoveal choroidal thickness (SFCT) ≤200 μm. Mean SFCT was 267.7 ± 118.5 μm for the entire cohort. Mean SFCT was 151.2 ± 35.0 μm in eyes with SFCT ≤200 μm (n = 124, 39%). In this subgroup, dilated Haller vessels (pachyvessels) were identified under the site of neovascular ingrowth in 117 eyes (94%). Choroidal thickness in the pachyvessel zone was greater (213.3 ± 52.2 μm) than SFCT (P < 0.001) with a significantly lower choriocapillaris/Sattler layer to total thickness ratio (P < 0.001). Qualitative alterations of the retinal pigment epithelium were observed in 60 eyes (51%). Eyes with normal or subnormal SFCT exhibited extrafoveal choroidal thickening at sites of polypoidal disease. The choriocapillaris and Sattler layers were attenuated at these locations, but Haller vessels were markedly dilated. These changes were topographically associated with sites of neovascular ingrowth and support the classification of polypoidal choroidal vasculopathy as a pachychoroid disorder.

  1. Central and Peripheral Corneal Thickness Measurement in Normal and Keratoconic Eyes Using Three Corneal Pachymeters

    PubMed Central

    Feizi, Sepehr; Jafarinasab, Mohammad Reza; Karimian, Farid; Hasanpour, Hosein; Masudi, Ali

    2014-01-01

    Purpose: To assess the agreement among ultrasonic pachymetry, the Galilei dual Scheimpflug analyzer, and Orbscan II for central and peripheral (Galilei vs. Orbscan) corneal thickness (CCT and PCT) measurement in normal and keratoconic eyes. Methods: In this prospective study, CCT and PCT were measured in 88 eyes of 88 refractive surgery candidates and 128 eyes of 69 keratoconic patients with ultrasonic pachymetry, the Galilei, and Orbscan II. The readings by the three instruments were compared using one-way analysis of normal variance. Agreement among the three devices was assessed using Pearson and intraclass correlation coefficients, and Bland–Altman plots. The same analyses were employed to evaluate agreement between Galilei and Orbscan II for PCT measurement. Results: In the normal group, mean CCT was 551.0±39.4, 566.9±33.5, and 565.5±40.9 μm measured by ultrasonic pachymetry, the Galilei, and Orbscan II, respectively (P<0.001). The corresponding figures in the keratoconus group were 492.0±61.7, 502.0±42.1, and 470.6±56.9 μm, respectively (P<0.001). Mean PCT was 612.5±35.3 and 640.9±38.0 μm in the normal group (P<0.001) and 567.6±35.2 and 595.1±41.4 μm in the keratoconus group (P<0.001) by the Galilei and Orbscan II, respectively. CCT and PCT measurements obtained by different devices were significantly correlated in both groups. Conclusion: To measure CCT, the Galilei and Orbscan II can be used interchangeably in normal eyes, but not in keratoconic eyes. For PCT, there is a systematic error between measurements obtained by the Galilei and Orbscan II. However, it is possible to change optical pachymeter readings into those obtained by ultrasonic pachymetry using a constant. PMID:25667728

  2. Measurement of Central Corneal Thickness Using Ultrasound Pachymetry and Orbscan II in Normal Eyes.

    PubMed

    Sadoughi, Mohammad Mehdi; Einollahi, Bahram; Einollahi, Neda; Rezaei, Javad; Roshandel, Danial; Feizi, Sepehr

    2015-01-01

    To compare ultrasound pachymetry and Orbscan II for measurement of central corneal thickness (CCT) in normal eyes. The current study was performed at Labbafinejad Medical Center (LMC), Tehran, Iran. Three hundred eyes from 150 healthy individuals referred for keratorefractive surgery were assessed first by Orbscan II and then by ultrasound pachymetry, and CCT values were recorded and compared. Overall, Orbscan II overestimated CCT as compared to ultrasound pachymetry by about 2.4% (mean values 547.6 ± 34.7 versus 534.8 ± 34.7, respectively, P < 0.001). The difference was more significant when CCT was less than 500 microns (mean values 493.2 ± 16.9 versus 479.9 ± 15.6, mean overestimation: 2.6%, P < 0.001). There was good linear correlation between the two methods (Pearson's correlation r = 0.968, P < 0.0001). Orbscan II has good correlation with ultrasound pachymetry for measurement of CCT in normal eyes; however Orbscan II should not be used to evaluate corneal thickness before keratorefractive surgeries, as it tends to overestimate corneal thickness and may result in undesirable, low residual stromal thickness.

  3. 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

  4. 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.

  5. Juxtapapillary choroid is thinner in normal-tension glaucoma than in healthy eyes.

    PubMed

    Lee, Kyoung Min; Lee, Eun Ji; Kim, Tae-Woo

    2016-12-01

    To measure the juxtapapillary choroidal thickness in eyes with normal-tension glaucoma (NTG) and to compare it with healthy eyes. Twelve radial B-scan images of the optic nerve head (ONH) were obtained from 96 patients with NTG and 48 healthy subjects matched by age using swept-source (SS) optical coherence tomography (OCT). The juxtapapillary choroidal thickness was defined as the average choroidal thickness within 500 μm from the border tissue of Elschnig. Choroidal thinning in patients with NTG was assessed by calculating the relative choroidal thickness, defined as the ratio of the measured juxtapapillary choroidal thickness in each meridian to the corresponding value in age-matched healthy controls. Retinal nerve fibre layer (RNFL) damage as reflected by circumpapillary RNFL thickness (measured using spectral-domain OCT) was also assessed. The juxtapapillary choroid was significantly thinner in NTG eyes than in healthy control eyes in the inferotemporal and superotemporal sectors. The relative choroidal thinning was topographically associated with the hemispheric location of dominant RNFL damage. The average juxtapapillary choroidal thickness was not associated with either the global RNFL thickness or the visual field mean deviation. Age and untreated intraocular pressure were significantly associated with the juxtapapillary choroidal thickness in NTG eyes in both univariate and multivariate analyses (all p < 0.05). Decreased microvascular circulation in the ONH as a result of juxtapapillary choroidal thinning could be an important part of the pathogenesis of optic nerve damage in NTG. © 2016 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  6. 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.

  7. 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

  8. Histologic effect of semiconductor diode laser transscleral cyclophotocoagulation on the normal equine eye.

    PubMed

    Morreale, Raymond J; Wilkie, David A; Gemensky-Metzler, Anne J; Weisbrode, Steven E; Willis, Michelle A

    2007-01-01

    To determine the acute histologic effects of semiconductor diode laser transscleral cyclophotocoagulation (TSCP) on the normal equine eye. Part 1: eight eyes of four horses. Part 2: 10 eyes of five horses. Part 1: TSCP was performed on four eyes at 4 mm and four eyes at 6 mm posterior to the limbus with 15 sites treated in four quadrants at 1800 mW for 1500 ms. The globes were sectioned transversely or sagitally to examine all quadrants and histologic sections were taken every 1 mm for the entire globe. Part 2: Based on the results from Part 1, TSCP was performed at 20 sites 4 mm posterior to the dorsotemporal limbus with a constant energy varying from 0.75 to 4 J/site. Histologic sections were taken every 1 mm for a total of 10 sections per eye and 20 sections per energy level group. Part 1: At 4 mm posterior to the limbus, coagulation of the nonpigmented epithelium (NPE) of the pars plicata was observed in the temporal (14%) and dorsal quadrants (12%). Retinal detachment was observed in the nasal quadrant (12%). Hemorrhage was common in the nasal (19%) and temporal (12%) quadrants. At 6 mm posterior to the limbus, coagulation of the NPE of the pars plicata was observed in the dorsal (14%), ventral (16%), nasal (2%), and temporal (2%) quadrants. Retinal detachment was observed in the dorsal (8%), ventral (18%), nasal (20%) and temporal (2%) quadrants. Part 2: Settings of 0.75 J/site were ineffective; 1.5, 2.25 and 3 J/site damaged the pars plicata without disruption of anatomy; and 4 J/site caused disruption of normal architecture. The most appropriate site for equine TSCP appears to be 4 mm posterior to the dorso- and ventrotemporal limbus avoiding the 3 and 9 o'clock positions and using an initial energy setting of 2.25 J/site. This results in effective damage to the pars plicata while minimizing surgical complications such as retinal detachment and hemorrhage.

  9. Chromosomal Microarray Analysis in Fetuses with Growth Restriction and Normal Karyotype: A Systematic Review and Meta-Analysis.

    PubMed

    Borrell, Antoni; Grande, Maribel; Pauta, Montse; Rodriguez-Revenga, Laia; Figueras, Francesc

    2017-09-09

    To perform a systematic review of the literature and a meta-analysis to estimate the incremental yield of chromosomal microarray analysis (CMA) over karyotyping in fetal growth restriction (FGR). This was a systematic review conducted in accordance with the PRISMA criteria. All articles identified in PubMed, Ovid Medline, and ISI Web of Knowledge (Web of Science) from January 2009 to November 2016 describing pathogenic copy number variants (CNVs) in fetuses with growth restriction were included. Case reports were excluded. Risk differences were pooled to estimate the overall and stratified CMA incremental yield. Ten studies with full data available met the inclusion criteria for analysis. Combined data from these studies revealed a 4% (95% confidence interval [CI] 1-6%) incremental yield of CMA over karyotyping in nonmalformed growth-restricted fetuses, and a 10% (95% CI 6-14%) incremental yield in FGR when associated with fetal malformations. The most frequently found pathogenic CNVs were 22q11.2 duplication, Xp22.3 deletion, and 7q11.23 deletion (Williams-Beuren syndrome), particularly in isolated FGR. The use of genomic CMA provides a 4% incremental yield of detecting pathogenic CNVs in fetuses with isolated growth restriction and normal karyotype. © 2017 S. Karger AG, Basel.

  10. [Application of chromosomal microarray analysis for the diagnosis of children with intellectual disability/developmental delay and a normal karytype].

    PubMed

    Hu, Ting; Zhu, Hongmei; Zhang, Zhu; Wang, Jiamin; Liu, Hongqian; Zhang, Xuemei; Zhang, Haixia; Du, Ze; Li, Lingping; Wang, He; Liu, Shanling

    2017-04-10

    To assess the value of chromosomal microarray analysis (CMA) for the diagnosis of children with intellectual disability/developmental delay (ID/DD) but a normal karytype. Peripheral blood samples from 92 ID/DD patients were analyzed with CMA using Affymetrix CytoScan 750K arrays. The results were analyzed by ChAS v3.0 software. Eighteen cases (19.57%) were detected with abnormalities by CMA, among which 10 cases were diagnosed with microdeletion/microduplication syndromes. These included 2 Williams-Beuren syndromes, 2 Angelman syndromes, 2 Russell-Silver syndromes, 1 Smith-Magenis syndromes, 1 Wolf-Hirschhorn syndromes, 1 15q26 overgrowth syndrome and 1 Xq28 (MECP2) duplication syndrome. In addition, 8 cases were diagnosed with pathogenic copy number variations (pCNV). CMA can significantly improve the diagnostic rate for patients with ID/DD, which is of great value for the treatment of such children and guidance of reproduction for their parents. Therefore, CMA should become the first-line diagnostic test for patients with ID/DD.

  11. 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.

  12. Choroid is thinner in inferior region of optic disks of normal eyes.

    PubMed

    Tanabe, Hirotaka; Ito, Yasuki; Terasaki, Hiroko

    2012-01-01

    To determine the thickness of the choroid across the posterior pole of normal eyes. Twenty-eight clinic-based normal eyes (54.1 ± 20.0 years, -3.6 ± 4.1 diopter) were studied. The macula and retina around the optic disk were scanned with a spectral-domain optical coherence tomographic instrument. The retinal mapping program with the enhanced depth imaging technique was used, and the borders of the choroid were drawn manually in each optical coherence tomographic image. A choroidal thickness map was constructed by the built-in program, and the choroidal thickness in the different sectors of the Early Treatment Diabetic Retinopathy Study grid was measured and compared. The choroid inferior to the optic disk was significantly thinner than that in the other sectors of the outer ring of the Early Treatment Diabetic Retinopathy Study grid (superior, 196 ± 62 μm; inferior, 146 ± 47 μm; nasal, 183 ± 80 μm; and temporal, 193 ± 64 μm, P < 0.001). The mean choroidal thickness at the nasal sector of the macular region was significantly thinner than other regions of the Early Treatment Diabetic Retinopathy Study grid (superior, 268 ± 74 μm; inferior, 245 ± 73 μm; nasal, 190 ± 68 μm; temporal, 268 ± 63 μm; and central, 258 ± 88 μm; P < 0.05). Choroidal thickness maps showed that the thinner choroidal area spreads around the optic disk and the inferior part of the posterior pole. The thinner choroid inferior to the optic disk may be a natural anatomical architecture of normal eyes, and this area may be more susceptible to hypoxia or to elevated intraocular pressures.

  13. Scanning Laser Polarimetry with Variable and Enhanced Corneal Compensation in Normal and Glaucomatous Eyes

    PubMed Central

    Sehi, Mitra; Guaqueta, Delia C.; Feuer, William J.; Greenfield, David S.

    2007-01-01

    Purpose To investigate whether correction for atypical birefringence pattern (ABP) using scanning laser polarimetry with enhanced corneal compensation (SLP-ECC) reduces the severity of ABP compared with variable corneal compensation (SLP-VCC), and improves the correlation with visual function. Design Prospective observational study. Methods Normal and glaucomatous eyes enrolled from 4 clinical sites underwent complete examination, automated perimetry, SLP-ECC and SLP-VCC. Eyes were characterized in 3 groups based upon the typical scan score (TSS): normal birefringence pattern (NBP) was defined as TSS 80, mild ABP as TSS 61–79, moderate-severe ABP as TSS 60. For each of 4 SLP parameters the area under the ROC curve (AUROC) was calculated to compare the ability of SLP-ECC and SLP-VCC to discriminate between normal and glaucomatous eyes. Results Eighty-four normal volunteers and 45 glaucoma patients were enrolled. Mean TSS was significantly (p<0.001) greater using SLP-ECC (98.0 ± 6.6) compared to SLP-VCC (83.4 ± 22.5). The frequency of moderate-severe ABP images was significantly (p<0.001, McNemar test) higher using SLP-VCC (18 of 129, 14%) compared to SLP-ECC (1 of 129, 0.8%). Two SLP-ECC parameters (TSNIT average and inferior average) had significantly (p=0.01, p<0.001) higher correlation (r=0.45, r=0.50 respectively) with MD compared to SLP-VCC (r=0.34, r=0.37). Among eyes with moderate-severe ABP (N = 18), inferior average obtained using SLP-ECC had significantly (p=0.03) greater AUROC (0.91 ± 0.07) compared with SLP-VCC (0.78 ± 0.11). Conclusions SLP-ECC significantly reduces the frequency and severity of ABP compared to SLP-VCC and improves the correlation between RNFL measures and visual function. PMID:17157800

  14. [A comparison study of pulsitile ocular blood flow in normal eyes and primary open angle glaucoma].

    PubMed

    Zhang, Ming-Zhi; Fu, Zhi-Fu; Liu, Xiao-Rui; Zheng, C

    2004-04-01

    To compare pulsatile ocular blood flow (POBF) and intraocular pressure (IOP) in primary open angle glaucoma (POAG) and normal control group matched for age, sex and refraction error, to investigate the rule of hem-dynamics in POAG and to determine the sensitivity and specificity of POBF measurement as a diagnostic test for glaucoma. Prior to the test a questionnaire was completed to determine age, sex, refractive error, family history of glaucoma, history of eye diseases, ocular medication, medical history and using of systemic beta-blockers. Patients of POAG were determined by following diagnostics standards: (1) Three IOP >25 mm Hg in different times of one day. (2) The fluctuate of IOP > 8 mm Hg during 24 hours. (3) Typical glaucoma changes in the visual field. (4) Typical glaucoma changes in optic disc. There were 100 POAG subjects with single eye observed (50 male and 50 female). We picked up 100 eyes randomly (50 male and 50 female) in 534 normal persons who matched for following conditions: (1) Sex. (2) Discrepancy of age less than 5 years. (3) Discrepancy of the refraction error less than +/- 2.00 DS. as the normal comparison group. The tonometer used was the POBF Tonometry. Pulse amplitude of IOP (PA), pulsatile ocular blood flow (POBF), pulse/heart rate (PR), maximum-IOP (max-IOP), minimum-IOP (min-IOP) and average IOP (aver-IOP) were obtained before the medical therapy and 1 or 2 weeks after the operation. The correlation between the POBF & mean value of the perimeter was analyzed. POBF was analyzed to determine the sensitivity and specificity of POBF measurement as a diagnostic test. The value of POBF in POAG and normal control was (9.72 +/- 3.47) microl/s and (12.04 +/- 4.68) microl/s, respectively. POAG patients' POBF, PV, PA, and AVE-IOP were less than those in the normal control, and the difference was statistically significant. There was no statistically significant correlation between the changes of visual field and POBF (r = 0.224, P = 0

  15. Risk factors for visual field damage progression in normal-tension glaucoma eyes.

    PubMed

    Daugeliene, L; Yamamoto, T; Kitazawa, Y

    1999-02-01

    This study was carried out to evaluate intraocular or systemic factors associated with the visual field damage progression in eyes with normal-tension glaucoma (NTG). Forty-seven NTG eyes with a minimum follow-up of 5 years were enrolled into the retrospective study. A stepwise regression analysis was performed to correlate the visual field damage progression, expressed as the mean deviation (MD) change per year, with several independent clinical factors including age, history of disc hemorrhage, initial MD, mean intraocular pressure (IOP), peak IOP, diurnal fluctuation of IOP, presence of a beta zone of peripapillary atrophy, and use of Ca(2+)-channel blockers. Statistical analysis revealed that non-use of Ca(2+)-channel blockers (P = 0.01), peripapillary atrophy (P = 0.03) and disc hemorrhage (P = 0.04) were associated with visual loss progression. Risk factors unrelated to IOP were suggested to be associated with progression of visual field loss. Systemic use of Ca(2+)-channel blockers has a favorable effect on visual field prognosis in NTG eyes.

  16. Lamina cribrosa microarchitecture in normal monkey eyes part 1: methods and initial results.

    PubMed

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

    2015-02-03

    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. 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. 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. 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. Copyright 2015 The Association for Research in Vision and Ophthalmology, Inc.

  17. 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

  18. Comparison of cytologic and histologic evaluations of the conjunctiva in the normal equine eye.

    PubMed

    Bourges-Abella, Nathalie; Raymond-Letron, Isabelle; Diquelou, Armelle; Guillot, Emilie; Regnier, Alain; Trumel, Catherine

    2007-01-01

    To describe the cells observed in conjunctival brush cytology (CBC) from normal horses and compare these findings with conjunctival structural histology so as to understand which cells are recovered from CBC. This study was divided into three parts. (1) Conjunctival brush smears were collected from 20 healthy horses on both eyes and a differential count on 300 cells was carried out on May Grünwald-Giemsa (MGG) smears. (2) A similar protocol was used for whole eyes from five horses obtained rapidly after death from a slaughterhouse. The eyes were then assessed for conjunctival histology. (3) Cytobrush smears were collected from five healthy horses. Smears were examined after MGG or periodic acid Schiff (PAS) staining. The differential cell count showed a majority of deep and intermediate epithelial cells with very few superficial and goblet cells in both eyes. A stratified columnar to cuboidal epithelium was observed on nearly the whole surface of the conjunctiva. A stratified squamous type was observed at the palpebral and bulbar edges. Areas with highest mucus cell indices were found from the nasal to the temporal edge of the equine inferior conjunctiva in the upper palpebral segment near the fornix and in a part of the nasal fornix. In MGG smears no mucus cells were identified; however, they were numerous in PAS smears (22.6% +/- 11) and were mostly cylindrical cells (42.5% +/- 14.4 PAS positive). Cytobrush smears in the healthy horse are characterized by a majority of polyhedral and cylindrical cells and a few squamous cells. The cylindrical cells may be mucous cells and probably originate from the main stratified columnar to cuboidal epithelium.

  19. 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.

  20. Usefulness of frequency-doubling technology for perimetrically normal eyes of open-angle glaucoma patients with unilateral field loss.

    PubMed

    Fan, Xiang; Wu, Ling-Ling; Ma, Zhi-Zhong; Xiao, Ge-Ge; Liu, Feng

    2010-08-01

    To determine whether frequency-doubling technology (FDT) perimetry detects visual field loss in perimetrically normal eyes of patients with open-angle glaucoma (OAG) and whether these visual field defects subsequently are detected by standard automated perimetry (SAP), and to explore the relating factors of the progression from abnormalities based on FDT to visual field loss based on SAP. Prospective cohort study. Sixty-eight OAG patients with unilateral field loss detected by SAP (Octopus, G2 program; Interzeig, Schlieren, Switzerland). Perimetrically normal eyes of participants were examined with the FDT N-30 threshold program (Humphrey Instruments, Welch-Allyn, Skaneateles, NY). The visual field examination was followed by a series of SAP examinations administered over 3 years. The relationship between FDT and subsequent SAP results in perimetrically normal eyes was analyzed. Glaucomatous optic neuropathy (GON), visual field indices, intraocular pressure (IOP), and central corneal thickness (CCT) were compared between converters (eyes with subsequent SAP abnormality) and nonconverters within perimetrically normal eyes with abnormal FDT results. Finally, the SAP test points were matched to the abnormal FDT sectors. The relative risk (RR) of subsequent SAP abnormality corresponding to FDT abnormal sectors was calculated. Sixty perimetrically normal eyes of 60 participants had complete data and a qualifying follow-up. Baseline FDT results were abnormal in 65%. Of the eyes with abnormal FDT results, 51% developed abnormal SAP results after 4 to 27 months, whereas none of the eyes with normal FDT results developed abnormal SAP results (P<0.05). In perimetrically normal eyes with abnormal FDT results, converters had a greater cup-to-disc ratio, more eyes with GON, larger and deeper cups, and worse FDT mean deviation than nonconverters (P<0.05). The IOP and CCT did not differ between the 2 groups. The RR of subsequent SAP abnormality corresponding to abnormal FDT

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

    PubMed

    Kinoshita, Takamasa; 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

    To determine the effects of dynamic exercise on the circulation and the luminal and stromal areas of the choroid in normal eyes. 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. 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. 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.

  2. 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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  5. Three-dimensional profile of macular retinal thickness in normal Japanese eyes.

    PubMed

    Ooto, Sotaro; Hangai, Masanori; Sakamoto, Atsushi; Tomidokoro, Atsuo; Araie, Makoto; Otani, Tomohiro; Kishi, Shoji; Matsushita, Kenji; Maeda, Naoyuki; Shirakashi, Motohiro; Abe, Haruki; Takeda, Hisashi; Sugiyama, Kazuhisa; Saito, Hitomi; Iwase, Aiko; Yoshimura, Nagahisa

    2010-01-01

    To demonstrate the three-dimensional macular thickness distribution in normal subjects by spectral domain optical coherence tomography (SD-OCT) and evaluate its association with sex, age, and axial length. Mean regional retinal thickness measurements on the Early Treatment Diabetic Retinopathy Study (ETDRS) layout were obtained by three-dimensional raster scanning (6 x 6 mm) using SD-OCT in 248 normal eyes of 248 Japanese subjects. Mean foveal thickness was 222 +/- 19 microm; it was significantly greater in men (226 +/- 19 microm) than in women (218 +/- 18 microm; P = 0.002) and did not correlate with age in either sex. Mean sectoral retinal thickness was also significantly greater in the men than in the women in all the quadrants of the inner ring (1-3 mm; P < 0.001 and P = 0.001-0.007) and in the temporal quadrant of the outer ring (3-6 mm; P < 0.001). The retinal thicknesses of each of the ETDRS sectors did not correlate significantly with axial length after adjustment for age in either sex. Retinal thickness in six of the eight sectors in the inner and outer rings showed a negative correlation with age after adjustment for axial length in the men (P < 0.001 and P = 0.001-0.018), whereas no correlation with age was observed in the women. SD-OCT demonstrated the three-dimensional macular thickness distribution in normal eyes. Macular thickness varied significantly with sex and age. These variables should be considered while evaluating macular thickness.

  6. Anatomical attributes of the optic nerve head in eyes with parafoveal scotoma in normal tension glaucoma.

    PubMed

    Rao, Aparna; Mukherjee, Sujoy

    2014-01-01

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

  7. 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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Comparison of corneal topographic measurements and high order aberrations in keratoconus and normal eyes.

    PubMed

    Colak, Hatice Nur; Kantarci, Feride Aylin; Yildirim, Aydin; Tatar, Mehmet Gurkan; Goker, Hasan; Uslu, Hasim; Gurler, Bulent

    2016-10-01

    The aim of this report was to compare corneal topographic measurements and anterior high order corneal aberrations in eyes with keratoconus and normal eyes by using Scheimpflug-Placido topography. Eighty cases diagnosed with mild (group 1), moderate (group 2), and advanced (group 3) stage keratoconus (KC) according to Amsler-Krumeich Classification and 81 healthy (control group) cases were retrospectively examined. The mean keratometric measurements (as both diopters (Kavg) and mm values (mmavg)), central corneal thickness values (CCT), high order aberration (HOA), total wavefront aberration (TWA), coma, trefoil, and spherical aberration measurements were performed using Sirius topography equipment. The topographic values were compared between the groups. There were 25 cases in group 1 KC (15.5%), 34 cases in group 2 KC (21.1%), 21 cases in group 3 KC (13.1%), and 81 cases (50.3%) in the control group. In terms of mean age and gender distributions, there was no statistically significant difference between the groups (p>0.05). However, there was significant difference between the groups in terms of Kavg, CCT, HOA, TWA, coma, trefoil, and spherical aberration values (p<0.01). Mean HOA, TWA, coma, trefoil, and spherical aberration values were observed to increase with the severity of KC disease. Anterior high order corneal aberrations were significantly increased in eyes with moderate and advanced keratoconus. Anterior high order corneal aberration measurements are a useful tool to guide the physician in diagnosis and classification of keratoconus. Copyright © 2016 British Contact Lens Association. Published by Elsevier Ltd. All rights reserved.

  9. How red is a white eye? Clinical grading of normal conjunctival hyperaemia.

    PubMed

    Murphy, P J; Lau, J S C; Sim, M M L; Woods, R L

    2007-05-01

    To quantify the level of normal bulbar conjunctival hyperaemia using the Cornea and Contact Lens Research Unit (CCLRU) grading scale, and to investigate inter-observer agreement. Bulbar conjunctival hyperaemia was assessed by two trained observers, using the CCLRU grading scale (zero to four units) interpolated into 0.1 increments, on the right eye of 121 healthy, non-contact lens-wearing subjects (male=58, female=63, median age=28 years, range 16-77). The eye was observed using a slit-lamp bio-microscope (x 10 magnification) under diffuse, white illumination. The subject's position of gaze was directed to allow grading of four quadrants: superior, nasal, inferior, and temporal conjunctiva. Bulbar redness was defined as the average of those four grades of conjunctival hyperaemia. A further twenty subjects were recruited to assess inter-observer agreement (male=8, female=12, median age=23 years). The average bulbar redness was 1.93 (+/-0.32 SD) units. The nasal (2.3+/-0.4) and temporal (2.1+/-0.4) quadrants were significantly redder than the superior (1.6+/-0.4) and inferior (1.7+/-0.4) quadrants (P<0.0001). Males had redder eyes than females by 0.2 units. Inter-observer 95% limits of agreement for bulbar redness was 0.38 units. The average bulbar redness of 1.9 units was higher than expected, reflecting the design of the grading scale. A bulbar redness of greater than 2.6 units may be considered abnormal, and a change in bulbar redness of > or =0.4 units may be significant.

  10. Dynamic Sensitivity of Corneal TRPM8 Receptors to Menthol Instillation in Dry Eye Versus Normal Subjects.

    PubMed

    Corcoran, Peter; Hollander, David A; Ousler, George W; Angjeli, Endri; Rimmer, David; Lane, Keith; Abelson, Mark B

    2017-09-21

    To assess the sensitivity of corneal cold receptors to a known transient receptor potential melastatin 8 (TRPM8) agonist, menthol, in dry eye and normals, and to determine whether factors such as disease duration or age affect responses. Dry eye disease (DED) (N = 33) and normal (N = 15) subjects were randomly assigned to receive Rohto(®) Hydra (0.01% menthol) or Systane(®) Ultra treatments (OU) in a prospective, double-blind, crossover study. DED subjects had documented disease and symptom response scores >2 on a 0- to 5-point scale. Normals had no history of DED and scores <2 on the same scale. Endpoints included mean cooling score (0 = not cool and 10 = very cool) evaluated at 0, 0.5, 1, 2, 3, and 4 min post-instillation, sum cooling scores (5 time points, range 0-60), and ocular signs and symptoms. Mean (±SD) ages were similar, 62.2 ± 8.6-year (DED) versus 53.5 ± 7.6-year (normal). Corneal sensitivity scores were not different between groups. Mean cooling scores at 0.5-4 min post-menthol instillation were significantly higher in DED subjects (P ≤ 0.03). Sum cooling scores were significantly higher (P = 0.04) in DED subjects with a disease duration <10 years (N = 18, 28.3 ± 2.58) versus ≥10 years (N = 15, 20.2 ± 2.76). Age did not affect cooling response in either group. DED subjects had greater sensitivity to cold than normal subjects. DED duration, and not age, was critical to cooling sensitivity. The finding that cooling scores were higher in subjects with DED for less than 10 years compared to more than 10 years suggests that corneal cold receptor sensitivity decreases as the duration of DED increases.

  11. Mast cells are present in the choroid of the normal eye in most vertebrate classes.

    PubMed

    McMenamin, Paul Gerard; Polla, Emily

    2013-07-01

    Mast cells are bone marrow-derived tissue-homing leukocytes, which have traditionally been regarded as effector cells in allergic disorders, responses against parasites, and regulation of blood flow, but a broader perspective of their functional heterogeneity, such as immunomodulation, angiogenesis, tissue repair, and remodeling after injury, is now emerging. The persistence of mast cells in connective tissues throughout the evolution of vertebrates is evidence of strong selective pressure suggesting that these cells must have multiple beneficial and important roles in normal homeostasis. While mast cells are present within the uveal tract of eutherian mammals, there is little known about their presence in the choroid of other vertebrate classes. Eye tissues from a range of vertebrate species (fish, amphibian, reptiles, birds, marsupials, monotreme, and eutherian mammals) were investigated. Tissues were fixed in either 2% glutaraldehyde, 2% paraformaldehyde or a mixture of both and processed for resin embedding. Semi-thin sections of the retina and choroid were cut and stained with toluidine blue. Mast cells were identified in the choroid of all classes of vertebrates investigated except sharks. Their morphology, location, and staining characteristics were remarkably similar from teleost fish through to eutherian mammals and bore close morphological resemblance to mammalian connective tissue mast cells. The similar morphology and distribution of mast cells in the choroid of all vertebrate classes studied suggest a basic physiological function that has been retained since the evolution of the vertebrate eye. © 2013 American College of Veterinary Ophthalmologists.

  12. 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

  13. 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

  14. Comparison of optic disc topography in non-glaucomatous eyes of children with juvenile diabetes mellitus and normal children.

    PubMed

    Elgin, Ufuk; Cankaya, Bülent; Simsek, Tulay; Batman, Aygen

    2010-01-01

    To compare the optic disc topography parameters of children with juvenile diabetes mellitus and normal children using the Heidelberg Retinal Tomograph (HRT III) (Heidelberg Engineering, Heidelberg, Germany). The topographic optic disc parameters (cup volume, cup area, rim volume, rim area, disc area, mean cup-to-disc ratio, and mean cup depth) of 28 non-glaucomatous eyes of 28 children with type 1 diabetes mellitus and 28 eyes of 28 age-matched healthy children were compared using the nonparametric Mann-Whitney U test. No statistically significant differences were found between cup volume (P = .782), cup area (P = .878), rim volume (P = .853), disc area (P = .452), mean cup-to-disc ratio (P = .852), and mean cup depth (P = .711) of eyes of cases with diabetes mellitus and normal subjects. This result suggests that non-glaucomatous eyes of children with type 1 diabetes mellitus and healthy subjects have similar topographic optic disc characteristics. Copyright 2010, SLACK Incorporated.

  15. Comparison of eye-movement patterns in schizophrenic and normal adults during examination of facial affect displays.

    PubMed

    Shimizu, T; Shimizu, A; Yamashita, K; Iwase, M; Kajimoto, O; Kawasaki, T

    2000-12-01

    Patients with schizophrenia are known to have deficits in facial affect recognition. Subjects were 25 schizophrenic patients and 25 normal subjects who were shown pairs of slides of laughing faces and asked to compare the intensity of laughter in the two slides. Eye movements were recorded using an infrared scleral reflection technique. Normal subjects efficiently compared the same facial features in the two slides, examining the eyes and mouth, important areas for recognizing laughter, for a longer time than other regions of the face. Schizophrenic patients spent less time ex amining the eyes and mouth and often examined other regions of the face or areas other than the face. Similar results were obtained for the number of fixation points. That schizophrenic patients may have employed an inefficient strategy with few effective eye movements in facial comparison and recognition may help to explain the deficits in facial recognition observed in schizophrenic patients.

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

    SciTech Connect

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

    1985-06-15

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

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

    PubMed

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

    2017-03-01

    To determine the diurnal variations of the luminal and stromal areas of the choroid in normal eyes. 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. 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. The changes in the luminal area are most likely responsible for the diurnal change in the CCT and subfoveal choroidal area. UMIN000019060, Pre-results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

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

    PubMed

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

    2017-01-01

    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. 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. 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. Eyes with mild POAG could be differentiated from pre-perimetric glaucoma eyes, which also could be differentiated from

  7. 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

  8. Spectral-Domain OCT Analysis of Regional Epithelial Thickness Profiles in Keratoconus, Postoperative Corneal Ectasia, and Normal Eyes

    PubMed Central

    Rocha, Karolinne Maia; Straziota, Claudia Perez; Stulting, R. Doyle; Randleman, J. Bradley

    2014-01-01

    PURPOSE To assess corneal microarchitecture and regional epithelial thickness profile in eyes with keratoconus, postoperative corneal ectasia, and normal unoperated eyes using spectral-domain optical coherence tomography (SD OCT). METHODS Regional corneal epithelial thickness profiles of eyes with keratoconus (KC) and postoperative corneal ectasia (Ectasia) were measured with anterior segment SC OCT (Optovue RTVue-100, Optovue Inc., Fremont, CA) and compared retrospectively to those of normal eyes (Control). Epithelial thickness was assessed at 21 points, 0.5 mm apart, across the central 6-mm of the corneal apex in the horizontal and vertical meridians. RESULTS One hundred twenty eyes were evaluated, including 49 eyes from 29 patients with KC, 32 eyes from 16 patients with Ectasia, and 39 eyes from 21 control patients. Average epithelial thickness at the corneal apex was 41.18±6.47μm (range 30 to 51 μm) in eyes with KC, 46.5±6.72μm in eyes with ectasia (range 34 to 60 μm), and 50.45±3.92 μm in normal eyes (range 42 to 55 μm). Apical epithelial thickness was significantly thinner in eyes with KC (p <.0001) and ectasia (p=.0007) than it was in controls. Epithelial thickness ranges in all other areas varied widely for KC (SD, range 21 to 101 μm) and ectasia (SD, range 30 to 82 μm) compared to controls (SD, range 43 to 64), p = .0063 CONCLUSION Central epithelial thickness was, on average, significantly thinner in ectatic corneas compared to controls; however, both central and regional epithelial thickness was highly irregular and variable in corneas with keratoconus and postoperative corneal ectasia. These thickness variations may alter preoperative topographic features and measurements in unpredictable ways, especially steepest K values. Regional epithelial thickness cannot be assumed to be uniform in ectatic corneas and therefore may require direct measurement when considering treatments for which underlying stromal thickness is particularly important

  9. Elastic modulus of orbicularis oculi muscle in normal humans, humans with Graves' eye disease, and cynomolgus monkeys.

    PubMed

    Oestreicher, J H; Frueh, B R

    1995-06-01

    We built an experimental apparatus to investigate the passive elastic characteristics of orbicularis oculi muscle and examined specimens from normal humans, humans with stable Graves' eye disease, and cynomolgus monkeys. Stress-strain curves were determined and found to be exponential. The elastic modulus (Young's modulus), analogous to the stiffness of the material, was calculated as a function of strain. Elastic modulus as a function of instantaneous stress was linear. Monkey elastic modulus values were determined, but did not allow meaningful interspecies comparison because of the small sample size. No significant difference was found between normal humans and humans with Graves' eye disease with respect to elastic modulus values.

  10. The effects of topical aqueous sirolimus on tear production in normal dogs and dogs with refractory dry eye.

    PubMed

    Spatola, Ronald; Nadelstein, Brad; Berdoulay, Andrew; English, Robert V

    2017-10-03

    To evaluate the effect of twice daily aqueous 0.02% sirolimus drops on tear production in normal dogs and dogs with refractory keratoconjunctivitis sicca (KCS). Two groups of dogs were studied. Ten normal dogs with no signs of ocular disease were administered topical 0.02% sirolimus ophthalmic solution in right eye, and a vehicle control in the left eye twice daily for 4 weeks. Complete ophthalmic examinations, including Schirmer tear test were performed weekly. Eighteen dogs with refractory KCS were randomly assigned to receive 0.02% sirolumus ophthalmic solution or 0.02% tacrolimus ophthalmic solution twice daily. Complete ophthalmic examinations were was performed at 2 and 6 weeks following treatment. Tear production in the sirolimus-treated eyes of normal dogs was greater when compared to vehicle controls with a mean difference over all time points of 3.46 mm (95% CI 1.17, 5.75; P = 0.006). After 4 weeks of treatment, the mean difference was 5 mm (95% CI 1.95, 8.05; P = 0.002). In dogs with refractory dry eye, 37.5% of eyes treated with sirolimus exhibited increased tear production >4 mm/min after 6 weeks of treatment, compared to 20% of eyes receiving tacrolimus (P = 0.433). One normal dog experienced topical irritation to both sirolimus and vehicle-treatment. Side effects were not reported in any treated eyes with chronic KCS. Topical 0.02% sirolimus might be an alternative treatment for canine patients with keratoconjunctivits sicca. The drug appears safe when applied topically in an aqueous suspension for up to 6 weeks. While initial results are promising, further studies are warranted. © 2017 American College of Veterinary Ophthalmologists.

  11. 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

  12. Comparative analysis of the relationship between anterior and posterior corneal shape analyzed by Scheimpflug photography in normal and keratoconus eyes.

    PubMed

    Montalbán, Raúl; Alio, Jorge L; Javaloy, Jaime; Piñero, David P

    2013-06-01

    To analyze and compare the relationship between anterior and posterior corneal shape evaluated by a tomographic system combining the Scheimpflug photography and Placido-disc in keratoconus and normal healthy eyes, as well as to evaluate its potential diagnostic value. Comparative case series including a sample of 161 eyes of 161 subjects with ages ranging from 7 to 66 years and divided into two groups: normal group including 100 healthy eyes of 100 subjects, and keratoconus group including 61 keratoconus eyes of 61 patients. All eyes received a comprehensive ophthalmologic examination including an anterior segment analysis with the Sirius system (CSO). Antero-posterior ratios for corneal curvature (k ratio) and shape factor (p ratio) were calculated. Logistic regression analysis was used to evaluate if some antero-posterior ratios combined with other clinical parameters were predictors of the presence of keratoconus. No statistically significant differences between groups were found in the antero-posterior k ratios for 3-, 5- and 7-mm diameter corneal areas (p ≥ 0.09). The antero-posterior p ratio for 4.5- and 8-mm diameter corneal areas was significantly higher in the normal group than in the keratoconus group (p<0.01). The k ratio for 3, 5, and 7 mm was significantly higher in the keratoconus grade IV subgroup than in the normal group (p<0.01). Furthermore, significant differences were found in the p ratio between the normal group and the keratoconus grade II subgroup (p ≤ 0.01). Finally, the logistic regression analysis identified as significant independent predictors of the presence of keratoconus (p<0.01) the 8-mm anterior shape factor, the anterior chamber depth, and the minimal corneal thickness. The antero-posterior k and p ratios are parameters with poor prediction ability for keratoconus, in spite of the trend to the presence of more prolate posterior corneal surfaces compared to the anterior in keratoconus eyes.

  13. Quality of life in glaucoma patients and normal subjects related to the severity of damage in each eye.

    PubMed

    Pujol Carreras, O; Anton, A; Mora, C; Pastor, L; Gudiña, S; Maull, R; Vega, Z; Castilla, M

    2017-06-07

    To assess the quality of life in glaucoma patients and normal subjects, and to assess its relationship with the severity of damage in each eye. A cross-sectional study was conducted with prospective selection of cases. The study included 464 subjects and were distributed into 4categories. Subjects included in group 1 had both eyes normal, that is with a normal intraocular pressure (IOP), optic disk and visual fields (VF), or mild glaucoma, defined as untreated IOP>21mmHg and abnormal VF with mean defect (MD) over -6dB. Group 2 consisted of patients with both eyes with mild or moderate glaucoma, defined as untreated IOP>21mmHg and abnormal VF with MD between -6 and -12dB. Group 3 included patients with moderate to severe glaucoma, that is, untreated IOP>21mmHg and abnormal VF with MD of less than -12dB in both eyes. Group 4 consisted of patients with asymmetric glaucoma damage, that is, they had one eye with severe glaucoma and the other eye normal or with mild glaucoma. All subjects completed 3 different questionnaires. Global quality of life was evaluated with EuroQol-5D (EQ-5D). Vision related quality of life was assessed with Visual Function Questionnaire (VFQ-25). Quality of life related to ocular surface disease was measured with Ocular Surface Disease Index (OSDI). VFQ-25 showed that group 3 had significantly lower scores than group 1 in mental health (P=.006), dependence (P=.006), colour vision (P=.002), and peripheral vision (P=.002). EQ-5D showed no significant differences between any group, but a trend was found to greater difficulty in group 3 than in groups 1 and 2, and in all dimensions. OSDI showed a higher score, or which was the same as a major disability, in groups 2 and 3 than group 1 (P=.021 and P=.014, respectively). VFQ-25 only found significant differences between group 1 and group 4. Dimensions with significant differences were found between group 1 and 3 (both eyes with advanced or moderate glaucoma). These were not found between group 1 and

  14. 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.

  15. Dynamic changes of anterior segment in patients with different stages of primary angle-closure in both eyes and normal subjects.

    PubMed

    Lin, Jialiu; Wang, Zhonghao; Chung, Chuchen; Xu, Jianan; Dai, Miaomiao; Huang, Jingjing

    2017-01-01

    To compare changes in anterior segment parameters under light and dark (light-to-dark) conditions among eyes with chronic primary angle-closure glaucoma (CPACG), fellow eyes with confirmed or suspect primary angle-closure (PAC or PACS), and age-matched healthy eyes. Consecutive patients with CPACG in one eye and PAC/PACS in the fellow eye, as well as age-matched healthy subjects were recruited. Anterior segment optical coherence tomography measurements were conducted under light and dark conditions, and anterior chamber, lens, and iris parameters compared. Demographic and biometric factors associated with light-to-dark change in iris area were analyzed by linear regression. Fifty-seven patients (mean age 59.6±8.9 years) and 30 normal subjects matched for age (60.6±9.3 years) and sex ratio were recruited. In regards to differences under light-to-dark conditions, angle opening distance at 500 μm (AOD500μm) and iris area during light-to-dark transition were smaller in CPACG eyes than fellow PACS/PAC eyes and normal eyes (P<0.017). Pupil diameter change was largest in normal eyes, and larger in PACS/PAC eyes than CPACG eyes (P<0.017). There was an average reduction of 0.145 mm2 in iris area for each millimeter of pupil diameter increase in CPACG eyes, 0.161 mm2 in fellow PAC/PACS eyes, and 0.165 mm2 in normal eyes. Larger iris curvature in the dark and diagnosis of PACG were significantly associated with less light-to-dark iris area changes. Dynamic changes in iris parameters with light-to-dark transition differed significantly among CPACG eyes, fellow PAC/PACS eyes, and normal eyes. Greater iris curvature under dark conditions was correlated with reduced light-to-dark change in iris area and pupil diameter, which may contribute to disease progression.

  16. Differences in the expression of genes between normal tissue and squamous cell carcinomas of head and neck using cancer-related gene cDNA microarray.

    PubMed

    Kainuma, Kazuyuki; Katsuno, Satoshi; Hashimoto, Shigenari; Oguchi, Tomohiro; Suzuki, Nobuyoshi; Asamura, Kenji; Usami, Shin-ichi

    2006-09-01

    This study clearly showed the molecular characteristics of head and neck squamous cell carcinoma (HNSCC) on the basis of gene expression patterns. cDNA microarray has recently been shown to have the ability to represent the expression patterns of large numbers of genes from a small amount of tissue, potentially enabling definition of groups of patients with similar biological behavior of cancer. Although gene expression profiling using this technique has proven helpful for predicting the prognosis in various cancers, little is known regarding HNSCC. The aim of this study was to investigate the differences in the expression of various genes between normal tissue and cancers of patients with HNSCC by cDNA microarray. We extracted mRNA from 17 HNSCC patients and used cDNA microarray analysis to investigate the gene expression patterns. The present study was not designed to perform an inclusive search for genes but rather to focus on cancer-related genes. Seven independent genes were found to be up-regulated in cancer tissues: matrix metalloproteinase-1, -3, and -10, interleukin-8, cadherin 3, hexabrachion, and interferon gamma-inducible protein 10. Hyaluronic acid-binding protein 2, keratin 4, and keratin 13 were categorized as down-regulated. The hierarchical clustering and dendrogram for 17 cancer samples and 425 genes could be grouped into three clusters.

  17. 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.

  18. Correlation of the KISA% index and Scheimpflug tomography in 'normal', 'subclinical', 'keratoconus-suspect' and 'clinically manifest' keratoconus eyes.

    PubMed

    Steinberg, Johannes; Aubke-Schultz, Silke; Frings, Andreas; Hülle, Jan; Druchkiv, Vasyl; Richard, Gisbert; Katz, Toam; Linke, Stephan J

    2015-05-01

    To analyse tomographic changes in eyes classified as 'normal', 'keratoconus-suspect' and 'clinically manifest keratoconus' based on the established KISA% definition of Rabinowitz and Rasheed and to develop the category of 'subclinical keratoconus eyes' to expand the classification into a 'subtopographic' range. Tomographic and topographic analyses of 670 eyes performed with a rotating Scheimpflug imaging system (Pentacam(®), Oculus Inc., Wetzlar, Germany) were retrospectively analysed. Based on the KISA% keratoconus classification system, eyes were assigned to a 'normal', 'keratoconus-suspect' or 'manifest keratoconus' group. In addition, a new group of 'subclinical keratoconus eyes' was analysed, comprising unsuspicious fellow eyes of patients with keratoconus. T-tests, Wilcoxon rank-sum test, receiver operating characteristics (ROC) and robust regression analyses were performed to correlate tomographic parameters with the increasing KISA% index. KISA%-grouped keratoconus eyes showed robust tomographic changes. By adding the subclinical group, although the concurrent topography was unchanged, we were able to demonstrate statistically significant changes for almost all tomographic parameters (parameters with highest sensitivity/specificity: ART_max, [0.69/0.69], BAD_D [0.66/0.66]). The highest coefficient of determination (R(2)) with the KISA% index was demonstrated for Ele_f_max (R(2) = 0.70), Ele_f_TP (R(2) = 0.69), Ele_b_TP (R(2) = 0.69) and BAD_D (R(2) = 0.68). We recommend the use of the expanded KISA% index (eKISA% index) as the basis for the definition of keratoconus and normal groups in future keratoconus research projects. © 2015 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  19. Alterations of Glutamate and γ-Aminobutyric Acid Expressions in Normal and Myopic Eye Development in Guinea Pigs.

    PubMed

    Guoping, Li; Xiang, Ye; Jianfeng, Wu; Dadong, Guo; Jie, Huang; Wenjun, Jiang; Junguo, Guo; Hongsheng, Bi

    2017-02-01

    The retina has an important role in the signal transmission related to eye development and myopia. Glutamate (Glu) and γ-aminobutyric acid (GABA) are the major excitatory and inhibitory neurotransmitters in the retina, which can affect the development of both the eye and myopia. Nevertheless, change in the balance between the excitatory and inhibitory neurotransmitters still is unclear during development of eyes and myopia. The purpose of this study was to explore the alterations of the ratio of Glu to GABA (RGG), which mediates the balance between the excitatory and inhibitory neurotransmitters in retina in the development of the eyes and lens-induced myopia (LIM) in a guinea pig model. An LIM guinea pig model was established using a -10 diopter (D) negative lens. The levels of Glu, GABA, and the dynamic change of RGG were measured in the retina in normal and myopia guinea pigs at four time points (i.e., 0, 2, 4, and 6 weeks after onset of LIM). Considering that Glu and GABA are related closely to the occurrence of myopia, we further studied the changes of RGG in the retina in LIM guinea pigs. Our results showed that the RGG was upregulated and was well correlated with diopter and axial length than either Glu or GABA during the development of normal eyes. Besides, we observed that the content of the RGG in the retina in myopia eyes was higher than that of Glu and GABA in normal subjects and was an obviously positive correlation. Taken together, our findings suggest that the RGG has a pivotal role in eye development and myopia. The abnormal retina signal induced by the unbalanced ratio between Glu and GABA is related closely to the occurrence of myopia.

  20. SD-OCT analysis of regional epithelial thickness profiles in keratoconus, postoperative corneal ectasia, and normal eyes.

    PubMed

    Rocha, Karolinne Maia; Perez-Straziota, Claudia E; Perez-Straziota, E; Stulting, R Doyle; Randleman, J Bradley

    2013-03-01

    To assess corneal microarchitecture and regional epithelial thickness profile in eyes with keratoconus, postoperative corneal ectasia (ectasia), and normal unoperated eyes (controls) using spectral-domain optical coherence tomography (SD-OCT). Regional corneal epithelial thickness profiles were measured with anterior segment SD-OCT (Optovue RTVue-100, Optovue Inc., Fremont, CA). Epithelial thickness was assessed at 21 points, 0.5 mm apart, across the central 6-mm of the corneal apex in the horizontal and vertical meridians. One hundred twenty eyes were evaluated, including 49 eyes from 29 patients with keratoconus, 32 eyes from 16 patients with ectasia, and 39 eyes from 21 control patients. Average epithelial thickness at the corneal apex was 41.18 ± 6.47 μm (range: 30 to 51 μm) for keratoconus, 46.5 ± 6.72 μm for ectasia (range: 34 to 60 μm), and 50.45 ± 3.92 μm for controls (range: 42 to 55 μm). Apical epithelial thickness was significantly thinner in eyes with keratoconus (P < .0001) and ectasia (P = .0007) than in controls. Epithelial thickness ranges in all other areas varied widely for keratoconus (range: 21 to 101 μm) and ectasia (range: 30 to 82 μm) compared to controls (range: 43 to 64) (P = .0063). SD-OCT demonstrated significant central and regional epithelial thickness profile differences between keratoconus, ectasia, and control eyes, with significant variability and unpredictability in ectatic eyes. This regional irregularity may necessitate direct epithelial thickness measurement for treatments where underlying stromal variations may be clinically relevant, including corneal collagen cross-linking or topography-guided ablations. Copyright 2013, SLACK Incorporated.

  1. 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…

  2. Psf2 plays important roles in normal eye development in Xenopus laevis

    PubMed Central

    Walter, Brian E.; Perry, Kimberly J.; Fukui, Lisa; Malloch, Erica L.; Wever, Jason

    2008-01-01

    Purpose Psf2 (partner of Sld5 2) represents a member of the GINS (go, ichi, ni, san) heterotetramer [1] and functions in DNA replication as a “sliding clamp.” Previous in situ hybridization analyses revealed that Psf2 is expressed during embryonic development in a tissue-specific manner, including the optic cup (retina) and the lens [2]. This article provides an analysis of Psf2 function during eye development in Xenopus laevis. Methods A morpholino targeted to Psf2 mRNA was designed to knockdown Psf2 translation and was injected into specific embryonic cells during early cleavage stages in the frog, Xenopus laevis. Injected embryos were assayed for specific defects in morphology, cell proliferation, and apoptosis. Synthetic Psf2 RNA was also co-injected with the morpholino to rescue morpholino-mediated developmental defects. It is well known that reciprocal inductive interactions control the development of the optic cup and lens. Therefore, control- and morpholino-injected embryos were used for reciprocal transplantation experiments to distinguish the intrinsic role of Psf2 in the development of the optic cup (retina) versus the lens. Results Morpholino-mediated knockdown of Psf2 expression resulted in dosage-dependent phenotypes, which included microphthalmia, incomplete closure of the ventral retinal fissure, and retinal and lens dysgenesis. Defects were also observed in other embryonic tissues that normally express Psf2 including the pharyngeal arches and the otic vesicle, although other tissues that express Psf2 were not found to be grossly defective. Eye defects could be rescued by co-injection of synthetic Psf2 RNA. Examination of cell proliferation via an antibody against phospho-histone H3 S10P revealed no significant differences in the retina and lens following Psf2 knockdown. However, there was a significant increase in the level of apoptosis in retinal as well as forebrain tissues, as revealed by TUNEL (terminal deoxynucleotide transferase dUTP nick

  3. 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.

  4. Normal standards of eye projection in Turkish children 6 to 17 years of age.

    PubMed

    Kara, Turgay; Kurtoglu, Selim; Mazicioglu, M Mumtaz; Ozturk, Ahmet; Ozdoğru, Mehtap; Ustunbas, Hasan Basri

    2010-12-01

    There are a few international and Turkish reports on children's eye projection references. This is a cross-sectional study. Data were obtained from the second study of the Determination of Anthropometric Measurements of Turkish Children and Adolescents study group (DAMTCA II).The study population was 4,533 primary and secondary school students aged 6 to 18 years (2,512 girls, 2,021 boys). A Hertel exophthalmometer was used; age- and gender-specific means and standard deviations and percentiles were calculated for eye projection. The 3rd, 5th, 10th, 25th, 50th, 75th, 80th, 85th, 90th, 95th, and 97th percentiles of right and left eye projection, and the mean and standard deviation for each age and gender were calculated. In 6-year-old children, the smoothed eye projection of the 3rd-97th percentiles for the right and left eye in boys were detected as 11.2 mm-17.0 mm for right eye and 11.1 mm-17.0 mm for left eye. In 17-year-old male adolescents, the 3rd-97th percentiles were detected as 11.9 mm-19.5 mm for the right eye and 11.8 mm-19.2 mm for the left eye. The 3rd-97th percentiles in 6-year-old girls were detected as 11.1 mm-17.1 mm for the right eye and 10.9 mm-17.1 mm for the left eye. In 17-year-old girls, the 3rd-97th percentiles were detected as 11.7 mm-19.4 mm for the right eye and 11.8-19.2 mm for the left eye. Age- and gender-specific references for exophthalmos provide important information both for the clinical decision-making process, and screening in the diagnosis of abnormal or pathological conditions which result in exophthalmos.

  5. Comparison of the visual effects of Fresnel prisms in normal and amblyopic eyes.

    PubMed

    Wright, David; Firth, Alison Y; Buckley, David

    2008-10-01

    To assess the effects of Fresnel prisms on visual acuity and peak contrast sensitivity in the amblyopic and sound eyes of participants with amblyopia and to determine whether these functions were affected by Fresnel prisms to a different degree than those of controls. The LogMAR visual acuity and peak contrast sensitivity of 10 unilateral amblyopic participants (mean age, 22.6 years) and 9 controls (mean age, 26.2 years) were tested with Fresnel prisms of powers 5(Delta), 10(Delta), 15(Delta), 20(Delta), and 25(Delta) and without a Fresnel prism. A statistically significant reduction in visual acuity with increasing prism power was found for all 3 groups, with the visual acuity of the amblyopic eyes being the least affected by the prisms. No statistically significant differences were found between the control and the sound eyes. No statistically significant differences in the effects of the prisms on peak contrast sensitivity could be detected between the 3 groups. Fresnel prisms were found to have a smaller effect on those amblyopic eyes with a poorer baseline visual acuity, indicating that these eyes may tolerate strong prisms without substantially impairing their visual acuity. Fresnel prisms have a lesser effect on the visual acuity of amblyopic eyes than on controls. In contrast, results for peak contrast sensitivity were very similar for each of the groups tested, and no significant differences were evident between the amblyopic, sound, and control eyes.

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

    PubMed

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

    2012-03-01

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

  7. Identification by cDNA microarray technology of genes modulated by artificial ultraviolet radiation in normal human melanocytes: relation to melanocarcinogenesis.

    PubMed

    Valéry, C; Grob, J J; Verrando, P

    2001-12-01

    Target genes of ultraviolet stress response in cutaneous melanocytes, potentially associated with solar-induced melanocarcinogenesis, were characterized by cDNA microarray technology. In cultured normal human melanocytes, 198 genes out of approximately 9000 arrayed were found modulated > or = 1.9 times following artificial ultraviolet minus sign mainly ultraviolet-B minus sign irradiation (100 mJ per cm(2)). Among them, 159 corresponded to known sequences, the encoded proteins being mostly involved in DNA or RNA binding/synthesis/modification, or ribosomal proteins. The others were transcription factors, receptors, tumor suppressors, and (proto)oncogenes. Members of these families have already been linked to melanoma. In addition, some of the modulated genes were borne by chromosomes harboring candidate melanoma loci. Comparisons with genes modified in melanoma samples reported in previous studies with similar microarray platform showed that 59% of the known genes sensitive to ultraviolet were modulated in the same way. Furthermore, 39 expressed sequence tags were modulated, and preliminary experiments showed that two expressed sequence tags displayed differential expressions both in melanoma cell lines and in melanoma tumors. These results provide a basis for further studies on the role of modulated genes in ultraviolet-induced melanoma. Because some of these genes are potential markers of the disease, they might help for developing new molecular-based strategies for risk prediction in patients.

  8. 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.

  9. Select Features of Diabetic Retinopathy on Swept-Source Optical Coherence Tomographic Angiography Compared With Fluorescein Angiography and Normal Eyes

    PubMed Central

    Salz, David A.; de Carlo, Talisa E.; Adhi, Mehreen; Moult, Eric; Choi, WhooJhon; Baumal, Caroline R.; Witkin, Andre J.; Duker, Jay S.; Fujimoto, James G.; Waheed, Nadia K.

    2017-01-01

    IMPORTANCE Optical coherence tomographic angiography (OCTA) is a recently developed noninvasive imaging technique that can visualize the retinal and choroidal microvasculature without the injection of exogenous dyes. OBJECTIVE To evaluate the potential clinical utility of OCTA using a prototype swept-source OCT (SS-OCT) device and compare it with fluorescein angiography (FA) for analysis of the retinal microvasculature in diabetic retinopathy. DESIGN, SETTING, AND PARTICIPANTS Prospective, observational cross-sectional study conducted at a tertiary care academic retina practice from November 2013 through November 2014. A cohort of diabetic and normal control eyes were imaged with a prototype SS-OCT system. The stage of diabetic retinopathy was determined by clinical examination. Imaging was performed using angiographic 3 × 3-mm and 6 × 6-mm SS-OCT scans to generate 3-dimensional en-face OCT angiograms for each eye. Two trained Boston Image Reading Center readers reviewed and graded FA and OCTA images independently. MAIN OUTCOMES AND MEASURES The size of the foveal nonflowzone and the perifoveal intercapillary area on OCTA were measured in both normal and diabetic eyes using Boston Image Reading Center image analysis software. RESULTS The study included 30 patients with diabetes (mean [SD] age, 55.7 [10] years) and 6 control individuals (mean [SD] age, 55.1 [6.4] years). A total of 43 diabetic and 11 normal control eyes were evaluated with OCTA. Fluorescein angiography was performed in 17 of 43 diabetic eyes within 8 weeks of the OCTA. Optical coherence tomographic angiography was able to identify a mean (SD) of 6.4 (4.0) microaneurysms (95% CI, 4.4–8.5), while FA identified a mean (SD) of 10 (6.9) microaneurysms (95% CI, 6.4–13.5). The exact intraretinal depth of microaneurysms on OCTA was localized in all cases (100%). The sensitivity of OCTA in detecting microaneuryms when compared with FA was 85% (95% CI, 53–97), while the specificity was 75% (95% CI, 21

  10. Comparison of Visual Function in Older Eyes in the Earliest Stages of Age-related Macular Degeneration to Those in Normal Macular Health.

    PubMed

    Owsley, Cynthia; Huisingh, Carrie; Clark, Mark E; Jackson, Gregory R; McGwin, Gerald

    2016-01-01

    To compare the ability of several visual functional tests in terms of the strength of their associations with the earliest phases of age-related macular degeneration (AMD), which bears on their potential to serve as functional endpoints in evaluating treatments for early AMD and prevention strategies. Eyes from adults ≥60 years old were identified as being in normal macular health or in the earliest stages of AMD (steps 2, 3 or 4) through grading of color stereo-fundus photos by an experienced grader masked to all other study variables who used the 9-step Age-Related Eye Disease Study (AREDS) classification system for AMD severity. Visual function was assessed using the following tests: best-corrected visual acuity, low luminance visual acuity, spatial contrast sensitivity, macular cone-mediated light sensitivity and rod-mediated dark adaptation. A total of 1260 eyes were tested from 640 participants; 1007 eyes were in normal macular health (defined as step 1 in AREDS system) and 253 eyes had early AMD (defined as steps 2, 3 or 4). Adjusting for age and gender, early AMD eyes had two times the odds of having delayed rod-mediated dark adaptation than eyes in normal macular health (p = 0.0019). Visual acuity, low luminance acuity, spatial contrast sensitivity and macular light sensitivity did not differ between normal eyes and early AMD eyes. Eyes in the earliest phases of AMD were two times more likely to have delayed rod-mediated dark adaptation, as assessed by the rod-intercept, as compared to older eyes in normal macular health, whereas there was no difference in early AMD versus normal eyes in tests of visual acuity, low luminance acuity, macular light sensitivity and spatial contrast sensitivity.

  11. Effects of 0.2% brimonidine and 0.2% brimonidine-0.5% timolol on intraocular pressure and pupil size in normal equine eyes.

    PubMed

    Von Zup, M; Lassaline, M; Kass, P H; Miller, P E; Thomasy, S M

    2017-05-04

    Brimonidine is an α2 -adrenergic agonist that decreases aqueous humour production and may increase uveoscleral outflow. It has not been evaluated in normal or glaucomatous equine eyes. To evaluate the efficacy and safety of brimonidine in lowering intraocular pressure (IOP), alone and in conjunction with timolol, as a treatment for equine glaucoma by comparing IOP in normal equine eyes treated with brimonidine and brimonidine-timolol, respectively, with IOP in control eyes. A balanced crossover design with 16 horses receiving one of two treatments, brimonidine and brimonidine-timolol, during each of two 10-day study phases, was used. Four horses were randomly assigned to each of four combinations of treated eye (right or left) and drug order within the two 10-day study phases (brimonidine first or brimonidine-timolol first). Pupil size and conjunctival hyperaemia were assessed twice per day and IOP was measured three times per day using rebound tonometry in both eyes of 16 normal horses throughout two 10-day study periods (brimonidine and brimonidine-timolol) separated by an 18-day washout period. One eye of each horse was treated with brimonidine or brimonidine-timolol and the opposite eye was treated with balanced salt solution (BSS). There were no adverse effects and no significant changes in pupil size in normal equine eyes treated with brimonidine or brimonidine-timolol. Average IOP in normal equine eyes treated with brimonidine (25.6 mmHg) was statistically higher than in eyes treated with brimonidine-timolol (24.6 mmHg) or BSS (24.5 mmHg). However, IOP differences were of ≤1 mmHg and thus not clinically important. Horses with normal eyes may not be as sensitive to the IOP-lowering effects of treatment as horses with glaucoma. Brimonidine and brimonidine-timolol are well tolerated in normal horses but do not decrease IOP. © 2017 EVJ Ltd.

  12. Measurement of Choroidal Thickness in Normal Eyes Using 3D OCT-1000 Spectral Domain Optical Coherence Tomography

    PubMed Central

    Shin, Joong Won; Shin, Yong Un; Cho, Hee Yoon

    2012-01-01

    Purpose To study choroidal thickness and its topographic profile in normal eyes using 3D OCT-1000 spectral domain optical coherence tomography and the correlation with age and refractive error. Methods Fifty-seven eyes (45 individuals) with no visual complaints or ocular disease underwent horizontal and vertical line scanning using 3D OCT-1000. The definition of choroidal thickness was the vertical distance between the posterior edge of the hyper-reflective retinal pigment epithelium and the choroid/sclera junction. Choroidal thickness was measured in the subfoveal area at 500 µm intervals from the fovea to 2,500 µm in the nasal, temporal, superior, and inferior regions. The spherical equivalent refractive error was measured by autorefractometry. Statistical analysis was used to confirm the correlations of choroidal thickness with age and refraction error. Results The mean age of the 45 participants (57 eyes) was 45.28 years. Detailed visualization of the choroid for measuring its thickness was possible in 63.3% of eyes. The mean subfoveal choroidal thickness was found to be 270.8 µm (standard deviation [SD], ±51 µm), in horizontal scanning and 275.0 µm (SD, ±49 µm) in vertical scanning. The temporal choroidal thickness was greater than any 500 µm interval in corresponding locations, and there was no significant difference between the superior and inferior choroid as far as 2,000 µm from the fovea. Age and refractive error were associated with subfoveal choroidal thickness in terms of regression (p < 0.05). Conclusions Choroidal thickness in normal Korean eyes can be measured using 3D OCT-1000 with high resolution line scanning. The topographical profile of choroidal thickness varies depending on its location. Age and refractive error are essential factors for interpretation of choroidal thickness. PMID:22870023

  13. Predictive Analysis Between Topographic, Pachymetric and Wavefront Parameters in Keratoconus, Suspects and Normal Eyes: Creating Unified Equations to Evaluate Keratoconus.

    PubMed

    Prakash, Gaurav; Suhail, Muhammad; Srivastava, Dhruv

    2016-01-01

    To perform prediction analysis between topographic, pachymetric and wavefront parameters in keratoconus, suspects, and normal cases and to look at the possibility of a unified equation to evaluate keratoconus. This cross-sectional, observational study was done in cornea services of a specialty hospital. Fifty eyes of 50 candidates with a diagnosis of normal, keratoconus suspect, and keratoconus were included in each group (total 150 eyes). All eyes underwent detailed analysis on Scheimplug + Placido device (Sirius, CSO, Italy). Main parameters evaluated were topographic [maximum keratometry (Max Km), average keratometry and astigmatism at 3, 5, and 7 mm], pachymetric [central and minimum corneal thickness (MCT) and their difference, corneal volume] and corneal aberrations [higher order aberrations root-mean-square (HOARMS), coma, spherical, residual].Central tendency, predictive fits and regression models, were computed. The measured variables had a significant difference in mean between the three groups (Kruskal-Wallis, p < 0.001). Max Km, MCT, and HOARMS had significant fits with other topographic, pachymetric and wavefront parameters, respectively. Inter-relations between these three (Max Km, MCT, and HOARMS) were also stronger for keratoconus (R(2) from 0.75 to 0.33) compared to suspect/normal eyes (R(2) from 0.15 to 0.003). These three variables (Max Km, MCT and HOARMS) were used as representative variables to create the unified equations. The equation for the pooled data was (Kmax = 59.5 + 2.3 × HOARMS-0.03 × MCT; R(2)= 0.7, p < 0.001). Major variables used for grading keratoconus (MaxKm, MCT, HOARMS) can be linked by linear regression equations to predict the pathology's behavior.

  14. Association between the percent tissue altered and post-laser in situ keratomileusis ectasia in eyes with normal preoperative topography.

    PubMed

    Santhiago, Marcony R; Smadja, David; Gomes, Beatriz F; Mello, Glauco R; Monteiro, Mario L R; Wilson, Steven E; Randleman, J Bradley

    2014-07-01

    To investigate the association of a novel metric, percent tissue altered, with the occurrence of ectasia after laser in situ keratomileusis (LASIK) in eyes with normal corneal topography and to compare this metric with other recognized risk factors. Retrospective case-control study. The study included 30 eyes from 16 patients with bilateral normal preoperative Placido-based corneal topography that developed ectasia after LASIK (ectasia group) and 174 eyes from 88 consecutive patients with uncomplicated LASIK and at least 3 years of postoperative follow-up. The following metrics were evaluated: age, preoperative central corneal thickness, residual stromal bed, Ectasia Risk Score System scores, and percent tissue altered, derived from [PTA = (FT + AD)/CCT], where FT = flap thickness, AD = ablation depth, and CCT = preoperative central corneal thickness. In the ectasia group, percent tissue altered ≥40 was the most prevalent factor (97%), followed by age <30 years (63%), residual stromal bed ≤300 μm (57%), and ectasia risk score ≥ 3 (43%) (P < .001 for all). Percent tissue altered ≥ 40 had the highest odds ratio (223), followed by residual stromal bed ≤ 300 μm (74) and ectasia risk score ≥ 4 (8). Stepwise logistic regression revealed percent tissue altered ≥ 40 as the single most significant independent variable (P < .0001). Percent tissue altered at the time of LASIK was significantly associated with the development of ectasia in eyes with normal preoperative topography and was a more robust indicator of risk than all other variables in this patient population. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    PubMed Central

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

    2014-01-01

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

  18. 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. PMID:28400890

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

    PubMed

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

    2017-01-01

    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. 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). 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. Comparison of the 3 ethnic databases did not reveal significant differences to differentiate early glaucomatous from normal Chinese eyes.

  20. 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).

  1. High-resolution imaging of the retinal nerve fiber layer in normal eyes using adaptive optics scanning laser ophthalmoscopy.

    PubMed

    Takayama, Kohei; Ooto, Sotaro; Hangai, Masanori; Arakawa, Naoko; Oshima, Susumu; Shibata, Naohisa; Hanebuchi, Masaaki; Inoue, Takashi; Yoshimura, Nagahisa

    2012-01-01

    To conduct high-resolution imaging of the retinal nerve fiber layer (RNFL) in normal eyes using adaptive optics scanning laser ophthalmoscopy (AO-SLO). AO-SLO images were obtained in 20 normal eyes at multiple locations in the posterior polar area and a circular path with a 3-4-mm diameter around the optic disc. For each eye, images focused on the RNFL were recorded and a montage of AO-SLO images was created. AO-SLO images for all eyes showed many hyperreflective bundles in the RNFL. Hyperreflective bundles above or below the fovea were seen in an arch from the temporal periphery on either side of a horizontal dividing line to the optic disc. The dark lines among the hyperreflective bundles were narrower around the optic disc compared with those in the temporal raphe. The hyperreflective bundles corresponded with the direction of the striations on SLO red-free images. The resolution and contrast of the bundles were much higher in AO-SLO images than in red-free fundus photography or SLO red-free images. The mean hyperreflective bundle width around the optic disc had a double-humped shape; the bundles at the temporal and nasal sides of the optic disc were narrower than those above and below the optic disc (P<0.001). RNFL thickness obtained by optical coherence tomography correlated with the hyperreflective bundle widths on AO-SLO (P<0.001) AO-SLO revealed hyperreflective bundles and dark lines in the RNFL, believed to be retinal nerve fiber bundles and Müller cell septa. The widths of the nerve fiber bundles appear to be proportional to the RNFL thickness at equivalent distances from the optic disc.

  2. Preface: The Aging Eye: Normal Changes, Age-Related Diseases, and Sight-Saving Approaches

    PubMed Central

    Chader, Gerald J.; Taylor, Allen

    2013-01-01

    This volume presents articles based on a workshop held June 14 to 16, 2013 in Rancho Palos Verde, CA sponsored by the Ocular Research Symposia Foundation (ORSF). The mission of the ORSF is to focus attention on unmet needs and current research opportunities in eye research with the objective of accelerating translation of research findings to effective clinical care. In this workshop, the subject of the “The Aging Eye” was addressed, including the prevalence of eye diseases in aging and the economic burden imposed by these diseases. New research work was highlighted on the genetics, biology, biochemistry, neurochemistry, and the impact of nutrition and the environment on function in the older eye. By identifying “low-hanging fruit” (i.e., the best opportunities for successful transition of laboratory research for the prevention of and new treatments and cures for ocular diseases), we seek to spur funding at both the basic research and clinical levels, resulting in sight-saving and sight-restoration measures in the near future. PMID:24335060

  3. 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. © 2014 Blackwell Verlag GmbH.

  4. Post-embryonic remodelling of neurocranial elements: a comparative study of normal versus abnormal eye migration in a flatfish, the Atlantic halibut

    PubMed Central

    Sæle, Øystein; Silva, Nadia; Pittman, Karin

    2006-01-01

    The process of eye migration in bilaterally symmetrical flatfish larvae starts with asymmetrical growth of the dorsomedial parts of the ethmoid plate together with the frontal bones, structures initially found in a symmetrical position between the eyes. The movement of these structures in the future ocular direction exerts a stretch on the fibroblasts in the connective tissue found between the moving structures and the eye that is to migrate. Secondarily, a dense cell population of fibroblasts ventral to the eye starts to proliferate, possibly cued by the pulling forces exerted by the eye. The increased growth ventral to the eye pushes the eye dorsally. Osteoblasts are deposited in the dense cell layer, forming the dermal part of the lateral ethmoid, and at full eye migration this will cover the area vacated by the migrated eye. When the migrating eye catches up with the previous migrated dermal bones, the frontals, these bones will be remodelled to accommodate the eye. Our findings suggest that a combination of extremely localized signals and more distant factors may impinge upon the outcome of the tissue remodelling. Early normal asymmetry of signalling factors may cascade on a series of events. PMID:16822267

  5. 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

  6. Healthy Eyes

    MedlinePlus

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

  7. 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

  8. "Harshlighting" small blemishes on microarrays

    PubMed Central

    Suárez-Fariñas, Mayte; Haider, Asifa; Wittkowski, Knut M

    2005-01-01

    Background Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans show similar artefacts, which affect the analysis, particularly when one tries to detect subtle changes. However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs). Results We present a method that harnesses the statistical power provided by having several HDONAs available, which are obtained under similar conditions except for the experimental factor. This method "harshlights" blemishes and renders them evident. We find empirically that about 25% of our chips are blemished, and we analyze the impact of masking them on screening for differentially expressed genes. Conclusion Experiments attempting to assess subtle expression changes should be carefully screened for blemishes on the chips. The proposed method provides investigators with a novel robust approach to improve the sensitivity of microarray analyses. By utilizing topological information to identify and mask blemishes prior to model based analyses, the method prevents artefacts from confounding the process of background correction, normalization, and summarization. PMID:15784152

  9. "Harshlighting" small blemishes on microarrays.

    PubMed

    Suárez-Fariñas, Mayte; Haider, Asifa; Wittkowski, Knut M

    2005-03-22

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

  10. The role of corneal afferent neurons in regulating tears under normal and dry eye conditions.

    PubMed

    Meng, Ian D; Kurose, Masayuki

    2013-12-01

    The cornea is one of several orofacial structures requiring glandular secretion for proper lubrication. Glandular secretion is regulated through a neural reflex initiated by trigeminal primary afferent neurons innervating the corneal epithelium. Corneal sensory afferents must respond to irritating and potentially damaging stimuli, as well as drying that occurs with evaporation of the tear film, and the physiological properties of corneal afferents are consistent with these requirements. Polymodal neurons are sensitive to noxious mechanical, thermal and chemical stimuli, mechanoreceptive neurons are selectively activated by mechanical stimuli, and cool cells respond to innocuous cooling. The central terminations of corneal primary afferents are located within two regions of the spinal trigeminal nucleus. The more rostral region, located at the transition between the trigeminal subnucleus caudalis and interpolaris, represents a critical relay for the regulation of the lacrimation reflex. From this region, major control of lacrimation is carried through projections to preganglionic parasympathetic neurons located in or around the superior salivatory nucleus. Dry eye syndrome may be caused by a dysfunction in the tear secreting glands themselves or in the neuronal circuit regulating these glands. Furthermore, the dry eye condition itself may modify the properties of corneal afferents and affect their ability to regulate secretion, a possibility just now being explored. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. The role of corneal afferent neurons in regulating tears under normal and dry eye conditions

    PubMed Central

    Meng, Ian D.; Kurose, Masayuki

    2013-01-01

    The cornea is one of several orofacial structures requiring glandular secretion for proper lubrication. Glandular secretion is regulated through a neural reflex initiated by trigeminal primary afferent neurons innervating the corneal epithelium. Corneal sensory afferents must respond to irritating and potentially damaging stimuli, as well as drying that occurs with evaporation of the tear film, and the physiological properties of corneal afferents are consistent with these requirements. Polymodal neurons are sensitive to noxious mechanical, thermal and chemical stimuli, mechanoreceptive neurons are selectively activated by mechanical stimuli, and cool cells respond to innocuous cooling. The central terminations of corneal primary afferents are located within two regions of the spinal trigeminal nucleus. The more rostral region, located at the transition between the trigeminal subnucleus caudalis and interpolaris, represents a critical relay for the regulation of the lacrimation reflex. From this region, major control of lacrimation is carried through projections to preganglionic parasympathetic neurons located in or around the superior salivatory nucleus. Dry eye syndrome may be caused by a dysfunction in the tear secreting glands themselves or in the neuronal circuit regulating these glands. Furthermore, the dry eye condition itself may modify the properties of corneal afferents and affect their ability to regulate secretion, a possibility just now being explored. PMID:23994439

  12. Comparative Evaluation of the Corneal and Anterior Chamber Parameters Derived From Scheimpflug Imaging in Arab and South Asian Normal Eyes.

    PubMed

    Prakash, Gaurav; Srivastava, Dhruv; Avadhani, Kavitha; Thirumalai, Sandeep M; Choudhuri, Sounak

    2015-11-01

    To evaluate the differences in the normal corneal and anterior segment Scheimpflug parameters in Arab and South Asian eyes. This hospital-based study was performed at a cornea and refractive surgery service in Abu Dhabi. A total of 600 consecutive normal candidates of South Asian (group 1, n = 300) and Arab (group 2, n = 300) origins underwent Scheimpflug imaging (Sirius; Costruzione Strumenti Oftalmici, Italy). One eye was randomly selected for evaluation. The age and sex distributions in both groups were comparable. The pachymetric variables were statistically higher in group 2 (group 2 vs. group 1, 544.3 ± 32.2 μm vs. 535.1 ± 31.4 μm for central corneal thickness, 541.0 ± 32.6 μm vs. 531.9 ± 31.5 μm for minimum corneal thickness, 571.7 ± 43.2 μm vs. 558.1 ± 42.3 μm for apical thickness, and 58.1 ± 4.2 vs. 57.3 ± 4.3 mm³ for the corneal volume; P < 0.05). The anterior chamber volume (group 2 vs. group 1: 166.4 ± 16.4 vs. 161.6 ± 20.5 mm³) and angle (group 2 vs. group 1: 44.6 ± 6.2 vs. 43.5 ± 5.8 degrees) were also higher for group 2 (P < 0.05). Central corneal curvature and apical corneal curvature (apex K) were higher in group 1 (P < 0.05) with comparable astigmatism. The flat keratometry (K), steep K, and apex K were 43.6 ± 2.2 diopters (D), 44.9 ± 1.8 D, and 45.7 ± 1.8 D for group 1, and 43.1 ± 2.2 D, 44.5 ± 2 D, and 45.2 ± 1.9 D for group 2. The effect size (Cohen d) for significant parameters ranged from 0.2 to 0.3. Normal eyes of Arab ethnicity tend to have statistically thicker and flatter corneas and less-crowded anterior segments than those of the South Asian counterparts. These epidemiological differences have a mild to moderate biological effect size (Cohen d), but they should be considered when evaluating these eyes for anterior segment or corneal procedures.

  13. Meta-analysis of Pentacam vs. ultrasound pachymetry in central corneal thickness measurement in normal, post-LASIK or PRK, and keratoconic or keratoconus-suspect eyes.

    PubMed

    Wu, Wenjing; Wang, Yan; Xu, Lulu

    2014-01-01

    The aim of this meta-analysis is to evaluate the central corneal thickness (CCT) measurement differences between Pentacam (Oculus Inc., Germany) and Ultrasound Pachymetry (USP) in normal (unoperated eyes , myopic and astigmatic eyes without corneal disease or topographic irregularity), after laser in situ keratomileusis (LASIK) or photorefractive keratectomy (PRK), and keratoconic or keratoconus suspected eyes. We assess whether Pentacam and USP have similar CCT differences in normal, thinner corneas after LASIK or PRK procedures, and kerotoconic or keratoconus suspected eyes. Data sources, including PubMed, Medline, EMBASE, and Cochrane Central Registry of Controlled Trials on the Cochrane Library, were searched to find the relevant studies. Primary outcome measures were CCT measurement between Pentacam and USP. Three groups of eyes were analyzed: normal; LASIK or PRK eyes; and keratoconus suspected or keratoconic eyes. Nineteen studies describing 1,908 eyes were enrolled in the normal group. Pentacam results were 1.47 μm ,95 % confidence interval (CI) -2.32 to 5.27, higher than USP without statistically significant difference (P = 0.45). Nine studies with total 539 eyes were included in the corneas after LASIK or PRK. The mean difference in the CCT measurement with Pentacam and ultrasound pachymetry was 1.03 μm, with the 95 % CI -3.36 to 5.42, there was no statistically difference (P = 0.64). Four studies with a total of 185 eyes were included in the keratoconic eyes or keratoconus-suspect group, however,the mean difference was -6.33 μm (95 % CI -9.17 to-3.49), which was statistically different between Pentacam and ultrasound pachymetry in the CCT measurement (P < 0.0001). Pentacam offers similar CCT results to ultrasound pachymetry in normal eyes, thinner corneas after LASIK or PRK procedures. However, in keratoconic or keratoconus-suspect eyes, Pentacam slightly underestimates the central corneal thickness than does ultrasound pachymetry

  14. Temperatures of the Ocular Surface, Lid, and Periorbital Regions of Sjögren's, Evaporative, and Aqueous-Deficient Dry Eyes Relative to Normals.

    PubMed

    Abreau, Kerstin; Callan, Christine; Kottaiyan, Ranjini; Zhang, Aizhong; Yoon, Geunyoung; Aquavella, James V; Zavislan, James; Hindman, Holly B

    2016-01-01

    To compare the temperatures of the ocular surface, eyelid, and periorbital skin in normal eyes with Sjögren's syndrome (SS) eyes, evaporative dry eyes (EDE), and aqueous deficient dry eyes (ADDE). 10 eyes were analyzed in each age-matched group (normal, SS, EDE, and ADDE). A noninvasive infrared thermal camera captured two-dimensional images in three regions of interest (ROI) in each of three areas: the ocular surface, the upper eyelid, and the periorbital skin within a controlled environmental chamber. Mean temperatures in each ROI were calculated from the videos. Ocular surface time-segmented cooling rates were calculated over a 5-s blink interval. Relative to normal eyes, dry eyes had lower initial central OSTs (SS -0.71°C, EDE -0.55°C, ADDE -0.95°C, KW P<.0001) and lower central upper lid temperatures (SS -0.24°C, ADDE -0.51°C, and EDE -0.54°C, KW P<.0001). ADDE eyes had the lowest initial central OST (P<.0001), while EDE eyes had the lowest central lid temperature and lower periorbital temperatures (P<.0001). Over the 5-s interblink interval, the greatest rate of temperature loss occurred following eyelid opening, but varied by group (normals -0.52, SS -0.73, EDE -0.63, and ADDE -0.75°C/s). The ADDE group also had the most substantial heat loss over the 5-s interblink interval (-0.97°C). Differences in OST may be related to thermal differences in lids and periorbita along with an altered tear film. Thermography of the ocular surface, lids, and surrounding tissues may help to differentiate between different etiologies of dry eye. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2016-05-17

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

  16. 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.

  17. 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

  18. 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

  19. Differences in Corneal Parameters Between Affected and Normal Contralateral Eyes in Patients With Hemifacial Spasm Treated With Botulinum Toxin-A: Outcomes During One Complete Treatment Cycle.

    PubMed

    Osaki, Teissy; Osaki, Midori H; Osaki, Tammy H; Hirai, Flavio E; Campos, Mauro

    2016-02-01

    To investigate possible temporary differences in corneal topographic parameters between affected and normal eyes in patients with hemifacial spasm (HFS) treated with botulinum toxin-A (BTX-A), over the course of 1 treatment cycle. This prospective study evaluated corneal topographic differences between affected and normal contralateral eyes during a 4-month period in patients with HFS treated with BTX-A (the duration of action of BTX-A for HFS ranges from 2 to 4 months). Corneal topographic analysis was performed using a conventional topographer (Atlas; Carl Zeiss Meditec, Dublin, CA). Steep K and astigmatism measurements were evaluated before BTX-A application and after 15 days and 2, 3, and 4 months. Twenty-four patients (16 women and 8 men) were evaluated. Steep K [46.9 ± 3.6 diopters (D)] and astigmatism values (2.6 ± 2.5 D) were significantly higher in affected eyes of HFS patients than in nonaffected eyes (45.0 ± 1.4 D and 0.9 ± 0.6 D) before treatment (P = 0.001 for steep K and P = 0.0003 for astigmatism). Astigmatism values also showed significant differences between the affected eye (1.4 ± 0.8 D) and nonaffected eye (0.9 ± 0.6 D) at 4 months (P = 0.006), whereas steep K showed significant differences between both eyes at 15 days (affected eye: 45.6 ± 1.5 D, nonaffected eye: 45.0 ± 1.4 D, P = 0.008), 3 months (affected eye: 45.6 ± 1.8 D, nonaffected eye: 45.1 ± 1.3 D, P = 0.03) and 4 months (affected eye: 45.8 ± 1.2 D, nonaffected eye: 45.1 ± 1.4 D, P = 0.003) after treatment. The differences in steep K, and especially in astigmatism values, between eyes tended to reduce during the period of action of BTX-A. At 4 months, when the BTX-A effect is considered to be over or very reduced, a significant difference between eyes for both parameters was noted again.

  20. Distribution of radii of curvature of anterior and posterior best fit sphere in a normal population: the Tehran Eye Study.

    PubMed

    Mehravaran, Shiva; Hashemi, Hassan; KhabazKhoob, Mehdi; Fotouhi, Akbar

    2013-08-01

    To determine the distribution and determinants of the radii of curvature of the anterior and posterior best fit spheres (ABFS and PBFS) of the cornea in a sample from the general normal population of Tehran. A stratified random cluster sampling was used to select samples from the first 4 districts of Tehran proportionate to the population of each stratum. We examined the distribution of the ABFS and PBFS, as measured with the Orbscan II in different groups of age, sex, and refractive error, and determined their relationship with other variables by using both univariate and multiple regression analyses. Valid data was collected from 800 eyes, and analyses were done with data from 399 right eyes only. Mean ABFS and PBFS in the studied sample were 43.31±1.79D and 52.67±3.04D, respectively. ABFS increased with age while PBFS showed no significant association; both showed significant inter-sex differences. In the multiple linear regression model, both ABFS and PBFS significantly correlated directly with age and average keratometry, and inversely with corneal diameter; PBFS correlated directly with anterior chamber depth as well. Mean PBFS/ABFS ratio was 1.22±0.05 which significantly decreased with age and was significantly higher in females. Knowledge of normal ranges of ABFS and PBFS and their determinants, including age, mean keratometry, and corneal diameter, as well as the choice of measurement device, is necessary for comparing information from different populations and interpreting results. Copyright © 2013 British Contact Lens Association. Published by Elsevier Ltd. All rights reserved.

  1. Long-term observation and evaluation of femtosecond laser-assisted thin-flap laser in situ keratomileusis in eyes with thin corneas but normal topography.

    PubMed

    Tomita, Minoru; Watabe, Miyuki; Mita, Mariko; Waring, George O

    2014-02-01

    To evaluate the long-term outcomes of thin-flap laser in situ keratomileusis (LASIK) in eyes with thin corneas (central corneal thickness [CCT] <500 μm) but normal topography. Private center, Tokyo, Japan. Retrospective randomized comparative study. The efficacy, safety, predictability, and topography of LASIK were evaluated in eyes with a CCT of less than 500 μm but with normal topography (thin-cornea group) to 6 years postoperatively. The LASIK outcomes in the thin-cornea group were compared with those in eyes with a CCT of 500 μm or greater (control group). Analysis was performed to determine whether there were differences between the groups at the last checkup 3 to 4 years postoperatively. In the thin-cornea group (291 eyes; 146 patients), no significant differences were observed in LASIK outcomes when eyes were subdivided by the time of final checkup (3, 4, and ≥ 5 years). There was a significant difference in visual and refractive outcomes between 3 months postoperatively and the last checkup in the thin-cornea group and the control group (371 eyes; 193 patients). No significant difference in visual, refractive, or topography outcomes was observed between the 2 groups at the last checkup. Laser in situ keratomileusis in eyes with thin corneas was as safe and effective as and showed similar long-term stability in eyes with a CCT of 500 μm or greater. No eye in either group had a postoperative complication. No author has a financial or proprietary interest in any material or method mentioned. Copyright © 2014 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  2. Vascular Normalization by ROCK Inhibitor: Therapeutic Potential of Ripasudil (K-115) Eye Drop in Retinal Angiogenesis and Hypoxia.

    PubMed

    Yamaguchi, Muneo; Nakao, Shintaro; Arita, Ryoichi; Kaizu, Yoshihiro; Arima, Mitsuru; Zhou, Yedi; Kita, Takeshi; Yoshida, Shigeo; Kimura, Kazuhiro; Isobe, Tomoyuki; Kaneko, Yoshio; Sonoda, Koh-Hei; Ishibashi, Tatsuro

    2016-04-01

    In this study, we investigated the therapeutic potential of a Rho-associated coiled-coil-containing protein kinase (ROCK) inhibitor ripasudil (K-115) eye drop on retinal neovascularization and hypoxia. In vitro, human retinal microvascular endothelial cells (HRMECs) were pretreated with ripasudil and then stimulated with VEGF. ROCK activity was evaluated by phosphorylation of myosin phosphatase target protein (MYPT)-1. Endothelial migration and cell viability were assessed by cell migration and MTT assay, respectively. The concentration of ripasudil in the retina was measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In vivo, normal saline, 0.4%, or 0.8% ripasudil were administered three times a day to mice with oxygen-induced retinopathy (OIR). The areas of neovascularization and avascular retina were also quantified with retinal flat-mounts at postnatal day (P) 15, P17, or P21. The retinal hypoxic area was evaluated using hypoxia-sensitive drug pimonidazole by immunohistochemistry at P17. The vascular normalization was also evaluated by immunohistochemistry at P17. Ripasudil but not fasudil significantly reduced VEGF-induced MYPT-1 phosphorylation in HRMECs at 30 μmol/L. Ripasudil significantly inhibited VEGF-induced HRMECs migration and proliferation. The concentration of ripasudil in the retina was 3.8 to 10.4 μmol/L and 6.8 to 14.8 μmol/L after 0.4% and 0.8% ripasudil treatment, respectively. In the 0.4% and 0.8% ripasudil treated OIR mice, the areas of neovascularization as well as avascular area in the retina was significantly reduced compared with those of saline-treated mice at P17 and P21. Pimonidazole staining revealed that treatment with 0.4% and 0.8% ripasudil significantly inhibited the increase in the hypoxic area compared with saline. 0.8% ripasudil could cause intraretinal vascular sprouting and increase retinal vascular perfusion. Novel ROCK inhibitor ripasudil eye drop has therapeutic potential in the treatment of retinal

  3. Optical coherence tomography angiography vessel density mapping at various retinal layers in healthy and normal tension glaucoma eyes.

    PubMed

    Shin, Joong Won; Sung, Kyung Rim; Lee, Ji Yun; Kwon, Junki; Seong, Mincheol

    2017-06-01

    To investigate peripapillary vessel density at various spatial locations and layers in healthy and normal tension glaucoma eyes using optical coherence tomography angiography (OCTA). A commercial OCTA device (AngioPlex; Carl Zeiss Meditec) was used to image microvasculature in a 6 × 6-mm optic disc region. Vessel densities of superficial and deep retinal layers were calculated using an automatic thresholding algorithm. Vessel density maps were plotted by averaging individual angiogram images. The spatial characteristics of vessel densities were analyzed at clock-hour sectors and in five 0.7-mm-thick concentric circles from a diameter of 2.0 to 5.5 mm. Areas under the receiver operating characteristics curves (AUCs) assessed the glaucoma diagnostic ability. Vessel density maps of superficial and deep retinal layers were significantly reduced at the 7 and 11 o'clock positions in glaucomatous eyes. In superficial layer, vessel density significantly decreased as the distance from the optic disc margin increased, except in the innermost circle (2.0-2.7-mm). There were significant differences in AUCs of superficial vessel density between innermost circle and the other outer circles. In the deep layer, the innermost circle showed significantly higher vessel density than the outer circles. Vessel density at 7 o'clock showed the best diagnostic performance (AUCs, 0.898 and 0.789) both in the superficial and deep layers. The innermost circle showed eccentric feature compared to the outer circles in terms of spatial characteristics and diagnostic ability. Understanding of the spatial characteristics of peripapillary vasculature may be helpful in clinical practice and determining the optimal measurement area of vessel density.

  4. Clinical validation of an algorithm to correct the error in the keratometric estimation of corneal power in normal eyes.

    PubMed

    Piñero, David P; Camps, Vicente J; Mateo, Verónica; Ruiz-Fortes, Pedro

    2012-08-01

    To validate clinically in a normal healthy population an algorithm to correct the error in the keratometric estimation of corneal power based on the use of a variable keratometric index of refraction (n(k)). Medimar International Hospital (Oftalmar) and University of Alicante, Alicante, Spain. Case series. Corneal power was measured with a Scheimpflug photography-based system (Pentacam software version 1.14r01) in healthy eyes with no previous ocular surgery. In all cases, keratometric corneal power was also estimated using an adjusted value of n(k) that is dependent on the anterior corneal radius (r(1c)) as follows: n(kadj) = -0.0064286 r(1c) +1.37688. Agreement between the Gaussian (P(c)(Gauss)) and adjusted keratometric (P(kadj)) corneal power values was evaluated. The study evaluated 92 eyes (92 patients; age range 15 to 64 years). The mean difference between P(c)(Gauss) and P(kadj) was -0.02 diopter (D) ± 0.22 (SD) (P=.43). A very strong, statistically significant correlation was found between both corneal powers (r = .994, P<.01). The range of agreement between P(c)(Gauss) and P(kadj) was 0.44 D, with limits of agreement of -0.46 and +0.42 D. In addition, a very strong, statistically significant correlation of the difference between P(c)(Gauss) and P(kadj) and the posterior corneal radius was found (r = 0.96, P<.01). The imprecision in the calculation of corneal power using keratometric estimation can be minimized in clinical practice by using a variable keratometric index that depends on the radius of the anterior corneal surface. No author has a financial or proprietary interest in any material or method mentioned. Copyright © 2012 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  5. 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

  6. The long-term effects of semiconductor diode laser transscleral cyclophotocoagulation on the normal equine eye and intraocular pressure(a).

    PubMed

    Cavens, Vanessa J Kuonen; Gemensky-Metzler, Anne J; Wilkie, David A; Weisbrode, Steven E; Lehman, Amy M

    2012-11-01

    To describe the long-term histologic and intraocular pressure (IOP) lowering effects of diode laser transscleral cyclophotocoagulation (TSCP) on the normal equine eye. Eight normal adult horses. TSCP was performed in one randomly assigned eye. Sixty spots were treated at settings of 1500 ms and 1500 mW. Two horses were randomly selected for euthanasia at 2, 4, 12, or 24 weeks post-TSCP. Both eyes were enucleated and histologically evaluated. Intraocular pressure was measured by applanation tonometry prior to TSCP, immediately post-TSCP, twice daily for 7 days post-TSCP and then monthly until study conclusion. A longitudinal model estimated the average IOP values for the treated and untreated eyes at 1 week, 1, 3, and 6 months post-TSCP. All treated eyes at all time periods exhibited four characteristic histologic lesions: scleral collagen hyalinization, ciliary body pigment dispersion and clumping, focal disruption of the ciliary body epithelium, and focal ciliary process atrophy. After TSCP, there were no significant changes in IOP from baseline for the control eyes, while the IOP in treated eyes was significantly decreased from baseline (P < 0.05) at all time periods. The estimated decrease in IOP in the treated eyes compared to baseline IOP at 6 months was -3.76 mmHg for an average decrease in IOP of 20% from baseline. Diode laser TSCP produces histologic lesions in the equine ciliary body that result in a significant and sustained decrease in IOP. TSCP may be an effective management for equine glaucoma. © 2012 American College of Veterinary Ophthalmologists.

  7. The effect of unilateral disruption of the centrifugal visual system on normal eye development in chicks raised under constant light conditions.

    PubMed

    Dillingham, Christopher Mark; Guggenheim, Jeremy Andrew; Erichsen, Jonathan Thor

    2017-04-01

    The centrifugal visual system (CVS) comprises a visually driven isthmic feedback projection to the retina. While its function has remained elusive, we have previously shown that, under otherwise normal conditions, unilateral disconnection of centrifugal neurons in the chick affected eye development, inducing a reduced rate of axial elongation that resulted in a unilateral hyperopia in the eye contralateral to the lesion. Here, we further investigate the role of centrifugal neurons in ocular development in chicks reared in an abnormal visual environment, namely constant light. The baseline ocular phenotype of constant light-reared chicks (n = 8) with intact centrifugal neurons was assessed over a 3-week post-hatch time period and, subsequently, compared to chicks raised in normal diurnal lighting (n = 8). Lesions of the isthmo-optic tract or sham surgeries were performed in another seventeen chicks, all raised under constant light. Ocular phenotyping was performed over a 21-day postoperative period to assess changes in refractive state (streak retinoscopy) and ocular component dimensions (A-scan ultrasonography). A pathway-tracing paradigm was employed to quantify lesion success. Chicks raised in constant light conditions with an intact CVS developed shallower anterior chambers combined with elongated vitreous chambers relative to chicks raised in normal diurnal lighting. Seven days following surgery to disrupt centrifugal neurons, a significant positive correlation between refractive error asymmetry between the eyes and lesion success was evident, characterized by hyperopia in the eye contralateral to the lesion. By 21 days post-surgery, these contralateral eyes had become emmetropic, while ipsilateral eyes had developed relative axial hyperopia. Our results provide further support for the hypothesis that the centrifugal visual system can modulate eye development.

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

    PubMed

    GRAHAM, C H; HSIA, Y

    1958-03-28

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

  9. 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

  10. Classification algorithms enhance the discrimination of glaucoma from normal eyes using high-definition optical coherence tomography.

    PubMed

    Baskaran, Mani; Ong, Ee-Lin; Li, Jia-Liang; Cheung, Carol Y; Chen, David; Perera, Shamira A; Ho, Ching Lin; Zheng, Ying-Feng; Aung, Tin

    2012-04-24

    To evaluate the diagnostic performance of classification algorithms based on Linear Discriminant Analysis (LDA) and Classification And Regression Tree (CART) methods, compared with optic nerve head (ONH) and retinal nerve fiber layer (RNFL) parameters measured by high-definition optical coherence tomography (Cirrus HD-OCT) for discriminating glaucoma subjects. Consecutive glaucoma subjects (Training data = 184; Validation data = 102) were recruited from an eye center and normal subjects (n = 508) from an ongoing Singaporean Chinese population-based study. ONH and RNFL parameters were measured using a 200 × 200 scan protocol. LDA and CART were computed and areas under the receiver operating characteristic curve (AUC) compared. Average RNFL thickness (AUC 0.92, 95% confidence interval [CI] 0.91, 0.93), inferior RNFL thickness (AUC 0.92, 95% CI 0.91, 0.93), vertical cup-disc ratio (AUC 0.91, 95% CI 0.90, 0.92) and rim area/disc area ratio (AUC 0.90, 95% CI 0.86, 0.93) discriminated glaucoma better than other parameters (P ≤ 0.033). LDA (AUC 0.96, 95% CI 0.95, 0.96) and CART (0.98, 95% CI 0.98, 0.99) outperformed all parameters for diagnostic accuracy (P ≤ 0.005). Misclassification rates in LDA (8%) and CART (5.6%) were found to be low. The AUC of LDA for the validation data was 0.98 (0.95, 0.99) and CART was 0.99 (0.99, 0.994). CART discriminated mild glaucoma from normal better than LDA (AUC 0.94 vs. 0.99, P < 0.0001). Classification algorithms based on LDA and CART can be used in HD-OCT analysis for glaucoma discrimination. The CART method was found to be superior to individual ONH and RNFL parameters for early glaucoma discrimination.

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

    PubMed

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

    2012-01-01

    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. Prospective study. 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. 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. 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.

  12. 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.

  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. 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.

  15. 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

  16. 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

  17. Identification, quantification and comparison of major non-polar lipids in normal and dry eye tear lipidomes by electrospray tandem mass spectrometry.

    PubMed

    Ham, Bryan M; Jacob, Jean T; Keese, Monica M; Cole, Richard B

    2004-11-01

    Millions of individuals suffer from a health condition known as keratoconjunctivitis sicca (KCS, also known as 'dry eye'). Studies have indicated that the lipids in the tear film layer, which covers the outer portion of the eye, may be directly correlated with the existence of dry eye syndrome. By identifying and comparing the major, non-polar lipids in normal eye tears with a dry eye model, it may be possible to identify a symptom of, or a contributing factor to, dry eye. Electrospray tandem mass spectrometry (ES-MS/MS) was used to identify and compare the non-polar lipids, detected as lithium adducts, from normal and dry eye tear samples obtained from rabbits. A limited number of normal human tear samples were also examined for lipid content, and a close resemblance to rabbit was observed. Three distinct regions were delineated in the ES mass spectra of the non polar lipids, m/z 20-500, 500-800 and 800-1100. A common feature noted among identified lipid components was a glycerol backbone with fatty acyl substituents attached. Product ion spectra were obtained for lithiated monoacyl-, 1,2- and 1,3-diacyl- and triacylglyceride standards. Newly proposed structures and fragmentation pathways for the major product ions are presented for the 1,2- and 1,3-diglycerides, and also for the monoglyceride. New approaches to distinguishing asymmetric 1,2-diglycerides and 1,2- from 1,3-diglycerides are proposed. For the rabbit tear samples, the m/z 20-500 range contains monoester diols with empirical formulas C(n)H(2n)O(4), the m/z 500-800 range includes diesters with empirical formulas C(n)H(2n-2)O(5) and the m/z 800-1100 range contains triesters with empirical formulas C(n)H(2n-4)O(6). Also found in the extracts were three isoprene acetals (terpenoids). Copyright (c) 2004 John Wiley & Sons, Ltd

  18. Genetic Networks Activated by Blast Injury to the Eye

    DTIC Science & Technology

    2014-08-01

    Major Finding: Collected retinas from 40 normal strains with 148 microarrays run. We have collected phenotypic data on corneal thickness, lOP and...pressure ( lOP ), central corneal thickness (CCT) and visual acuity. Task 2) Define the genetic networks activated by blast injury in the eye and in...retina. Accomplishments Under These Goals: Taskl: At the present time we have measured lOP and central corneal thickness on 27 strains of mice

  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

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

    2015-01-01

    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. 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. 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. The reproducibility of peripapillary RNFL measurements obtained with SLP-ECC was excellent, indicating that SLP-ECC is sufficiently accurate for monitoring glaucoma progression.

  20. 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; Pajarin, Ana B.

    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

  1. 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…

  2. 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…

  3. 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.

  4. 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

  5. Normal Morning Melanin-Concentrating Hormone Levels and No Association with Rapid Eye Movement or Non-Rapid Eye Movement Sleep Parameters in Narcolepsy Type 1 and Type 2

    PubMed Central

    Schrölkamp, Maren; Jennum, Poul J.; Gammeltoft, Steen; Holm, Anja; Kornum, Birgitte R.; Knudsen, Stine

    2017-01-01

    Study Objectives: Other than hypocretin-1 (HCRT-1) deficiency in narcolepsy type 1 (NT1), the neurochemical imbalance of NT1 and narcolepsy type 2 (NT2) with normal HCRT-1 levels is largely unknown. The neuropeptide melanin-concentrating hormone (MCH) is mainly secreted during sleep and is involved in rapid eye movement (REM) and non-rapid eye movement (NREM) sleep regulation. Hypocretin neurons reciprocally interact with MCH neurons. We hypothesized that altered MCH secretion contributes to the symptoms and sleep abnormalities of narcolepsy and that this is reflected in morning cerebrospinal fluid (CSF) MCH levels, in contrast to previously reported normal evening/afternoon levels. Methods: Lumbar CSF and plasma were collected from 07:00 to 10:00 from 57 patients with narcolepsy (subtypes: 47 NT1; 10 NT2) diagnosed according to International Classification of Sleep Disorders, Third Edition (ICSD-3) and 20 healthy controls. HCRT-1 and MCH levels were quantified by radioimmunoassay and correlated with clinical symptoms, polysomnography (PSG), and Multiple Sleep Latency Test (MSLT) parameters. Results: CSF and plasma MCH levels were not significantly different between narcolepsy patients regardless of ICSD-3 subtype, HCRT-1 levels, or compared to controls. CSF MCH and HCRT-1 levels were not significantly correlated. Multivariate regression models of CSF MCH levels, age, sex, and body mass index predicting clinical, PSG, and MSLT parameters did not reveal any significant associations to CSF MCH levels. Conclusions: Our study shows that MCH levels in CSF collected in the morning are normal in narcolepsy and not associated with the clinical symptoms, REM sleep abnormalities, nor number of muscle movements during REM or NREM sleep of the patients. We conclude that morning lumbar CSF MCH measurement is not an informative diagnostic marker for narcolepsy. Citation: Schrölkamp M, Jennum PJ, Gammeltoft S, Holm A, Kornum BR, Knudsen S. Normal morning melanin

  6. 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

  7. 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.

  8. 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. © 2013 John Wiley & Sons Ltd.

  9. The fluorescence lifetime of lipofuscin granule fluorophores contained in the retinal pigment epithelium cells from human cadaver eyes in normal state and in the case of visualized pathology.

    PubMed

    Yakovleva, M A; Feldman, T B; Arbukhanova, P M; Borzenok, S A; Kuzmin, V A; Ostrovsky, M A

    2017-05-01

    A comparative analysis of fluorescence lifetime of lipofuscin granule fluorophores contained in the retinal pigment epithelium cells from human cadaver eyes in normal state and in the case of visualized pathology was carried out. Measurements of fluorescence lifetimes of bis-retinoids and their photooxidation and photodegradation products were carried out using the method of counting time-correlated photons. Comparative analysis showed that, in the case of visualized pathology, the contribution of photooxidation and photodegradation products of bis-retinoids to the total fluorescence of the retinal pigment epithelium cell suspension increases in comparison with the norm.

  10. Funduscopic versus HRT III Confocal Scanner Vertical Cup-Disc Ratio Assessment in Normal Tension and Primary Open Angle Glaucoma (The Leuven Eye Study).

    PubMed

    Willekens, Koen; Bataillie, Sophie; Sarens, Inge; Odent, Sofie; Abegão Pinto, Luìs; Vandewalle, Evelien; Van Keer, Karel; Stalmans, Ingeborg

    2017-01-01

    To compare funduscopic and confocal scanning vertical cup-disc ratio (VCDR) assessments and their respective predictive value for estimating functional glaucomatous damage. Data from a single eye of open angle glaucoma patients from the Leuven Eye Study were included: age, gender, intra-ocular pressure, visual acuity, refractive error, visual field mean deviation and pattern standard deviation, funduscopic and HRT III VCDRs as well as mean retinal nerve fibre layer thickness. Non-parametric tests to compare differences within and between diagnostic groups were used, and receiver-operating characteristic curves as well as Bland-Altman plots constructed. Three hundred and one eyes of 301 subjects with primary open angle glaucoma (POAG) and normal tension glaucoma (NTG) were included. The average VCDR assessed with HRT III was significantly smaller than the funduscopic measurement (0.69 ± 0.16 vs. 0.81 ± 0.14, respectively; p < 0.001). The predictive value of both measurement techniques did not differ in NTG patients, but the funduscopic estimate yielded a significantly larger predictive power in patients with severe POAG. Funduscopic and confocal scanner estimates of VCDR differ significantly and should not be used interchangeably. In POAG patients with severe glaucoma, a subjective VCDR predicts functional glaucomatous damage significantly better. © 2016 S. Karger AG, Basel.

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

    PubMed Central

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

    2016-01-01

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

  12. 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.

  13. Corneal thickness and elevation measurements using swept-source optical coherence tomography and slit scanning topography in normal and keratoconic eyes.

    PubMed

    Jhanji, Vishal; Yang, Bingzhi; Yu, Marco; Ye, Cong; Leung, Christopher K S

    2013-11-01

    To compare corneal thickness and corneal elevation using swept source optical coherence tomography and slit scanning topography. Prospective study. 41 normal and 46 keratoconus subjects. All eyes were imaged using swept source optical coherence tomography and slit scanning tomography during the same visit. Mean corneal thickness and best-fit sphere measurements were compared between the instruments. Agreement of measurements between swept source optical coherence tomography and scanning slit topography was analyzed. Intra-rater reproducibility coefficient and intraclass correlation coefficient were evaluated. In normal eyes, central corneal thickness measured by swept source optical coherence tomography was thinner compared with slit scanning topography (p < 0.0001) and ultrasound pachymetry (p = < .0001). Ultrasound pachymetry readings had better 95% limits of agreement with swept source optical coherence tomography than slit scanning topography. In keratoconus eyes, central corneal thickness was thinner on swept source optical coherence tomography than slit scanning topography (p = 0.081) and ultrasound pachymetry (p = 0.001). There were significant differences between thinnest corneal thickness, and, anterior and posterior best-fit sphere measurements between both instruments (p < 0.05 for all). Overall, reproducibility coefficients and intraclass correlation coefficients were significantly better with swept source optical coherence tomography for measurement of central corneal thickness, anterior best-fit sphere and, posterior best-fit sphere (all p < 0.001). Corneal thickness and elevation measurements were significantly different between swept source optical coherence tomography and slit scanning topography. With better reproducibility coefficients and intraclass correlation coefficients, swept source optical coherence tomography may provide a reliable alternative for measurement of corneal parameters. © 2013 The Authors. Clinical

  14. Evaluation of Segmentation of the Superficial and Deep Vascular Layers of the Retina by Optical Coherence Tomography Angiography Instruments in Normal Eyes.

    PubMed

    Spaide, Richard F; Curcio, Christine A

    2017-03-01

    Correct attribution of vascular features in optical coherence tomography (OCT) angiography depends on accurate segmentation of retinal layers. To evaluate the segmentation of retinal layers among 3 OCT angiography instruments in the central macula, an area where the superficial and deep vascular plexuses terminate. A retrospective review of a representative OCT angiogram from 1 patient and an evaluation of the vascular pattern in an autopsied eye were conducted at a community retina practice at a university laboratory. A set of 3 × 3-mm scans centered on the fovea using the Cirrus 5000, RTVue XR Avanti, and Triton DRI OCT platforms with default layer segmentations were used to evaluate segmentation accuracy of a normal macula of a white man in his 60s as an emblematic example. A representative histologic section from the central macula of a normal eye was used as an exemplar. Retinal layer segmentation and resultant vascular image compared with vessels as seen in histologic section. The segmentation slab designed to isolate the superficial vascular plexus included the deep vascular plexus in the central macula for all 3 instruments. None of the instruments produced segmented regions that followed the relevant anatomic layers correctly. Because of inherent errors in segmentation, studies of the superficial and deep vascular plexuses using manufacturer-recommended default settings are likely to be biased. A proposal for an improved segmentation strategy is presented.

  15. Number of blastocysts biopsied as a predictive indicator to obtain at least one normal/balanced embryo following preimplantation genetic diagnosis with single nucleotide polymorphism microarray in translocation cases.

    PubMed

    Wang, Yi-Zi; Ding, Chen-Hui; Wang, Jing; Zeng, Yan-Hong; Zhou, Wen; Li, Rong; Zhou, Can-Quan; Deng, Ming-Fen; Xu, Yan-Wen

    2017-01-01

    The aim of this study is to investigate the minimum number of blastocysts for biopsy to increase the likelihood of obtaining at least one normal/balanced embryo in preimplantation genetic diagnosis (PGD) for translocation carriers. This blinded retrospective study included 55 PGD cycles for Robertsonian translocation (RT) and 181 cycles for reciprocal translocation (rcp) to indicate when only one of the couples carried a translocation. Single-nucleotide polymorphism microarray after trophectoderm biopsy was performed. Reliable results were obtained for 355/379 (93.7 %) biopsied blastocysts in RT group and 986/1053 (93.6 %) in rcp group. Mean numbers of biopsied embryos per patient, normal/balanced embryos per patient, and mean normal/balanced embryo rate per patient were 7.4, 3.1, and 40.7 % in RT group and 8.0, 2.1, and 27.3 %, respectively, in rcp group. In a regression model, three factors significantly affected the number of genetically transferrable embryos: number of biopsied embryos (P = 0.001), basal FSH level (P = 0.040), and maternal age (P = 0.027). ROC analysis with a cutoff of 1.5 was calculated for the number of biopsied embryos required to obtain at least one normal/balanced embryo for RT carriers. For rcp carriers, the cutoff was 3.5. The clinical pregnancy rate per embryo transfer was 44.2 and 42.6 % in RT and rcp groups (P = 0.836). The minimum numbers of blastocysts to obtain at least one normal/balanced embryo for RT and rcp were 2 and 4 under the conditions of female age < 37 years with a basal FSH level < 11.4 IU/L.

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

    PubMed Central

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

    2014-01-01

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

  17. Evaluation of the transforming growth factor-beta activity in normal and dry eye human tears by CCL-185 cell bioassay.

    PubMed

    Zheng, Xiaofen; De Paiva, Cintia S; Rao, Kavita; Li, De-Quan; Farley, William J; Stern, Michael; Pflugfelder, Stephen C

    2010-09-01

    To develop a new bioassay method using human lung epithelial cells (CCL-185) to assess activity of transforming growth factor beta (TGF-beta) in human tear fluid from normal subjects and patients with dry eye. Two epithelial cell lines, mink lung cells (CCL-64) and human lung cells (CCL-185), were compared to detect the active form of TGF-beta by BrdU incorporation (quantitation of cell DNA synthesis) and WST assay (metabolic activity of viable cells). The effect of TGF-beta on the growth of CCL-185 cells was observed microscopically. Human tears from normal control subjects and patients with dry eye (DE) with and without Sjögren syndrome were evaluated for TGF-beta concentration by Luminex microbead assay, and TGF-beta activity by the CCL-185 cell growth inhibition bioassay. The metabolic activity of viable CCL-185 cells, measured by WST, was shown to be proportional to the TGF-beta1 concentration (R = 0.919) and confirmed by BrdU assay (R = 0.969). Compared with CCL-185, metabolic activity of viable cells and DNA synthesis, measured by WST and BrdU incorporation assays, were shown to be less proportional to the TGF-beta1 concentration in the CCL-64 line (R = 0.42 and 0.17, respectively). Coincubation with human anti-TGF-beta1 antibody (MAB-240) yielded a dose-dependent inhibition of TGF-beta1 (0.3 ng/mL) activity. CCL-185 cell growth observed microscopically was noted to decrease in response to increasing TGF-beta1 concentrations. Levels of immuodetectable TGF-beta1 and TGF-beta2 were similar in normal and DE tears. TGF-beta bioactivity in DE human tears measured by the CCL-185 cells assay was found to be higher (9777.5 +/- 10481.9 pg/mL) than those in normal controls (4129.3 +/- 1342.9 pg/mL) (P < 0.05). Among patients with DE, TGF-beta bioactivity was highest in those with Sjögren syndrome. Approximately, 79.1% of TGF-beta in DE tears and 37.6% TGF-beta in normal tears were found to be biologically active. The CCL-185 cell assay was found to be a suitable

  18. 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

  19. 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 ...

  20. Eye Infections

    MedlinePlus

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

  1. Spotting effect in microarray experiments

    PubMed Central

    Mary-Huard, Tristan; Daudin, Jean-Jacques; Robin, Stéphane; Bitton, Frédérique; Cabannes, Eric; Hilson, Pierre

    2004-01-01

    Background Microarray data must be normalized because they suffer from multiple biases. We have identified a source of spatial experimental variability that significantly affects data obtained with Cy3/Cy5 spotted glass arrays. It yields a periodic pattern altering both signal (Cy3/Cy5 ratio) and intensity across the array. Results Using the variogram, a geostatistical tool, we characterized the observed variability, called here the spotting effect because it most probably arises during steps in the array printing procedure. Conclusions The spotting effect is not appropriately corrected by current normalization methods, even by those addressing spatial variability. Importantly, the spotting effect may alter differential and clustering analysis. PMID:15151695

  2. 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

  3. Witnessing the first sign of retinitis pigmentosa onset in the allegedly normal eye of a case of unilateral RP: a 30-year follow-up.

    PubMed

    Gauvin, Mathieu; Chakor, Hadi; Koenekoop, Robert K; Little, John M; Lina, Jean-Marc; Lachapelle, Pierre

    2016-06-01

    A patient initially presented with constricted visual field, attenuated retinal vasculature, pigmentary clumping and reduced ERG in OS only, suggestive of unilateral retinitis pigmentosa (RP). This patient was subsequently seen on eight occasions (over three decades), and, with time, the initially normal eye (OD) gradually showed signs of RP-like degeneration. The purpose of this study was to evaluate which clinical modality (visual field, funduscopy or electroretinography) could have first predicted this fate. At each time points, data obtained from our patient were compared to normative data using Z tests. At initial visit, all tests were significantly (p < 0.05) altered in OS and normal in OD. Visual field and retinal vessel diameter in OD reduced gradually to reach statistical significance at the 5th visit and 6th visit (21 and 22 years after the first examination, respectively). In OD, the amplitude of the scotopic and photopic ERGs reduced gradually and was significantly smaller than normal at the 2nd visit (after 11 years) and 3rd visit (after 18 years), respectively. When the photopic ERG was analyzed using the discrete wavelet transform (DWT), we were able to detect a significant change at the 2nd visit (after 11 years) instead of the 3rd visit (18 years). Our study allowed us to witness the earliest manifestation of an RP disease process. The ERG was the first test to detect significant RP changes. A significantly earlier detection of ERG anomalies was obtained when the DWT was used, demonstrating its advantage for early detection of ERG changes.

  4. 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

  5. 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

  6. 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.

  7. 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

  8. Sensitivity and specificity for detecting early glaucoma in eyes with high myopia from normative database of macular ganglion cell complex thickness obtained from normal non-myopic or highly myopic Asian eyes.

    PubMed

    Nakanishi, Hideo; Akagi, Tadamichi; Hangai, Masanori; Kimura, Yugo; Suda, Kenji; Kumagai, Kyoko Kawashima; Morooka, Satoshi; Ikeda, Hanako Ohashi; Yoshimura, Nagahisa

    2015-07-01

    We aimed to determine the sensitivity and specificity of the normative database of non-myopic and highly myopic eyes of the macular ganglion cell complex (mGCC) thickness embedded in the NIDEK RS-3000 spectral-domain optical coherence tomography (SD-OCT) for detecting early glaucoma in highly myopic eyes. Forty-seven highly myopic eyes (axial length ≥26.0 mm) of 47 subjects were studied. The SD-OCT images were used to determine the mGCC thickness within a 9-mm diameter circle centered on the fovea. The sensitivity and specificity of the non-myopic database were compared to that of the highly myopic database for distinguishing the early glaucomatous eyes from the non-glaucomatous eyes. The mGCC scans were classified as abnormal if at least one of the eight sectors of the significance map was < 1 % of the normative thickness. Twenty-one eyes were diagnosed to be non-glaucomatous and 26 eyes to have early glaucoma. . The average mGCC thickness was significantly thinner (80.9 ± 8.5 μm) in the early glaucoma group than in the non-glaucomatous group (91.2 ± 7.5 μm; p <1 × 10(-4)). The sensitivity was 96.2 % and specificity was 47.6 % when the non-myopic database was used, and the sensitivity was 92.3 % and the specificity was 90.5 % when the highly myopic database was used. The difference in the specificity was significant (p < 0.01). The significantly higher specificity of the myopic normative database for detecting early glaucoma in highly myopic eyes will lead to fewer false positive diagnoses. The database obtained from highly myopic eyes should be used when evaluating the mGCC thickness of highly myopic eyes.

  9. 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 ...

  10. Scleral micro-RNA signatures in adult and fetal eyes.

    PubMed

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

    2013-01-01

    In human eyes, ocular enlargement/growth reflects active extracellular matrix remodeling of the outer scleral shell. Micro-RNAs are small non-coding RNAs that regulate gene expression by base pairing with target sequences. They serve as nodes of signaling networks. We hypothesized that the sclera, like most tissues, expresses micro-RNAs, some of which modulate genes regulating ocular growth. In this study, the scleral micro-RNA expression profile of rapidly growing human fetal eyes was compared with that of stable adult donor eyes using high-throughput microarray and quantitative PCR analyses. Scleral samples from normal human fetal (24 wk) and normal adult donor eyes were obtained (n=4 to 6, each group), and RNA extracted. Genome-wide micro-RNA profiling was performed using the Agilent micro-RNA microarray platform. Micro-RNA target predictions were obtained using Microcosm, TargetScan and PicTar algorithms. TaqMan® micro-RNA assays targeting micro-RNAs showing either highest significance, detection, or fold differences, and collagen specificity, were applied to scleral samples from posterior and peripheral ocular regions (n=7, each group). Microarray data were analyzed using R, and quantitative PCR data with 2^-deltaCt methods. Human sclera was found to express micro-RNAs, and comparison of microarray results for adult and fetal samples revealed many to be differentially expressed (p<0.01, min p= 6.5x10(11)). Specifically, fetal sclera showed increased expression of mir-214, let-7c, let-7e, mir-103, mir-107, and mir-98 (1.5 to 4 fold changes, p<0.01). However, no significant regionally specific differences .i.e., posterior vs. peripheral sclera, were observed for either adult or fetal samples. For the first time, micro-RNA expression has been catalogued in human sclera. Some micro-RNAs show age-related differential regulation, higher in the sclera of rapidly growing fetal eyes, consistent with a role in ocular growth regulation. Thus micro-RNAs represent

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

    PubMed Central

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

    2013-01-01

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

  12. 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

  13. DNA Microarray Technology

    SciTech Connect

    WERNER-WASHBURNE, MARGARET; DAVIDSON, GEORGE S.

    2002-01-01

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

  14. 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.

  15. Lasik eye surgery - slideshow

    MedlinePlus

    ... presentations/100206.htm Lasik eye surgery - series—Normal anatomy To use the sharing features on this page, ... Bethesda, MD 20894 U.S. Department of Health and Human Services National Institutes of Health Page last updated: ...

  16. H5 avian influenza virus pathotyping using oligonucleotide microarray.

    PubMed

    Wang, Lih-Chiann; Huang, Dean; Cheng, Ming-Chu; Lee, Shu-Hwae; Wang, Ching-Ho

    2015-08-01

    The H5 avian influenza virus subtype has huge impact on the poultry industry. Rapid diagnosis and accurate identification of the highly pathogenic avian influenza virus and low-pathogenicity avian influenza virus is essential, especially during H5 outbreaks and surveillance. To this end, a novel and rapid strategy for H5 virus molecular pathotyping is presented. The specific hemagglutinin gene of the H5 virus and the basic amino acid number of the motif at the hemagglutinin precursor protein cleavage site were detected using oligonucleotide microarray. Highly pathogenic and low-pathogenicity avian influenza viruses in Taiwan were differentiated using 13 microarray probes with the naked eye. The detection limit reached 3.4 viral RNA copies, 1000 times more sensitive than reverse transcription polymerase chain reaction. Thus, the oligonucleotide microarray would provide an alternative H5 pathogenicity determination using the naked eye for laboratories lacking facilities. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    PubMed

    Monsudi, Kehinde F; Ayanniyi, Abdulkabir A

    2011-04-01

    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.

  18. 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

  19. 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

  20. Chromosomal microarray versus karyotyping for prenatal diagnosis.

    PubMed

    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

    2012-12-06

    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. 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. 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. 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.).

  1. Functional GPCR microarrays.

    PubMed

    Hong, Yulong; Webb, Brian L; Su, Hui; Mozdy, Eric J; Fang, Ye; Wu, Qi; Liu, Li; Beck, Jonathan; Ferrie, Ann M; Raghavan, Srikanth; Mauro, John; Carre, Alain; Müeller, Dirk; Lai, Fang; Rasnow, Brian; Johnson, Michael; Min, Hosung; Salon, John; Lahiri, Joydeep

    2005-11-09

    This paper describes G-protein-coupled receptor (GPCR) microarrays on porous glass substrates and functional assays based on the binding of a europium-labeled GTP analogue. The porous glass slides were made by casting a glass frit on impermeable glass slides and then coating with gamma-aminopropyl silane (GAPS). The emitted fluorescence was captured on an imager with a time-gated intensified CCD detector. Microarrays of the neurotensin receptor 1, the cholinergic receptor muscarinic 2, the opioid receptor mu, and the cannabinoid receptor 1 were fabricated by pin printing. The selective agonism of each of the receptors was observed. The screening of potential antagonists was demonstrated using a cocktail of agonists. The amount of activation observed was sufficient to permit determinations of EC50 and IC50. Such microarrays could potentially streamline drug discovery by helping integrate primary screening with selectivity and safety screening without compromising the essential functional information obtainable from cellular assays.

  2. Nanotechnologies in protein microarrays.

    PubMed

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

    2015-01-01

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

  3. 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.

  4. Eye Diseases

    MedlinePlus

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

  5. 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 ...

  6. 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 ...

  7. Eye Allergies

    MedlinePlus

    ... Sep. 01, 2016 Eye allergies, also called allergic conjunctivitis, are quite common. They occur when the eyes ... can tear and burn. Unlike other kinds of conjunctivitis, eye allergies are not spread from person to ...

  8. 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 ...

  9. Autocorrelation analysis reveals widespread spatial biases in microarray experiments

    PubMed Central

    Koren, Amnon; Tirosh, Itay; Barkai, Naama

    2007-01-01

    Background DNA microarrays provide the ability to interrogate multiple genes in a single experiment and have revolutionized genomic research. However, the microarray technology suffers from various forms of biases and relatively low reproducibility. A particular source of false data has been described, in which non-random placement of gene probes on the microarray surface is associated with spurious correlations between genes. Results In order to assess the prevalence of this effect and better understand its origins, we applied an autocorrelation analysis of the relationship between chromosomal position and expression level to a database of over 2000 individual yeast microarray experiments. We show that at least 60% of these experiments exhibit spurious chromosomal position-dependent gene correlations, which nonetheless appear in a stochastic manner within each experimental dataset. Using computer simulations, we show that large spatial biases caused in the microarray hybridization step and independently of printing procedures can exclusively account for the observed spurious correlations, in contrast to previous suggestions. Our data suggest that such biases may generate more than 15% false data per experiment. Importantly, spatial biases are expected to occur regardless of microarray design and over a wide range of microarray platforms, organisms and experimental procedures. Conclusions Spatial biases comprise a major source of noise in microarray studies; revision of routine experimental practices and normalizations to account for these biases may significantly and comprehensively improve the quality of new as well as existing DNA microarray data. PMID:17565680

  10. Autocorrelation analysis reveals widespread spatial biases in microarray experiments.

    PubMed

    Koren, Amnon; Tirosh, Itay; Barkai, Naama

    2007-06-12

    DNA microarrays provide the ability to interrogate multiple genes in a single experiment and have revolutionized genomic research. However, the microarray technology suffers from various forms of biases and relatively low reproducibility. A particular source of false data has been described, in which non-random placement of gene probes on the microarray surface is associated with spurious correlations between genes. In order to assess the prevalence of this effect and better understand its origins, we applied an autocorrelation analysis of the relationship between chromosomal position and expression level to a database of over 2000 individual yeast microarray experiments. We show that at least 60% of these experiments exhibit spurious chromosomal position-dependent gene correlations, which nonetheless appear in a stochastic manner within each experimental dataset. Using computer simulations, we show that large spatial biases caused in the microarray hybridization step and independently of printing procedures can exclusively account for the observed spurious correlations, in contrast to previous suggestions. Our data suggest that such biases may generate more than 15% false data per experiment. Importantly, spatial biases are expected to occur regardless of microarray design and over a wide range of microarray platforms, organisms and experimental procedures. Spatial biases comprise a major source of noise in microarray studies; revision of routine experimental practices and normalizations to account for these biases may significantly and comprehensively improve the quality of new as well as existing DNA microarray data.

  11. 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

  12. [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.

  13. 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…

  14. 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

  15. 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…

  16. 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.

  17. Performing custom microRNA microarray experiments.

    PubMed

    Zhang, Xiaoxiao; Zeng, Yan

    2011-10-28

    microRNAs (miRNAs) are a large family of ˜ 22 nucleotides (nt) long RNA molecules that are widely expressed in eukaryotes (1). Complex genomes encode at least hundreds of miRNAs, which primarily inhibit the expression of a vast number of target genes post-transcriptionally (2, 3). miRNAs control a broad range of biological processes (1). In addition, altered miRNA expression has been associated with human diseases such as cancers, and miRNAs may serve as biomarkers for diseases and prognosis (4, 5). It is important, therefore, to understand the expression and functions of miRNAs under many different conditions. Three major approaches have been employed to profile miRNA expression: real-time PCR, microarray, and deep sequencing. The technique of miRNA microarray has the advantage of being high-throughput, generally less expensive, and most of the experimental and analysis steps can be carried out in a molecular biology laboratory at most universities, medical schools and associated hospitals. Here, we describe a method for performing custom miRNA microarray experiments. A miRNA probe set will be printed on glass slides to produce miRNA microarrays. RNA is isolated using a method or reagent that preserves small RNA species, and then labeled with a fluorescence dye. As a control, reference DNA oligonucleotides corresponding to a subset of miRNAs are also labeled with a different fluorescence dye. The reference DNA will serve to demonstrate the quality of the slide and hybridization and will also be used for data normalization. The RNA and DNA are mixed and hybridized to a microarray slide containing probes for most of the miRNAs in the database. After washing, the slide is scanned to obtain images, and intensities of the individual spots quantified. These raw signals will be further processed and analyzed as the expression data of the corresponding miRNAs. Microarray slides can be stripped and regenerated to reduce the cost of microarrays and to enhance the

  18. Reproducibility of peripapillary retinal nerve fiber layer thickness with spectral domain cirrus high-definition optical coherence tomography in normal eyes.

    PubMed

    Hong, Samin; Kim, Chan Yun; Lee, Won Seok; Seong, Gong Je

    2010-01-01

    To assess the reproducibility of the new spectral domain Cirrus high-definition optical coherence tomography (HD-OCT; Carl Zeiss Meditec, Dublin, CA, USA) for analysis of peripapillary retinal nerve fiber layer (RNFL) thickness in healthy eyes. Thirty healthy Korean volunteers were enrolled. Three optic disc cube 200 x 200 Cirrus HD-OCT scans were taken on the same day in discontinuous sessions by the same operator without using the repeat scan function. The reproducibility of the calculated RNFL thickness and probability code were determined by the intraclass correlation coefficient (ICC), coefficient of variation (CV), test-retest variability, and Fleiss' generalized kappa (kappa). Thirty-six eyes were analyzed. For average RNFL thickness, the ICC was 0.970, CV was 2.38%, and test-retest variability was 4.5 microm. For all quadrants except the nasal, ICCs were 0.972 or higher and CVs were 4.26% or less. Overall test-retest variability ranged from 5.8 to 8.1 microm. The kappa value of probability codes for average RNFL thickness was 0.690. The kappa values of quadrants and clock-hour sectors were lower in the nasal areas than in other areas. The reproducibility of Cirrus HD-OCT to analyze peripapillary RNFL thickness in healthy eyes was excellent compared with the previous reports for time domain Stratus OCT. For the calculated RNFL thickness and probability code, variability was relatively higher in the nasal area, and more careful analyses are needed.

  19. Biolog phenotype microarrays.

    PubMed

    Shea, April; Wolcott, Mark; Daefler, Simon; Rozak, David A

    2012-01-01

    Phenotype microarrays nicely complement traditional genomic, transcriptomic, and proteomic analysis by offering opportunities for researchers to ground microbial systems analysis and modeling in a broad yet quantitative assessment of the organism's physiological response to different metabolites and environments. Biolog phenotype assays achieve this by coupling tetrazolium dyes with minimally defined nutrients to measure the impact of hundreds of carbon, nitrogen, phosphorous, and sulfur sources on redox reactions that result from compound-induced effects on the electron transport chain. Over the years, we have used Biolog's reproducible and highly sensitive assays to distinguish closely related bacterial isolates, to understand their metabolic differences, and to model their metabolic behavior using flux balance analysis. This chapter describes Biolog phenotype microarray system components, reagents, and methods, particularly as they apply to bacterial identification, characterization, and metabolic analysis.

  20. 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.

  1. Eye Absence Does Not Regulate Planarian Stem Cells during Eye Regeneration.

    PubMed

    LoCascio, Samuel A; Lapan, Sylvain W; Reddien, Peter W

    2017-02-27

    Dividing cells called neoblasts contain pluripotent stem cells and drive planarian flatworm regeneration from diverse injuries. A long-standing question is whether neoblasts directly sense and respond to the identity of missing tissues during regeneration. We used the eye to investigate this question. Surprisingly, eye removal was neither sufficient nor necessary for neoblasts to increase eye progenitor production. Neoblasts normally increase eye progenitor production following decapitation, facilitating regeneration. Eye removal alone, however, did not induce this response. Eye regeneration following eye-specific resection resulted from homeostatic rates of eye progenitor production and less cell death in the regenerating eye. Conversely, large head injuries that left eyes intact increased eye progenitor production. Large injuries also non-specifically increased progenitor production for multiple uninjured tissues. We propose a model for eye regeneration in which eye tissue production by planarian stem cells is not directly regulated by the absence of the eye itself. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. When is red eye not just conjunctivitis?

    PubMed

    Vafidis, Gilli

    2002-07-01

    Red eyes are not 'just conjunctivitis' when there is significant pain or associated loss of sight. However, you are pretty safe to treat pain-free eyes and the normally seeing red eye with reasurance, lid hygiene advice and bland topical medication. But beware patients wearing soft lenses, and the red eyes of tiny babies or elderly patients, particularly those with apparent acute gastroenteritis.

  3. 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…

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. Gene Profiling in Experimental Models of Eye Growth: Clues to Myopia Pathogenesis

    PubMed Central

    Stone, Richard A.; Khurana, Tejvir S.

    2010-01-01

    To understand the complex regulatory pathways that underlie the development of refractive errors, expression profiling has evaluated gene expression in ocular tissues of well-characterized experimental models that alter postnatal eye growth and induce refractive errors. Derived from a variety of platforms (e.g. differential display, spotted microarrays or Affymetrix GeneChips), gene expression patterns are now being identified in species that include chicken, mouse and primate. Reconciling available results is hindered by varied experimental designs and analytical/statistical features. Continued application of these methods offers promise to provide the much-needed mechanistic framework to develop therapies to normalize refractive development in children. PMID:20363242

  10. 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 ...

  11. 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 ...

  12. Eye emergencies

    MedlinePlus

    ... by common household products such as cleaning solutions, garden chemicals, solvents, or other types of chemicals. Fumes ... in the eye with a ball, such as indoor racket sports Images Eye First aid kit References ...

  13. Eye Emergencies

    MedlinePlus

    ... The Marfan Foundation 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 ...

  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. Challenges for MicroRNA Microarray Data Analysis

    PubMed Central

    Wang, Bin; Xi, Yaguang

    2013-01-01

    Microarray is a high throughput discovery tool that has been broadly used for genomic research. Probe-target hybridization is the central concept of this technology to determine the relative abundance of nucleic acid sequences through fluorescence-based detection. In microarray experiments, variations of expression measurements can be attributed to many different sources that influence the stability and reproducibility of microarray platforms. Normalization is an essential step to reduce non-biological errors and to convert raw image data from multiple arrays (channels) to quality data for further analysis. In general, for the traditional microarray analysis, most established normalization methods are based on two assumptions: (1) the total number of target genes is large enough (>10,000); and (2) the expression level of the majority of genes is kept constant. However, microRNA (miRNA) arrays are usually spotted in low density, due to the fact that the total number of miRNAs is less than 2,000 and the majority of miRNAs are weakly or not expressed. As a result, normalization methods based on the above two assumptions are not applicable to miRNA profiling studies. In this review, we discuss a few representative microarray platforms on the market for miRNA profiling and compare the traditional methods with a few novel strategies specific for miRNA microarrays. PMID:24163754

  16. 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.

  17. 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

  18. 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

  19. New screening methods for donor eye-bank eyes.

    PubMed

    Terry, M A; Ousley, P J

    1999-07-01

    Current methods of screening donor eyes for corneal transplantation are not always effective in excluding corneas with abnormal topography. We used the Orbscan to determine whether corneal-thickness maps could be used as a technique for donor tissue screening. Forty eye-bank eyes were measured with the Orbscan, and a corneal-thickness map was generated. Average central pachymetry measurements from each map were compared with the thinnest midperipheral thickness reading. Two eyes from a donor who had photorefractive keratectomy (PRK) and two eyes from a donor with keratoconus were then compared with the normal donor eye results. The average difference between the thinnest midperipheral pachymetry and the central pachymetry in the control group was 0.040 +/- 0.026 mm. The eyes from the donor with PRK showed larger disparities between the central and midperipheral thicknesses because of the thinned central cornea, with differences of 0.154 mm in the right eye and 0.106 mm in the left eye. The eyes from the donor with keratoconus had midperipheral corneas that were thinner than the center, indicating eccentric, ectatic cones. The differences in thickness between the center and midperiphery in the eyes from the donor with PRK and the donor with keratoconus differed from the control group by >2 SD. Diseases or surgery that affect the relationship between the central and midperipheral corneal thickness may be screened through Orbscan pachymetry mapping with comparison with a normal range.

  20. 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.

  1. Gene Expression and Functional Studies of the Optic Nerve Head Astrocyte Transcriptome from Normal African Americans and Caucasian Americans Donors

    PubMed Central

    Miao, Haixi; Chen, Lin; Riordan, Sean M.; Li, Wenjun; Juarez, Santiago; Crabb, Andrea M.; Lukas, Thomas J.; Du, Pan; Lin, Simon M.; Wise, Alexandria; Agapova, Olga A.; Yang, Ping; Gu, Charles C.; Hernandez, M. Rosario

    2008-01-01

    Purpose To determine whether optic nerve head (ONH) astrocytes, a key cellular component of glaucomatous neuropathy, exhibit differential gene expression in primary cultures of astrocytes from normal African American (AA) donors compared to astrocytes from normal Caucasian American (CA) donors. Methods We used oligonucleotide Affymetrix microarray (HG U133A & HG U133A 2.0 chips) to compare gene expression levels in cultured ONH astrocytes from twelve CA and twelve AA normal age matched donor eyes. Chips were normalized with Robust Microarray Analysis (RMA) in R using Bioconductor. Significant differential gene expression levels were detected using mixed effects modeling and Statistical Analysis of Microarray (SAM). Functional analysis and Gene Ontology were used to classify differentially expressed genes. Differential gene expression was validated by quantitative real time RT-PCR. Protein levels were detected by Western blots and ELISA. Cell adhesion and migration assays tested physiological responses. Glutathione (GSH) assay detected levels of intracellular GSH. Results Multiple analyses selected 87 genes differentially expressed between normal AA and CA (P<0.01). The most relevant genes expressed in AA were categorized by function, including: signal transduction, response to stress, ECM genes, migration and cell adhesion. Conclusions These data show that normal astrocytes from AA and CA normal donors display distinct expression profiles that impact astrocyte functions in the ONH. Our data suggests that differences in gene expression in ONH astrocytes may be specific to the development and/or progression of glaucoma in AA. PMID:18716680

  2. 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.

  3. 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.

  4. Methods in molecular cardiology: microarray technology

    PubMed Central

    van den Bosch, B.; Doevendans, P.A.; Lips, D.; Smeets, H.J.M.

    2003-01-01

    It has become more and more evident that changes in expression levels of genes can play an important role in cardiovascular diseases. Specific gene expression profiles may explain, for example, the pathophysiology of myocardial hypertrophy and pump failure and may provide clues for therapeutic interventions. Knowledge of gene expression patterns can also be applied for diagnostic and prognostic purposes, in which differences in gene activity can be used for classification. DNA microarray technology has become the method of choice to simultaneously study the expression of many different genes in a single assay. Each microarray contains many thousands of different DNA sequences attached to a glass slide. The amount of messenger RNA, which is a measure of gene activity, is compared for each gene on the microarray by labelling the mRNA with different fluorescently labelled nucleotides (Cy3 or Cy5) for the test and reference samples. After hybridisation to the microarray the relative amounts of a particular gene transcript in the two samples can be determined by measuring the signal intensities for the fluorescent groups (Cy3 and Cy5) and calculating signal ratios. This paper describes the development of in-house microarray technology, using commercially available cDNA collections. Several technical approaches will be compared and an overview of the pitfalls and possibilities will be presented. The technology will be explained in the context of our project to determine gene expression differences between normal, hypertrophic and failing heart. ImagesFigure 1Figure 2Figure 3Figure 4Figure 5Figure 6Figure 7Figure 9 PMID:25696214

  5. Ecotoxicogenomics: Microarray interlaboratory comparability.

    PubMed

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

    2016-02-01

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

  6. 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

  7. Test–Retest Repeatability of the Pupil Light Response to Blue and Red Light Stimuli in Normal Human Eyes Using a Novel Pupillometer

    PubMed Central

    Herbst, Kristina; Sander, Birgit; Milea, Dan; Lund-Andersen, Henrik; Kawasaki, Aki

    2011-01-01

    In this study, we evaluated the repeatability of pupil responses to colored light stimuli in healthy subjects using a prototype chromatic pupillometer. One eye of 10 healthy subjects was tested twice in the same day using monochromatic light exposure at two selected wavelengths (660 and 470 nm, intensity 300 cd/m2) presented continuously for 20 s. Pupil responses were recorded in real-time before, during, and after light exposure. Maximal contraction amplitude and sustained contraction amplitude were calculated. In addition, we quantified the summed pupil response during continuous light stimulation as the total area between a reference line representing baseline pupil size and the line representing actual pupil size over 20 s (area under the curve). There was no significant difference in the repeated measure compared to the first test for any of the pupil response parameters. In conclusion, we have developed a novel prototype of color pupillometer which demonstrates good repeatability in evoking and recording the pupillary response to a bright blue and red light stimulus. PMID:21442043

  8. DNA microarray technology for the microbiologist: an overview.

    PubMed

    Ehrenreich, Armin

    2006-11-01

    DNA microarrays have found widespread use as a flexible tool to investigate bacterial metabolism. Their main advantage is the comprehensive data they produce on the transcriptional response of the whole genome to an environmental or genetic stimulus. This allows the microbiologist to monitor metabolism and to define stimulons and regulons. Other fields of application are the identification of microorganisms or the comparison of genomes. The importance of this technology increases with the number of sequenced genomes and the falling prices for equipment and oligonucleotides. Knowledge of DNA microarrays is of rising relevance for many areas in microbiological research. Much literature has been published on various specific aspects of this technique that can be daunting to the casual user and beginner. This article offers a comprehensive outline of microarray technology for transcription analysis in microbiology. It shortly discusses the types of DNA microarrays available, the printing of custom arrays, common labeling strategies for targets, hybridization, scanning, normalization, and clustering of expression data.

  9. Retinoblastoma in a microphthalmic eye.

    PubMed

    Axelsen, I

    1978-01-01

    A case of simultaneous occurrence of microphthalmus and retinoblastoma in an eye removed from a 1-year-old monozygote twin with bilateral retinoblastoma, is reported. The other eye was of normal size, and was treated with irradiation (local application of Stallard disc). This case seems to be the first one published showing that one cannot be usre of the absence of tumours in small eyes although it is extremely rare.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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 ...

  15. 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 ...

  16. LASIK Eye Surgery

    MedlinePlus

    ... performed. In general, a special type of cutting laser is used to precisely change the shape of your cornea — the dome-shaped transparent tissue at the front of your eye — to improve vision. Normally, images are clearly focused ...

  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. 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

  19. 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 ...

  20. 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.

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

    PubMed

    Dionne, Karen; Redfern, Rachel L; Nichols, Jason J; Nichols, Kelly K

    2016-01-01

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

  2. Reverse Phase Protein Microarrays.

    PubMed

    Baldelli, Elisa; Calvert, Valerie; Hodge, Alex; VanMeter, Amy; Petricoin, Emanuel F; Pierobon, Mariaelena

    2017-01-01

    While genes and RNA encode information about cellular status, proteins are considered the engine of the cellular machine, as they are the effective elements that drive all cellular functions including proliferation, migration, differentiation, and apoptosis. Consequently, investigations of the cellular protein network are considered a fundamental tool for understanding cellular functions.Alteration of the cellular homeostasis driven by elaborate intra- and extracellular interactions has become one of the most studied fields in the era of personalized medicine and targeted therapy. Increasing interest has been focused on developing and improving proteomic technologies that are suitable for analysis of clinical samples. In this context, reverse-phase protein microarrays (RPPA) is a sensitive, quantitative, high-throughput immunoassay for protein analyses of tissue samples, cells, and body fluids.RPPA is well suited for broad proteomic profiling and is capable of capturing protein activation as well as biochemical reactions such as phosphorylation, glycosylation, ubiquitination, protein cleavage, and conformational alterations across hundreds of samples using a limited amount of biological material. For these reasons, RPPA represents a valid tool for protein analyses and generates data that help elucidate the functional signaling architecture through protein-protein interaction and protein activation mapping for the identification of critical nodes for individualized or combinatorial targeted therapy.

  3. What Causes Eye Pain?

    PubMed

    Belmonte, Carlos; Acosta, M Carmen; Merayo-Lloves, Jesus; Gallar, Juana

    Eye pain is an unpleasant sensory and emotional experience including sensory-discriminative, emotional, cognitive, and behavioral components and supported by distinct, interconnected peripheral and central nervous system elements. Normal or physiological pain results of the stimulation by noxious stimuli of sensory axons of trigeminal ganglion (TG) neurons innervating the eye. These are functionally heterogeneous. Mechano-nociceptors are only excited by noxious mechanical forces. Polymodal nociceptors also respond to heat, exogenous irritants, and endogenous inflammatory mediators, whereas cold thermoreceptors detect moderate temperature changes. Their distinct sensitivity to stimulating forces is determined by the expression of specific classes of ion channels: Piezo2 for mechanical forces, TRPV1 and TRPA1 for heat and chemical agents, and TRPM8 for cold. Pricking pain is evoked by mechano-nociceptors, while polymodal nociceptors are responsible of burning and stinging eye pain; sensations of dryness appear to be mainly evoked by cold thermoreceptors. Mediators released by local inflammation, increase the excitability of eye polymodal nociceptors causing their sensitization and the augmented pain sensations. During chronic inflammation, additional, long-lasting changes in the expression and function of stimulus-transducing and voltage-sensitive ion channels develop, thereby altering polymodal terminal's excitability and evoking chronic inflammatory pain. When trauma, infections, or metabolic processes directly damage eye nerve terminals, these display aberrant impulse firing due to an abnormal expression of transducing and excitability-modulating ion channels. This malfunction evokes 'neuropathic pain' which may also result from abnormal function of higher brain structures where ocular TG neurons project. Eye diseases or ocular surface surgery cause different levels of inflammation and/or nerve injury, which in turn activate sensory fibers of the eye in a variable

  4. 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

  5. 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

  6. Schirmer tear test type I readings and intraocular pressure values assessed by applanation tonometry (Tonopen® XL) in normal eyes of four European species of birds of prey.

    PubMed

    Barsotti, Giovanni; Briganti, Angela; Spratte, Johanna R; Ceccherelli, Renato; Breghi, Gloria

    2013-09-01

    To determine normal values for Schirmer tear test I and intraocular pressure in four European species of birds of prey. Twenty birds from each of the following species: Eurasian Tawny owl (Strix aluco), Little owl (Athene noctua), Common buzzard (Buteo buteo), and European kestrel (Falco tinnunculus). Both eyes of all birds (80 eyes) underwent a complete ophthalmic examination, which included a Schirmer tear test type I (STT-I) performed with commercially available strips and the assessment of the intraocular pressure (IOP) by applanation tonometry, employing the Tonopen-XL(®) device. The animals, which had been taken to a rescue center, were examined for ocular lesions prior to their eventual release into the wild. STT-I readings and IOP values were expressed as means ± standard deviation. Schirmer tear test type I readings were as follows: Eurasian Tawny owls: 3.12 ± 1.92 mm/min; Little owls: 3.5 ± 1.96 mm/min; Common buzzards: 12.47 ± 2.66 mm/min; European kestrels: 6.20 ± 3.67 mm/min. IOP values were as follows: Eurasian Tawny owls: 11.21 ± 3.12 mmHg; Little owls: 9.83 ± 3.41 mmHg; Common buzzards: 17.2 ± 3.53 mmHg; European kestrels: 8.53 ± 1.59 mmHg. The results of this study give representative values for STT-I and IOP in four of the most common species of birds of prey in Europe. © 2012 American College of Veterinary Ophthalmologists.

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

    PubMed

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

    2016-11-30

    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.

  8. 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

  9. 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 ...

  10. 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 ...

  11. Eye Infections

    MedlinePlus

    ... become red, he probably has a condition called conjunctivitis . Also known as pinkeye, this inflammation, which can be painful and itchy, ... bacteria, antibiotic eye drops are the usual treatment. Conjunctivitis caused by viruses should not be treated with ...

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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. ...

  17. Comparison of hydroxylated print additives on antibody microarray performance

    PubMed Central

    Wu, Peng; Grainger, David W.

    2008-01-01

    Various hydroxylated additives were added to antibody print buffers at different concentrations to stabilize printed antibodies during normal array spot desiccation on commercial polymer-coated microarray slides. Polyvinyl alcohol addition to print buffers produced the most regular spot morphologies, homogenous intra-spot antibody distribution, uniform fluorescence intensity, and improved analyte capture activity, maintained up to 1 month at 4°C for capturing model analytes, anti-human IL-1β, IL-4 and TNFα, on these microarraying slides. PMID:17081047

  18. 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.

  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. 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.

  1. Scanometric analysis of DNA microarrays using DNA intercalator-conjugated gold nanoparticles.

    PubMed

    Cho, Hyunmin; Jung, Juyeon; Chung, Bong Hyun

    2012-08-07

    We introduce a scanometric detection method for the analysis of DNA microarrays using DNA intercalator-conjugated gold nanoparticles that can be analyzed with the naked eye or with an optical scanner after the enhancement of the AuNPs. Moreover, we successfully detected a hemagglutinin-subtyping DNA array using this method.

  2. 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

  3. 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.

  4. Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data.

    PubMed

    Guo, Yan; Sheng, Quanhu; Li, Jiang; Ye, Fei; Samuels, David C; Shyr, Yu

    2013-01-01

    RNAseq and microarray methods are frequently used to measure gene expression level. While similar in purpose, there are fundamental differences between the two technologies. Here, we present the largest comparative study between microarray and RNAseq methods to date using The Cancer Genome Atlas (TCGA) data. We found high correlations between expression data obtained from the Affymetrix one-channel microarray and RNAseq (Spearman correlations coefficients of ∼0.8). We also observed that the low abundance genes had poorer correlations between microarray and RNAseq data than high abundance genes. As expected, due to measurement and normalization differences, Agilent two-channel microarray and RNAseq data were poorly correlated (Spearman correlations coefficients of only ∼0.2). By examining the differentially expressed genes between tumor and normal samples we observed reasonable concordance in directionality between Agilent two-channel microarray and RNAseq data, although a small group of genes were found to have expression changes reported in opposite directions using these two technologies. Overall, RNAseq produces comparable results to microarray technologies in term of expression profiling. The RNAseq normalization methods RPKM and RSEM produce similar results on the gene level and reasonably concordant results on the exon level. Longer exons tended to have better concordance between the two normalization methods than shorter exons.

  5. Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data

    PubMed Central

    Li, Jiang; Ye, Fei; Samuels, David C.; Shyr, Yu

    2013-01-01

    RNAseq and microarray methods are frequently used to measure gene expression level. While similar in purpose, there are fundamental differences between the two technologies. Here, we present the largest comparative study between microarray and RNAseq methods to date using The Cancer Genome Atlas (TCGA) data. We found high correlations between expression data obtained from the Affymetrix one-channel microarray and RNAseq (Spearman correlations coefficients of ∼0.8). We also observed that the low abundance genes had poorer correlations between microarray and RNAseq data than high abundance genes. As expected, due to measurement and normalization differences, Agilent two-channel microarray and RNAseq data were poorly correlated (Spearman correlations coefficients of only ∼0.2). By examining the differentially expressed genes between tumor and normal samples we observed reasonable concordance in directionality between Agilent two-channel microarray and RNAseq data, although a small group of genes were found to have expression changes reported in opposite directions using these two technologies. Overall, RNAseq produces comparable results to microarray technologies in term of expression profiling. The RNAseq normalization methods RPKM and RSEM produce similar results on the gene level and reasonably concordant results on the exon level. Longer exons tended to have better concordance between the two normalization methods than shorter exons. PMID:23977046

  6. 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.

  7. Microarray analysis of papillary thyroid cancers in Korean.

    PubMed

    Kim, Hyun Sook; Kim, Do Hyung; Kim, Ji Yeon; Jeoung, Nam Ho; Lee, In Kyu; Bong, Jin Gu; Jung, Eui Dal

    2010-12-01

    Papillary thyroid cancer (PTC) is the most common malignancy of the thyroid gland. It involves several molecular mechanisms. The BRAF V600E mutation has been identified as the most common genetic abnormality in PTC. Moreover, it is known to be more prevalent in Korean PTC patients than in patients from other countries. We investigated distinct genetic profiles in Korean PTC through cDNA microarray analysis. Transcriptional profiles of five PTC samples and five paired normal thyroid tissue samples were generated using cDNA microarrays. The tumors were genotyped for BRAF mutations. The results of the cDNA microarray gene expression analysis were confirmed by real-time PCR and immunohistochemistry analysis of 35 PTC patients. Four of the five patients whose PTC tissues were subjected to microarray analysis were found to carry the BRAF V600E mutation. Microarrays analysis of the five PTC tissue samples showed the expression of 96 genes to be increased and that of 16 genes decreased. Real-time reverse transcription-polymerase chain reaction (RT-PCR) confirmed increased expression of SLC34A2, TM7SF4, COMP, KLK7, and KCNJ2 and decreased expression of FOXA2, SLC4A4, LYVE-1, and TFCP2L1 in PTC compared with normal tissue. Of these genes, TFCP2L1, LYVE-1, and KLK7 were previously unidentified in PTC microarray analysis. Notably, Foxa2 activity in PTC was reduced, as shown by its cytoplasmic localization, in immunohistochemical analyses. These findings demonstrate both similarities and differences between our results and previous reports. In Korean cases of PTC, Foxa2 activity was reduced with its cytoplasmic accumulation. Further studies are needed to confirm the relationship between FOXA2 and BRAF mutations in Korean cases of PTC.

  8. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    PubMed Central

    2009-01-01

    The web application D-Maps provides a user-friendly interface to researchers performing studies based on microarrays. The program was developed to manage and process one- or two-color microarray data obtained from several platforms (currently, GeneTAC, ScanArray, CodeLink, NimbleGen and Affymetrix). Despite the availability of many algorithms and many software programs designed to perform microarray analysis on the internet, these usually require sophisticated knowledge of mathematics, statistics and computation. D-maps was developed to overcome the requirement of high performance computers or programming experience. D-Maps performs raw data processing, normalization and statistical analysis, allowing access to the analyzed data in text or graphical format. An original feature presented by D-Maps is GEO (Gene Expression Omnibus) submission format service. The D-MaPs application was already used for analysis of oligonucleotide microarrays and PCR-spotted arrays (one- and two-color, laser and light scanner). In conclusion, D-Maps is a valuable tool for microarray research community, especially in the case of groups without a bioinformatic core. PMID:21637530

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

    PubMed

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

    2009-07-01

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

  11. 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 ...

  12. Eye Twitching

    MedlinePlus

    ... aspects of life. Hemifacial spasm involves twitches of muscles on one side of the face, including the eyelid. Eye twitching usually goes away on its own within a few days or weeks with rest, stress relief and decreased caffeine. Schedule an appointment with your doctor if: The ...

  13. Googly Eyes

    ERIC Educational Resources Information Center

    Boss, Susan

    2009-01-01

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

  14. DNA microarray integromics analysis platform.

    PubMed

    Waller, Tomasz; Gubała, Tomasz; Sarapata, Krzysztof; Piwowar, Monika; Jurkowski, Wiktor

    2015-01-01

    The study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray Integromics Analysis Platform, a unique web application that focuses on computational integration and analysis of "multi-omics" data. Our tool supports a range of complex analyses, including - among others - low- and high-level analyses of DNA microarray data, integrated analysis of transcriptomics and lipidomics data and the ability to infer miRNA-mRNA interactions. We demonstrate the characteristics and benefits of the DNA Microarray Integromics Analysis Platform using two different test cases. The first test case involves the analysis of the nutrimouse dataset, which contains measurements of the expression of genes involved in nutritional problems and the concentrations of hepatic fatty acids. The second test case involves the analysis of miRNA-mRNA interactions in polysaccharide-stimulated human dermal fibroblasts infected with porcine endogenous retroviruses. The DNA Microarray Integromics Analysis Platform is a web-based graphical user interface for "multi-omics" data management and analysis. Its intuitive nature and wide range of available workflows make it an effective tool for molecular biology research. The platform is hosted at https://lifescience.plgrid.pl/.

  15. Microfluidic microarray systems and methods thereof

    DOEpatents

    West, Jay A. A. [Castro Valley, CA; Hukari, Kyle W [San Ramon, CA; Hux, Gary A [Tracy, CA

    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.

  16. Native antigen fractionation protein microarrays for biomarker discovery.

    PubMed

    Caiazzo, Robert J; O'Rourke, Dennis J; Barder, Timothy J; Nelson, Bryce P; Liu, Brian C-S

    2011-01-01

    In this protocol, we used the T24 human bladder cancer cell line as a source of native antigens to construct fractionated lysate microarrays. Subsequently, these microarrays were used to compare the autoantibody responses of individuals with interstitial cystitis/painful bladder syndrome (IC/PBS) to those of normal female controls. To accomplish this, T24 cells were lysed under nondenaturing conditions to obtain native antigens. These native antigens were then fractionated in 2D using a PF-2D liquid chromatography; the first dimension separated the proteins by their isoelectric points, and the second separated them according to hydrophobicity. The resulting protein fractions were printed onto nitrocellulose-coated glass slides (PATH slides) to create a set of fractionated lysate microarrays. To compare the autoantibody responses of IC/PBS patients with normal controls, the fractionated lysate arrays were competitively hybridized with fluorescently labeled IgG samples purified from both IC/PBS and control sera. This protocol presents a detailed description of the creation and use of native antigen fractionated lysate microarrays for autoantibody profiling.

  17. Diagnostic utility of microarray testing in pregnancy loss.

    PubMed

    Rosenfeld, J A; Tucker, M E; Escobar, L F; Neill, N J; Torchia, B S; McDaniel, L D; Schultz, R A; Chong, K; Chitayat, D

    2015-10-01

    To determine the frequency of clinically significant chromosomal abnormalities identified by chromosomal microarray in pregnancy losses at any gestational age and to compare microarray performance with that of traditional cytogenetic analysis when testing pregnancy losses. Among 535 fetal demise specimens of any gestational age, clinical microarray-based comparative genomic hybridization (aCGH) was performed successfully on 515, and a subset of 107 specimens underwent additional single nucleotide polymorphism (SNP) analysis. Overall, clinically significant abnormalities were identified in 12.8% (64/499) of specimens referred with normal or unknown karyotypes. Detection rates were significantly higher with earlier gestational age. In the subset with normal karyotype, clinically significant abnormalities were identified in 6.9% (20/288). This detection rate did not vary significantly with gestational age, suggesting that, unlike aneuploidy, the contribution of submicroscopic chromosomal abnormalities to fetal demise does not vary with gestational age. In the 107 specimens that underwent aCGH and SNP analysis, seven cases (6.5%) had abnormalities of potential clinical significance detected by the SNP component, including female triploidy. aCGH failed to yield fetal results in 8.3%, which is an improvement over traditional cytogenetic analysis of fetal demise specimens. Both the provision of results in cases in which karyotype fails and the detection of abnormalities in the presence of a normal karyotype demonstrate the increased diagnostic utility of microarray in pregnancy loss. Thus, chromosomal microarray testing is a preferable, robust method of analyzing cases of pregnancy loss to better delineate possible genetic etiologies, regardless of gestational age. Copyright © 2015 ISUOG. Published by John Wiley & Sons Ltd.

  18. 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.

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

    PubMed Central

    Lapan, Sylvain W.; Reddien, Peter W.

    2013-01-01

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

  20. 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.

  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. 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,…

  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. 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

  5. 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.

  6. 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 ...

  7. 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. ...

  8. 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 ...

  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 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 ...

  11. 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 ...

  12. Why Do Eyes Water?

    MedlinePlus

    ... Lifesaver Kids Talk About: Coaches Why Do Eyes Water? KidsHealth > For Kids > Why Do Eyes Water? Print ... out of your nose. continue Why Do Eyes Water? Eyes water for lots of different reasons besides ...

  13. 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 ...

  14. 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.

  15. 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

  16. Characterizing dye bias in microarray experiments.

    PubMed

    Dobbin, K K; Kawasaki, E S; Petersen, D W; Simon, R M

    2005-05-15

    Spot intensity serves as a proxy for gene expression in dual-label microarray experiments. Dye bias is defined as an intensity difference between samples labeled with different dyes attributable to the dyes instead of the gene expression in the samples. Dye bias that is not removed by array normalization can introduce bias into comparisons between samples of interest. But if the bias is consistent across samples for the same gene, it can be corrected by proper experimental design and analysis. If the dye bias is not consistent across samples for the same gene, but is different for different samples, then removing the bias becomes more problematic, perhaps indicating a technical limitation to the ability of fluorescent signals to accurately represent gene expression. Thus, it is important to characterize dye bias to determine: (1) whether it will be removed for all genes by array normalization, (2) whether it will not be removed by normalization but can be removed by proper experimental design and analysis and (3) whether dye bias correction is more problematic than either of these and is not easily removable. We analyzed two large (each >27 arrays) tissue culture experiments with extensive dye swap arrays to better characterize dye bias. Indirect, amino-allyl labeling was used in both experiments. We found that post-normalization dye bias that is consistent across samples does appear to exist for many genes, and that controlling and correcting for this type of dye bias in design and analysis is advisable. The extent of this type of dye bias remained unchanged under a wide range of normalization methods (median-centering, various loess normalizations) and statistical analysis techniques (parametric, rank based, permutation based, etc.). We also found dye bias related to the individual samples for a much smaller subset of genes. But these sample-specific dye biases appeared to have minimal impact on estimated gene-expression differences between the cell lines.

  17. Black Eye: First Aid

    MedlinePlus

    First aid Black eye: First aid Black eye: First aid By Mayo Clinic Staff A black eye is caused by bleeding under the skin around the eye. Most injuries that cause a black eye aren't serious. But a black eye ...

  18. 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.

  19. 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.

  20. 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

  1. Incorporating Nonlinear Relationships in Microarray Missing Value Imputation.

    PubMed

    Yu, Tianwei; Peng, Hesen; Sun, Wei

    2011-01-01

    Microarray gene expression data often contain missing values. Accurate estimation of the missing values is important for downstream data analyses that require complete data. Nonlinear relationships between gene expression levels have not been well-utilized in missing value imputation. We propose an imputation scheme based on nonlinear dependencies between genes. By simulations based on real microarray data, we show that incorporating nonlinear relationships could improve the accuracy of missing value imputation, both in terms of normalized root-mean-squared error and in terms of the preservation of the list of significant genes in statistical testing. In addition, we studied the impact of artificial dependencies introduced by data normalization on the simulation results. Our results suggest that methods relying on global correlation structures may yield overly optimistic simulation results when the data have been subjected to row (gene)-wise mean removal.

  2. Incorporating nonlinear relationships in microarray missing value imputation

    PubMed Central

    Yu, Tianwei; Peng, Hesen; Sun, Wei

    2013-01-01

    Microarray gene expression data often contain missing values. Accurate estimation of the missing values is important for down-stream data analyses that require complete data. Nonlinear relationships between gene expression levels have not been well-utilized in missing value imputation. We propose an imputation scheme based on nonlinear dependencies between genes. By simulations based on real microarray data, we show that incorporating non-linear relationships could improve the accuracy of missing value imputation, both in terms of normalized root mean squared error and in terms of the preservation of the list of significant genes in statistical testing. In addition, we studied the impact of artificial dependencies introduced by data normalization on the simulation results. Our results suggest that methods relying on global correlation structures may yield overly optimistic simulation results when the data has been subjected to row (gene) – wise mean removal. PMID:20733236

  3. 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.

  4. 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.

  5. Searching eye movement, smooth pursuit eye movement and schizophrenia.

    PubMed

    Yan, W; Xia, M; Xing, Z; Cai, Z; Li, G; Huang, F

    1996-07-01

    To detect whether the smooth pursuit eye movement (SPEM) and searching eye movement (SEM) could be considered as a biological marker of schizophrenia, and used as a tool in helping diagnosis of schizophrenia. 88 schizophrenics, 77 patients with mood disorders, 32 with "neurosis", and 74 normal healthy controls were examined for SPEM and SEM individually. The authors verified the results in all the first-visit 150 outpatients in March 1993 by comparing the examination results with the clinical diagnoses after a 6-month follow-up. Significant differences were found in the number of eye fixation (NEF) and total eye scanning length (TESL) of SEM between schizophrenics and normal controls or patients with other disorders. Less NEF and shorter TESL could be helpful in differential diagnosis, and the agreement rate, Kappa coefficient was 0.62. No significant differences were found in SPEM in this investigation between non-medicated schizophrenics and normal controls. Searching eye movement (SEM) might be considered as a biological marker of schizophrenia and might be used as a supplementary tool in its diagnosis.

  6. 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

  7. 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.

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

    PubMed

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

    2016-12-01

    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. 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. 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). 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 bone formation.Cite this article: J. J

  9. 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.

  10. 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. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. 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

  12. 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

  13. Microarray Inspector: tissue cross contamination detection tool for microarray data.

    PubMed

    Stępniak, Piotr; Maycock, Matthew; Wojdan, Konrad; Markowska, Monika; Perun, Serhiy; Srivastava, Aashish; Wyrwicz, Lucjan S; Świrski, Konrad

    2013-01-01

    Microarray technology changed the landscape of contemporary life sciences by providing vast amounts of expression data. Researchers are building up repositories of experiment results with various conditions and samples which serve the scientific community as a precious resource. Ensuring that the sample is of high quality is of utmost importance to this effort. The task is complicated by the fact that in many cases datasets lack information concerning pre-experimental quality assessment. Transcription profiling of tissue samples may be invalidated by an error caused by heterogeneity of the material. The risk of tissue cross contamination is especially high in oncological studies, where it is often difficult to extract the sample. Therefore, there is a need of developing a method detecting tissue contamination in a post-experimental phase. We propose Microarray Inspector: customizable, user-friendly software that enables easy detection of samples containing mixed tissue types. The advantage of the tool is that it uses raw expression data files and analyses each array independently. In addition, the system allows the user to adjust the criteria of the analysis to conform to individual needs and research requirements. The final output of the program contains comfortable to read reports about tissue contamination assessment with detailed information about the test parameters and results. Microarray Inspector provides a list of contaminant biomarkers needed in the analysis of adipose tissue contamination. Using real data (datasets from public repositories) and our tool, we confirmed high specificity of the software in detecting contamination. The results indicated the presence of adipose tissue admixture in a range from approximately 4% to 13% in several tested surgical samples.

  14. Lagophthalmos in enophthalmic eyes

    PubMed Central

    Yip, C-C; Gonzalez-Candial, M; Jain, A; Goldberg, R A; McCann, J D

    2005-01-01

    Aims: To report a case series of enophthalmic patients with lagophthalmos. Methods: A retrospective review of the electronic medical records at a tertiary health care centre of all patients with the diagnoses of “enophthalmos” and “lagophthalmos”. Patients who had a history of diseases (such as Graves’ orbitopathy), trauma or surgery of the orbit and eyelid were excluded. Enophthalmos was defined as exophthalmometric reading of 14 mm or less in both eyes. Results: Seven patients (14 eyes) with bilateral enophthalmos were found to have concomitant lagophthalmos. All patients had deep superior sulci bilaterally. The upper eyelids were seen to be severely retro-placed behind the superior orbital rim. The extraocular motilities were full with no focal neurological deficit. The orbicularis oculi function was normal with no facial paralysis. The orbits were soft on retropulsion and no facial asymmetry was noted. The mean exophthalmolmetry reading measured 12.6 (SD 1.1) mm. The lagophthalmos varied from 1–5 mm. One patient (one eye) with 3 mm lagophthalmos developed a corneal ulcer and was treated with topical antibiotics and gold weight placement in the upper eyelid. Conclusion: Enophthalmic patients with deep superior sulci and retro-placed upper eyelids may present with lagophthalmos and exposure keratopathy. PMID:15923500

  15. Lagophthalmos in enophthalmic eyes.

    PubMed

    Yip, C-C; Gonzalez-Candial, M; Jain, A; Goldberg, R A; McCann, J D

    2005-06-01

    To report a case series of enophthalmic patients with lagophthalmos. A retrospective review of the electronic medical records at a tertiary health care centre of all patients with the diagnoses of "enophthalmos" and "lagophthalmos". Patients who had a history of diseases (such as Graves' orbitopathy), trauma or surgery of the orbit and eyelid were excluded. Enophthalmos was defined as exophthalmometric reading of 14 mm or less in both eyes. Seven patients (14 eyes) with bilateral enophthalmos were found to have concomitant lagophthalmos. All patients had deep superior sulci bilaterally. The upper eyelids were seen to be severely retro-placed behind the superior orbital rim. The extraocular motilities were full with no focal neurological deficit. The orbicularis oculi function was normal with no facial paralysis. The orbits were soft on retropulsion and no facial asymmetry was noted. The mean exophthalmolmetry reading measured 12.6 (SD 1.1) mm. The lagophthalmos varied from 1-5 mm. One patient (one eye) with 3 mm lagophthalmos developed a corneal ulcer and was treated with topical antibiotics and gold weight placement in the upper eyelid. Enophthalmic patients with deep superior sulci and retro-placed upper eyelids may present with lagophthalmos and exposure keratopathy.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. Billie's eyes.

    PubMed

    Dunning, S E

    1993-03-01

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

  1. 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.

  2. 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.

  3. 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.

  4. 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...

  5. 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...

  6. 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

  7. 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.

  8. 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

  9. Novel R Pipeline for Analyzing Biolog Phenotypic Microarray Data

    PubMed Central

    Vehkala, Minna; Shubin, Mikhail; Connor, Thomas R; Thomson, Nicholas R; Corander, Jukka

    2015-01-01

    Data produced by Biolog Phenotype MicroArrays are longitudinal measurements of cells’ respiration on distinct substrates. We introduce a three-step pipeline to analyze phenotypic microarray data with novel procedures for grouping, normalization and effect identification. Grouping and normalization are standard problems in the analysis of phenotype microarrays defined as categorizing bacterial responses into active and non-active, and removing systematic errors from the experimental data, respectively. We expand existing solutions by introducing an important assumption that active and non-active bacteria manifest completely different metabolism and thus should be treated separately. Effect identification, in turn, provides new insights into detecting differing respiration patterns between experimental conditions, e.g. between different combinations of strains and temperatures, as not only the main effects but also their interactions can be evaluated. In the effect identification, the multilevel data are effectively processed by a hierarchical model in the Bayesian framework. The pipeline is tested on a data set of 12 phenotypic plates with bacterium Yersinia enterocolitica. Our pipeline is implemented in R language on the top of opm R package and is freely available for research purposes. PMID:25786143

  10. Statistical designs for two-color spotted microarray experiments.

    PubMed

    Chai, Feng-Shun; Liao, Chen-Tuo; Tsai, Shin-Fu

    2007-04-01

    Two-color cDNA or oligonucleotide-based spotted microarrays have been commonly used in measuring the expression levels of thousands of genes simultaneously. To realize the immense potential of this powerful new technology, budgeted within limited resources or other constraints, practical designs with high efficiencies are in demand. In this study, we address the design issue concerning the arrangement of the mRNA samples labeled with fluorescent dyes and hybridized on the slides. A normalization model is proposed to characterize major sources of systematic variation in a two-color microarray experiment. This normalization model establishes a connection between designs for two-color microarray experiments with a particular class of classical row-column designs. A heuristic algorithm for constructing A-optimal or highly efficient designs is provided. Statistical optimality results are found for some of the designs generated from the algorithm. It is believed that the constructed designs are the best or very close to the best possible for estimating the relative gene expression levels among the mRNA samples of interest.

  11. 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 ...

  12. 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 ...

  13. 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 ...

  14. Dilating Eye Drops

    MedlinePlus

    ... sometimes used to treat eye diseases, such as amblyopia and inflammation. How long do dilating drops last? ... used to treat certain eye diseases, such as amblyopia and inflammation in the eye. These therapeutic dilating ...

  15. 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.

  16. 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...

  17. 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...

  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. 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.

  20. 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

  1. 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.

  2. Development of a microarray chip for gene expression in rabbit ocular research.

    PubMed

    Popp, Michael P; Liu, Li; Timmers, Adrian; Esson, Douglas W; Shiroma, Lineu; Meyers, Craig; Berceli, Scott; Tao, Ming; Wistow, Graeme; Schultz, Gregory S; Sherwood, Mark B

    2007-02-02

    To develop a microarray for the rabbit that can be used for ocular gene expression research. Messenger RNA was isolated from anterior segment tissues (cornea, conjunctiva, and iris) and posterior segment tissues (lens, retina, and sclera) of rabbit eyes and used to create two independent cDNA libraries through the NEIBank project. Clones from each of these libraries were sequenced from both the 5' and 3' ends. These sequences and those from the National Center for Biotechnology Information (NCBI) taxonomy database for rabbit were combined and electronically assembled into a set of unique nonoverlapping continuous sequences (contigs). For each contig, a homology search was performed using BLASTX and BLASTN against both the NCBI NR and NT databases to provide gene annotation. Unique contigs were sent to Agilent Technologies, where 60 base oligonucleotide probes were designed and synthesized, in situ, on two different arrays in an 8 array x 1900 element format. Glaucoma filtration surgery was performed on one eye of six rabbits. After 14 days, tissue was harvested from the conjunctiva and Tenon's capsule of both the surgically treated and untreated control eyes. Total RNA from each sample was labeled with cyanine dyes and hybridized to our custom microarrays. Of the 3,154 total probes present on the two arrays, 2,522 had a signal value above the background. The expression of 315 genes was significantly altered by glaucoma filtration surgery. Genes whose expression was altered included proteins associated with inflammatory response, defense response, and proteins involved in synthesis of the extracellular matrix. The results of this rabbit microarray study are consistent with those from other wound healing studies, indicating that this array can provide valid information on broad patterns of gene expression. This is the first microarray available for rabbit studies and is a valuable tool that can be used to study molecular events in the eye.

  3. Eye dominance in children: a longitudinal study.

    PubMed

    Dellatolas, G; Curt, F; Dargent-Paré, C; De Agostini, M

    1998-05-01

    In a sample of 807 normal preschool children aged from 3 to 6, examined eye dominance was not associated with the declared eye dominance of their parents. Forty percent of the children showed left-eyedness. Eyedness was associated with handedness and not significantly related to age group or sex. A strong relationship between the answers of the two parents concerning eye preference was observed. Two hundred forty-four children were followed-up for 2 years. The examinations were carried out once every 6 months. Two thirds of the children showed perfect stability in eye dominance. There was some evidence that stability in eye use tends to increase with age and to be lower in left-handed children with left-handed parents. There is, at present, very little evidence of a positive association between eye dominance in parents and that in their children.

  4. 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.

  5. Measuring eye states in functional MRI.

    PubMed

    Brodoehl, Stefan; Witte, Otto W; Klingner, Carsten M

    2016-07-13

    In many functional magnetic resonance imaging (fMRI) studies, experimental design often depends on the eye state (i.e., whether the participants had their eyes open or closed). Closed eyes during an fMRI is the general convention, particularly when patients are in a resting-state, but the eye state is difficult to verify. Although knowledge of the impact of the eye state on brain activity is steadily growing, only a few research groups have implemented standardized procedures to monitor eye movements and eye state. These procedures involve advanced methods that are costly (e.g., fMRI-compatible cameras) and often time-consuming (e.g., EEG/EOG). We present a simple method that distinguishes open from closed eyes utilizing functional MR images alone. The utility of this method was demonstrated on fMRI data from 14 healthy subjects who had to open and close their eyes according to a predetermined protocol (3.0 T MRI scanner, EPI sequence with 3 × 3 × 3 mm voxels, TR 2.52 s). The method presented herein is capable of extracting the movement direction of the eyes. All described methods are applicable for pre- and post-normalized MR images and are freely available through a MATLAB toolbox.

  6. 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.

  7. 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.

  8. 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…

  9. 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…

  10. Diurnal intraocular pressure changes in eyes affected with acute primary angle closure and fellow eyes after laser peripheral iridotomy.

    PubMed

    Park, Han Seok; Kim, Joon Mo; Shim, Seong Hee; Kim, Hyun Tae; Bae, Jeong Hun; Choi, Chul Young; Park, Ki Ho

    2015-09-01

    To evaluate diurnal curves of intraocular pressure (IOP) in eyes affected with unilateral acute primary angle closure (APAC) after laser peripheral iridotomy (LPI), and fellow eyes. The medical records of 22 female patients (44 eyes) with unilateral APAC and LPI performed OU were reviewed along with those of 48 normal control subjects (48 eyes). None of the subjects used glaucoma medications after LPI. IOP was measured with a Goldman applanation tonometer during waking hours and in a sitting position every 2 h between 09:00 and 23:00. IOP profiles were compared including the means, peaks, trough IOPs, and IOP fluctuations of the affected, fellow, and normal eyes. The IOPs of the affected eyes were significantly higher than those of normal eyes at every time point measured, including peak and trough IOPs. The diurnal IOPs of fellow eyes were higher than those of normal eyes, though not significantly. There were no significant differences in IOP fluctuation between the affected, fellow, and normal eyes. IOP diurnal curves for APAC affected, fellow, and normal eyes were not statistically different (repeated measures ANOVA, p = 0.865). The mean coefficient of IOP in affected and fellow eyes ranged from 0.486 to 0.604. There were no clinically significant differences among the three groups in terms of IOP diurnal curves, and thus LPI did not have a significant effect on diurnal patterns of IOP. Though the diurnal IOPs of affected eyes after LPI was significantly higher than those of normal eyes, the IOP range was not acute.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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…

  19. 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…

  20. Eye Injuries (For Parents)

    MedlinePlus

    ... the eye nausea or vomiting after an eye injury Think Prevention! Kids who play sports should wear protective goggles or unbreakable glasses as needed. Keep chemicals and other potentially dangerous objects out of the reach of children. Reviewed by: Steven Dowshen, ... (Conjunctivitis) Eyes Corneal Abrasions Styes Activity: Eyes ...

  1. Eye Injuries in Sports

    MedlinePlus

    ... and Fitness Sports Safety Eye Injuries in Sports Eye Injuries in Sports Exercise and FitnessPrevention and WellnessSports Safety Share Eye Injuries ... injury, detached retina, patient education, patient information, penetrating eye ... Exercise and Fitness, Prevention and Wellness, Sports Safety June ...

  2. 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.

  3. Molecular Inflammation in the Contralateral Eye After Cataract Surgery in the First Eye.

    PubMed

    Zhu, Xiang-Jia; Wolff, Don; Zhang, Ke-Ke; He, Wen-Wen; Sun, Xing-Huai; Lu, Yi; Zhou, Peng

    2015-08-01

    The purpose of this study was to assess the inflammatory status of the aqueous humor in the fellow eye after uneventful cataract surgery in the first eye. At the screening stage, aqueous humor samples from 15 first-eye and 15 second-eye cataract patients were collected just before cataract surgery and assayed using human cytokine antibody array. Screened cytokines were then verified using a suspension array system with aqueous humor samples obtained from 35 first-eye and 36 second-eye cataract patients. The cytokine antibody array revealed that interleukin-1 receptor antagonist (Il-1ra) and macrophage inflammatory protein (MIP)-1a and MIP-1b were expressed at high levels in first-eye patients and were lower in second-eye patients, whereas opposite trends were found for monocyte chemoattractant protein 1 (MCP-1) and for regulated on activation, normal T expressed and secreted (RANTES) (all, P < 0.05, Student's t-test). However, only MCP-1 and IL-1ra were significantly different between the two groups after Bonferroni correction (both P < 0.00125). In the replication stage, the suspension cytokine array revealed that only MCP-1 expression was significantly greater in the aqueous humor of second-eye patients than in that of first-eye patients (P = 0.0067, Student's t-test). This study revealed that expression of MCP-1, a pain-related inflammatory chemokine, was significantly increased in aqueous humor in the contralateral eye after first-eye cataract surgery. This suggests there may be a sympathetic ophthalmic type uveitis in the contralateral eye after first-eye cataract surgery and that may help to explain why second-eye phacoemulsification is often more painful. (ClinicalTrials.gov number, NCT01824927.)

  4. 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.

  5. 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.

  6. 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

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

    PubMed Central

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

    2010-01-01

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

  8. 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.

  9. ArrayPipe: a flexible processing pipeline for microarray data

    PubMed Central

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

    2004-01-01

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

  10. 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

  11. 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.

  12. 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.

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

    PubMed Central

    Rehrauer, Hubert; Zoller, Stefan; Schlapbach, Ralph

    2007-01-01

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

  14. 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.

  15. 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.

  16. 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

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

    PubMed

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

    2015-01-01

    Most studies employing experimental models of unilateral glaucoma have used the normotensive contralateral eye as the normal control. However, some studies have recently reported the activation of the retinal macroglia and microglia in the uninjured eye, suggesting that the eye contralateral to experimental glaucoma should not be used as a control. This review analyzes the studies describing the contralateral findings and discusses some of the routes through which the signals can reach the contralateral eye to initiate the glial reactivation. © 2015 Elsevier B.V. All rights reserved.

  18. 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

  19. 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

  20. Metric learning for DNA microarray data analysis

    NASA Astrophysics Data System (ADS)

    Takeuchi, Ichiro; Nakagawa, Masao; Seto, Masao

    2009-12-01

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

  1. 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

  2. Demystified...tissue microarray technology.

    PubMed

    Packeisen, J; Korsching, E; Herbst, H; Boecker, W; Buerger, H

    2003-08-01

    Several "high throughput methods" have been introduced into research and routine laboratories during the past decade. Providing a new approach to the analysis of genomic alterations and RNA or protein expression patterns, these new techniques generate a plethora of new data in a relatively short time, and promise to deliver clues to the diagnosis and treatment of human cancer. Along with these revolutionary developments, new tools for the interpretation of these large sets of data became necessary and are now widely available. Tissue microarray (TMA) technology is one of these new tools. It is based on the idea of applying miniaturisation and a high throughput approach to the analysis of intact tissues. The potential and the scientific value of TMAs in modern research have been demonstrated in a logarithmically increasing number of studies. The spectrum for additional applications is widening rapidly, and comprises quality control in histotechnology, longterm tissue banking, and the continuing education of pathologists. This review covers the basic technical aspects of TMA production and discusses the current and potential future applications of TMA technology.

  3. 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.

  4. 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

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

    PubMed

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

    2014-10-31

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

  6. 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

  7. 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. © The Author(s) 2015.

  8. Genetic regulation of vertebrate eye development.

    PubMed

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

    2014-11-01

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

  9. 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.

  10. [DNA microarrays in parasitology and medical sciences].

    PubMed

    Jaros, Sławomir

    2006-01-01

    The article presents the current knowledge on the microarray technique and its applications in medical sciences and parasitology. The first part of the article is focused on the technical aspects (microarray preparation, different microarray platforms, probes preparation, hybridization and signal detection). The article also describes possible ways of proceeding during laboratory work on organism of which the genome sequence is not known or has been only partially sequenced. The second part of the review describes how microarray technique have been, or possibly will be, used for better understanding parasite life cycles and development, host-parasite relationship, comparative genomics of virulent organisms, develpoment vaccines against the most virulent parasites and host responses to infection.

  11. 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

  12. 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.

  13. Eye Movements of Flatfish for Different Gravity Condition

    NASA Astrophysics Data System (ADS)

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

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

  14. 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.

  15. 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.

  16. 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

  17. Evaluation of Surface Chemistries for Antibody Microarrays

    SciTech Connect

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

    2007-12-01

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

  18. 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

  19. Sustained eye closure slows saccades

    PubMed Central

    Shaikh, Aasef G.; Wong, Aaron L.; Optican, Lance M.; Miura, Kenichiro; Solomon, David; Zee, David S.

    2010-01-01

    Saccadic eye movements rapidly orient the line of sight towards the object of interest. Pre-motor burst neurons (BNs) controlling saccades receive excitation from superior colliculus and cerebellum, but inhibition by omnipause neurons (OPNs) prevents saccades. When the OPNs pause, BNs begin to fire. It has been presumed that part of the BN burst comes from post-inhibitory rebound (PIR). We hypothesized that in the absence of prior inhibition from OPNs there would be no PIR, and thus the increase in initial firing rate of BNs would be reduced. Consequently, saccade acceleration would be reduced. We measured eye movements and showed that sustained eye closure, which inhibits the activity of OPNs and thus hypothetically should weaken PIR, reduced the peak velocity, acceleration, and deceleration of saccades in healthy human subjects. Saccades under closed eyelids also had irregular trajectories; the frequency of the oscillations underlying this irregularity was similar to that of high-frequency ocular flutter (back-to-back saccades) often seen in normal subjects during attempted fixation at straight ahead while eyes are closed. Saccades and quick phases of nystagmus are generated by the same pre-motor neurons, and we found that the quick-phase velocity of nystagmus was also reduced by lid closure. These changes were not due to a mechanical hindrance to the eyes, because lid closure did not affect the peak velocities or accelerations of the eyes in the “slow-phase” response to rapid head movements of comparable speeds to those of saccades. These results indicate a role for OPNs in generating the abrupt onset and high velocities of saccades. We hypothesize that the mechanism involved is PIR in pre-motor burst neurons. PMID:20573593

  20. 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…

  1. 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…

  2. 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.

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

    PubMed

    Strickler, Allen G; Jeffery, William R

    2009-03-01

    Changes in gene expression were examined by microarray analysis during development of the eyed surface dwelling (surface fish) and blind cave-dwelling (cavefish) forms of the teleost Astyanax mexicanus De Filippi, 1853. The cross-species microarray used surface and cavefish RNA hybridized to a DNA chip prepared from a closely related species, the zebrafish Danio rerio Hamilton, 1822. We identified a total of 67 differentially expressed probe sets at three days post-fertilization: six upregulated and 61 downregulated in cavefish relative to surface fish. Many of these genes function either in eye development and/or maintenance, or in programmed cell death. The upregulated probe set showing the highest mean fold change was similar to the human ubiquitin specific protease 53 gene. The downregulated probe sets showing some of the highest fold changes corresponded to genes with roles in eye development, including those encoding gamma crystallins, the guanine nucleotide binding proteins Gnat1 and Gant2, a BarH-like homeodomain transcription factor, and rhodopsin. Downregulation of gamma-crystallin and rhodopsin was confirmed by in situ hybridization and immunostaining with specific antibodies. Additional downregulated genes encode molecules that inhibit or activate programmed cell death. The results suggest that cross-species microarray can be used for identifying differentially expressed genes in cavefish, that many of these genes might be involved in eye degeneration via apoptotic processes, and that more genes are downregulated than upregulated in cavefish, consistent with the predominance of morphological losses over gains during regressive evolution. © 2009 ISZS, Blackwell Publishing and IOZ/CAS.

  4. 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.

  5. 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.

  6. 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.

  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 muscle test (image)

    MedlinePlus

    ... the extraocular muscles which results in uncontrolled eye movements. The test involves moving the eyes in six different directions in space to evaluate the proper functioning of the extraocular ...

  9. 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 ...

  10. 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. ...

  11. 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 ...

  12. 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 ...

  13. LASIK Eye Surgery

    MedlinePlus

    ... conditions. These conditions include: Autoimmune disorders, such as rheumatoid arthritis Immunodeficiency conditions caused by immunosuppressive medications or HIV Persistent dry eyes Unstable vision due to medications, hormonal changes, pregnancy, breast-feeding or age Several eye conditions, such ...

  14. Diabetes and eye disease

    MedlinePlus

    ... have damage to the blood vessels in your eye, some types of exercise can make the problem worse. Check with your health care provider before starting an exercise program. Other eye problems that can occur in people with diabetes ...

  15. 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

  16. Eye drop neurology.

    PubMed

    Bennetto, Luke; Guly, Catherine; Ormerod, Ian; Plant, Gordon T

    2014-06-01

    Eye drops can help to diagnose and prevent complications of neurological disorders. Guttae ophthalmicae (eye drops) are generally safe because the drugs rarely achieve significant systemic concentrations, although there are rare exceptions. This article covers contemporary pharmacological pupil testing; how to dilate a pupil safely; common reasons why pupils do not respond to drops; and corneal lubrication to prevent complications of weak eye closure.

  17. 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…

  18. Fish eye optics

    NASA Astrophysics Data System (ADS)

    Hudec, R.; Michalova, S.

    2017-07-01

    We report on small student (high—school) project of the Czech Academy of Sciences dealing with animal (fish) eyes and possible application in science and technology. Albeit most fishes have refractive eyes, the recent discoveries confirm that some fishes have reflective eyes with strange arrangements as well.

  19. 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…

  20. 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…

  1. 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…

  2. Neural constraints on eye motion in human eye-head saccades.

    PubMed

    Misslisch, H; Tweed, D; Vilis, T

    1998-02-01

    We examined two ways in which the neural control system for eye-head saccades constrains the motion of the eye in the head. The first constraint involves Listing's law, which holds ocular torsion at zero during head-fixed saccades. During eye-head saccades, does this law govern the eye's motion in space or in the head? Our subjects, instructed to saccade between space-fixed targets with the head held still in different positions, systematically violated Listing's law of the eye in space in a way that approximately, but not perfectly, preserved Listing's law of the eye in head. This finding implies that the brain does not compute desired eye position based on the desired gaze direction alone but also considers head position. The second constraint we studied was saturation, the process where desired-eye-position commands in the brain are "clipped" to keep them within an effective oculomotor range (EOMR), which is smaller than the mechanical range of eye motion. We studied the adaptability of the EOMR by asking subjects to make head-only saccades. As predicted by current eye-head models, subjects failed to hold their eyes still in their orbits. Unexpectedly, though, the range of eye-in-head motion in the horizontal-vertical plane was on average 31% smaller in area than during normal eye-head saccades, suggesting that the EOMR had been reduced by effort of will. Larger reductions were possible with altered visual input: when subjects donned pinhole glasses, the EOMR immediately shrank by 80%. But even with its reduced EOMR, the eye still moved into the "blind" region beyond the pinhole aperture during eye-head saccades. Then, as the head movement brought the saccade target toward the pinhole, the eyes reversed their motion, anticipating or roughly matching the target's motion even though it was still outside the pinhole and therefore invisible. This finding shows that the backward rotation of the eye is timed by internal computations, not by vision. When subjects wore

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  4. 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.

  5. 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.

  6. 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.

  7. 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)