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Sample records for aberration analysis dosimetria

  1. Differential algebraic method for aberration analysis of typical electrostatic lenses.

    PubMed

    Liu, Zhixiong

    2006-02-01

    In this paper up to fifth-order geometric and third-order chromatic aberration coefficients of typical electrostatic lenses are calculated by means of the charged particle optics code, COSY INFINITY, based on the differential algebraic (DA) method. A two-tube immersion lens and a symmetric einzel lens have been chosen as two examples, whose axial potential distributions are numerically calculated by a FORTRAN program using the finite difference method. The DA results are in good agreement with those evaluated by the aberration integrals in electron optics. The DA method presented here can easily be extended to aberration analysis of other numerically computed electron lenses, including magnetic lenses. PMID:16125845

  2. Eye aberration analysis with Zernike polynomials

    NASA Astrophysics Data System (ADS)

    Molebny, Vasyl V.; Chyzh, Igor H.; Sokurenko, Vyacheslav M.; Pallikaris, Ioannis G.; Naoumidis, Leonidas P.

    1998-06-01

    New horizons for accurate photorefractive sight correction, afforded by novel flying spot technologies, require adequate measurements of photorefractive properties of an eye. Proposed techniques of eye refraction mapping present results of measurements for finite number of points of eye aperture, requiring to approximate these data by 3D surface. A technique of wave front approximation with Zernike polynomials is described, using optimization of the number of polynomial coefficients. Criterion of optimization is the nearest proximity of the resulted continuous surface to the values calculated for given discrete points. Methodology includes statistical evaluation of minimal root mean square deviation (RMSD) of transverse aberrations, in particular, varying consecutively the values of maximal coefficient indices of Zernike polynomials, recalculating the coefficients, and computing the value of RMSD. Optimization is finished at minimal value of RMSD. Formulas are given for computing ametropia, size of the spot of light on retina, caused by spherical aberration, coma, and astigmatism. Results are illustrated by experimental data, that could be of interest for other applications, where detailed evaluation of eye parameters is needed.

  3. Quantitative analysis of radiation-induced chromosome aberrations.

    PubMed

    Sachs, R K; Levy, D; Hahnfeldt, P; Hlatky, L

    2004-01-01

    We review chromosome aberration modeling and its applications, especially to biodosimetry and to characterizing chromosome geometry. Standard results on aberration formation pathways, randomness, dose-response, proximity effects, transmissibility, kinetics, and relations to other radiobiological endpoints are summarized. We also outline recent work on graph-theoretical descriptions of aberrations, Monte-Carlo computer simulations of aberration spectra, software for quantifying aberration complexity, and systematic links of apparently incomplete with complete or truly incomplete aberrations. PMID:15162028

  4. Evaluation of an automated karyotyping system for chromosome aberration analysis

    NASA Technical Reports Server (NTRS)

    Prichard, Howard M.

    1987-01-01

    Chromosome aberration analysis is a promising complement to conventional radiation dosimetry, particularly in the complex radiation fields encountered in the space environment. The capabilities of a recently developed automated karyotyping system were evaluated both to determine current capabilities and limitations and to suggest areas where future development should be emphasized. Cells exposed to radiometric chemicals and to photon and particulate radiation were evaluated by manual inspection and by automated karyotyping. It was demonstrated that the evaluated programs were appropriate for image digitization, storage, and transmission. However, automated and semi-automated scoring techniques must be advanced significantly if in-flight chromosome aberration analysis is to be practical. A degree of artificial intelligence may be necessary to realize this goal.

  5. Optimal principal component analysis-based numerical phase aberration compensation method for digital holography.

    PubMed

    Sun, Jiasong; Chen, Qian; Zhang, Yuzhen; Zuo, Chao

    2016-03-15

    In this Letter, an accurate and highly efficient numerical phase aberration compensation method is proposed for digital holographic microscopy. Considering that most parts of the phase aberration resides in the low spatial frequency domain, a Fourier-domain mask is introduced to extract the aberrated frequency components, while rejecting components that are unrelated to the phase aberration estimation. Principal component analysis (PCA) is then performed only on the reduced-sized spectrum, and the aberration terms can be extracted from the first principal component obtained. Finally, by oversampling the reduced-sized aberration terms, the precise phase aberration map is obtained and thus can be compensated by multiplying with its conjugation. Because the phase aberration is estimated from the limited but more relevant raw data, the compensation precision is improved and meanwhile the computation time can be significantly reduced. Experimental results demonstrate that our proposed technique could achieve both high compensating accuracy and robustness compared with other developed compensation methods. PMID:26977692

  6. Aberration analysis calculations for synchrotron radiation beamline design

    SciTech Connect

    McKinney, W.R.; Howells, M.; Padmore, H.A.

    1997-09-01

    The application of ray deviation calculations based on aberration coefficients for a single optical surface for the design of beamline optical systems is reviewed. A systematic development is presented which allows insight into which aberration may be causing the rays to deviate from perfect focus. A new development allowing analytical calculation of line shape is presented.

  7. Lens aberration measurement and analysis using a novel pattern

    NASA Astrophysics Data System (ADS)

    Nam, Byung-Ho; Cho, Byeong-Ho; Park, Jong O.; Kim, Dong-Seok; Baek, SungJin; Jeong, JongHo; Nam, ByungSub; Hwang, Young J.; Song, Young Jin

    2001-09-01

    Lens aberration of the exposure tool causes pattern deformation and position shift. As design rule shrinks, the ratio of printed feature size to applied wavelength for optical lithography is driven inexorably toward resolution limit. In this study, we devised an efficient method to evaluate lens aberration using multi-ring pattern on an attenuated phase-shift mask. Adoption of multi-ring pattern can cut down measurement time and improve measurement repeatability. These patterns are uniformly distributed through entire field in 7 by 7 manner. Lens aberration was evaluated by multi-ring pattern array under conventional or off-axis illumination with KrF stepper of NA 0.65. Multi-ring critical dimension (CD) data was discussed together with the issue of lens aberration such as coma, astigmatism, field curvature, etc. We can apply this new measurement technique to select better lens system efficiently. multi-ring, field size, pattern deformation

  8. Aberration analysis of a wedge-plate display system.

    PubMed

    Cheng, Yi-Kai; Chung, Sen-Nien; Chern, Jyh-Long

    2007-08-01

    The aberration characteristics of a wedge-plate display optical system are analyzed. The study shows that a kink-like feature is inherent in the ray-intercept curve due to either the onset of the dark zone in imaging or the coincidence of the ray direction with the vertex. Third-order aberration coefficients are deduced, and the total amount of aberration is investigated to illustrate the basic limitations of image quality in this type of display. The issue of design optimization is also investigated based on the aberration characteristics. A numerical example of a 50 in. display with a 1:10 thickness and a diagonal screen length ratio is also provided. PMID:17621338

  9. The Spot of Arago and its role in aberration analysis

    NASA Astrophysics Data System (ADS)

    Erbschloe, D. R.

    1983-12-01

    The Spot of Arago is the bright diffraction spot in the center of the shadow behind a circular obstacle. Because this pattern is the result of diffraction at the edge of the obstacle, the spot contains information about the incident beam. If the incident beam contains aberrations, the shape and intensity of the diffraction pattern should change. For points on and near the optical axis, analytical solutions to the Rayleigh-Sommerfeld diffraction integral are possible for a circular obscuration and an annular aperture illuminated by a plane wave of uniform or gaussian intensity distribution and containing defocus and/or spherical aberration. Computer studies of these cases show excellent agreement with experiment. The amount of defocus and spherical aberration can be deduced by intensity measurements and shift in positions of on axis intensity extrema behind an annular aperture. An empirical study of astigmatism revealed a predictable change in the diffraction pattern allowing for the verification of the aberration to within .05 wavelengths. The Spot of Arago is inherent in many optical systems due to the geometry of components. The technique of aberration determination by changes in the diffraction pattern should be useful in such systems.

  10. Aberration analysis and efficiency improvement of a bidirectional optical subassembly

    NASA Astrophysics Data System (ADS)

    Wu, Hao; Huang, Zhangdi; Yu, Ziyan; Qian, Xiaoshi; Xu, Fei; Chen, Beckham; Lu, Yanqing

    2009-10-01

    An approach to improve the coupling efficiency of bidirectional optical subassembly (BOSA) modules is proposed and experimentally demonstrated. We analyzed the wavefront aberration coefficients of a typical BOSA. It was found that the 45-deg wavelength filter induces coma and astigmatism, and then it further deteriorates the laser diode to fiber coupling. We measured the BOSA efficiencies based on a series of different filters. For a typical 0.5-mm filter, 25% coupling efficiency improvement was achieved by optimizing the filter parameters.

  11. Painting Analysis of Chromosome Aberrations Induced by Energetic Heavy Ions in Human Cells

    NASA Technical Reports Server (NTRS)

    Wu, Honglu

    2006-01-01

    FISH, mFISH, mBAND, telomere and centromere probes have been used to study chromosome aberrations induced in human cells exposed to low-and high-LET radiation in vitro. High-LET induced damages are mostly a single track effect. Unrejoined chromosome breaks (incomplete exchanges) and complex type aberrations were higher for high-LET. Biosignatures may depend on the method the samples are collected. Recent mBAND analysis has revealed more information about the nature of intra-chromosome exchanges. Whether space flight/microgravity affects radiation-induced chromosome aberration frequencies is still an open question.

  12. Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq

    PubMed Central

    Weissbein, Uri; Schachter, Maya; Egli, Dieter; Benvenisty, Nissim

    2016-01-01

    Genomic instability has profound effects on cellular phenotypes. Studies have shown that pluripotent cells with abnormal karyotypes may grow faster, differentiate less and become more resistance to apoptosis. Previously, we showed that microarray gene expression profiles can be utilized for the analysis of chromosomal aberrations by comparing gene expression levels between normal and aneuploid samples. Here we adopted this method for RNA-Seq data and present eSNP-Karyotyping for the detection of chromosomal aberrations, based on measuring the ratio of expression between the two alleles. We demonstrate its ability to detect chromosomal gains and losses in pluripotent cells and their derivatives, as well as meiotic recombination patterns. This method is advantageous since it does not require matched diploid samples for comparison, is less sensitive to global expression changes caused by the aberration and utilizes already available gene expression profiles to determine chromosomal aberrations. PMID:27385103

  13. Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq.

    PubMed

    Weissbein, Uri; Schachter, Maya; Egli, Dieter; Benvenisty, Nissim

    2016-01-01

    Genomic instability has profound effects on cellular phenotypes. Studies have shown that pluripotent cells with abnormal karyotypes may grow faster, differentiate less and become more resistance to apoptosis. Previously, we showed that microarray gene expression profiles can be utilized for the analysis of chromosomal aberrations by comparing gene expression levels between normal and aneuploid samples. Here we adopted this method for RNA-Seq data and present eSNP-Karyotyping for the detection of chromosomal aberrations, based on measuring the ratio of expression between the two alleles. We demonstrate its ability to detect chromosomal gains and losses in pluripotent cells and their derivatives, as well as meiotic recombination patterns. This method is advantageous since it does not require matched diploid samples for comparison, is less sensitive to global expression changes caused by the aberration and utilizes already available gene expression profiles to determine chromosomal aberrations. PMID:27385103

  14. Polarization Aberrations

    NASA Technical Reports Server (NTRS)

    Mcguire, James P., Jr.; Chipman, Russell A.

    1990-01-01

    The analysis of the polarization characteristics displayed by optical systems can be divided into two categories: geometrical and physical. Geometrical analysis calculates the change in polarization of a wavefront between pupils in an optical instrument. Physical analysis propagates the polarized fields wherever the geometrical analysis is not valid, i.e., near the edges of stops, near images, in anisotropic media, etc. Polarization aberration theory provides a starting point for geometrical design and facilitates subsequent optimization. The polarization aberrations described arise from differences in the transmitted (or reflected) amplitudes and phases at interfaces. The polarization aberration matrix (PAM) is calculated for isotropic rotationally symmetric systems through fourth order and includes the interface phase, amplitude, linear diattenuation, and linear retardance aberrations. The exponential form of Jones matrices used are discussed. The PAM in Jones matrix is introduced. The exact calculation of polarization aberrations through polarization ray tracing is described. The report is divided into three sections: I. Rotationally Symmetric Optical Systems; II. Tilted and Decentered Optical Systems; and Polarization Analysis of LIDARs.

  15. Gene expression analysis of aberrant signaling pathways in meningiomas

    PubMed Central

    TORRES-MARTÍN, MIGUEL; MARTINEZ-GLEZ, VICTOR; PEÑA-GRANERO, CAROLINA; ISLA, ALBERTO; LASSALETTA, LUIS; DE CAMPOS, JOSE M.; PINTO, GIOVANNY R.; BURBANO, ROMMEL R.; MELÉNDEZ, BÁRBARA; CASTRESANA, JAVIER S.; REY, JUAN A.

    2013-01-01

    Examining aberrant pathway alterations is one method for understanding the abnormal signals that are involved in tumorigenesis and tumor progression. In the present study, expression arrays were performed on tumor-related genes in meningiomas. The GE Array Q Series HS-006 was used to determine the expression levels of 96 genes that corresponded to six primary biological regulatory pathways in a series of 42 meningiomas, including 32 grade I, four recurrent grade I and six grade II tumors, in addition to three normal tissue controls. Results showed that 25 genes that were primarily associated with apoptosis and angiogenesis functions were downregulated and 13 genes frequently involving DNA damage repair functions were upregulated. In addition to the inactivation of the neurofibromin gene, NF2, which is considered to be an early step in tumorigenesis, variations of other biological regulatory pathways may play a significant role in the development of meningioma. PMID:23946817

  16. Gene expression analysis of aberrant signaling pathways in meningiomas.

    PubMed

    Torres-Martín, Miguel; Martinez-Glez, Victor; Peña-Granero, Carolina; Isla, Alberto; Lassaletta, Luis; DE Campos, Jose M; Pinto, Giovanny R; Burbano, Rommel R; Meléndez, Bárbara; Castresana, Javier S; Rey, Juan A

    2013-07-01

    Examining aberrant pathway alterations is one method for understanding the abnormal signals that are involved in tumorigenesis and tumor progression. In the present study, expression arrays were performed on tumor-related genes in meningiomas. The GE Array Q Series HS-006 was used to determine the expression levels of 96 genes that corresponded to six primary biological regulatory pathways in a series of 42 meningiomas, including 32 grade I, four recurrent grade I and six grade II tumors, in addition to three normal tissue controls. Results showed that 25 genes that were primarily associated with apoptosis and angiogenesis functions were downregulated and 13 genes frequently involving DNA damage repair functions were upregulated. In addition to the inactivation of the neurofibromin gene, NF2, which is considered to be an early step in tumorigenesis, variations of other biological regulatory pathways may play a significant role in the development of meningioma. PMID:23946817

  17. Factor Analysis of the Aberrant Behavior Checklist in Individuals with Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Brinkley, Jason; Nations, Laura; Abramson, Ruth K.; Hall, Alicia; Wright, Harry H.; Gabriels, Robin; Gilbert, John R.; Pericak-Vance, Margaret A. O.; Cuccaro, Michael L.

    2007-01-01

    Exploratory factor analysis (varimax and promax rotations) of the aberrant behavior checklist-community version (ABC) in 275 individuals with Autism spectrum disorder (ASD) identified four- and five-factor solutions which accounted for greater than 70% of the variance. Confirmatory factor analysis (Lisrel 8.7) revealed indices of moderate fit for…

  18. The Gaussian beam mode analysis of off-axis aberrations in long wavelength optical systems

    NASA Astrophysics Data System (ADS)

    Finn, T. J.; Trappe, N.; Murphy, J. A.; Withington, S.

    2008-03-01

    An issue of major concern in the design of long wavelength systems is optical aberration or distortion, which can be particularly severe in off-axis systems. Aberrations occur in both lenses and mirrors and in this paper we present a novel method capable of modelling off-axis mirror configurations. Aberrations degrade fundamental receiver coupling coefficients such as aperture efficiency while increasing spillover power losses. For single pixel instruments this will lead to much longer integration times and the possibility of stray light. For imaging arrays the aberrations cause a departure from perfect point imaging by increasing coupling to array detectors located at angles further off the bore sight of the telescope. This paper verifies a matrix-based scheme using Gaussian beam mode analysis (GBMA) for predicting aberrations from off-axis mirrors. The applied technique was originally described in (S. Withington, A. Murphy, G. Isaak, Representation of mirrors in beam waveguides as inclined phase transforming surfaces, Infrared Phys. Tech. 36(3) (1995) 723-734. [1]) and in this paper we exploit the theory and validate the approach with a series of examples using off-axis conic sections. We present the predictions for both a fundamental Gaussian and a scalar horn field illuminating various off-axis mirror configurations including different angles of incidence. A commercially available physical optics (PO) software package, GRASP8™, is used to validate the accuracy of these scalar GBMA predictions.

  19. High order surface aberration contributions from phase space analysis of differential rays.

    PubMed

    Chen, Bo; Herkommer, Alois M

    2016-03-21

    Phase space methods are very popular for illumination systems or paraxial system analysis. In this paper it will be shown that it is also a promising tool to visualize and quantify surface aberration contributions, including all orders. The method is based on the calculation and propagation of a differential ray pair. In order to validate the method we compare to Aldis calculus, an exact method to determine high order aberrations in rotational symmetric systems. A triplet lens is used as an example to visualize the results. The analysis indicates that the phase space method is a very good approximation to Aldis calculus and moreover it is not limited to any symmetry assumptions. PMID:27136789

  20. mBAND Analysis of Late Chromosome Aberrations in Human Lymphocytes Induced by Gamma Rays and Fe Ions

    NASA Technical Reports Server (NTRS)

    Sunagawa, Mayumi; Zhang, Ye; Yeshitla, Samrawit; Kadhim, Munira; Wilson, Bobby; Wu, Honglu

    2014-01-01

    Chromosomal translocations and inversions are considered stable, and cells containing these types of chromosome aberrations can survive multiple cell divisions. An efficient method to detect an inversion is multi-color banding fluorescent in situ hybridization (mBAND) which allows identification of both inter- and intrachromosome aberrations simultaneously. Post irradiation, chromosome aberrations may also arise after multiple cell divisions as a result of genomic instability. To investigate the stable or late-arising chromosome aberrations induced after radiation exposure, we exposed human lymphocytes to gamma rays and Fe ions ex vivo, and cultured the cells for multiple generations. Chromosome aberrations were analyzed in cells collected at first mitosis and at several time intervals during the culture period post irradiation. With gamma irradiation, about half of the damages observed at first mitosis remained after 7 day- and 14 day- culture, suggesting the transmissibility of damages to the surviving progeny. Detailed analysis of chromosome break ends participating in exchanges revealed a greater fraction of break ends involved in intrachromosome aberrations in the 7- and 14-day samples in comparison to the fraction at first mitosis. In particular, simple inversions were found at 7 and 14 days, but not at the first mitosis, suggesting that some of the aberrations might be formed days post irradiation. In contrast, at the doses that produced similar frequencies of gamma-induced chromosome aberrations as observed at first mitosis, a significantly lower yield of aberrations remained at the same population doublings after Fe ion exposure. At these equitoxic doses, more complex type aberrations were observed for Fe ions, indicating that Fe ion-induced initial chromosome damages are more severe and may lead to cell death. Comparison between low and high doses of Fe ion irradiation in the induction of late damages will also be discussed.

  1. Comparative methylome analysis in solid tumors reveals aberrant methylation at chromosome 6p in nasopharyngeal carcinoma

    PubMed Central

    Dai, Wei; Cheung, Arthur Kwok Leung; Ko, Josephine Mun Yee; Cheng, Yue; Zheng, Hong; Ngan, Roger Kai Cheong; Ng, Wai Tong; Lee, Anne Wing Mui; Yau, Chun Chung; Lee, Victor Ho Fu; Lung, Maria Li

    2015-01-01

    Altered patterns of DNA methylation are key features of cancer. Nasopharyngeal carcinoma (NPC) has the highest incidence in Southern China. Aberrant methylation at the promoter region of tumor suppressors is frequently reported in NPC; however, genome-wide methylation changes have not been comprehensively investigated. Therefore, we systematically analyzed methylome data in 25 primary NPC tumors and nontumor counterparts using a high-throughput approach with the Illumina HumanMethylation450 BeadChip. Comparatively, we examined the methylome data of 11 types of solid tumors collected by The Cancer Genome Atlas (TCGA). In NPC, the hypermethylation pattern was more dominant than hypomethylation and the majority of de novo methylated loci were within or close to CpG islands in tumors. The comparative methylome analysis reveals hypermethylation at chromosome 6p21.3 frequently occurred in NPC (false discovery rate; FDR=1.33 × 10−9), but was less obvious in other types of solid tumors except for prostate and Epstein–Barr virus (EBV)-positive gastric cancer (FDR<10−3). Bisulfite pyrosequencing results further confirmed the aberrant methylation at 6p in an additional patient cohort. Evident enrichment of the repressive mark H3K27me3 and active mark H3K4me3 derived from human embryonic stem cells were found at these regions, indicating both DNA methylation and histone modification function together, leading to epigenetic deregulation in NPC. Our study highlights the importance of epigenetic deregulation in NPC. Polycomb Complex 2 (PRC2), responsible for H3K27 trimethylation, is a promising therapeutic target. A key genomic region on 6p with aberrant methylation was identified. This region contains several important genes having potential use as biomarkers for NPC detection. PMID:25924914

  2. Efficacy, safety, predictability, aberrations and corneal biomechnical parameters after SMILE and FLEx: Meta-analysis

    PubMed Central

    Ma, Jing; Cao, Nan-Jue; Xia, Li-Kun

    2016-01-01

    AIM To identify possible differences of efficacy, safety, predictability, higher-order aberrations and corneal biomechnical parameters after small-incision lenticule extraction (SMILE) and femtosecond lenticule extraction (FLEx). METHODS A systematic literature retrieval was conducted in Medline, Embase and the Cochrane Library, up to October, 2015. The included studies were subject to a Meta-analysis. Comparison between SMILE and FLEx was measured as pooled odds ratio (OR) or weighted mean differences (WMD). Of 95% confidence intervals (CI) were used to analyze data. RESULTS A total of seven studies were included. Firstly, there were no differences in uncorrected distance visual acuity (UDVA) 20/20 or better (OR, 1.37; 95% CI, 0.69 to 2.69; P=0.37) and logMAR UDVA (WMD, -0.02; 95% CI, -0.05 to 0.01; P=0.17) after SMILE versus FLEx. We found no differences in corrected distance visual acuity (CDVA) unchanged (OR, 0.98; 95% CI, 0.46 to 2.11; P=0.97) and logMAR CDVA (WMD, -0.00; 95% CI, -0.01 to 0.01; P=0.90) either. Secondly, we found no differences in refraction within ±1.00 D (OR, 0.98; 95% CI, 0.13 to 7.28; P=0.99) and ±0.50 D (OR, 1.62; 95% CI, 0.62 to 4.28; P=0.33) of target postoperatively. Thirdly, for higher-order aberrations, we found no differences in the total higher-order aberrations (WMD, -0.04; 95% CI, -0.09 to 0.01; P=0.14), coma (WMD, -0.04; 95% CI, -0.09 to 0.01; P=0.11), spherical (WMD, 0.01; 95% CI, -0.02 to 0.03; P=0.60) and trefoil (WMD, -0.00; 95% CI, -0.04 to 0.03; P=0.76). Furthermore, for corneal biomechanical parameters, we also found no differences (WMD, 0.08; 95% CI, -0.17 to 0.33; P=0.54) after SMILE versus FLEx. CONCLUSION There are no statistically differences in efficacy, safety, predictability, higher-order aberrations and corneal biomechnical parameters postoperative between SMILE and FLEx. PMID:27275436

  3. Rapid Analysis of Chromosome Aberrations in Mouse B Lymphocytes by PNA-FISH

    PubMed Central

    Misenko, Sarah M.; Bunting, Samuel F.

    2014-01-01

    Defective DNA repair leads to increased genomic instability, which is the root cause of mutations that lead to tumorigenesis. Analysis of the frequency and type of chromosome aberrations in different cell types allows defects in DNA repair pathways to be elucidated. Understanding mammalian DNA repair biology has been greatly helped by the production of mice with knockouts in specific genes. The goal of this protocol is to quantify genomic instability in mouse B lymphocytes. Labeling of the telomeres using PNA-FISH probes (peptide nucleic acid - fluorescent in situ hybridization) facilitates the rapid analysis of genomic instability in metaphase chromosome spreads. B cells have specific advantages relative to fibroblasts, because they have normal ploidy and a higher mitotic index. Short-term culture of B cells therefore enables precise measurement of genomic instability in a primary cell population which is likely to have fewer secondary genetic mutations than what is typically found in transformed fibroblasts or patient cell lines. PMID:25177909

  4. Factor Analysis and Norms for Parent Ratings on the Aberrant Behavior Checklist-Community for Young People in Special Education.

    ERIC Educational Resources Information Center

    Brown, Elaine C.; Aman, Michael G.; Havercamp, Susan M.

    2002-01-01

    Parents of 601 children and adolescents with mental retardation rated their children on the Aberrant Behavior Checklist-Community (ABC). Factor analysis revealed a factor structure similar to the original ABC but without the inappropriate speech factor. Analysis of subject variables revealed main effects for gender, age, and classroom assignment…

  5. Improved Statistical Analysis for Array CGH-Based DNA Copy Number Aberrations

    PubMed Central

    Jiang, Hongmei; Zhu, Zhong-Zheng; Yu, Yue; Lin, Simon; Hou, Lifang

    2011-01-01

    Array-based comparative genomic hybridization (aCGH) allows measuring DNA copy number at the whole genome scale. In cancer studies, one may be interested in identifying DNA copy number aberrations (CNAs) associated with certain clinicopathological characteristics such as cancer metastasis. We proposed to define test regions based on copy number pattern profiles across multiple samples, using either smoothed log2-ratio or discrete data of copy number gain/loss calls. Association test performed on the refined test regions instead of the probes has improved power due to reduced number of tests. We also compared three types of measurement of copy number levels, normalized log2-ratio, smoothed log2-ratio, and copy number gain or loss calls in statistical hypothesis testing. The relative strengths and weaknesses of the proposed method were demonstrated using both simulation studies and real data analysis of a liver cancer study. PMID:22084565

  6. Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA

    NASA Astrophysics Data System (ADS)

    Bercovici, Sivan; Geiger, Dan

    Admixture mapping is a gene mapping approach used for the identification of genomic regions harboring disease susceptibility genes in the case of recently admixed populations such as African Americans. We present a novel method for admixture mapping, called admixture aberration analysis (AAA), that uses a DNA pool of affected admixed individuals. We demonstrate through simulations that AAA is a powerful and economical mapping method under a range of scenarios, capturing complex human diseases such as hypertension and end stage kidney disease. The method has a low false-positive rate and is robust to deviation from model assumptions. Finally, we apply AAA on 600 prostate cancer-affected African Americans, replicating a known risk locus. Simulation results indicate that the method can yield over 96% reduction in genotyping. Our method is implemented as a Java program called AAAmap and is freely available.

  7. Analysis of genomic aberrations and gene expression profiling identifies novel lesions and pathways in myeloproliferative neoplasms

    PubMed Central

    Rice, K L; Lin, X; Wolniak, K; Ebert, B L; Berkofsky-Fessler, W; Buzzai, M; Sun, Y; Xi, C; Elkin, P; Levine, R; Golub, T; Gilliland, D G; Crispino, J D; Licht, J D; Zhang, W

    2011-01-01

    Polycythemia vera (PV), essential thrombocythemia and primary myelofibrosis, are myeloproliferative neoplasms (MPNs) with distinct clinical features and are associated with the JAK2V617F mutation. To identify genomic anomalies involved in the pathogenesis of these disorders, we profiled 87 MPN patients using Affymetrix 250K single-nucleotide polymorphism (SNP) arrays. Aberrations affecting chr9 were the most frequently observed and included 9pLOH (n=16), trisomy 9 (n=6) and amplifications of 9p13.3–23.3 (n=1), 9q33.1–34.13 (n=1) and 9q34.13 (n=6). Patients with trisomy 9 were associated with elevated JAK2V617F mutant allele burden, suggesting that gain of chr9 represents an alternative mechanism for increasing JAK2V617F dosage. Gene expression profiling of patients with and without chr9 abnormalities (+9, 9pLOH), identified genes potentially involved in disease pathogenesis including JAK2, STAT5B and MAPK14. We also observed recurrent gains of 1p36.31–36.33 (n=6), 17q21.2–q21.31 (n=5) and 17q25.1–25.3 (n=5) and deletions affecting 18p11.31–11.32 (n=8). Combined SNP and gene expression analysis identified aberrations affecting components of a non-canonical PRC2 complex (EZH1, SUZ12 and JARID2) and genes comprising a ‘HSC signature' (MLLT3, SMARCA2 and PBX1). We show that NFIB, which is amplified in 7/87 MPN patients and upregulated in PV CD34+ cells, protects cells from apoptosis induced by cytokine withdrawal. PMID:22829077

  8. Analysis of laser beam quality degradation caused by quartic phase aberrations.

    PubMed

    Siegman, A E

    1993-10-20

    Simple formulas are derived for the degradation in the beam-quality factor, M(2), of an arbitrary laser beam caused by quartic phase distortions such as those that might occur in a spherically aberrated optical component, a thermally aberrated laser output window, or a divergent beam emerging from a high-index dielectric medium as in a wide-stripe, unstable-resonator diode laser. A new formula for the defocus correction that is needed to collimate optimally a beam with quartic phase aberration is also derived. Analytical results and numerical examples are given for both radially aberrated and one-dimensionaltransversely aberrated cases, and a simple experimental measurement of the beam-quality degradation produced by a thin plano-convex lens is shown to be in good agreement with the theory. PMID:20856411

  9. Clinical Presentation and Microarray Analysis of Peruvian Children with Atypical Development and/or Aberrant Behavior

    PubMed Central

    Butler, Merlin G.; Usrey, Kelly; Roberts, Jennifer L.; Schroeder, Stephen R.

    2014-01-01

    We report our experience with high resolution microarray analysis in infants and young children with developmental disability and/or aberrant behavior enrolled at the Centro Ann Sullivan del Peru in Lima, Peru, a low income country. Buccal cells were collected with cotton swabs from 233 participants for later DNA isolation and identification of copy number variation (deletions/duplications) and regions of homozygosity (ROH) for estimating consanguinity status in 15 infants and young children (12 males, 3 females; mean age ± SD = 28.1 m ±  7.9 m; age range 14 m–41 m) randomly selected for microarray analysis. An adequate DNA yield was found in about one-half of the enrolled participants. Ten participants showed deletions or duplications containing candidate genes reported to impact behavior or cognitive development. Five children had ROHs which could have harbored recessive gene alleles contributing to their clinical presentation. The coefficient of inbreeding was calculated and three participants showed first-second cousin relationships, indicating consanguinity. Our preliminary study showed that DNA isolated from buccal cells using cotton swabs was suboptimal, but yet in a subset of participants the yield was adequate for high resolution microarray analysis and several genes were found that impact development and behavior and ROHs identified to determine consanguinity status. PMID:25400949

  10. Eigenfunction analysis of stochastic backscatter for characterization of acoustic aberration in medical ultrasound imaging

    NASA Astrophysics Data System (ADS)

    Varslot, Trond; Krogstad, Harald; Mo, Eirik; Angelsen, Bjørn A.

    2004-06-01

    Presented here is a characterization of aberration in medical ultrasound imaging. The characterization is optimal in the sense of maximizing the expected energy in a modified beamformer output of the received acoustic backscatter. Aberration correction based on this characterization takes the form of an aberration correction filter. The situation considered is frequently found in applications when imaging organs through a body wall: aberration is introduced in a layer close to the transducer, and acoustic backscatter from a scattering region behind the body wall is measured at the transducer surface. The scattering region consists of scatterers randomly distributed with very short correlation length compared to the acoustic wavelength of the transmit pulse. The scatterer distribution is therefore assumed to be δ correlated. This paper shows how maximizing the expected energy in a modified beamformer output signal naturally leads to eigenfunctions of a Fredholm integral operator, where the associated kernel function is a spatial correlation function of the received stochastic signal. Aberration characterization and aberration correction are presented for simulated data constructed to mimic aberration introduced by the abdominal wall. The results compare well with what is obtainable using data from a simulated point source.

  11. Analysis of nodal aberration properties in off-axis freeform system design.

    PubMed

    Shi, Haodong; Jiang, Huilin; Zhang, Xin; Wang, Chao; Liu, Tao

    2016-08-20

    Freeform surfaces have the advantage of balancing off-axis aberration. In this paper, based on the framework of nodal aberration theory (NAT) applied to the coaxial system, the third-order astigmatism and coma wave aberration expressions of an off-axis system with Zernike polynomial surfaces are derived. The relationship between the off-axis and surface shape acting on the nodal distributions is revealed. The nodal aberration properties of the off-axis freeform system are analyzed and validated by using full-field displays (FFDs). It has been demonstrated that adding Zernike terms, up to nine, to the off-axis system modifies the nodal locations, but the field dependence of the third-order aberration does not change. On this basis, an off-axis two-mirror freeform system with 500 mm effective focal length (EFL) and 300 mm entrance pupil diameter (EPD) working in long-wave infrared is designed. The field constant aberrations induced by surface tilting are corrected by selecting specific Zernike terms. The design results show that the nodes of third-order astigmatism and coma move back into the field of view (FOV). The modulation transfer function (MTF) curves are above 0.4 at 20 line pairs per millimeter (lp/mm) which meets the infrared reconnaissance requirement. This work provides essential insight and guidance for aberration correction in off-axis freeform system design. PMID:27557003

  12. Aberration analysis and calculation in system of Gaussian beam illuminates lenslet array

    NASA Astrophysics Data System (ADS)

    Zhao, Zhu; Hui, Mei; Zhou, Ping; Su, Tianquan; Feng, Yun; Zhao, Yuejin

    2014-09-01

    Low order aberration was founded when focused Gaussian beam imaging at Kodak KAI -16000 image detector, which is integrated with lenslet array. Effect of focused Gaussian beam and numerical simulation calculation of the aberration were presented in this paper. First, we set up a model of optical imaging system based on previous experiment. Focused Gaussian beam passed through a pinhole and was received by Kodak KAI -16000 image detector whose microlenses of lenslet array were exactly focused on sensor surface. Then, we illustrated the characteristics of focused Gaussian beam and the effect of relative space position relations between waist of Gaussian beam and front spherical surface of microlenses to the aberration. Finally, we analyzed the main element of low order aberration and calculated the spherical aberration caused by lenslet array according to the results of above two steps. Our theoretical calculations shown that , the numerical simulation had a good agreement with the experimental result. Our research results proved that spherical aberration was the main element and made up about 93.44% of the 48 nm error, which was demonstrated in previous experiment. The spherical aberration is inversely proportional to the value of divergence distance between microlens and waist, and directly proportional to the value of the Gaussian beam waist radius.

  13. Aberrant Functional Whole-Brain Network Architecture in Patients With Schizophrenia: A Meta-analysis.

    PubMed

    Kambeitz, Joseph; Kambeitz-Ilankovic, Lana; Cabral, Carlos; Dwyer, Dominic B; Calhoun, Vince D; van den Heuvel, Martijn P; Falkai, Peter; Koutsouleris, Nikolaos; Malchow, Berend

    2016-07-01

    Findings from multiple lines of research provide evidence of aberrant functional brain connectivity in schizophrenia. By using graph-analytical measures, recent studies indicate that patients with schizophrenia exhibit changes in the organizational principles of whole-brain networks and that these changes relate to cognitive symptoms. However, there has not been a systematic investigation of functional brain network changes in schizophrenia to test the consistency of these changes across multiple studies. A comprehensive literature search was conducted to identify all available functional graph-analytical studies in patients with schizophrenia. Effect size measures were derived from each study and entered in a random-effects meta-analytical model. All models were tested for effects of potential moderator variables as well as for the presence of publication bias. The results of a total of n = 13 functional neuroimaging studies indicated that brain networks in patients with schizophrenia exhibit significant decreases in measures of local organization (g = -0.56, P = .02) and significant decreases in small-worldness (g = -0.65, P = .01) whereas global short communication paths seemed to be preserved (g = 0.26, P = .32). There was no evidence for a publication bias or moderator effects. The present meta- analysis demonstrates significant changes in whole brain network architecture associated with schizophrenia across studies. PMID:27460615

  14. M-Band Analysis of Chromosome Aberrations in Human Epithelial Cells Induced By Low- and High-Let Radiations

    NASA Technical Reports Server (NTRS)

    Hada, M.; Gersey, B.; Saganti, P. B.; Wilkins, R.; Gonda, S. R.; Cucinotta, F. A.; Wu, H.

    2007-01-01

    Energetic primary and secondary particles pose a health risk to astronauts in extended ISS and future Lunar and Mars missions. High-LET radiation is much more effective than low-LET radiation in the induction of various biological effects, including cell inactivation, genetic mutations, cataracts and cancer. Most of these biological endpoints are closely correlated to chromosomal damage, which can be utilized as a biomarker for radiation insult. In this study, human epithelial cells were exposed in vitro to gamma rays, 1 GeV/nucleon Fe ions and secondary neutrons whose spectrum is similar to that measured inside the Space Station. Chromosomes were condensed using a premature chromosome condensation technique and chromosome aberrations were analyzed with the multi-color banding (mBAND) technique. With this technique, individually painted chromosomal bands on one chromosome allowed the identification of both interchromosomal (translocation to unpainted chromosomes) and intrachromosomal aberrations (inversions and deletions within a single painted chromosome). Results of the study confirmed the observation of higher incidence of inversions for high-LET irradiation. However, detailed analysis of the inversion type revealed that all of the three radiation types in the study induced a low incidence of simple inversions. Half of the inversions observed in the low-LET irradiated samples were accompanied by other types of intrachromosome aberrations, but few inversions were accompanied by interchromosome aberrations. In contrast, Fe ions induced a significant fraction of inversions that involved complex rearrangements of both the inter- and intrachromosome exchanges.

  15. Microarray expression profile analysis of aberrant long non-coding RNAs in esophageal squamous cell carcinoma.

    PubMed

    Yao, Juan; Huang, Jun-Xing; Lin, Mei; Wu, Zheng-Dong; Yu, Hong; Wang, Peng-Cheng; Ye, Jun; Chen, Ping; Wu, Jing; Zhao, Guo-Jun

    2016-06-01

    Increasing evidence indicates that long non-coding RNA (lncRNA) plays an important role in tumorigenesis. However, the function and regulatory mechanism of lncRNAs are still unclear in esophageal squamous cell carcinoma (ESCC). To address this challenge, we screened lncRNAs expression profiles in 3 pairs of ESCC and matched non-cancerous tissues by microarray assay and identified the relationship between lncRNAs expression in ESCC tissue and clinicopathological characteristics and prognosis of patients with ESCC. We found 182 lncRNAs that were significantly differently expressed in ESCC tissues versus the matched non-cancerous tissues. Gene ontology and pathway analysis results suggested that the primary biological processes of these genes were involved in extracellular matrix, immune responses, cell differentiation and cell proliferation. Through cis and trans analyzing, we found 4 lncRNAs (ENST00000480669, NONHSAT104436, NONHSAT126998 and NONHSAT112918) may play important roles in tumorigenesis of ESCC. The four lncRNAs were checked in 73 patients with ESCC. The results showed that they mainly related to tumor metastasis. Kaplan-Meier survival analysis showed that high expression of NONHSAT104436, NONHSAT126998 and low expression of ENST00000480669 were related to poor 3-year overall survival (P=0.003, 0.032 and 0.040, respectively). Multivariate analysis showed that NONHSAT104436 was an independent prognostic factor (P=0.017). Thus we concluded that, lncRNAs showed differently expression patterns in ESCC versus matched non-cancerous tissues, and aberrantly expressed lncRNA may play important roles in ESCC development and progression. Interestingly, the overexpression of NONHSAT104436 was tightly correlated with distant metastasis and, poor survival rate, which might indicate that NONHSAT104436 might play a very important part in ESCC tumor progression. PMID:27035335

  16. Analysis of Chromosomal Aberrations in the Blood Lymphocytes of Astronauts after Space Flight

    NASA Technical Reports Server (NTRS)

    George, K.; Kim, M. Y.; Elliott, T.; Cucinotta, F. A.

    2007-01-01

    It is a NASA requirement that biodosimetry analysis be performed on all US astronauts who participate in long duration missions of 3 months or more onboard the International Space Station. Cytogenetic analysis of blood lymphocytes is the most sensitive and reliable biodosimetry method available at present, especially if chromosome damage is assessed before as well as after space flight. Results provide a direct measurement of space radiation damage in vivo that takes into account individual radiosensitivity and considers the influence of microgravity and other stress conditions. We present data obtained from all twenty-five of the crewmembers who have participated in the biodosimetry program so far. The yield of chromosome exchanges, measured using fluorescence in situ hybridization (FISH) technique with chromosome painting probes, increased after space flight for all these individuals. In vivo dose was derived from frequencies of chromosome exchanges using preflight calibration curves of in vitro exposed cells from the same individual, and RBE was compared with individually measured physically absorbed dose and projected organ dose equivalents. Biodosimetry estimates using samples collected within a few weeks of return from space lie within the range expected from physical dosimetry. For some of these individuals chromosome aberrations were assessed again several months after their respective missions and a temporal decline in stable exchanges was observed in some cases, suggesting that translocations are unstable with time after whole body exposure to space radiation. This may indicate complications with the use of translocations for retrospective dose reconstruction. Data from one crewmember who has participated in two separate long duration space missions and has been followed up for over 10 years provides limited data on the effect of repeat flights and shows a possible adaptive response to space radiation exposure.

  17. Chromosome Aberrations in Human Epithelial Cells Exposed Los Alamos High-Energy Secondary Neutrons: M-BAND Analysis

    NASA Technical Reports Server (NTRS)

    Hada, M.; Saganti, P. B.; Gersey, B.; Wilkins, R.; Cucinotta, F. A.; Wu, H.

    2007-01-01

    High-energy secondary neutrons, produced by the interaction of galactic cosmic rays (GCR) with the atmosphere, spacecraft structure and planetary surfaces, contribute a significant fraction to the dose equivalent radiation measurement in crew members and passengers of commercial aviation travel as well as astronauts in space missions. The Los Alamos Nuclear Science Center (LANSCE) neutron facility's 30L beam line (4FP30L-A/ICE House) is known to generate neutrons that simulate the secondary neutron spectrum of the Earth's atmosphere at high altitude. The neutron spectrum is also similar to that measured onboard spacecrafts like the MIR and the International Space Station (ISS). To evaluate the biological damage, we exposed human epithelial cells in vitro to the LANSCE neutron beams with an entrance dose rate of 2.5 cGy/hr, and studied the induction of chromosome aberrations that were identified with multicolor-banding in situ hybridization (mBAND) technique. With this technique, individually painted chromosomal bands on one chromosome allowed the identification of inter-chromosomal aberrations (translocation to unpainted chromosomes) and intra-chromosomal aberrations (inversions and deletions within a single painted chromosome). Compared to our previous results with gamma-rays and 600 MeV/nucleon Fe ions of high dose rate at NSRL (NASA Space Radiation Laboratory at Brookhaven National Laboratory), the neutron data from the LANSCE experiments showed significantly higher frequency of chromosome aberrations. However, detailed analysis of the inversion type revealed that all of the three radiation types in the study induced a low incidence of simple inversions. Most of the inversions in gamma-ray irradiated samples were accompanied by other types of intrachromosomal aberrations but few inversions were accompanied by interchromosomal aberrations. In contrast, neutrons and Fe ions induced a significant fraction of inversions that involved complex rearrangements of both

  18. Analysis of the optical field on the human retina from wavefront aberration data.

    PubMed

    Barbero, Sergio; Marcos, Susana

    2008-09-01

    Wave aberrations in the human eye are usually known with respect to the ideal spherical wavefront in the exit pupil. Using Kirchhoff's diffraction theory, we have derived a diffraction integral to compute the optical field on the retina from the wave aberration data. We have proposed a numerical algorithm based on the Stamnes-Spjelkavik-Pedersen (SSP) method to solve that integral. We have shown which approximations are admissible to reduce the complexity of the diffraction integral. In addition, we have compared our results with those of the conventional procedure used to compute intensities on the retina. We have found significant differences between our results and the conventional ones. PMID:18758554

  19. Analysis of Chromosomal Aberrations after Low and High Dose Rate Gamma Irradiation in ATM or NBS Suppressed Human Fibroblast Cells

    NASA Technical Reports Server (NTRS)

    Hada, M.; Huff, J. L.; Patel, Z.; Pluth, J. M.; George, K. A.; Cucinotta, F. A.

    2009-01-01

    A detailed understanding of the biological effects of heavy nuclei is needed for space radiation protection and for cancer therapy. High-LET radiation produces more complex DNA lesions that may be non-repairable or that may require additional processing steps compared to endogenous DSBs, increasing the possibility of misrepair. Interplay between radiation sensitivity, dose, and radiation quality has not been studied extensively. Previously we studied chromosome aberrations induced by low- and high- LET radiation in several cell lines deficient in ATM (ataxia telangactasia mutated; product of the gene that is mutated in ataxia telangiectasia patients) or NBS (nibrin; product of the gene mutated in the Nijmegen breakage syndrome), and gliomablastoma cells that are proficient or lacking in DNA-dependent protein kinase (DNA-PK) activity. We found that the yields of both simple and complex chromosomal aberrations were significantly increased in the DSB repair defective cells compared to normal cells. The increased aberrations observed for the ATM and NBS defective lines was due to a significantly larger quadratic dose-response term compared to normal fibroblasts for both simple and complex aberrations, while the linear dose-response term was significantly higher in NBS cells only for simple exchanges. These results point to the importance of the functions of ATM and NBS in chromatin modifications that function to facilitate correct DSB repair and minimize aberration formation. To further understand the sensitivity differences that were observed in ATM and NBS deficient cells, in this study, chromosomal aberration analysis was performed in normal lung fibroblast cells treated with KU-55933, a specific ATM kinase inhibitor, or Mirin, an MRN complex inhibitor involved in activation of ATM. We are also testing siRNA knockdown of these proteins. Normal and ATM or NBS suppressed cells were irradiated with gamma-rays and chromosomes were collected with a premature chromosome

  20. Prognostic value of numerical chromosome aberrations in multiple myeloma: A FISH analysis of 15 different chromosomes.

    PubMed

    Pérez-Simón, J A; García-Sanz, R; Tabernero, M D; Almeida, J; González, M; Fernández-Calvo, J; Moro, M J; Hernández, J M; San Miguel, J F; Orfão, A

    1998-05-01

    Recent observations indicate that chromosome aberrations are important prognostic factors in patients with multiple myeloma (MM) treated with high-dose chemotherapy. Nevertheless, the inherent problems of conventional cytogenetics have hampered the systematic evaluation of this parameter in series of patients treated with conventional chemotherapy. Fluorescence in situ hybridization (FISH) analysis is an attractive alternative for evaluation of numerical chromosomal changes. In the present study, we analyze the relationship between aneuploidies of 15 different chromosomes assessed by FISH and prognosis in a series of 63 patients with MM treated with conventional chemotherapy. After a median follow-up of 61 months (range, 6 to 109), 49% of patients are still alive with a median survival of 33 months. The overall incidence of numerical chromosome abnormalities was 70%. This incidence significantly increased when seven or more chromosomes were analyzed (53 patients), reaching 81%. Trisomies of chromosomes 6, 9, and 17 were associated with prolonged survival (P = .033, P = .035, and P = .026, respectively); by contrast, overall survival (OS) was lower in cases with monosomy 13 (as assessed by deletion of Rb gene, P = .0012). From the clinical point of view, loss of Rb gene was associated with a poor performance status; low hemoglobin levels; high creatinine, C-reactive protein, and lactic dehydrogenase serum levels; high percentage of bone marrow plasma cells (BMPC); extensive bone lytic lesions; and advanced clinical stage. Other chromosome abnormalities such as trisomy of chromosome 9 and 17 were associated with good prognostic features including high hemoglobin levels, early clinical stage, beta2microglobulin less than 6 micro/mL, and low percentage of BMPC. A multivariate analysis for OS showed that S-phase PC greater than 3% (P = .010) and beta2microglobulin serum levels greater than 6 micro/mL (P = .024), together with monosomy of chromosome 13 (P = .031) and

  1. Using Automated Image Analysis Algorithms to Distinguish Normal, Aberrant, and Degenerate Mitotic Figures Induced by Eg5 Inhibition.

    PubMed

    Bigley, Alison L; Klein, Stephanie K; Davies, Barry; Williams, Leigh; Rudmann, Daniel G

    2016-07-01

    Modulation of the cell cycle may underlie the toxicologic or pharmacologic responses of a potential therapeutic agent and contributes to decisions on its preclinical and clinical safety and efficacy. The descriptive and quantitative assessment of normal, aberrant, and degenerate mitotic figures in tissue sections is an important end point characterizing the effect of xenobiotics on the cell cycle. Historically, pathologists used manual counting and special staining visualization techniques such as immunohistochemistry for quantification of normal, aberrant, and degenerate mitotic figures. We designed an automated image analysis algorithm for measuring these mitotic figures in hematoxylin and eosin (H&E)-stained sections. Algorithm validation methods used data generated from a subcutaneous human transitional cell carcinoma xenograft model in nude rats treated with the cell cycle inhibitor Eg5. In these studies, we scanned and digitized H&E-stained xenografts and applied a complex ruleset of sequential mathematical filters and shape discriminators for classification of cell populations demonstrating normal, aberrant, or degenerate mitotic figures. The resultant classification system enabled the representations of three identifiable degrees of morphological change associated with tumor differentiation and compound effects. The numbers of mitotic figure variants and mitotic indices data generated corresponded to a manual assessment by a pathologist and supported automated algorithm verification and application for both efficacy and toxicity studies. PMID:26936079

  2. Cytogenetic analysis of 101 giant cell tumors of bone: nonrandom patterns of telomeric associations and other structural aberrations.

    PubMed

    Gorunova, Ludmila; Vult von Steyern, Fredrik; Storlazzi, Clelia Tiziana; Bjerkehagen, Bodil; Follerås, Gunnar; Heim, Sverre; Mandahl, Nils; Mertens, Fredrik

    2009-07-01

    Giant cell tumor of bone (GCTB) is a benign but locally aggressive tumor with metastatic potential. We performed cytogenetic analysis on 101 GCTB from 92 patients. Karyotypes were obtained from 95 tumors, 47 of which had clonal aberrations. The majority of the cytogenetically abnormal GCTB had multiple, up to 28 per tumor, clones. Clonal telomeric associations (tas) and other structural and numerical changes were found in about 70, 60, and 30%, respectively, of clonally abnormal tumors. Forty-seven aberrations were recurrent, of which 35 are novel. The vast majority of the recurrent aberrations were tas, confirming the important role of telomeric fusions in the development of GCTB. The frequency of tas in GCTB cultures increased with passaging, suggesting a selective advantage of tas-positive cells in vitro. The termini most frequently involved in tas were 22p, 13p, 15p, 21p, 14p, 19q, 1q, 12p, 11p, and 20q. The frequency of tas (irrespective of their clonality) was significantly higher in tumors carrying clonal changes, indicating that tas are precursors of other types of aberrations. In line with this assumption, the chromosomes preferentially involved in tas in a given tumor were also the ones most often affected by other rearrangements. We did not find the previously reported amplicon in 20q11.1, assessed by fluorescence in situ hybridization in 10 tumors. Nor did we find any association between cytogenetic features and adverse clinical outcome. Thus, local recurrences probably depend more on the adequacy of surgical treatment than on the intrinsic biology of the tumors. PMID:19396867

  3. Performance analysis of grazing incidence imaging systems. [X ray telescope aberrations

    NASA Technical Reports Server (NTRS)

    Winkler, C. E.; Korsch, D.

    1977-01-01

    An exact expression relating the coordinates of a point on the incident ray, a point of reflection from an arbitrary surface, and a point on the reflected ray is derived. The exact relation is then specialized for the case of grazing incidence, and first order and third order systematic analyses are carried out for a single reflective surface and then for a combination of two surfaces. The third order treatment yields a complete set of primary aberrations for single element and two element systems. The importance of a judicious choice for a coordinate system in showing field curvature to clearly be the predominant aberration for a two element system is discussed. The validity of the theory is verified through comparisons with the exact ray trace results for the case of the telescope.

  4. Painting Analysis of Chromosome Aberrations Induced by Energetic Heavy Ions in Human Cells

    NASA Technical Reports Server (NTRS)

    Wu, Honglu; Hada, Megumi; Cucinotta, Francis

    2007-01-01

    This viewgraph presentation reviews some of the techniques used to analyze the damage done to chromosome from ion radiation. Fluorescence in situ hybridization (FISH), mFISH, mBAND, telomere and centromereprobes have been used to study chromosome aberrations induced in human cells exposed to low-and high-LET radiation in vitro. There is some comparison of the different results from the various techniques. The results of the study are summarized.

  5. Analysis of pupil and corneal wave aberration data supplied by the SN CT 1000 topography system

    NASA Astrophysics Data System (ADS)

    Comastri, S. A.; Martin, G.; Pfortner, T.

    2006-11-01

    Ocular aberrations depend on pupil size and centring and the retinal image quality under natural conditions differs from that corresponding to laboratory ones. In the present article, pupil and wave aberration data supplied by the Shin Nippon CT 1000 (SN CT 1000) topography system are analysed. Two groups of eyes under natural viewing conditions are considered ((260+/-20) lux at the eye under study). The first group consists of 10 normal eyes (-1.25 to 3 D sphere; 0 to -1.75 D cylinder) of five young subjects (age between 18 and 33 years). For this group, five determinations per eye are performed and the repeatability of results is analysed. Pupil centre is displaced from corneal vertex towards the temporal region, the largest displacement being (0.5+/-0.1) mm. The variation of pupil diameter in each eye is less than 21% while the inter-subject variability is large since diameters are between (3+/-0.3) and (5.3+/-0.6) mm. Aberrations are evaluated for two different pupil sizes, the natural one and a fictitious one of 6 mm. The corneal higher-order root-mean square wavefront error (RMSHO) for a 6 mm pupil centred in the corneal vertex, averaged across all eyes, is (0.37+/-0.06) [mu]m while, considering the natural pupil diameter, the average in each eye is significantly lower, up to eight times smaller. The fourth-order spherical aberration is an important aberration in the considered eyes, its maximum value for a 6 mm pupil being (0.38+/-0.02) [mu]m. The second group consists of 24 eyes of 12 subjects (age between 25 and 68 years) such that four eyes are of normal adults (1.25 to +6 D sphere; 0 to -0.5 D cylinder), eight have astigmatisms (-5.5 to +3.25 D sphere; -1.5 to -4.5 D cylinder), six have post-refractive surgery (+0.5 to +3.5 D sphere; -0.5 to -4 D cylinder) and six have keratoconus (-9.5 to +1 D sphere; -1 to -4.5 D cylinder). For this group only one determination per eye is performed. Pupil centre is displaced from corneal vertex towards the temporal

  6. Analysis of Heavy Ion-Induced Chromosome Aberrations in Human Fibroblast Cells Using In Situ Hybridization

    NASA Technical Reports Server (NTRS)

    Wu, Honglu; Durante, Marco; Furusawa, Yoshiya; George, Kerry; Kawata, Tetsuya; Cucinotta, Francis A.

    2003-01-01

    Confluent human fibroblast cells (AG1522) were irradiated with gamma rays, 490 MeV/nucleon Si, or with Fe ions at either 200 or 500 MeV/nucleon. The cells were allowed to repair at 37 0 C for 24 hours after exposure, and a chemically induced premature chromosome condensation (PCC) technique was used to condense chromosomes in the G2 phase of the cell cycle. Unrejoined chromosomal breaks and complex exchanges were analyzed in the irradiated samples. In order to verify that chromosomal breaks were truly unrejoined, chromosome aberrations were analyzed using a combination of whole chromosome specific probes and probes specific for the telomere region of the chromosome. Results showed that the frequency of unrejoined chromosome breaks was higher after high-LET radiation, and consequently, the ratio of incomplete to complete exchanges increased steadily with LET up to 440 keV/micron, the highest LET value in the present study. For samples exposed to 200 MeV/nucleon Fe ions, chromosome aberrations were analyzed using the multicolor FISH (mFISH) technique that allows identification of both complex and truly incomplete exchanges. Results of the mFISH study showed that 0.7 and 3 Gy dose of the Fe ions produced similar ratios of complex to simple exchanges and incomplete to complete exchanges, values for which were higher than those obtained after a 6 Gy gamma exposure. After 0.7 Gy of Fe ions, most complex aberrations were found to involve three or four chromosomes, indicating the maximum number of chromosome domains traversed by a single Fe ion track. 2

  7. Quantitative analysis of aberrant protein glycosylation in liver cancer plasma by AAL-enrichment and MRM mass spectrometry.

    PubMed

    Ahn, Yeong Hee; Shin, Park Min; Kim, Yong-Sam; Oh, Na Ree; Ji, Eun Sun; Kim, Kwang Hoe; Lee, Yeon Jung; Kim, Sung Ho; Yoo, Jong Shin

    2013-11-01

    A lectin-coupled mass spectrometry (MS) approach was employed to quantitatively monitor aberrant protein glycosylation in liver cancer plasma. To do this, we compared the difference in the total protein abundance of a target glycoprotein between hepatocellular carcinoma (HCC) plasmas and hepatitis B virus (HBV) plasmas, as well as the difference in lectin-specific protein glycoform abundance of the target glycoprotein. Capturing the lectin-specific protein glycoforms from a plasma sample was accomplished by using a fucose-specific aleuria aurantia lectin (AAL) immobilized onto magnetic beads via a biotin-streptavidin conjugate. Following tryptic digestion of both the total plasma and its AAL-captured fraction of each HCC and HBV sample, targeted proteomic mass spectrometry was conducted quantitatively by a multiple reaction monitoring (MRM) technique. From the MRM-based analysis of the total plasmas and AAL-captured fractions, differences between HCC and HBV plasma groups in fucosylated glycoform levels of target glycoproteins were confirmed to arise from both the change in the total protein abundance of the target proteins and the change incurred by aberrant fucosylation on target glycoproteins in HCC plasma, even when no significant change occurs in the total protein abundance level. Combining the MRM-based analysis method with the lectin-capturing technique proved to be a successful means of quantitatively investigating aberrant protein glycosylation in cancer plasma samples. Additionally, it was elucidated that the differences between HCC and control groups in fucosylated biomarker candidates A1AT and FETUA mainly originated from an increase in fucosylation levels on these target glycoproteins, rather than an increase in the total protein abundance of the target glycoproteins. PMID:24027776

  8. Adaptive Optics Analysis of Visual Benefit with Higher-order Aberrations Correction of Human Eye - Poster Paper

    NASA Astrophysics Data System (ADS)

    Xue, Lixia; Dai, Yun; Rao, Xuejun; Wang, Cheng; Hu, Yiyun; Liu, Qian; Jiang, Wenhan

    2008-01-01

    Higher-order aberrations correction can improve visual performance of human eye to some extent. To evaluate how much visual benefit can be obtained with higher-order aberrations correction we developed an adaptive optics vision simulator (AOVS). Dynamic real time optimized modal compensation was used to implement various customized higher-order ocular aberrations correction strategies. The experimental results indicate that higher-order aberrations correction can improve visual performance of human eye comparing with only lower-order aberration correction but the improvement degree and higher-order aberration correction strategy are different from each individual. Some subjects can acquire great visual benefit when higher-order aberrations were corrected but some subjects acquire little visual benefit even though all higher-order aberrations were corrected. Therefore, relative to general lower-order aberrations correction strategy, customized higher-order aberrations correction strategy is needed to obtain optimal visual improvement for each individual. AOVS provides an effective tool for higher-order ocular aberrations optometry for customized ocular aberrations correction.

  9. Wavefront aberration measurement method for a hyper-NA lithographic projection lens based on principal component analysis of an aerial image.

    PubMed

    Zhu, Boer; Wang, Xiangzhao; Li, Sikun; Yan, Guanyong; Shen, Lina; Duan, Lifeng

    2016-04-20

    A wavefront aberration measurement method for a hyper-NA lithographic projection lens by use of an aerial image based on principal component analysis is proposed. Aerial images of the hyper-NA lithographic projection lens are expressed accurately by using polarized light and a vector imaging model, as well as by considering the polarization properties. As a result, the wavefront aberrations of the hyper-NA lithographic projection lens are measured accurately. The lithographic simulator PROLITH is used to validate the accuracies of the wavefront aberration measurement and analyze the impact of the polarization rotation of illumination on the accuracy of the wavefront aberration measurement, as well as the degree of polarized light and the sample interval of aerial images. The result shows that the proposed method can retrieve 33 terms of Zernike coefficients (Z5-Z37) with a maximum error of less than 0.00085λ. PMID:27140087

  10. Interfacial atomic structure analysis at sub-angstrom resolution using aberration-corrected STEM

    PubMed Central

    2014-01-01

    The atomic structure of a SiGe/Si epitaxial interface grown via molecular beam epitaxy on a single crystal silicon substrate was investigated using an aberration-corrected scanning transmittance electron microscope equipped with a high-angle annular dark-field detector and an energy-dispersive spectrometer. The accuracy required for compensation of the various residual aberration coefficients to achieve sub-angstrom resolution with the electron optics system was also evaluated. It was found that the interfacial layer was composed of a silicon single crystal, connected coherently to epitaxial SiGe nanolaminates. In addition, the distance between the dumbbell structures of the Si and Ge atoms was approximately 0.136 nm at the SiGe/Si interface in the [110] orientation. The corresponding fast Fourier transform exhibited a sub-angstrom scale point resolution of 0.78 Å. Furthermore, the relative positions of the atoms in the chemical composition line scan signals could be directly interpreted from the corresponding incoherent high-angle annular dark-field image. PMID:25426003

  11. Design of eye models used in quantitative analysis of interaction between chromatic and higher-order aberrations of eye

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Special kinds of eye models are constructed by means of optical system design to quantitatively investigate impacts of longitudinal chromatic aberration (LCA), transverse chromatic aberration (TCA) and LCA+TCA on retina image quality and on depth of focus (DOF), as well as interaction between chromatic and higher-order aberrations. Results show that LCA plays a main role in enhancement of DOF and higher-order aberrations further increase DOF. For most of the eyes the impact of higher-order aberrations on vision is much smaller than that of LCA+TCA and the presence of LCA+TCA further reduces the impact of higher-order aberrations. The impact of LCA approximates to that of LCA+TCA, and the impact of TCA approximates to that of normal level of higher-order aberrations and is negligible.

  12. Chromosome aberration analysis in peripheral lymphocytes of Gulf War and Balkans War veterans.

    PubMed

    Schröder, H; Heimers, A; Frentzel-Beyme, R; Schott, A; Hoffmann, W

    2003-01-01

    Chromosome aberrations and sister chromatid exchanges (SCEs) were determined in standard peripheral lymphocyte metaphase preparations of 13 British Gulf War veterans, two veterans of the recent war in the Balkans and one veteran of both wars. All 16 volunteers suspect exposures to depleted uranium (DU) while deployed at the two different theatres of war in 1990 and later on. The Bremen laboratory control served as a reference in this study. Compared with this control there was a statistically significant increase in the frequency of dicentric chromosomes (dic) and centric ring chromosomes (cR) in the veterans' group. indicating a previous exposure to ionising radiation. The statistically significant overdispersion of die and cR indicates non-uniform irradiation as would be expected after non-uniform exposure and/or exposure to radiation with a high linear energy transfer (LET). The frequency of SCEs was decreased when compared with the laboratory control. PMID:12678382

  13. Analysis of higher order optical aberrations in the SLC final focus using Lie Algebra techniques

    SciTech Connect

    Walker, N.J.; Irwin, J.; Woodley, M.

    1993-04-01

    The SLC final focus system is designed to have an overall demagnification of 30:1, with a {beta} at the interaction point ({beta}*) of 5 mm, and an energy band pass of {approximately}0.4%. Strong sextupole pairs are used to cancel the large chromaticity which accrues primarily from the final triplet. Third-order aberrations limit the performance of the system, the dominating terms being U{sub 1266} and U{sub 3466} terms (in the notation of K. Brown). Using Lie Algebra techniques, it is possible to analytically calculate the soave of these terms in addition to understanding their origin. Analytical calculations (using Lie Algebra packages developed in the Mathematica language) are presented of the bandwidth and minimum spot size as a function of divergence at the interaction point (IP). Comparisons of the analytical results from the Lie Algebra maps and results from particle tracking (TURTLE) are also presented.

  14. Transcriptome Meta-Analysis of Lung Cancer Reveals Recurrent Aberrations in NRG1 and Hippo Pathway Genes

    PubMed Central

    Dhanasekaran, Saravana M.; Balbin, O. Alejandro; Chen, Guoan; Nadal, Ernest; Kalyana-Sundaram, Shanker; Pan, Jincheng; Veeneman, Brendan; Cao, Xuhong; Malik, Rohit; Vats, Pankaj; Wang, Rui; Huang, Stephanie; Zhong, Jinjie; Jing, Xiaojun; Iyer, Matthew; Wu, Yi-Mi; Harms, Paul W.; Lin, Jules; Reddy, Rishindra; Brennan, Christine; Palanisamy, Nallasivam; Chang, Andrew C.; Truini, Anna; Truini, Mauro; Robinson, Dan R.; Beer, David G.; Chinnaiyan, Arul M.

    2014-01-01

    Lung cancer is emerging as a paradigm for disease molecular subtyping, facilitating targeted therapy based on driving somatic alterations. Here, we perform transcriptome analysis of 153 samples representing lung adenocarcinomas, squamous cell carcinomas, large cell lung cancer, adenoid cystic carcinomas and cell lines. By integrating our data with The Cancer Genome Atlas and published sources, we analyze 753 lung cancer samples for gene fusions and other transcriptomic alterations. We show that higher numbers of gene fusions is an independent prognostic factor for poor survival in lung cancer. Our analysis confirms the recently reported CD74-NRG1 fusion and suggests that NRG1, NF1 and Hippo pathway fusions may play important roles in tumors without known driver mutations. In addition, we observe exon skipping events in c-MET, which are attributable to splice site mutations. These classes of genetic aberrations may play a significant role in the genesis of lung cancers lacking known driver mutations. PMID:25531467

  15. Epidemiology of Colonic Aberrant Crypt Foci: Review and Analysis of Existing Studies

    PubMed Central

    Stevens, Richard G.; Swede, Helen; Rosenberg, Daniel W.

    2007-01-01

    Since first described in a rodent model in 1987, aberrant crypt foci (ACF) in the colon have been shown to exhibit many of the molecular features of the more advanced colonic neoplasms including cancer. Therefore, they may be early lesions with potential for progression, and be valuable biomarkers for reduction of risk of colorectal cancer (CRC). For this review, we searched PubMed, and reference lists of recent publications, for studies which reported on associations of features of ACF in humans, such as number or size, with subject characteristics, such as age or family history of CRC. Over 150 papers have reported on ACF in humans. However, the vast majority of these publications are concerned with molecular and morphological features of biopsied lesions, and not their epidemiology. None of the epidemiological studies were of optimum design, primarily due to their absence of a well-defined subject sampling frame or method. Given their ‘first-generation’ nature, consistent findings were of increased ACF number with age and with synchronous advanced colonic neoplasia. One study reported a higher mean number of ACF in subjects with a family history of CRC than in those without. The strongest evidence on the ability of ACF to predict a diagnosis of CRC will be from prospective studies with baseline ACF assessment in a large sample of disease-free persons (many thousands) who are followed carefully for many years. In the interim, because ACF are asymptomatic, well-designed cross-sectional studies are feasible and will yield valuable information on the relation of ACF to the known risk factors for CRC. This information can then be used to improve the design of prospective studies, and of clinical intervention trials that use ACF as an intermediate endpoint. PMID:17182176

  16. Role of quercetin on mitomycin C induced genotoxicity: analysis of micronucleus and chromosome aberrations in vivo.

    PubMed

    Mazumdar, Mehnaz; Giri, Sarbani; Giri, Anirudha

    2011-04-01

    Quercetin, a flavonol group of plant flavonoid, has generated immense interest because of its potential antioxidant, anti-proliferative, chemoprotective, anti-inflammatory and gene expression modulating properties. However, the pro-oxidant chemistry of quercetin is important as it is related to the generation of mutagenic quinone-type metabolites. In the present study, 25mg/kg, 50mg/kg and 100mg/kg of quercetin given through the intra peritoneal (i.p.) route induced 2.31 ± 0.27%, 4.72 ± 0.58% and 6.38 ± 0.68% (control value=0.67 ± 0.30%) respectively, of cells with micronucleus (MN) in polychromatic erythrocytes in bone marrow cells and 10.93 ± 0.98%, 10.00 ± 0.89% and 14.27 ± 3.94% (control 2.61 ± 0.48) of cells with chromosome aberrations (CA) following 24h of the treatments. Higher frequencies of MN and CA were also observed after 48h of the treatments. To verify the effect of route of treatment on the quercetin induced damage, 100mg/kg b.w. was given through oral route which declined frequency of MN (P<0.001) as well as CA (P<0.05) as compared to the i.p. route for the same dose. Quercetin also induced higher frequency of metaphases with sticky chromosomes and C-mitosis. Pre-treatment with quercetin significantly reduced the frequency of mitomycin C (MMC) induced MN as well as CA, but no clear correlation between the dose and effect could be observed. Further studies are required to elucidate the possible interaction of quercetin with DNA as well as with other DNA damaging agents like MMC in vivo. The protective action of quercetin was not enhanced when given orally. Our findings suggest that quercetin may result in genomic instability in the tested dose range and significant reduction in MMC induced genotoxicity in the highest dose tested. These effects of quercetin are to be taken into consideration while evaluating the possible use of quercetin as a therapeutic agent. PMID:21256974

  17. Identification and Comparison of Aberrant Key Regulatory Networks in Breast, Colon, Liver, Lung, and Stomach Cancers through Methylome Database Analysis

    PubMed Central

    Kim, Byungtak; Kang, Seongeun; Jeong, Gookjoo; Park, Sung-Bin; Kim, Sun Jung

    2014-01-01

    Aberrant methylation of specific CpG sites at the promoter is widely responsible for genesis and development of various cancer types. Even though the microarray-based methylome analyzing techniques have contributed to the elucidation of the methylation change at the genome-wide level, the identification of key methylation markers or top regulatory networks appearing common in highly incident cancers through comparison analysis is still limited. In this study, we in silico performed the genome-wide methylation analysis on each 10 sets of normal and cancer pairs of five tissues: breast, colon, liver, lung, and stomach. The methylation array covers 27,578 CpG sites, corresponding to 14,495 genes, and significantly hypermethylated or hypomethylated genes in the cancer were collected (FDR adjusted p-value <0.05; methylation difference >0.3). Analysis of the dataset confirmed the methylation of previously known methylation markers and further identified novel methylation markers, such as GPX2, CLDN15, and KL. Cluster analysis using the methylome dataset resulted in a diagram with a bipartite mode distinguishing cancer cells from normal cells regardless of tissue types. The analysis further revealed that breast cancer was closest with lung cancer, whereas it was farthest from colon cancer. Pathway analysis identified that either the “cancer” related network or the “cancer” related bio-function appeared as the highest confidence in all the five cancers, whereas each cancer type represents its tissue-specific gene sets. Our results contribute toward understanding the essential abnormal epigenetic pathways involved in carcinogenesis. Further, the novel methylation markers could be applied to establish markers for cancer prognosis. PMID:24842468

  18. Wave-front aberrations analysis by Zernike polynomials based on the annular sub-aperture stitching system

    NASA Astrophysics Data System (ADS)

    Duan, Lei; Hui, Mei; Deng, Jiayuan; Gong, Cheng; Zhao, Yuejin

    2012-11-01

    Annular sub-aperture stitching method was developed for testing large-aperture aspheric surfaces without using of any compensating element for measurement. It is necessary to correct measurement of aspheric optical aberrations and create mathematical description to describe wave-front aberrations. Zernike polynomials are suitable to describe wave aberration functions and data fitting of experimental measurements for the annular sub-aperture stitching system. This paper uses Zernike polynomials to describe the wave-front aberrations of full wave-front and reconstructed wave-front by annular sub-aperture stitching algorithm. At the same time, the imaging quality of the aspheric optical element can be contrasted. The stitching result shows good agreement with the full aperture result.

  19. Aberration analysis of the putative projector for Lorenzo Lotto's Husband and wife: image analysis through computer ray-tracing

    NASA Astrophysics Data System (ADS)

    Robinson, Dirk; Stork, David G.

    2008-02-01

    A recent theory claims that the late-Italian Renaissance painter Lorenzo Lotto secretly built a concave-mirror projector to project an image of a carpet onto his canvas and trace it during the execution of Husband and wife (c. 1543). Key evidence adduced to support this claim includes "perspective anomalies" and changes in "magnification" that the theory's proponents ascribe to Lotto refocusing his projector to overcome its limitations in depth of field. We find, though, that there are important geometrical constraints upon such a putative optical projector not incorporated into the proponents' analyses, and that when properly included, the argument for the use of optics loses its force. We used Zemax optical design software to create a simple model of Lotto's studio and putative projector, and incorporated the optical properties proponents inferred from geometrical properties of the depicted carpet. Our central contribution derives from including the 116-cm-wide canvas screen; we found that this screen forces the incident light to strike the concave mirror at large angles (>= 15°) and that this, in turn, means that the projected image would reveal severe off-axis aberrations, particularly astigmatism. Such aberrations are roughly as severe as the defocus blur claimed to have led Lotto to refocus the projector. In short, we find that the projected images would not have gone in and out of focus in the way claimed by proponents, a result that undercuts their claim that Lotto used a projector for this painting. We speculate on the value of further uses of sophisticated ray-tracing analyses in the study of fine arts.

  20. Evaluation of chronic lymphocytic leukemia by oligonucleotide-based microarray analysis uncovers novel aberrations not detected by FISH or cytogenetic analysis

    PubMed Central

    2011-01-01

    Background Cytogenetic evaluation is a key component of the diagnosis and prognosis of chronic lymphocytic leukemia (CLL). We performed oligonucleotide-based comparative genomic hybridization microarray analysis on 34 samples with CLL and known abnormal karyotypes previously determined by cytogenetics and/or fluorescence in situ hybridization (FISH). Results Using a custom designed microarray that targets >1800 genes involved in hematologic disease and other malignancies, we identified additional cryptic aberrations and novel findings in 59% of cases. These included gains and losses of genes associated with cell cycle regulation, apoptosis and susceptibility loci on 3p21.31, 5q35.2q35.3, 10q23.31q23.33, 11q22.3, and 22q11.23. Conclusions Our results show that microarray analysis will detect known aberrations, including microscopic and cryptic alterations. In addition, novel genomic changes will be uncovered that may become important prognostic predictors or treatment targets for CLL in the future. PMID:22087757

  1. Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes

    PubMed Central

    Kim, Tae-Min; Xi, Ruibin; Luquette, Lovelace J.; Park, Richard W.; Johnson, Mark D.; Park, Peter J.

    2013-01-01

    A large database of copy number profiles from cancer genomes can facilitate the identification of recurrent chromosomal alterations that often contain key cancer-related genes. It can also be used to explore low-prevalence genomic events such as chromothripsis. In this study, we report an analysis of 8227 human cancer copy number profiles obtained from 107 array comparative genomic hybridization (CGH) studies. Our analysis reveals similarity of chromosomal arm-level alterations among developmentally related tumor types as well as a number of co-occurring pairs of arm-level alterations. Recurrent (“pan-lineage”) focal alterations identified across diverse tumor types show an enrichment of known cancer-related genes and genes with relevant functions in cancer-associated phenotypes (e.g., kinase and cell cycle). Tumor type-specific (“lineage-restricted”) alterations and their enriched functional categories were also identified. Furthermore, we developed an algorithm for detecting regions in which the copy number oscillates rapidly between fixed levels, indicative of chromothripsis. We observed these massive genomic rearrangements in 1%–2% of the samples with variable tumor type-specific incidence rates. Taken together, our comprehensive view of copy number alterations provides a framework for understanding the functional significance of various genomic alterations in cancer genomes. PMID:23132910

  2. [The number of aberrations in aberrant cells as a parameter of chromosomal instability. 1. Characterization of dose dependency].

    PubMed

    Kutsokon', N K; Bezrukov, V F; Lazarenko, L M; Rashydov, N M; Hrodzyns'kyĭ, D M

    2003-01-01

    Analysis of chromosome instability (CI) is of great importance in view of pollution of the environment by genotoxic factors. Frequency of aberrant cells, spectrum of chromosome aberrations, damages of aberrant cell and distribution of aberrations in the cells are the most conventional parameters of CI. We have carried out the comparative analysis of the frequency of aberrant cells and the dynamics of aberrant cell damages induced by different mutagenic factors (alpha-irradiation from 241Am, gamma-irradiation from 60Co and tioTEPA) in Allium-test. This comparative analysis denotes that the studied parameters have different dynamics characterizing different mechanisms of CI in Allium cepa L. PMID:14569619

  3. Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish.

    PubMed

    Moore, Finola E; Garcia, Elaine G; Lobbardi, Riadh; Jain, Esha; Tang, Qin; Moore, John C; Cortes, Mauricio; Molodtsov, Aleksey; Kasheta, Melissa; Luo, Christina C; Garcia, Amaris J; Mylvaganam, Ravi; Yoder, Jeffrey A; Blackburn, Jessica S; Sadreyev, Ruslan I; Ceol, Craig J; North, Trista E; Langenau, David M

    2016-05-30

    Hematopoiesis culminates in the production of functionally heterogeneous blood cell types. In zebrafish, the lack of cell surface antibodies has compelled researchers to use fluorescent transgenic reporter lines to label specific blood cell fractions. However, these approaches are limited by the availability of transgenic lines and fluorescent protein combinations that can be distinguished. Here, we have transcriptionally profiled single hematopoietic cells from zebrafish to define erythroid, myeloid, B, and T cell lineages. We also used our approach to identify hematopoietic stem and progenitor cells and a novel NK-lysin 4(+) cell type, representing a putative cytotoxic T/NK cell. Our platform also quantified hematopoietic defects in rag2(E450fs) mutant fish and showed that these fish have reduced T cells with a subsequent expansion of NK-lysin 4(+) cells and myeloid cells. These data suggest compensatory regulation of the innate immune system in rag2(E450fs) mutant zebrafish. Finally, analysis of Myc-induced T cell acute lymphoblastic leukemia showed that cells are arrested at the CD4(+)/CD8(+) cortical thymocyte stage and that a subset of leukemia cells inappropriately reexpress stem cell genes, including bmi1 and cmyb In total, our experiments provide new tools and biological insights into single-cell heterogeneity found in zebrafish blood and leukemia. PMID:27139488

  4. M-BAND Analysis of Chromosome Aberration In Human Epithelial Cells exposed to Gamma-ray and Secondary Neutrons of Low Dose Rate

    NASA Technical Reports Server (NTRS)

    Hada, M.; Saganti, P. B.; Gersey, B.; Wilkins, R.; Cucinotta, F. A.; Wu, H.

    2007-01-01

    High-energy secondary neutrons, produced by the interaction of galactic cosmic rays with the atmosphere, spacecraft structure and planetary surfaces, contribute to a significant fraction to the dose equivalent in crew members and passengers during commercial aviation travel, and astronauts in space missions. The Los Alamos Nuclear Science Center (LANSCE) neutron facility's "30L" beam line is known to generate neutrons that simulate the secondary neutron spectrum of the Earth's atmosphere at high altitude. The neutron spectrum is also similar to that measured onboard spacecraft like the MIR and the International Space Station (ISS). To evaluate the biological damage, we exposed human epithelial cells in vitro to the LANSCE neutron beams at an entrance dose rate of 2.5 cGy/hr or gamma-ray at 1.7cGy/hr, and assessed the induction of chromosome aberrations that were identified with mBAND. With this technique, individually painted chromosomal bands on one chromosome allowed the identification of inter-chromosomal aberrations (translocation to unpainted chromosomes) and intra-chromosomal aberrations (inversions and deletions within a single painted chromosome). Compared to our previous results for gamma-rays and 600 MeV/nucleon Fe ions of high dose rate, the neutron data showed a higher frequency of chromosome aberrations. However, detailed analysis of the inversion type revealed that all of the three radiation types in the study induced a low incidence of simple inversions. The low dose rate gamma-rays induced a lower frequency of chromosome aberrations than high dose rate gamma-rays, but the inversion spectrum was similar for the same cytotoxic effect. The distribution of damage sites on chromosome 3 for different radiation types will also be discussed.

  5. Chromosome aberrations in peripheral blood lymphocytes of welders and characterization of their exposure by biological samples analysis

    SciTech Connect

    Elias, Z.; Mur, J.M.; Pierre, F.; Gilgenkrantz, S.; Schneider, O.; Baruthio, F.; Daniere, M.C.; Fontana, J.M.

    1989-05-01

    Chromosomal aberrations in cultured lymphocytes obtained from 55 welders and 55 matched controls were analyzed. Depending on the welding techniques and the nature of the consumables and metals welded, three separate groups of welders were examined. Chromium, nickel, and manganese levels in serum and urine were measured to assess the exposure to welding fumes. A statistically significant increase of chromosomal aberrations was found in one of the three analyzed groups of welders. This group used the semi-automatic metal active gas welding process with cored wire containing nickel for welding mild steel. These welders had significantly higher concentrations of serum and urine manganese and, unlike the other welders, significantly elevated concentrations of nickel, both in serum and urine. However, no significant correlations between nickel or manganese levels and the frequency of chromosomal aberrations were found. There was a significant correlation between the length of welding employment of these welders and the frequency of chromosomal breaks, although there was no significant correlation between age and the frequency of chromosomal aberrations. The other two groups of welders, for which the analyses of biologic fluids proved chromium and manganese exposure, had no statistically significant higher frequency of chromosomal aberrations. One of these groups used the manual metal arc welding process with coated electrodes for welding mainly mild steel and the other group used the tungsten inert gas welding process for welding stainless steel. A significant correlation between the daily amount of cigarettes smoked and the frequency of chromosomal breakages, in controls as in welders, was observed. The present data indicate that certain welding processes may generate fumes that seem to have a clastogenic activity.

  6. Interpreting Chromosome Aberration Spectra

    NASA Technical Reports Server (NTRS)

    Levy, Dan; Reeder, Christopher; Loucas, Bradford; Hlatky, Lynn; Chen, Allen; Cornforth, Michael; Sachs, Rainer

    2007-01-01

    Ionizing radiation can damage cells by breaking both strands of DNA in multiple locations, essentially cutting chromosomes into pieces. The cell has enzymatic mechanisms to repair such breaks; however, these mechanisms are imperfect and, in an exchange process, may produce a large-scale rearrangement of the genome, called a chromosome aberration. Chromosome aberrations are important in killing cells, during carcinogenesis, in characterizing repair/misrepair pathways, in retrospective radiation biodosimetry, and in a number of other ways. DNA staining techniques such as mFISH ( multicolor fluorescent in situ hybridization) provide a means for analyzing aberration spectra by examining observed final patterns. Unfortunately, an mFISH observed final pattern often does not uniquely determine the underlying exchange process. Further, resolution limitations in the painting protocol sometimes lead to apparently incomplete final patterns. We here describe an algorithm for systematically finding exchange processes consistent with any observed final pattern. This algorithm uses aberration multigraphs, a mathematical formalism that links the various aspects of aberration formation. By applying a measure to the space of consistent multigraphs, we will show how to generate model-specific distributions of aberration processes from mFISH experimental data. The approach is implemented by software freely available over the internet. As a sample application, we apply these algorithms to an aberration data set, obtaining a distribution of exchange cycle sizes, which serves to measure aberration complexity. Estimating complexity, in turn, helps indicate how damaging the aberrations are and may facilitate identification of radiation type in retrospective biodosimetry.

  7. High-resolution detection of recurrent aberrations in lung adenocarcinomas by array comparative genomic hybridization and expression analysis of selective genes by quantitative PCR.

    PubMed

    Zhu, Hong; Wong, Maria Pik; Tin, Vicky

    2014-06-01

    Genomic abnormalities are the hallmark of cancers and may harbor potential candidate genes important for cancer development and progression. We performed array comparative genomic hybridization (array CGH) on 36 cases of primary lung adenocarcinoma (AD) using an array containing 2621 BAC or PAC clones spanning the genome at an average interval of 1 Mb. Array CGH identified the commonest aberrations consisting of DNA gains within 1p, 1q, 5p, 5q, 7p, 7q, 8q, 11q, 12p, 13q, 16p, 17q, 20q, and losses with 6q, 9p, 10q and 18q. High-level copy gains involved mainly 7p21-p15 and 20q13.3. Dual color fluorescence in situ hybridization (FISH) was performed on a selective locus for validation of array CGH results. Genomic aberrations were compared with different clinicopathological features and a trend of higher number of aberrations in tumors with aggressive phenotypes and current tobacco exposure was identified. According to array CGH data, 23 candidate genes were selected for quantitative PCR (qPCR) analysis. The concordance observed between the genomic and expression changes in most of the genes suggested that they could be candidate cancer-related genes that contributed to the development of lung AD. PMID:24728343

  8. The Aberration Corrected SEM

    SciTech Connect

    Joy, David C.

    2005-09-09

    The performance of the conventional low-energy CD-SEM is limited by the aberrations inherent in the probe forming lens. Multi-pole correctors are now available which can reduce or eliminate these aberrations. An SEM equipped with such a corrector offers higher spatial resolution and more probe current from a given electron source, and other aspects of the optical performance are also improved, but the much higher numerical aperture associated with an aberration corrected lens results in a reduction in imaging depth of field.

  9. Analysis of chromosome aberrations and sister chromatid exchanges in peripheral blood lymphocytes of newborns after vitamin K prophylaxis at birth.

    PubMed

    Cornelissen, M; Smeets, D; Merkx, G; De Abreu, R; Kollee, L; Monnens, L

    1991-12-01

    In many countries vitamin K prophylaxis at birth is recommended to prevent bleeding in infants due to vitamin K deficiency. Because the incidence of clinical vitamin K deficiency is very low, such a vitamin K administration should be completely safe. However, an increase in sister chromatid exchanges in lymphocytes of fetal sheep 24 h after injection of vitamin K1 has been reported. Therefore, a study concerning genotoxicity of vitamin K1 in man was conducted. Sister chromatid exchanges and chromosome aberrations were analyzed in peripheral blood lymphocytes of six newborns 24 h after intramuscular administration of 1 mg vitamin K1 and in six control neonates. The mean number of sister chromatid exchanges per metaphase in the vitamin K group was 8.88 +/- 1.22 as compared with 9.05 +/- 1.14 in the control group (NS). The mean number of chromosome aberrations per 100 mitoses was 3.00 +/- 2.61 in the vitamin K group and 2.50 +/- 1.87 in the control group (NS). Vitamin K1 plasma concentrations ranged from 115 to 1150 ng/mL (255 to 2555 x 10(-9) M) in the supplemented group, a 5000-fold rise as compared with the control group (p less than 0.01). We did not find any evidence for genetic toxicity due to the administration of 1 mg vitamin K1 intramuscularly to the newborn child. PMID:1805152

  10. Contrast Sensitivity and Spherical Aberration in Eyes Implanted with AcrySof IQ and AcrySof Natural Intraocular Lens: the Results of a Meta-Analysis

    PubMed Central

    Liu, Jianping; Zhao, Jiangyue; Ma, Liwei; Liu, Guangcong; Wu, Di; Zhang, Jinsong

    2013-01-01

    Background To systematically evaluate the visual performance of aspheric AcrySof IQ and spherical AcrySof Natural intraocular lens (IOL) after cataract surgery. Methodology/Principal Findings Potential randomized controlled trials (RCTs) that involved implanting AcrySof IQ and AcrySof Natural were searched from PubMed, Web of science, EMBASE, Chinese Science and Technology Periodicals Databases and Cochrane Central Register of Controlled Trials. The methodological quality of the studies was assessed by the Jadad method. Standardized mean differences (SMDs) with 95% confidence intervals (CIs) of best-corrected visual acuity (BCVA), contrast sensitivity and spherical aberration were pooled using a random-effects model. Seven studies were identified and analyzed to compare AcrySof IQ (236 eyes) with AcrySof Natural (232 eyes) after phacoemulsification. There was no significant difference in postoperative BCVA between AcrySof IQ and AcrySof Natural (p =0.137) after a follow up of 3 months. For contrast sensitivity, these differences reached statistical significance under photopic conditions at two spatial frequencies (3 cycles per degree (cpd), 6 cpd, 12 cpd, and 18 cpd; p =0.022, p =0.017, p = 0.065, and p=0.191, respectively) and under mesopic conditions at three spatial frequencies (3 cpd, 6 cpd, 12 cpd, and 18 cpd; p =0.007, p =0.033, p =0.030, and p =0.080, respectively). Eyes with AcrySof IQ also had statistically significant less spherical aberration than eyes with AcrySof Natural (p<0.001). Sensitivity analysis showed that the results were relatively stable and reliable. Conclusions/Significance The overall findings indicate that AcrySof IQ with a modified aspheric surface induced significantly less spherical aberration than AcrySof Natural. Contrast sensitivity in eyes with AcrySof IQ is better than that in eyes with AcrySof Natural, especially under mesopic conditions. PMID:24205001

  11. An integrative genomic and transcriptomic analysis reveals molecular pathways and networks regulated by copy number aberrations in basal-like, HER2 and luminal cancers.

    PubMed

    Natrajan, Rachael; Weigelt, Britta; Mackay, Alan; Geyer, Felipe C; Grigoriadis, Anita; Tan, David S P; Jones, Chris; Lord, Christopher J; Vatcheva, Radost; Rodriguez-Pinilla, Socorro M; Palacios, Jose; Ashworth, Alan; Reis-Filho, Jorge S

    2010-06-01

    Breast cancer is a heterogeneous disease caused by the accumulation of genetic changes in neoplastic cells. We hypothesised that molecular subtypes of breast cancer may be driven by specific constellations of genes whose expression is regulated by gene copy number aberrations. To address this question, we analysed a series of 48 microdissected grade III ductal carcinomas using high resolution microarray comparative genomic hybridisation and mRNA expression arrays. There were 5,931 genes whose expression significantly correlates with copy number identified; out of these, 1,897 genes were significantly differentially expressed between basal-like, HER2 and luminal tumours. Ingenuity Pathway Analysis (IPA) revealed that 'G1/S cell cycle regulation' and 'BRCA1 in DNA damage control' pathways were significantly enriched for genes whose expression correlates with copy number and are differentially expressed between the molecular subtypes of breast cancer. IPA of genes whose expression significantly correlates with copy number in each molecular subtype individually revealed that canonical pathways involved in oestrogen receptor (ER) signalling and DNA repair are enriched for these genes. We also identified 32, 157 and 265 genes significantly overexpressed when amplified in basal-like, HER2 and luminal cancers, respectively. These lists include known and novel potential therapeutic targets (e.g. HER2 and PPM1D in HER2 cancers). Our results provide strong circumstantial evidence that different patterns of genetic aberrations in distinct molecular subtypes of breast cancer contribute to their specific transcriptomic profiles and that biological phenomena characteristic of each subtype (e.g. proliferation, HER2 and ER signalling) may be driven by specific patterns of copy number aberrations. PMID:19688261

  12. Post DSAEK Optical Changes: A Comprehensive Prospective Analysis on the Role of Ocular Wavefront Aberrations, Haze, and Corneal Thickness

    PubMed Central

    Hindman, Holly B.; Huxlin, Krystel R.; Pantanelli, Seth M.; Callan, Christine L.; Sabesan, Ramkumar; Ching, Steven S.T.; Miller, Brooke E.; Martin, Tim; Yoon, Geunyoung

    2014-01-01

    Purpose To assess the visual impact of ocular wavefront aberrations, corneal thickness, and corneal light scatter prospectively after Descemet’s Stripping Automated Endothelial Keratoplasty (DSAEK) in humans. Methods Data were obtained prospectively from 20 eyes pre-operatively and at 1, 3, 6, and 12 months post- DSAEK. At each visit, best spectacle corrected visual acuity (BSCVA) and visual acuity with glare (Brightness Acuity Testing - BAT) were recorded and ocular wavefront measurements and corneal Optical Coherence Tomography (OCT) performed. Magnitude and sign of individual Zernike terms (higher order aberrations HOA) were determined. Epithelial, host stromal, donor stromal, and total corneal thickness were quantified. Brightness, intensity profiles of OCT images were generated to quantify light scatter in the whole cornea, subepithelial region, anterior and posterior host stroma, interface, and donor stroma. Results Mean BSCVA and glare disability at low light levels improved from 1 to 12 months post-DSAEK. All corneal thicknesses and ocular lower- and HOAs were stable from 1 through 12 months, whereas total corneal, host stromal, and interface brightness intensities decreased significantly over the same period. A repeated measures ANOVA across the follow up period found that the change in scatter, but not the change in higher order aberrations, could account for the variability occurring in acuity from 1 to 12 months post-DSAEK. Conclusions While ocular HOAs and scatter are both elevated over normal post-DSAEK, our results demonstrate that improvements in visual performance occurring over the first year post-DSAEK are associated with decreasing light scatter. In contrast, there were no significant changes in ocular HOAs during this time. Because corneal light scatter decreased between 1 and 12 months despite stable corneal thicknesses over the same period, we conclude that factors that induced light scatter, other than tissue thickness or swelling (corneal

  13. Uterine smooth muscle tumors with features suggesting fumarate hydratase aberration: detailed morphologic analysis and correlation with S-(2-succino)-cysteine immunohistochemistry

    PubMed Central

    Reyes, Carolina; Karamurzin, Yevgeniy; Frizzell, Norma; Garg, Karuna; Nonaka, Daisuke; Chen, Ying-Bei; Soslow, Robert A.

    2013-01-01

    Rare, sporadic uterine leiomyomas arise in the setting of severe metabolic aberration due to somatic fumarate hydratase mutation. Germline mutations account for the Hereditary Leiomyomatosis and Renal Cell Carcinoma syndrome, which predisposes for cutaneous and uterine leiomyomas and aggressive renal cell carcinomas. Altered fumarate hydratase leads to fumarate accumulates in affected cells with formation of S-(2-succino)-cysteine, which can be detected with polyclonal antibody. High levels of these modified cysteine residues are found characteristically in fumarate hydratase-deficient cells, but not in normal tissues or tumors unassociated with Hereditary Leiomyomatosis and Renal Cell Carcinoma syndrome. We hypothesized that S-(2-succino)-cysteine-positive leiomyomas, indicating fumarate hydratase aberration, have morphologic features that differ from those without S-(2-succino)-cysteine positivity. Hematoxylin and eosin-stained slides of uterine smooth muscle tumors were prospectively analyzed for features suggesting Hereditary Leiomyomatosis and Renal Cell Carcinoma Syndrome, such as prominent eosinophilic macronucleoli with perinucleolar halos, yielding 9 cases. Germline genetic testing for fumarate hydratase mutations was performed in 3 cases. A detailed morphological analysis was undertaken, and S-(2-succino)-cysteine immunohistochemistry was performed with controls from a tissue microarray [leiomyomas (19), leiomyosarcomas (29), and endometrial stromal tumors (15)]. Of the 9 study cases, 4 had multiple uterine smooth muscle tumors. All cases had increased cellularity, staghorn vasculature, and fibrillary cytoplasm with pink globules. All cases had inclusion-like nucleoli with perinuclear halos (7 diffuse, 1 focal). All showed diffuse granular cytoplasmic labeling with the S-(2-succino)-cysteine antibody. Two of 3 tested patients had germline fumarate hydratase mutations. Only 1 leiomyoma from the tissue microarray controls was immunohistochemically positive

  14. Biomarker for Space Radiation Risk: Painting Analysis of Chromosome Aberrations Induced by Energetic Heavy Ions in Human Cells

    NASA Technical Reports Server (NTRS)

    Hada, Megumi; George, Kerry; Cucinotta, Francis A.; Wu, Honglu

    2007-01-01

    Energetic heavy ions pose a great health risk to astronauts in extended ISS and future Lunar and Mars missions. High-LET heavy ions are particularly effective in causing various biological effects, including cell inactivation, genetic mutations, cataracts and cancer induction. Most of these biological endpoints are closely related to chromosomal damage, which can be utilized as a biomarker for radiation insults. Over the years, we have studied chromosomal damage in human fibroblast, epithelia and lymphocyte cells exposed in vitro to energetic charged particles generated at several accelerator facilities in the world. We have also studied chromosome aberrations in astronaut s peripheral blood lymphocytes before and after space flight. Various fluorescence in situ hybridization painting techniques have been used to identify from only the telomere region of the chromosome to every chromosome in a human cell. We will summarize the results of the investigations, and discuss the unique radiation signatures and biomarkers for space radiation exposure.

  15. High-frequency aberrantly methylated targets in pancreatic adenocarcinoma identified via global DNA methylation analysis using methylCap-seq

    PubMed Central

    2014-01-01

    Background Extensive reprogramming and dysregulation of DNA methylation is an important characteristic of pancreatic cancer (PC). Our study aimed to characterize the genomic methylation patterns in various genomic contexts of PC. The methyl capture sequencing (methylCap-seq) method was used to map differently methylated regions (DMRs) in pooled samples from ten PC tissues and ten adjacent non-tumor (PN) tissues. A selection of DMRs was validated in an independent set of PC and PN samples using methylation-specific PCR (MSP), bisulfite sequencing PCR (BSP), and methylation sensitive restriction enzyme-based qPCR (MSRE-qPCR). The mRNA and expressed sequence tag (EST) expression of the corresponding genes was investigated using RT-qPCR. Results A total of 1,131 PC-specific and 727 PN-specific hypermethylated DMRs were identified in association with CpG islands (CGIs), including gene-associated CGIs and orphan CGIs; 2,955 PC-specific and 2,386 PN-specific hypermethylated DMRs were associated with gene promoters, including promoters containing or lacking CGIs. Moreover, 1,744 PC-specific and 1,488 PN-specific hypermethylated DMRs were found to be associated with CGIs or CGI shores. These results suggested that aberrant hypermethylation in PC typically occurs in regions surrounding the transcription start site (TSS). The BSP, MSP, MSRE-qPCR, and RT-qPCR data indicated that the aberrant DNA methylation in PC tissue and in PC cell lines was associated with gene (or corresponding EST) expression. Conclusions Our study characterized the genome-wide DNA methylation patterns in PC and identified DMRs that were distributed among various genomic contexts that might influence the expression of corresponding genes or transcripts to promote PC. These DMRs might serve as diagnostic biomarkers or therapeutic targets for PC. PMID:25276247

  16. Chromosome aberrations in decondensed sperm DNA

    SciTech Connect

    Preston, R.J.

    1982-01-01

    Factors that could influence the chromosomal aberration frequency observed at first cleavage following in vivo exposure of germ cells to chemical mutagens are discussed. The techniques of chromosome aberration analysis following sperm DNA condensation by in vitro fertilization or fusion seem to be viable research areas for providing information of human germ cell exposures. However, the potential sensitivity of the assay needs to be better understood, and factors that can influence this sensitivity require a great deal of further study using animal models.

  17. Spherical aberration in electrically thin flat lenses.

    PubMed

    Ruphuy, Miguel; Ramahi, Omar M

    2016-08-01

    We analyze the spherical aberration of a new generation of lenses made of flat electrically thin inhomogeneous media. For such lenses, spherical aberration is analyzed quantitatively and qualitatively, and comparison is made to the classical gradient index rod. Both flat thin and thick lenses are made of gradient index materials, but the physical mechanisms and design equations are different. Using full-wave three-dimensional numerical simulation, we evaluate the spherical aberrations using the Maréchal criterion and show that the thin lens gives significantly better performance than the thick lens (rod). Additionally, based on ray tracing formulation, third-order analysis for longitudinal aberration and optical path difference are presented, showing strong overall performance of thin lenses in comparison to classical rod lenses. PMID:27505651

  18. Epigenomic Analysis of Sézary Syndrome Defines Patterns of Aberrant DNA Methylation and Identifies Diagnostic Markers.

    PubMed

    van Doorn, Remco; Slieker, Roderick C; Boonk, Stéphanie E; Zoutman, Willem H; Goeman, Jelle J; Bagot, Martine; Michel, Laurence; Tensen, Cornelis P; Willemze, Rein; Heijmans, Bas T; Vermeer, Maarten H

    2016-09-01

    Sézary syndrome (Sz) is a malignancy of skin-homing CD4(+) memory T cells that is clinically characterized by erythroderma, lymphadenopathy, and blood involvement. Distinction of Sz from erythroderma secondary to inflammatory skin diseases (erythrodermic inflammatory dermatosis [EID]) is often challenging. Recent studies identified recurrent mutations in epigenetic enzymes involved in DNA modification in Sz. Here we defined the DNA methylomes of purified CD4(+) T cells from patients with Sz, EID, and healthy control subjects. Sz showed extensive global DNA methylation alterations, with 7.8% of 473,921 interrogated autosomal CpG sites showing hypomethylation and 3.2% hypermethylation. Promoter CpG islands were markedly enriched for hypermethylation. The 126 genes with recurrent promoter hypermethylation in Sz included multiple candidate tumor suppressors that showed transcriptional repression, implicating aberrant methylation in the pathogenesis of Sz. Validation in an independent sample set showed promoter hypermethylation of CMTM2, C2orf40, G0S2, HSPB6, PROM1, and PAM in 94-100% of Sz samples but not in EID samples. Notably, promoter hypermethylation of a single gene, the chemokine-like factor CMTM2, was sufficient to accurately distinguish Sz from EID in all cases. This study shows that Sz is characterized by widespread yet distinct DNA methylation alterations, which can be used clinically as epigenetic diagnostic markers. PMID:27113428

  19. Analysis and Compensation for Lateral Chromatic Aberration in a Color Coding Structured Light 3D Measurement System.

    PubMed

    Huang, Junhui; Xue, Qi; Wang, Zhao; Gao, Jianmin

    2016-01-01

    While color-coding methods have improved the measuring efficiency of a structured light three-dimensional (3D) measurement system, they decreased the measuring accuracy significantly due to lateral chromatic aberration (LCA). In this study, the LCA in a structured light measurement system is analyzed, and a method is proposed to compensate the error caused by the LCA. Firstly, based on the projective transformation, a 3D error map of LCA is constructed in the projector images by using a flat board and comparing the image coordinates of red, green and blue circles with the coordinates of white circles at preselected sample points within the measurement volume. The 3D map consists of the errors, which are the equivalent errors caused by LCA of the camera and projector. Then in measurements, error values of LCA are calculated and compensated to correct the projector image coordinates through the 3D error map and a tri-linear interpolation method. Eventually, 3D coordinates with higher accuracy are re-calculated according to the compensated image coordinates. The effectiveness of the proposed method is verified in the following experiments. PMID:27598174

  20. Analysis of Terminal Deletions using a Generalized Time-Dependent Model of Radiation-Induced Formation of Chromosomal Aberrations

    NASA Technical Reports Server (NTRS)

    Ponomarev, Artem L.; George, K.; Cucinotta, Francis A.

    2011-01-01

    We have developed a model that can simulate different types of radiation induced chromosomal aberrations (CA's) and can provide predictions on the frequency and size of chromosomes with terminal deletions. Chromosomes with terminal deletions lack telomeres and this can elicit sister chromatid unions and the prolonged breakage/fusion/bridge (B/F/B) cycles that have been observed in mammalian tumors. The loss of a single telomere has been shown to cause extensive genomic instability through the B/F/B cycle process. Our model uses a stochastic process of DNA broken end joining, in which a realistic spectrum of CA's is created from improperly joined DNA free ends formed by DNA double strand breaks (DSBs). The distribution of the DNA free ends is given by a mechanistic model that takes into account the chromatin structure and track structure for high-LET radiation. The model allows for DSB clustering from high-LET radiation and simulates the formation of CA's in stages that correspond to the actual time after radiation exposure. The time scale for CA formation is derived from experimental data on DSB repair kinetics. At any given time a nucleus may have intact chromosomes, CA's, and/or unrepaired fragments, some of which are defined as terminal deletions, if they are capped by one telomere. The model produces a spectrum of terminal deletions with their corresponding probabilities and size distributions for different heavy ions exposures for the first division after exposure. This data provides valuable information because there is limited experimental data available in the literature on the on the actual size of terminal deletions. We compare our model output to the available experimental data and make a reasonable extrapolation on the number of chromosomes lacking telomeres in human lymphocytes exposed to heavy ions. This model generates data which may lead to predictions on the rate of genomic instability in cells after exposure to high charge and energy nuclei

  1. Genomic copy number analysis of a spectrum of blue nevi identifies recurrent aberrations of entire chromosomal arms in melanoma ex blue nevus.

    PubMed

    Chan, May P; Andea, Aleodor A; Harms, Paul W; Durham, Alison B; Patel, Rajiv M; Wang, Min; Robichaud, Patrick; Fisher, Gary J; Johnson, Timothy M; Fullen, Douglas R

    2016-03-01

    Blue nevi may display significant atypia or undergo malignant transformation. Morphologic diagnosis of this spectrum of lesions is notoriously difficult, and molecular tools are increasingly used to improve diagnostic accuracy. We studied copy number aberrations in a cohort of cellular blue nevi, atypical cellular blue nevi, and melanomas ex blue nevi using Affymetrix's OncoScan platform. Cases with sufficient DNA were analyzed for GNAQ, GNA11, and HRAS mutations. Copy number aberrations were detected in 0 of 5 (0%) cellular blue nevi, 3 of 12 (25%) atypical cellular blue nevi, and 6 of 9 (67%) melanomas ex blue nevi. None of the atypical cellular blue nevi displayed more than one aberration, whereas complex aberrations involving four or more regions were seen exclusively in melanomas ex blue nevi. Gains and losses of entire chromosomal arms were identified in four of five melanomas ex blue nevi with copy number aberrations. In particular, gains of 1q, 4p, 6p, and 8q, and losses of 1p and 4q were each found in at least two melanomas. Whole chromosome aberrations were also common, and represented the sole finding in one atypical cellular blue nevus. When seen in melanomas, however, whole chromosome aberrations were invariably accompanied by partial aberrations of other chromosomes. Three melanomas ex blue nevi harbored aberrations, which were absent or negligible in their precursor components, suggesting progression in tumor biology. Gene mutations involving GNAQ and GNA11 were each detected in two of eight melanomas ex blue nevi. In conclusion, copy number aberrations are more common and often complex in melanomas ex blue nevi compared with cellular and atypical cellular blue nevi. Identification of recurrent gains and losses of entire chromosomal arms in melanomas ex blue nevi suggests that development of new probes targeting these regions may improve detection and risk stratification of these lesions. PMID:26743478

  2. Effect of lET and track structure on the statistical analysis of chromosome aberrations: Use of the convoluted Poisson-Neyman distribution.

    NASA Astrophysics Data System (ADS)

    Gudowska-Nowak, E.; Lee, R.; Nasonova, E.; Scholz, M.

    Chromosome aberration data obtained for various types of mammalian cells including human lymphocytes after exposure to low and high LET clearly demonstrate the differences in the energy deposition pattern of both radiation qualities In our paper the distribution of chromosome aberrations observed in human peripheral blood lymphocytes after exposure to 900 MeV u Fe ions are analyzed and compared to the effects of 250 kV X-rays After low LET exposure the distribution of aberrations among cells at the first post-irradiation mitosis is characterized by a Poisson distribution reflecting a simple random distribution of damages as expected according to the homogeneous pattern of energy distribution On the contrary after high LET exposure the distribution of aberrations reflects the microscopic inhomogeneity of energy depositions If particle hits to the cell nucleus can be viewed as independent events each contributing with an average number of aberrations per hit the overall distribution of aberrations can be represented by a compound Poisson Neyman statistics However in the case of high energetic particles the radial extension of the particle tracks cannot be neglected due to overlap effects from different tracks the particle traversals cannot be treated as independent In this case the distribution of aberrations is characterized by a mixture of a Neyman distribution with a background of a Poisson-type distribution representing the contributions from the center part of the tracks and the outer overlapping part of the tracks respectively

  3. Aberrations for Grazing Incidence Optics

    NASA Technical Reports Server (NTRS)

    Saha, Timo T.

    2008-01-01

    Large number of grazing incidence telescope configurations have been designed and studied. Wolte1 telescopes are commonly used in astronomical applications. Wolter telescopes consist of a paraboloidal primary mirror and a hyperboloidal or an ellipsoidal secondary mirror. There are 8 possible combinations of Wolter telescopes. Out of these possible designs only type 1 and type 2 telescopes are widely used. Type 1 telescope is typically used for x-ray applications and type 2 telescopes are used for EUV applications. Wolter-Schwarzshild (WS) telescopes offer improved image quality over a small field of view. The WS designs are stigmatic and free of third order coma and, therefore, the PSF is significantly better over a small field of view. Typically the image is more symmetric about its centroid. As for the Wolter telescopes there are 8 possible combinations of WS telescopes. These designs have not been widely used because the surface equations are complex parametric equations complicating the analysis and typically the resolution requirements are too low to take full advantage of the WS designs. There are several other design options. Most notable are wide field x-ray telescope designs. Polynomial designs were originally suggested by Burrows4 and hyperboloid-hyperboloid designs for solar physics applications were designed by Harvey5. No general aberration theory exists for grazing incidence telescopes that would cover all the design options. Several authors have studied the aberrations of grazing incidence telescopes. A comprehensive theory of Wolter type 1 and 2 telescopes has been developed. Later this theory was expanded to include all possible combinations of grazing incidence and also normal incidence paraboloid-hyperboloid and paraboloid-ellipsoid telescopes. In this article the aberration theory of Wolter type telescopes is briefly reviewed.

  4. Aberrant Gene Expression in Humans

    PubMed Central

    Yang, Ence; Ji, Guoli; Brinkmeyer-Langford, Candice L.; Cai, James J.

    2015-01-01

    Gene expression as an intermediate molecular phenotype has been a focus of research interest. In particular, studies of expression quantitative trait loci (eQTL) have offered promise for understanding gene regulation through the discovery of genetic variants that explain variation in gene expression levels. Existing eQTL methods are designed for assessing the effects of common variants, but not rare variants. Here, we address the problem by establishing a novel analytical framework for evaluating the effects of rare or private variants on gene expression. Our method starts from the identification of outlier individuals that show markedly different gene expression from the majority of a population, and then reveals the contributions of private SNPs to the aberrant gene expression in these outliers. Using population-scale mRNA sequencing data, we identify outlier individuals using a multivariate approach. We find that outlier individuals are more readily detected with respect to gene sets that include genes involved in cellular regulation and signal transduction, and less likely to be detected with respect to the gene sets with genes involved in metabolic pathways and other fundamental molecular functions. Analysis of polymorphic data suggests that private SNPs of outlier individuals are enriched in the enhancer and promoter regions of corresponding aberrantly-expressed genes, suggesting a specific regulatory role of private SNPs, while the commonly-occurring regulatory genetic variants (i.e., eQTL SNPs) show little evidence of involvement. Additional data suggest that non-genetic factors may also underlie aberrant gene expression. Taken together, our findings advance a novel viewpoint relevant to situations wherein common eQTLs fail to predict gene expression when heritable, rare inter-individual variation exists. The analytical framework we describe, taking into consideration the reality of differential phenotypic robustness, may be valuable for investigating

  5. Aberrant methylation during cervical carcinogenesis.

    PubMed

    Virmani, A K; Muller, C; Rathi, A; Zoechbauer-Mueller, S; Mathis, M; Gazdar, A F

    2001-03-01

    We studied the pattern of aberrant methylation during the multistage pathogenesis of cervical cancers. We analyzed a total of 73 patient samples and 10 cervical cancer cell lines. In addition, tissue samples [peripheral blood lymphocytes (n = 10) and buccal epithelial cells (n = 12)] were obtained from 22 healthy volunteers. On the basis of the results of preliminary analysis, the cervical samples were grouped into three categories: (a) nondysplasia/low-grade cervical intraepithelial neoplasia (CIN; n = 37); (b) high-grade CIN (n = 17); and (c) invasive cancer (n = 19). The methylation status of six genes was determined (p16, RARbeta, FHIT, GSTP1, MGMT, and hMLH1). Our main findings are as follows: (a) methylation was completely absent in control tissues; (b) the frequencies of methylation for all of the genes except hMLH1 were >20% in cervical cancers; (c) aberrant methylation commenced early during multistage pathogenesis and methylation of at least one gene was noted in 30% of the nondysplasia/low-grade CIN group; (d) an increasing trend for methylation was seen with increasing pathological change; (e) methylation of RARbeta and GSTP1 were early events, p16 and MGMT methylation were intermediate events, and FHIT methylation was a late, tumor-associated event; and (f) methylation occurred independently of other risk factors including papillomavirus infection, smoking history, or hormone use. Although our findings need to be extended to a larger series, they suggest that the pattern of aberrant methylation in women with or without dysplasia may help identify subgroups at increased risk for histological progression or cancer development. PMID:11297252

  6. mFISH analysis of chromosome aberrations induced in vitro by α-particle radiation: examination of dose-response relationships.

    PubMed

    Curwen, Gillian B; Tawn, E Janet; Cadwell, Kevin K; Guyatt, Laura; Thompson, James; Hill, Mark A

    2012-11-01

    A multicolored FISH (mFISH) technique was used to characterize the cytogenetic damage associated with exposure to α-particle radiation with particular emphasis on the quality and quantity that is likely to be transmitted through cell division to descendant cells. Peripheral blood lymphocytes were irradiated in vitro with (238)Pu α particles with a range of mean doses up to 936 mGy and were cultured for 47 h. The dose responses for total aberrant cells, stable and unstable cells, and cells with one simple chromosome aberration and multiple chromosome aberrations were predominantly linear for doses that resulted in cell nuclei receiving a single α-particle traversal. However, there was a decrease per unit dose in aberrant cells of all types at higher doses because of cells increasingly receiving multiple traversals. The proportion of radiation-induced aberrant cells containing multiple aberrations ranged from 48 to 74% with little evidence of dose dependency. Ninety-one percent of all cells with multiple aberrations were classified as unstable. Resolving the chromosome rearrangements into simple categories resulted in a linear dose response for dicentrics of 24.9 ± 3.3 × 10(-2) per Gy. The predominant aberration in stable transmissible cells was a single translocation with a dose response for predominantly single hit cell nuclei of 4.1 ± 1.3 × 10(-2) per Gy. Thus, translocations are the most likely aberration to be observed in peripheral blood lymphocytes from individuals with incorporated α-emitting radionuclides resulting in long-term chronic exposure. PMID:23083107

  7. A Method for Serial Tissue Processing and Parallel Analysis of Aberrant Crypt Morphology, Mucin Depletion, and Beta-Catenin Staining in an Experimental Model of Colon Carcinogenesis

    PubMed Central

    2010-01-01

    The use of architectural and morphological characteristics of cells for establishing prognostic indicators by which individual pathologies are assigned grade and stage is a well-accepted practice. Advances in automated micro- and macroscopic image acquisition and digital image analysis have created new opportunities in the field of prognostic assessment; but, one area in experimental pathology, animal models for colon cancer, has not taken advantage of these opportunities. This situation is primarily due to the methods available to evaluate the colon of the rodent for the presence of premalignant and malignant pathologies. We report a new method for the excision and processing of the entire colon of the rat and illustrate how this procedure permitted the quantitative assessment of aberrant crypt foci (ACF), a premalignant colon pathology, for characteristics consistent with progression to malignancy. ACF were detected by methylene blue staining and subjected to quantitative morphometric analysis. Colons were then restained with high iron diamine–alcian blue for assessment of mucin depletion using an image overlay to associate morphometric data with mucin depletion. The subsequent evaluation of ACF for beta-catenin staining is also demonstrated. The methods described are particularly relevant to the screening of compounds for cancer chemopreventive activity. PMID:21406072

  8. Prospects for aberration corrected electron precession.

    PubMed

    Own, C S; Sinkler, W; Marks, L D

    2007-01-01

    Recent developments in aberration control in the TEM have yielded a tremendous enhancement of direct imaging capabilities for studying atomic structures. However, aberration correction also has substantial benefits for achieving ultra-resolution in the TEM through reciprocal space techniques. Several tools are available that allow very accurate detection of the electron distribution in surfaces allowing precise atomic-scale characterization through statistical inversion techniques from diffraction data. The precession technique now appears to extend this capability to the bulk. This article covers some of the progress in this area and details requirements for a next-generation analytical diffraction instrument. An analysis of the contributions offered by aberration correction for precision electron precession is included. PMID:17207934

  9. Covariation Analysis of Serumal and Urinary Metabolites Suggests Aberrant Glycine and Fatty Acid Metabolism in Chronic Hepatitis B

    PubMed Central

    Yang, Xue; Kong, Xiangliang; Cao, Zhiwei; Zhang, Yongyu; Hu, Yiyang; Tang, Kailin

    2016-01-01

    Background Chronic hepatitis b (CHB) is one of the most serious viral diseases threatening human health by putting patients at lifelong risk of cirrhosis and hepatocellular carcinoma (HCC). Although some proofs of altered metabolites in CHB were accumulated, its metabolic mechanism remains poorly understood. Analyzing covariations between metabolites may provide new hints toward underlying metabolic pathogenesis in CHB patients. Methods The present study collected paired urine and serum samples from the same subjects including 145 CHB and 23 healthy controls. A large-scale analysis of metabolites’ covariation within and across biofluids was systematically done to explore the underlying biological evidences for reprogrammed metabolism in CHB. Randomization and relative ranking difference were introduced to reduce bias caused by different sample size. More importantly, functional indication was interpreted by mapping differentially changed covariations to known metabolic pathways. Results Our results suggested reprogrammed pathways related to glycine metabolism, fatty acids metabolism and TCA cycle in CHB patients. With further improvement, the covariation analysis combined with network association study would pave new alternative way to interpret functional clues in clinical multi-omics data. PMID:27228119

  10. Association between aberrant APC promoter methylation and breast cancer pathogenesis: a meta-analysis of 35 observational studies.

    PubMed

    Zhou, Dan; Tang, Weiwei; Wang, Wenyi; Pan, Xiaoyan; An, Han-Xiang; Zhang, Yun

    2016-01-01

    Background. Adenomatous polyposis coli (APC) is widely known as an antagonist of the Wnt signaling pathway via the inactivation of β-catenin. An increasing number of studies have reported that APC methylation contributes to the predisposition to breast cancer (BC). However, recent studies have yielded conflicting results. Methods. Herein, we systematically carried out a meta-analysis to assess the correlation between APC methylation and BC risk. Based on searches of the Cochrane Library, PubMed, Web of Science and Embase databases, the odds ratio (OR) with 95% confidence interval (CI) values were pooled and summarized. Results. A total of 31 articles involving 35 observational studies with 2,483 cases and 1,218 controls met the inclusion criteria. The results demonstrated that the frequency of APC methylation was significantly higher in BC cases than controls under a random effect model (OR = 8.92, 95% CI [5.12-15.52]). Subgroup analysis further confirmed the reliable results, regardless of the sample types detected, methylation detection methods applied and different regions included. Interestingly, our results also showed that the frequency of APC methylation was significantly lower in early-stage BC patients than late-stage ones (OR = 0.62, 95% CI [0.42-0.93]). Conclusion. APC methylation might play an indispensable role in the pathogenesis of BC and could be regarded as a potential biomarker for the diagnosis of BC. PMID:27478702

  11. Association between aberrant APC promoter methylation and breast cancer pathogenesis: a meta-analysis of 35 observational studies

    PubMed Central

    Zhou, Dan; Tang, Weiwei; Wang, Wenyi; Pan, Xiaoyan

    2016-01-01

    Background. Adenomatous polyposis coli (APC) is widely known as an antagonist of the Wnt signaling pathway via the inactivation of β-catenin. An increasing number of studies have reported that APC methylation contributes to the predisposition to breast cancer (BC). However, recent studies have yielded conflicting results. Methods. Herein, we systematically carried out a meta-analysis to assess the correlation between APC methylation and BC risk. Based on searches of the Cochrane Library, PubMed, Web of Science and Embase databases, the odds ratio (OR) with 95% confidence interval (CI) values were pooled and summarized. Results. A total of 31 articles involving 35 observational studies with 2,483 cases and 1,218 controls met the inclusion criteria. The results demonstrated that the frequency of APC methylation was significantly higher in BC cases than controls under a random effect model (OR = 8.92, 95% CI [5.12–15.52]). Subgroup analysis further confirmed the reliable results, regardless of the sample types detected, methylation detection methods applied and different regions included. Interestingly, our results also showed that the frequency of APC methylation was significantly lower in early-stage BC patients than late-stage ones (OR = 0.62, 95% CI [0.42–0.93]). Conclusion. APC methylation might play an indispensable role in the pathogenesis of BC and could be regarded as a potential biomarker for the diagnosis of BC. PMID:27478702

  12. Aberration correction of unstable resonators

    NASA Technical Reports Server (NTRS)

    Lang, Robert J. (Inventor)

    1994-01-01

    Construction of aspheric reflectors for unstable resonator lasers to provide an arbitrary laser mode inside the resonator to correct aberrations of an output beam by the construction of the shape of an end reflector opposite the output reflector of the resonator cavity, such as aberrations resulting from refraction of a beam exiting the solid of the resonator having an index of refraction greater than 1 or to produce an aberration in the output beam that will precisely compensate for the aberration of an optical train into which the resonator beam is coupled.

  13. Aberrant Methylation of RASSF1A gene Contribute to the Risk of Renal Cell Carcinoma: a Meta-Analysis.

    PubMed

    Yu, Gan-Shen; Lai, Cai-Yong; Xu, Yin; Bu, Chen-Feng; Su, Ze-Xuan

    2015-01-01

    The aim of this study was to assess the diagnostic value of RASSF1A methylation in renal cell carcinoma. Systematically search were performed using the Pubmed, ProQest and Web of Science for all articles on the association between RASSF1A methylation and renal cell carcinoma before 15 April 2015. After the filtration, 13 studies involving 677 cases and 497 controls met our criteria. Our meta-analysis suggested that hypermethylation of RASSF1A gene was associated with the increased risk of RCC(OR:4.14, 95%CI:1.06-16.1). Stratified analyses showed a similar risk in qualitative detection method(OR:28.4, 95%CI:10.2-79.6), body fluid sample(OR:12.8, 95%CI:5.35-30.8), and American(OR:10.5, 95%CI:1.97-55.9). Our result identified that RASSF1A methylation had a strong potential in prediction the risk of Renal cell carcinoma. PMID:26107221

  14. Genome-wide analysis of aberrantly expressed microRNAs in bronchoalveolar lavage fluid from patients with silicosis.

    PubMed

    Zhang, Yang; Wang, Faxuan; Zhou, Dingzi; Ren, Xiaohui; Zhou, Dinglun; Gao, Xiaosi; Lan, Yajia; Zhang, Qin; Xie, Xiaoqi

    2016-08-01

    Background To identify differentially expressed miRNAs profiles in bronchoalveolar lavage fluid (BALF) from patients with silicosis and consider the potential contribution of miRNAs to silicosis.Methods miRNAs expression profiling were performed in the cell fraction of BALF samples obtained from 9 subjects (3 silicosis observation subjects, 3 stage I and stage II silicosis patients, respectively). The differential expression of two selected miRNAs hsa-miR-181c-5p and hsa-miR-29a-3p were confirmed by RT-qPCR. Furthermore, miRNAs Gene Ontology Enrichment categories and target mRNAs were determined based on miRWalk.Results We found 110 dysregulated miRNAs in silicosis samples, most of which showed a down-regulation trend. Microarray results were confirmed by RT-qPCR. With the observation group samples set as standards, stage I samples showed 123 differentially expressed miRNAs, and stage II 46. 23 miRNAs were dysregulated in both stages. Finally, functional enrichment analysis indicated that these miRNAs played an important role in various biological processes, including ECM-receptor interaction and endocytosis.Conclusions This is the first time to acquire the BALF-derived microRNAs expression profiling targeting to human silicosis. These results contribute to unravelling miRNAs involved in the pathogenesis of silicosis, and provide new tools of potential use of as biomarkers for diagnosis and/or therapeutic purposes. PMID:26903263

  15. Genome-wide analysis of aberrantly expressed microRNAs in bronchoalveolar lavage fluid from patients with silicosis

    PubMed Central

    ZHANG, Yang; WANG, Faxuan; ZHOU, Dingzi; REN, Xiaohui; ZHOU, Dinglun; GAO, Xiaosi; LAN, Yajia; ZHANG, Qin; XIE, Xiaoqi

    2016-01-01

    Background To identify differentially expressed miRNAs profiles in bronchoalveolar lavage fluid (BALF) from patients with silicosis and consider the potential contribution of miRNAs to silicosis. Methods miRNAs expression profiling were performed in the cell fraction of BALF samples obtained from 9 subjects (3 silicosis observation subjects, 3 stage I and stage II silicosis patients, respectively). The differential expression of two selected miRNAs hsa-miR-181c-5p and hsa-miR-29a-3p were confirmed by RT-qPCR. Furthermore, miRNAs Gene Ontology Enrichment categories and target mRNAs were determined based on miRWalk. Results We found 110 dysregulated miRNAs in silicosis samples, most of which showed a down-regulation trend. Microarray results were confirmed by RT-qPCR. With the observation group samples set as standards, stage I samples showed 123 differentially expressed miRNAs, and stage II 46. 23 miRNAs were dysregulated in both stages. Finally, functional enrichment analysis indicated that these miRNAs played an important role in various biological processes, including ECM-receptor interaction and endocytosis. Conclusions This is the first time to acquire the BALF-derived microRNAs expression profiling targeting to human silicosis. These results contribute to unravelling miRNAs involved in the pathogenesis of silicosis, and provide new tools of potential use of as biomarkers for diagnosis and/or therapeutic purposes. PMID:26903263

  16. Adaptive aberration correction using a triode hyperbolic electron mirror.

    PubMed

    Fitzgerald, J P S; Word, R C; Könenkamp, R

    2011-01-01

    A converging electron mirror can be used to compensate spherical and chromatic aberrations in an electron microscope. This paper presents an analytical solution to a novel triode (three electrode) hyperbolic mirror as an improvement to the well-known diode (two electrode) hyperbolic mirror for aberration correction. A weakness of the diode mirror is a lack of flexibility in changing the chromatic and spherical aberration coefficients independently without changes in the mirror geometry. In order to remove this limitation, a third electrode can be added. We calculate the optical properties of the resulting triode mirror analytically on the basis of a simple model field distribution. We present the optical properties-the object/image distance, z(0), and the coefficients of spherical and chromatic aberration, C(s) and C(c), of both mirror types from an analysis of electron trajectories in the mirror field. From this analysis, we demonstrate that while the properties of both designs are similar, the additional parameters in the triode mirror improve the range of aberration that can be corrected. The triode mirror is also able to provide a dynamic adjustment range of chromatic aberration for fixed spherical aberration and focal length, or any permutation of these three parameters. While the dynamic range depends on the values of aberration correction needed, a nominal 10% tuning range is possible for most configurations accompanied by less than 1% change in the other two properties. PMID:21930022

  17. ANALYSIS OF THE DISTRIBUTION AND DOSE RESPONSE OF CHROMOSOME ABERRATIONS IN HUMAN LYMPHOCYTES AFTER IN VITRO EXPOSURE TO (137) CESIUM GAMMA RADIATION

    EPA Science Inventory

    The chromosome aberration yield for human lymphocytes exposed in vitro to various doses of (137) Cesium has been studied. Dicentric, total acentric, and excess acentric data were seen to follow a Poisson distribution. Calculated total hits demonstrated over-dispersion which could...

  18. Chromosome Aberrations in Astronauts

    NASA Technical Reports Server (NTRS)

    George, Kerry A.; Durante, M.; Cucinotta, Francis A.

    2007-01-01

    A review of currently available data on in vivo induced chromosome damage in the blood lymphocytes of astronauts proves that, after protracted exposure of a few months or more to space radiation, cytogenetic biodosimetry analyses of blood collected within a week or two of return from space provides a reliable estimate of equivalent radiation dose and risk. Recent studies indicate that biodosimetry estimates from single spaceflights lie within the range expected from physical dosimetry and biophysical models, but very large uncertainties are associated with single individual measurements and the total sample population remains low. Retrospective doses may be more difficult to estimate because of the fairly rapid time-dependent loss of "stable" aberrations in blood lymphocytes. Also, biodosimetry estimates from individuals who participate in multiple missions, or very long (interplanetary) missions, may be complicated by an adaptive response to space radiation and/or changes in lymphocyte survival and repopulation. A discussion of published data is presented and specific issues related to space radiation biodosimetry protocols are discussed.

  19. Coating-induced wavefront aberrations

    NASA Astrophysics Data System (ADS)

    Reiley, Daniel J.; Chipman, Russell A.

    1992-12-01

    The coatings which are used on telescope mirrors and other optical interfaces can have a profound effect on the image quality formed by an optical system. This paper evaluates the defocus and astigmatism which are caused by the s- and p-phase shifts of coatings. These coating-induced wavefront aberrations are usually insignificant, but can, under certain circumstances, overshadow the geometric wavefront aberrations of the system. The wavefront aberrations induced by reflection-enhanced coatings on an f/1.5 Cassegrain telescope are numerically evaluated as an example.

  20. Correction of Distributed Optical Aberrations

    SciTech Connect

    Baker, K; Olivier, S; Carrano, C; Phillion, D

    2006-02-12

    The objective of this project was to demonstrate the use of multiple distributed deformable mirrors (DMs) to improve the performance of optical systems with distributed aberrations. This concept is expected to provide dramatic improvement in the optical performance of systems in applications where the aberrations are distributed along the optical path or within the instrument itself. Our approach used multiple actuated DMs distributed to match the aberration distribution. The project developed the algorithms necessary to determine the required corrections and simulate the performance of these multiple DM systems.

  1. M-BAND analysis of chromosome aberration induced by Fe-ions in human epithelial cells cultured in 3-dimensional matrices

    NASA Astrophysics Data System (ADS)

    Hada, Megumi; Cucinotta, Francis A.; Wu, Honglu

    Energetic heavy ions pose a great health risk to astronauts in extended ISS and future lunar and Mars missions. High-LET heavy ions are particularly effective in causing various biological effects, including cell inactivation, genetic mutations, cataracts and cancer induction. Most of these biological endpoints are closely related to chromosomal damage, which can be utilized as a biomarker for radiation insults. Previously, we had studied lowand high-LET radiationinduced chromosome aberrations in human epithelial cells cultured in 2-dimension (2D) using the multicolor banding fluorescence in situ hybridization (mBAND) technique. However, it has been realized that the biological response to radiation insult in a 2D cellular environment in vitro can differ significantly from the response in 3-dimension (3D) or at the actual tissue level. In this study, we cultured human epithelial cells in 3D to provide a more suitable model for human tissue. Human mammary epithelial cells (CH184B5F5/M10) were grown in Matrigel to form 3D structures, and exposed to Fe-ions at NASA Space Radiation Laboratory (NSRL) at the Brookhaven National Laboratory or 137 Cs-gamma radiation source at the University of Texas MD Anderson Cancer Center. After exposure, cells were allowed to repair for 16hr before dissociation and subcultured at low density in 2D. G2 and metaphase chromosomes in the first cell cycle were collected using a chemical-induced premature chromosome condensation (PCC) technique, and chromosome aberrations were analyzed using mBAND technique. With this technique, individually painted chromosomal bands on one chromosome allowed the identification of interchromosomal aberrations (translocation to unpainted chromosomes) and intrachromosomal aberrations (inversions and deletions within a single painted chromosome). Our data indicate a significant difference of the chromosome aberration yield between 2D and 3D cell cultures for gamma exposures, but not for Fe ion exposures

  2. M-BAND Analysis of Chromosome Aberration Induced by Fe-Ions in Human Epithelial Cells Cultured in 3-Dimensional Matrices

    NASA Technical Reports Server (NTRS)

    Hada, M.; Cucinotta, F. A.; Wu, H.

    2008-01-01

    Energetic heavy ions pose a great health risk to astronauts in extended ISS and future lunar and Mars missions. High-LET heavy ions are particularly effective in causing various biological effects, including cell inactivation, genetic mutations, cataracts and cancer induction. Most of these biological endpoints are closely related to chromosomal damage, which can be utilized as a biomarker for radiation insults. Previously, we had studied low- and high-LET radiation-induced chromosome aberrations in human epithelial cells cultured in 2-dimension (2D) using the multicolor banding fluorescence in situ hybridization (mBAND) technique. However, it has been realized that the biological response to radiation insult in a 2D cellular environment in vitro can differ significantly from the response in 3-dimension (3D) or at the actual tissue level. In this study, we cultured human epithelial cells in 3D to provide a more suitable model for human tissue. Human mammary epithelia cells (CH184B5F5/M10) were grown in Matrigel to form 3D structures, and exposed to Fe-ions at NASA Space Radiation Laboratory (NSRL) at the Brookhaven National Laboratory or 137Cs-gamma radiation source at the University of Texas MD Anderson Cancer Center. After exposure, cells were allowed to repair for 16hr before dissociation and subcultued at low density in 2D. G2 and metaphase chromosomes in the first cell cycle were collected using a chemical-induced premature chromosome condensation (PCC) technique, and chromosome aberrations were analyzed using mBAND technique. With this technique, individually painted chromosomal bands on one chromosome allowed the identification of interchromosomal aberrations (translocation to unpainted chromosomes) and intrachromosomal aberrations (inversions and deletions within a single painted chromosome). Our data indicate a significant difference of the chromosome aberration yield between 2D and 3D cell cultures for gamma exposures, but not for Fe ion exposures

  3. Historical aspects of aberration correction.

    PubMed

    Rose, Harald H

    2009-06-01

    A brief history of the development of direct aberration correction in electron microscopy is outlined starting from the famous Scherzer theorem established in 1936. Aberration correction is the long story of many seemingly fruitless efforts to improve the resolution of electron microscopes by compensating for the unavoidable resolution-limiting aberrations of round electron lenses over a period of 50 years. The successful breakthrough, in 1997, can be considered as a quantum step in electron microscopy because it provides genuine atomic resolution approaching the size of the radius of the hydrogen atom. The additional realization of monochromators, aberration-free imaging energy filters and spectrometers has been leading to a new generation of analytical electron microscopes providing elemental and electronic information about the object on an atomic scale. PMID:19254915

  4. mBAND analysis of chromosome aberrations in human epithelial cells induced by gamma-rays and secondary neutrons of low dose rate.

    PubMed

    Hada, M; Gersey, B; Saganti, P B; Wilkins, R; Cucinotta, F A; Wu, H

    2010-08-14

    Human risks from chronic exposures to both low- and high-LET radiation are of intensive research interest in recent years. In the present study, human epithelial cells were exposed in vitro to gamma-rays at a dose rate of 17 mGy/h or secondary neutrons of 25 mGy/h. The secondary neutrons have a broad energy spectrum that simulates the Earth's atmosphere at high altitude, as well as the environment inside spacecrafts like the Russian MIR station and the International Space Station (ISS). Chromosome aberrations in the exposed cells were analyzed using the multicolor banding in situ hybridization (mBAND) technique with chromosome 3 painted in 23 colored bands that allows identification of both inter- and intrachromosome exchanges including inversions. Comparison of present dose responses between gamma-rays and neutron irradiations for the fraction of cells with damaged chromosome 3 yielded a relative biological effectiveness (RBE) value of 26+/-4 for the secondary neutrons. Our results also revealed that secondary neutrons of low dose rate induced a higher fraction of intrachromosome exchanges than gamma-rays, but the fractions of inversions observed between these two radiation types were indistinguishable. Similar to the previous findings after acute radiation exposures, most of the inversions observed in the present study were accompanied by other aberrations. The fractions of complex type aberrations and of unrejoined chromosomal breakages were also found to be higher in the neutron-exposed cells than after gamma-rays. We further analyzed the location of the breaks involved in chromosome aberrations along chromosome 3, and observed hot spots after gamma-ray, but not neutron, exposures. PMID:20338263

  5. Aberrant expression of anaplastic lymphoma kinase in lung adenocarcinoma: Analysis of circulating free tumor RNA using one-step reverse transcription-polymerase chain reaction.

    PubMed

    Bruno, Rossella; Giordano, Mirella; Giannini, Riccardo; Alì, Greta; Puppo, Gianfranco; Ribechini, Alessandro; Chella, Antonio; Fontanini, Gabriella

    2016-09-01

    Lung adenocarcinoma patients harboring anaplastic lymphoma kinase (ALK) gene rearrangements respond well to approved ALK inhibitors. However, to date, limited evidence is available regarding whether using circulating free tumor mRNA to identify aberrant ALK expression is possible, and its feasibility remains to be clearly addressed. The present study evaluated ALK expression by a one-step reverse transcription‑polymerase chain reaction (PCR) assay on the circulating free tumor mRNA from 12 lung adenocarcinoma patients. Additionally, the present study tested for ALK rearrangements by fluorescence in situ hybridization (FISH) and immunohistochemistry. A molecular genetic characterization was performed on tumor tissues and plasma samples. Aberrant ALK expression was detected in 2/12 patients using mRNA purified from plasma specimens and the results agreed with the FISH and immunohistochemistry findings of solid biopsy samples. The detection of aberrant ALK expression on circulating free tumor RNA may be feasible using a one‑step real‑time PCR assay and may be particularly helpful when a solid biopsy sample is not available. PMID:27430882

  6. Sexual aberration or instinctual vicissitude? Revisiting freud's "the sexual aberrations".

    PubMed

    Phillips, Sidney H

    2014-04-01

    The author reconsiders Freud's "The Sexual Aberrations," the first of his Three Essays on the Theory of Sexuality (1905), in light of contemporary psychoanalytic theory. Are the concepts of sexual aberration and norm still viable? The author argues that they are necessary but insufficient elements in current theory. He then presents a competing model in which sexuality can be reduced to a more elemental level of disturbance and wish, where it is an expression of a nonsexual wish--for example, to possess or control the object to eliminate separateness. The author presents clinical material to demonstrate this alternative model. PMID:24777366

  7. Aberrations in asymmetrical electron lenses.

    PubMed

    Fitzgerald, J P S; Word, R C; Könenkamp, R

    2012-08-01

    Starting from well established knowledge in light-optics we explore the question if electron-optical aberration can be improved in asymmetrical electron lenses. We show that spherical as well as chromatic aberration coefficients are reduced in asymmetric electrostatic einzel lenses when the center electrode is moved away from the center position towards the entrance electrode. Relative improvements up to 40% for both the chromatic and the spherical aberration coefficients can be obtained. We use analytical and numerical calculations to confirm this result for exemplary cases of a lens with fixed length and working distance. The agreement of the two calculation methods is very good. We then derive an estimate for the electron-optical aberration coefficients from light-optics. The derived expressions for chromatic and spherical aberrations are somewhat simpler than the ones derived from electron-optics as they involve integrals only over the electrostatic potential, not over the electron paths. The estimated formulas still agree well with the electron optical calculations. Overall, we are tempted to suggest that the enormous knowledge base of light optics can provide considerable guidance for electron-optical applications. PMID:22206603

  8. Dimensions of driving anger and their relationships with aberrant driving.

    PubMed

    Zhang, Tingru; Chan, Alan H S; Zhang, Wei

    2015-08-01

    The purpose of this study was to investigate the relationship between driving anger and aberrant driving behaviours. An internet-based questionnaire survey was administered to a sample of Chinese drivers, with driving anger measured by a 14-item short Driving Anger Scale (DAS) and the aberrant driving behaviours measured by a 23-item Driver Behaviour Questionnaire (DBQ). The results of Confirmatory Factor Analysis demonstrated that the three-factor model (hostile gesture, arrival-blocking and safety-blocking) of the DAS fitted the driving anger data well. The Exploratory Factor Analysis on DBQ data differentiated four types of aberrant driving, viz. emotional violation, error, deliberate violation and maintaining progress violation. For the anger-aberration relation, it was found that only "arrival-blocking" anger was a significant positive predictor for all four types of aberrant driving behaviours. The "safety-blocking" anger revealed a negative impact on deliberate violations, a finding different from previously established positive anger-aberration relation. These results suggest that drivers with different patterns of driving anger would show different behavioural tendencies and as a result intervention strategies may be differentially effective for drivers of different profiles. PMID:25984643

  9. The Correlation Analysis between Corneal Biomechanical Properties and the Surgically Induced Corneal High-Order Aberrations after Small Incision Lenticule Extraction and Femtosecond Laser In Situ Keratomileusis

    PubMed Central

    Wu, Wenjing; Wang, Yan

    2015-01-01

    Background. To investigate the correlation between corneal biomechanics and the surgically induced corneal high-order aberrations (HOAs) after small incision lenticule extraction (SMILE) and femtosecond laser in situ keratomileusis (FS-LASIK). Methods. A total of 150 right myopic eyes that underwent SMILE or FS-LASIK surgery were included in this retrospective study, 75 eyes in each group. The corneal hysteresis (CH) and the corneal resistance factor (CRF) with the corneal HOAs of the anterior, posterior, and total cornea were assessed preoperatively and three months postoperatively. Multivariate linear regression was applied to determine the correlations. Results. The preoperative CRF was significantly correlated with the induced 3rd–6th-order HOAs and spherical aberration of the anterior surface and the total cornea after SMILE and FS-LASIK surgeries (P < 0.05), postoperatively. The CRF was significantly correlated with the induced vertical coma of the anterior and posterior surfaces and the total cornea after SMILE surgery (P < 0.05). There was a significant correlation between the CRF and the induced posterior corneal horizontal coma after FS-LASIK surgery (P = 0.013). Conclusions. The corneal biomechanics affect the surgically induced corneal HOAs after SMILE and FS-LASIK surgery, which may be meaningful for screening the patients preoperatively and optimizing the visual qualities postoperatively. PMID:26483975

  10. Chromosome Aberrations by Heavy Ions

    NASA Astrophysics Data System (ADS)

    Ballarini, Francesca; Ottolenghi, Andrea

    It is well known that mammalian cells exposed to ionizing radiation can show different types of chromosome aberrations (CAs) including dicentrics, translocations, rings, deletions and complex exchanges. Chromosome aberrations are a particularly relevant endpoint in radiobiology, because they play a fundamental role in the pathways leading either to cell death, or to cell conversion to malignancy. In particular, reciprocal translocations involving pairs of specific genes are strongly correlated (and probably also causally-related) with specific tumour types; a typical example is the BCR-ABL translocation for Chronic Myeloid Leukaemia. Furthermore, aberrations can be used for applications in biodosimetry and more generally as biomarkers of exposure and risk, that is the case for cancer patients monitored during Carbon-ion therapy and astronauts exposed to space radiation. Indeed hadron therapy and astronauts' exposure to space radiation represent two of the few scenarios where human beings can be exposed to heavy ions. After a brief introduction on the main general features of chromosome aberrations, in this work we will address key aspects of the current knowledge on chromosome aberration induction, both from an experimental and from a theoretical point of view. More specifically, in vitro data will be summarized and discussed, outlining important issues such as the role of interphase death/mitotic delay and that of complex-exchange scoring. Some available in vivo data on cancer patients and astronauts will be also reported, together with possible interpretation problems. Finally, two of the few available models of chromosome aberration induction by ionizing radiation (including heavy ions) will be described and compared, focusing on the different assumptions adopted by the authors and on how these models can deal with heavy ions.

  11. How To Measure Gravitational Aberration?

    NASA Astrophysics Data System (ADS)

    Krizek, M.; Solcova, A.

    2007-08-01

    In 1905, Henri Poincaré predicted the existence of gravitational waves and assumed that their speed c[g] would be that of the speed of light c. If the gravitational aberration would also have the same magnitude as the aberration of light, we would observe several paradoxical phenomena. For instance, the orbit of two bodies of equal mass would be unstable, since two attractive forces arise that are not in line and hence form a couple. This tends to increase the angular momentum, period, and total energy of the system. This can be modelled by a system of ordinary differential equations with delay. A big advantage of computer simulation is that we can easily perform many test for various possible values of the speed of gravity [1]. In [2], Carlip showed that gravitational aberration in general relativity is almost cancelled out by velocity-dependent interactions. This means that rays of sunlight are not parallel to the attractive gravitational force of the Sun, i.e., we do not see the Sun in the direction of its attractive force, but slightly shifted about an angle less than 20``. We show how the actual value of the gravitational aberration can be obtained by measurement of a single angle at a suitable time instant T corresponding to the perihelion of an elliptic orbit. We also derive an a priori error estimate that expresses how acurately T has to be determined to attain the gravitational aberration to a prescribed tolerance. [1] M. Křížek: Numerical experience with the finite speed of gravitational interaction, Math. Comput. Simulation 50 (1999), 237-245. [2] S. Carlip: Aberration and the speed of gravity, Phys. Lett. A 267 (2000), 81-87.

  12. Analysis of chromosomal aberrations, sister-chromatid exchanges and micronuclei in peripheral lymphocytes of pharmacists before and after working with cytostatic drugs.

    PubMed

    Roth, S; Norppa, H; Järventaus, H; Kyyrönen, P; Ahonen, M; Lehtomäki, J; Sainio, H; Sorsa, M

    1994-12-01

    The frequencies of chromosome aberrations, SCEs and micronuclei (cytokinesis-block method) in blood lymphocytes were compared among six nonsmoking female pharmacists before and after 1 year of working with cytostatic drugs. All possible precautions were taken to avoid exposure to cytostatics, including proper protective clothing and a monitored, negative-pressured working environment with vertical laminar flow cabinet. As referents, an age-matched group of six nonsmoking female hospital workers not dealing with cytostatics was simultaneously sampled twice with the same time interval. The pharmacists showed a marginally higher mean frequency of SCEs/cell (6.3; P = 0.049) after the working period than 1 year earlier (5.8). On the other hand, the referents, with no obvious exposure, had a higher mean number of cells with chromatid-type aberrations, gaps excluded, in the second sampling (2.0%; P = 0.048) than in the first one (0.5%). In addition, a slight (P = 0.055) trend towards a higher frequency of micronucleated binucleate cells was observed in the second sampling for both the exposed and control subjects. As such findings suggest technical variation in the cytogenetic parameters, the small difference observed in SCEs for the pharmacists between the two samplings was probably not related to the cytostatics exposure. No statistically significant differences were observed for any of the cytogenetic parameters in comparisons between the pharmacists and the referents. The findings suggest that caution should be exercised in comparing results obtained from two different samplings in prospective cytogenetic studies. PMID:7527908

  13. Distortion of ultrashort pulses caused by aberrations

    NASA Astrophysics Data System (ADS)

    Horváth, Z. L.; Kovács, A. P.; Bor, Zs.

    The effect of the primary wave aberrations (spherical aberration, astigmatism and coma) on ultrashort pulses is studied by the Nijboer-Zernike theory. The results of the geometrical and the wave optical treatments are compared.

  14. Polarization aberrations in the solar activity measurements experiments (SAMEX) solar vector magnetograph

    NASA Technical Reports Server (NTRS)

    Mcguire, James P., Jr.; Chipman, Russell A.

    1989-01-01

    An optical design and polarization analysis of the Air Force/NASA Solar Activity Measurements Experiments solar vector magnetograph optical system is performed. Polarization aberration theory demonstrates that conventional telescope coating designs introduce unacceptably high levels of polarization aberrations into the optical system. Several ultralow polarization mirror and lens coatings designs for this instrument are discussed. Balancing of polarization aberrations at different surfaces is demonstrated.

  15. Using geometric algebra to study optical aberrations

    SciTech Connect

    Hanlon, J.; Ziock, H.

    1997-05-01

    This paper uses Geometric Algebra (GA) to study vector aberrations in optical systems with square and round pupils. GA is a new way to produce the classical optical aberration spot diagrams on the Gaussian image plane and surfaces near the Gaussian image plane. Spot diagrams of the third, fifth and seventh order aberrations for square and round pupils are developed to illustrate the theory.

  16. Acute Effect of Cigarette Smoking on Pupil Size and Ocular Aberrations: A Pre- and Postsmoking Study

    PubMed Central

    Erdem, Uzeyir; Gundogan, Fatih C.; Dinc, Umut Aslı; Yolcu, Umit; Ilhan, Abdullah; Altun, Salih

    2015-01-01

    Aim. To evaluate the acute effects of cigarette smoking on photopic and mesopic pupil sizes and wavefront aberrations. Methods. Cigarette smoker volunteers were recruited in the study. Photopic and mesopic pupil sizes and total ocular aberrations were measured before smoking and immediately after smoking. All volunteers were asked to smoke a single cigarette containing 1.0 mg nicotine. Pupil sizes and total ocular aberrations were assessed by optical path difference scanning system (OPD-Scan II ARK-10000, NIDEK). Only the right eyes were considered for statistical analysis. The changes of pupil size and total ocular aberrations after smoking were tested for significance by Wilcoxon signed ranks test. Results. Mean photopic pupil size decreased from 3.52 ± 0.73 mm to 3.29 ± 0.58 mm (P = 0.001) after smoking. Mean mesopic pupil size was also decreased from 6.42 ± 0.75 mm to 6.14 ± 0.75 mm after smoking (P = 0.001). There was a decrease in all the measured components of aberrations (total wavefront aberration, higher-order aberration, total coma, total trefoil, total tetrafoil, total spherical aberration and total higher-order aberration) after smoking; however the differences were insignificant for all (P > 0.05). Conclusion. Our results indicate that pupil constricts after smoking. On the other hand, smoking does not alter ocular aberrations. PMID:25699189

  17. The Silencing of CCND2 by Promoter Aberrant Methylation in Renal Cell Cancer and Analysis of the Correlation between CCND2 Methylation Status and Clinical Features.

    PubMed

    Wang, Lu; Cui, Yun; Zhang, Lian; Sheng, Jindong; Yang, Yang; Kuang, Guanyu; Fan, Yu; Zhang, Qian; Jin, Jie

    2016-01-01

    Cyclin D2 (CCND2) is a member of the D-type cyclins, which plays a pivotal role in cell cycle regulation, differentiation and malignant transformation. However, its expression status and relative regulation mechanism remains unclear in renal cell cancer (RCC). In our study, the mRNA expression level of CCND2 is down-regulated in 22/23 paired RCC tissues (p<0.05). In addition, its protein expression level is also decreased in 43/43 RCC tumor tissues compared with its corresponding non-malignant tissues (p<0.001). We further detected that CCND2 was down-regulated or silenced in 6/7 RCC cell lines, but expressed in "normal" human proximal tubular (HK-2) cell line. Subsequently, MSP and BGS results showed that the methylation status in CCND2 promoter region is closely associated with its expression level in RCC cell lines. Treatment with 5-Aza with or without TSA restored CCND2 expression in several methylated RCC cell lines. Among the 102 RCC tumors, methylation of CCND2 was detected in 29/102 (28%) cases. Only 2/23 (8.7%) adjacent non-malignant tissues showed methylation. We then analyzed the correlation of clinical features and its promoter methylation. Collectively, our data suggested that loss of CCND2 expression is closely associated with the promoter aberrant methylation. PMID:27583477

  18. M-FISH Analysis of Chromosome Aberrations in Human Fibroblast Cells After In Vitro Exposure to Low- and High-LET Radiation

    NASA Technical Reports Server (NTRS)

    Wu, Honglu; Furusawa, Yoshiya; George, Kerry; Kawata, Tetsuya; Cucinotta, Francis

    2002-01-01

    The recently commercialized multiplex fluorescence in situ hybridization (m-FISH) technique, which allows human chromosomes to be painted in 24 different colors, was used to analyze chromosome aberrations in diploid human fibroblast cells after in vitro radiation exposure. Confluent flasks of a normal primary fibroblast cell line (AG 1522) were irradiated at high dose rates with either gamma rays or 200 MeV/nucleon Fe ions (LET = 440 keV/micron), incubated at 37 C for 24 hours after exposure, and subsequently subcultured. A chemically induced premature chromosome condensation technique was used to collect chromosome samples 32 hours after subculture. Results showed that the fraction of exchanges which were identified as complex, i.e. involving misrejoining of three or more DSB, were higher in the Fe-irradiated samples compared with the gamma-irradiated samples, as has been shown previously using FISH with one or two painted chromosomes . The ratios of complex/simple type exchanges were similar for samples irradiated with 0.7 Gy and 3 Gy of Fe ions, although exchanges involving five or more breaks were found only in 3 Gy irradiated samples. The fraction of incomplete exchanges was also higher in Fe- than gamma-irradiated samples. Data on the distribution of individual chromosome involvement in interchromosomal exchanges will be presented.

  19. Inferring primary tumor sites from mutation spectra: a meta-analysis of histology-specific aberrations in cancer-derived cell lines.

    PubMed

    Dietlein, Felix; Eschner, Wolfgang

    2014-03-15

    Next-generation sequencing technologies have led to profound characterization of mutation spectra for several cancer types. Hence, we sought to systematically compare genomic aberrations between primary tumors and cancer lines. For this, we compiled publically available sequencing data of 1651 genes across 905 cell lines. We used them to characterize 23 distinct primary tumor sites by a novel approach that is based on Bayesian spam-filtering techniques. Thereby, we confirmed the strong overall similarity of alterations between patient samples and cell culture. However, we also identified several suspicious mutations, which had not been associated with their cancer types before. Based on these characterizations, we developed the inferring cancer origins from mutation spectra (ICOMS) tool. On our cell line collection, the algorithm reached a prediction specificity rate of 79%, which strongly variegated between primary cancer sites. On an independent validation cohort of 431 primary tumor samples, we observed a similar accuracy of 71%. Additionally, we found that ICOMS could be employed to deduce further attributes from mutation spectra, including sub-histology and compound sensitivity. Thus, thorough classification of site-specific mutation spectra for cell lines may decipher further genome-phenotype associations in cancer. PMID:24163242

  20. Chromosomal aberrations in ISS crew members

    NASA Astrophysics Data System (ADS)

    Johannes, Christian; Goedecke, Wolfgang; Antonopoulos, Alexandra

    2012-07-01

    High energy radiation is a major risk factor in manned space missions. Astronauts and cosmonauts are exposed to ionising radiations of cosmic and solar origin, while on the Earth's surface people are well protected by the atmosphere and a deflecting magnetic field. There are now data available describing the dose and the quality of ionising radiation on-board of the International Space Station (ISS). Nonetheless, the effect of increased radiation dose on mutation rates of ISS crew members are hard to predict. Therefore, direct measurements of mutation rates are required in order to better estimate the radiation risk for longer duration missions. The analysis of chromosomal aberrations in peripheral blood lymphocytes is a well established method to measure radiation-induced mutations. We present data of chromosome aberration analyses from lymphocyte metaphase spreads of ISS crew members participating in short term (10-14 days) or long term (around 6 months) missions. From each subject we received two blood samples. The first sample was drawn about 10 days before launch and a second one within 3 days after return from flight. From lymphocyte cultures metaphase plates were prepared on glass slides. Giemsa stained and in situ hybridised metaphases were scored for chromosome changes in pre-flight and post-flight blood samples and the mutation rates were compared. Results obtained in chromosomal studies on long-term flight crew members showed pronounced inter-individual differences in the response to elevated radiation levels. Overall slight but significant elevations of typical radiation induced aberrations, i.e., dicentric chromosomes and reciprocal translocations have been observed. Our data indicate no elevation of mutation rates due to short term stays on-board the ISS.

  1. Efficient estimation and large-scale evaluation of lateral chromatic aberration for digital image forensics

    NASA Astrophysics Data System (ADS)

    Gloe, Thomas; Borowka, Karsten; Winkler, Antje

    2010-01-01

    The analysis of lateral chromatic aberration forms another ingredient for a well equipped toolbox of an image forensic investigator. Previous work proposed its application to forgery detection1 and image source identification.2 This paper takes a closer look on the current state-of-the-art method to analyse lateral chromatic aberration and presents a new approach to estimate lateral chromatic aberration in a runtime-efficient way. Employing a set of 11 different camera models including 43 devices, the characteristic of lateral chromatic aberration is investigated in a large-scale. The reported results point to general difficulties that have to be considered in real world investigations.

  2. The Gaussian formula and spherical aberrations of static and relativistic curved mirrors from Fermat's principle

    NASA Astrophysics Data System (ADS)

    Sutanto, Sylvia H.; Tjiang, Paulus C.

    2011-10-01

    The Gaussian formula and spherical aberrations of static and relativistic curved mirrors are analyzed using the optical path length (OPL) and Fermat's principle. The geometrical figures generated by the rotation of conic sections about their symmetry axes are considered for the shapes of the mirrors. By comparing the results in static and relativistic cases, it is shown that the focal lengths and the spherical aberration relations of the relativistic mirrors obey the Lorentz contraction. Further analysis of the spherical aberrations for both static and relativistic cases have resulted in information about the limits for the paraxial approximation, as well as for the minimum speed of the systems to reduce the spherical aberrations.

  3. Erratum: cosmological parameter estimation: impact of CMB aberration Erratum: cosmological parameter estimation: impact of CMB aberration

    NASA Astrophysics Data System (ADS)

    Catena, Riccardo; Notari, Alessio

    2013-07-01

    The peculiar motion of an observer with respect to the CMB rest frame induces an apparent deflection of the observed CMB photons, i.e. aberration, and a shift in their frequency, i.e. Doppler effect. Both effects distort the temperature multipoles alm's via a mixing matrix at any l. The common lore when performing a CMB based cosmological parameter estimation is to consider that Doppler affects only the l = 1 multipole, and neglect any other corrections. In ref. [1] we checked the validity of this assumption in parameter estimation for a Planck-like angular resolution, both for a full-sky ideal experiment and also when sky cuts are included to model CMB foreground contaminations with a sky fraction similar to the Planck satellite. The result to this analysis was that aberration and Doppler have a sizable impact on a CMB based parameter estimation. In this erratum we correct an error made in ref. [1] when comparing pseudo angular power spectra computed in the CMB rest frame with the ones measured by a moving observer. Properly comparing the two spectra we find now that although the corrections to the Cl due to aberration and Doppler are larger than the cosmic variance at l > 1000 and potentially important, the resulting bias on the parameters is negligible for Planck.

  4. Correlations between corneal and total wavefront aberrations

    NASA Astrophysics Data System (ADS)

    Mrochen, Michael; Jankov, Mirko; Bueeler, Michael; Seiler, Theo

    2002-06-01

    Purpose: Corneal topography data expressed as corneal aberrations are frequently used to report corneal laser surgery results. However, the optical image quality at the retina depends on all optical elements of the eye such as the human lens. Thus, the aim of this study was to investigate the correlations between the corneal and total wavefront aberrations and to discuss the importance of corneal aberrations for representing corneal laser surgery results. Methods: Thirty three eyes of 22 myopic subjects were measured with a corneal topography system and a Tschernig-type wavefront analyzer after the pupils were dilated to at least 6 mm in diameter. All measurements were centered with respect to the line of sight. Corneal and total wavefront aberrations were calculated up to the 6th Zernike order in the same reference plane. Results: Statistically significant correlations (p < 0.05) between the corneal and total wavefront aberrations were found for the astigmatism (C3,C5) and all 3rd Zernike order coefficients such as coma (C7,C8). No statistically significant correlations were found for all 4th to 6th order Zernike coefficients except for the 5th order horizontal coma C18 (p equals 0.003). On average, all Zernike coefficients for the corneal aberrations were found to be larger compared to Zernike coefficients for the total wavefront aberrations. Conclusions: Corneal aberrations are only of limited use for representing the optical quality of the human eye after corneal laser surgery. This is due to the lack of correlation between corneal and total wavefront aberrations in most of the higher order aberrations. Besides this, the data present in this study yield towards an aberration balancing between corneal aberrations and the optical elements within the eye that reduces the aberration from the cornea by a certain degree. Consequently, ideal customized ablations have to take both, corneal and total wavefront aberrations, into consideration.

  5. Array-Based Comparative Genomic Hybridization Analysis Reveals Chromosomal Copy Number Aberrations Associated with Clinical Outcome in Canine Diffuse Large B-Cell Lymphoma

    PubMed Central

    Bresolin, Silvia; Marconato, Laura; Comazzi, Stefano; Te Kronnie, Geertruy; Aresu, Luca

    2014-01-01

    Canine Diffuse Large B-cell Lymphoma (cDLBCL) is an aggressive cancer with variable clinical response. Despite recent attempts by gene expression profiling to identify the dog as a potential animal model for human DLBCL, this tumor remains biologically heterogeneous with no prognostic biomarkers to predict prognosis. The aim of this work was to identify copy number aberrations (CNAs) by high-resolution array comparative genomic hybridization (aCGH) in 12 dogs with newly diagnosed DLBCL. In a subset of these dogs, the genetic profiles at the end of therapy and at relapse were also assessed. In primary DLBCLs, 90 different genomic imbalances were counted, consisting of 46 gains and 44 losses. Two gains in chr13 were significantly correlated with clinical stage. In addition, specific regions of gains and losses were significantly associated to duration of remission. In primary DLBCLs, individual variability was found, however 14 recurrent CNAs (>30%) were identified. Losses involving IGK, IGL and IGH were always found, and gains along the length of chr13 and chr31 were often observed (>41%). In these segments, MYC, LDHB, HSF1, KIT and PDGFRα are annotated. At the end of therapy, dogs in remission showed four new CNAs, whereas three new CNAs were observed in dogs at relapse compared with the previous profiles. One ex novo CNA, involving TCR, was present in dogs in remission after therapy, possibly induced by the autologous vaccine. Overall, aCGH identified small CNAs associated with outcome, which, along with future expression studies, may reveal target genes relevant to cDLBCL. PMID:25372838

  6. Risk estimation based on chromosomal aberrations induced by radiation

    NASA Technical Reports Server (NTRS)

    Durante, M.; Bonassi, S.; George, K.; Cucinotta, F. A.

    2001-01-01

    The presence of a causal association between the frequency of chromosomal aberrations in peripheral blood lymphocytes and the risk of cancer has been substantiated recently by epidemiological studies. Cytogenetic analyses of crew members of the Mir Space Station have shown that a significant increase in the frequency of chromosomal aberrations can be detected after flight, and that such an increase is likely to be attributed to the radiation exposure. The risk of cancer can be estimated directly from the yields of chromosomal aberrations, taking into account some aspects of individual susceptibility and other factors unrelated to radiation. However, the use of an appropriate technique for the collection and analysis of chromosomes and the choice of the structural aberrations to be measured are crucial in providing sound results. Based on the fraction of aberrant lymphocytes detected before and after flight, the relative risk after a long-term Mir mission is estimated to be about 1.2-1.3. The new technique of mFISH can provide useful insights into the quantification of risk on an individual basis.

  7. Primary aberrations for grazing incidence. [in X-ray telescopes

    NASA Technical Reports Server (NTRS)

    Winkler, C. E.; Korsch, D.

    1977-01-01

    Beginning with exact relations between object and image coordinates for a single reflective surface, a systematic analysis of general grazing incidence systems is presented. A complete set of primary aberrations for single-element and two-element systems is developed. The importance of a judicious choice for a coordinate system in showing field curvature to be clearly the predominant aberration for a two-element system is discussed. The validity of the theory is verified through comparisons with the exact ray-trace results for the case of a telescope.

  8. Chromosome aberrations induced by zebularine in triticale.

    PubMed

    Ma, Xuhui; Wang, Qing; Wang, Yanzhi; Ma, Jieyun; Wu, Nan; Ni, Shuang; Luo, Tengxiao; Zhuang, Lifang; Chu, Chenggen; Cho, Seong-Woo; Tsujimoto, Hisashi; Qi, Zengjun

    2016-07-01

    Chromosome engineering is an important approach for generating wheat germplasm. Efficient development of chromosome aberrations will facilitate the introgression and application of alien genes in wheat. In this study, zebularine, a DNA methylation transferase inhibitor, was successfully used to induce chromosome aberrations in the octoploid triticale cultivar Jinghui#1. Dry seeds were soaked in zebularine solutions (250, 500, and 750 μmol/L) for 24 h, and the 500 μmol/L treatment was tested in three additional treatment times, i.e., 12, 36, and 48 h. All treatments induced aberrations involving wheat and rye chromosomes. Of the 920 cells observed in 67 M1 plants, 340 (37.0%) carried 817 aberrations with an average of 0.89 aberrations per cell (range: 0-12). The aberrations included probable deletions, telosomes and acentric fragments (49.0%), large segmental translocations (28.9%), small segmental translocations (17.1%), intercalary translocations (2.6%), long chromosomes that could carry more than one centromere (2.0%), and ring chromosomes (0.5%). Of 510 M2 plants analyzed, 110 (21.6%) were found to carry stable aberrations. Such aberrations included 79 with varied rye chromosome numbers, 7 with wheat and rye chromosome translocations, 15 with possible rye telosomes/deletions, and 9 with complex aberrations involving variation in rye chromosome number and wheat-rye translocations. These indicated that aberrations induced by zebularine can be steadily transmitted, suggesting that zebularine is a new efficient agent for chromosome manipulation. PMID:27334255

  9. [Radioulnar synostosis as characteristic feature of chromosome aberrations (author's transl)].

    PubMed

    Küsswetter, W; Heisel, A

    1981-02-01

    Among 13 patients with congenital proximal radioulnar synostosis the chromosomal analysis revealed a 47, XXY-constellation in an 8 years old boy and a 47, XXX-syndrome in a 12-year-old girl. The investigations show, that the congenital radio-ulnar synostosis may be combined with the chromosome aberration more often than it was commonly thought. PMID:7281903

  10. Correcting aberration in aspheric surfaces

    NASA Astrophysics Data System (ADS)

    Ahmed, K.; Khan, A. N.; Rauf, A.; Gul, A.

    2014-06-01

    New technique eases aspheric lens fabrication and overcome traditional limitation. An aspheric lens has been designed by using optical designing software to replace the achromat (Doublet) lens of eyepiece assembly of telescope. The devised physical parameters of aspheric lens have been incorporated into the CNC Aspheric machine to fabricate the lens. The antireflection coating for visible region has been carried out on lens by employing PVD technique. In this report diminished aberration effects due to non-spherical surface profile and comparison of optical parameters of achromat (doublet) and aspheric lens is presented.

  11. Optimal incision sites to reduce corneal aberration variations after small incision phacoemulsification cataract surgery

    PubMed Central

    Chu, Ling; Zhao, Jiang-Yue; Zhang, Jin-Song; Meng, Jie; Wang, Ming-Wu; Yang, Ya-Jing; Yu, Jia-Ming

    2016-01-01

    AIM To analyze the effect of steep meridian small incision phacoemulsification cataract surgery on anterior, posterior and total corneal wavefront aberration. METHODS Steep meridian small incision phacoemulsification cataract surgery was performed in age-related cataract patients which were divided into three groups according to the incision site: 12 o'clock, 9 o'clock and between 9 and 12 o'clock (BENT) incision groups. The preoperative and 3-month postoperative root mean square (RMS) values of anterior, posterior and total corneal wavefront aberration including coma, spherical aberration, and total higher-order aberrations (HOAs), were measured by Pentacam scheimpflug imaging. The mean preoperative and postoperative corneal wavefront aberrations were documented. RESULTS Total corneal aberration and total lower-order aberrations decreased significantly in three groups after operation. RMS value of total HOAs decreased significantly postoperatively in the 12 o'clock incision group (P<0.001). Corneal spherical aberration was statistically significantly lower after steep meridian small incision phacoemulsification cataract surgery in BENT incision group (P<0.05) and Pearson correlation analysis indicated that spherical aberration changes had no significant relationship with total astigmatism changes in all three corneal incision location. CONCLUSION Corneal incision of phacoemulsification cataract surgery can affect corneal wavefront aberration. The 12 o'clock corneal incision eliminated more HOAs and the spherical aberrations decreased in BENT incision group obviously when we selected steep meridian small incision. Cataract lens replacement using wavefront-corrected intraocular lens combined with optimized corneal incision site would improve ocular aberration results. PMID:27162725

  12. Phase and birefringence aberration correction

    DOEpatents

    Bowers, M.; Hankla, A.

    1996-07-09

    A Brillouin enhanced four wave mixing phase conjugate mirror corrects phase aberrations of a coherent electromagnetic beam and birefringence induced upon that beam. The stimulated Brillouin scattering (SBS) phase conjugation technique is augmented to include Brillouin enhanced four wave mixing (BEFWM). A seed beam is generated by a main oscillator which arrives at the phase conjugate cell before the signal beams in order to initiate the Brillouin effect. The signal beam which is being amplified through the amplifier chain is split into two perpendicularly polarized beams. One of the two beams is chosen to be the same polarization as some component of the seed beam, the other orthogonal to the first. The polarization of the orthogonal beam is then rotated 90{degree} such that it is parallel to the other signal beam. The three beams are then focused into cell containing a medium capable of Brillouin excitation. The two signal beams are focused such that they cross the seed beam path before their respective beam waists in order to achieve BEFWM or the two signal beams are focused to a point or points contained within the focused cone angle of the seed beam to achieve seeded SBS, and thus negate the effects of all birefringent and material aberrations in the system. 5 figs.

  13. Phase and birefringence aberration correction

    DOEpatents

    Bowers, Mark; Hankla, Allen

    1996-01-01

    A Brillouin enhanced four wave mixing phase conjugate mirror corrects phase aberrations of a coherent electromagnetic beam and birefringence induced upon that beam. The stimulated Brillouin scattering (SBS) phase conjugation technique is augmented to include Brillouin enhanced four wave mixing (BEFWM). A seed beam is generated by a main oscillator which arrives at the phase conjugate cell before the signal beams in order to initiate the Brillouin effect. The signal beam which is being amplified through the amplifier chain is split into two perpendicularly polarized beams. One of the two beams is chosen to be the same polarization as some component of the seed beam, the other orthogonal to the first. The polarization of the orthogonal beam is then rotated 90.degree. such that it is parallel to the other signal beam. The three beams are then focused into cell containing a medium capable of Brillouin excitation. The two signal beams are focused such that they cross the seed beam path before their respective beam waists in order to achieve BEFWM or the two signal beams are focused to a point or points contained within the focused cone angle of the seed beam to achieve seeded SBS, and thus negate the effects of all birefringent and material aberrations in the system.

  14. Aberrations of ellipsoidal reflectors for unit magnification.

    PubMed

    Mielenz, K D

    1974-12-01

    Ellipsoidal reflectors are useful for the 1:1 imaging of small objects without spherical and chromatic aberration. The magnitude of the off-axis aberrations of such reflectors is computed by application of Fermat's principle to the Hamiltonian point characteristic. The limiting form of the mirror aperture for which these aberrations do not exceed a set tolerance is an ellipse whose semiaxes depend on object size and angle of incidence. PMID:20134811

  15. Correlation between Post-LASIK Starburst Symptom and Ocular Wavefront Aberrations

    NASA Astrophysics Data System (ADS)

    Liu, Yong-Ji; Mu, Guo-Guang; Wang, Zhao-Qi; Wang-Yan

    2006-06-01

    Monochromatic aberrations in post laser in-situ keratomileusis (LASIK) eyes are measured. The data are categorized into reference group and starburst group according to the visual symptoms. Statistic analysis has been made to find the correlation between the ocular wavefront aberrations and the starburst symptom. The rms aberrations of the 3rd and 4th orders for the starburst group are significantly larger than those for the reference group. The starburst symptom shows a strong correlation with vertical coma, total coma, spherical aberrations. For 3-mm pupil size and 5.8-mm pupil size, the modulation transfer function (MTF) of the starburst group are lower than those of the reference group, but their visual acuities are close. MTF and PSF analyses are made for two groups, and the results are consistent with the statistical analysis, which means the difference between the two groups is mainly due to the third- and fourth-order Zernike aberrations.

  16. Influence of aberrations in microholographic recording

    NASA Astrophysics Data System (ADS)

    Katayama, Ryuichi

    2015-11-01

    The influence of various types of aberrations (spherical, coma, and astigmatic) of recording and readout beams on the readout signal in a microholographic recording was investigated through a numerical simulation. The simulation conditions were that the wavelength of the laser was 405 nm and the numerical aperture of the objective lenses was 0.85. The tolerance of the root-mean-square (RMS) wavefront aberrations was defined as the aberration when the normalized signal level decreased to 0.8. Among the three types of aberrations, the influence of the spherical aberration was the most significant. When both the recording and readout beams were aberrated and the signs of the aberrations were in the worst case, the tolerance of the RMS wavefront aberrations was less than half of the Maréchal's criterion. Moreover, when the RMS wavefront aberrations of the recording and readout beams were within the above tolerance, the bit intervals of 0.13 and 0.65 μm in the inplane and vertical directions, respectively, which correspond to the recording density of 91 bit/μm3 (recording capacity of 16 TB for a 120-mm-diameter optical disk having a 300-μm-thick recording layer), were shown to be feasible for confocal detection with an allowable signal-to-noise ratio.

  17. mBAND and mFISH analysis of chromosomal aberrations and breakpoint distribution in chromosome 1 of AG01522 human fibroblasts that were exposed to radiation of different qualities.

    PubMed

    Berardinelli, F; De Vitis, M; Nieri, D; Cherubini, R; De Nadal, V; Gerardi, S; Tanzarella, C; Sgura, A; Antoccia, A

    2015-11-01

    High-resolution multicolour banding FISH (mBAND) and multiplex FISH (mFISH) were used to analyse the aberrations of chromosome 1 in irradiated-AG01522 human primary fibroblasts. The cells were exposed to 1Gy of a panel of radiation of different qualities, such as X-rays, low-energy protons (28keV/μm), helium-ions (62keV/μm) and carbon-ions (96 and 252keV/μm). mBAND and mFISH analysis in calyculin-A G2-condensed chromosome spreads allowed us to detect intra- and interchromosome aberrations involving chromosome 1, including simple and complex-type exchanges, inversions (both para- and pericentric ones), deletions and rings. The data indicate that the induction of chromosomal exchanges was influenced by both Linear energy transfer (LET) and particle types. Moreover, the complex-to-simple exchanges ratio (C-ratio) and interchromosome to intrachromosome exchanges ratio (F-ratio) were evaluated by mFISH and mBAND techniques, respectively. Our results indicate that the C-ratio is a more reliable marker of radiation quality, with values that increased linearly in an LET-dependent manner. In addition, by means of mBAND analysis, the distribution of radiation-induced breakpoints along chromosome 1 was analyzed and compared with the expected distributions of the breaks. The expected values were calculated assuming a random distribution of the breakpoints. The data indicate that, irrespective of the radiation that was used, the breakpoints were non-randomly distributed along chromosome 1. In particular, breaks in the pericentromeric region were encountered at a higher frequency than expected. A deeper analysis revealed that breaks were not located in the constitutive heterochromatin (G-bands 1p11/1q11 and 1q12), but rather in a region comprised between 1p11.2 and 1p22.1, which includes G-light and G-dark bands. PMID:26520373

  18. Some Useful Correspondences In Aberration Theory

    NASA Astrophysics Data System (ADS)

    Shafer, David

    1986-10-01

    There are many correspondences between the behavior of monochromatic aberrations and chromatic aberrations. Usually the behavior of the chromatic aberrations is of a lower order than the corresponding monochromatic behavior. The cause of the 5th-order mono-chromatic astigmatism, for example, is similar in type to the cause of the chromatic variation of 3rd-order astigmatism. The stop-shift behavior of 3rd-order monochromatic coma is similar to that of first-order lateral color, and so on. These correspondences are interesting for two reasons. One is that they have not been commented on much before, despite the value of one's being aware of these relationships. Methods used to control a monochromatic aberration may also apply to the corresponding chromatic aberration, and vice-versa, for example. The other benefit to studying this topic is that the chromatic aberrations, which are of a lower order than their monochro-matic correspondences, are much easier to understand and visualize. A simple diagram can illustrate the stop-shift behavior of lateral color much more easily than trying to do the same thing with 3rd-order coma. Finally, the very important distinction between intrinsic and induced aberrations can be best illustrated with chromatic aberrations, because of their lower order.

  19. Rooting Out Aberrant Behavior in Training.

    ERIC Educational Resources Information Center

    Kokalis, Jerry, Jr.; Paquin, Dave

    1989-01-01

    Discusses aberrant, or disruptive, behavior in an industrial/business, classroom-based, instructor-led training setting. Three examples of aberrant behavior are described, typical case studies are provided for each, and preventive (long-term) and corrective (on-the-spot) strategies for dealing with the problems are discussed. (LRW)

  20. Harmonic oscillator states in aberration optics

    NASA Technical Reports Server (NTRS)

    Wolf, Kurt Bernardo

    1993-01-01

    The states of the three-dimensional quantum harmonic oscillator classify optical aberrations of axis-symmetric systems due to the isomorphism between the two mathematical structures. Cartesian quanta and angular momentum classifications have their corresponding aberration classifications. The operation of concatenation of optical elements introduces a new operation between harmonic oscillator states.

  1. Aberrant Radial Artery Causing Carpal Tunnel Syndrome

    PubMed Central

    Kokkalis, Zinon T.; Tolis, Konstantinos E.; Megaloikonomos, Panayiotis D.; Panagopoulos, Georgios N.; Igoumenou, Vasilios G.; Mavrogenis, Andreas F.

    2016-01-01

    Anatomical vascular variations are rare causes of carpal tunnel syndrome. An aberrant medial artery is the most common vascular variation, while an aberrant radial artery causing carpal tunnel syndrome is even more rare, with an incidence ranging less than 3%. This article reports a patient with compression of the median nerve at the carpal tunnel by an aberrant superficial branch of the radial artery. An 80- year- old man presented with a 5-year history of right hand carpal tunnel syndrome; Tinel sign, Phalen test and neurophysiological studies were positive. Open carpal tunnel release showed an aberrant superficial branch of the radial artery with its accompanying veins running from radially to medially, almost parallel to the median nerve, ending at the superficial palmar arterial arch. The median nerve was decompressed without ligating the aberrant artery. At the last follow-up, 2 years after diagnosis and treatment the patient is asymptomatic. PMID:27517078

  2. Nodal aberration theory applied to freeform surfaces

    NASA Astrophysics Data System (ADS)

    Fuerschbach, Kyle; Rolland, Jannick P.; Thompson, Kevin P.

    2014-12-01

    When new three-dimensional packages are developed for imaging optical systems, the rotational symmetry of the optical system is often broken, changing its imaging behavior and making the optical performance worse. A method to restore the performance is to use freeform optical surfaces that compensate directly the aberrations introduced from tilting and decentering the optical surfaces. In order to effectively optimize the shape of a freeform surface to restore optical functionality, it is helpful to understand the aberration effect the surface may induce. Using nodal aberration theory the aberration fields induced by a freeform surface in an optical system are explored. These theoretical predications are experimentally validated with the design and implementation of an aberration generating telescope.

  3. Aberrant Radial Artery Causing Carpal Tunnel Syndrome.

    PubMed

    Kokkalis, Zinon T; Tolis, Konstantinos E; Megaloikonomos, Panayiotis D; Panagopoulos, Georgios N; Igoumenou, Vasilios G; Mavrogenis, Andreas F

    2016-06-01

    Anatomical vascular variations are rare causes of carpal tunnel syndrome. An aberrant medial artery is the most common vascular variation, while an aberrant radial artery causing carpal tunnel syndrome is even more rare, with an incidence ranging less than 3%. This article reports a patient with compression of the median nerve at the carpal tunnel by an aberrant superficial branch of the radial artery. An 80- year- old man presented with a 5-year history of right hand carpal tunnel syndrome; Tinel sign, Phalen test and neurophysiological studies were positive. Open carpal tunnel release showed an aberrant superficial branch of the radial artery with its accompanying veins running from radially to medially, almost parallel to the median nerve, ending at the superficial palmar arterial arch. The median nerve was decompressed without ligating the aberrant artery. At the last follow-up, 2 years after diagnosis and treatment the patient is asymptomatic. PMID:27517078

  4. High-resolution genomic analysis suggests the absence of recurrent genomic alterations other than SMARCB1 aberrations in atypical teratoid/rhabdoid tumors.

    PubMed

    Hasselblatt, Martin; Isken, Sarah; Linge, Anna; Eikmeier, Kristin; Jeibmann, Astrid; Oyen, Florian; Nagel, Inga; Richter, Julia; Bartelheim, Kerstin; Kordes, Uwe; Schneppenheim, Reinhard; Frühwald, Michael; Siebert, Reiner; Paulus, Werner

    2013-02-01

    Atypical teratoid/rhabdoid tumor (AT/RT) is a rare malignant pediatric brain tumor characterized by genetic alterations affecting the SMARCB1 (hSNF5/INI1) locus in chromosome band 22q11.2. To identify potential additional genetic alterations, high-resolution genome-wide analysis was performed using a molecular inversion probe single-nucleotide polymorphism (MIP SNP) assay (Affymetrix OncoScan formalin-fixed paraffin-embedded express) on DNA isolated from 18 formalin-fixed paraffin-embedded archival samples. Alterations affecting the SMARCB1 locus could be demonstrated by MIP SNP in 15 out of 16 evaluable cases (94%). These comprised five tumors with homozygous deletions, six tumors with heterozygous deletions, and four tumors with copy number neutral loss of heterozygosity (LOH) involving chromosome band 22q11.2. Remarkably, MIB SNP analysis did not yield any further recurrent chromosomal gains, losses, or copy neutral LOH. On MIP SNP screening for somatic mutations, the presence of a SMARCB1 mutation (c.472C>T p.R158X) was confirmed, but no recurrent mutations of other cancer relevant genes could be identified. Results of fluorescence in situ hybridization, multiplex ligation-dependent probe amplification, and SMARCB1 sequencing were highly congruent with that of the MIP SNP assay. In conclusion, these data further suggest the absence of recurrent genomic alterations other than SMARCB1 in AT/RT. PMID:23074045

  5. Image-based EUVL aberration metrology

    NASA Astrophysics Data System (ADS)

    Fenger, Germain Louis

    A significant factor in the degradation of nanolithographic image fidelity is optical wavefront aberration. As resolution of nanolithography systems increases, effects of wavefront aberrations on aerial image become more influential. The tolerance of such aberrations is governed by the requirements of features that are being imaged, often requiring lenses that can be corrected with a high degree of accuracy and precision. Resolution of lithographic systems is driven by scaling wavelength down and numerical aperture (NA) up. However, aberrations are also affected from the changes in wavelength and NA. Reduction in wavelength or increase in NA result in greater impact of aberrations, where the latter shows a quadratic dependence. Current demands in semiconductor manufacturing are constantly pushing lithographic systems to operate at the diffraction limit; hence, prompting a need to reduce all degrading effects on image properties to achieve maximum performance. Therefore, the need for highly accurate in-situ aberration measurement and correction is paramount. In this work, an approach has been developed in which several targets including phase wheel, phase disk, phase edges, and binary structures are used to generate optical images to detect and monitor aberrations in extreme ultraviolet (EUV) lithographic systems. The benefit of using printed patterns as opposed to other techniques is that the lithography system is tested under standard operating conditions. Mathematical models in conjunction with iterative lithographic simulations are used to determine pupil phase wavefront errors and describe them as combinations of Zernike polynomials.

  6. Aberration correction past and present.

    PubMed

    Hawkes, P W

    2009-09-28

    Electron lenses are extremely poor: if glass lenses were as bad, we should see as well with the naked eye as with a microscope! The demonstration by Otto Scherzer in 1936 that skillful lens design could never eliminate the spherical and chromatic aberrations of rotationally symmetric electron lenses was therefore most unwelcome and the other great electron optician of those years, Walter Glaser, never ceased striving to find a loophole in Scherzer's proof. In the wartime and early post-war years, the first proposals for correcting C(s) were made and in 1947, in a second milestone paper, Scherzer listed these and other ways of correcting lenses; soon after, Dennis Gabor invented holography for the same purpose. These approaches will be briefly summarized and the work that led to the successful implementation of quadupole-octopole and sextupole correctors in the 1990 s will be analysed. In conclusion, the elegant role of image algebra in describing image formation and processing and, above all, in developing new methods will be mentioned. PMID:19687058

  7. Non-Gaussianity and CMB aberration and Doppler

    SciTech Connect

    Catena, Riccardo; Liguori, Michele; Renzi, Alessandro; Notari, Alessio E-mail: michele.liguori@pd.infn.it E-mail: arenzi@pd.infn.it

    2013-09-01

    The peculiar motion of an observer with respect to the CMB rest frame induces a deflection in the arrival direction of the observed photons (also known as CMB aberration) and a Doppler shift in the measured photon frequencies. As a consequence, aberration and Doppler effects induce non trivial correlations between the harmonic coefficients of the observed CMB temperature maps. In this paper we investigate whether these correlations generate a bias on non-Gaussianity estimators f{sub NL}. We perform this analysis simulating a large number of temperature maps with Planck-like resolution (lmax = 2000) as different realizations of the same cosmological fiducial model (WMAP7yr). We then add to these maps aberration and Doppler effects employing a modified version of the HEALPix code. We finally evaluate a generalization of the Komatsu, Spergel and Wandelt non-Gaussianity estimator for all the simulated maps, both when peculiar velocity effects have been considered and when these phenomena have been neglected. Using the value v/c = 1.23 × 10{sup −3} for our peculiar velocity, we found that the aberration/Doppler induced non-Gaussian signal is at most of about half of the cosmic variance σ for f{sub NL} both in a full-sky and in a cut-sky experimental configuration, for local, equilateral and orthogonal estimators. We conclude therefore that when estimating f{sub NL} it is safe to ignore aberration and Doppler effects if the primordial map is already Gaussian. More work is necessary however to assess whether a map which contains non-Gaussianity can be significantly distorted by a peculiar velocity.

  8. Canine urothelial carcinoma: genomically aberrant and comparatively relevant

    PubMed Central

    Shapiro, S. G.; Raghunath, S.; Williams, C.; Motsinger-Reif, A. A.; Cullen, J. M.; Liu, T.; Albertson, D.; Ruvolo, M.; Lucas, A. Bergstrom; Jin, J.; Knapp, D. W.; Schiffman, J. D.

    2015-01-01

    Urothelial carcinoma (UC), also referred to as transitional cell carcinoma (TCC), is the most common bladder malignancy in both human and canine populations. In human UC, numerous studies have demonstrated the prevalence of chromosomal imbalances. Although the histopathology of the disease is similar in both species, studies evaluating the genomic profile of canine UC are lacking, limiting the discovery of key comparative molecular markers associated with driving UC pathogenesis. In the present study, we evaluated 31 primary canine UC biopsies by oligonucleotide array comparative genomic hybridization (oaCGH). Results highlighted the presence of three highly recurrent numerical aberrations: gain of dog chromosome (CFA) 13 and 36 and loss of CFA 19. Regional gains of CFA 13 and 36 were present in 97% and 84% of cases, respectively, and losses on CFA 19 were present in 77% of cases. Fluorescence in situ hybridization (FISH), using targeted bacterial artificial chromosome (BAC) clones and custom Agilent SureFISH probes, was performed to detect and quantify these regions in paraffin-embedded biopsy sections and urine-derived urothelial cells. The data indicate that these three aberrations are potentially diagnostic of UC. Comparison of our canine oaCGH data with that of 285 human cases identified a series of shared copy number aberrations. Using an informatics approach to interrogate the frequency of copy number aberrations across both species, we identified those that had the highest joint probability of association with UC. The most significant joint region contained the gene PABPC1, which should be considered further for its role in UC progression. In addition, cross-species filtering of genome-wide copy number data highlighted several genes as high-profile candidates for further analysis, including CDKN2A, S100A8/9, and LRP1B. We propose that these common aberrations are indicative of an evolutionarily conserved mechanism of pathogenesis and harbor genes key to

  9. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

    PubMed Central

    Biankin, Andrew V.; Waddell, Nicola; Kassahn, Karin S.; Gingras, Marie-Claude; Muthuswamy, Lakshmi B.; Johns, Amber L.; Miller, David K.; Wilson, Peter J.; Patch, Ann-Marie; Wu, Jianmin; Chang, David K.; Cowley, Mark J.; Gardiner, Brooke B.; Song, Sarah; Harliwong, Ivon; Idrisoglu, Senel; Nourse, Craig; Nourbakhsh, Ehsan; Manning, Suzanne; Wani, Shivangi; Gongora, Milena; Pajic, Marina; Scarlett, Christopher J.; Gill, Anthony J.; Pinho, Andreia V.; Rooman, Ilse; Anderson, Matthew; Holmes, Oliver; Leonard, Conrad; Taylor, Darrin; Wood, Scott; Xu, Qinying; Nones, Katia; Fink, J. Lynn; Christ, Angelika; Bruxner, Tim; Cloonan, Nicole; Kolle, Gabriel; Newell, Felicity; Pinese, Mark; Mead, R. Scott; Humphris, Jeremy L.; Kaplan, Warren; Jones, Marc D.; Colvin, Emily K.; Nagrial, Adnan M.; Humphrey, Emily S.; Chou, Angela; Chin, Venessa T.; Chantrill, Lorraine A.; Mawson, Amanda; Samra, Jaswinder S.; Kench, James G.; Lovell, Jessica A.; Daly, Roger J.; Merrett, Neil D.; Toon, Christopher; Epari, Krishna; Nguyen, Nam Q.; Barbour, Andrew; Zeps, Nikolajs; Kakkar, Nipun; Zhao, Fengmei; Wu, Yuan Qing; Wang, Min; Muzny, Donna M.; Fisher, William E.; Brunicardi, F. Charles; Hodges, Sally E.; Reid, Jeffrey G.; Drummond, Jennifer; Chang, Kyle; Han, Yi; Lewis, Lora R.; Dinh, Huyen; Buhay, Christian J.; Beck, Timothy; Timms, Lee; Sam, Michelle; Begley, Kimberly; Brown, Andrew; Pai, Deepa; Panchal, Ami; Buchner, Nicholas; De Borja, Richard; Denroche, Robert E.; Yung, Christina K.; Serra, Stefano; Onetto, Nicole; Mukhopadhyay, Debabrata; Tsao, Ming-Sound; Shaw, Patricia A.; Petersen, Gloria M.; Gallinger, Steven; Hruban, Ralph H.; Maitra, Anirban; Iacobuzio-Donahue, Christine A.; Schulick, Richard D.; Wolfgang, Christopher L.; Morgan, Richard A.; Lawlor, Rita T.; Capelli, Paola; Corbo, Vincenzo; Scardoni, Maria; Tortora, Giampaolo; Tempero, Margaret A.; Mann, Karen M.; Jenkins, Nancy A.; Perez-Mancera, Pedro A.; Adams, David J.; Largaespada, David A.; Wessels, Lodewyk F. A.; Rust, Alistair G.; Stein, Lincoln D.; Tuveson, David A.; Copeland, Neal G.; Musgrove, Elizabeth A.; Scarpa, Aldo; Eshleman, James R.; Hudson, Thomas J.; Sutherland, Robert L.; Wheeler, David A.; Pearson, John V.; McPherson, John D.; Gibbs, Richard A.; Grimmond, Sean M.

    2012-01-01

    Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis. PMID:23103869

  10. Effect of aberrations in vortex spatial filtering

    NASA Astrophysics Data System (ADS)

    Sharma, Manoj Kumar; Joseph, Joby; Senthilkumaran, P.

    2012-11-01

    Edge enhancement is a very important operation in image processing and a spiral phase plate can be used as a radial Hilbert mask for isotropic edge enhancement. In this paper we analyze the effect of various Seidel aberrations on the performance of radial Hilbert mask or the vortex phase mask. The aberrated vortex phase mask is implemented optically with the help of a high resolution, spatial light modulator (SLM). It has also been shown that out of various aberrations astigmatism can introduce anisotropy in the Hilbert mask which causes selective edge enhancement.

  11. Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets.

    PubMed

    Zhang, Lu; Liu, Xiaoqiao; Zhang, Xuegong; Chen, Ronghua

    2016-06-01

    Hepatocellular carcinoma (HCC) is an aggressive and deadly cancer. The molecular pathogenesis of the disease remains poorly understood. To better understand HCC biology and explore potential biomarkers and therapeutic targets, we investigated the whole transcriptome of HCC. Considering the genetic heterogeneity of HCC, four datasets from four studies consisting of 15 pairs of HCC and adjacent normal samples were analyzed. We observed that the number of lncRNAs expressed in each HCC sample was consistently greater than the adjacent normal sample. Moreover, 15 lncRNAs were identified expressed in five to seven HCC tissues but were not detected in any adjacent normal tissue. Differential expression analysis detected 35 up- and 80 down-regulated lncRNAs in HCC samples compared with adjacent normal samples. In addition, five differentially expressed lncRNAs were predicted to play a role in oxidation and reduction process. With regard to splicing alterations, we identified nine highly recurrent differential splicing events belonging to eight genes USO1, RPS24, CCDC50, THNSL2, NUMB, FN1 (two events), SLC39A14 and NR1I3. Of them, splicing alterations of SLC39A14 and NR1I3 were reported for the association with HCC for the first time. The splicing dysregulation in HCC may be influenced by three splicing factors ESRP2, CELF2 and SRSF5 which were significantly down-regulated in HCC samples. This study revealed uncharacterized aspects of HCC transcriptome and identified important lncRNAs and splicing isoforms with the potential to serve as biomarkers and therapeutic targets for the disease. PMID:26711644

  12. Ploidy status and copy number aberrations in primary glioblastomas defined by integrated analysis of allelic ratios, signal ratios and loss of heterozygosity using 500K SNP Mapping Arrays

    PubMed Central

    Gardina, Paul J; Lo, Ken C; Lee, Walter; Cowell, John K; Turpaz, Yaron

    2008-01-01

    Background Genomic hybridization platforms, including BAC-CGH and genotyping arrays, have been used to estimate chromosome copy number (CN) in tumor samples by detecting the relative strength of genomic signal. The methods rely on the assumption that the predominant chromosomal background of the samples is diploid, an assumption that is frequently incorrect for tumor samples. In addition to generally greater resolution, an advantage of genotyping arrays over CGH arrays is the ability to detect signals from individual alleles, allowing estimation of loss-of-heterozygosity (LOH) and allelic ratios to enhance the interpretation of copy number alterations. Copy number events associated with LOH potentially have the same genetic consequences as deletions. Results We have utilized allelic ratios to detect patterns that are indicative of higher ploidy levels. An integrated analysis using allelic ratios, total signal and LOH indicates that many or most of the chromosomes from 24 glioblastoma tumors are in fact aneuploid. Some putative whole-chromosome losses actually represent trisomy, and many apparent sub-chromosomal losses are in fact relative losses against a triploid or tetraploid background. Conclusion These results suggest a re-interpretation of previous findings based only on total signal ratios. One interesting observation is that many single or multiple-copy deletions occur at common putative tumor suppressor sites subsequent to chromosomal duplication; these losses do not necessarily result in LOH, but nonetheless occur in conspicuous patterns. The 500 K Mapping array was also capable of detecting many sub-mega base losses and gains that were overlooked by CGH-BAC arrays, and was superior to CGH-BAC arrays in resolving regions of complex CN variation. PMID:18928532

  13. Image Ellipticity from Atmospheric Aberrations

    SciTech Connect

    de Vries, W H; Olivier, S S; Asztalos, S J; Rosenberg, L J; Baker, K L

    2007-03-06

    We investigate the ellipticity of the point-spread function (PSF) produced by imaging an unresolved source with a telescope, subject to the effects of atmospheric turbulence. It is important to quantify these effects in order to understand the errors in shape measurements of astronomical objects, such as those used to study weak gravitational lensing of field galaxies. The PSF modeling involves either a Fourier transform of the phase information in the pupil plane or a ray-tracing approach, which has the advantage of requiring fewer computations than the Fourier transform. Using a standard method, involving the Gaussian weighted second moments of intensity, we then calculate the ellipticity of the PSF patterns. We find significant ellipticity for the instantaneous patterns (up to more than 10%). Longer exposures, which we approximate by combining multiple (N) images from uncorrelated atmospheric realizations, yield progressively lower ellipticity (as 1/{radical}N). We also verify that the measured ellipticity does not depend on the sampling interval in the pupil plane using the Fourier method. However, we find that the results using the ray-tracing technique do depend on the pupil sampling interval, representing a gradual breakdown of the geometric approximation at high spatial frequencies. Therefore, ray tracing is generally not an accurate method of modeling PSF ellipticity induced by atmospheric turbulence unless some additional procedure is implemented to correctly account for the effects of high spatial frequency aberrations. The Fourier method, however, can be used directly to accurately model PSF ellipticity, which can give insights into errors in the statistics of field galaxy shapes used in studies of weak gravitational lensing.

  14. Transverse chromatic aberration after corneal refractive surgery

    NASA Astrophysics Data System (ADS)

    Anera, R. G.; Jiménez, J. R.; Jiménez del Barco, L.; Hita, E.

    2005-05-01

    An expression has been deduced theoretically from a schematic-eye model, for the transverse or lateral chromatic aberration (TCA) after refractive surgery. The aim was to investigate analytically how chromatic aberration varies after the emmetropization process. These changes in the TCA have been characterized from changes in corneal asphericity. The results indicate that TCA after refractive surgery diminishes as the degree of myopia increases, a trend contrary to that occurring with monochromatic aberrations, such as spherical or coma. These results can explain the fact that the real deterioration of the visual function under photopic conditions detected in those operated on for myopia is less than expected when only monochromatic aberrations are taken into account.

  15. Aberrations of a horizontal-vertical depolarizer

    NASA Technical Reports Server (NTRS)

    Mcclain, Stephen C.; Chipman, Russell A.; Hillman, Lloyd W.

    1992-01-01

    Ray-trace equations for uniaxial birefringent materials are used here to derive third-order estimates for aberrations that are produced in imaging through uniaxial plates and horizontal-vertical (HV) depolarizers. An HV depolarizer is a spatial pseudodepolarizer; it converts a uniform input polarization state into a continuum of spatially varying polarization states in an output beam. An HV depolarizer consists of two birefringent wedges whose crystal axes are crossed at 90 deg. The interface between the wedges is included, which leads to a spatially varying retardance that provides the spatial pseudodepolarization. In HV depolarizers, spherical aberration, astigmatism, and image doubling are the principal aberrations for on-axis objects. Only spherical aberration occurs in isotropic plates, while the presence of birefringent wedges introduces astigmatism and image doubling. It is shown that image separation is proportional to the magnitude of the retardance variation.

  16. Simultaneous and independent adaptive correction of spherical and chromatic aberration using an electron mirror and lens combination.

    PubMed

    Fitzgerald, J P S; Word, R C; Könenkamp, R

    2012-04-01

    We present a theoretical analysis of an electrostatic triode mirror combined with an einzel lens for the correction of spherical and chromatic aberration. We show that this device adaptively corrects spherical and chromatic aberration simultaneously and independently. Chromatic aberration can be compensated over a relative range of -38% to +100%, and spherical aberration over ±100% range. We compare the analytic calculation with a numerical simulation and show that the two descriptions agree to within 5% in the relevant operating regime of the device. PMID:22459116

  17. Sensing Phase Aberrations behind Lyot Coronagraphs

    NASA Astrophysics Data System (ADS)

    Sivaramakrishnan, Anand; Soummer, Rémi; Pueyo, Laurent; Wallace, J. Kent; Shao, Michael

    2008-11-01

    Direct detection of young extrasolar planets orbiting nearby stars can be accomplished from the ground with extreme adaptive optics and coronagraphy in the near-infrared, as long as this combination can provide an image with a dynamic range of 107 after the data are processed. Slowly varying speckles due to residual phase aberrations that are not measured by the primary wave-front sensor are the primary obstacle to achieving such a dynamic range. In particular, non-common optical path aberrations occurring between the wave-front sensor and the coronagraphic occulting spot degrade performance the most. We analyze the passage of both low and high spatial frequency phase ripples, as well as low-order Zernike aberrations, through an apodized pupil Lyot coronagraph in order to demonstrate the way coronagraphic filtering affects various aberrations. We derive the coronagraphically induced cutoff frequency of the filtering and estimate coronagraphic contrast losses due to low-order Zernike aberrations: tilt, astigmatism, defocus, coma, and spherical aberration. Such slowly varying path errors can be measured behind a coronagraph and corrected by a slowly updated optical path delay precompensation or offset asserted on the wave front by the adaptive optics (AO) system. We suggest ways of measuring and correcting all but the lowest spatial frequency aberrations using Lyot plane wave-front data, in spite of the complex interaction between the coronagraph and those mid-spatial frequency aberrations that cause image plane speckles near the coronagraphic focal plane mask occulter's edge. This investigation provides guidance for next-generation coronagraphic instruments currently under construction.

  18. Prediction of Visual Acuity from Wavefront Aberrations

    NASA Technical Reports Server (NTRS)

    Watson, Andrew B. (Inventor); Ahumada, Albert J. (Inventor)

    2013-01-01

    A method for generating a visual acuity metric, based on wavefront aberrations (WFAs), associated with a test subject and representing classes of imperfections, such as defocus, astigmatism, coma and spherical aberrations, of the subject's visual system. The metric allows choices of different image template, can predict acuity for different target probabilities, can incorporate different and possibly subject-specific neural transfer functions, can predict acuity for different subject templates, and incorporates a model of the optotype identification task.

  19. Accommodation to Wavefront Vergence and Chromatic Aberration

    PubMed Central

    Wang, Yinan; Kruger, Philip B.; Li, James S.; Lin, Peter L.; Stark, Lawrence R.

    2011-01-01

    Purpose Longitudinal chromatic aberration (LCA) provides a cue to accommodation with small pupils. However, large pupils increase monochromatic aberrations, which may obscure chromatic blur. In the present study, we examined the effect of pupil size and LCA on accommodation. Methods Accommodation was recorded by infrared optometer while observers (nine normal trichromats) viewed a sinusoidally moving Maltese cross target in a Badal stimulus system. There were two illumination conditions: white (3000 K; 20 cd/m2) and monochromatic (550 nm with 10 nm bandwidth; 20 cd/m2) and two artificial pupil conditions (3 mm and 5.7 mm). Separately, static measurements of wavefront aberration were made with the eye accommodating to targets between 0 and 4 D (COAS, Wavefront Sciences). Results Large individual differences in accommodation to wavefront vergence and to LCA are a hallmark of accommodation. LCA continues to provide a signal at large pupil sizes despite higher levels of monochromatic aberrations. Conclusions Monochromatic aberrations may defend against chromatic blur at high spatial frequencies, but accommodation responds best to optical vergence and to LCA at 3 c/deg where blur from higher order aberrations is less. PMID:21317666

  20. Study on intra-ocular lens aberration measurement in-air

    NASA Astrophysics Data System (ADS)

    Wang, Yuanyuan; Chen, Jiaojie; Fen, Haihua; Hu, Chuan; Li, Yiyi

    2010-10-01

    In clinical ophthalmology, the wavefront aberration of human eyes is expressed by Zernike polynomial after cataract surgery and intraocular lens implantation, the human eyes aberration will change. The problem of objective evaluation of wavefront aberration introduced by the Intra-ocular (IOL) in-vivo remains unsolved. This paper introduced the measurement principal of IOL wavefront aberration with expression by Zernike polynominal in air. A Hartmann-Shack wavefront sensor system was constructed to measure the wavefront of IOL and to get the corresponding grid patterns. After a series of computer image processing steps, 7th order with 35 items Zernike coefficients was obtained. The IOL of 20.0D power was measured 5 times by this system to get the spherical aberration about 6.73+/-0.02μm, demonstrating the good repeatability of the system. Ten IOLs with the same 20.0D power but difference in surface curvature were chosen for measurement. The spherical aberration observed were in the range of 2.74μm-11.26μm. These results are valuable for the optical design of IOLs and the aberration analysis of human eyes post-operation.

  1. Depth aberrations characterization in linear and nonlinear microscopy schemes using a Shack-Hartmann wavefront sensor

    NASA Astrophysics Data System (ADS)

    Aviles-Espinosa, Rodrigo; Andilla, Jordi; Porcar-Guezenec, Rafael; Levecq, Xavier; Artigas, David; Loza-Alvarez, Pablo

    2012-03-01

    The performance of imaging devices such as linear and nonlinear microscopes (NLM) can be limited by the optical properties of the imaged sample. Such an important aspect has already been described using theoretical models due to the difficulties of implementing a direct wavefront sensing scheme. However, these only stand for simple interfaces and cannot be generalized to biological samples given its structural complexity. This has leaded to the development of sensor-less adaptive optics (AO) implementations. In this approach, aberrations are iteratively corrected trough an image related parameter (aberrations are not measured), being prone of causing sample damage. In this work, we perform a practical implementation of a Shack-Hartman wavefront sensor to compensate for sample induced aberrations, demonstrating its applicability in linear and NLM. We perform an extensive analysis of wavefront distortion effects through different depths employing phantom samples. Aberration effects originated by the refractive index mismatch and depth are quantified using the linear and nonlinear guide-star concept. More over we analyze offaxis aberrations in NLM, an important aspect that is commonly overlooked. In this case spherical aberration behaves similarly to the wavefront error compared with the on-axis case. Finally we give examples of aberration compensation using epi-fluorescence and nonlinear microscopy.

  2. Cytogenetic heterogeneity and their serial dynamic changes during acquisition of cytogenetic aberrations in cultured mesenchymal stem cells.

    PubMed

    Kim, Jung-Ah; Im, Kyong Ok; Park, Si Nae; Kwon, Ji Seok; Kim, Seon Young; Oh, Keunhee; Lee, Dong-Sup; Kim, Min Kyung; Kim, Seong Who; Jang, Mi; Lee, Gene; Oh, Yeon-Mok; Lee, Sang Do; Lee, Dong Soon

    2015-07-01

    To minimize the risk of tumorigenesis in mesenchymal stem cells (MSCs), G-banding analysis is widely used to detect chromosomal aberrations in MSCs. However, a critical limitation of G-banding is that it only reflects the status of metaphase cells, which can represent as few as 0.01% of tested cells. During routine cytogenetic testing in MSCs, we often detect chromosomal aberrations in minor cell populations. Therefore, we aimed to investigate whether such a minority of cells can expand over time or if they ultimately disappear during MSC passaging. We passaged MSCs serially while monitoring quantitative changes for each aberrant clone among heterogeneous MSCs. To investigate the cytogenetic status of interphase cells, which represent the main population, we also performed interphase FISH analysis, in combination with G-banding and telomere length determination. In human adipose tissue-derived MSCs, 4 types of chromosomal aberrations were found during culturing, and in umbilical cord MSCs, 2 types of chromosomal aberrations were observed. Sequential dynamic changes among heterogeneous aberrant clones during passaging were similar to the dynamic changes observed in cancer stem cells during disease progression. Throughout all passages, the quantitative G-banding results were inconsistent with those of the interphase FISH analysis. Interphase FISH revealed hidden aberrations in stem cell populations with normal karyotypes by G-banding analysis. We found that telomere length gradually decreased during passaging until the point at which cytogenetic aberrations appeared. The present study demonstrates that rare aberrant clones at earlier passages can become predominant clones during later passages. Considering the risk of tumorigenesis due to aberrant MSCs, we believe that our results will help to establish proper safety guidelines for MSC use. In particular, we believe it is critical to test for chromosomal aberrations using both G-banding and FISH to ensure the safety

  3. Development of a combined chemical and enzymatic approach for the mass spectrometric identification and quantification of aberrant N-glycosylation.

    PubMed

    Chen, Rui; Wang, Fangjun; Tan, Yexiong; Sun, Zhen; Song, Chunxia; Ye, Mingliang; Wang, Hongyang; Zou, Hanfa

    2012-02-16

    Direct mass spectrometric analysis of aberrant protein glycosylation is a challenge to the current analytical techniques. Except lectin affinity chromatography, no other glycosylation enrichment techniques are available for analysis of aberrant glycosylation. In this study, we developed a combined chemical and enzymatic strategy as an alternative for the mass spectrometric analysis of aberrant glycosylation. Sialylated glycopeptides were enriched with reverse glycoblotting, cleaved by endoglycosidase F3 and analyzed by mass spectrometry with both neutral loss triggered MS(3) in collision induced dissociation (CID) and electron transfer dissociation (ETD). Interestingly, a great part of resulted glycopeptides were found with fucose attached to the N-acetylglucosamine (N-GlcNAc), which indicated that the aberrant glycosylation that is carrying both terminal sialylation and core fucosylation was identified. Totally, 69 aberrant N-glycosylation sites were identified in sera samples from hepatocellular carcinoma (HCC) patients. Following the identification, quantification of the level of this aberrant glycosylation was also carried out using stable isotope dimethyl labeling and pooled sera sample from liver cirrhosis and HCC was compared. Six glycosylation sites demonstrated elevated level of aberrancy, which demonstrated that our developed strategy was effective in both qualitative and quantitative studies of aberrant glycosylation. PMID:22202184

  4. Multiple aberrant hormone receptors in Cushing's syndrome.

    PubMed

    El Ghorayeb, Nada; Bourdeau, Isabelle; Lacroix, André

    2015-10-01

    The mechanisms regulating cortisol production when ACTH of pituitary origin is suppressed in primary adrenal causes of Cushing's syndrome (CS) include diverse genetic and molecular mechanisms. These can lead either to constitutive activation of the cAMP system and steroidogenesis or to its regulation exerted by the aberrant adrenal expression of several hormone receptors, particularly G-protein coupled hormone receptors (GPCR) and their ligands. Screening for aberrant expression of GPCR in bilateral macronodular adrenal hyperplasia (BMAH) and unilateral adrenal tumors of patients with overt or subclinical CS demonstrates the frequent co-expression of several receptors. Aberrant hormone receptors can also exert their activity by regulating the paracrine secretion of ACTH or other ligands for those receptors in BMAH or unilateral tumors. The aberrant expression of hormone receptors is not limited to adrenal CS but can be implicated in other endocrine tumors including primary aldosteronism and Cushing's disease. Targeted therapies to block the aberrant receptors or their ligands could become useful in the future. PMID:25971648

  5. Aberration in proper motions for Galactic stars

    NASA Astrophysics Data System (ADS)

    Liu, J.-C.; Xie, Y.; Zhu, Z.

    2014-12-01

    Accelerations of both the solar system barycenter (SSB) and stars in the MilkyWay cause a systematic observational effect on the stellar proper motions, which was first studied by J. Kovalevsky (2003). This paper intends to extend that work and aims to estimate the magnitude and significance of the aberration in proper motions of stars, especially in the region near the Galactic center (GC). We adopt two models for the Galactic rotation curve to evaluate the aberrational effect on the Galactic plane. We show that the effect of aberration in proper motions depends on the galactocentric distance of stars; it is dominated by the acceleration of stars in the central region of the Galaxy. Then we investigate the applicability of the theoretical expressions: if the orbital period of stars is only a fraction of the light time from the star to the SSB, the expression with approximation proposed by Kovalevsky is not appropriate. With a more suitable formulation, we found that the aberration has no effect on the determination of the stellar orbits on the celestial sphere. In the future this aberrational effect under consideration should be considered with high-accurate astrometry, particularly in constructing the Gaia celestial reference system realized by Galactic stars.

  6. Coma aberrations in combined two- and three-dimensional STED nanoscopy

    PubMed Central

    Antonello, Jacopo; Kromann, Emil B.; Burke, Daniel; Bewersdorf, Joerg; Booth, Martin J.

    2016-01-01

    Stimulated emission depletion (STED) microscopes, like all super-resolution methods, are sensitive to aberrations. Of particular importance are aberrations that affect the quality of the depletion focus, which requires a point of near-zero intensity surrounded by strong illumination. We present analysis, modeling, and experimental measurements that show the effects of coma aberrations on depletion patterns of two-dimensional (2D) and three-dimensional (3D) STED configurations. Specifically, we find that identical coma aberrations create focal shifts in opposite directions in 2D and 3D STED. This phenomenon could affect the precision of microscopic measurements and has ramifications for the efficacy of combined 2D/3D STED systems. PMID:27472636

  7. Identification of Genomic Aberrations in Cancer Subclones from Heterogeneous Tumor Samples.

    PubMed

    Xia, Hong; Liu, Yuanning; Wang, Minghui; Li, Ao

    2015-01-01

    Tumor samples are usually heterogeneous, containing admixture of more than one kind of tumor subclones. Studies of genomic aberrations from heterogeneous tumor data are hindered by the mixed signal of tumor subclone cells. Most of the existing algorithms cannot distinguish contributions of different subclones from the measured single nucleotide polymorphism (SNP) array signals, which may cause erroneous estimation of genomic aberrations. Here, we have introduced a computational method, Cancer Heterogeneity Analysis from SNP-array Experiments (CHASE), to automatically detect subclone proportions and genomic aberrations from heterogeneous tumor samples. Our method is based on HMM, and incorporates EM algorithm to build a statistical model for modeling mixed signal of multiple tumor subclones. We tested the proposed approach on simulated datasets and two real datasets, and the results show that the proposed method can efficiently estimate tumor subclone proportions and recovery the genomic aberrations. PMID:26357278

  8. Observation of lens aberrations for high resolution electron microscopy II: simple expressions for optimal estimates.

    PubMed

    Saxton, W Owen

    2015-04-01

    This paper lists simple closed-form expressions estimating aberration coefficients (defocus, astigmatism, three-fold astigmatism, coma / misalignment, spherical aberration) on the basis of image shift or diffractogram shape measurements as a function of injected beam tilt. Simple estimators are given for a large number of injected tilt configurations, optimal in the sense of least-squares fitting of all the measurements, and so better than most reported previously. Standard errors are given for most, allowing different approaches to be compared. Special attention is given to the measurement of the spherical aberration, for which several simple procedures are given, and the effect of foreknowledge of this on other aberration estimates is noted. Details and optimal expressions are also given for a new and simple method of analysis, requiring measurements of the diffractogram mirror axis direction only, which are simpler to make than the focus and astigmatism measurements otherwise required. PMID:25728295

  9. Coma aberrations in combined two- and three-dimensional STED nanoscopy.

    PubMed

    Antonello, Jacopo; Kromann, Emil B; Burke, Daniel; Bewersdorf, Joerg; Booth, Martin J

    2016-08-01

    Stimulated emission depletion (STED) microscopes, like all super-resolution methods, are sensitive to aberrations. Of particular importance are aberrations that affect the quality of the depletion focus, which requires a point of near-zero intensity surrounded by strong illumination. We present analysis, modeling, and experimental measurements that show the effects of coma aberrations on depletion patterns of two-dimensional (2D) and three-dimensional (3D) STED configurations. Specifically, we find that identical coma aberrations create focal shifts in opposite directions in 2D and 3D STED. This phenomenon could affect the precision of microscopic measurements and has ramifications for the efficacy of combined 2D/3D STED systems. PMID:27472636

  10. Modeling aberrations in the Advanced Camera for Surveys

    NASA Astrophysics Data System (ADS)

    Houairi, K.; Casertano, S.; Lallo, M.; Makidon, R. B.

    2006-10-01

    We present an analysis of the optical model for HST and ACS that shows the possible impact of misalignments of various optical elements on apparent image aberrations. The analysis was aimed at identifying possible causes for apparent variations in coma and astigmatism seen on orbital time scales in HST images. Results indicate that any combinations of mirrors and motions that reproduce the observed coma and astigmatism changes, also predict either large shifts in the image, which is not observed, or require unrealistically large movements of the elements.

  11. Properties of second-order geometrical aberrations

    NASA Astrophysics Data System (ADS)

    Grammatin, A. P.

    1994-08-01

    This paper analyzes the properties of second-order aberrations that arise in centered optical systems that contain an aspherical surface whose sagittal equation contains a term proportional to the cube of the distance from a surface point to the optical axis. It is shown that the second-order spherical aberration decreases from the center of the field to its edge. No astigmatism appears in wide, oblique beams in the central part of the field. Coma increases linearly from zero at the center of the field to a value equal to the spherical aberration, and then remains constant over the field. A proof is given of the possibility of correcting the image curvature by using an aspherical surface of the type described above.

  12. Optical mechanism for aberration of starlight.

    PubMed

    Woodruff, Robert A

    2012-07-01

    We present a physical-optics-based theory for aberration of starlight and show that the influence of the moving sensor on the incident stellar wavefront combined with a finite velocity of light within the sensor can fully account for the aberration phenomena. Our treatment differs from all previous derivations because we include wavefront-imaging physics within the sensor model. Our predictions match existing Earth-based aberration measurements but differ from predictions of the special relativistic-based theory for larger velocities. We derive design parameters for an experiment using an Earth-based sensor containing a refractive optical medium that would experimentally differentiate between these two theories and yield an independent experimental test of time dilation. PMID:22751386

  13. An aberrant precision account of autism

    PubMed Central

    Lawson, Rebecca P.; Rees, Geraint; Friston, Karl J.

    2014-01-01

    Autism is a neurodevelopmental disorder characterized by problems with social-communication, restricted interests and repetitive behavior. A recent and thought-provoking article presented a normative explanation for the perceptual symptoms of autism in terms of a failure of Bayesian inference (Pellicano and Burr, 2012). In response, we suggested that when Bayesian inference is grounded in its neural instantiation—namely, predictive coding—many features of autistic perception can be attributed to aberrant precision (or beliefs about precision) within the context of hierarchical message passing in the brain (Friston et al., 2013). Here, we unpack the aberrant precision account of autism. Specifically, we consider how empirical findings—that speak directly or indirectly to neurobiological mechanisms—are consistent with the aberrant encoding of precision in autism; in particular, an imbalance of the precision ascribed to sensory evidence relative to prior beliefs. PMID:24860482

  14. Aberrant immunophenotypes of mantle cell lymphomas.

    PubMed

    Wohlschlaeger, Ch; Lange, K; Merz, H; Feller, A C

    2003-02-01

    Mantle cell lymphomas (MCL) are characterized by cytomorphological criteria, a distinct immunophenotype and a characteristic chromosomal aberration (t(11;14)). In morphological variants of MCL the immunohistochemical constellation with CD5-positivity and CD23-negativity is a helpful and decisive diagnostic aid to differentiate MCL from other B-cell-lymphomas, e.g. lymphocytic lymphomas (B-CLL). In this study the morphological, immunophenotypical, and genetical features of 50 MCL were analysed. Five cases revealed an aberrant immunophenotype with lacking expression of CD5 (n = 3) and positive reactivity to CD23 (n = 2) while cyclin D1 expression could be demonstrated in all 5 cases. These constellations show that there is, besides morphological subgroups, a small group of MCL with aberrant immunophenotypes, which has to be taken into account in the differential diagnosis to lymphocytic lymphoma and other lymphomas. PMID:12688344

  15. VLBI measurement of the secular aberration drift

    NASA Astrophysics Data System (ADS)

    Titov, O.; Lambert, S. B.; Gontier, A.-M.

    2011-05-01

    Aims: While analyzing decades of very long baseline interferometry (VLBI) data, we detected the secular aberration drift of the extragalatic radio source proper motions caused by the rotation of the Solar System barycenter around the Galactic center. Our results agree with the predicted estimate to be 4-6 micro arcseconds per year (μas/yr) towards α = 266° and δ = -29°. In addition, we tried to detect the quadrupole systematics of the velocity field. Methods: The analysis method consisted of three steps. First, we analyzed geodetic and astrometric VLBI data to produce radio source coordinate time series. Second, we fitted proper motions of 555 sources with long observational histories over the period 1990-2010 to their respective coordinate time series. Finally, we fitted vector spherical harmonic components of degrees 1 and 2 to the proper motion field. Results: Within the error bars, the magnitude and the direction of the dipole component agree with predictions. The dipole vector has an amplitude of 6.4 ± 1.5 μas/yr and is directed towards equatorial coordinates α = 263° and δ = -20°. The quadrupole component has not been detected. The primordial gravitational wave density, integrated over a range of frequencies less than 10-9 Hz, has a limit of 0.0042h-2 where h is the normalized Hubble constant is H0/(100 km s-1). We dedicate this work to the memory of Anne-Marie Gontier, our colleague and personal friend, and a widely recognized specialist of VLBI. She passed away shortly after this paper was submitted.Proper motion data is only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/529/A91

  16. Aberrations of diffracted wave fields. II. Diffraction gratings.

    PubMed

    Mahajan, V N

    2000-12-01

    The Rayleigh-Sommerfeld theory is applied to diffraction of a spherical wave by a grating. The grating equation is obtained from the aberration-free diffraction pattern, and its aberrations are shown to be the same as the conventional aberrations obtained by using Fermat's principle. These aberrations are shown to be not associated with the diffraction process. Moreover, it is shown that the irradiance distribution of a certain diffraction order is the Fraunhofer diffraction pattern of the grating aperture as a whole aberrated by the aberration of that order. PMID:11140481

  17. Aberration averaging using point spread function for scanning projection systems

    NASA Astrophysics Data System (ADS)

    Ooki, Hiroshi; Noda, Tomoya; Matsumoto, Koichi

    2000-07-01

    Scanning projection system plays a leading part in current DUV optical lithography. It is frequently pointed out that the mechanically induced distortion and field curvature degrade image quality after scanning. On the other hand, the aberration of the projection lens is averaged along the scanning direction. This averaging effect reduces the residual aberration significantly. The aberration averaging based on the point spread function and phase retrieval technique in order to estimate the effective wavefront aberration after scanning is described in this paper. Our averaging method is tested using specified wavefront aberration, and its accuracy is discussed based on the measured wavefront aberration of recent Nikon projection lens.

  18. Use of field aberrations in the alignment of the Large Binocular Telescope optics

    NASA Astrophysics Data System (ADS)

    Rakich, A.; Hill, J. M.; Biddick, C. J.; Miller, D. L.; Leibold, T.

    2008-07-01

    It is now well-known that measurement of field-aberration, and in particular the asymmetric field-astigmatism, is required to break the degeneracy of tip-induced and de-centre-induced aberration that exists when only on-axis misalignment aberrations are considered. This paper discusses the application of the measurement of field-aberrations to the alignment of LBT optics. This application ranges from the use of wide field out-of-focus images to determine corrector tip for the red and blue prime-focus correctors, to the use of data acquired by off-axis Shack-Hartman wavefront sensors to actively reposition the hexapod-mounted primary and secondary mirrors so as to simultaneously remove both de-centre and tip/tilt such that the only remaining field-astigmatism has rotational symmetry about the centre of the detector. Also introduced is a novel method to calculate the misalignment aberrations based on an extension of the plate-diagram analysis. It is shown that this method is readily applicable to the calculation of misalignment aberrations for systems of three-or-more powered mirrors, with almost no more computational difficulty than that of the two-mirror case. Results are discussed, as well as work in progress in this area.

  19. On-line measurement of wavefront aberration on optics caused by intense lasers

    NASA Astrophysics Data System (ADS)

    Xu, Zuodong; Liu, Fuhua; Jiang, Chang; Wang, Fei; Shao, Bibo; Ji, Yunfeng

    2015-05-01

    It is presented that the thermally induced transmitted wavefront aberration of a high-reflectivity sampling mirror was detected on line using a Shack-Hartmann wavefront sensor (SHWS) in the beam quality measurement of an intense laser. As a result of heat absorption in the sampling mirror with active aperture of 120 mm, thermally induced wavefront aberration emerged when the mirror was exposed to high laser intensity of several kilowatts per centimeter square. Time-dependent wavefront aberration curves were acquired, and the transmitted wavefronts were reconstructed based on Zernike mode reconstruction theory. The experimental results indicate that the magnitude of the dynamic transmitted wavefront aberration increases gradually with the growing heat deposit during laser irradiation. The maximum of wavefront aberration observed after irradiation for 5 seconds reaches 0.11 μm of root-mean-square value. After further analysis, the experimental results of dynamic aberration can be applied in modifications for the measurement results of intense laser beam quality or tests for the thermal stability of optics used in the intense laser systems.

  20. Designing refractive beam shapers via aberration theory

    NASA Astrophysics Data System (ADS)

    Laskin, Alexander; Shealy, David

    2014-10-01

    In this paper, we use aberration theory to design a refractive laser beam shaper in the configuration of two-aspheric lenses, whose analytical equations are known, but rather complicated. Specifically, we use results from third order aberration theory to obtain the parameters of the refracting laser beam shaper from the transverse aberration, which are then used as a starting point for further optimization by using optical design software. This approach was developed during the beginning of the twentieth century, works well for systems with a low numerical aperture, and allows one to define the following parameters of an optical system: radii of curvature, indices of refraction, thicknesses or air gaps, and conic constants of second order aspheric surfaces. We shall consider surfaces of the second-order spherical and conic sections and shall consider the example of designing of a two-lens beam shaper of the Keplerian 1-to-1 telescopic design providing a theoretical flat phase front and a flat-top irradiance profile of the output beam, where the ray mapping function from the input aperture to the output aperture is known from the literature. Explicit expression for third order longitudinal aberration and the Seidel coefficients are expressed in terms beam waist and input beam geometrical parameter, indices, lens radii and conic constants.

  1. Aberration features in directional dark matter detection

    SciTech Connect

    Bozorgnia, Nassim; Gelmini, Graciela B.; Gondolo, Paolo E-mail: gelmini@physics.ucla.edu

    2012-08-01

    The motion of the Earth around the Sun causes an annual change in the magnitude and direction of the arrival velocity of dark matter particles on Earth, in a way analogous to aberration of stellar light. In directional detectors, aberration of weakly interacting massive particles (WIMPs) modulates the pattern of nuclear recoil directions in a way that depends on the orbital velocity of the Earth and the local galactic distribution of WIMP velocities. Knowing the former, WIMP aberration can give information on the latter, besides being a curious way of confirming the revolution of the Earth and the extraterrestrial provenance of WIMPs. While observing the full aberration pattern requires extremely large exposures, we claim that the annual variation of the mean recoil direction or of the event counts over specific solid angles may be detectable with moderately large exposures. For example, integrated counts over Galactic hemispheres separated by planes perpendicular to Earth's orbit would modulate annually, resulting in Galactic Hemisphere Annual Modulations (GHAM) with amplitudes larger than the usual non-directional annual modulation.

  2. Cosmological parameter estimation: impact of CMB aberration

    NASA Astrophysics Data System (ADS)

    Catena, Riccardo; Notari, Alessio

    2013-04-01

    The peculiar motion of an observer with respect to the CMB rest frame induces an apparent deflection of the observed CMB photons, i.e. aberration, and a shift in their frequency, i.e. Doppler effect. Both effects distort the temperature multipoles alm's via a mixing matrix at any l. The common lore when performing a CMB based cosmological parameter estimation is to consider that Doppler affects only the l = 1 multipole, and neglect any other corrections. In this paper we reconsider the validity of this assumption, showing that it is actually not robust when sky cuts are included to model CMB foreground contaminations. Assuming a simple fiducial cosmological model with five parameters, we simulated CMB temperature maps of the sky in a WMAP-like and in a Planck-like experiment and added aberration and Doppler effects to the maps. We then analyzed with a MCMC in a Bayesian framework the maps with and without aberration and Doppler effects in order to assess the ability of reconstructing the parameters of the fiducial model. We find that, depending on the specific realization of the simulated data, the parameters can be biased up to one standard deviation for WMAP and almost two standard deviations for Planck. Therefore we conclude that in general it is not a solid assumption to neglect aberration in a CMB based cosmological parameter estimation.

  3. Determining the accommodative response from wavefront aberrations.

    PubMed

    Tarrant, Janice; Roorda, Austin; Wildsoet, Christine F

    2010-01-01

    The purpose of this study was to evaluate some of the methods used to calculate objective refractions from wavefront aberrations, to determine their applicability for accommodation research. A wavefront analyzer was used to measure the ocular aberrations of 13 emmetropes and 17 myopes at distance, and 4 near target vergences: 2, 3, 4, and 5 D. The accommodative response was calculated using the following techniques: least squares fitting (Zernike defocus), paraxial curvature matching (Seidel defocus), and 5 optical quality metrics (PFWc, PFSc, PFCc, NS, and VSMTF). We also evaluated a task-specific method of determining optimum focus that used a through-focus procedure to select the image that best optimized both contrast amplitude and gradient (CAG). Neither Zernike nor Seidel defocus appears to be the best method for determining the accommodative response from wavefront aberrations. When the eye has negative spherical aberration, Zernike defocus tends to underestimate, whereas Seidel defocus tends to overestimate the accommodative response. A better approach is to first determine the best image plane using a suitable optical quality metric and then calculate the accommodative error relative to this plane. Of the metrics evaluated, both NS and VSMTF were reasonable choices, with the CAG algorithm being a less preferred alternate. PMID:20616123

  4. Cosmological parameter estimation: impact of CMB aberration

    SciTech Connect

    Catena, Riccardo; Notari, Alessio E-mail: notari@ffn.ub.es

    2013-04-01

    The peculiar motion of an observer with respect to the CMB rest frame induces an apparent deflection of the observed CMB photons, i.e. aberration, and a shift in their frequency, i.e. Doppler effect. Both effects distort the temperature multipoles a{sub lm}'s via a mixing matrix at any l. The common lore when performing a CMB based cosmological parameter estimation is to consider that Doppler affects only the l = 1 multipole, and neglect any other corrections. In this paper we reconsider the validity of this assumption, showing that it is actually not robust when sky cuts are included to model CMB foreground contaminations. Assuming a simple fiducial cosmological model with five parameters, we simulated CMB temperature maps of the sky in a WMAP-like and in a Planck-like experiment and added aberration and Doppler effects to the maps. We then analyzed with a MCMC in a Bayesian framework the maps with and without aberration and Doppler effects in order to assess the ability of reconstructing the parameters of the fiducial model. We find that, depending on the specific realization of the simulated data, the parameters can be biased up to one standard deviation for WMAP and almost two standard deviations for Planck. Therefore we conclude that in general it is not a solid assumption to neglect aberration in a CMB based cosmological parameter estimation.

  5. Anti-forensics of chromatic aberration

    NASA Astrophysics Data System (ADS)

    Mayer, Owen; Stamm, Matthew C.

    2015-03-01

    Over the past decade, a number of information forensic techniques have been developed to identify digital image manipulation and falsification. Recent research has shown, however, that an intelligent forger can use anti-forensic countermeasures to disguise their forgeries. In this paper, an anti-forensic technique is proposed to falsify the lateral chromatic aberration present in a digital image. Lateral chromatic aberration corresponds to the relative contraction or expansion between an image's color channels that occurs due to a lens's inability to focus all wavelengths of light on the same point. Previous work has used localized inconsistencies in an image's chromatic aberration to expose cut-and-paste image forgeries. The anti-forensic technique presented in this paper operates by estimating the expected lateral chromatic aberration at an image location, then removing deviations from this estimate caused by tampering or falsification. Experimental results are presented that demonstrate that our anti-forensic technique can be used to effectively disguise evidence of an image forgery.

  6. Optical advantages of astigmatic aberration corrected heliostats

    NASA Astrophysics Data System (ADS)

    van Rooyen, De Wet; Schöttl, Peter; Bern, Gregor; Heimsath, Anna; Nitz, Peter

    2016-05-01

    Astigmatic aberration corrected heliostats adapt their shape in dependence of the incidence angle of the sun on the heliostat. Simulations show that this optical correction leads to a higher concentration ratio at the target and thus in a decrease in required receiver aperture in particular for smaller heliostat fields.

  7. Corneal Aberrations Before and After Photorefractive Keratectomy

    PubMed Central

    Rosa, Nicola; De Bernardo, Maddalena; Lanza, Michele; Borrelli, Maria; Fusco, Fabrizia; Flagiello, Antimo

    2010-01-01

    Purpose To determine whether - and which - higher-order corneal aberrations, up to the sixth order, are induced by photorefractive keratectomy (PRK). Methods 197 eyes of 197 patients have been examined with a corneal aberrometer for a 3.5 and a 6.0 mm pupil simulation, both before and 1, 3, 6 months after myopic PRK treatment ranging from −15.25 D to -0.5 D (mean −5.31±2.95 D). The statistical evaluation was performed using a paired Student's T-test. Results After PRK there is a clear-cut increase in almost all the higher-order corneal aberrations for both a 3.5 and a 6.0 mm pupil simulation. These aberrations tend to normalize after 3 and 6 months mainly for a 3.5 mm simulation, whereas such normalization is not present for a 6.0 mm simulation. Conclusions PRK induces significant aberrations both for 3.5 and 6 mm pupils, 1 month after PRK, but a trend towards normalization is evident at the 6 month follow-up for the smaller pupil size.

  8. Research on stitching interferometry aspheric surface with correcting systemic aberration

    NASA Astrophysics Data System (ADS)

    Qiao, Yujing; Han, Guihua

    2010-10-01

    Sub-aperture stitching interferometry was originally used for measurement of large-diameter plane and spherical, it is a technological means that uses small-caliber interferometer to test each parts of optical component, and then all the subaperture data are combined or stitched together to create a map of the full surface. Correcting adjust errors of three directions is currently stitching algorithm for realizing the stitching testing aspheric surface. But without spatial analysis for bias errors of positioning mechanism, we can't know exactly the actual appearance of bias errors, consequently will not be able to implement a accuracy stitching.. Because the accuracy of individual stitching can't meet the accuracy requirements, the test result of stitching interferometry aspheric surface will not meet requirements of accuracy due to the errors accumulation. Correcting systemic aberration method is presented to solve the problem mentioned above. It is based on the analysis of the actual impact appearance of location components' bias error in interferometry. The actual appearance is exactly the same after comparing with the Seidle aberration. a correction bias errors model of stitching measure is found based on the analysis, and it proposed an accuracy stitching measurement for quadric surface measurement. It gets the stitching coefficients with least square fitting method, and acquires the estimate values of bias errors in sub-aperture stitching components, and corrects the high-order systemic aberration, therefore improve the fitting accuracy in sub-apertures overlap zone. The experiment result shows, the stitching accuracy of this stitching method is higher than traditional stitching method.

  9. Primary aberrations in focused radially polarized vortex beams

    NASA Astrophysics Data System (ADS)

    Biss, David P.; Brown, T. G.

    2004-02-01

    We study the effect of primary aberrations on the 3-D polarization of the electric field in a focused lowest order radially polarized beam. A full vector diffraction treatment of the focused beams is used. Attention is given to the effects of primary spherical, astigmatic, and comatic aberrations on the local polarization, Strehl ratio, and aberration induced degradation of the longitudinal field at focus

  10. Genomic Aberrations in Lung Adenocarcinoma in Never Smokers

    PubMed Central

    Beau-Faller, Michèle; Camilleri-Broët, Sophie; Girard, Philippe; Hofman, Paul; Mazières, Julien; Toujani, Saloua; Lacroix, Ludovic; Laffaire, Julien; Dessen, Philippe; Fouret, Pierre

    2010-01-01

    Background Lung cancer in never smokers would rank as the seventh most common cause of cancer death worldwide. Methods and Findings We performed high-resolution array comparative genomic hybridization analysis of lung adenocarcinoma in sixty never smokers and identified fourteen new minimal common regions (MCR) of gain or loss, of which five contained a single gene (MOCS2, NSUN3, KHDRBS2, SNTG1 and ST18). One larger MCR of gain contained NSD1. One focal amplification and nine gains contained FUS. NSD1 and FUS are oncogenes hitherto not known to be associated with lung cancer. FISH showed that the amplicon containing FUS was joined to the next telomeric amplicon at 16p11.2. FUS was over-expressed in 10 tumors with gain of 16p11.2 compared to 30 tumors without that gain. Other cancer genes present in aberrations included ARNT, BCL9, CDK4, CDKN2B, EGFR, ERBB2, MDM2, MDM4, MET, MYC and KRAS. Unsupervised hierarchical clustering with adjustment for false-discovery rate revealed clusters differing by the level and pattern of aberrations and displaying particular tumor characteristics. One cluster was strongly associated with gain of MYC. Another cluster was characterized by extensive losses containing tumor suppressor genes of which RB1 and WRN. Tumors in that cluster frequently harbored a central scar-like fibrosis. A third cluster was associated with gains on 7p and 7q, containing ETV1 and BRAF, and displayed the highest rate of EGFR mutations. SNP array analysis validated copy-number aberrations and revealed that RB1 and WRN were altered by recurrent copy-neutral loss of heterozygosity. Conclusions The present study has uncovered new aberrations containing cancer genes. The oncogene FUS is a candidate gene in the 16p region that is frequently gained in never smokers. Multiple genetic pathways defined by gains of MYC, deletions of RB1 and WRN or gains on 7p and 7q are involved in lung adenocarcinoma in never smokers. PMID:21151896

  11. The correction of electron lens aberrations.

    PubMed

    Hawkes, P W

    2015-09-01

    The progress of electron lens aberration correction from about 1990 onwards is chronicled. Reasonably complete lists of publications on this and related topics are appended. A present for Max Haider and Ondrej Krivanek in the year of their 65th birthdays. By a happy coincidence, this review was completed in the year that both Max Haider and Ondrej Krivanek reached the age of 65. It is a pleasure to dedicate it to the two leading actors in the saga of aberration corrector design and construction. They would both wish to associate their colleagues with such a tribute but it is the names of Haider and Krivanek (not forgetting Joachim Zach) that will remain in the annals of electron optics, next to that of Harald Rose. I am proud to know that both regard me as a friend as well as a colleague. PMID:26025209

  12. A challenging case due to uncommon aberrancies.

    PubMed

    Waleed, Mohammad; Raza, Ali; Minhaj, Tariq; Houghton, Timothy

    2015-01-01

    A 71-year-old man was referred to a rapid access chest pain clinic by his general practitioner. He presented with a 6-month history of twice weekly central chest pain lasting 2-3 min with walking and exertion, relieved with rest or co-codamol tablets. After initial investigations and a positive myoview scan, he was listed for an elective coronary angiogram. Unfortunately, the procedure was abandoned due to unclear course of the guide wire and a possible aberrant aortic course. Further non-invasive tests were arranged to clarify the anatomy of the vessels. After getting a clear idea of the aberrancies, coronary angiogram was replanned, and the patient underwent successful angiography with angioplasty to one of the coronary arteries, without any complications. PMID:26404545

  13. Comparison between two different methods to obtain the wavefront aberration function

    NASA Astrophysics Data System (ADS)

    Cruz Félix, Angel S.; Ibarra, Jorge; López, Estela; Rosales, Marco A.; Tepichín, Eduardo

    2010-08-01

    The analysis and measurement of the wavefront aberration function are very important tools that allow us to evaluate the performance of any specified optical system. This technology has been adopted in visual optics for the analysis of optical aberrations in the human eye, before and after being subjected to laser refractive surgery. We have been working in the characterization and evaluation of the objective performance of human eyes that have been subjected to two different surface ablation techniques known as ASA and PASA1. However, optical aberrations in the human eye are time-dependent2 and, hence, difficult to analyze. In order to obtain a static profile from the post-operatory wavefront aberration function we applied these ablation techniques directly over hard contact lenses. In this work we show the comparison between two different methods to obtain the wavefront aberration function from a reference refractive surface, in order to generalize this method and being able to fully characterize hard contact lenses which have been subjected to different ablation techniques typically used in refractive surgery for vision correction. For the first method we used a Shack-Hartmann wavefront sensor, and in the second method we used a Mach-Zehnder type interferometer. We show the preliminary results of this characterization.

  14. Risk of cancer in an occupationally exposed cohort with increased level of chromosomal aberrations.

    PubMed Central

    Smerhovsky, Z; Landa, K; Rössner, P; Brabec, M; Zudova, Z; Hola, N; Pokorna, Z; Mareckova, J; Hurychova, D

    2001-01-01

    We used cytogenetic analysis to carry out a cohort study in which the major objective was to test the association between frequency of chromosomal aberrations and subsequent risk of cancer. In spite of the extensive use of the cytogenetic analysis of human peripheral blood lymphocytes in biomonitoring of exposure to various mutagens and carcinogens on an ecologic level, the long-term effects of an increased frequency of chromosomal aberrations in individuals are still uncertain. Few epidemiologic studies have addressed this issue, and a moderate risk of cancer in individuals with an elevated frequency of chromosomal aberrations has been observed. In the present study, we analyzed data on 8,962 cytogenetic tests and 3,973 subjects. We found a significant and strong association between the frequency of chromosomal aberrations and cancer incidence in a group of miners exposed to radon, where a 1% increase in frequency of chromosomal aberrations was followed by a 64% increase in risk of cancer (p < 0.000). In contrast, the collected data are inadequate for a critical evaluation of the association with exposure to other chemicals. PMID:11171523

  15. Effect of correction of aberration dynamics on chaos in human ocular accommodation.

    PubMed

    Hampson, Karen M; Cufflin, Matthew P; Mallen, Edward A H

    2013-11-15

    We used adaptive optics to determine the effect of monochromatic aberration dynamics on the level of chaos in the accommodation control system. Four participants viewed a stationary target while the dynamics of their aberrations were either left uncorrected, defocus was corrected, or all aberrations except defocus were corrected. Chaos theory analysis was used to discern changes in the accommodative microfluctuations. We found a statistically significant reduction in the chaotic nature of the accommodation microfluctuations during correction of defocus, but not when all aberrations except defocus were corrected. The Lyapunov exponent decreased from 0.71 ± 0.07 D/s (baseline) to 0.55 ± 0.03 D/s (correction of defocus fluctuations). As the reduction of chaos in physiological signals is indicative of stress to the system, the results indicate that for the participants included in this study, fluctuations in defocus have a more profound effect than those of the other aberrations. There were no changes in the power spectrum between experimental conditions. Hence chaos theory analysis is a more subtle marker of changes in the accommodation control system and will be of value in the study of myopia onset and progression. PMID:24322122

  16. The prevalence of chromosomal aberrations associated with myelodysplastic syndromes in China.

    PubMed

    Hu, Qinyong; Chu, Yuxin; Song, Qibin; Yao, Yi; Yang, Weihong; Huang, Shiang

    2016-08-01

    This study aims to investigate the prevalence and distribution of diverse chromosomal aberrations associated with myelodysplastic syndromes (MDS) in China. Bone marrow samples were collected from multiple cities in China. Metaphase cytogenetic (MC) analysis and fluorescence in situ hybridization (FISH) were initially used to test chromosomal lesions. Affymetrix CytoScan 750 K genechip platform performed a genome-wide detection of chromosomal aberrations. Chromosomal gain was identified in 76 patients; the most prevalent was trisomy 8(17.9 %). New chromosomal gain was detected on chromosome 9, 19p, and X. Chromosomal loss was detected in 101 patients. The most frequent was loss 5q (21.0 %). Some loss and gain were not identified by MC or FISH but identified by genechip. UPD was solely identified by genechip in 51 patients; the most prevalent were UPD 7q (4.94 %) and UPD 17p (4.32 %). Furthermore, complex chromosomal aberrations were detected in 56 patients. In conclusion, Affymetrix CytoScan 750 K genechip was more precise than MC and FISH in detection of cryptic chromosomal aberrations relevant to MDS. Analysis of the prevalence and distribution of diverse chromosomal aberrations in China may improve strategies for MDS diagnosis and therapies. PMID:27225263

  17. Detection of recurrent cytogenetic aberrations in multiple myeloma: A comparison between MLPA and iFISH

    PubMed Central

    Yu, Zhen; Li, Fei; Yi, Shuhua; Ai, Xiaofei; Qin, Xiaoqi; Feng, Xiaoyan; Zhou, Wen; Xu, Yan; Li, Zengjun; Hao, Mu; Sui, Weiwei; Deng, Shuhui; Acharya, Chirag; Zhao, Yaozhong; Ru, Kun; Qiu, Lugui; An, Gang

    2015-01-01

    Multiple myeloma (MM) is a genetically heterogeneous disease with diverse clinical characteristics and outcomes. Recently, multiplex ligation-dependent probe amplification (MLPA) has emerged as an effective and robust method for the detection of cytogenetic aberrations in MM patients. In the present study, MLPA analysis was applied to analyze cytogenetics of CD138 tumor cells of 59 MM samples, and its result was compared, retrospectively, with the interphase fluorescence in situ hybridization (iFISH) data. We firstly established the normal range of each of the 42 diagnostic probes using healthy donor samples. A total of 151 aberrations were detected in 59 patient samples, and 49/59 cases (83.1%) harbored at least one copy number variation. Overall, 0–7 aberrations were detected per case using MLPA, indicating the heterogeneity and complexity of MM cytogenetics. We showed the high efficiency of MLPA and the high congruency of the two methods to assess cytogenetic aberrations. Considering that MLPA analysis is not reliable when the aberration only exits in a small population of tumor cells, it is essential to use both MLPA and iFISH as complementary techniques for the diagnosis of MM. PMID:26416457

  18. Nonrandom chromosomal aberrations and cytogenetic heterogeneity in gallbladder carcinomas.

    PubMed

    Gorunova, L; Parada, L A; Limon, J; Jin, Y; Hallén, M; Hägerstrand, I; Iliszko, M; Wajda, Z; Johansson, B

    1999-12-01

    Chromosome banding analysis of 11 short-term cultured gallbladder carcinomas revealed acquired clonal aberrations in seven tumors (five primary and two metastases). Three of these had one clone, whereas the remaining four were cytogenetically heterogeneous, displaying two to seven aberrant clones. Of a total of 21 abnormal clones, 18 had highly complex karyotypes and three exhibited simple numerical deviations. Double minutes and homogeneously staining regions were observed in one and two carcinomas, respectively. To characterize the karyotypic profile of gallbladder cancer more precisely, we have combined the present findings with our three previously reported cases, thereby providing the largest cytogenetic database on this tumor type to date. A total of 287 chromosomal breakpoints were identified, 251 of which were found in the present study. Chromosome 7 was rearranged most frequently, followed by chromosomes 1, 3, 11, 6, 5, and 8. The bands preferentially involved were 1p32, 1p36, 1q32, 3p21, 6p21, 7p13, 7q11, 7q32, 19p13, 19q13, and 22q13. Nine recurrent abnormalities could, for the first time, be identified in gallbladder carcinoma: del(3)(p13), i(5)(p10), del(6)(q13), del(9)(p13), del(16)(q22), del(17)(p11), i(17)(q10), del(19)(p13), and i(21)(q10). The most common partial or whole-arm gains involved 3q, 5p, 7p, 7q, 8q, 11q, 13q, and 17q, and the most frequent partial or whole-arm losses affected 3p, 4q, 5q, 9p, 10p, 10q, 11p, 14p, 14q, 15p, 17p, 19p, 21p, 21q, and Xp. These chromosomal aberrations and imbalances provide some starting points for molecular analyses of genomic regions that may harbor genes of pathogenetic importance in gallbladder carcinogenesis. Genes Chromosomes Cancer 26:312-321, 1999. PMID:10534766

  19. Aberrant phenotypes in Kikuchi’s disease

    PubMed Central

    Wei, Xue-Jing; Zhou, Xiao-Ge; Xie, Jian-Lan; Zheng, Xiao-Dan; Zheng, Yuan-Yuan

    2014-01-01

    Initial reports emphasized the immunophenotypic similarities between benign and malignant T cell populations, while some previous studies indicating that aberrant T-cell antigen loss is a good marker for detecting malignant T-cell proliferation. Recently, we found a very interesting and thought-provoking phenomenon: In benign disease-28 of 38 (73.7%) cases of Kikuchi’s disease also showed aberrant phenotypes with loss of pan-T cell antigens, which makes the differential diagnosis between Kikuchi’s disease and T cell lymphoma more challenging. In our study, 38 cases of Kikuchi’s disease and 30 cases of reactive lymphoid hyperplasia (RLH) were studied by EliVision immunohistochemical staining. As well as TCR gene rearrangement using PCR was negative in 10 tested cases of the Kikuchi’s disease. Among these cases, the most common antigen deficiency was CD5 (22 cases), then CD7 (11 cases), CD2 (8 cases) and CD3 (2 cases). Compared with proliferative and xanthomatous types of Kikuchi’s disease, antigens tended to be lost in necrotizing type. Based on follow-up data, a correlation was not found between the occurrence of aberrant phenotypes and prognosis. In RLH, obvious pan-T cell antigen loss was also not found. In conclusion, this is the first study to demonstrate distinct patterns of antigen loss in Kikuchi’s disease, suggesting that T cell antigen loss is not reliable as an auxiliary diagnostic standard for T cell lymphoma. PMID:25337197

  20. Ocular higher-order aberrations and mesopic pupil size in individuals screened for refractive surgery

    PubMed Central

    Hashemian, Seyed Javad; Soleimani, Mohammad; Foroutan, Alireza; Joshaghani, Mahmood; Ghaempanah, Mohammad Jafar; Jafari, Mohammad Ebrahim; Yaseri, Mehdi

    2012-01-01

    AIM To study the distribution of ocular higher-order aberrations(HOAs) and mesopic pupil size in individuals screened for refractive surgery. METHODS Ocular HOAs and mesopic pupil size were studied in 2 458 eyes of 1 240 patients with myopia, myopic astigmatism and compound myopic astigmatism and 215 eyes of 110 patients with hyperopia, hyperopic astigmatism and compound hyperopic astigmatism using the Zywave aberrometer (Busch& Lomb). All patients had correctable refractive errors without a history of refractive surgery or underlying diseases. Root-mean-square values of HOAs, total spherical aberration, total coma and mesopic pupil size were analyzed. Ocular HOAs were measured across a ≥ 6.0 mm pupil, and pupil size measurements were performed under the mesopic condition. RESULTS The mean values of HOAs, total spherical aberration and total coma in the myopic group were 0.369µm, ±0.233, 0.133± 0.112µm and 0.330±0.188µm, respectively. In the hyperopic group the mean values of HOAs, total spherical aberration and total coma were 0.418µm ±0.214, 0.202±0.209µm and 0.343±0.201µm, respectively. Hyperopes showed greater total HOAs (P<0.01) and total spherical aberration (P<0.01) compared to myopes. In age-matched analysis, only the amount of total spherical aberration was higher in the hyperopic group (P=0.05). Mesopic pupil size in the myopic group was larger (P≤0.05). CONCLUSION The results suggested that significant levels of HOAs were found in both groups which are important for planning refractive surgeries on Iranians. There were significantly higher levels of total spherical aberration in hyperopes compared to myopes. Mesopic pupil size was larger in myopic group. PMID:22762055

  1. DNA Repair Defects and Chromosomal Aberrations

    NASA Technical Reports Server (NTRS)

    Hada, Megumi; George, K. A.; Huff, J. L.; Pluth, J. M.; Cucinotta, F. A.

    2009-01-01

    Yields of chromosome aberrations were assessed in cells deficient in DNA doublestrand break (DSB) repair, after exposure to acute or to low-dose-rate (0.018 Gy/hr) gamma rays or acute high LET iron nuclei. We studied several cell lines including fibroblasts deficient in ATM (ataxia telangiectasia mutated; product of the gene that is mutated in ataxia telangiectasia patients) or NBS (nibrin; product of the gene mutated in the Nijmegen breakage syndrome), and gliomablastoma cells that are proficient or lacking in DNA-dependent protein kinase (DNA-PK) activity. Chromosomes were analyzed using the fluorescence in situ hybridization (FISH) chromosome painting method in cells at the first division post irradiation, and chromosome aberrations were identified as either simple exchanges (translocations and dicentrics) or complex exchanges (involving >2 breaks in 2 or more chromosomes). Gamma irradiation induced greater yields of both simple and complex exchanges in the DSB repair-defective cells than in the normal cells. The quadratic dose-response terms for both simple and complex chromosome exchanges were significantly higher for the ATM- and NBS-deficient lines than for normal fibroblasts. However, in the NBS cells the linear dose-response term was significantly higher only for simple exchanges. The large increases in the quadratic dose-response terms in these repair-defective cell lines points the importance of the functions of ATM and NBS in chromatin modifications to facilitate correct DSB repair and minimize the formation of aberrations. The differences found between ATM- and NBS-deficient cells at low doses suggest that important questions should with regard to applying observations of radiation sensitivity at high dose to low-dose exposures. For aberrations induced by iron nuclei, regression models preferred purely linear dose responses for simple exchanges and quadratic dose responses for complex exchanges. Relative biological effectiveness (RBE) factors of all of

  2. Chromatic variation of aberration: the role of induced aberrations and raytrace direction

    NASA Astrophysics Data System (ADS)

    Berner, A.; Nobis, T.; Shafer, D.; Gross, H.

    2015-09-01

    The design and optimization process of an optical system contains several first order steps. The definition of the appropriate lens type and the fixation of the raytrace direction are some of them. The latter can be understood as a hidden assumption rather than an aware design step. This is usually followed by the determination of the paraxial lens layout calculated for the primary wavelength. It is obvious, that for this primary wavelength the paraxial calculations are independent of raytrace direction. Today, most of the lens designs are specified not to work only for one wavelength, but in a certain wavelength range. Considering such rays of other wavelengths, one can observe that depending on the direction there will already occur differences in the first order chromatic aberrations and additionally in the chromatic variation of the third-order aberrations. The reason for this effect are induced aberrations emerging from one surface to the following surfaces by perturbed ray heights and ray angles. It can be shown, that the total amount of surface-resolved first order chromatic aberrations and the chromatic variation of the five primary aberrations can be split into an intrinsic part and an induced part. The intrinsic part is independent of the raytrace direction whereas the induced part is not.

  3. 3D resolved mapping of optical aberrations in thick tissues

    PubMed Central

    Zeng, Jun; Mahou, Pierre; Schanne-Klein, Marie-Claire; Beaurepaire, Emmanuel; Débarre, Delphine

    2012-01-01

    We demonstrate a simple method for mapping optical aberrations with 3D resolution within thick samples. The method relies on the local measurement of the variation in image quality with externally applied aberrations. We discuss the accuracy of the method as a function of the signal strength and of the aberration amplitude and we derive the achievable resolution for the resulting measurements. We then report on measured 3D aberration maps in human skin biopsies and mouse brain slices. From these data, we analyse the consequences of tissue structure and refractive index distribution on aberrations and imaging depth in normal and cleared tissue samples. The aberration maps allow the estimation of the typical aplanetism region size over which aberrations can be uniformly corrected. This method and data pave the way towards efficient correction strategies for tissue imaging applications. PMID:22876353

  4. Aberration-Corrected Scanning Transmission Electron Microscope (STEM) Through-Focus Imaging for Three-Dimensional Atomic Analysis of Bismuth Segregation on Copper [001]/33° Twist Bicrystal Grain Boundaries.

    PubMed

    Wade, Charles Austin; McLean, Mark J; Vinci, Richard P; Watanabe, Masashi

    2016-06-01

    Scanning transmission electron microscope (STEM) through-focus imaging (TFI) has been used to determine the three-dimensional atomic structure of Bi segregation-induced brittle Cu grain boundaries (GBs). With TFI, it is possible to observe single Bi atom distributions along Cu [001] twist GBs using an aberration-corrected STEM operating at 200 kV. The depth resolution is ~5 nm. Specimens with GBs intentionally inclined with respect to the microscope's optic axis were used to investigate Bi segregant atom distributions along and through the Cu GB. It was found that Bi atoms exist at most once per Cu unit cell along the GB, meaning that no continuous GB film is present. Therefore, the reduced fracture toughness of this particular Bi-doped Cu boundary would not be caused by fracture of Bi-Bi bonds. PMID:27145975

  5. Aberrant functional brain connectome in people with antisocial personality disorder

    PubMed Central

    Tang, Yan; Long, Jun; Wang, Wei; Liao, Jian; Xie, Hua; Zhao, Guihu; Zhang, Hao

    2016-01-01

    Antisocial personality disorder (ASPD) is characterised by a disregard for social obligations and callous unconcern for the feelings of others. Studies have demonstrated that ASPD is associated with abnormalities in brain regions and aberrant functional connectivity. In this paper, topological organisation was examined in resting-state fMRI data obtained from 32 ASPD patients and 32 non-ASPD controls. The frequency-dependent functional networks were constructed using wavelet-based correlations over 90 brain regions. The topology of the functional networks of ASPD subjects was analysed via graph theoretical analysis. Furthermore, the abnormal functional connectivity was determined with a network-based statistic (NBS) approach. Our results revealed that, compared with the controls, the ASPD patients exhibited altered topological configuration of the functional connectome in the frequency interval of 0.016–0.031 Hz, as indicated by the increased clustering coefficient and decreased betweenness centrality in the medial superior frontal gyrus, precentral gyrus, Rolandic operculum, superior parietal gyrus, angular gyrus, and middle temporal pole. In addition, the ASPD patients showed increased functional connectivity mainly located in the default-mode network. The present study reveals an aberrant topological organisation of the functional brain network in individuals with ASPD. Our findings provide novel insight into the neuropathological mechanisms of ASPD. PMID:27257047

  6. Aberrant functional brain connectome in people with antisocial personality disorder.

    PubMed

    Tang, Yan; Long, Jun; Wang, Wei; Liao, Jian; Xie, Hua; Zhao, Guihu; Zhang, Hao

    2016-01-01

    Antisocial personality disorder (ASPD) is characterised by a disregard for social obligations and callous unconcern for the feelings of others. Studies have demonstrated that ASPD is associated with abnormalities in brain regions and aberrant functional connectivity. In this paper, topological organisation was examined in resting-state fMRI data obtained from 32 ASPD patients and 32 non-ASPD controls. The frequency-dependent functional networks were constructed using wavelet-based correlations over 90 brain regions. The topology of the functional networks of ASPD subjects was analysed via graph theoretical analysis. Furthermore, the abnormal functional connectivity was determined with a network-based statistic (NBS) approach. Our results revealed that, compared with the controls, the ASPD patients exhibited altered topological configuration of the functional connectome in the frequency interval of 0.016-0.031 Hz, as indicated by the increased clustering coefficient and decreased betweenness centrality in the medial superior frontal gyrus, precentral gyrus, Rolandic operculum, superior parietal gyrus, angular gyrus, and middle temporal pole. In addition, the ASPD patients showed increased functional connectivity mainly located in the default-mode network. The present study reveals an aberrant topological organisation of the functional brain network in individuals with ASPD. Our findings provide novel insight into the neuropathological mechanisms of ASPD. PMID:27257047

  7. Enhanced Deletion Formation by Aberrant DNA Replication in Escherichia Coli

    PubMed Central

    Saveson, C. J.; Lovett, S. T.

    1997-01-01

    Repeated genes and sequences are prone to genetic rearrangements including deletions. We have investigated deletion formation in Escherichia coli strains mutant for various replication functions. Deletion was selected between 787 base pair tandem repeats carried either on a ColE1-derived plasmid or on the E. coli chromosome. Only mutations in functions associated with DNA Polymerase III elevated deletion rates in our assays. Especially large increases were observed in strains mutant in dnaQ, the ε editing subunit of Pol III, and dnaB, the replication fork helicase. Mutations in several other functions also altered deletion formation: the α polymerase (dnaE), the γ clamp loader complex (holC, dnaX), and the β clamp (dnaN) subunits of Pol III and the primosomal proteins, dnaC and priA. Aberrant replication stimulated deletions through several pathways. Whereas the elevation in dnaB strains was mostly recA- and lexA-dependent, that in dnaQ strains was mostly recA- and lexA-independent. Deletion product analysis suggested that slipped mispairing, producing monomeric replicon products, may be preferentially increased in a dnaQ mutant and sister-strand exchange, producing dimeric replicon products, may be elevated in dnaE mutants. We conclude that aberrant Polymerase III replication can stimulate deletion events through several mechanisms of deletion and via both recA-dependent and independent pathways. PMID:9177997

  8. Correlation-based aberration correction in the presence of inoperable elements.

    PubMed

    O'Donnell, M; Engeler, W E

    1992-01-01

    Estimation of phase aberrations using correlation processing between neighboring elements in a phased array is explored in the presence of inoperable elements. Using a CORDIC-based implementation of a complex baseband correlator, inactive elements can be identified simultaneous with correlation processing. Following detection of inoperable elements, a simple rerouting of the adaptive beam former is used to eliminate these elements from correlation analysis. Experimental results on a 3.33-MHz, 64-element array system with four contiguous, inactive elements demonstrate the robustness of the simple rerouting method for accurate phase aberration estimation. PMID:18267685

  9. Angular-dispersion-induced spatiotemporal aberrations in noncollinear optical parametric amplifiers

    SciTech Connect

    Bromage, Jake; Dorrer, Christophe; Zuegel, Jonathan D.

    2010-01-01

    We characterize spatiotemporal aberrations induced in noncollinear optical parametric amplifiers (NOPAs), for the first time (to our knowledge), using spatially resolved spectral interferometry. Measurements show that when the submillimeter pump and signal beams are not correctly aligned, several degrees of pulse-front tilt caused by angular dispersion are introduced by the NOPA angular-dependent gain, without significant loss of bandwidth. After eliminating the pulse-front tilt, analysis of the residual higher-order aberrations shows that far-field intensities reaching 80% of the theoretical limit can be achieved without complex spatiospectral phase optimization.

  10. Display depth analyses with the wave aberration for the auto-stereoscopic 3D display

    NASA Astrophysics Data System (ADS)

    Gao, Xin; Sang, Xinzhu; Yu, Xunbo; Chen, Duo; Chen, Zhidong; Zhang, Wanlu; Yan, Binbin; Yuan, Jinhui; Wang, Kuiru; Yu, Chongxiu; Dou, Wenhua; Xiao, Liquan

    2016-07-01

    Because the aberration severely affects the display performances of the auto-stereoscopic 3D display, the diffraction theory is used to analyze the diffraction field distribution and the display depth through aberration analysis. Based on the proposed method, the display depth of central and marginal reconstructed images is discussed. The experimental results agree with the theoretical analyses. Increasing the viewing distance or decreasing the lens aperture can improve the display depth. Different viewing distances and the LCD with two lens-arrays are used to verify the conclusion.

  11. Changes in aberrations and retinal image quality due to tear film dynamics.

    PubMed

    Li, Kaccie Y; Yoon, Geunyoung

    2006-12-11

    A reliable and objective method to measure aberration changes due to the tear film is essential in improving clinical assessment of the tear film and in vivo retinal imaging. The tear film of 11 subjects are studied by acquiring continuous wavefront measurements in real-time with a customized Shack-Hartmann wavefront sensor. The device has a high resolution lenslet array (190 mum) and a topographer unit with an infrared pupil illuminator (940 nm). A Fourier transform reconstructor algorithm [1] was used to estimate the eyes' wavefront aberrations from slope measurements. Increasing irregularities in the tear film produced observable wavefront variations. The temporal behavior of tear induced aberrations and retinal image quality was evaluated by the root mean squared (RMS) error of the residual wavefront and the volume modulation transfer function (MTF). Similar trends were observed from both metrics. Our analysis demonstrates the applicability of the SH wavefront sensor to assessing the dynamics of the human tear film. PMID:19529690

  12. The correction of aberrations computed in the aperture plane of multifrequency microwave radiometer antennas

    NASA Technical Reports Server (NTRS)

    Schmidt, R. F.

    1984-01-01

    An analytical/numerical approach to identifying and correcting the aberrations introduced by a general displacement of the feed from the focal point of a single offset paraboloid antenna used in deployable radiometer systems is developed. A 15 meter reflector with 18 meter focal length is assumed for the analysis, which considers far field radiation pattern quality, focal region fields, and aberrations appearing in the aperture plane. The latter are obtained by ray tracing in the transmit mode and are expressed in terms of optical notation. Attention is given to the physical restraints imposed on corrective elements by real microwave systems and to the intermediate near field aspects of the problem in three dimensions. The subject of wave fronts and caustics in the receive mode is introduced for comparative purposes. Several specific examples are given for aberration reduction at eight beamwidths of scan at a frequency of 1.414 GHz.

  13. Calibration for the errors resulted from aberration in long focal length measurement

    NASA Astrophysics Data System (ADS)

    Yao, Jiang; Luo, Jia; He, Fan; Bai, Jian; Wang, Kaiwei; Hou, Xiyun; Hou, Changlun

    2014-09-01

    In this paper, a high-accuracy calibration method for errors resulted from aberration in long focal length measurement, is presented. Generally, Gaussian Equation is used for calculation without consideration of the errors caused by aberration. However, the errors are the key factor affecting the accuracy in the measurement system of a large aperture and long focal length lens. We creatively introduce an effective way to calibrate the errors, with detailed analysis of the long focal length measurement based on divergent light and Talbot interferometry. Aberration errors are simulated by Zemax. Then, we achieve auto-correction with the help of Visual C++ software and the experimental results reveal that the relative accuracy is better than 0.01%.By comparing modified values with experimental results obtained in knife-edge testing measurement, the proposed method is proved to be highly effective and reliable.

  14. Detecting independent and recurrent copy number aberrations using interval graphs

    PubMed Central

    Wu, Hsin-Ta; Hajirasouliha, Iman; Raphael, Benjamin J.

    2014-01-01

    Motivation: Somatic copy number aberrations (SCNAs) are frequent in cancer genomes, but many of these are random, passenger events. A common strategy to distinguish functional aberrations from passengers is to identify those aberrations that are recurrent across multiple samples. However, the extensive variability in the length and position of SCNAs makes the problem of identifying recurrent aberrations notoriously difficult. Results: We introduce a combinatorial approach to the problem of identifying independent and recurrent SCNAs, focusing on the key challenging of separating the overlaps in aberrations across individuals into independent events. We derive independent and recurrent SCNAs as maximal cliques in an interval graph constructed from overlaps between aberrations. We efficiently enumerate all such cliques, and derive a dynamic programming algorithm to find an optimal selection of non-overlapping cliques, resulting in a very fast algorithm, which we call RAIG (Recurrent Aberrations from Interval Graphs). We show that RAIG outperforms other methods on simulated data and also performs well on data from three cancer types from The Cancer Genome Atlas (TCGA). In contrast to existing approaches that employ various heuristics to select independent aberrations, RAIG optimizes a well-defined objective function. We show that this allows RAIG to identify rare aberrations that are likely functional, but are obscured by overlaps with larger passenger aberrations. Availability: http://compbio.cs.brown.edu/software. Contact: braphael@brown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24931984

  15. Peripheral Aberrations and Image Quality for Contact Lens Correction

    PubMed Central

    Shen, Jie; Thibos, Larry N.

    2011-01-01

    Purpose Contact lenses reduced the degree of hyperopic field curvature present in myopic eyes and rigid contact lenses reduced sphero-cylindrical image blur on the peripheral retina, but their effect on higher order aberrations and overall optical quality of the eye in the peripheral visual field is still unknown. The purpose of our study was to evaluate peripheral wavefront aberrations and image quality across the visual field before and after contact lens correction. Methods A commercial Hartmann-Shack aberrometer was used to measure ocular wavefront errors in 5° steps out to 30° of eccentricity along the horizontal meridian in uncorrected eyes and when the same eyes are corrected with soft or rigid contact lenses. Wavefront aberrations and image quality were determined for the full elliptical pupil encountered in off-axis measurements. Results Ocular higher-order aberrations increase away from fovea in the uncorrected eye. Third-order aberrations are larger and increase faster with eccentricity compared to the other higher-order aberrations. Contact lenses increase all higher-order aberrations except 3rd-order Zernike terms. Nevertheless, a net increase in image quality across the horizontal visual field for objects located at the foveal far point is achieved with rigid lenses, whereas soft contact lenses reduce image quality. Conclusions Second order aberrations limit image quality more than higher-order aberrations in the periphery. Although second-order aberrations are reduced by contact lenses, the resulting gain in image quality is partially offset by increased amounts of higher-order aberrations. To fully realize the benefits of correcting higher-order aberrations in the peripheral field requires improved correction of second-order aberrations as well. PMID:21873925

  16. Aberration-Corrected Stem of Q-Rich Separates from the Saratov (L4) Meteorite

    NASA Astrophysics Data System (ADS)

    Stroud, R. M.; Chisholm, M. F.; Amari, A.; Matsuda, J.

    2012-09-01

    TEM and aberration-corrected STEM analysis of two nanodiamond- and SiC-free Saratov (L4) separates, AJ (most Q-rich) and AI (Q-rich), show that the carrier is porous carbon consisting of nanoscale graphene platelets.

  17. Hexapod kinematics for secondary mirror aberration control .

    NASA Astrophysics Data System (ADS)

    Schipani, P.

    This work deals with active correction of the aberrations in a telescope by moving the secondary mirror. A special attention is dedicated to the case of a secondary mirror whose motions are controlled by a 6-6 Stewart Platform (generally called by astronomers simply "hexapod", even if this term is more general). The kinematics of the device is studied. The non trivial forward kinematics problem is solved by an iterative algorithm fitting the necessities of an active optics system and fast enough to be used in a closed loop feedback control.

  18. Aberrations in Fresnel Lenses and Mirrors

    NASA Technical Reports Server (NTRS)

    Gregory, Don

    1999-01-01

    The NASA/MSFC Shooting Star program revealed a number of technical problems that must be solved before solar thermal propulsion can become a reality. The fundamental problem of interest here is the collection of solar energy. This is the first step in the propulsion process and indeed the most important. Everything else depends on the efficiency and focusing ability of the collection lens or mirror. An initial model of Fresnel lens behavior using a wave optics approach has been completed and the results were encouraging enough to warrant an experimental investigation. This experimental investigation confirmed some of the effects predicted and produced invaluable photographic evidence of coherence based diffraction and aberration.

  19. Aberrant splicing and drug resistance in AML.

    PubMed

    de Necochea-Campion, Rosalia; Shouse, Geoffrey P; Zhou, Qi; Mirshahidi, Saied; Chen, Chien-Shing

    2016-01-01

    The advent of next-generation sequencing technologies has unveiled a new window into the heterogeneity of acute myeloid leukemia (AML). In particular, recurrent mutations in spliceosome machinery and genome-wide aberrant splicing events have been recognized as a prominent component of this disease. This review will focus on how these factors influence drug resistance through altered splicing of tumor suppressor and oncogenes and dysregulation of the apoptotic signaling network. A better understanding of these factors in disease progression is necessary to design appropriate therapeutic strategies recognizing specific alternatively spliced or mutated oncogenic targets. PMID:27613060

  20. Memory aberrations, transliminality, and delusional ideation.

    PubMed

    Dagnall, Neil; Munley, Gary; Parker, Andrew

    2008-02-01

    This study investigated the relationships between cognitive-perceptual personality dimensions (transliminality and delusional ideation) and self-report measures of memory error (Oblivion Scale and the Prospective and Retrospective Memory Questionnaire). 100 full- and part-time psychology undergraduate students completed the measures (18 men and 82 women; M = 19.3 yr., SD = 4.4). A positive correlation was found between transliminality and reported memory aberrations (Oblivion Scale scores) and also between transliminality and Prospective and Retrospective Memory Questionnaire scores. Correlations were positive between Peters, et al. Delusions Inventory and the self-report memory measures. Transliminality and Peters, et al. Delusions Inventory scores predicted the number of memory aberrations or slips reported on the Oblivion Scale and Prospective and Retrospective Memory Questionnaire. To explore whether transliminality explained additional variance to that accounted for by the Peters, et al. Delusions Inventory, forward regression was applied and showed aspects of transliminality not accounted for by Peters, et al. Delusions Inventory did not explain additional variance within the self-report memory measures. PMID:18459357

  1. Lymphocyte chromosomal aberration assay in radiation biodosimetry

    PubMed Central

    Agrawala, Paban K.; Adhikari, J. S.; Chaudhury, N. K.

    2010-01-01

    Exposure to ionizing radiations, whether medical, occupational or accidental, leads to deleterious biological consequences like mortality or carcinogenesis. It is considered that no dose of ionizing radiation exposure is safe. However, once the accurate absorbed dose is estimated, one can be given appropriate medical care and the severe consequences can be minimized. Though several accurate physical dose estimation modalities exist, it is essential to estimate the absorbed dose in biological system taking into account the individual variation in radiation response, so as to plan suitable medical care. Over the last several decades, lots of efforts have been taken to design a rapid and easy biological dosimeter requiring minimum invasive procedures. The metaphase chromosomal aberration assay in human lymphocytes, though is labor intensive and requires skilled individuals, still remains the gold standard for radiation biodosimetry. The current review aims at discussing the human lymphocyte metaphase chromosomal aberration assay and recent developments involving the application of molecular cytogenetic approaches and other technological advancements to make the assay more authentic and simple to use even in the events of mass radiation casualties. PMID:21829315

  2. Relationships between chromosome structure and chromosomal aberrations

    NASA Astrophysics Data System (ADS)

    Eidelman, Yuri; Andreev, Sergey

    An interphase nucleus of human lymphocyte was simulated by the novel Monte Carlo tech-nique. The main features of interphase chromosome structure and packaging were taken into account: different levels of chromatin organisation; nonrandom localisation of chromosomes within a nucleus; chromosome loci dynamics. All chromosomes in a nucleus were modelled as polymer globules. A dynamic pattern of intra/interchromosomal contacts was simulated. The detailed information about chromosomal contacts, such as distribution of intrachromoso-mal contacts over the length of each chromosome and dependence of contact probability on genomic separation between chromosome loci, were calculated and compared to the new exper-imental data obtained by the Hi-C technique. Types and frequencies of simple and complex radiation-induced chromosomal exchange aberrations (CA) induced by X-rays were predicted with taking formation and decay of chromosomal contacts into account. Distance dependence of exchange formation probability was calculated directly. mFISH data for human lymphocytes were analysed. The calculated frequencies of simple CA agreed with the experimental data. Complex CA were underestimated despite the dense packaging of chromosome territories within a nucleus. Possible influence of chromosome-nucleus structural organisation on the frequency and spectrum of radiation-induced chromosome aberrations is discussed.

  3. Effects of optical aberration on chromotomographic reconstruction

    NASA Astrophysics Data System (ADS)

    Tervo, Ryan; Hawks, Michael; Perram, Glen; Fickus, Matthew

    2014-06-01

    Chromotomography is a form of hyperspectral imaging that utilizes a spinning diffractive element to resolve a rapidly evolving scene. The system captures both spatial dimensions and the spectral dimension at the same time. Advanced algorithms take the recorded dispersed images and use them to construct the data cube in which each reconstructed image is the recorded scene at a specific wavelength. A simulation tool has been developed which uses Zemax to accurately trace rays through real or proposed optical systems. The simulation is used here to explore the limitations of tomographic reconstruction in both idealized and aberrated imaging systems. Results of the study show the accuracy of reconstructed images depends upon the content of the original target scene, the number of projections measured, and the angle through which the prism is rotated. For cases studied here, 20 projections are sufficient to achieve image quality 99.5±1% of the max value. Reconstructed image quality degrades with aberrations, but no worse than equivalent conventional imagers.

  4. Correcting Aberrations in Complex Magnet Systems for Muon Cooling Channels

    SciTech Connect

    J.A. Maloney, B. Erdelyi, A. Afanaciev, R.P. Johnson, Y.S. Derbenev, V.S. Morozov

    2011-03-01

    Designing and simulating complex magnet systems needed for cooling channels in both neutrino factories and muon colliders requires innovative techniques to correct for both chromatic and spherical aberrations. Optimizing complex systems, such as helical magnets for example, is also difficult but essential. By using COSY INFINITY, a differential algebra based code, the transfer and aberration maps can be examined to discover what critical terms have the greatest influence on these aberrations.

  5. Aberrations caused by mechanical misalignments in electrostatic quadrupole lens systems

    NASA Astrophysics Data System (ADS)

    Baranova, L. A.; Read, F. H.

    Image aberrations resulting from small misalignments in quadrupole lenses multiplets have been analysed. Analytical formulas for the coefficients of the beam displacement, astigmatism and coma associated with misalignments in a general quadrupole lens system have been derived. Numerical computations of systems of three and four quadrupole lenses have also been carried out. The aberration figures obtained for systems with and without a mechanical defect are compared. The aberration coefficients that have been obtained can be used for estimating tolerance limits for lens misalignments.

  6. Comparison of Aberrations After Standard and Customized Refractive Surgery

    NASA Astrophysics Data System (ADS)

    Fang, L.; He, X.; Wang, Y.

    2013-09-01

    To detect possible differences in residual wavefront aberrations between standard and customized laser refractive surgery based onmathematical modeling, the residual optical aberrations after conventional and customized laser refractive surgery were compared accordingto the ablation profile with transition zone. The results indicated that ablation profile has a significant impact on the residual aberrations.The amount of residual aberrations for conventional correction is higher than that for customized correction. Additionally, the residualaberrations for high myopia eyes are markedly larger than those for moderate myopia eyes. For a 5 mm pupil, the main residual aberrationterm is coma and yet it is spherical aberration for a 7 mm pupil. When the pupil diameter is the same as optical zone or greater, themagnitudes of residual aberrations is obviously larger than that for a smaller pupil. In addition, the magnitudes of the residual fifth orsixth order aberrations are relatively large, especially secondary coma in a 6 mm pupil and secondary spherical aberration in a 7 mm pupil.Therefore, the customized ablation profile may be superior to the conventional correction even though the transition zone and treatmentdecentration are taken into account. However, the customized ablation profile will still induce significant amount of residual aberrations.

  7. Striatal Activity is Associated with Deficits of Cognitive Control and Aberrant Salience for Patients with Schizophrenia

    PubMed Central

    Ceaser, Alan E.; Barch, Deanna M.

    2016-01-01

    A recent meta-analysis has shown that a large dopamine abnormality exists in the striatum when comparing patients with schizophrenia and controls, and this abnormality is thought to contribute to aberrant salience assignment (or a misattribution of relevance to irrelevant stimuli). This abnormality may also disrupt striatal contributions to cognitive control processing. We examined the relationship between striatal involvement in cognition and aberrant salience symptoms using a task of cognitive control that involves updating, interference control, and simple maintenance. The current study included a sample of 22 patients with schizophrenia and 20 healthy controls and used a slow event-related fMRI design. We predicted that (1) aberrant salience symptoms would be greater for patient's, (2) patients would demonstrate increased errors during interference control trials, given that patients may be inappropriately assigning salience to distracters, and (3) striatal activity during those errors would be correlated with aberrant salience symptoms. We found a trend toward a significant difference between patients and controls on aberrant salience symptoms, and a significant difference between groups on select task conditions. During interference control trials, patients were more likely to inappropriately encode distracters. For patients, both prefrontal and striatal activity was significantly greater when patients inappropriately identified the distracter as correct compared to activity during distracter rejection. During updating, patient prefrontal and striatal activity was significantly lower for incorrect than correct updating trials. Finally, as predicted, for patients the increase of activity during incorrect distracter trials was positively correlated with aberrant salience symptoms, but only for the striatal region. These relationships may have implications for treatments that improve cognitive function and reduce symptom expression. PMID:26869912

  8. Sphere-cone-polynomial special window with good aberration characteristic

    NASA Astrophysics Data System (ADS)

    Wang, Chao; Zhang, Xin; Qu, He-Meng; Wang, Ling-Jie; Wang, Yu

    2013-07-01

    Optical windows with external surfaces shaped to satisfy operational environment needs are known as special windows. A novel special window, a sphere-cone-polynomial (SCP) window, is proposed. The formulas of this window shape are given. An SCP MgF2 window with a fineness ratio of 1.33 is designed as an example. The field-of-regard (FOR) angle is ±75°. From the window system simulation results obtained with the calculated fluid dynamics (CFD) and optical design software, we find that compared to the conventional window forms, the SCP shape can not only introduce relatively less drag in the airflow, but also have the minimal effect on imaging. So the SCP window optical system can achieve a high image quality across a super wide FOR without adding extra aberration correctors. The tolerance analysis results show that the optical performance can be maintained with a reasonable fabricating tolerance to manufacturing errors.

  9. Cancer cells express aberrant DNMT3B transcripts encoding truncated proteins

    PubMed Central

    Ostler, KR; Davis, EM; Payne, SL; Gosalia, BB; Expósito-Céspedes, J; Le Beau, MM; Godley, LA

    2008-01-01

    Cancer cells display an altered distribution of DNA methylation relative to normal cells. Certain tumor suppressor gene promoters are hypermethylated and transcriptionally inactivated, whereas repetitive DNA is hypomethylated and transcriptionally active. Little is understood about how the abnormal DNA methylation patterns of cancer cells are established and maintained. Here, we identify over 20 DNMT3B transcripts from many cancer cell lines and primary acute leukemia cells that contain aberrant splicing at the 5′ end of the gene, encoding truncated proteins lacking the C-terminal catalytic domain. Many of these aberrant transcripts retain intron sequences. Although the aberrant transcripts represent a minority of the DNMT3B transcripts present, Western blot analysis demonstrates truncated DNMT3B isoforms in the nuclear protein extracts of cancer cells. To test if expression of a truncated DNMT3B protein could alter the DNA methylation patterns within cells, we expressed DNMT3B7, the most frequently expressed aberrant transcript, in 293 cells. DNMT3B7-expressing 293 cells have altered gene expression as identified by microarray analysis. Some of these changes in gene expression correlate with altered DNA methylation of corresponding CpG islands. These results suggest that truncated DNMT3B proteins could play a role in the abnormal distribution of DNA methylation found in cancer cells. PMID:17353906

  10. Chromosomal aberrations in lymphocytes from car painters.

    PubMed

    Silva, J M; Santos-Mello, R

    1996-05-01

    In the present paper we report the results of biological monitoring of a group of 25 car painters working in different automobile shops in Brasília. There was a significantly higher frequency of aneuplodies and chromosome deletions in the peripheral lymphocytes of car painters than in control subjects. We also detected a significant correlation between the time worked as a car painter and the frequency of aneuploidy. Smoking habits do not represent a significant factor in terms of production of the various types of chromosome aberrations among car painters. These results permitted us to conclude that the individuals studied represent a risk group and should be medically followed up with judicious periodic examinations. PMID:8637507

  11. Patterns of Chromosomal Aberrations in Solid Tumors.

    PubMed

    Grade, Marian; Difilippantonio, Michael J; Camps, Jordi

    2015-01-01

    Chromosomal abnormalities are a defining feature of solid tumors. Such cytogenetic alterations are mainly classified into structural chromosomal aberrations and copy number alterations, giving rise to aneuploid karyotypes. The increasing detection of these genetic changes allowed the description of specific tumor entities and the associated patterns of gene expression. In fact, tumor-specific landscapes of gross genomic copy number changes, including aneuploidies of entire chromosome arms and chromosomes result in a global deregulation of the transcriptome of cancer cells. Furthermore, the molecular characterization of cytogenetic abnormalities has provided insights into the mechanisms of tumorigenesis and has, in a few instances, led to the clinical implementation of effective diagnostic and prognostic tools, as well as treatment strategies that target a specific genetic abnormality. PMID:26376875

  12. Overlapped Fourier coding for optical aberration removal

    PubMed Central

    Horstmeyer, Roarke; Ou, Xiaoze; Chung, Jaebum; Zheng, Guoan; Yang, Changhuei

    2014-01-01

    We present an imaging procedure that simultaneously optimizes a camera’s resolution and retrieves a sample’s phase over a sequence of snapshots. The technique, termed overlapped Fourier coding (OFC), first digitally pans a small aperture across a camera’s pupil plane with a spatial light modulator. At each aperture location, a unique image is acquired. The OFC algorithm then fuses these low-resolution images into a full-resolution estimate of the complex optical field incident upon the detector. Simultaneously, the algorithm utilizes redundancies within the acquired dataset to computationally estimate and remove unknown optical aberrations and system misalignments via simulated annealing. The result is an imaging system that can computationally overcome its optical imperfections to offer enhanced resolution, at the expense of taking multiple snapshots over time. PMID:25321982

  13. Patterns of Chromosomal Aberrations in Solid Tumors

    PubMed Central

    Grade, Marian; Difilippantonio, Michael J.

    2016-01-01

    Chromosomal abnormalities are a defining feature of solid tumors. Such cytogenetic alterations are mainly classified into structural chromosomal aberrations and copy number alterations, giving rise to aneuploid karyotypes. The increasing detection of these genetic changes allowed the description of specific tumor entities and the associated patterns of gene expression. In fact, tumor-specific landscapes of gross genomic copy number changes, including aneuploidies of entire chromosome arms and chromosomes result in a global deregulation of the transcriptome of cancer cells. Furthermore, the molecular characterization of cytogenetic abnormalities has provided insights into the mechanisms of tumorigenesis and has, in a few instances, led to the clinical implementation of effective diagnostic and prognostic tools, as well as treatment strategies that target a specific genetic abnormality. PMID:26376875

  14. Congenital Aberrant Tearing: A Re-Look

    PubMed Central

    Miller, Marilyn T.; Strömland, Kerstin; Ventura, Liana

    2008-01-01

    Purpose Congenital aberrant tearing is characterized by tearing when eating (“crocodile tears”), lack of emotional tearing, or both. Most reported cases are associated with Duane syndrome. In our previous studies we observed aberrant tearing in individuals with thalidomide embryopathy and Möbius sequence. This report summarizes the literature on the subject and adds 3 new studies that give information on this unusual condition. Methods Twenty-eight individuals with Möbius sequence were interviewed about tearing symptoms at a support group meeting in Italy. In Sweden 30 adults primarily from the original thalidomide series were reexamined. In this latter study, a Schirmer test was done at baseline and repeated 5 minutes after eating. Twenty families in Brazil who have children with Möbius sequence were questioned about tearing symptoms and exposure to misoprostol during pregnancy. Results In the 28 Italian individuals, either “crocodile tears” or lack of emotional tearing was noted in 7 cases. In the thalidomide study, 10 of 30 patients had tearing when eating and 7 had no emotional tearing. Low Schirmer scores or increased tearing after eating was noted in a few asymptomatic individuals. Among the 20 Brazilian children with Möbius sequence, 10 had some tearing abnormality. Conclusion Congenital anomalous lacrimation is rare but usually associated with Duane syndrome or abduction deficits, as in Möbius sequence and, less frequently, facial nerve palsy. Studies implicate an early insult in development at 4 to 6 weeks. At that time the facial nerve, sixth nerve, and lacrimal nucleus are in close proximity in the embryo. PMID:19277226

  15. Analysis of aberrant methylation on promoter sequences of tumor suppressor genes and total DNA in sputum samples: a promising tool for early detection of COPD and lung cancer in smokers

    PubMed Central

    2012-01-01

    Background Chronic obstructive pulmonary disease (COPD) is a disorder associated to cigarette smoke and lung cancer (LC). Since epigenetic changes in oncogenes and tumor suppressor genes (TSGs) are clearly important in the development of LC. In this study, we hypothesize that tobacco smokers are susceptible for methylation in the promoter region of TSGs in airway epithelial cells when compared with non-smoker subjects. The purpose of this study was to investigate the usefulness of detection of genes promoter methylation in sputum specimens, as a complementary tool to identify LC biomarkers among smokers with early COPD. Methods We determined the amount of DNA in induced sputum from patients with COPD (n = 23), LC (n = 26), as well as in healthy subjects (CTR) (n = 33), using a commercial kit for DNA purification, followed by absorbance measurement at 260 nm. The frequency of CDKN2A, CDH1 and MGMT promoter methylation in the same groups was determined by methylation-specific polymerase chain reaction (MSP). The Fisher’s exact test was employed to compare frequency of results between different groups. Results DNA concentration was 7.4 and 5.8 times higher in LC and COPD compared to the (CTR) (p < 0.0001), respectively. Methylation status of CDKN2A and MGMT was significantly higher in COPD and LC patients compared with CTR group (p < 0.0001). Frequency of CDH1 methylation only showed a statistically significant difference between LC patients and CTR group (p < 0.05). Conclusions We provide evidence that aberrant methylation of TSGs in samples of induced sputum is a useful tool for early diagnostic of lung diseases (LC and COPD) in smoker subjects. Virtual slides The abstract MUST finish with the following text: Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1127865005664160 PMID:22818553

  16. Using nodal aberration theory to understand the aberrations of multiple unobscured three mirror anastigmatic (TMA) telescopes

    NASA Astrophysics Data System (ADS)

    Thompson, Kevin P.; Fuerschbach, Kyle; Schmid, Tobias; Rolland, Jannick P.

    2009-08-01

    The alignment of three mirror anastigmatic (TMA) telescopes has been studied since their invention in the 60s. Recently, Thompson et al.1 reported that other than the conventional uniform coma over the field caused by misalignment, TMA telescopes display only one other misalignment induced aberration, field-asymmetric, field-linear astigmatism. Currently, an instrument with three TMAs is under development as the primary spectrometer on the James Webb Space Telescope. This paper will report on the application of Nodal Aberration Theory (NAT) to understanding the optical design of an optical system with multiple TMAs as a first step towards investigating and potentially independently analyzing the sensitivities to alignment of this key instrument.

  17. Crash risk and aberrant driving behaviors among bus drivers: the role of personality and attitudes towards traffic safety.

    PubMed

    Mallia, Luca; Lazuras, Lambros; Violani, Cristiano; Lucidi, Fabio

    2015-06-01

    Several studies have shown that personality traits and attitudes toward traffic safety predict aberrant driving behaviors and crash involvement. However, this process has not been adequately investigated in professional drivers, such as bus drivers. The present study used a personality-attitudes model to assess whether personality traits predicted aberrant self-reported driving behaviors (driving violations, lapses, and errors) both directly and indirectly, through the effects of attitudes towards traffic safety in a large sample of bus drivers. Additionally, the relationship between aberrant self-reported driving behaviors and crash risk was also assessed. Three hundred and one bus drivers (mean age=39.1, SD=10.7 years) completed a structured and anonymous questionnaire measuring personality traits, attitudes toward traffic safety, self-reported aberrant driving behaviors (i.e., errors, lapses, and traffic violations), and accident risk in the last 12 months. Structural equation modeling analysis revealed that personality traits were associated to aberrant driving behaviors both directly and indirectly. In particular altruism, excitement seeking, and normlessness directly predicted bus drivers' attitudes toward traffic safety which, in turn, were negatively associated with the three types of self-reported aberrant driving behaviors. Personality traits relevant to emotionality directly predicted bus drivers' aberrant driving behaviors, without any mediation of attitudes. Finally, only self-reported violations were related to bus drivers' accident risk. The present findings suggest that the hypothesized personality-attitudes model accounts for aberrant driving behaviors in bus drivers, and provide the empirical basis for evidence-based road safety interventions in the context of public transport. PMID:25823904

  18. M-BAND Study of Radiation-Induced Chromosome Aberrations in Human Epithelial Cells: Radiation Quality and Dose Rate Effects

    NASA Technical Reports Server (NTRS)

    Hada, Megumi; Cucinotta, Francis; Wu, Honglu

    2009-01-01

    The advantage of the multicolor banding in situ hybridization (mBAND) technique is its ability to identify both inter- (translocation to unpainted chromosomes) and intra- (inversions and deletions within a single painted chromosome) chromosome aberrations simultaneously. To study the detailed rearrangement of low- and high-LET radiation induced chromosome aberrations in human epithelial cells (CH184B5F5/M10) in vitro, we performed a series of experiments with Cs-137 gamma rays of both low and high dose rates, neutrons of low dose rate and 600 MeV/u Fe ions of high dose rate, with chromosome 3 painted with multi-binding colors. We also compared the chromosome aberrations in both 2- and 3-dimensional cell cultures. Results of these experiments revealed the highest chromosome aberration frequencies after low dose rate neutron exposures. However, detailed analysis of the radiation induced inversions revealed that all three radiation types induced a low incidence of simple inversions. Most of the inversions in gamma-ray irradiated samples were accompanied by other types of intra-chromosomal aberrations but few inversions were accompanied by inter-chromosomal aberrations. In contrast, neutrons and Fe ions induced a significant fraction of inversions that involved complex rearrangements of both inter- and intrachromosomal exchanges. The location of the breaks involved in chromosome exchanges was analyzed along the painted chromosome. The breakpoint distribution was found to be randomly localized on chromosome 3 after neutron or Fe ion exposure, whereas non-random distribution with clustering breakpoints was observed after -ray exposure. Our comparison of chromosome aberration yields between 2- and 3-dimensional cell cultures indicated a significant difference for gamma exposures, but not for Fe ion exposures. These experimental results indicated that the track structure of the radiation and the cellular/chromosome structure can both affect radiation-induced chromosome

  19. Canine Mammary Tumours Are Affected by Frequent Copy Number Aberrations, including Amplification of MYC and Loss of PTEN

    PubMed Central

    Borge, Kaja S.; Nord, Silje; Van Loo, Peter; Lingjærde, Ole C.; Gunnes, Gjermund; Alnæs, Grethe I. G.; Solvang, Hiroko K.; Lüders, Torben; Kristensen, Vessela N.; Børresen-Dale, Anne-Lise; Lingaas, Frode

    2015-01-01

    Background Copy number aberrations frequently occur during the development of many cancers. Such events affect dosage of involved genes and may cause further genomic instability and progression of cancer. In this survey, canine SNP microarrays were used to study 117 canine mammary tumours from 69 dogs. Results We found a high occurrence of copy number aberrations in canine mammary tumours, losses being more frequent than gains. Increased frequency of aberrations and loss of heterozygosity were positively correlated with increased malignancy in terms of histopathological diagnosis. One of the most highly recurrently amplified regions harbored the MYC gene. PTEN was located to a frequently lost region and also homozygously deleted in five tumours. Thus, deregulation of these genes due to copy number aberrations appears to be an important event in canine mammary tumour development. Other potential contributors to canine mammary tumour pathogenesis are COL9A3, INPP5A, CYP2E1 and RB1. The present study also shows that a more detailed analysis of chromosomal aberrations associated with histopathological parameters may aid in identifying specific genes associated with canine mammary tumour progression. Conclusions The high frequency of copy number aberrations is a prominent feature of canine mammary tumours as seen in other canine and human cancers. Our findings share several features with corresponding studies in human breast tumours and strengthen the dog as a suitable model organism for this disease. PMID:25955013

  20. Optical aberrations and alignment of the eye with age.

    PubMed

    Berrio, Esther; Tabernero, Juan; Artal, Pablo

    2010-01-01

    We explored the relative changes in ocular, corneal, and internal aberrations associated with normal aging with special emphasis in the role of ocular alignment and lens shape factor in the balance of aberrations. Ocular and corneal aberrations together with the angle kappa were measured for a 5-mm pupil diameter in 46 eyes with low refractive errors and ages ranging between 20 and 77 years. The root mean square (RMS) of the higher order ocular and corneal aberrations increased with age at a rate of 0.0032 μm/year and 0.0015 μm/year, respectively. While in young eyes the partial compensation of aberrations by the internal surfaces was clear, no significant difference was found between corneal and ocular RMS in the older group. The ocular spherical aberration (0.0011 μm/year) and horizontal coma (0.0017 μm/year) increased moderately with age. This is not due to changes in the optical alignment, since angle kappa did not vary significantly with age. Age-related variations in the radii of curvature of the crystalline lens modify slightly its shape factor, reducing the compensation of lateral coma. This suggests that geometrical changes in the crystalline lens with age contribute to modify its aberration structure, reducing the compensation mechanism and explaining most of the measured increment of ocular aberrations with age. PMID:21196516

  1. Sextupole system for the correction of spherical aberration

    DOEpatents

    Crewe, A.V.; Kopf, D.A.

    In an electron beam device in which an electron beam is developed and then focused by a lens to a particular spot, there is provided a means for eliminating spherical aberration. A sextupole electromagnetic lens is positioned between two focusing lenses. The interaction of the sextupole with the beam compensates for spherical aberration. (GHT)

  2. Modified Matching Ronchi Test to Visualize Lens Aberrations

    ERIC Educational Resources Information Center

    Hassani, Kh; Ziafi, H. Hooshmand

    2011-01-01

    We introduce a modification to the matching Ronchi test to visualize lens aberrations with simple and inexpensive equipment available in educational optics labs. This method can help instructors and students to observe and estimate lens aberrations in real time. It is also a semi-quantitative tool for primary tests in research labs. In this work…

  3. Optical aberrations measurement with a low cost optometric instrument

    NASA Astrophysics Data System (ADS)

    Furlan, Walter D.; Muñoz-Escrivá, L.; Pons, A.; Martínez-Corral, M.

    2002-08-01

    A simple experimental method for measuring optical aberrations of a single lens is proposed. The technique is based on the use of an optometric instrument employed for the assessment of the refractive state of the eye: the retinoscope. Experimental results for spherical aberration and astigmatism are obtained.

  4. Using Brief Assessments to Evaluate Aberrant Behavior Maintained by Attention.

    ERIC Educational Resources Information Center

    O'Reilly, Mark F.; Lancioni, Giulio E.; King, Lisa; Lally, Grainne; Dhomhnaill, Orla Nic

    2000-01-01

    Functional assessments were conducted for two Irish individuals with severe disabilities and aberrant behavior. A modified attention condition was introduced, which involved both parents interacting with a third person. Aberrant behavior occurred only in the modified attention condition. Successful treatment consisted of delivery of attention on a…

  5. Aberrant regeneration in idiopathic oculomotor nerve palsy: case report.

    PubMed

    Laguna, J F; Smith, M S

    1980-06-01

    Aberrant regeneration of the oculomotor nerve usually follows injury to the nerve by posterior communicating arty aneurysms or trauma. A case of idiopathic third nerve palsy with pupillary involvement occurred in an otherwise healthy 38-year-old man. Follow-up examination 32 months later showed evidence of oculomotor function with aberrant regeneration. PMID:7381547

  6. Genomic aberrations frequently alter chromatin regulatory genes in chordoma.

    PubMed

    Wang, Lu; Zehir, Ahmet; Nafa, Khedoudja; Zhou, Nengyi; Berger, Michael F; Casanova, Jacklyn; Sadowska, Justyna; Lu, Chao; Allis, C David; Gounder, Mrinal; Chandhanayingyong, Chandhanarat; Ladanyi, Marc; Boland, Patrick J; Hameed, Meera

    2016-07-01

    Chordoma is a rare primary bone neoplasm that is resistant to standard chemotherapies. Despite aggressive surgical management, local recurrence and metastasis is not uncommon. To identify the specific genetic aberrations that play key roles in chordoma pathogenesis, we utilized a genome-wide high-resolution SNP-array and next generation sequencing (NGS)-based molecular profiling platform to study 24 patient samples with typical histopathologic features of chordoma. Matching normal tissues were available for 16 samples. SNP-array analysis revealed nonrandom copy number losses across the genome, frequently involving 3, 9p, 1p, 14, 10, and 13. In contrast, copy number gain is uncommon in chordomas. Two minimum deleted regions were observed on 3p within a ∼8 Mb segment at 3p21.1-p21.31, which overlaps SETD2, BAP1 and PBRM1. The minimum deleted region on 9p was mapped to CDKN2A locus at 9p21.3, and homozygous deletion of CDKN2A was detected in 5/22 chordomas (∼23%). NGS-based molecular profiling demonstrated an extremely low level of mutation rate in chordomas, with an average of 0.5 mutations per sample for the 16 cases with matched normal. When the mutated genes were grouped based on molecular functions, many of the mutation events (∼40%) were found in chromatin regulatory genes. The combined copy number and mutation profiling revealed that SETD2 is the single gene affected most frequently in chordomas, either by deletion or by mutations. Our study demonstrated that chordoma belongs to the C-class (copy number changes) tumors whose oncogenic signature is non-random multiple copy number losses across the genome and genomic aberrations frequently alter chromatin regulatory genes. © 2016 Wiley Periodicals, Inc. PMID:27072194

  7. Aberrant Immune Responses in a Mouse with Behavioral Disorders

    PubMed Central

    Gao, Donghong; Miller, Veronica M.; Lawrence, David A.

    2011-01-01

    BTBR T+tf/J (BTBR) mice have recently been reported to have behaviors that resemble those of autistic individuals, in that this strain has impairments in social interactions and a restricted repetitive and stereotyped pattern of behaviors. Since immune responses, including autoimmune responses, are known to affect behavior, and individuals with autism have aberrant immune activities, we evaluated the immune system of BTBR mice, and compared their immunity and degree of neuroinflammation with that of C57BL/6 (B6) mice, a highly social control strain, and with F1 offspring. Mice were assessed at postnatal day (pnd) 21 and after behavioral analysis at pnd70. BTBR mice had significantly higher amounts of serum IgG and IgE, of IgG anti-brain antibodies (Abs), and of IgG and IgE deposited in the brain, elevated expression of cytokines, especially IL-33 IL-18, and IL-1β in the brain, and an increased proportion of MHC class II-expressing microglia compared to B6 mice. The F1 mice had intermediate levels of Abs and cytokines as well as social activity. The high Ab levels of BTBR mice are in agreement with their increased numbers of CD40hi/I-Ahi B cells and IgG-secreting B cells. Upon immunization with KLH, the BTBR mice produced 2–3 times more anti-KLH Abs than B6 mice. In contrast to humoral immunity, BTBR mice are significantly more susceptible to listeriosis than B6 or BALB/c mice. The Th2-like immune profile of the BTBR mice and their constitutive neuroinflammation suggests that an autoimmune profile is implicated in their aberrant behaviors, as has been suggested for some humans with autism. PMID:21799730

  8. Chaos in ocular aberration dynamics of the human eye

    PubMed Central

    Hampson, Karen M.; Mallen, Edward A. H.

    2012-01-01

    Since the characterization of the eye’s monochromatic aberration fluctuations in 2001, the power spectrum has remained the most widely used method for analyzing their dynamics. However, the power spectrum does not capture the complexities of the fluctuations. We measured the monochromatic aberration dynamics of six subjects using a Shack-Hartmann sensor sampling at 21 Hz. We characterized the dynamics using techniques from chaos theory. We found that the attractor embedding dimension for all aberrations, for all subjects, was equal to three. The embedding lag averaged across aberrations and subjects was 0.31 ± 0.07 s. The Lyapunov exponent of the rms wavefront error was positive for each subject, with an average value of 0.44 ± 0.15 µm/s. This indicates that the aberration dynamics are chaotic. Implications for future modeling are discussed. PMID:22567581

  9. Aberrations of the cathode objective lens up to fifth order.

    PubMed

    Tromp, R M; Wan, W; Schramm, S M

    2012-08-01

    In this paper we discuss a topic that was close to Prof. Gertrude Rempfer s interests for many years. On this occasion of her 100th birthday, we remember and honor Gertrude for her many outstanding contributions, and for the inspiring example that she set. We derive theoretical expressions for the aberration coefficients of the uniform electrostatic field up to 5th order and compare these with raytracing calculations for the cathode lens used in Low Energy Electron Microscopy and Photo Electron Emission Microscopy experiments. These higher order aberration coefficients are of interest for aberration corrected experiments in which chromatic (C(c)) and spherical (C₃) aberrations of the microscope are set to zero. The theoretical predictions are in good agreement with the results of raytracing. Calculations of image resolution using the Contrast Transfer Function method show that sub-nanometer resolution is achievable in an aberration corrected LEEM system. PMID:22188906

  10. Surgical and healing changes to ocular aberrations following refractive surgery

    NASA Astrophysics Data System (ADS)

    Straub, Jochen; Schwiegerling, Jim

    2003-07-01

    Purpose: To measure ocular aberrations before and at several time periods after LASIK surgery to determine the change to the aberration structure of the eye. Methods: A Shack-Hartmann wavefront sensor was used to measure 88 LASIK patients pre-operatively and at 1 week and 12 months following surgery. Reconstructed wavefront errors are compared to look at induced differences. Manifest refraction was measured at 1 week, 1 month, 3 months, 6 months and 12 months following surgery. Sphere, cylinder, spherical aberration, and pupil diameter are analyzed. Results: A dramatic elevation in spherical aberration is seen following surgery. This elevation appears almost immediately and remains for the duration of the study. A temporary increase in pupil size is seen following surgery. Conclusions: LASIK surgery dramatically reduces defocus and astigmatism in the eye, but simultaneously increases spherical aberration levels. This increase occurs at the time of surgery and is not an effect of the healing response.