WorldWideScience

Sample records for chromosome image analysis

  1. Cytogenetic analysis of quinoa chromosomes using nanoscale imaging and spectroscopy techniques

    Science.gov (United States)

    Yangquanwei, Zhong; Neethirajan, Suresh; Karunakaran, Chithra

    2013-11-01

    Here we present a high-resolution chromosomal spectral map derived from synchrotron-based soft X-ray spectromicroscopy applied to quinoa species. The label-free characterization of quinoa metaphase chromosomes shows that it consists of organized substructures of DNA-protein complex. The analysis of spectra of chromosomes using the scanning transmission X-ray microscope (STXM) and its superposition of the pattern with the atomic force microscopy (AFM) and scanning electron microscopy (SEM) images proves that it is possible to precisely locate the gene loci and the DNA packaging inside the chromosomes. STXM has been successfully used to distinguish and quantify the DNA and protein components inside the quinoa chromosomes by visualizing the interphase at up to 30-nm spatial resolution. Our study represents the successful attempt of non-intrusive interrogation and integrating imaging techniques of chromosomes using synchrotron STXM and AFM techniques. The methodology developed for 3-D imaging of chromosomes with chemical specificity and temporal resolution will allow the nanoscale imaging tools to emerge from scientific research and development into broad practical applications such as gene loci tools and biomarker libraries.

  2. Cytogenetic analysis of quinoa chromosomes using nanoscale imaging and spectroscopy techniques.

    Science.gov (United States)

    Yangquanwei, Zhong; Neethirajan, Suresh; Karunakaran, Chithra

    2013-01-01

    Here we present a high-resolution chromosomal spectral map derived from synchrotron-based soft X-ray spectromicroscopy applied to quinoa species. The label-free characterization of quinoa metaphase chromosomes shows that it consists of organized substructures of DNA-protein complex. The analysis of spectra of chromosomes using the scanning transmission X-ray microscope (STXM) and its superposition of the pattern with the atomic force microscopy (AFM) and scanning electron microscopy (SEM) images proves that it is possible to precisely locate the gene loci and the DNA packaging inside the chromosomes. STXM has been successfully used to distinguish and quantify the DNA and protein components inside the quinoa chromosomes by visualizing the interphase at up to 30-nm spatial resolution. Our study represents the successful attempt of non-intrusive interrogation and integrating imaging techniques of chromosomes using synchrotron STXM and AFM techniques. The methodology developed for 3-D imaging of chromosomes with chemical specificity and temporal resolution will allow the nanoscale imaging tools to emerge from scientific research and development into broad practical applications such as gene loci tools and biomarker libraries.

  3. Morphological images analysis and chromosomic aberrations classification based on fuzzy logic

    International Nuclear Information System (INIS)

    This work has implemented a methodology for automation of images analysis of chromosomes of human cells irradiated at IEA-R1 nuclear reactor (located at IPEN, Sao Paulo, Brazil), and therefore subject to morphological aberrations. This methodology intends to be a tool for helping cytogeneticists on identification, characterization and classification of chromosomal metaphasic analysis. The methodology development has included the creation of a software application based on artificial intelligence techniques using Fuzzy Logic combined with image processing techniques. The developed application was named CHRIMAN and is composed of modules that contain the methodological steps which are important requirements in order to achieve an automated analysis. The first step is the standardization of the bi-dimensional digital image acquisition procedure through coupling a simple digital camera to the ocular of the conventional metaphasic analysis microscope. Second step is related to the image treatment achieved through digital filters application; storing and organization of information obtained both from image content itself, and from selected extracted features, for further use on pattern recognition algorithms. The third step consists on characterizing, counting and classification of stored digital images and extracted features information. The accuracy in the recognition of chromosome images is 93.9%. This classification is based on classical standards obtained at Buckton [1973], and enables support to geneticist on chromosomic analysis procedure, decreasing analysis time, and creating conditions to include this method on a broader evaluation system on human cell damage due to ionizing radiation exposure. (author)

  4. Development of an integrated computerized scheme for metaphase chromosome image analysis: a robustness experiment

    Science.gov (United States)

    Wang, Xingwei; Zheng, Bin; Li, Shibo; Mulvihill, John J.; Wood, Marc C.; Yuan, Chaowei; Chen, Wei; Liu, Hong

    2008-02-01

    Our integrated computer-aided detection (CAD) scheme includes three basic modules. The first module detects whether a microscopic digital image depicts a metaphase chromosome cell. If a cell is detected, the scheme will justify whether it is analyzable with a decision tree. Once an analyzable cell is detected, the second module is applied to segment individual chromosomes and to compute two important features. Specifically, the scheme utilizes a modified thinning algorithm to identify the medial axis of a chromosome. By tracking perpendicular lines along the medial axis, the scheme computes four feature profiles, identifies centromeres, and assigns polarities of chromosomes based on a set of pre-optimized rules. The third module is followed to classify chromosomes into 24 types. In this module, each chromosome is initially represented by a vector of 31 features. A two-layer classifier with 8 artificial neural networks (ANN) is optimized by a genetic algorithm. A testing chromosome is first classified into one of the seven groups by the ANN in the first layer. Another ANN is then automatically selected from the seven ANNs in the second layer (one for each group) to further classify this chromosome into one of 24 types. To test the performance and robustness of this CAD scheme, we randomly selected and assembled an independent testing dataset. The dataset contains 100 microscopic digital images including 50 analyzable and 50 un-analyzable metphase cells identified by the experts. The centromere location, the corresponding polarity, and karyotype for each individual chromosome were recorded in the "truth" file. The performance of the CAD scheme applied to this image dataset is analyzed and compared with the results in the true file. The assessment accuracies are 93% for the first module, 90.8% for centromere identification and 93.2% for polarity assignment in the second module, over 96% for six chromosome groups and 81.8% for one group in the third module

  5. Fluorescence imaging of chromosomal DNA using click chemistry

    Science.gov (United States)

    Ishizuka, Takumi; Liu, Hong Shan; Ito, Kenichiro; Xu, Yan

    2016-01-01

    Chromosome visualization is essential for chromosome analysis and genetic diagnostics. Here, we developed a click chemistry approach for multicolor imaging of chromosomal DNA instead of the traditional dye method. We first demonstrated that the commercially available reagents allow for the multicolor staining of chromosomes. We then prepared two pro-fluorophore moieties that served as light-up reporters to stain chromosomal DNA based on click reaction and visualized the clear chromosomes in multicolor. We applied this strategy in fluorescence in situ hybridization (FISH) and identified, with high sensitivity and specificity, telomere DNA at the end of the chromosome. We further extended this approach to observe several basic stages of cell division. We found that the click reaction enables direct visualization of the chromosome behavior in cell division. These results suggest that the technique can be broadly used for imaging chromosomes and may serve as a new approach for chromosome analysis and genetic diagnostics. PMID:27620982

  6. Fetal chromosome analysis: screening for chromosome disease?

    DEFF Research Database (Denmark)

    Philip, J; Tabor, Ann; Bang, J;

    1983-01-01

    The aim of the study was to investigate the rationale of the current indications for fetal chromosome analysis. 5372 women had 5423 amniocentesis performed, this group constituting a consecutive sample at the chromosome laboratory, Rigshospitalet, Copenhagen from March 1973 to September 1980 (Group...... A + B). Pregnant women 35 years of age, women who previously had a chromosomally abnormal child, families with translocation carriers or other heritable chromosomal disease, families where the father was 50 years or more and women in families with a history of Down's syndrome (group A), were compared...... to women having amniocentesis, although considered not to have any increased risk of fetal chromosome abnormality (1390 pregnancies, group B). They were also compared with 750 consecutive pregnancies in women 25-34 years of age, in whom all heritable diseases were excluded (group C). The risk of unbalanced...

  7. System for the analysis of plant chromosomes

    International Nuclear Information System (INIS)

    The paper describes a computer system for the automation workers of recognition analysis and interpretation of plant chromosomes. This system permit to carry out the analysis in a more comfortable and faster way, using the image processing techniques

  8. Morphological images analysis and chromosomic aberrations classification based on fuzzy logic; Analise morfologica de imagens e classificacao de aberracoes cromossomicas por meio de logica fuzzy

    Energy Technology Data Exchange (ETDEWEB)

    Souza, Leonardo Peres

    2011-07-01

    This work has implemented a methodology for automation of images analysis of chromosomes of human cells irradiated at IEA-R1 nuclear reactor (located at IPEN, Sao Paulo, Brazil), and therefore subject to morphological aberrations. This methodology intends to be a tool for helping cytogeneticists on identification, characterization and classification of chromosomal metaphasic analysis. The methodology development has included the creation of a software application based on artificial intelligence techniques using Fuzzy Logic combined with image processing techniques. The developed application was named CHRIMAN and is composed of modules that contain the methodological steps which are important requirements in order to achieve an automated analysis. The first step is the standardization of the bi-dimensional digital image acquisition procedure through coupling a simple digital camera to the ocular of the conventional metaphasic analysis microscope. Second step is related to the image treatment achieved through digital filters application; storing and organization of information obtained both from image content itself, and from selected extracted features, for further use on pattern recognition algorithms. The third step consists on characterizing, counting and classification of stored digital images and extracted features information. The accuracy in the recognition of chromosome images is 93.9%. This classification is based on classical standards obtained at Buckton [1973], and enables support to geneticist on chromosomic analysis procedure, decreasing analysis time, and creating conditions to include this method on a broader evaluation system on human cell damage due to ionizing radiation exposure. (author)

  9. A review of metaphase chromosome image selection techniques for automatic karyotype generation.

    Science.gov (United States)

    Arora, Tanvi; Dhir, Renu

    2016-08-01

    The karyotype is analyzed to detect the genetic abnormalities. It is generated by arranging the chromosomes after extracting them from the metaphase chromosome images. The chromosomes are non-rigid bodies that contain the genetic information of an individual. The metaphase chromosome image spread contains the chromosomes, but these chromosomes are not distinct bodies; they can either be individual chromosomes or be touching one another; they may be bent or even may be overlapping and thus forming a cluster of chromosomes. The extraction of chromosomes from these touching and overlapping chromosomes is a very tedious process. The segmentation of a random metaphase chromosome image may not give us correct and accurate results. Therefore, before taking up a metaphase chromosome image for analysis, it must be analyzed for the orientation of the chromosomes it contains. The various reported methods for metaphase chromosome image selection for automatic karyotype generation are compared in this paper. After analysis, it has been concluded that each metaphase chromosome image selection method has its advantages and disadvantages.

  10. A review of metaphase chromosome image selection techniques for automatic karyotype generation.

    Science.gov (United States)

    Arora, Tanvi; Dhir, Renu

    2016-08-01

    The karyotype is analyzed to detect the genetic abnormalities. It is generated by arranging the chromosomes after extracting them from the metaphase chromosome images. The chromosomes are non-rigid bodies that contain the genetic information of an individual. The metaphase chromosome image spread contains the chromosomes, but these chromosomes are not distinct bodies; they can either be individual chromosomes or be touching one another; they may be bent or even may be overlapping and thus forming a cluster of chromosomes. The extraction of chromosomes from these touching and overlapping chromosomes is a very tedious process. The segmentation of a random metaphase chromosome image may not give us correct and accurate results. Therefore, before taking up a metaphase chromosome image for analysis, it must be analyzed for the orientation of the chromosomes it contains. The various reported methods for metaphase chromosome image selection for automatic karyotype generation are compared in this paper. After analysis, it has been concluded that each metaphase chromosome image selection method has its advantages and disadvantages. PMID:26676686

  11. An approach to automated chromosome analysis

    International Nuclear Information System (INIS)

    The methods of approach developed with a view to automatic processing of the different stages of chromosome analysis are described in this study divided into three parts. Part 1 relates the study of automated selection of metaphase spreads, which operates a decision process in order to reject ail the non-pertinent images and keep the good ones. This approach has been achieved by Computing a simulation program that has allowed to establish the proper selection algorithms in order to design a kit of electronic logical units. Part 2 deals with the automatic processing of the morphological study of the chromosome complements in a metaphase: the metaphase photographs are processed by an optical-to-digital converter which extracts the image information and writes it out as a digital data set on a magnetic tape. For one metaphase image this data set includes some 200 000 grey values, encoded according to a 16, 32 or 64 grey-level scale, and is processed by a pattern recognition program isolating the chromosomes and investigating their characteristic features (arm tips, centromere areas), in order to get measurements equivalent to the lengths of the four arms. Part 3 studies a program of automated karyotyping by optimized pairing of human chromosomes. The data are derived from direct digitizing of the arm lengths by means of a BENSON digital reader. The program supplies' 1/ a list of the pairs, 2/ a graphic representation of the pairs so constituted according to their respective lengths and centromeric indexes, and 3/ another BENSON graphic drawing according to the author's own representation of the chromosomes, i.e. crosses with orthogonal arms, each branch being the accurate measurement of the corresponding chromosome arm. This conventionalized karyotype indicates on the last line the really abnormal or non-standard images unpaired by the program, which are of special interest for the biologist. (author)

  12. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    Directory of Open Access Journals (Sweden)

    Tsap Leonid V

    2006-01-01

    Full Text Available The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell, and its state. Analysis of chromosome structure is significant in the detection of diseases, identification of chromosomal abnormalities, study of DNA structural conformation, in-depth study of chromosomal surface morphology, observation of in vivo behavior of the chromosomes over time, and in monitoring environmental gene mutations. The methodology incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  13. Transillumination spatially modulated illumination microscopy for human chromosome imaging

    Science.gov (United States)

    Pitris, Costas; Heracleous, Peter; Patsalis, Philippos

    2005-03-01

    Human chromosome analysis is an essential task in cytogenetics, especially in prenatal screening, genetic syndrome diagnosis, cancer pathology research and mutagen dosimetry. Chromosomal analysis begins with the creation of a karyotype, which is a layout of chromosome images organized by decreasing size in pairs. Both manual and automatic classification of chromosomes are limited by the resolution of the microscope and imaging system used. One way to improve the results of classification and even detect subtleties now remaining undetected, is to enhance the resolution of the images. It is possible to achieve lateral resolution beyond the classical limit, by using spatially modulated illumination (SMI) in a wide-field, non-confocal microscope. In this case, the sample is illuminated with spatially modulated light, which makes normally inaccessible high-resolution information visible in the observed image by shifting higher frequencies within the OTF limits of the microscope. Although, SMI microscopes have been reported in the past, this manuscript reports the development of a transillumination microscope for opaque, non-fluorescent samples. The illumination path consisted of a light source illuminating a ruled grating which was subsequently imaged on the sample. The grating was mounted on a rotating and translating stage so that the magnification and rotation of the pattern could be adjusted. The imaging lens was a 1.25 NA oil immersion objective. Test samples showed resolution improvement, as judged from a comparison of the experimentally obtained FWHM. Further studies using smaller fringe distance or laser interference pattern illumination will be evaluated to further optimize the SMI results.

  14. Chromosome analysis of arsenic affected cattle

    Directory of Open Access Journals (Sweden)

    S. Shekhar

    2014-10-01

    Full Text Available Aim: The aim was to study the chromosome analysis of arsenic affected cattle. Materials and Methods: 27 female cattle (21 arsenic affected and 6 normal were selected for cytogenetical study. The blood samples were collected, incubated, and cultured using appropriate media and specific methods. The samples were analyzed for chromosome number and morphology, relative length of the chromosome, arm ratio, and centromere index of X chromosome and chromosomal abnormalities in arsenic affected cattle to that of normal ones. Results: The diploid number of metaphase chromosomes in arsenic affected cattle as well as in normal cattle were all 2n=60, 58 being autosomes and 2 being sex chromosomes. From the centromeric position, karyotyping studies revealed that all the 29 pair of autosomes was found to be acrocentric or telocentric, and the sex chromosomes (XX were submetacentric in both normal and arsenic affected cattle. The relative length of all the autosome pairs and sex chrosomosome pair was found to be higher in normal than that of arsenic affected cattle. The mean arm ratio of X-chromosome was higher in normal than that of arsenic affected cattle, but it is reverse in case of centromere index value of X-chromosome. There was no significant difference of arm ratio and centromere index of X-chromosomes between arsenic affected and normal cattle. No chromosomal abnormalities were found in arsenic affected cattle. Conclusion: The chromosome analysis of arsenic affected cattle in West Bengal reported for the first time in this present study which may serve as a guideline for future studies in other species. These reference values will also help in comparison of cytological studies of arsenic affected cattle to that of various toxicants.

  15. Inherited unbalanced structural chromosome abnormalities at prenatal chromosome analysis are rarely ascertained through recurrent miscarriage

    NARCIS (Netherlands)

    Franssen, M. T. M.; Korevaar, J. C.; Tjoa, W. M.; Leschot, N. J.; Bossuyt, P. M. M.; Knegt, A. C.; Suykerbuyk, R. F.; Hochstenbach, R.; van der Veen, F.; Goddijn, M.

    2008-01-01

    Objective To determine the mode of ascertainment of inherited unbalanced structural chromosome abnormalities detected at prenatal chromosome analysis. Methods From the databases of three centres for clinical genetics in the Netherlands, all cases of inherited unbalanced structural chromosome abnorma

  16. IMACULAT - an open access package for the quantitative analysis of chromosome localization in the nucleus.

    Directory of Open Access Journals (Sweden)

    Ishita Mehta

    Full Text Available The alteration in the location of the chromosomes within the nucleus upon action of internal or external stimuli has been implicated in altering genome function. The effect of stimuli at a whole genome level is studied by using two-dimensional fluorescence in situ hybridization (FISH to delineate whole chromosome territories within a cell nucleus, followed by a quantitative analysis of the spatial distribution of the chromosome. However, to the best of our knowledge, open access software capable of quantifying spatial distribution of whole chromosomes within cell nucleus is not available. In the current work, we present a software package that computes localization of whole chromosomes - Image Analysis of Chromosomes for computing localization (IMACULAT. We partition the nucleus into concentric elliptical compartments of equal area and the variance in the quantity of any chromosome in these shells is used to determine its localization in the nucleus. The images are pre-processed to remove the smudges outside the cell boundary. Automation allows high throughput analysis for deriving statistics. Proliferating normal human dermal fibroblasts were subjected to standard a two-dimensional FISH to delineate territories for all human chromosomes. Approximately 100 images from each chromosome were analyzed using IMACULAT. The analysis corroborated that these chromosome territories have non-random gene density based organization within the interphase nuclei of human fibroblasts. The ImageMagick Perl API has been used for pre-processing the images. The source code is made available at www.sanchak.com/imaculat.html.

  17. Multimodality hard-x-ray imaging of a chromosome with nanoscale spatial resolution

    Science.gov (United States)

    Yan, Hanfei; Nazaretski, Evgeny; Lauer, Kenneth; Huang, Xiaojing; Wagner, Ulrich; Rau, Christoph; Yusuf, Mohammed; Robinson, Ian; Kalbfleisch, Sebastian; Li, Li; Bouet, Nathalie; Zhou, Juan; Conley, Ray; Chu, Yong S.

    2016-02-01

    We developed a scanning hard x-ray microscope using a new class of x-ray nano-focusing optic called a multilayer Laue lens and imaged a chromosome with nanoscale spatial resolution. The combination of the hard x-ray’s superior penetration power, high sensitivity to elemental composition, high spatial-resolution and quantitative analysis creates a unique tool with capabilities that other microscopy techniques cannot provide. Using this microscope, we simultaneously obtained absorption-, phase-, and fluorescence-contrast images of Pt-stained human chromosome samples. The high spatial-resolution of the microscope and its multi-modality imaging capabilities enabled us to observe the internal ultra-structures of a thick chromosome without sectioning it.

  18. DETECTION OF CHROMOSOME ABERRATIONS IN TWELVE PRIMARY GASTRIC CANCERS BY DIRECT CHROMOSOME ANALYSIS AND FISH

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Direct chromosome analysis and FISH were performed on twelve primary gastric carcinomas. Two of them had simple chromosome changes: 48,XX, +8, +20, and 49, XY, +2, +8, +9, and the others had complicated chromosome changes, which includes much more numerical and structural chromosome aberrations. Frequent structural changes in the complicated types involved chromosome 7, 3, 1, 5 and 12 etc. The del 7q was noted in eight cases. The del (3p) and del (1p) were noted in six and five cases, respectively. The results provide some important clues for isolation of the genes related to gastric cancer.

  19. Y chromosomal STR analysis using Pyrosequencing technology.

    Science.gov (United States)

    Edlund, Hanna; Allen, Marie

    2009-03-01

    Analysis of Y chromosome STR markers has proven to be useful in forensic cases where the samples contain a mixture of DNA from several individuals. STR markers are commonly genotyped based on length separation of PCR products. In this study we evaluated if Pyrosequencing can be used as an alternative method for determining Y-STR variants. In total 70 unrelated Swedish males were typed for the Y chromosomal markers (DYS19, DYS389 I-II, DYS390, DYS391, DYS392, DYS393 and DYS438) using Pyrosequencing. Using the 8 markers, 57 unique haplotypes were observed with a discrimination capacity of 0.81. At four loci, the Pyrosequencing analysis revealed sequence variants. The sequence variants were found in the DYS389 II, DYS390, DYS391, and DYS393 loci in frequencies between 1.43% and 14.3%. Pyrosequencing has here been shown to be a useful tool for typing Y chromosomal STRs and the method can provide a complement to conventional forensic Y STR analyses. Moreover, the Pyrosequencing method can be used to rapidly evaluate novel markers. PMID:19215881

  20. Chromosome

    Science.gov (United States)

    Chromosomes are structures found in the center (nucleus) of cells that carry long pieces of DNA. DNA ... is the building block of the human body. Chromosomes also contain proteins that help DNA exist in ...

  1. Image Analysis

    DEFF Research Database (Denmark)

    . The topics of the accepted papers range from novel applications of vision systems, pattern recognition, machine learning, feature extraction, segmentation, 3D vision, to medical and biomedical image analysis. The papers originate from all the Scandinavian countries and several other European countries......The 19th Scandinavian Conference on Image Analysis was held at the IT University of Copenhagen in Denmark during June 15-17, 2015. The SCIA conference series has been an ongoing biannual event for more than 30 years and over the years it has nurtured a world-class regional research and development...

  2. Flow analysis of human chromosome sets by means of mixing-stirring device

    Science.gov (United States)

    Zenin, Valeri V.; Aksenov, Nicolay D.; Shatrova, Alla N.; Klopov, Nicolay V.; Cram, L. Scott; Poletaev, Andrey I.

    1997-05-01

    A new mixing and stirring device (MSD) was used to perform flow karyotype analysis of single human mitotic chromosomes analyzed so as to maintain the identity of chromosomes derived from the same cell. An improved method for cell preparation and intracellular staining of chromosomes was developed. The method includes enzyme treatment, incubation with saponin and separation of prestained cells from debris on a sucrose gradient. Mitotic cells are injected one by one in the MSD which is located inside the flow chamber where cells are ruptured, thereby releasing chromosomes. The set of chromosomes proceeds to flow in single file fashion to the point of analysis. The device works in a stepwise manner. The concentration of cells in the sample must be kept low to ensure that only one cell at a time enters the breaking chamber. Time-gated accumulation of data in listmode files makes it possible to separate chromosome sets comprising of single cells. The software that was developed classifies chromosome sets according to different criteria: total number of chromosomes, overall DNA content in the set, and the number of chromosomes of certain types. This approach combines the high performance of flow cytometry with the advantages of image analysis. Examples obtained with different human cell lines are presented.

  3. Chromosome analysis of three species of Myoxidae

    Directory of Open Access Journals (Sweden)

    Maria Vittoria Civitelli

    1995-05-01

    Full Text Available Abstract Karyotype analysis was carried out on three species of dormice: Myoxus glis, 4 populations from Northern and Southern Italy and from Turkey; Dryomys nitedula, 4 populations from Northern and Southern Italy, from Israel and from Turkey; Myomimus roachi, 1 specimen from Turkey. Myoxus glis shows 2n=62; comparison of our specimens from different localities shows complete correspondence between karyotypes, both for the autosomes and the heterochromosomes. Dryomys nitedula shows 2n=48. All populations we studied, show the same karyotypic pattern, except for the NOR-bearing chromosomes. Myomimus roachi, here studied for the first time, shows 2n=44. All the autosomes are biarmed of decreasing size. The X-chromosome is a medium size metacentric, while the Y-chromosome is the smallest one. All the three species we studied, show one pair of NOR-bearing chromosomes, Ag-NORs always correspond to the secondary constriction. Differences in the fundamental number and in heterochromosome morphology, have been observed by other authors, in different European populations. This variability is analysed and discussed. Riassunto Analisi cromosomica in tre specie di Myoxidae - L'analisi cromosomica è stata condotta su popolazioni europee di tre specie di Myoxidae: Myoxus glis, 4 popolazioni provenienti dal Nord e Sud Italia, e dalla Turchia; Dryomys nitedula, 4 popolazioni provenienti dal Nord e Sud Italia, da Israele e dalla Turchia; Myomimus roachi, 1 esemplare, proveniente dalla Turchia. Myoxus glis presenta 2n=62. Gli esemplari, provenienti dalle diverse popolazioni, mostrano corrispondenza nella morfologia sia degli autosomi che degli eterocromosomi. Dryomys nitedula presenta 2n=48. La morfologia dei cromosomi nei cariotipi appare corrispondente mentre diversa è la localizzazione degli Ag-NOR.

  4. DNA sequence and analysis of human chromosome 18.

    Science.gov (United States)

    Nusbaum, Chad; Zody, Michael C; Borowsky, Mark L; Kamal, Michael; Kodira, Chinnappa D; Taylor, Todd D; Whittaker, Charles A; Chang, Jean L; Cuomo, Christina A; Dewar, Ken; FitzGerald, Michael G; Yang, Xiaoping; Abouelleil, Amr; Allen, Nicole R; Anderson, Scott; Bloom, Toby; Bugalter, Boris; Butler, Jonathan; Cook, April; DeCaprio, David; Engels, Reinhard; Garber, Manuel; Gnirke, Andreas; Hafez, Nabil; Hall, Jennifer L; Norman, Catherine Hosage; Itoh, Takehiko; Jaffe, David B; Kuroki, Yoko; Lehoczky, Jessica; Lui, Annie; Macdonald, Pendexter; Mauceli, Evan; Mikkelsen, Tarjei S; Naylor, Jerome W; Nicol, Robert; Nguyen, Cindy; Noguchi, Hideki; O'Leary, Sinéad B; O'Neill, Keith; Piqani, Bruno; Smith, Cherylyn L; Talamas, Jessica A; Topham, Kerri; Totoki, Yasushi; Toyoda, Atsushi; Wain, Hester M; Young, Sarah K; Zeng, Qiandong; Zimmer, Andrew R; Fujiyama, Asao; Hattori, Masahira; Birren, Bruce W; Sakaki, Yoshiyuki; Lander, Eric S

    2005-09-22

    Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements. PMID:16177791

  5. Cytogenetic analysis of chromosomal abnormalities in Sri Lankan children

    Institute of Scientific and Technical Information of China (English)

    Colombo; Sri Lanka

    2015-01-01

    Background: Cytogenetic analysis is a valuable investigation in the diagnostic work up of children with suspected chromosomal disorders. The objective of this study was to describe the prevalence of various types of chromosomal abnormalities in Sri Lankan children undergoing cytogenetic analysis. Methods: Cytogenetic reports of 1554 consecutive children with suspected chromosomal disorders who underwent karyotyping in two genetic centers in Sri Lanka from January 2006 to December 2011 were reviewed retrospectively. Results: A total of 1548 children were successfully karyotyped. Abnormal karyotypes were found in 783 (50.6%) children. Numerical and structural abnormalities accounted for 90.8% and 9.2%, respectively. Down syndrome was the commonest aneuploidy identifi ed. Other various autosomal and sex chromosomal aneuploidies as well as micro-deletion syndromes were also detected. Conclusions: The prevalence of chromosomal abnormalities in Sri Lankan children undergoing cytogenetic analysis for suspected chromosomal disorders was relatively higher than that in Caucasian and other Asian populations.

  6. The DNA sequence, annotation and analysis of human chromosome 3

    DEFF Research Database (Denmark)

    Muzny, Donna M; Scherer, Steven E; Kaul, Rajinder;

    2006-01-01

    After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chr...

  7. The DNA sequence and comparative analysis of human chromosome 10.

    Science.gov (United States)

    Deloukas, P; Earthrowl, M E; Grafham, D V; Rubenfield, M; French, L; Steward, C A; Sims, S K; Jones, M C; Searle, S; Scott, C; Howe, K; Hunt, S E; Andrews, T D; Gilbert, J G R; Swarbreck, D; Ashurst, J L; Taylor, A; Battles, J; Bird, C P; Ainscough, R; Almeida, J P; Ashwell, R I S; Ambrose, K D; Babbage, A K; Bagguley, C L; Bailey, J; Banerjee, R; Bates, K; Beasley, H; Bray-Allen, S; Brown, A J; Brown, J Y; Burford, D C; Burrill, W; Burton, J; Cahill, P; Camire, D; Carter, N P; Chapman, J C; Clark, S Y; Clarke, G; Clee, C M; Clegg, S; Corby, N; Coulson, A; Dhami, P; Dutta, I; Dunn, M; Faulkner, L; Frankish, A; Frankland, J A; Garner, P; Garnett, J; Gribble, S; Griffiths, C; Grocock, R; Gustafson, E; Hammond, S; Harley, J L; Hart, E; Heath, P D; Ho, T P; Hopkins, B; Horne, J; Howden, P J; Huckle, E; Hynds, C; Johnson, C; Johnson, D; Kana, A; Kay, M; Kimberley, A M; Kershaw, J K; Kokkinaki, M; Laird, G K; Lawlor, S; Lee, H M; Leongamornlert, D A; Laird, G; Lloyd, C; Lloyd, D M; Loveland, J; Lovell, J; McLaren, S; McLay, K E; McMurray, A; Mashreghi-Mohammadi, M; Matthews, L; Milne, S; Nickerson, T; Nguyen, M; Overton-Larty, E; Palmer, S A; Pearce, A V; Peck, A I; Pelan, S; Phillimore, B; Porter, K; Rice, C M; Rogosin, A; Ross, M T; Sarafidou, T; Sehra, H K; Shownkeen, R; Skuce, C D; Smith, M; Standring, L; Sycamore, N; Tester, J; Thorpe, A; Torcasso, W; Tracey, A; Tromans, A; Tsolas, J; Wall, M; Walsh, J; Wang, H; Weinstock, K; West, A P; Willey, D L; Whitehead, S L; Wilming, L; Wray, P W; Young, L; Chen, Y; Lovering, R C; Moschonas, N K; Siebert, R; Fechtel, K; Bentley, D; Durbin, R; Hubbard, T; Doucette-Stamm, L; Beck, S; Smith, D R; Rogers, J

    2004-05-27

    The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence. PMID:15164054

  8. Spinal imaging and image analysis

    CERN Document Server

    Yao, Jianhua

    2015-01-01

    This book is instrumental to building a bridge between scientists and clinicians in the field of spine imaging by introducing state-of-the-art computational methods in the context of clinical applications.  Spine imaging via computed tomography, magnetic resonance imaging, and other radiologic imaging modalities, is essential for noninvasively visualizing and assessing spinal pathology. Computational methods support and enhance the physician’s ability to utilize these imaging techniques for diagnosis, non-invasive treatment, and intervention in clinical practice. Chapters cover a broad range of topics encompassing radiological imaging modalities, clinical imaging applications for common spine diseases, image processing, computer-aided diagnosis, quantitative analysis, data reconstruction and visualization, statistical modeling, image-guided spine intervention, and robotic surgery. This volume serves a broad audience as  contributions were written by both clinicians and researchers, which reflects the inte...

  9. Human oocyte chromosome analysis: complicated cases and major pitfalls

    Indian Academy of Sciences (India)

    Bernd Rosenbusch; Michael Schneider; Hans Wilhelm Michelmann

    2008-08-01

    Human oocytes that remained unfertilized in programmes of assisted reproduction have been analysed cytogenetically for more than 20 years to assess the incidence of aneuploidy in female gametes. However, the results obtained so far are not indisputable as a consequence of difficulties in evaluating oocyte chromosome preparations. Because of the lack of guidelines, we decided to summarize for the first time, the possible pitfalls in human oocyte chromosome analysis. Therefore, we screened the material from our previous studies and compiled representative, complicated cases with recommendations for their cytogenetic classification. We point out that maturity and size of the oocyte are important parameters and that fixation artefacts, as well as the particular structure of oocyte chromosomes, may predispose one to misinterpretations. Moreover, phenomena related to oocyte activation and fertilization are illustrated and explained. This compilation may help to avoid major problems in future studies and contribute to a more precise, and uniform assessment of human oocyte chromosomes.

  10. Biological dosimetry: chromosomal aberration analysis for dose assessment

    International Nuclear Information System (INIS)

    In view of the growing importance of chromosomal aberration analysis as a biological dosimeter, the present report provides a concise summary of the scientific background of the subject and a comprehensive source of information at the technical level. After a review of the basic principles of radiation dosimetry and radiation biology basic information on the biology of lymphocytes, the structure of chromosomes and the classification of chromosomal aberrations are presented. This is followed by a presentation of techniques for collecting blood, storing, transporting, culturing, making chromosomal preparations and scaring of aberrations. The physical and statistical parameters involved in dose assessment are discussed and examples of actual dose assessments taken from the scientific literature are given

  11. Advanced biomedical image analysis

    CERN Document Server

    Haidekker, Mark A

    2010-01-01

    "This book covers the four major areas of image processing: Image enhancement and restoration, image segmentation, image quantification and classification, and image visualization. Image registration, storage, and compression are also covered. The text focuses on recently developed image processing and analysis operators and covers topical research"--Provided by publisher.

  12. Retinal imaging and image analysis

    NARCIS (Netherlands)

    Abramoff, M.D.; Garvin, Mona K.; Sonka, Milan

    2010-01-01

    Many important eye diseases as well as systemic diseases manifest themselves in the retina. While a number of other anatomical structures contribute to the process of vision, this review focuses on retinal imaging and image analysis. Following a brief overview of the most prevalent causes of blindne

  13. Real-time imaging of meiotic chromosomes in S. cerevisiae

    Science.gov (United States)

    Koszul, Romain; Weiner, Beth M.

    2016-01-01

    Important information on cellular physiology can be obtained by directly observing living cells. The nucleus and the chromatin within are of particular interest to many researchers. Monitoring the behavior of specific DNA loci in the living cell is now commonly achieved through the insertion of binding sites for fluorescently tagged proteins at the sequence of interest (e.g. reference 1). However, visualizing the behavior of full length chromosomes can only be achieved when they constitute discrete, relatively well individualized units. During meiotic mid-prophase, chromosomes of budding yeast are well-organized structures that present such characteristics, making them remarkably suited for visualization. Here we describe the optimized protocols and techniques that allow monitoring of chromosome behavior during meiotic prophase in budding yeast. PMID:19685320

  14. Chromosome aberration analysis based on a beta-binomial distribution

    International Nuclear Information System (INIS)

    Analyses carried out here generalized on earlier studies of chromosomal aberrations in the populations of Hiroshima and Nagasaki, by allowing extra-binomial variation in aberrant cell counts corresponding to within-subject correlations in cell aberrations. Strong within-subject correlations were detected with corresponding standard errors for the average number of aberrant cells that were often substantially larger than was previously assumed. The extra-binomial variation is accomodated in the analysis in the present report, as described in the section on dose-response models, by using a beta-binomial (B-B) variance structure. It is emphasized that we have generally satisfactory agreement between the observed and the B-B fitted frequencies by city-dose category. The chromosomal aberration data considered here are not extensive enough to allow a precise discrimination between competing dose-response models. A quadratic gamma ray and linear neutron model, however, most closely fits the chromosome data. (author)

  15. Biological dosimetry of ionizing radiation by chromosomal aberration analysis

    International Nuclear Information System (INIS)

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical, and cytogenetic data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable. In this case, the study ol chromosomal aberrations, normally dicentric chromosomes, in peripheral lymphocytes can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using dicentric chromosomes analysis, X-rays at 300 kVp, 114 rad/min and temperature 37 degree celsius has been produced. Experimental data is fitted to model Y =α + β1D + β2D 2 , where Y is the number of dicentrics per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 14 refs

  16. Delimiting the origin of a B chromosome by FISH mapping, chromosome painting and DNA sequence analysis in Astyanax paranae (Teleostei, Characiformes.

    Directory of Open Access Journals (Sweden)

    Duílio M Z de A Silva

    Full Text Available Supernumerary (B chromosomes have been shown to contain a wide variety of repetitive sequences. For this reason, fluorescent in situ hybridisation (FISH is a useful tool for ascertaining the origin of these genomic elements, especially when combined with painting from microdissected B chromosomes. In order to investigate the origin of B chromosomes in the fish species Astyanax paranae, these two approaches were used along with PCR amplification of specific DNA sequences obtained from the B chromosomes and its comparison with those residing in the A chromosomes. Remarkably, chromosome painting with the one-arm metacentric B chromosome probe showed hybridization signals on entire B chromosome, while FISH mapping revealed the presence of H1 histone and 18S rDNA genes symmetrically placed in both arms of the B chromosome. These results support the hypothesis that the B chromosome of A. paranae is an isochromosome. Additionally, the chromosome pairs Nos. 2 or 23 are considered the possible B chromosome ancestors since both contain syntenic H1 and 18S rRNA sequences. The analysis of DNA sequence fragments of the histone and rRNA genes obtained from the microdissected B chromosomes showed high similarity with those obtained from 0B individuals, which supports the intraspecific origin of B chromosomes in A. paranae. Finally, the population hereby analysed showed a female-biased B chromosome presence suggesting that B chromosomes in this species could influence sex determinism.

  17. Mouse Karyotype Obtained by Combining DAPI Staining with Image Analysis

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    In this study, mitotic metaphase chromosomes in mouse were identified by a new chromosome fluorescence banding technique combining DAPI staining with image analysis. Clear 4', 6-diamidino-2-phenylindole (DAPI) multiple bands like G-bands could be produced in mouse. The MetaMorph software was then used to generate linescans of pixel intensity for the banded chromosomes from short arm to long arm. These linescans were sufficient not only to identify each individual chromosome but also analyze the physical sites of bands in chromosome. Based on the results, the clear and accurate karyotype of mouse metaphase chromosomes was established. The technique is therefore considered to be a new method for cytological studies of mouse.

  18. Molecular-Cytological Identification and Chromosome Behavior Analysis of Telotetrasomic in Rice

    Institute of Scientific and Technical Information of China (English)

    GONG Zhi-yun; GAO Qing-song; YU Heng-xiu; YI Chuan-deng; GU Ming-hong

    2008-01-01

    From the progenies of a telotrisomic of chromosome 9 short arm of an indica rice variety, Zhongxian 3037, a phenotypical variant was selected. The variant plant had rolled leaves, dispersed plant type, as well as a low seed-setting rate. Cytological and molecular cytological investigations revealed two extra chromosomes, which were the shortest in somatic cells of the variant. Fluorescent in situ hybridization (FISH) analysis using a rice centromere specific DNA (RCS2) and a DNA sequence specific for chromosome 9 on premetaphase and pachytene chromosomes showed that these two chromosomes were the short arms of chromosome 9. That is to say, the variant was a telotetrasomic of chromosome 9. Among the 25 pachytene cells, the two telosomic chromosomes paired each other to form a bivalent and didn't pair with other normal chromosome 9 as multivalents in 96% cells. However, the bivalent was easy to disassociate in advance.

  19. High-Throughput Live-Cell Microscopy Analysis of Association Between Chromosome Domains and the Nucleolus in S. cerevisiae.

    Science.gov (United States)

    Wang, Renjie; Normand, Christophe; Gadal, Olivier

    2016-01-01

    Spatial organization of the genome has important impacts on all aspects of chromosome biology, including transcription, replication, and DNA repair. Frequent interactions of some chromosome domains with specific nuclear compartments, such as the nucleolus, are now well documented using genome-scale methods. However, direct measurement of distance and interaction frequency between loci requires microscopic observation of specific genomic domains and the nucleolus, followed by image analysis to allow quantification. The fluorescent repressor operator system (FROS) is an invaluable method to fluorescently tag DNA sequences and investigate chromosome position and dynamics in living cells. This chapter describes a combination of methods to define motion and region of confinement of a locus relative to the nucleolus in cell's nucleus, from fluorescence acquisition to automated image analysis using two dedicated pipelines. PMID:27576709

  20. High-Throughput Live-Cell Microscopy Analysis of Association Between Chromosome Domains and the Nucleolus in S. cerevisiae.

    Science.gov (United States)

    Wang, Renjie; Normand, Christophe; Gadal, Olivier

    2016-01-01

    Spatial organization of the genome has important impacts on all aspects of chromosome biology, including transcription, replication, and DNA repair. Frequent interactions of some chromosome domains with specific nuclear compartments, such as the nucleolus, are now well documented using genome-scale methods. However, direct measurement of distance and interaction frequency between loci requires microscopic observation of specific genomic domains and the nucleolus, followed by image analysis to allow quantification. The fluorescent repressor operator system (FROS) is an invaluable method to fluorescently tag DNA sequences and investigate chromosome position and dynamics in living cells. This chapter describes a combination of methods to define motion and region of confinement of a locus relative to the nucleolus in cell's nucleus, from fluorescence acquisition to automated image analysis using two dedicated pipelines.

  1. Chromosome aberration analysis for biological dosimetry: a review

    International Nuclear Information System (INIS)

    Among various biological dosimetry techniques, dicentric chromosome aberration method appears to be the method of choice in analysing accidental radiation exposure in most of the laboratories. The major advantage of this method is its sensitivity as the number of dicentric chromosomes present in control population is too small and more importantly radiation induces mainly dicentric chromosome aberration among unstable aberration. This report brings out the historical development of various cytogenetic methods, the basic structure of DNA, chromosomes and different forms of chromosome aberrations. It also highlights the construction of dose-response curve for dicentric chromosome and its use in the estimation of radiation dose. (author)

  2. Towards single particle imaging of human chromosomes at SACLA

    Science.gov (United States)

    Robinson, Ian; Schwenke, Joerg; Yusuf, Mohammed; Estandarte, Ana; Zhang, Fucai; Chen, Bo; Clark, Jesse; Song, Changyong; Nam, Daewoong; Joti, Yasumasa; Tono, Kensuke; Yabashi, Makina; Ratnasari, Gina; Kaneyoshi, Kohei; Takata, Hideaki; Fukui, Kiichi

    2015-12-01

    Single particle imaging (SPI) is one of the front-page opportunities which were used to motivate the construction of the first x-ray free electron lasers (XFELs). SPI’s big advantage is that it avoids radiation damage to biological samples because the diffraction takes place in femtosecond single shots before any atomic motion can take place in the sample, hence before the onset of radiation damage. This is the ‘diffract before destruction’ theme, destruction being assured from the high x-ray doses used. This article reports our collaboration’s first attempt at SPI using the SACLA XFEL facility in June 2015. The report is limited to experience with the instrumentation and examples of data because we have not yet had time to invert them to images.

  3. Applying deep learning technology to automatically identify metaphase chromosomes using scanning microscopic images: an initial investigation

    Science.gov (United States)

    Qiu, Yuchen; Lu, Xianglan; Yan, Shiju; Tan, Maxine; Cheng, Samuel; Li, Shibo; Liu, Hong; Zheng, Bin

    2016-03-01

    Automated high throughput scanning microscopy is a fast developing screening technology used in cytogenetic laboratories for the diagnosis of leukemia or other genetic diseases. However, one of the major challenges of using this new technology is how to efficiently detect the analyzable metaphase chromosomes during the scanning process. The purpose of this investigation is to develop a computer aided detection (CAD) scheme based on deep learning technology, which can identify the metaphase chromosomes with high accuracy. The CAD scheme includes an eight layer neural network. The first six layers compose of an automatic feature extraction module, which has an architecture of three convolution-max-pooling layer pairs. The 1st, 2nd and 3rd pair contains 30, 20, 20 feature maps, respectively. The seventh and eighth layers compose of a multiple layer perception (MLP) based classifier, which is used to identify the analyzable metaphase chromosomes. The performance of new CAD scheme was assessed by receiver operation characteristic (ROC) method. A number of 150 regions of interest (ROIs) were selected to test the performance of our new CAD scheme. Each ROI contains either interphase cell or metaphase chromosomes. The results indicate that new scheme is able to achieve an area under the ROC curve (AUC) of 0.886+/-0.043. This investigation demonstrates that applying a deep learning technique may enable to significantly improve the accuracy of the metaphase chromosome detection using a scanning microscopic imaging technology in the future.

  4. MORPHOMETRIC ANALYSIS ON CHROMOSOMES OF TROPICAL Pinus SPECIES

    Directory of Open Access Journals (Sweden)

    Lília Rosário Ribeiro

    2009-01-01

    Full Text Available Karyotypic analysis of Pinus oocarpa Schiede ex Schltdl., Pinus patula Schltdl. & Cham. and of provenances Jócon Yoro, Las Camelias and San Rafael del Norte of Pinus tecunumanii Eguiluz & J. P. Perry were accomplished to provide information for definition of Pinus tecunumanii taxonomic status. Characterization of mitotic chromosomes stained with Giemsa and with 4', 6-diamidino-2- phenylindoldihydrochlorid (DAPI fluorochrome confirmed the karyotypic pattern reported for most of the Pinus species, which present eleven pairs of metacentric chromosomes, very similar in regard to length and morphology, and a submetacentric pair for all the taxa studied. Sharp definition of secondary constrictionsrevealed by DAPI staining allowed distinction of species and provenances by the number and position of this cytological marker. Pinus tecunumanii was also different from the other two species in regard to total length of haploid set. The results support the species status for Pinus tecunumanii as well as present evidence that in addition to point mutations, structural alterations contributed toward intra and interspecies differentiation into the genus Pinus.

  5. A Geometric Approach For Fully Automatic Chromosome Segmentation

    CERN Document Server

    Minaee, Shervin; Khalaj, Babak Hossein

    2011-01-01

    Chromosome segmentation is a fundamental task in human chromosome analysis. Most of previous methods for separation between touching chromosomes require human intervention. In this paper, a geometry based method is used for automatic chromosome segmentation. This method can be divided into two phases. In the first phase, chromosome clusters are detected using three geometric criteria and in the second phase chromosome clusters are separated using a proper cut line. However, most earlier methods do not work well with chromosome clusters that contain more than two chromosomes. Our method, on the other hand, has a high efficiency in separation of chromosome clusters in such scenarios. Another advantage of the proposed method is that it can easily apply to any type of images such as binary images. This is due to the fact that the proposed scheme uses the geometric features of chromosomes which are independent of the type of images. The performance of the proposed scheme is demonstrated on a database containing to...

  6. Linkage analysis on chromosome 2 in essential hypotension pedigrees

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    It is a new approach to study the important genes related to the control of blood pressure by probing into hypotension and hypertension at the same time. Genome scanning on whole chromosome 2 in 8 hypotension pedigrees has been done and parameter (LOD score) and non-pa- rameter (NPL score) were used in the linkage analysis by GENEHUNTER software. The results show the evidence of linkage between D2S112 and D2S117, indicating a number of critical genes may lie in thisregion and contribute to the mechanism of blood pressure regulation. Also this region has been found in the previous study in hypertension pedigrees. These genes may play an important role in the regulation of blood pressure and can also be the important candidate genes in hypertension studies.

  7. Computer aided analysis of additional chromosome aberrations in Philadelphia chromosome positive acute lymphoblastic leukaemia using a simplified computer readable cytogenetic notation

    Directory of Open Access Journals (Sweden)

    Mohr Brigitte

    2003-01-01

    Full Text Available Abstract Background The analysis of complex cytogenetic databases of distinct leukaemia entities may help to detect rare recurring chromosome aberrations, minimal common regions of gains and losses, and also hot spots of genomic rearrangements. The patterns of the karyotype alterations may provide insights into the genetic pathways of disease progression. Results We developed a simplified computer readable cytogenetic notation (SCCN by which chromosome findings are normalised at a resolution of 400 bands. Lost or gained chromosomes or chromosome segments are specified in detail, and ranges of chromosome breakpoint assignments are recorded. Software modules were written to summarise the recorded chromosome changes with regard to the respective chromosome involvement. To assess the degree of karyotype alterations the ploidy levels and numbers of numerical and structural changes were recorded separately, and summarised in a complex karyotype aberration score (CKAS. The SCCN and CKAS were used to analyse the extend and the spectrum of additional chromosome aberrations in 94 patients with Philadelphia chromosome positive (Ph-positive acute lymphoblastic leukemia (ALL and secondary chromosome anomalies. Dosage changes of chromosomal material represented 92.1% of all additional events. Recurring regions of chromosome losses were identified. Structural rearrangements affecting (pericentromeric chromosome regions were recorded in 24.6% of the cases. Conclusions SCCN and CKAS provide unifying elements between karyotypes and computer processable data formats. They proved to be useful in the investigation of additional chromosome aberrations in Ph-positive ALL, and may represent a step towards full automation of the analysis of large and complex karyotype databases.

  8. High-resolution image analysis.

    Science.gov (United States)

    Preston, K

    1986-01-01

    In many departments of cytology, cytogenetics, hematology, and pathology, research projects using high-resolution computerized microscopy are now being mounted for computation of morphometric measurements on various structural components, as well as for determination of cellular DNA content. The majority of these measurements are made in a partially automated, computer-assisted mode, wherein there is strong interaction between the user and the computerized microscope. At the same time, full automation has been accomplished for both sample preparation and sample examination for clinical determination of the white blood cell differential count. At the time of writing, approximately 1,000 robot differential counting microscopes are in the field, analyzing images of human white blood cells, red blood cells, and platelets at the overall rate of about 100,000 slides per day. This mammoth through-put represents a major accomplishment in the application of machine vision to automated microscopy for hematology. In other areas of automated high-resolution microscopy, such as cytology and cytogenetics, no commercial instruments are available (although a few metaphase-finding machines are available and other new machines have been announced during the past year). This is a disappointing product, considering the nearly half century of research effort in these areas. This paper provides examples of the state of the art in automation of cell analysis for blood smears, cervical smears, and chromosome preparations. Also treated are new developments in multi-resolution automated microscopy, where images are now being generated and analyzed by a single machine over a range of 64:1 magnification and from 10,000 X 20,000 to 500 X 500 in total picture elements (pixels). Examples of images of human lymph node and liver tissue are presented. Semi-automated systems are not treated, although there is mention of recent research in the automation of tissue analysis.

  9. Digital image analysis

    DEFF Research Database (Denmark)

    Riber-Hansen, Rikke; Vainer, Ben; Steiniche, Torben

    2012-01-01

    Digital image analysis (DIA) is increasingly implemented in histopathological research to facilitate truly quantitative measurements, decrease inter-observer variation and reduce hands-on time. Originally, efforts were made to enable DIA to reproduce manually obtained results on histological slides...... reproducibility, application of stereology-based quantitative measurements, time consumption, optimization of histological slides, regions of interest selection and recent developments in staining and imaging techniques....

  10. Detection of skewed X-chromosome inactivation in Fragile X syndrome and X chromosome aneuploidy using quantitative melt analysis.

    Science.gov (United States)

    Godler, David E; Inaba, Yoshimi; Schwartz, Charles E; Bui, Quang M; Shi, Elva Z; Li, Xin; Herlihy, Amy S; Skinner, Cindy; Hagerman, Randi J; Francis, David; Amor, David J; Metcalfe, Sylvia A; Hopper, John L; Slater, Howard R

    2015-07-01

    Methylation of the fragile X mental retardation 1 (FMR1) exon 1/intron 1 boundary positioned fragile X related epigenetic element 2 (FREE2), reveals skewed X-chromosome inactivation (XCI) in fragile X syndrome full mutation (FM: CGG > 200) females. XCI skewing has been also linked to abnormal X-linked gene expression with the broader clinical impact for sex chromosome aneuploidies (SCAs). In this study, 10 FREE2 CpG sites were targeted using methylation specific quantitative melt analysis (MS-QMA), including 3 sites that could not be analysed with previously used EpiTYPER system. The method was applied for detection of skewed XCI in FM females and in different types of SCA. We tested venous blood and saliva DNA collected from 107 controls (CGG chromosome test; (ii) locus-specific XCI skewing towards the hypomethylated state in FM females; and (iii) skewed XCI towards the hypermethylated state in SCA with 3 or more X chromosomes, and in 5% of the 47,XXY individuals. MS-QMA output also showed significant correlation with the EpiTYPER reference method in FM males and females (P < 0.0001) and SCAs (P < 0.05). In conclusion, we demonstrate use of MS-QMA to quantify skewed XCI in two applications with diagnostic utility.

  11. Direct ChromOSOme Analysis and FISH Detection of Primary Gastric cancer

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Objective: To investigate chromosome aberrations and their role in the genesis and development of primary gastric cancer. Methods: An improved, direct chromosome preparation from solid tumors was adopted for G-banding analysis followed by FISH on decolored G-banding chromosomes so that chromosome aberrations could be confirmed at DNA level. Results: A total of 28 primary gastric cancer specimens were studies. Case 1 and case 2 had simple chromosome numerical changes: 49, XY, +2, +8, +9 and 48, +8, +20, respectively. All but case 1 and 2 had complicated chromosome abnormalities. Chromosome structural of frequent occurrence involved del(7q)(21/26), del(3p)(14/26), del(lp)(l1/26) and del(17p)(10/26). The chromosome abnormalities could be simple and complicated. In former, numerical changes involving 1 to 3 chromosome could be observed. Trisomies 8 and 9 might represent a cytogenetic subgroup of primary gastric cancer. In the later, the del(7q) was the most consistent aberration. 7q32-qter was the commonly lost segment. Conclusion: Numerical and structural alterations of chromosomes are present in primary gastric cancer. Del(7q) is one of the structural change characteristic of primary gastric cancer. In the 7q32-qter fragment, a tumor suppressor gene probably exists and it may have close relation to the genesis and progression of gastric cancer.

  12. [Chromosomal organization of the genomes of small-chromosome plants].

    Science.gov (United States)

    Muravenko, O V; Zelenin, A V

    2009-11-01

    An effective approach to study the chromosome organization in genomes of plants with small chromosomes and/or with low-informative C-banding patterns was developed in the course of investigation of the karyotypes of cotton plant, camomile, flax, and pea. To increase the resolving power of chromosome analysis, methods were worked out for revealing early replication patterns on chromosomes and for artificial impairment of mitotic chromosome condensation with the use of a DNA intercalator, 9-aminoacridine (9-AMA). To estimate polymorphism of the patterns of C-banding of small chromosomes on preparations obtained with the use of 9-AMA, it is necessary to choose a length interval that must not exceed three average sizes of metaphase chromosomes without the intercalator. The use of 9-AMA increases the resolution of differential C- and OR-banding and the precision of physical chromosome mapping by the FISH method. Of particular importance in studying small chromosomes is optimization of the computer-aided methods used to obtain and process chromosome images. The complex approach developed for analysis of the chromosome organization in plant genomes was used to study the karyotypes of 24 species of the genus Linum L. It permitted their chromosomes to be identified for the first time, and, in addition, B chromosomes were discovered and studied in the karyotypes of the species of the section Syllinum. By similarity of the karyotypes, the studied flax species were distributed in eight groups in agreement with the clusterization of these species according to the results of RAPD analysis performed in parallel. Systematic positions and phylogenetic relationships of the studied flax species were verified. Out results can serve as an important argument in favour of the proposal to develop a special program for sequencing the genome of cultivated flax (L. usitatissimum L.), which is a major representative of small-chromosome species. PMID:20058798

  13. Hyperspectral image analysis. A tutorial

    DEFF Research Database (Denmark)

    Amigo Rubio, Jose Manuel; Babamoradi, Hamid; Elcoroaristizabal Martin, Saioa

    2015-01-01

    This tutorial aims at providing guidelines and practical tools to assist with the analysis of hyperspectral images. Topics like hyperspectral image acquisition, image pre-processing, multivariate exploratory analysis, hyperspectral image resolution, classification and final digital image processi...... to differentiate between several types of plastics by using Near infrared hyperspectral imaging and Partial Least Squares - Discriminant Analysis. Thus, the reader is guided through every single step and oriented in order to adapt those strategies to the user's case....

  14. Single-Molecule Analysis of Replicating Yeast Chromosomes.

    Science.gov (United States)

    Gallo, David; Wang, Gang; Yip, Christopher M; Brown, Grant W

    2016-02-01

    The faithful replication of eukaryotic chromosomal DNA occurs during S phase once per cell cycle. Replication is highly regulated and is initiated at special structures, termed origins, from which replication forks move out bidirectionally. A wide variety of techniques have been developed to study the features and kinetics of replication. Many of these, such as those based on flow cytometry and two-dimensional and pulsed-field gel electrophoresis, give a population-level view of replication. However, an alternative approach, DNA fiber analysis, which was originally developed more than 50 years ago, has the advantage of revealing features of replication at the level of individual DNA fibers. Initially based on autoradiography, this technique has been superseded by immunofluorescence-based detection of incorporated halogenated thymidine analogs. Furthermore, derivations of this technique have been developed to distribute and stretch the labeled DNA fibers uniformly on optically clear surfaces. As described here, one such technique-DNA combing, in which DNA is combed onto silanized coverslips-has been used successfully to monitor replication fork progression and origin usage in budding yeast. PMID:26832692

  15. Systematic analysis of S. cerevisiae chromosome VIII genes.

    Science.gov (United States)

    Niedenthal, R; Riles, L; Güldener, U; Klein, S; Johnston, M; Hegemann, J H

    1999-12-01

    To begin genome-wide functional analysis, we analysed the consequences of deleting each of the 265 genes of chromosome VIII of Saccharomyces cerevisiae. For 33% of the deletion strains a growth phenotype could be detected: 18% of the genes are essential for growth on complete glucose medium, and 15% grow significantly more slowly than the wild-type strain or exhibit a conditional phenotype when incubated under one of 20 different growth conditions. Two-thirds of the mutants that exhibit conditional phenotypes are pleiotropic; about one-third of the mutants exhibit only one phenotype. We also measured the level of expression directed by the promoter of each gene. About half of the promoters direct detectable transcription in rich glucose medium, and most of these exhibited only low or medium activity. Only 1% of the genes are expressed at about the same level as ACT1. The number of active promoters increased to 76% upon growth on a non-fermentable carbon source, and to 93% in minimal glucose medium. The majority of promoters fluctuated in strength, depending on the medium.

  16. An investigation of ring and dicentric chromosomes found in three Turner's syndrome patients using DNA analysis and in situ hybridisation with X and Y chromosome specific probes.

    OpenAIRE

    Cooper, C; Crolla, J. A.; Laister, C; Johnston, D I; Cooke, P.

    1991-01-01

    We have studied three patients with features of Turner's syndrome, two with a 45,X/46,X,r(?) and the third with a 45,X/46,X,dic?(Y) karyotype. Because Turner's syndrome patients with a mosaic karyotype containing a Y chromosome are known to have a high risk of developing gonadal tumours, we used DNA analysis and in situ hybridisation with X and Y specific probes to identify the chromosomal origin of the rings and dicentric chromosomes in the three index patients. Both ring chromosomes were sh...

  17. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

    Science.gov (United States)

    Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

    2016-05-01

    Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies. PMID:26758200

  18. DNA sequence and analysis of human chromosome 8.

    Science.gov (United States)

    Nusbaum, Chad; Mikkelsen, Tarjei S; Zody, Michael C; Asakawa, Shuichi; Taudien, Stefan; Garber, Manuel; Kodira, Chinnappa D; Schueler, Mary G; Shimizu, Atsushi; Whittaker, Charles A; Chang, Jean L; Cuomo, Christina A; Dewar, Ken; FitzGerald, Michael G; Yang, Xiaoping; Allen, Nicole R; Anderson, Scott; Asakawa, Teruyo; Blechschmidt, Karin; Bloom, Toby; Borowsky, Mark L; Butler, Jonathan; Cook, April; Corum, Benjamin; DeArellano, Kurt; DeCaprio, David; Dooley, Kathleen T; Dorris, Lester; Engels, Reinhard; Glöckner, Gernot; Hafez, Nabil; Hagopian, Daniel S; Hall, Jennifer L; Ishikawa, Sabine K; Jaffe, David B; Kamat, Asha; Kudoh, Jun; Lehmann, Rüdiger; Lokitsang, Tashi; Macdonald, Pendexter; Major, John E; Matthews, Charles D; Mauceli, Evan; Menzel, Uwe; Mihalev, Atanas H; Minoshima, Shinsei; Murayama, Yuji; Naylor, Jerome W; Nicol, Robert; Nguyen, Cindy; O'Leary, Sinéad B; O'Neill, Keith; Parker, Stephen C J; Polley, Andreas; Raymond, Christina K; Reichwald, Kathrin; Rodriguez, Joseph; Sasaki, Takashi; Schilhabel, Markus; Siddiqui, Roman; Smith, Cherylyn L; Sneddon, Tam P; Talamas, Jessica A; Tenzin, Pema; Topham, Kerri; Venkataraman, Vijay; Wen, Gaiping; Yamazaki, Satoru; Young, Sarah K; Zeng, Qiandong; Zimmer, Andrew R; Rosenthal, Andre; Birren, Bruce W; Platzer, Matthias; Shimizu, Nobuyoshi; Lander, Eric S

    2006-01-19

    The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution. PMID:16421571

  19. Gene expression meta-analysis identifies chromosomal regions involved in ovarian cancer survival

    DEFF Research Database (Denmark)

    Thomassen, Mads; Jochumsen, Kirsten M; Mogensen, Ole;

    2009-01-01

    the relation of gene expression and chromosomal position to identify chromosomal regions of importance for early recurrence of ovarian cancer. By use of *Gene Set Enrichment Analysis*, we have ranked chromosomal regions according to their association to survival. Over-representation analysis including 1......Ovarian cancer cells exhibit complex karyotypic alterations causing deregulation of numerous genes. Some of these genes are probably causal for cancer formation and local growth, whereas others are causal for metastasis and recurrence. By using publicly available data sets, we have investigated......-4 consecutive cytogenetic bands identified regions with increased expression for chromosome 5q12-14, and a very large region of chromosome 7 with the strongest signal at 7p15-13 among tumors from short-living patients. Reduced gene expression was identified at 4q26-32, 6p12-q15, 9p21-q32, and 11p14-11. We...

  20. Achievement report for fiscal 1999 on research and development of technologies for medical welfare equipment. Chromosome image analysis and diagnosis device with confocal scanning laser microscope; 1999 nendo iryo fukushi kiki gijutsu kenkyu kaihatsu seika hokokusho. Kyoshoten laser kenbikyo ni yoru zensenshokutai gazo kaiseki shindan sochi

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-05-01

    The device is now satisfactorily capable of all image processing functions (bi-levelling, color deviation, brilliance adjustment, etc.) with the exception the karyotyping function. A substance that emits fluorescence by laser excitation is developed (for labelling the probe). A direct labelling method is studied, in which nucleic acid probes (nucleic acid labelled for chromosomal identification) will prove to be remarkably high in sensitivity. A new fluorescent reagent is synthesized, which is a BHHCT-4-dUTP to act as a nucleic acid probe. It is found that the new substance is superior to the conventional fluorescent substances in terms of stability and that all chromosomes may be forced into hybridization (selective combination of a probe with a peculiar chromosome) when various probes are labelled by this substance. A programing unit is constructed for a chromosomal aberration database. Items needed relative to chromosomes and parameters relative to chromosomal aberration data are appropriately arranged, and conditions to satisfy for their development into a database are studied. A rough design of an interface is complete. (NEDO)

  1. CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR-Cas system.

    Science.gov (United States)

    Yan, Meng; Zhou, Shi-Rong; Xue, Hong-Wei

    2015-07-01

    The clustered regularly interspaced short palindromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user-friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present CRISPR Primer Designer for researchers to design primers for CRISPR applications. The program has a user-friendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRISPR-Cas system-based chromosome imaging system.

  2. CRISPR Primer Designer:Design primers for knockout and chromosome imaging CRISPR-Cas system

    Institute of Scientific and Technical Information of China (English)

    Meng Yan; Shi-Rong Zhou; Hong-Wei Xue

    2015-01-01

    The clustered regularly interspaced short palin-dromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especial y the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran local y and acquired a user-friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were stil no tools helping users to generate specific end-user spacers. We herein present CRISPR Primer Designer for researchers to design primers for CRISPR applications. The program has a user-friendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs local y and can be used to search spacer clusters, and exports primers for the CRISPR-Cas system-based chromosome imaging system.

  3. Risk of chromosomal abnormalities in early spontaneous abortion after assisted reproductive technology: a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Jun-Zhen Qin

    Full Text Available BACKGROUND: Studies on the risk of chromosomal abnormalities in early spontaneous abortion after assisted reproductive technology (ART are relatively controversial and insufficient. Thus, to obtain a more precise evaluation of the risk of embryonic chromosomal abnormalities in first-trimester miscarriage after ART, we performed a meta-analysis of all available case-control studies relating to the cytogenetic analysis of chromosomal abnormalities in first-trimester miscarriage after ART. METHODS: Literature search in the electronic databases MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials (CENTRAL based on the established strategy. Meta-regression, subgroup analysis, and Galbraith plots were conducted to explore the sources of heterogeneity. RESULTS: A total of 15 studies with 1,896 cases and 1,186 controls relevant to the risk of chromosomal abnormalities in first- trimester miscarriage after ART, and 8 studies with 601 cases and 602 controls evaluating frequency of chromosome anomaly for maternal age≥35 versus <35 were eligible for the meta-analysis. No statistical difference was found in risk of chromosomally abnormal miscarriage compared to natural conception and the different types of ART utilized, whereas the risk of fetal aneuploidy significantly increased with maternal age≥35 (OR 2.88, 95% CI: 1.74-4.77. CONCLUSIONS: ART treatment does not present an increased risk for chromosomal abnormalities occurring in a first trimester miscarriage, but incidence of fetal aneuploidy could increase significantly with advancing maternal age.

  4. Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat

    Directory of Open Access Journals (Sweden)

    Sehgal Sunish K

    2012-05-01

    Full Text Available Abstract Background Bread wheat, one of the world’s staple food crops, has the largest, highly repetitive and polyploid genome among the cereal crops. The wheat genome holds the key to crop genetic improvement against challenges such as climate change, environmental degradation, and water scarcity. To unravel the complex wheat genome, the International Wheat Genome Sequencing Consortium (IWGSC is pursuing a chromosome- and chromosome arm-based approach to physical mapping and sequencing. Here we report on the use of a BAC library made from flow-sorted telosomic chromosome 3A short arm (t3AS for marker development and analysis of sequence composition and comparative evolution of homoeologous genomes of hexaploid wheat. Results The end-sequencing of 9,984 random BACs from a chromosome arm 3AS-specific library (TaaCsp3AShA generated 11,014,359 bp of high quality sequence from 17,591 BAC-ends with an average length of 626 bp. The sequence represents 3.2% of t3AS with an average DNA sequence read every 19 kb. Overall, 79% of the sequence consisted of repetitive elements, 1.38% as coding regions (estimated 2,850 genes and another 19% of unknown origin. Comparative sequence analysis suggested that 70-77% of the genes present in both 3A and 3B were syntenic with model species. Among the transposable elements, gypsy/sabrina (12.4% was the most abundant repeat and was significantly more frequent in 3A compared to homoeologous chromosome 3B. Twenty novel repetitive sequences were also identified using de novo repeat identification. BESs were screened to identify simple sequence repeats (SSR and transposable element junctions. A total of 1,057 SSRs were identified with a density of one per 10.4 kb, and 7,928 junctions between transposable elements (TE and other sequences were identified with a density of one per 1.39 kb. With the objective of enhancing the marker density of chromosome 3AS, oligonucleotide primers were successfully designed from

  5. Medical Image Analysis Facility

    Science.gov (United States)

    1978-01-01

    To improve the quality of photos sent to Earth by unmanned spacecraft. NASA's Jet Propulsion Laboratory (JPL) developed a computerized image enhancement process that brings out detail not visible in the basic photo. JPL is now applying this technology to biomedical research in its Medical lrnage Analysis Facility, which employs computer enhancement techniques to analyze x-ray films of internal organs, such as the heart and lung. A major objective is study of the effects of I stress on persons with heart disease. In animal tests, computerized image processing is being used to study coronary artery lesions and the degree to which they reduce arterial blood flow when stress is applied. The photos illustrate the enhancement process. The upper picture is an x-ray photo in which the artery (dotted line) is barely discernible; in the post-enhancement photo at right, the whole artery and the lesions along its wall are clearly visible. The Medical lrnage Analysis Facility offers a faster means of studying the effects of complex coronary lesions in humans, and the research now being conducted on animals is expected to have important application to diagnosis and treatment of human coronary disease. Other uses of the facility's image processing capability include analysis of muscle biopsy and pap smear specimens, and study of the microscopic structure of fibroprotein in the human lung. Working with JPL on experiments are NASA's Ames Research Center, the University of Southern California School of Medicine, and Rancho Los Amigos Hospital, Downey, California.

  6. Radar image analysis utilizing junctive image metamorphosis

    Science.gov (United States)

    Krueger, Peter G.; Gouge, Sally B.; Gouge, Jim O.

    1998-09-01

    A feasibility study was initiated to investigate the ability of algorithms developed for medical sonogram image analysis, to be trained for extraction of cartographic information from synthetic aperture radar imagery. BioComputer Research Inc. has applied proprietary `junctive image metamorphosis' algorithms to cancer cell recognition and identification in ultrasound prostate images. These algorithms have been shown to support automatic radar image feature detection and identification. Training set images were used to develop determinants for representative point, line and area features, which were used on test images to identify and localize the features of interest. The software is computationally conservative; operating on a PC platform in real time. The algorithms are robust; having applicability to be trained for feature recognition on any digital imagery, not just those formed from reflected energy, such as sonograms and radar images. Applications include land mass characterization, feature identification, target recognition, and change detection.

  7. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.

    Science.gov (United States)

    Salanoubat, M; Lemcke, K; Rieger, M; Ansorge, W; Unseld, M; Fartmann, B; Valle, G; Blöcker, H; Perez-Alonso, M; Obermaier, B; Delseny, M; Boutry, M; Grivell, L A; Mache, R; Puigdomènech, P; De Simone, V; Choisne, N; Artiguenave, F; Robert, C; Brottier, P; Wincker, P; Cattolico, L; Weissenbach, J; Saurin, W; Quétier, F; Schäfer, M; Müller-Auer, S; Gabel, C; Fuchs, M; Benes, V; Wurmbach, E; Drzonek, H; Erfle, H; Jordan, N; Bangert, S; Wiedelmann, R; Kranz, H; Voss, H; Holland, R; Brandt, P; Nyakatura, G; Vezzi, A; D'Angelo, M; Pallavicini, A; Toppo, S; Simionati, B; Conrad, A; Hornischer, K; Kauer, G; Löhnert, T H; Nordsiek, G; Reichelt, J; Scharfe, M; Schön, O; Bargues, M; Terol, J; Climent, J; Navarro, P; Collado, C; Perez-Perez, A; Ottenwälder, B; Duchemin, D; Cooke, R; Laudie, M; Berger-Llauro, C; Purnelle, B; Masuy, D; de Haan, M; Maarse, A C; Alcaraz, J P; Cottet, A; Casacuberta, E; Monfort, A; Argiriou, A; flores, M; Liguori, R; Vitale, D; Mannhaupt, G; Haase, D; Schoof, H; Rudd, S; Zaccaria, P; Mewes, H W; Mayer, K F; Kaul, S; Town, C D; Koo, H L; Tallon, L J; Jenkins, J; Rooney, T; Rizzo, M; Walts, A; Utterback, T; Fujii, C Y; Shea, T P; Creasy, T H; Haas, B; Maiti, R; Wu, D; Peterson, J; Van Aken, S; Pai, G; Militscher, J; Sellers, P; Gill, J E; Feldblyum, T V; Preuss, D; Lin, X; Nierman, W C; Salzberg, S L; White, O; Venter, J C; Fraser, C M; Kaneko, T; Nakamura, Y; Sato, S; Kato, T; Asamizu, E; Sasamoto, S; Kimura, T; Idesawa, K; Kawashima, K; Kishida, Y; Kiyokawa, C; Kohara, M; Matsumoto, M; Matsuno, A; Muraki, A; Nakayama, S; Nakazaki, N; Shinpo, S; Takeuchi, C; Wada, T; Watanabe, A; Yamada, M; Yasuda, M; Tabata, S

    2000-12-14

    Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes. PMID:11130713

  8. Chromosomal evolution in the Drosophila cardini group (Diptera: Drosophilidae): photomaps and inversion analysis.

    Science.gov (United States)

    Cordeiro, Juliana; De Toni, Daniela Cristina; da Silva, Gisele de Souza; Valente, Vera Lucia da Silva

    2014-10-01

    Detailed chromosome photomaps are the first step to develop further chromosomal analysis to study the evolution of the genetic architecture in any set of species, considering that chromosomal rearrangements, such as inversions, are common features of genome evolution. In this report, we analyzed inversion polymorphisms in 25 different populations belonging to six neotropical species in the cardini group: Drosophila cardini, D. cardinoides, D. neocardini, D. neomorpha, D. parthenogenetica and D. polymorpha. Furthermore, we present the first reference photomaps for the Neotropical D. cardini and D. parthenogenetica and improved photomaps for D. cardinoides, D. neocardini and D. polymorpha. We found 19 new inversions for these species. An exhaustive pairwise comparison of the polytene chromosomes was conducted for the six species in order to understand evolutionary patterns of their chromosomes.

  9. Gabor Analysis for Imaging

    DEFF Research Database (Denmark)

    Christensen, Ole; Feichtinger, Hans G.; Paukner, Stephan

    2015-01-01

    In contrast to classical Fourier analysis, time–frequency analysis is concerned with localized Fourier transforms. Gabor analysis is an important branch of time–frequency analysis. Although significantly different, it shares with the wavelet transform methods the ability to describe the smoothness...... of a given function in a location-dependent way. The main tool is the sliding window Fourier transform or short-time Fourier transform (STFT) in the context of audio signals. It describes the correlation of a signal with the time–frequency shifted copies of a fixed function (or window or atom). Thus......, it characterizes a function by its transform over phase space, which is the time–frequency plane (TF-plane) in a musical context or the location–wave-number domain in the context of image processing. Since the transition from the signal domain to the phase space domain introduces an enormous amount of data...

  10. The sequence and analysis of duplication rich human chromosome 16

    Energy Technology Data Exchange (ETDEWEB)

    Martin, J; Han, C; Gordon, L A; Terry, A; Prabhakar, S; She, X; Xie, G; Hellsten, U; Chan, Y M; Altherr, M; Couronne, O; Aerts, A; Bajorek, E; Black, S; Blumer, H; Branscomb, E; Brown, N; Bruno, W J; Buckingham, J; Callen, D F; Campbell, C S; Campbell, M L; Campbell, E W; Caoile, C; Challacombe, J F; Chasteen, L A; Chertkov, O; Chi, H C; Christensen, M; Clark, L M; Cohn, J D; Denys, M; Detter, J C; Dickson, M; Dimitrijevic-Bussod, M; Escobar, J; Fawcett, J J; Flowers, D; Fotopulos, D; Glavina, T; Gomez, M; Gonzales, E; Goodstein, D; Goodwin, L A; Grady, D L; Grigoriev, I; Groza, M; Hammon, N; Hawkins, T; Haydu, L; Hildebrand, C E; Huang, W; Israni, S; Jett, J; Jewett, P B; Kadner, K; Kimball, H; Kobayashi, A; Krawczyk, M; Leyba, T; Longmire, J L; Lopez, F; Lou, Y; Lowry, S; Ludeman, T; Manohar, C F; Mark, G A; McMurray, K L; Meincke, L J; Morgan, J; Moyzis, R K; Mundt, M O; Munk, A C; Nandkeshwar, R D; Pitluck, S; Pollard, M; Predki, P; Parson-Quintana, B; Ramirez, L; Rash, S; Retterer, J; Ricke, D O; Robinson, D; Rodriguez, A; Salamov, A; Saunders, E H; Scott, D; Shough, T; Stallings, R L; Stalvey, M; Sutherland, R D; Tapia, R; Tesmer, J G; Thayer, N; Thompson, L S; Tice, H; Torney, D C; Tran-Gyamfi, M; Tsai, M; Ulanovsky, L E; Ustaszewska, A; Vo, N; White, P S; Williams, A L; Wills, P L; Wu, J; Wu, K; Yang, J; DeJong, P; Bruce, D; Doggett, N A; Deaven, L; Schmutz, J; Grimwood, J; Richardson, P; Rokhsar, D S; Eichler, E E; Gilna, P; Lucas, S M; Myers, R M; Rubin, E M; Pennacchio, L A

    2005-04-06

    Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes, and 3 RNA pseudogenes. These genes include metallothionein, cadherin, and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. While the segmental duplications of chromosome 16 are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events likely to have had an impact on the evolution of primates and human disease susceptibility.

  11. Novel Integrated Lab-on-Chip System for Chromosome Translocations Analysis

    DEFF Research Database (Denmark)

    Svendsen, Winnie Edith; Lange, Jacob Moresco; Shah, Pranjul Jaykumar;

    2009-01-01

    This presentation will focus on the development of a chromosome total analysis system (C-TAS) starting from the design strategy and simulations to the integration into a final monolithic plug and play device. Individual modules which perform the sample preprocessing and analysis tasks like - cell...... isolation, cell culture, cell lysing, chromosome extraction and Fluorescence In-Situ Hybridization will be presented. How we solved connecting the individual chips and adjusting the microfluidic flows, by using simulations will be discussed....

  12. Shannon Information and Power Law Analysis of the Chromosome Code

    Directory of Open Access Journals (Sweden)

    J. A. Tenreiro Machado

    2012-01-01

    Full Text Available This paper studies the information content of the chromosomes of twenty-three species. Several statistics considering different number of bases for alphabet character encoding are derived. Based on the resulting histograms, word delimiters and character relative frequencies are identified. The knowledge of this data allows moving along each chromosome while evaluating the flow of characters and words. The resulting flux of information is captured by means of Shannon entropy. The results are explored in the perspective of power law relationships allowing a quantitative evaluation of the DNA of the species.

  13. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  14. Analysis of chromosome aberration data by hybrid-scale models

    Energy Technology Data Exchange (ETDEWEB)

    Indrawati, Iwiq [Research and Development on Radiation and Nuclear Biomedical Center, National Nuclear Energy Agency (Indonesia); Kumazawa, Shigeru [Nuclear Technology and Education Center, Japan Atomic Energy Research Institute, Honkomagome, Tokyo (Japan)

    2000-02-01

    This paper presents a new methodology for analyzing data of chromosome aberrations, which is useful to understand the characteristics of dose-response relationships and to construct the calibration curves for the biological dosimetry. The hybrid scale of linear and logarithmic scales brings a particular plotting paper, where the normal section paper, two types of semi-log papers and the log-log paper are continuously connected. The hybrid-hybrid plotting paper may contain nine kinds of linear relationships, and these are conveniently called hybrid scale models. One can systematically select the best-fit model among the nine models by among the conditions for a straight line of data points. A biological interpretation is possible with some hybrid-scale models. In this report, the hybrid scale models were applied to separately reported data on chromosome aberrations in human lymphocytes as well as on chromosome breaks in Tradescantia. The results proved that the proposed models fit the data better than the linear-quadratic model, despite the demerit of the increased number of model parameters. We showed that the hybrid-hybrid model (both variables of dose and response using the hybrid scale) provides the best-fit straight lines to be used as the reliable and readable calibration curves of chromosome aberrations. (author)

  15. A sugar beet (Beta vulgaris L.) reference FISH karyotype for chromosome and chromosome-arm identification, integration of genetic linkage groups and analysis of major repeat family distribution.

    Science.gov (United States)

    Paesold, Susanne; Borchardt, Dietrich; Schmidt, Thomas; Dechyeva, Daryna

    2012-11-01

    We developed a reference karyotype for B. vulgaris which is applicable to all beet cultivars and provides a consistent numbering of chromosomes and genetic linkage groups. Linkage groups of sugar beet were assigned to physical chromosome arms by FISH (fluorescent in situ hybridization) using a set of 18 genetically anchored BAC (bacterial artificial chromosome) markers. Genetic maps of sugar beet were correlated to chromosome arms, and North-South orientation of linkage groups was established. The FISH karyotype provides a technical platform for genome studies and can be applied for numbering and identification of chromosomes in related wild beet species. The discrimination of all nine chromosomes by BAC probes enabled the study of chromosome-specific distribution of the major repetitive components of sugar beet genome comprising pericentromeric, intercalary and subtelomeric satellites and 18S-5.8S-25S and 5S rRNA gene arrays. We developed a multicolor FISH procedure allowing the identification of all nine sugar beet chromosome pairs in a single hybridization using a pool of satellite DNA probes. Fiber-FISH was applied to analyse five chromosome arms in which the furthermost genetic marker of the linkage group was mapped adjacently to terminal repetitive sequences on pachytene chromosomes. Only on two arms telomere arrays and the markers are physically linked, hence these linkage groups can be considered as terminally closed making the further identification of distal informative markers difficult. The results support genetic mapping by marker localization, the anchoring of contigs and scaffolds for the annotation of the sugar beet genome sequence and the analysis of the chromosomal distribution patterns of major families of repetitive DNA.

  16. A sugar beet (Beta vulgaris L.) reference FISH karyotype for chromosome and chromosome-arm identification, integration of genetic linkage groups and analysis of major repeat family distribution.

    Science.gov (United States)

    Paesold, Susanne; Borchardt, Dietrich; Schmidt, Thomas; Dechyeva, Daryna

    2012-11-01

    We developed a reference karyotype for B. vulgaris which is applicable to all beet cultivars and provides a consistent numbering of chromosomes and genetic linkage groups. Linkage groups of sugar beet were assigned to physical chromosome arms by FISH (fluorescent in situ hybridization) using a set of 18 genetically anchored BAC (bacterial artificial chromosome) markers. Genetic maps of sugar beet were correlated to chromosome arms, and North-South orientation of linkage groups was established. The FISH karyotype provides a technical platform for genome studies and can be applied for numbering and identification of chromosomes in related wild beet species. The discrimination of all nine chromosomes by BAC probes enabled the study of chromosome-specific distribution of the major repetitive components of sugar beet genome comprising pericentromeric, intercalary and subtelomeric satellites and 18S-5.8S-25S and 5S rRNA gene arrays. We developed a multicolor FISH procedure allowing the identification of all nine sugar beet chromosome pairs in a single hybridization using a pool of satellite DNA probes. Fiber-FISH was applied to analyse five chromosome arms in which the furthermost genetic marker of the linkage group was mapped adjacently to terminal repetitive sequences on pachytene chromosomes. Only on two arms telomere arrays and the markers are physically linked, hence these linkage groups can be considered as terminally closed making the further identification of distal informative markers difficult. The results support genetic mapping by marker localization, the anchoring of contigs and scaffolds for the annotation of the sugar beet genome sequence and the analysis of the chromosomal distribution patterns of major families of repetitive DNA. PMID:22775355

  17. Chromosomal analysis of Physalaemus kroyeri and Physalaemus cicada (Anura, Leptodactylidae)

    Science.gov (United States)

    Vittorazzi, Stenio Eder; Lourenço, Luciana Bolsoni; Solé, Mirco; Faria, Renato Gomes; Recco-Pimentel, Shirlei Maria

    2016-01-01

    Abstract All the species of Physalaemus Fitzinger, 1826 karyotyped up until now have been classified as 2n = 22. The species of the Physalaemus cuvieri group analyzed by C-banding present a block of heterochromatin in the interstitial region of the short arm of pair 5. Physalaemus cicada Bokermann, 1966 has been considered to be a member of the Physalaemus cuvieri species group, although its interspecific phylogenetic relationships remain unknown. The PcP190 satellite DNA has been mapped on the chromosomes of most of the species of the Physalaemus cuvieri group. For two species, Physalaemus cicada and Physalaemus kroyeri (Reinhardt & Lütken, 1862), however, only the chromosome number and morphology are known. Given this, the objective of the present study was to analyze the chromosomes of Physalaemus cicada and Physalaemus kroyeri, primarily by C-banding and PcP190 mapping. The results indicate that Physalaemus kroyeri and Physalaemus cicada have similar karyotypes, which were typical of Physalaemus. In both species, the NORs are located on the long arm of pair 8, and the C-banding indicated that, among other features, Physalaemus kroyeri has the interstitial band on chromosome 5, which is however absent in Physalaemus cicada. Even so, a number of telomeric bands were observed in Physalaemus cicada. The mapping of the PcP190 satellite DNA highlighted areas of the centromeric region of the chromosomes of pair 1 in both species, although in Physalaemus kroyeri, heteromorphism was also observed in pair 3. The cytogenetic evidence does not support the inclusion of Physalaemus cicada in the Physalaemus cuvieri group. In the case of Physalaemus kroyeri, the interstitial band on pair 5 is consistent with the existence of a cytogenetic synapomorphy in the Physalaemus cuvieri species group. PMID:27551351

  18. Genomic Imbalances in Neonates With Birth Defects: High Detection Rates by Using Chromosomal Microarray Analysis

    Science.gov (United States)

    Lu, Xin-Yan; Phung, Mai T.; Shaw, Chad A.; Pham, Kim; Neil, Sarah E.; Patel, Ankita; Sahoo, Trilochan; Bacino, Carlos A.; Stankiewicz, Pawel; Lee Kang, Sung-Hae; Lalani, Seema; Chinault, A. Craig; Lupski, James R.; Cheung, Sau W.; Beaudet, Arthur L.

    2009-01-01

    OBJECTIVES Our aim was to determine the frequency of genomic imbalances in neonates with birth defects by using targeted array-based comparative genomic hybridization, also known as chromosomal microarray analysis. METHODS Between March 2006 and September 2007, 638 neonates with various birth defects were referred for chromosomal microarray analysis. Three consecutive chromosomal microarray analysis versions were used: bacterial artificial chromosome-based versions V5 and V6 and bacterial artificial chromosome emulated oligonucleotide-based version V6 Oligo. Each version had targeted but increasingly extensive genomic coverage and interrogated >150 disease loci with enhanced coverage in genomic rearrangement-prone pericentromeric and subtelomeric regions. RESULTS Overall, 109 (17.1%) patients were identified with clinically significant abnormalities with detection rates of 13.7%, 16.6%, and 19.9% on V5, V6, and V6 Oligo, respectively. The majority of these abnormalities would not be defined by using karyotype analysis. The clinically significant detection rates by use of chromosomal microarray analysis for various clinical indications were 66.7% for “possible chromosomal abnormality” ± “others” (other clinical indications), 33.3% for ambiguous genitalia ± others, 27.1% for dysmorphic features + multiple congenital anomalies ± others, 24.6% for dysmorphic features ± others, 21.8% for congenital heart disease ± others, 17.9% for multiple congenital anomalies ± others, and 9.5% for the patients referred for others that were different from the groups defined. In all, 16 (2.5%) patients had chromosomal aneuploidies, and 81 (12.7%) patients had segmental aneusomies including common microdeletion or microduplication syndromes and other genomic disorders. Chromosomal mosaicism was found in 12 (1.9%) neonates. CONCLUSIONS Chromosomal microarray analysis is a valuable clinical diagnostic tool that allows precise and rapid identification of genomic imbalances

  19. Image processing system for mammalian and human cytogenetic analysis

    International Nuclear Information System (INIS)

    Scoring of chromosomal abnormalities, dicentrics and rings, frequency of micronuclei in human peripheral blood lymphocytes are some of the important cytogenetic parameters which are currently being used as good biological dosimeter in accidental radiation exposure cases. This paper describes the image processing system and details of techniques applied to karyotyping, numerical counting of chromosomes at metaphase and area measurement of cell nucleus and micronucleus in cytochalasin-B blocked human lymphocytes. These functions make use of quantitative measurements of object parameters to carry out the desired analysis on the samples. 3 refs

  20. Prenatal Chromosomal Microarray Analysis and Identification of Genetic Variants in Congenital Diaphragmatic Hernia.

    OpenAIRE

    Brady, Paul

    2014-01-01

    Chromosomal microarray analysis has gradually replaced conventional karyotyping over recent years in the postnatal setting which has revolutionized whole genome screening for genomic imbalances in patients. We sought to evaluate the benefits and the challenges of applying chromosomal microarrays to prenatal diagnosis for referrals with abnormal ultrasound findings. Our findings, presented in Chapter 3, demonstrate a diagnostic yield of ~10%. Importantly, ~3% are caused by submicroscopic CN...

  1. The sequence and analysis of duplication rich human chromosome 16

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Joel; Han, Cliff; Gordon, Laurie A.; Terry, Astrid; Prabhakar, Shyam; She, Xinwei; Xie, Gary; Hellsten, Uffe; Man Chan, Yee; Altherr, Michael; Couronne, Olivier; Aerts, Andrea; Bajorek, Eva; Black, Stacey; Blumer, Heather; Branscomb, Elbert; Brown, Nancy C.; Bruno, William J.; Buckingham, Judith M.; Callen, David F.; Campbell, Connie S.; Campbell, Mary L.; Campbell, Evelyn W.; Caoile, Chenier; Challacombe, Jean F.; Chasteen, Leslie A.; Chertkov, Olga; Chi, Han C.; Christensen, Mari; Clark, Lynn M.; Cohn, Judith D.; Denys, Mirian; Detter, John C.; Dickson, Mark; Dimitrijevic-Bussod, Mira; Escobar, Julio; Fawcett, Joseph J.; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Goodwin, Lynne A.; Grady, Deborah L.; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Hildebrand, Carl E.; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Jewett, Phillip E.; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Krawczyk, Marie-Claude; Leyba, Tina; Longmire, Jonathan L.; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Ludeman, Thom; Mark, Graham A.; Mcmurray, Kimberly L.; Meincke, Linda J.; Morgan, Jenna; Moyzis, Robert K.; Mundt, Mark O.; Munk, A. Christine; Nandkeshwar, Richard D.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Parson-Quintana, Beverly; Ramirez, Lucia; Rash, Sam; Retterer, James; Ricke, Darryl O.; Robinson, Donna L.; Rodriguez, Alex; Salamov, Asaf; Saunders, Elizabeth H.; Scott, Duncan; Shough, Timothy; Stallings, Raymond L.; Stalvey, Malinda; Sutherland, Robert D.; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Torney, David C.; Tran-Gyamfi, Mary; Tsai, Ming; Ulanovsky, Levy E.; Ustaszewska, Anna; Vo, Nu; White, P. Scott; Williams, Albert L.; Wills, Patricia L.; Wu, Jung-Rung; Wu, Kevin; Yang, Joan; DeJong, Pieter; Bruce, David; Doggett, Norman; Deaven, Larry; Schmutz, Jeremy; Grimwood, Jane; Richardson, Paul; et al.

    2004-08-01

    We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes and 3 RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobasepairs were identified and result in gene content differences across humans. One of the unique features of chromosome 16 is its high level of segmental duplication, ranked among the highest of the human autosomes. While the segmental duplications are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events which are likely to have had an impact on the evolution of primates and human disease susceptibility.

  2. The Sequence and Analysis of Duplication Rich Human Chromosome 16

    Science.gov (United States)

    Martin, Joel; Han, Cliff; Gordon, Laurie A.; Terry, Astrid; Prabhakar, Shyam; She, Xinwei; Xie, Gary; Hellsten, Uffe; Man Chan, Yee; Altherr, Michael; Couronne, Olivier; Aerts, Andrea; Bajorek, Eva; Black, Stacey; Blumer, Heather; Branscomb, Elbert; Brown, Nancy C.; Bruno, William J.; Buckingham, Judith M.; Callen, David F.; Campbell, Connie S.; Campbell, Mary L.; Campbell, Evelyn W.; Caoile, Chenier; Challacombe, Jean F.; Chasteen, Leslie A.; Chertkov, Olga; Chi, Han C.; Christensen, Mari; Clark, Lynn M.; Cohn, Judith D.; Denys, Mirian; Detter, John C.; Dickson, Mark; Dimitrijevic-Bussod, Mira; Escobar, Julio; Fawcett, Joseph J.; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Goodwin, Lynne A.; Grady, Deborah L.; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Hildebrand, Carl E.; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Jewett, Phillip E.; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Krawczyk, Marie-Claude; Leyba, Tina; Longmire, Jonathan L.; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Ludeman, Thom; Mark, Graham A.; Mcmurray, Kimberly L.; Meincke, Linda J.; Morgan, Jenna; Moyzis, Robert K.; Mundt, Mark O.; Munk, A. Christine; Nandkeshwar, Richard D.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Parson-Quintana, Beverly; Ramirez, Lucia; Rash, Sam; Retterer, James; Ricke, Darryl O.; Robinson, Donna L.; Rodriguez, Alex; Salamov, Asaf; Saunders, Elizabeth H.; Scott, Duncan; Shough, Timothy; Stallings, Raymond L.; Stalvey, Malinda; Sutherland, Robert D.; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Torney, David C.; Tran-Gyamfi, Mary; Tsai, Ming; Ulanovsky, Levy E.; Ustaszewska, Anna; Vo, Nu; White, P. Scott; Williams, Albert L.; Wills, Patricia L.; Wu, Jung-Rung; Wu, Kevin; Yang, Joan; DeJong, Pieter; Bruce, David; Doggett, Norman; Deaven, Larry; Schmutz, Jeremy; Grimwood, Jane; Richardson, Paul; et al.

    2004-01-01

    We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes and 3 RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobasepairs were identified and result in gene content differences across humans. One of the unique features of chromosome 16 is its high level of segmental duplication, ranked among the highest of the human autosomes. While the segmental duplications are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events which are likely to have had an impact on the evolution of primates and human disease susceptibility.

  3. Chromosome region-specific libraries for human genome analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kao, Fa-Ten.

    1992-08-01

    During the grant period progress has been made in the successful demonstration of regional mapping of microclones derived from microdissection libraries; successful demonstration of the feasibility of converting microclones with short inserts into yeast artificial chromosome clones with very large inserts for high resolution physical mapping of the dissected region; Successful demonstration of the usefulness of region-specific microclones to isolate region-specific cDNA clones as candidate genes to facilitate search for the crucial genes underlying genetic diseases assigned to the dissected region; and the successful construction of four region-specific microdissection libraries for human chromosome 2, including 2q35-q37, 2q33-q35, 2p23-p25 and 2p2l-p23. The 2q35-q37 library has been characterized in detail. The characterization of the other three libraries is in progress. These region-specific microdissection libraries and the unique sequence microclones derived from the libraries will be valuable resources for investigators engaged in high resolution physical mapping and isolation of disease-related genes residing in these chromosomal regions.

  4. Chromosomal aberration analysis of persons occupationally exposed to radiation in Iran (2)

    International Nuclear Information System (INIS)

    The results of chromosome aberration analysis on lymphocytes from 333 persons suspected of being overexposed to X and gamma rays in recent years at Iran is presented. 91 persons were associated with industrial radiography, 124 with radiology and 118 with medical research and therapy centers. The total yields of chromosome aberration per 100 cells were respectively 3.76, 2.92 and 2.96. The frequencies of dicentrics which are important in biological dosimetry were respectively 0.18, 0.17 and 0.21. In this investigation, 50 subjects were also examined as control with a mean aberration of 1.14 per 100 cells. With regard to incidence of chromosome aberrations as mentioned, the rate of chromosome aberrations in industrial radiographers was the most significant

  5. Physical mapping, expression analysis and polymorphism survey of resistance gene analogues on chromosome 11 of rice

    Indian Academy of Sciences (India)

    Irfan A Ghazi; Prem S Srivastava; Vivek Dalal; Kishor Gaikwad; Ashok K Singh; Tilak R Sharma; Nagendra K Singh; Trilochan Mohapatra

    2009-06-01

    Rice is the first cereal genome with a finished sequence and a model crop that has important syntenic relationships with other cereal species. The objectives of our study were to identify resistance gene analogue (RGA) sequences from chromosome 11 of rice, understand their expression in other cereals and dicots by in silico analysis, determine their presence on other rice chromosomes, and evaluate the extent of polymorphism and actual expression in a set of rice genotypes. A total of 195 RGAs were predicted and physically localised. Of these, 91.79% expressed in rice, and 51.28% expressed in wheat, which was the highest among other cereals. Among monocots, sugarcane showed the highest (78.92%) expression, while among dicots, RGAs were maximally expressed in Arabidopsis (11.79%). Interestingly, two of the chromosome 11-specific RGAs were found to be expressing in all the organisms studied. Eighty RGAs of chromosome 11 had significant homology with chromosome 12, which was the maximum among all the rice chromosomes. Thirty-one per cent of the RGAs used in polymerase chain reaction (PCR) amplification showed polymorphism in a set of rice genotypes. Actual gene expression analysis revealed post-inoculation induction of one RGA in the rice line IRBB-4 carrying the bacterial blight resistance gene Xa-4. Our results have implications for the development of sequence-based markers and functional validation of specific RGAs in rice.

  6. Reflections on ultrasound image analysis.

    Science.gov (United States)

    Alison Noble, J

    2016-10-01

    Ultrasound (US) image analysis has advanced considerably in twenty years. Progress in ultrasound image analysis has always been fundamental to the advancement of image-guided interventions research due to the real-time acquisition capability of ultrasound and this has remained true over the two decades. But in quantitative ultrasound image analysis - which takes US images and turns them into more meaningful clinical information - thinking has perhaps more fundamentally changed. From roots as a poor cousin to Computed Tomography (CT) and Magnetic Resonance (MR) image analysis, both of which have richer anatomical definition and thus were better suited to the earlier eras of medical image analysis which were dominated by model-based methods, ultrasound image analysis has now entered an exciting new era, assisted by advances in machine learning and the growing clinical and commercial interest in employing low-cost portable ultrasound devices outside traditional hospital-based clinical settings. This short article provides a perspective on this change, and highlights some challenges ahead and potential opportunities in ultrasound image analysis which may both have high impact on healthcare delivery worldwide in the future but may also, perhaps, take the subject further away from CT and MR image analysis research with time. PMID:27503078

  7. Reflections on ultrasound image analysis.

    Science.gov (United States)

    Alison Noble, J

    2016-10-01

    Ultrasound (US) image analysis has advanced considerably in twenty years. Progress in ultrasound image analysis has always been fundamental to the advancement of image-guided interventions research due to the real-time acquisition capability of ultrasound and this has remained true over the two decades. But in quantitative ultrasound image analysis - which takes US images and turns them into more meaningful clinical information - thinking has perhaps more fundamentally changed. From roots as a poor cousin to Computed Tomography (CT) and Magnetic Resonance (MR) image analysis, both of which have richer anatomical definition and thus were better suited to the earlier eras of medical image analysis which were dominated by model-based methods, ultrasound image analysis has now entered an exciting new era, assisted by advances in machine learning and the growing clinical and commercial interest in employing low-cost portable ultrasound devices outside traditional hospital-based clinical settings. This short article provides a perspective on this change, and highlights some challenges ahead and potential opportunities in ultrasound image analysis which may both have high impact on healthcare delivery worldwide in the future but may also, perhaps, take the subject further away from CT and MR image analysis research with time.

  8. ANALYSIS OF FUNDUS IMAGES

    DEFF Research Database (Denmark)

    2000-01-01

    A method classifying objects man image as respective arterial or venous vessels comprising: identifying pixels of the said modified image which are located on a line object, determining which of the said image points is associated with crossing point or a bifurcation of the respective line object......; (e) vessel length. Furthermore methods for detecting size and positions of features of eye fundus images.......A method classifying objects man image as respective arterial or venous vessels comprising: identifying pixels of the said modified image which are located on a line object, determining which of the said image points is associated with crossing point or a bifurcation of the respective line object......, wherein a crossing point is represented by an image point which is the intersection of four line segments, performing a matching operation on pairs of said line segments for each said crossing point, to determine the path of blood vessels in the image, thereby classifying the line objects in the original...

  9. Image Analysis in CT Angiography

    NARCIS (Netherlands)

    Manniesing, R.

    2006-01-01

    In this thesis we develop and validate novel image processing techniques for the analysis of vascular structures in medical images. First a new type of filter is proposed which is capable of enhancing vascular structures while suppressing noise in the remainder of the image. This filter is based on

  10. Chromosomal imbalances in nasopharyngeal carcinoma: a meta-analysis of comparative genomic hybridization results

    Directory of Open Access Journals (Sweden)

    Jin Ping

    2006-01-01

    Full Text Available Abstract Nasopharyngeal carcinoma (NPC is a highly prevalent disease in Southeast Asia and its prevalence is clearly affected by genetic background. Various theories have been suggested for its high incidence in this geographical region but to these days no conclusive explanation has been identified. Chromosomal imbalances identifiable through comparative genomic hybridization may shed some light on common genetic alterations that may be of relevance to the onset and progression of NPC. Review of the literature, however, reveals contradictory results among reported findings possibly related to factors associated with patient selection, stage of disease, differences in methodological details etc. To increase the power of the analysis and attempt to identify commonalities among the reported findings, we performed a meta-analysis of results described in NPC tissues based on chromosomal comparative genomic hybridization (CGH. This meta-analysis revealed consistent patters in chromosomal abnormalities that appeared to cluster in specific "hot spots" along the genome following a stage-dependent progression.

  11. Digital Images Analysis

    OpenAIRE

    Roman-Gonzalez, Avid

    2012-01-01

    International audience; A specific field of image processing focuses on the evaluation of image quality and assessment of their authenticity. A loss of image quality may be due to the various processes by which it passes. In assessing the authenticity of the image we detect forgeries, detection of hidden messages, etc. In this work, we present an overview of these areas; these areas have in common the need to develop theories and techniques to detect changes in the image that it is not detect...

  12. Cytogenetic analysis of B chromosomes in one population of the fish Moenkhausia sanctaefilomenae (Steindachner, 1907) (Teleostei, Characiformes)

    OpenAIRE

    Diogo Hashimoto; Tatiana Voltolin; Ana Paes; Fausto Foresti; Jehud Bortolozzi; Fabio Porto-Foresti

    2012-01-01

    The aim of this study was to characterize cytogenetically one population of the fish Moenkhausia sanctaefilomenae (Steindachner, 1907), with emphasis on the analysis of B chromosomes. The nucleolar activity in the B microchromosomes was characterized, and an analysis of mitotic instability of these microchromosomes was accomplished. The results showed a diploid chromosome number of 50 chromosomes. In all individuals, we observed the presence of B microchromosomes with intra- and inter-individ...

  13. Linkage analysis of chromosome 14 and essential hypertension in Chinese population

    Institute of Scientific and Technical Information of China (English)

    ZHAO Wei-yan; HUANG Jian-feng; GE Dong-liang; SU Shao-yong; LI Biao; GU Dong-feng

    2005-01-01

    Background Hypertension is a complex biological trait that influenced by multiple factors. The encouraging results for hypertension research showed that the linkage analysis can be used to replicate other studies and discover new genetic risk factors. Previous studies linked human chromosome 14 to essential hypertension or blood pressure traits. With a Chinese population, we tried to replicate these findings. Methods A linkage scan was performed on chromosome 14 with 14-microsatellite markers with a density of about 10 centi Morgen (cM) in 147 Chinese hypertensive nuclear families. Multipoint non-parametric linkage analysis and exclusion mapping were performed with the GENEHUNTER software, whereas quantitative analysis was performed with the variance component method integrated in the SOLAR package. Results In the qualitative analysis, the highest non-parametric linkage score is 1.0 (P=0.14) at D14S261 in the single point analysis, and no loci achieved non-parametric linkage score more than 1.0 in the multipoint analysis. Maximum-likelihood mapping showed no significant results, either. Subsequently the traditional exclusion criteria of the log-of-the-odds score-2 were adopted, and the chromosome 14 with λs≥2.4 was excluded. In the quantitative analysis of blood pressure with the SOLAR software, two-point analysis and multipoint analysis suggested no evidence for linkage occurred on chromosome 14 for systolic and diastolic blood pressure. Conclusion There was no substantial evidence to support the linkage of chromosome 14 and essential hypertension or blood pressure trait in Chinese hypertensive subjects in this study.

  14. Analysis of the DNA sequence and duplication history of human chromosome 15.

    Science.gov (United States)

    Zody, Michael C; Garber, Manuel; Sharpe, Ted; Young, Sarah K; Rowen, Lee; O'Neill, Keith; Whittaker, Charles A; Kamal, Michael; Chang, Jean L; Cuomo, Christina A; Dewar, Ken; FitzGerald, Michael G; Kodira, Chinnappa D; Madan, Anup; Qin, Shizhen; Yang, Xiaoping; Abbasi, Nissa; Abouelleil, Amr; Arachchi, Harindra M; Baradarani, Lida; Birditt, Brian; Bloom, Scott; Bloom, Toby; Borowsky, Mark L; Burke, Jeremy; Butler, Jonathan; Cook, April; DeArellano, Kurt; DeCaprio, David; Dorris, Lester; Dors, Monica; Eichler, Evan E; Engels, Reinhard; Fahey, Jessica; Fleetwood, Peter; Friedman, Cynthia; Gearin, Gary; Hall, Jennifer L; Hensley, Grace; Johnson, Ericka; Jones, Charlien; Kamat, Asha; Kaur, Amardeep; Locke, Devin P; Madan, Anuradha; Munson, Glen; Jaffe, David B; Lui, Annie; Macdonald, Pendexter; Mauceli, Evan; Naylor, Jerome W; Nesbitt, Ryan; Nicol, Robert; O'Leary, Sinéad B; Ratcliffe, Amber; Rounsley, Steven; She, Xinwei; Sneddon, Katherine M B; Stewart, Sandra; Sougnez, Carrie; Stone, Sabrina M; Topham, Kerri; Vincent, Dascena; Wang, Shunguang; Zimmer, Andrew R; Birren, Bruce W; Hood, Leroy; Lander, Eric S; Nusbaum, Chad

    2006-03-30

    Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome. PMID:16572171

  15. Stochastic geometry for image analysis

    CERN Document Server

    Descombes, Xavier

    2013-01-01

    This book develops the stochastic geometry framework for image analysis purpose. Two main frameworks are  described: marked point process and random closed sets models. We derive the main issues for defining an appropriate model. The algorithms for sampling and optimizing the models as well as for estimating parameters are reviewed.  Numerous applications, covering remote sensing images, biological and medical imaging, are detailed.  This book provides all the necessary tools for developing an image analysis application based on modern stochastic modeling.

  16. In Vivo Enhancer Analysis Chromosome 16 Conserved NoncodingSequences

    Energy Technology Data Exchange (ETDEWEB)

    Pennacchio, Len A.; Ahituv, Nadav; Moses, Alan M.; Nobrega,Marcelo; Prabhakar, Shyam; Shoukry, Malak; Minovitsky, Simon; Visel,Axel; Dubchak, Inna; Holt, Amy; Lewis, Keith D.; Plajzer-Frick, Ingrid; Akiyama, Jennifer; De Val, Sarah; Afzal, Veena; Black, Brian L.; Couronne, Olivier; Eisen, Michael B.; Rubin, Edward M.

    2006-02-01

    The identification of enhancers with predicted specificitiesin vertebrate genomes remains a significant challenge that is hampered bya lack of experimentally validated training sets. In this study, weleveraged extreme evolutionary sequence conservation as a filter toidentify putative gene regulatory elements and characterized the in vivoenhancer activity of human-fish conserved and ultraconserved1 noncodingelements on human chromosome 16 as well as such elements from elsewherein the genome. We initially tested 165 of these extremely conservedsequences in a transgenic mouse enhancer assay and observed that 48percent (79/165) functioned reproducibly as tissue-specific enhancers ofgene expression at embryonic day 11.5. While driving expression in abroad range of anatomical structures in the embryo, the majority of the79 enhancers drove expression in various regions of the developingnervous system. Studying a set of DNA elements that specifically droveforebrain expression, we identified DNA signatures specifically enrichedin these elements and used these parameters to rank all ~;3,400human-fugu conserved noncoding elements in the human genome. The testingof the top predictions in transgenic mice resulted in a three-foldenrichment for sequences with forebrain enhancer activity. These datadramatically expand the catalogue of in vivo-characterized human geneenhancers and illustrate the future utility of such training sets for avariety of iological applications including decoding the regulatoryvocabulary of the human genome.

  17. Linkage analysis of neurofibromatosis type I, using chromosome 17 DNA markers.

    OpenAIRE

    Kittur, S D; Bagdon, M M; Lubs, M L; Phillips, J. A.; Murray, J C; Slaugenhaupt, S A; Chakravarti, A; Adler, W. H.

    1989-01-01

    The gene for von Recklinghausen neurofibromatosis type 1 (NF1) has recently been mapped to the pericentromeric region of human chromosome 17. To further localize the NF1 gene, linkage analysis using chromosome 17 DNA markers was performed on 11 multigeneration families with 175 individuals, 57 of whom were affected. The markers used were D17Z1 (p17H8), D17S58 (EW301), D17S54 (EW203), D17S57 (EW206), D17S73 (EW207), CRI-L946, HOX-2, and growth hormone. Tight linkage was found between NF1 and D...

  18. Diagnostic Yield of Chromosomal Microarray Analysis in an Autism Primary Care Practice: Which Guidelines to Implement?

    Science.gov (United States)

    McGrew, Susan G.; Peters, Brittany R.; Crittendon, Julie A.; Veenstra-VanderWeele, Jeremy

    2012-01-01

    Genetic testing is recommended for patients with ASD; however specific recommendations vary by specialty. American Academy of Pediatrics and American Academy of Neurology guidelines recommend G-banded karyotype and Fragile X DNA. The American College of Medical Genetics recommends Chromosomal Microarray Analysis (CMA). We determined the yield of…

  19. Transcriptomic analysis of fiber strength in upland cotton chromosome introgression lines carrying different Gossypium barbadense chromosomal segments.

    Directory of Open Access Journals (Sweden)

    Lei Fang

    Full Text Available Fiber strength is the key trait that determines fiber quality in cotton, and it is closely related to secondary cell wall synthesis. To understand the mechanism underlying fiber strength, we compared fiber transcriptomes from different G. barbadense chromosome introgression lines (CSILs that had higher fiber strengths than their recipient, G. hirsutum acc. TM-1. A total of 18,288 differentially expressed genes (DEGs were detected between CSIL-35431 and CSIL-31010, two CSILs with stronger fiber and TM-1 during secondary cell wall synthesis. Functional classification and enrichment analysis revealed that these DEGs were enriched for secondary cell wall biogenesis, glucuronoxylan biosynthesis, cellulose biosynthesis, sugar-mediated signaling pathways, and fatty acid biosynthesis. Pathway analysis showed that these DEGs participated in starch and sucrose metabolism (328 genes, glycolysis/gluconeogenesis (122 genes, phenylpropanoid biosynthesis (101 genes, and oxidative phosphorylation (87 genes, etc. Moreover, the expression of MYB- and NAC-type transcription factor genes were also dramatically different between the CSILs and TM-1. Being different to those of CSIL-31134, CSIL-35431 and CSIL-31010, there were many genes for fatty acid degradation and biosynthesis, and also for carbohydrate metabolism that were down-regulated in CSIL-35368. Metabolic pathway analysis in the CSILs showed that different pathways were changed, and some changes at the same developmental stage in some pathways. Our results extended our understanding that carbonhydrate metabolic pathway and secondary cell wall biosynthesis can affect the fiber strength and suggested more genes and/or pathways be related to complex fiber strength formation process.

  20. Topological analysis of weather images

    OpenAIRE

    MUBI, GREGOR

    2015-01-01

    In this thesis computational topology is used to analyse weather data. The goal is to analyse weather images and discern, if it is possible to expose certain parameters, which could improve humid mass classification. For this reason we were observing how those masses appear and merge on sequences of images. We used topological method named persistence. For data analysis we obtained weather radar images. We also wrote around 20 scripts in computing environment MATLAB, which served for data co...

  1. Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes

    Directory of Open Access Journals (Sweden)

    Sanchez-Alberola Neus

    2012-02-01

    Full Text Available Abstract Background The SOS response is a well-known regulatory network present in most bacteria and aimed at addressing DNA damage. It has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. Recently, the SOS response has been shown to regulate the activity of integrases in the chromosomal superintegrons of the Vibrionaceae, which encompasses a wide range of pathogenic species harboring multiple chromosomes. Here we combine in silico and in vitro techniques to perform a comparative genomics analysis of the SOS regulon in the Vibrionaceae, and we extend the methodology to map this transcriptional network in other bacterial species harboring multiple chromosomes. Results Our analysis provides the first comprehensive description of the SOS response in a family (Vibrionaceae that includes major human pathogens. It also identifies several previously unreported members of the SOS transcriptional network, including two proteins of unknown function. The analysis of the SOS response in other bacterial species with multiple chromosomes uncovers additional regulon members and reveals that there is a conserved core of SOS genes, and that specialized additions to this basic network take place in different phylogenetic groups. Our results also indicate that across all groups the main elements of the SOS response are always found in the large chromosome, whereas specialized additions are found in the smaller chromosomes and plasmids. Conclusions Our findings confirm that the SOS response of the Vibrionaceae is strongly linked with pathogenicity and dissemination of antibiotic resistance, and suggest that the characterization of the newly identified members of this regulon could provide key insights into the pathogenesis of Vibrio. The persistent location of key SOS genes in the large chromosome across several bacterial groups confirms that the SOS response plays an

  2. Multispectral analysis of multimodal images

    International Nuclear Information System (INIS)

    An increasing number of multimodal images represent a valuable increase in available image information, but at the same time it complicates the extraction of diagnostic information across the images. Multispectral analysis (MSA) has the potential to simplify this problem substantially as unlimited number of images can be combined, and tissue properties across the images can be extracted automatically. Materials and methods. We have developed a software solution for MSA containing two algorithms for unsupervised classification, an EM-algorithm finding multinormal class descriptions and the k-means clustering algorithm, and two for supervised classification, a Bayesian classifier using multinormal class descriptions and a kNN-algorithm. The software has an efficient user interface for the creation and manipulation of class descriptions, and it has proper tools for displaying the results. Results. The software has been tested on different sets of images. One application is to segment cross-sectional images of brain tissue (T1- and T2-weighted MR images) into its main normal tissues and brain tumors. Another interesting set of images are the perfusion maps and diffusion maps, derived images from raw MR images. The software returns segmentation that seem to be sensible. Discussion. The MSA software appears to be a valuable tool for image analysis with multimodal images at hand. It readily gives a segmentation of image volumes that visually seems to be sensible. However, to really learn how to use MSA, it will be necessary to gain more insight into what tissues the different segments contain, and the upcoming work will therefore be focused on examining the tissues through for example histological sections

  3. Image Harvest: an open-source platform for high-throughput plant image processing and analysis.

    Science.gov (United States)

    Knecht, Avi C; Campbell, Malachy T; Caprez, Adam; Swanson, David R; Walia, Harkamal

    2016-05-01

    High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources required for processing large image datasets at no cost. Image Harvest also offers functionalities to extract digital traits from images to interpret plant architecture-related characteristics. To demonstrate the applications of these digital traits, a rice (Oryza sativa) diversity panel was phenotyped and genome-wide association mapping was performed using digital traits that are used to describe different plant ideotypes. Three major quantitative trait loci were identified on rice chromosomes 4 and 6, which co-localize with quantitative trait loci known to regulate agronomically important traits in rice. Image Harvest is an open-source software for high-throughput image processing that requires a minimal learning curve for plant biologists to analyzephenomics datasets. PMID:27141917

  4. Image Analysis for Tongue Characterization

    Institute of Scientific and Technical Information of China (English)

    SHENLansun; WEIBaoguo; CAIYiheng; ZHANGXinfeng; WANGYanqing; CHENJing; KONGLingbiao

    2003-01-01

    Tongue diagnosis is one of the essential methods in traditional Chinese medical diagnosis. The ac-curacy of tongue diagnosis can be improved by tongue char-acterization. This paper investigates the use of image anal-ysis techniques for tongue characterization by evaluating visual features obtained from images. A tongue imaging and analysis instrument (TIAI) was developed to acquire digital color tongue images. Several novel approaches are presented for color calibration, tongue area segmentation,quantitative analysis and qualitative description for the colors of tongue and its coating, the thickness and moisture of coating and quantification of the cracks of the toilgue.The overall accuracy of the automatic analysis of the colors of tongue and the thickness of tongue coating exceeds 85%.This work shows the promising future of tongue character-ization.

  5. Flightspeed Integral Image Analysis Toolkit

    Science.gov (United States)

    Thompson, David R.

    2009-01-01

    The Flightspeed Integral Image Analysis Toolkit (FIIAT) is a C library that provides image analysis functions in a single, portable package. It provides basic low-level filtering, texture analysis, and subwindow descriptor for applications dealing with image interpretation and object recognition. Designed with spaceflight in mind, it addresses: Ease of integration (minimal external dependencies) Fast, real-time operation using integer arithmetic where possible (useful for platforms lacking a dedicated floatingpoint processor) Written entirely in C (easily modified) Mostly static memory allocation 8-bit image data The basic goal of the FIIAT library is to compute meaningful numerical descriptors for images or rectangular image regions. These n-vectors can then be used directly for novelty detection or pattern recognition, or as a feature space for higher-level pattern recognition tasks. The library provides routines for leveraging training data to derive descriptors that are most useful for a specific data set. Its runtime algorithms exploit a structure known as the "integral image." This is a caching method that permits fast summation of values within rectangular regions of an image. This integral frame facilitates a wide range of fast image-processing functions. This toolkit has applicability to a wide range of autonomous image analysis tasks in the space-flight domain, including novelty detection, object and scene classification, target detection for autonomous instrument placement, and science analysis of geomorphology. It makes real-time texture and pattern recognition possible for platforms with severe computational restraints. The software provides an order of magnitude speed increase over alternative software libraries currently in use by the research community. FIIAT can commercially support intelligent video cameras used in intelligent surveillance. It is also useful for object recognition by robots or other autonomous vehicles

  6. X chromosome-linked and mitochondrial gene control of Leber hereditary optic neuropathy: Evidence from segregation analysis for dependence on X chromosome inactivation

    Energy Technology Data Exchange (ETDEWEB)

    Xiangdong Bu; Rotter, J.I. (Cedars-Sinai Medical Center, Los Angeles, CA (United States) Univ. of California, Los Angeles (United States))

    1991-09-15

    Leber hereditary optic neuropathy (LHON) has been shown to involve mutation(s) of mitochondrial DNA, yet there remain several confusing aspects of its inheritance not explained by mitochondrial inheritance alone, including male predominance, reduced penetrance, and a later age of onset in females. By extending segregation analysis methods to disorders that involve both a mitochondrial and a nuclear gene locus, the authors show that the available pedigree data for LHON are most consistent with a two-locus disorder, with one responsible gene being mitochondrial and the other nuclear and X chromosome-linked. Furthermore, they have been able to extend the two-locus analytic method and demonstrate that a proportion of affected females are likely heterozygous at the X chromosome-linked locus and are affected due to unfortunate X chromosome inactivation, thus providing an explanation for the later age of onset in females. The estimated penetrance for a heterozygous female is 0.11{plus minus}0.02. The calculated frequency of the X chromosome-linked gene for LHON is 0.l08. Among affected females, 60% are expected to be heterozygous, and the remainder are expected to be homozygous at the responsible X chromosome-linked locus.

  7. Introduction to Medical Image Analysis

    DEFF Research Database (Denmark)

    Paulsen, Rasmus Reinhold; Moeslund, Thomas B.

    This book is a result of a collaboration between DTU Informatics at the Technical University of Denmark and the Laboratory of Computer Vision and Media Technology at Aalborg University. It is partly based on the book ”Image and Video Processing”, second edition by Thomas Moeslund. The aim...... of the book is to present the fascinating world of medical image analysis in an easy and interesting way. Compared to many standard books on image analysis, the approach we have chosen is less mathematical and more casual. Some of the key algorithms are exemplified in C-code. Please note that the code...

  8. Shape analysis in medical image analysis

    CERN Document Server

    Tavares, João

    2014-01-01

    This book contains thirteen contributions from invited experts of international recognition addressing important issues in shape analysis in medical image analysis, including techniques for image segmentation, registration, modelling and classification, and applications in biology, as well as in cardiac, brain, spine, chest, lung and clinical practice. This volume treats topics such as, anatomic and functional shape representation and matching; shape-based medical image segmentation; shape registration; statistical shape analysis; shape deformation; shape-based abnormity detection; shape tracking and longitudinal shape analysis; machine learning for shape modeling and analysis; shape-based computer-aided-diagnosis; shape-based medical navigation; benchmark and validation of shape representation, analysis and modeling algorithms. This work will be of interest to researchers, students, and manufacturers in the fields of artificial intelligence, bioengineering, biomechanics, computational mechanics, computationa...

  9. Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan

    Directory of Open Access Journals (Sweden)

    Thomas George H

    2006-01-01

    Full Text Available Abstract Background A variety of diseases are caused by chromosomal abnormalities such as aneuploidies (having an abnormal number of chromosomes, microdeletions, microduplications, and uniparental disomy. High density single nucleotide polymorphism (SNP microarrays provide information on chromosomal copy number changes, as well as genotype (heterozygosity and homozygosity. SNP array studies generate multiple types of data for each SNP site, some with more than 100,000 SNPs represented on each array. The identification of different classes of anomalies within SNP data has been challenging. Results We have developed SNPscan, a web-accessible tool to analyze and visualize high density SNP data. It enables researchers (1 to visually and quantitatively assess the quality of user-generated SNP data relative to a benchmark data set derived from a control population, (2 to display SNP intensity and allelic call data in order to detect chromosomal copy number anomalies (duplications and deletions, (3 to display uniparental isodisomy based on loss of heterozygosity (LOH across genomic regions, (4 to compare paired samples (e.g. tumor and normal, and (5 to generate a file type for viewing SNP data in the University of California, Santa Cruz (UCSC Human Genome Browser. SNPscan accepts data exported from Affymetrix Copy Number Analysis Tool as its input. We validated SNPscan using data generated from patients with known deletions, duplications, and uniparental disomy. We also inspected previously generated SNP data from 90 apparently normal individuals from the Centre d'Étude du Polymorphisme Humain (CEPH collection, and identified three cases of uniparental isodisomy, four females having an apparently mosaic X chromosome, two mislabelled SNP data sets, and one microdeletion on chromosome 2 with mosaicism from an apparently normal female. These previously unrecognized abnormalities were all detected using SNPscan. The microdeletion was independently

  10. An Allometric Analysis of Sex and Sex Chromosome Dosage Effects on Subcortical Anatomy in Humans.

    Science.gov (United States)

    Reardon, Paul Kirkpatrick; Clasen, Liv; Giedd, Jay N; Blumenthal, Jonathan; Lerch, Jason P; Chakravarty, M Mallar; Raznahan, Armin

    2016-02-24

    Structural neuroimaging of humans with typical and atypical sex-chromosome complements has established the marked influence of both Yand X-/Y-chromosome dosage on total brain volume (TBV) and identified potential cortical substrates for the psychiatric phenotypes associated with sex-chromosome aneuploidy (SCA). Here, in a cohort of 354 humans with varying karyotypes (XX, XY, XXX, XXY, XYY, XXYY, XXXXY), we investigate sex and SCA effects on subcortical size and shape; focusing on the striatum, pallidum and thalamus. We find large effect-size differences in the volume and shape of all three structures as a function of sex and SCA. We correct for TBV effects with a novel allometric method harnessing normative scaling rules for subcortical size and shape in humans, which we derive here for the first time. We show that all three subcortical volumes scale sublinearly with TBV among healthy humans, mirroring known relationships between subcortical volume and TBV among species. Traditional TBV correction methods assume linear scaling and can therefore invert or exaggerate sex and SCA effects on subcortical anatomy. Allometric analysis restricts sex-differences to: (1) greater pallidal volume (PV) in males, and (2) relative caudate head expansion and ventral striatum contraction in females. Allometric analysis of SCA reveals that supernumerary X- and Y-chromosomes both cause disproportionate reductions in PV, and coordinated deformations of striatopallidal shape. Our study provides a novel understanding of sex and sex-chromosome dosage effects on subcortical organization, using an allometric approach that can be generalized to other basic and clinical structural neuroimaging settings.

  11. An Allometric Analysis of Sex and Sex Chromosome Dosage Effects on Subcortical Anatomy in Humans.

    Science.gov (United States)

    Reardon, Paul Kirkpatrick; Clasen, Liv; Giedd, Jay N; Blumenthal, Jonathan; Lerch, Jason P; Chakravarty, M Mallar; Raznahan, Armin

    2016-02-24

    Structural neuroimaging of humans with typical and atypical sex-chromosome complements has established the marked influence of both Yand X-/Y-chromosome dosage on total brain volume (TBV) and identified potential cortical substrates for the psychiatric phenotypes associated with sex-chromosome aneuploidy (SCA). Here, in a cohort of 354 humans with varying karyotypes (XX, XY, XXX, XXY, XYY, XXYY, XXXXY), we investigate sex and SCA effects on subcortical size and shape; focusing on the striatum, pallidum and thalamus. We find large effect-size differences in the volume and shape of all three structures as a function of sex and SCA. We correct for TBV effects with a novel allometric method harnessing normative scaling rules for subcortical size and shape in humans, which we derive here for the first time. We show that all three subcortical volumes scale sublinearly with TBV among healthy humans, mirroring known relationships between subcortical volume and TBV among species. Traditional TBV correction methods assume linear scaling and can therefore invert or exaggerate sex and SCA effects on subcortical anatomy. Allometric analysis restricts sex-differences to: (1) greater pallidal volume (PV) in males, and (2) relative caudate head expansion and ventral striatum contraction in females. Allometric analysis of SCA reveals that supernumerary X- and Y-chromosomes both cause disproportionate reductions in PV, and coordinated deformations of striatopallidal shape. Our study provides a novel understanding of sex and sex-chromosome dosage effects on subcortical organization, using an allometric approach that can be generalized to other basic and clinical structural neuroimaging settings. PMID:26911691

  12. Quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes

    Directory of Open Access Journals (Sweden)

    Chen Carton W

    2007-08-01

    Full Text Available Abstract Background Most bacterial chromosomes exhibit asymmetry of base composition with respect to leading vs. lagging strands (GC and AT skews. These skews reflect mainly those in protein coding sequences, which are driven by asymmetric mutation pressures during replication and transcription (notably asymmetric cytosine deamination plus subsequent selection for preferred structures, signals, amino acid or codons. The transcription-associated effects but not the replication-associated effects contribute to the overall skews through the uneven distribution of the coding sequences on the leading and lagging strands. Results Analysis of 185 representative bacterial chromosomes showed diverse and characteristic patterns of skews among different clades. The base composition skews in the coding sequences were used to derive quantitatively the effect of replication-driven mutation plus subsequent selection ('replication-associated pressure', RAP, and the effect of transcription-driven mutation plus subsequent selection at translation level ('transcription-associate pressure', TAP. While different clades exhibit distinct patterns of RAP and TAP, RAP is absent or nearly absent in some bacteria, but TAP is present in all. The selection pressure at the translation level is evident in all bacteria based on the analysis of the skews at the three codon positions. Contribution of asymmetric cytosine deamination was found to be weak to TAP in most phyla, and strong to RAP in all the Proteobacteria but weak in most of the Firmicutes. This possibly reflects the differences in their chromosomal replication machineries. A strong negative correlation between TAP and G+C content and between TAP and chromosomal size were also revealed. Conclusion The study reveals the diverse mutation and selection forces associated with replication and transcription in various groups of bacteria that shape the distinct patterns of base composition skews in the chromosomes during

  13. Document image analysis: A primer

    Indian Academy of Sciences (India)

    Rangachar Kasturi; Lawrence O’Gorman; Venu Govindaraju

    2002-02-01

    Document image analysis refers to algorithms and techniques that are applied to images of documents to obtain a computer-readable description from pixel data. A well-known document image analysis product is the Optical Character Recognition (OCR) software that recognizes characters in a scanned document. OCR makes it possible for the user to edit or search the document’s contents. In this paper we briefly describe various components of a document analysis system. Many of these basic building blocks are found in most document analysis systems, irrespective of the particular domain or language to which they are applied. We hope that this paper will help the reader by providing the background necessary to understand the detailed descriptions of specific techniques presented in other papers in this issue.

  14. The scale and nature of Viking settlement in Ireland from Y-chromosome admixture analysis.

    Science.gov (United States)

    McEvoy, Brian; Brady, Claire; Moore, Laoise T; Bradley, Daniel G

    2006-12-01

    The Vikings (or Norse) played a prominent role in Irish history but, despite this, their genetic legacy in Ireland, which may provide insights into the nature and scale of their immigration, is largely unexplored. Irish surnames, some of which are thought to have Norse roots, are paternally inherited in a similar manner to Y-chromosomes. The correspondence of Scandinavian patrilineal ancestry in a cohort of Irish men bearing surnames of putative Norse origin was examined using both slow mutating unique event polymorphisms and relatively rapidly changing short tandem repeat Y-chromosome markers. Irish and Scandinavian admixture proportions were explored for both systems using six different admixture estimators, allowing a parallel investigation of the impact of method and marker type in Y-chromosome admixture analysis. Admixture proportion estimates in the putative Norse surname group were highly consistent and detected little trace of Scandinavian ancestry. In addition, there is scant evidence of Scandinavian Y-chromosome introgression in a general Irish population sample. Although conclusions are largely dependent on the accurate identification of Norse surnames, the findings are consistent with a relatively small number of Norse settlers (and descendents) migrating to Ireland during the Viking period (ca. AD 800-1200) suggesting that Norse colonial settlements might have been largely composed of indigenous Irish. This observation adds to previous genetic studies that point to a flexible Viking settlement approach across North Atlantic Europe.

  15. Molecular analysis of sex chromosome-linked mutants in the silkworm Bombyx mori

    Indian Academy of Sciences (India)

    Tsuguru Fujii; Hiroaki Abe; Toru Shimada

    2010-09-01

    In Bombyx mori, the W chromosome determines the female sex. A few W chromosome-linked mutations that cause masculinization of the female genitalia have been found. In female antennae of a recently isolated mutant, both female-type and male-type Bmdsx mRNAs were expressed, and BmOr1 (bombykol receptor) and BmOr3 (bombykal receptor), which are predominantly expressed in the antennae of male moths, were expressed about 50 times more abundantly in the antennae of mutant females than in those of normal females. These mutants are valuable resources for the molecular analysis of the sex-determination system. Besides the Fem gene, the quantitative egg size-determining gene Esd is thought to be present on the W chromosome, based on the observation that ZWW triploid moths produce larger eggs than ZZW triploids. The most recently updated B. mori genome assembly comprises 20.5 Mb of Z chromosome sequence. Using these sequence data, responsible genes or candidate genes for four Z-linked mutants have been reported. The od (distinct oily) and spli (soft and pliable) are caused by mutation in BmBLOS2 and Bmacj6, respectively. Bmap is a candidate gene for $V_g$ (vestigial). Similarly, Bmprm is a candidate gene for Md (muscle dystrophy), causing abnormal development of indirect flight muscle.

  16. Pocket pumped image analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kotov, I.V., E-mail: kotov@bnl.gov [Brookhaven National Laboratory, Upton, NY 11973 (United States); O' Connor, P. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Murray, N. [Centre for Electronic Imaging, Open University, Milton Keynes, MK7 6AA (United Kingdom)

    2015-07-01

    The pocket pumping technique is used to detect small electron trap sites. These traps, if present, degrade CCD charge transfer efficiency. To reveal traps in the active area, a CCD is illuminated with a flat field and, before image is read out, accumulated charges are moved back and forth number of times in parallel direction. As charges are moved over a trap, an electron is removed from the original pocket and re-emitted in the following pocket. As process repeats one pocket gets depleted and the neighboring pocket gets excess of charges. As a result a “dipole” signal appears on the otherwise flat background level. The amplitude of the dipole signal depends on the trap pumping efficiency. This paper is focused on trap identification technique and particularly on new methods developed for this purpose. The sensor with bad segments was deliberately chosen for algorithms development and to demonstrate sensitivity and power of new methods in uncovering sensor defects.

  17. Chromosome analysis in the Kruger National Park - the chromosomes of the saddle-backed jackal Canis Mesomelas

    Directory of Open Access Journals (Sweden)

    C. Wallace

    1977-08-01

    Full Text Available Among the present-day members of the Canidae family are included the dogs and foxes (Wurster and Benirschke 1968. The genus Canis is represented in Africa by four species of jackal (Bigaike 1972. This paper presents the chromosome Findings in a male saddle-backed jackal Canis mesomelas studied in the Kruger National Park, Republic of South Africa.

  18. Imaging spectroscopy for scene analysis

    CERN Document Server

    Robles-Kelly, Antonio

    2012-01-01

    This book presents a detailed analysis of spectral imaging, describing how it can be used for the purposes of material identification, object recognition and scene understanding. The opportunities and challenges of combining spatial and spectral information are explored in depth, as are a wide range of applications. Features: discusses spectral image acquisition by hyperspectral cameras, and the process of spectral image formation; examines models of surface reflectance, the recovery of photometric invariants, and the estimation of the illuminant power spectrum from spectral imagery; describes

  19. Analysis of a 26,756 bp segment from the left arm of yeast chromosome IV.

    Science.gov (United States)

    Wölfl, S; Hanemann, V; Saluz, H P

    1996-12-01

    The nucleotide sequence of a 26.7 kb DNA segment from the left arm of Saccharomyces cerevisiae chromosome IV is presented. An analysis of this segment revealed 11 open reading frames (ORFs) longer than 300 bp and one split gene. These ORFs include the genes encoding the large subunit of RNA polymerase II, the biotin apo-protein ligase, an ADP-ribosylation factor (ARF 2), the 'L35'-ribosomal protein, a rho GDP dissociation factor, and the sequence encoding the protein phosphatase 2A. Further sequence analysis revealed a short ORF encoding the ribosomal protein YL41B, an intron in a 5' untranslated region and an extended homology with another cosmid (X83276) located on the same chromosome. The potential biological relevance of these findings is discussed. PMID:8972577

  20. Multispectral Imaging Broadens Cellular Analysis

    Science.gov (United States)

    2007-01-01

    Amnis Corporation, a Seattle-based biotechnology company, developed ImageStream to produce sensitive fluorescence images of cells in flow. The company responded to an SBIR solicitation from Ames Research Center, and proposed to evaluate several methods of extending the depth of field for its ImageStream system and implement the best as an upgrade to its commercial products. This would allow users to view whole cells at the same time, rather than just one section of each cell. Through Phase I and II SBIR contracts, Ames provided Amnis the funding the company needed to develop this extended functionality. For NASA, the resulting high-speed image flow cytometry process made its way into Medusa, a life-detection instrument built to collect, store, and analyze sample organisms from erupting hydrothermal vents, and has the potential to benefit space flight health monitoring. On the commercial end, Amnis has implemented the process in ImageStream, combining high-resolution microscopy and flow cytometry in a single instrument, giving researchers the power to conduct quantitative analyses of individual cells and cell populations at the same time, in the same experiment. ImageStream is also built for many other applications, including cell signaling and pathway analysis; classification and characterization of peripheral blood mononuclear cell populations; quantitative morphology; apoptosis (cell death) assays; gene expression analysis; analysis of cell conjugates; molecular distribution; and receptor mapping and distribution.

  1. Molecular analysis of the distribution of chromosomal breakpoints: characterization of a 'hot' region for breaks in human chromosome 11

    International Nuclear Information System (INIS)

    Full text: Ionizing radiation randomly damages DNA and chromosomes whereas subsequent chromosome breaks are non-random. Assuming, as an ideal and naive but useful proposition, that breaks are equally likely anywhere in the chromosome and that a deletion always occurs between two breaks, the frequency of fragments would decrease linearly with increasing fragment size. This simple distribution is not, however, observed. To shed light on the 'real' situation of break formation we mapped breakpoints in the human chromosome no. 11 of 353 independent CD59- mutants isolated from human/hamster hybrid AL cells exposed to radiations (high and low dose-rate gamma rays, high LET carbon or nitrogen ions, protons) or chemicals (arsenic or irradiated, mutagenic histidine) or unexposed. The number of breaks per unit length of DNA differed significantly in different regions of chromosome 11.The highest level of breaks (140/mbp) were in the 0.8 mbp segment between CD59 and Catalase (CAT). Finer mapping of break points was carried out using 26 PCR primer pairs spread across this interval in 15 independent mutants. In two mutants, the break point was in a 107 bp fragment; in the other 13 the breaks were in a single 35 mbp fragment, but not all were at exactly the same site; 4 of 13 occurred in 3 different 3 mbp sub-segments. We are sequencing these fragments to look for such features as repeats: 'colder' regions like that between CD59 and WT will also be analyzed. But, since at least some breaks occurred at different sites and the frequency and distribution of breaks was about the same for all treatments, our we postulate that hot (and cold spots) may be due more to structural features or specific repair than to sequence or type of damage

  2. Chromosome analysis of nuclear power plant workers using fluorescence in situ hybridization and Giemsa assay

    Science.gov (United States)

    Hristova, Rositsa; Hadjidekova, Valeria; Grigorova, Mira; Nikolova, Teodora; Bulanova, Minka; Popova, Ljubomira; Staynova, Albena; Benova, Donka

    2013-01-01

    The aim of this study was to evaluate the genotoxic effects of ionizing radiation in vivo in exposed Bulgarian nuclear power plant workers by using classical cytogenetic and molecular cytogenetic analyses of peripheral lymphocytes. Chromosome analysis using fluorescence in situ hybrydization (FISH) and Giemsa techniques was undertaken on 63 workers and 45 administrative staff controls from the Bulgarian Nuclear Power Plant. Using the Giemsa method, the frequencies of cells studied with chromosome aberrations, dicentrics plus rings and chromosome fragments in the radiation workers were significantly higher compared with the control group (P = 0.044, P = 0.014, and P = 0.033, respectively). A significant association between frequencies of dicentrics plus rings and accumulated doses was registered (P < 0.01). In the present study, a FISH cocktail of whole chromosome paints for chromosomes 1, 4 and 11 was used. A significant association between frequency of translocations and accumulated doses was also observed (P < 0.001). Within the control group, a correlation was found between age and the spontaneous frequency of translocations. No correlation was found between smoking status and frequency of translocations. When compared with the control group, workers with accumulated doses up to 100 mSv showed no increase in genome translocation frequency, whereas workers with accumulated doses from 101 to 200 mSv showed a statistically significant doubling of genome translocation frequency (P = 0.009). Thus, in cases of chronic exposure and for purposes of retrospective dosimetry, the genome frequency of translocations is a more useful marker for evaluation of genotoxic effects than dicentric frequency. PMID:23536543

  3. Analysis of human chromosome 21 for a locus conferring susceptibility to Hirschsprung Disease

    Energy Technology Data Exchange (ETDEWEB)

    Bolk, S.; Duggan, D.J.; Chakravarti, A. [Case Western Reserve Univ., Cleveland, OH (United States)

    1994-09-01

    It has been estimated that approximately 5% of patients diagnosed with Hirschsprung disease (HSCR), or aganglionic megacolon, have trisomy 21. Since the incidence of Hirschsprung disease is 1/5000 live births and the incidence of trisomy 21 is approximately 1/1000 live births, the observed occurrence of HSCR in trisomy 21 is fifty times higher than expected. We propose that at least one locus on chromosome 21 predisposes to HSCR. Although at fifty times elevated risk, only 1% of Down Syndrome cases have HSCR. Thus additional genes or genetic events are necessary for HSCR to manifest in patients with trisomy 21. Based on segregation analysis, Badner et al. postulated that recessive genes may be responsible for up to 80% of HSCR. We postulate that at least one such gene is on chromosome 21 and increased homozygosity for common recessive HSCR mutations may be one cause for the elevated risk of HSCR in cases of trisomy 21. To map such a chromosome 21 locus, we are searching for segments of human chromosome 21 which are identical by descent from the parent in whom non-disjunction occurred. These segments will arise either from meiosis I (followed by a crossover between the centromere and the locus) or from meiosis II (followed by no crossovers). Nine nuclear families with a proband diagnosed with HSCR and Down Syndrome have been genotyped for 18 microsatellite markers spanning human chromosome 21q. In all nine cases analyzed thus far, trisomy 21 resulted from maternal non-disjunction at meiosis I. At this point no single IBD region is apparent. Therefore, additional families are being ascertained and additional markers at high density are being genotyped to map the HSCR locus.

  4. Doses in radiation accidents investigated by chromosome aberration analysis

    International Nuclear Information System (INIS)

    Results from cytogenetic investigations into 55 cases of suspected over-exposure to radiation during 1977 are reviewed. This report is the seventh in an annual series (previous results were published in NRPB-R5, R10, R23, R35, R41 and R57) which together contain data on 327 studies. Results from all investigations have been pooled for general analysis. Brief accounts are given in an appendix of the circumstances behind the past year's investigations and, where possible, physical estimates of dose have been included for comparison. Two cases are described in more detail: the first concerned a non-classified worker who put an iridium-192 source in his pocket and took it home; and the second involved the accidental contamination of two people with tritium gas. In a second appendix, the confidence limits on cytogenetic dosimetry for X- and γ-ray over-exposures are given and the derivation of these limits is discussed. (author)

  5. Analysis of chromosomal and organellar DNA of somatic hybrids between Triticum aestiuvm and Haynaldia villosa Schur.

    Science.gov (United States)

    Zhou, A; Xia, G; Zhang, X; Chen, H; Hu, H

    2001-05-01

    Intergeneric somatic hybridization between wheat (cv. Jinan 177) protoplasts that have 24-28 chromosomes and Haynaldia villosa protoplasts containing 11-14 chromosomes was carried out by the polyethylene glycol (PEG) method. A high frequency of hybrid calli and plants were obtained from the fusion products, as revealed by cytological and biochemical techniques and by PCR analysis of 5S rDNA spacer sequences. GISH (genomic in situ hybridization) analysis confirmed the presence of chromosomes from both parents in the hybrid clones and the common occurrence of translocations between them. The RFLP analysis of the organellar DNA using mitochondrion- and chloroplast-specific probes revealed that mitochondria from both parents existed in the cells of hybrid calli and their recombination, whereas chloroplasts segregated and recombined randomly. The gross morphology of hybrid plants resembled that of wheat, but the gross morphology of their ovaries and anthers were intermediate between those of the two parents. The relationship between hybrid plant regeneration and the balance of genetic materials in hybrid clones is discussed. PMID:11405621

  6. Chromosome analysis of 427 cases with primary amenorrhea%原发性闭经427例患者染色体核型分析

    Institute of Scientific and Technical Information of China (English)

    彭琳; 王楠; 邓东锐; 左伟; 程琛; 党静; 郝海燕; 周媛; 蒋敏; 凌霞珍

    2012-01-01

    目的 对原发性闭经患者进行细胞遗传学分析,探讨原发性闭经与染色体异常的关系,用以指导临床诊断及处理.方法 对427例原发性闭经患者进行外周血淋巴细胞培养、染色体制备及核型分析.结果 427例原发性闭经患者中共检出染色体异常核型118例,异常检出率为27.6℅﹙118∕427﹚.性染色体异常中,X染色体数目异常59例、结构异常25例、嵌合体24例,其中有单纯X染色体与常染色体平衡易位1例,合并X的部分缺失2例.常染色体结构异常10例,包括染色体倒位﹙4例﹚、平衡易位﹙4例﹚以及染色体大小异常﹙2例﹚,涉及到第6、7、9、14、15、16、22号常染色体.结论 结合临床表现、影像学检查以及染色体核型检查,可以为原发性闭经患者寻找病因提供理论依据,同时有利于处理措施的制定.%Objective To carry out chromosome analysis of patients with primary amenorrhea and investigate the relationship between primary amenorrhea and chromosome abnormalities, so as to guide clinical diagnosis and treatment. Methods Peripheral blood lymphocyte culture, chromosome preparation and karyotype analysis were done to 427 cases of patients with primary amenorrhea. Results There were 118 cases of abnormal chromosome karyotype with primary amenorrhea, and the anomaly detection rate was 27. 6% ( 118/427 ). In cases with sex chromosome abnormalities, there were 59 patients with numerical abnormalities of X chromosome, 25 patients with X chromosome structural abnormality, and 24 cases of mosaicism. Among them, there was one case of simple reciprocal translocation between X chromosome and autosome, and two cases of consolidation with terminal deletion of X chromosome. There were cases of autosomal structural abnormalities, including chromosomal inversion ( 4 cases ), balanced translocation ( 4 cases ) and abnormal chromosome size ( 2 cases ). Autosomal abnormalities happened on the sixth, seventh, ninth

  7. Cytogenetic Analysis of Chromosome 3 in DROSOPHILA MELANOGASTER: The Homoeotic Gene Complex in Polytene Chromosome Interval 84a-B

    OpenAIRE

    Kaufman, Thomas C.; Lewis, Ricki; Wakimoto, Barbara

    1980-01-01

    Cytogenetic evidence is presented demonstrating that the 84A-B interval in the proximal portion of the right arm of chromosome 3 is the residence of a homoeotic gene complex similar to the bithorax locus. This complex, originally defined by the Antennapedia (Antp) mutation, controls segmentation in the anterior portion of the organism. Different lesions within this complex homoeotically transform portions of the prothorax, proboscis, antenna and eye and present clear analogies to similar lesi...

  8. The frequency of chromosome exchanges in critical groups of Chernobyl accident victims according to conventional chromosome analysis and FISH method

    International Nuclear Information System (INIS)

    Conventional cytogenetic with group karyotyping and FISH analyses were performed in 16 Chernobyl accident liquidators diagnosed in 1986 with acute radiation sickness of different degree of severity. The data received confirmed the validity of FISH both as for evaluation of stable chromosome aberrations in peripheral lymphocytes of irradiated persons as enough high sensitivity of FISH for the tentative retrospective dose evaluation in the remote period after acute irradiation and during chronic radiation exposure in doses above 0.25 Gy

  9. Cloning, sequencing, and analysis of inv8 chromosome breakpoints associated with recombinant 8 syndrome.

    Science.gov (United States)

    Graw, S L; Sample, T; Bleskan, J; Sujansky, E; Patterson, D

    2000-03-01

    Rec8 syndrome (also known as "recombinant 8 syndrome" and "San Luis Valley syndrome") is a chromosomal disorder found in individuals of Hispanic descent with ancestry from the San Luis Valley of southern Colorado and northern New Mexico. Affected individuals typically have mental retardation, congenital heart defects, seizures, a characteristic facial appearance, and other manifestations. The recombinant chromosome is rec(8)dup(8q)inv(8)(p23.1q22.1), and is derived from a parental pericentric inversion, inv(8)(p23.1q22.1). Here we report on the cloning, sequencing, and characterization of the 8p23.1 and 8q22 breakpoints from the inversion 8 chromosome associated with Rec8 syndrome. Analysis of the breakpoint regions indicates that they are highly repetitive. Of 6 kb surrounding the 8p23.1 breakpoint, 75% consists of repetitive gene family members-including Alu, LINE, and LTR elements-and the inversion took place in a small single-copy region flanked by repetitive elements. Analysis of 3.7 kb surrounding the 8q22 breakpoint region reveals that it is 99% repetitive and contains multiple LTR elements, and that the 8q inversion site is within one of the LTR elements.

  10. Proteomics Analysis with a Nano Random Forest Approach Reveals Novel Functional Interactions Regulated by SMC Complexes on Mitotic Chromosomes.

    Science.gov (United States)

    Ohta, Shinya; Montaño-Gutierrez, Luis F; de Lima Alves, Flavia; Ogawa, Hiromi; Toramoto, Iyo; Sato, Nobuko; Morrison, Ciaran G; Takeda, Shunichi; Hudson, Damien F; Rappsilber, Juri; Earnshaw, William C

    2016-08-01

    Packaging of DNA into condensed chromosomes during mitosis is essential for the faithful segregation of the genome into daughter nuclei. Although the structure and composition of mitotic chromosomes have been studied for over 30 years, these aspects are yet to be fully elucidated. Here, we used stable isotope labeling with amino acids in cell culture to compare the proteomes of mitotic chromosomes isolated from cell lines harboring conditional knockouts of members of the condensin (SMC2, CAP-H, CAP-D3), cohesin (Scc1/Rad21), and SMC5/6 (SMC5) complexes. Our analysis revealed that these complexes associate with chromosomes independently of each other, with the SMC5/6 complex showing no significant dependence on any other chromosomal proteins during mitosis. To identify subtle relationships between chromosomal proteins, we employed a nano Random Forest (nanoRF) approach to detect protein complexes and the relationships between them. Our nanoRF results suggested that as few as 113 of 5058 detected chromosomal proteins are functionally linked to chromosome structure and segregation. Furthermore, nanoRF data revealed 23 proteins that were not previously suspected to have functional interactions with complexes playing important roles in mitosis. Subsequent small-interfering-RNA-based validation and localization tracking by green fluorescent protein-tagging highlighted novel candidates that might play significant roles in mitotic progression. PMID:27231315

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

    Science.gov (United States)

    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.

  12. Signal and image multiresolution analysis

    CERN Document Server

    Ouahabi, Abdelialil

    2012-01-01

    Multiresolution analysis using the wavelet transform has received considerable attention in recent years by researchers in various fields. It is a powerful tool for efficiently representing signals and images at multiple levels of detail with many inherent advantages, including compression, level-of-detail display, progressive transmission, level-of-detail editing, filtering, modeling, fractals and multifractals, etc.This book aims to provide a simple formalization and new clarity on multiresolution analysis, rendering accessible obscure techniques, and merging, unifying or completing

  13. Molecular analysis of recombination in a family with Duchenne muscular dystrophy and a large pericentric X chromosome inversion

    Energy Technology Data Exchange (ETDEWEB)

    Shashi, V.; Golden, W.L.; Allinson, P.S. [Univ. of Virginia Health Sciences Center, Charlottesville, VA (United States)] [and others

    1996-06-01

    It has been demonstrated in animal studies that, in animals heterozygous for pericentric chromosomal inversions, loop formation is greatly reduced during meiosis. This results in absence of recombination within the inverted segment, with recombination seen only outside the inversion. A recent study in yeast has shown that telomeres, rather than centromeres, lead in chromosome movement just prior to meiosis and may be involved in promoting recombination. We studied by cytogenetic analysis and DNA polymorphisms the nature of meiotic recombination in a three-generation family with a large pericentric X chromosome inversion, inv(X)(p21.1q26), in which Duchenne muscular dystrophy (DMD) was cosegregating with the inversion. On DNA analysis there was no evidence of meiotic recombination between the inverted and normal X chromosomes in the inverted segment. Recombination was seen at the telomeric regions, Xp22 and Xq27-28. No deletion or point mutation was found on analysis of the DMD gene. On the basis of the FISH results, we believe that the X inversion is the mutation responsible for DMD in this family. Our results indicate that (1) pericentric X chromosome inversions result in reduction of recombination between the normal and inverted X chromosomes; (2) meiotic X chromosome pairing in these individuals is likely initiated at the telomeres; and (3) in this family DMD is caused by the pericentric inversion. 50 refs., 7 figs., 1 tab.

  14. Teaching image analysis at DIKU

    DEFF Research Database (Denmark)

    Johansen, Peter

    2011-01-01

    The early development of computer vision at Department of Computer Science at University of Copenhagen (DIKU) is briefly described. The different disciplines in computer vision are introduced, and the principles for teaching two courses, an image analysis course, and a robot lab class are outlined....

  15. The architecture of chicken chromosome territories changes during differentiation

    Directory of Open Access Journals (Sweden)

    Stadler Sonja

    2004-11-01

    Full Text Available Abstract Background Between cell divisions the chromatin fiber of each chromosome is restricted to a subvolume of the interphase cell nucleus called chromosome territory. The internal organization of these chromosome territories is still largely unknown. Results We compared the large-scale chromatin structure of chromosome territories between several hematopoietic chicken cell types at various differentiation stages. Chromosome territories were labeled by fluorescence in situ hybridization in structurally preserved nuclei, recorded by confocal microscopy and evaluated visually and by quantitative image analysis. Chromosome territories in multipotent myeloid precursor cells appeared homogeneously stained and compact. The inactive lysozyme gene as well as the centromere of the lysozyme gene harboring chromosome located to the interior of the chromosome territory. In further differentiated cell types such as myeloblasts, macrophages and erythroblasts chromosome territories appeared increasingly diffuse, disaggregating to separable substructures. The lysozyme gene, which is gradually activated during the differentiation to activated macrophages, as well as the centromere were relocated increasingly to more external positions. Conclusions Our results reveal a cell type specific constitution of chromosome territories. The data suggest that a repositioning of chromosomal loci during differentiation may be a consequence of general changes in chromosome territory morphology, not necessarily related to transcriptional changes.

  16. Molecular cytogenetic analysis of monoecious hemp (Cannabis sativa L.) cultivars reveals its karyotype variations and sex chromosomes constitution.

    Science.gov (United States)

    Razumova, Olga V; Alexandrov, Oleg S; Divashuk, Mikhail G; Sukhorada, Tatiana I; Karlov, Gennady I

    2016-05-01

    Hemp (Cannabis sativa L., 2n = 20) is a dioecious plant. Sex expression is controlled by an X-to-autosome balance system consisting of the heteromorphic sex chromosomes XY for males and XX for females. Genetically monoecious hemp offers several agronomic advantages compared to the dioecious cultivars that are widely used in hemp cultivation. The male or female origin of monoecious maternal plants is unknown. Additionally, the sex chromosome composition of monoecious hemp forms remains unknown. In this study, we examine the sex chromosome makeup in monoecious hemp using a cytogenetic approach. Eight monoecious and two dioecious cultivars were used. The DNA of 210 monoecious plants was used for PCR analysis with the male-associated markers MADC2 and SCAR323. All monoecious plants showed female amplification patterns. Fluorescence in situ hybridization (FISH) with the subtelomeric CS-1 probe to chromosomes plates and karyotyping revealed a lack of Y chromosome and presence of XX sex chromosomes in monoecious cultivars with the chromosome number 2n = 20. There was a high level of intra- and intercultivar karyotype variation detected. The results of this study can be used for further analysis of the genetic basis of sex expression in plants.

  17. The murine ufo receptor: molecular cloning, chromosomal localization and in situ expression analysis.

    Science.gov (United States)

    Faust, M; Ebensperger, C; Schulz, A S; Schleithoff, L; Hameister, H; Bartram, C R; Janssen, J W

    1992-07-01

    We have cloned the mouse homologue of the ufo oncogene. It encodes a novel tyrosine kinase receptor characterized by a unique extracellular domain containing two immunoglobulin-like and two fibronectin type III repeats. Comparison of the predicted ufo amino acid sequences of mouse and man revealed an overall identity of 87.6%. The ufo locus maps to mouse chromosome 7A3-B1 and thereby extends the known conserved linkage group between mouse chromosome 7 and human chromosome 19. RNA in situ hybridization analysis established the onset of specific ufo expression in the late embryogenesis at day 12.5 post coitum (p.c.) and localized ufo transcription to distinct substructures of a broad spectrum of developing tissues (e.g. subepidermal cells of the skin, mesenchymal cells of the periosteum). In adult animals ufo is expressed in cells forming organ capsules as well as in connective tissue structures. ufo may function as a signal transducer between specific cell types of mesodermal origin.

  18. Cri-Du-Chat Syndrome: Clinical Profile and Chromosomal Microarray Analysis in Six Patients

    Directory of Open Access Journals (Sweden)

    Layla Damasceno Espirito Santo

    2016-01-01

    Full Text Available Cri-du-chat syndrome is a chromosomal disorder caused by a deletion of the short arm of chromosome 5. The disease severity, levels of intellectual and developmental delay, and patient prognosis have been related to the size and position of the deletion. Aiming to establish genotype-phenotype correlations, we applied array-CGH to evaluate six patients carrying cytogenetically detected deletions of the short arm of chromosome 5 who were followed at a genetics community service. The patients’ cytogenetic and clinical profiles were reevaluated. A database review was performed to predict additional genes and regulatory elements responsible for the characteristic phenotypic and behavioral traits of this disorder. Array-CGH analysis allowed for delineation of the terminal deletions, which ranged in size from approximately 11.2 Mb to 28.6 Mb, with breakpoints from 5p15.2 to 5p13. An additional dup(8(p23 (3.5 Mb, considered to be a benign copy number variation, was also observed in one patient. The correlation coefficient value (ρ=0.13 calculated indicated the presence of a weak relationship between developmental delay and deletion size. Genetic background, family history, epigenetic factors, quantitative trait locus polymorphisms, and environmental factors may also affect patient phenotype and must be taken into account in genotype-phenotype correlations.

  19. Effects of colcemid concentration on chromosome aberration analysis in human lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Kanda, Reiko; Hayata, Isamu; Kobayashi, Sadayoshi (National Inst. of Radiological Sciences, Chiba (Japan)); Jiang, Tao

    1994-03-01

    As a part of technical improvements of chromosome aberration analysis on human peripheral lymphocytes for biological radiation dosimetry, we examined the optimal conditions for the use of colcemid in chromosome preparation in order to obtain enough number of cells at metaphase in the first cell division. When treated with colcemid at concentrations below 0.01 [mu]g/ml from the beginning of culture, cultures harvested at 48 hours had low mitotic indices. Colcemid treatment at 0.025 to 0.05 [mu]g/ml during 48 hours resulted in high mitotic indices (8 to 15%) and almost of the mitotic cells remaining in the 1st cell division, suggesting that this range of colcemid concentration was appropriate for continuous treatment with colcemid. We further examined the effect of colcemid concentration on the quantitative consistency of the yields of radiation-induced chromosome aberration. Repeated experiments showed that the yield of dicentrics and centric rings in the culture having colcemid at 0.025 [mu]g/ml concentration were larger than that at 0.05 [mu]g/ml. These data indicate the importance of assuring the accuracy of colcemid concentration in the lymphocyte culture for cytogenetic radiation dosimetry. (author).

  20. Astronomical Image and Data Analysis

    CERN Document Server

    Starck, J.-L

    2006-01-01

    With information and scale as central themes, this comprehensive survey explains how to handle real problems in astronomical data analysis using a modern arsenal of powerful techniques. It treats those innovative methods of image, signal, and data processing that are proving to be both effective and widely relevant. The authors are leaders in this rapidly developing field and draw upon decades of experience. They have been playing leading roles in international projects such as the Virtual Observatory and the Grid. The book addresses not only students and professional astronomers and astrophysicists, but also serious amateur astronomers and specialists in earth observation, medical imaging, and data mining. The coverage includes chapters or appendices on: detection and filtering; image compression; multichannel, multiscale, and catalog data analytical methods; wavelets transforms, Picard iteration, and software tools. This second edition of Starck and Murtagh's highly appreciated reference again deals with to...

  1. Automated image analysis techniques for cardiovascular magnetic resonance imaging

    NARCIS (Netherlands)

    Geest, Robertus Jacobus van der

    2011-01-01

    The introductory chapter provides an overview of various aspects related to quantitative analysis of cardiovascular MR (CMR) imaging studies. Subsequently, the thesis describes several automated methods for quantitative assessment of left ventricular function from CMR imaging studies. Several novel

  2. Target identification by image analysis.

    Science.gov (United States)

    Fetz, V; Prochnow, H; Brönstrup, M; Sasse, F

    2016-05-01

    Covering: 1997 to the end of 2015Each biologically active compound induces phenotypic changes in target cells that are characteristic for its mode of action. These phenotypic alterations can be directly observed under the microscope or made visible by labelling structural elements or selected proteins of the cells with dyes. A comparison of the cellular phenotype induced by a compound of interest with the phenotypes of reference compounds with known cellular targets allows predicting its mode of action. While this approach has been successfully applied to the characterization of natural products based on a visual inspection of images, recent studies used automated microscopy and analysis software to increase speed and to reduce subjective interpretation. In this review, we give a general outline of the workflow for manual and automated image analysis, and we highlight natural products whose bacterial and eucaryotic targets could be identified through such approaches. PMID:26777141

  3. Undetected sex chromosome aneuploidy by chromosomal microarray.

    Science.gov (United States)

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

    2012-11-01

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

  4. Analysis of 22 Y chromosomal STR haplotypes and Y haplogroup distribution in Pathans of Pakistan.

    Science.gov (United States)

    Lee, Eun Young; Shin, Kyoung-Jin; Rakha, Allah; Sim, Jeong Eun; Park, Myung Jin; Kim, Na Young; Yang, Woo Ick; Lee, Hwan Young

    2014-07-01

    We analyzed haplotypes for 22 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) and five additional STRs (DYS388, DYS446, DYS447, DYS449 and DYS464), and Y chromosomal haplogroup distribution in 270 unrelated individuals from the Pathans residing in the Federally Administered Tribal Areas and the North-West Frontier Province of Pakistan using in-house multiplex PCR systems. Each Y-STR showed diversities ranging from 0.2506 to 0.8538, and the discriminatory capacity (DC) was 73.7% with 199 observed haplotypes using 17 Yfiler loci. By the addition of 5 Y-STRs to the Yfiler system, the DC was increased to 85.2% while showing 230 observed haplotypes. Among the additional 5 Y-STRs, DYS446, DYS447 and DYS449 were major contributors to enhancing discrimination. In the analysis of molecular variance, the Pathans of this study showed significant differences from other Pathan populations as well as neighboring population sets. In Y-SNP analysis, a total of 12 Y chromosomal haplogroups were observed and the most frequent haplogroup was R1a1a with 49.3% frequency. To obtain insights on the origin of Pathans, the network analysis was performed for the haplogroups G and Q observed from the Pathans and the Jewish population groups including Ashkenazim and Sephardim, but little support for a Jewish origin could be found. In the present study, we report Y-STR population data in Pathans of Pakistan, and we emphasize the need for adding additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory capacity in a population with low genetic diversity. PMID:24709582

  5. Porcine gamma-synuclein: molecular cloning, expression analysis, chromosomal localization and functional expression

    DEFF Research Database (Denmark)

    Frandsen, Pernille Munk; Madsen, Lone Bruhn; Bendixen, Christian;

    2009-01-01

    and pituitary gland. Expression analysis also showed that porcine SNCG transcripts could be detected in different brain regions during early stages of embryo development. The porcine SNCG orthologue was mapped to chromosome 14q25-q29. The distribution of recombinant porcine γ-synuclein was studied in three......The γ-synuclein protein is involved in breast carcinogenesis and has also been implicated in other forms of cancer and in ocular diseases. Furthermore, γ-synuclein is believed to have a role in certain neurodegenerative diseases, such as Parkinson's disease and Alzheimer's disease. This work...... different transfected cell lines and the protein was found to be predominantly localized in the cytoplasm...

  6. Mesh Processing in Medical Image Analysis

    DEFF Research Database (Denmark)

    The following topics are dealt with: mesh processing; medical image analysis; interactive freeform modeling; statistical shape analysis; clinical CT images; statistical surface recovery; automated segmentation; cerebral aneurysms; and real-time particle-based representation....

  7. Live cell imaging of the nascent inactive X chromosome during the early differentiation process of naive ES cells towards epiblast stem cells.

    Directory of Open Access Journals (Sweden)

    Aurélia Guyochin

    Full Text Available Random X-chromosome inactivation ensures dosage compensation in mammals through the transcriptional silencing of one of the two X chromosomes present in each female cell. Silencing is initiated in the differentiating epiblast of the mouse female embryos through coating of the nascent inactive X chromosome by the non-coding RNA Xist, which subsequently recruits the Polycomb Complex PRC2 leading to histone H3-K27 methylation. Here we examined in mouse ES cells the early steps of the transition from naive ES cells towards epiblast stem cells as a model for inducing X chromosome inactivation in vitro. We show that these conditions efficiently induce random XCI. Importantly, in a transient phase of this differentiation pathway, both X chromosomes are coated with Xist RNA in up to 15% of the XX cells. In an attempt to determine the dynamics of this process, we designed a strategy aimed at visualizing the nascent inactive X-chromosome in live cells. We generated transgenic female XX ES cells expressing the PRC2 component Ezh2 fused to the fluorescent protein Venus. The fluorescent fusion protein was expressed at sub-physiological levels and located in nuclei of ES cells. Upon differentiation of ES cell towards epiblast stem cell fate, Venus-fluorescent territories appearing in interphase nuclei were identified as nascent inactive X chromosomes by their association with Xist RNA. Imaging of Ezh2-Venus for up to 24 hours during the differentiation process showed survival of some cells with two fluorescent domains and a surprising dynamics of the fluorescent territories across cell division and in the course of the differentiation process. Our data reveal a strategy for visualizing the nascent inactive X chromosome and suggests the possibility for a large plasticity of the nascent inactive X chromosome.

  8. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

    OpenAIRE

    Zody, Michael C; Garber, Manuel; Adams, David J.; Sharpe, Ted; Harrow, Jennifer; James R. Lupski; Nicholson, Christine; Searle, Steven M.; Wilming, Laurens; Young, Sarah K.; Abouelleil, Amr; Van Allen, Nicole R; Bi, Weimin; Bloom, Toby; Borowsky, Mark L

    2006-01-01

    Chromosome 17 is unusual among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome1, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second highest gene density in the genome2,3. It is also enriched in segmental duplications, ranking third in density among the autosomes4. Here we report a finished sequence for human chromosome 17, as well as a structural ...

  9. Plasmodium falciparum: analysis of chromosomes separated by contour-clamped homogenous electric fields.

    Science.gov (United States)

    Gu, H; Inselburg, J W; Bzik, D J; Li, W B

    1990-08-01

    We have established improved conditions for separating the chromosomes of Plasmodium falciparum by pulsed field gradient gel electrophoresis (PFG) using a contour-clamped homogenous electric field (CHEF) apparatus. Thirteen clearly separable chromosomal bands were reproducibly isolated from the strain FCR3 and their sizes have been determined. Evidence that indicates one band may contain two chromosomes is presented. The relationship between the PFG separable DNA and the number of unique chromosomes in P. falciparum is considered. We have established a relationship between the maximum resolvable sizes of the chromosomes and the pulse times. The chromosomal location of twenty-seven P. falciparum DNA probes is also reported. PMID:2197113

  10. Comparative genomic hybridization analysis shows different epidemiology of chromosomal and plasmid-borne cpe-carrying Clostridium perfringens type A.

    Directory of Open Access Journals (Sweden)

    Päivi Lahti

    Full Text Available Clostridium perfringens, one of the most common causes of food poisonings, can carry the enterotoxin gene, cpe, in its chromosome or on a plasmid. C. perfringens food poisonings are more frequently caused by the chromosomal cpe-carrying strains, while the plasmid-borne cpe-positive genotypes are more commonly found in the human feces and environmental samples. Different tolerance to food processing conditions by the plasmid-borne and chromosomal cpe-carrying strains has been reported, but the reservoirs and contamination routes of enterotoxin-producing C. perfringens remain unknown. A comparative genomic hybridization (CGH analysis with a DNA microarray based on three C. perfringens type A genomes was conducted to shed light on the epidemiology of C. perfringens food poisonings caused by plasmid-borne and chromosomal cpe-carrying strains by comparing chromosomal and plasmid-borne cpe-positive and cpe-negative C. perfringens isolates from human, animal, environmental, and food samples. The chromosomal and plasmid-borne cpe-positive C. perfringens genotypes formed two distinct clusters. Variable genes were involved with myo-inositol, ethanolamine and cellobiose metabolism, suggesting a new epidemiological model for C. perfringens food poisonings. The CGH results were complemented with growth studies, which demonstrated different myo-inositol, ethanolamine, and cellobiose metabolism between the chromosomal and plasmid-borne cpe-carrying strains. These findings support a ubiquitous occurrence of the plasmid-borne cpe-positive strains and their adaptation to the mammalian intestine, whereas the chromosomal cpe-positive strains appear to have a narrow niche in environments containing degrading plant material. Thus the epidemiology of the food poisonings caused by two populations appears different, the plasmid-borne cpe-positive strains probably contaminating foods via humans and the chromosomal strains being connected to plant material.

  11. Analysis of Y chromosome microdeletions and CFTR gene mutations as genetic markers of infertility in Serbian men

    Directory of Open Access Journals (Sweden)

    Dinić Jelena

    2007-01-01

    Full Text Available Background/Aim. Impaired fertility of a male partner is the main cause of infertility in up to one half of all infertile couples. At the genetic level, male infertility can be caused by chromosome aberrations or gene mutations. The presence and types of Y chromosome microdeletions and cystic fybrosis transmembrane conductance regulator (CFTR gene mutations as genetic cause of male infertility was tested in Serbian men. The aim of this study was to analyze CFTR gene mutations and Y chromosome microdelations as potential causes of male infertility in Serbian patients, as well as to test the hypothesis that CFTR mutations in infertile men are predominantly located in the several last exons of the gene. Methods. This study has encompassed 33 men with oligo- or azoospermia. The screening for Y chromosome microdeletions in the azoospermia factor (AZF region was performed by multiplex PCR analysis. The screening of the CFTR gene was performed by denaturing gradient gel electrophoresis (DGGE method. Results. Deletions on Y chromosome were detected in four patients, predominantly in AZFc region (four of total six deletions. Mutations in the CFTR gene were detected on eight out of 66 analyzed chromosomes of infertile men. The most common mutation was F508del (six of total eight mutations. Conclusion. This study confirmed that both Y chromosome microdeletions and CFTR gene mutations played important role in etiology of male infertility in Serbian infertile men. Genetic testing for Y chromosome microdeletions and CFTR gene mutations has been introduced in routine diagnostics and offered to couples undergoing assisted reproduction techniques. Considering that both the type of Y chromosome microdeletion and the type of CFTR mutation have a prognostic value, it is recommended that AZF and CFTR genotyping should not only be performed in patients with reduced sperm quality before undergoing assisted reproduction, but also for the purpose of preimplantation and

  12. Mesh Processing in Medical Image Analysis

    DEFF Research Database (Denmark)

    The following topics are dealt with: mesh processing; medical image analysis; interactive freeform modeling; statistical shape analysis; clinical CT images; statistical surface recovery; automated segmentation; cerebral aneurysms; and real-time particle-based representation.......The following topics are dealt with: mesh processing; medical image analysis; interactive freeform modeling; statistical shape analysis; clinical CT images; statistical surface recovery; automated segmentation; cerebral aneurysms; and real-time particle-based representation....

  13. [The construction of the genetic map and QTL locating analysis on chromosome 2 in swine].

    Science.gov (United States)

    Qu, Yan-Chun; Deng, Chang-Yan; Xiong, Yuan-Zhu; Zheng, Rong; Yu, Li; Su, Yu-Hong; Liu, Gui-Lan

    2002-01-01

    The study constructed the genetic linkage map of porcine chromosome 2 and further analysis of quantitative trait loci was conducted. The results of the study demonstrated that all 7 microsatellite loci we chose were with relatively high polymorphism, and its polymorphic information content was from 0.40182 to 0.58477. The genetic map we constructed for resource family was 152.9 cM in length, with the order of all loci highly consistent with the USDA map. All marker intervals were longer than USDA map with the interval between marker Sw2516 and Sw1201 as an exception. Furthermore, we conducted QTLs locating analysis by combining the genetic map with the phenotypic data. QTLs affecting lively estimated traits such as lean meat percentage, were located at 60-65 cM on chromosome 2, while QTLs for the height and marbling of Longissmus dorsi muscle were located at 20 cM and 55 cM, respectively Among them, QTL for estimated lean meat percentage was significant at chromosome-wise level (P < 0.01) and was responsible for 21.55% of the phenotypic variance. QTLs for the height and marbling of Longissmus dorsi muscle were responsible for 10.12% and 10.97% of the phenotypic variance, respectively. The additive and dominance effect of lively estimated traits were in the inverse tendency, while the QTL for the height of Longissmus dorsi muscle had its additive and dominance effect in the same tendency and was with advantageous allele in Large White. The QTLs we detected had relatively large effect on phenotype and built a basis for molecular marker assisted selection and breeding.

  14. [The construction of the genetic map and QTL locating analysis on chromosome 2 in swine].

    Science.gov (United States)

    Qu, Yan-Chun; Deng, Chang-Yan; Xiong, Yuan-Zhu; Zheng, Rong; Yu, Li; Su, Yu-Hong; Liu, Gui-Lan

    2002-01-01

    The study constructed the genetic linkage map of porcine chromosome 2 and further analysis of quantitative trait loci was conducted. The results of the study demonstrated that all 7 microsatellite loci we chose were with relatively high polymorphism, and its polymorphic information content was from 0.40182 to 0.58477. The genetic map we constructed for resource family was 152.9 cM in length, with the order of all loci highly consistent with the USDA map. All marker intervals were longer than USDA map with the interval between marker Sw2516 and Sw1201 as an exception. Furthermore, we conducted QTLs locating analysis by combining the genetic map with the phenotypic data. QTLs affecting lively estimated traits such as lean meat percentage, were located at 60-65 cM on chromosome 2, while QTLs for the height and marbling of Longissmus dorsi muscle were located at 20 cM and 55 cM, respectively Among them, QTL for estimated lean meat percentage was significant at chromosome-wise level (P < 0.01) and was responsible for 21.55% of the phenotypic variance. QTLs for the height and marbling of Longissmus dorsi muscle were responsible for 10.12% and 10.97% of the phenotypic variance, respectively. The additive and dominance effect of lively estimated traits were in the inverse tendency, while the QTL for the height of Longissmus dorsi muscle had its additive and dominance effect in the same tendency and was with advantageous allele in Large White. The QTLs we detected had relatively large effect on phenotype and built a basis for molecular marker assisted selection and breeding. PMID:12645259

  15. Cytogenetic analysis of the Amazon stingless bee Melipona seminigra merrillae reveals different chromosome number for the genus

    Directory of Open Access Journals (Sweden)

    Izaura Bezerra Francini

    2011-10-01

    Full Text Available Cytogenetic analysis of the Amazon stingless bee Melipona seminigra merrillae, by conventional Giemsa staining and C-banding, revealed a different chromosome number for Melipona: 2n = 22 for females and diploid drones while the haploid drones present n = 11. There is no evidence of B chromosomes. This result contrasts with previous studies, in which the chromosome number of 19 Melipona species was determined as 2n = 18 for females and n = 9 for haploid males. Based on cytogenetic information available for other Melipona species, we propose that M. s. merrillae has a more derived diploid number. This indicates that chromosome number is not a conservative characteristic within the genus as previously thought. Cytogenetic data for stingless bees are scarce, especially in Amazon region. Additional studies will be very important in order to promote Melipona karyoevolution discussion and consequently a taxonomy review.

  16. Evaluation of genetic potential of Bacopa monnieri extract in Mouse bone marrow cells by chromosomal analysis test

    Directory of Open Access Journals (Sweden)

    Shilki Vishnoi

    2013-06-01

    Full Text Available Herbs have always been used as a common source of medicines, the Bacopa monnieri is an important herb used in Aruveda as a traditional medicinal system of India. In the present investigations, the genotoxic potential of Bacopa monnieri Hydromethanolic extract (BMH was evaluated employing Chromosomal analysis assay invivo. BMH was administered to Swiss Albino mice as i.p. dose of 80mg/kg, 160mg/kg, 240mg/kg body wt., 24 hours prior the administration of cyclophosphamide (CP (positive control at the dose of 50 mg/kg body wt. A dose-dependent, significant decrease in chromosome aberration was observed with respect to control. Result suggested that BMHhave a preventive potential against CP induced chromosomal aberration in Swiss albino mouse bone marrow cells at the dose tested. Therefore seems to have a preventive potential against Chromosomal aberrations in Swiss Albinomouse bone marrow cells.

  17. SYNAPTONEMAL COMPLEX ANALYSIS OF MUTAGEN EFFECTS ON MEIOTIC CHROMOSOME STRUCTURE AND BEHAVIOR

    Science.gov (United States)

    Homologous chromosome synapsis and crossing-over at meiosis are basic to mammalian gamete development. hey achieve genetic recombination, regulate chromosome segregation, and are believed to function in repair and maturation. ynaptonemal complexes (SCs) are axial correlates of me...

  18. Independent clonal origin of multiple uterine leiomyomas that was determined by X chromosome inactivation and microsatellite analysis

    DEFF Research Database (Denmark)

    Canevari, Renata A; Pontes, Anaglória; Rosa, Fabíola E;

    2005-01-01

    OBJECTIVE: In an attempt to clarify the clonality and genetic relationships that are involved in the tumorigenesis of uterine leiomyomas, we used a total of 43 multiple leiomyomas from 14 patients and analyzed the allelic status with 15 microsatellite markers and X chromosome inactivation analysis....... STUDY DESIGN: We have used a set of 15 microsatellite polymorphism markers mapped on 3q, 7p, 11, and 15q by automated analysis. The X chromosome inactivation was evaluated by the methylation status of the X-linked androgen receptor gene. RESULTS: Loss of heterozygosity analysis showed a different...... pattern in 7 of the 8 cases with allelic loss for at least 1 of 15 microsatellite markers that were analyzed. A similar loss of heterozygosity findings at 7p22-15 was detected in 3 samples from the same patient. X chromosome inactivation analysis demonstrated the same inactivated allele in all tumors...

  19. Integration Platform for Biomedical Image Analysis

    OpenAIRE

    Rantanen, Ville

    2015-01-01

    Images provide invaluable information to Biomedicine. Especially, microscopy as an information source has been providing knowledge for research and clinical diagnostics. We have moved away from simply looking at the images to quantifiable computerized image analysis. Over the last decades, image analysis developers have prepared algorithms and software to address various scientific enquiries using images. These software are often created for a single purpose. Naturally, not even the most gene...

  20. SKY analysis revealed recurrent numerical and structural chromosome changes in BDII rat endometrial carcinomas

    Directory of Open Access Journals (Sweden)

    Behboudi Afrouz

    2011-06-01

    Full Text Available Abstract Background Genomic alterations are common features of cancer cells, and some of these changes are proven to be neoplastic-specific. Such alterations may serve as valuable tools for diagnosis and classification of tumors, prediction of clinical outcome, disease monitoring, and choice of therapy as well as for providing clues to the location of crucial cancer-related genes. Endometrial carcinoma (EC is the most frequently diagnosed malignancy of the female genital tract, ranking fourth among all invasive tumors affecting women. Cytogenetic studies of human ECs have not produced very conclusive data, since many of these studies are based on karyotyping of limited number of cases and no really specific karyotypic changes have yet been identified. As the majority of the genes are conserved among mammals, the use of inbred animal model systems may serve as a tool for identification of underlying genes and pathways involved in tumorigenesis in humans. In the present work we used spectral karyotyping (SKY to identify cancer-related aberrations in a well-characterized experimental model for spontaneous endometrial carcinoma in the BDII rat tumor model. Results Analysis of 21 experimental ECs revealed specific nonrandom numerical and structural chromosomal changes. The most recurrent numerical alterations were gains in rat chromosome 4 (RNO4 and losses in RNO15. The most commonly structural changes were mainly in form of chromosomal translocations and were detected in RNO3, RNO6, RNO10, RNO11, RNO12, and RNO20. Unbalanced chromosomal translocations involving RNO3p was the most commonly observed structural changes in this material followed by RNO11p and RNO10 translocations. Conclusion The non-random nature of these events, as documented by their high frequencies of incidence, is suggesting for dynamic selection of these changes during experimental EC tumorigenesis and therefore for their potential contribution into development of this malignancy

  1. Analysis of the terminus region of the Caulobacter crescentus chromosome and identification of the dif site

    DEFF Research Database (Denmark)

    Jensen, Rasmus Bugge

    2006-01-01

    The terminus region of the Caulobacter crescentus chromosome and the dif chromosome dimer resolution site were characterized. The Caulobacter genome contains skewed sequences that abruptly switch strands at dif and may have roles in chromosome maintenance and segregation. Absence of dif or the Xer...

  2. Chromosomal microarray analysis as a first-tier clinical diagnostic test: Estonian experience.

    Science.gov (United States)

    Zilina, Olga; Teek, Rita; Tammur, Pille; Kuuse, Kati; Yakoreva, Maria; Vaidla, Eve; Mölter-Väär, Triin; Reimand, Tiia; Kurg, Ants; Ounap, Katrin

    2014-03-01

    Chromosomal microarray analysis (CMA) is now established as the first-tier cytogenetic diagnostic test for fast and accurate detection of chromosomal abnormalities in patients with developmental delay/intellectual disability (DD/ID), multiple congenital anomalies (MCA), and autism spectrum disorders (ASD). We present our experience with using CMA for postnatal and prenatal diagnosis in Estonian patients during 2009-2012. Since 2011, CMA is on the official service list of the Estonian Health Insurance Fund and is performed as the first-tier cytogenetic test for patients with DD/ID, MCA or ASD. A total of 1191 patients were analyzed, including postnatal (1072 [90%] patients and 59 [5%] family members) and prenatal referrals (60 [5%] fetuses). Abnormal results were reported in 298 (25%) patients, with a total of 351 findings (1-3 per individual): 147 (42%) deletions, 106 (30%) duplications, 89 (25%) long contiguous stretches of homozygosity (LCSH) events (>5 Mb), and nine (3%) aneuploidies. Of all findings, 143 (41%) were defined as pathogenic or likely pathogenic; for another 143 findings (41%), most of which were LCSH, the clinical significance remained unknown, while 61 (18%) reported findings can now be reclassified as benign or likely benign. Clinically relevant findings were detected in 126 (11%) patients. However, the proportion of variants of unknown clinical significance was quite high (41% of all findings). It seems that our ability to detect chromosomal abnormalities has far outpaced our ability to understand their role in disease. Thus, the interpretation of CMA findings remains a rather difficult task requiring a close collaboration between clinicians and cytogeneticists.

  3. Cytogenetic analysis of B chromosomes in one population of the fish Moenkhausia sanctaefilomenae (Steindachner, 1907 (Teleostei, Characiformes

    Directory of Open Access Journals (Sweden)

    Diogo Hashimoto

    2012-04-01

    Full Text Available The aim of this study was to characterize cytogenetically one population of the fish Moenkhausia sanctaefilomenae (Steindachner, 1907, with emphasis on the analysis of B chromosomes. The nucleolar activity in the B microchromosomes was characterized, and an analysis of mitotic instability of these microchromosomes was accomplished. The results showed a diploid chromosome number of 50 chromosomes. In all individuals, we observed the presence of B microchromosomes with intra- and inter-individual variability. The analysis of the nucleolus organizing regions (NORs by silver nitrate staining demonstrated multiple NORs. We observed active sites of ribosomal DNA in the B microchromosomes, with a frequency of 20% in the analyzed cells, which shows gene activity in these chromosomal elements. The analysis of constitutive heterochromatin patterns showed that the B microchromosomes are heterochromatic or euchromatic, which demonstrates differentiation of DNA composition between these genomic elements. The calculation of the mitotic instability index implied that B chromosomes in this species might be in a final stage of instability.

  4. Cytogenetic analysis of B chromosomes in one population of the fish Moenkhausia sanctaefilomenae (Steindachner, 1907) (Teleostei, Characiformes).

    Science.gov (United States)

    Voltolin, Diogo Teruo Hashimoto Tatiana Aparecida; Paes, Ana Danyelle Noitel Valim de Arruda; Foresti, Fausto; Bortolozzi, Jehud; Porto-Foresti, Fábio

    2012-01-01

    The aim of this study was to characterize cytogenetically one population of the fish Moenkhausia sanctaefilomenae (Steindachner, 1907), with emphasis on the analysis of B chromosomes. The nucleolar activity in the B microchromosomes was characterized, and an analysis of mitotic instability of these microchromosomes was accomplished. The results showed a diploid chromosome number of 50 chromosomes. In all individuals, we observed the presence of B microchromosomes with intra- and inter-individual variability. The analysis of the nucleolus organizing regions (NORs) by silver nitrate staining demonstrated multiple NORs. We observed active sites of ribosomal DNA in the B microchromosomes, with a frequency of 20% in the analyzed cells, which shows gene activity in these chromosomal elements. The analysis of constitutive heterochromatin patterns showed that the B microchromosomes are heterochromatic or euchromatic, which demonstrates differentiation of DNA composition between these genomic elements. The calculation of the mitotic instability index implied that B chromosomes in this species might be in a final stage of instability. PMID:24260658

  5. Analysis of Plasmid and Chromosomal DNA of Multidrug-Resistant Salmonella enterica Serovar Typhi from Asia

    Science.gov (United States)

    Mirza, S.; Kariuki, S.; Mamun, K. Z.; Beeching, N. J.; Hart, C. A.

    2000-01-01

    Molecular analysis of chromosomal DNA from 193 multidrug-resistant (MDR) Salmonella enterica serovar Typhi isolates from 1990 to 1995 from Pakistan, Kuwait, Malaysia, Bangladesh, and India produced a total of five major different pulsed-field gel electrophoresis (PFGE) patterns. Even within a particular country MDR S. enterica serovar Typhi DNA was found to be in different PFGE groups. Similar self-transferable 98-MDa plasmids belonging to either incompatibility group incHI1 or incHI1/FIIA were implicated in the MDR phenotype in S. enterica serovar Typhi isolates from all the locations except Quetta, Pakistan, where the majority were of incFIA. A total of five different PFGE genotypes with six different plasmids, based on incompatibility and restriction endonuclease analysis groups, were found among these MDR S. enterica serovar Typhi isolates. PMID:10747124

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

    Science.gov (United States)

    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

  7. Analysis of the Trojan Y-Chromosome eradication strategy for an invasive species

    KAUST Repository

    Wang, Xueying

    2013-05-24

    The Trojan Y-Chromosome (TYC) strategy, an autocidal genetic biocontrol method, has been proposed to eliminate invasive alien species. In this work, we analyze the dynamical system model of the TYC strategy, with the aim of studying the viability of the TYC eradication and control strategy of an invasive species. In particular, because the constant introduction of sex-reversed trojan females for all time is not possible in practice, there arises the question: What happens if this injection is stopped after some time? Can the invasive species recover? To answer that question, we perform a rigorous bifurcation analysis and study the basin of attraction of the recovery state and the extinction state in both the full model and a certain reduced model. In particular, we find a theoretical condition for the eradication strategy to work. Additionally, the consideration of an Allee effect and the possibility of a Turing instability are also studied in this work. Our results show that: (1) with the inclusion of an Allee effect, the number of the invasive females is not required to be very low when the introduction of the sex-reversed trojan females is stopped, and the remaining Trojan Y-Chromosome population is sufficient to induce extinction of the invasive females; (2) incorporating diffusive spatial spread does not produce a Turing instability, which would have suggested that the TYC eradication strategy might be only partially effective, leaving a patchy distribution of the invasive species. © 2013 Springer-Verlag Berlin Heidelberg.

  8. Chromosome Mapping, Expression and Polymorphism Analysis of CRABP1 Gene in Pigs

    Institute of Scientific and Technical Information of China (English)

    ZHAO Shuan-ping; TANG Zhong-lin; ZHOU Rong; QU Chang-qing; ZHENG Jian-wei; LI Kui

    2014-01-01

    Cellular retinoic acid-binding protein 1 (CRABP1) is a well-conserved member of cytosolic lipid-binding protein family. It is an important modulator of retinoic acid signaling. Long serial analysis of gene expression (LongSAGE) analysis suggested that CRABP1 gene was differentially expressed during prenatal skeletal muscle development in porcine. Here, we obtained the full-length coding region sequence and genomic sequence of the porcine CRABP1 gene and analyzed its genomic structures. Subsequently, we examined CRABP1 chromosome assignment using INRA-University of Minnesota 7 000 porcine radiation hybrid panel (IMpRH) and explored its tissue distribution in adult Tongcheng pigs and dynamical expression proifles in prenatal skeletal muscle (33, 65 and 90 days post coitus, dpc) from Landrace (lean-type) (described as L33, L65 and L90) and Tongcheng pigs (obese-type) (described as T33, T65 and T90). The CRABP1 gene was mapped to chromosome 7q11-q23 and closely linked to the microsatellite marker SWR1928. Quantitative real-time PCR showed that CRABP1 mRNA was highly expressed in lung and stomach, moderately expressed in placenta and uterus, and weakly expressed in other tissues. Moreover, CRABP1 gene was down-regulated during prenatal skeletal muscle development in both Landrace and Tongcheng pigs and it was expressed much higher in T33 than L33. Two single-nucleotide polymorphisms (SNPs) were detected by sequencing and mass spectrometry methods, allele frequency analysis indicated that g. 281 (G>A) and g. 2992 (G>A) were deviated from Hardy-Weinberg equilibrium in the Landrace and DLY (Duroc×(Landrace×Yorkshire)) pig breeds.

  9. A reasoning system for image analysis

    Directory of Open Access Journals (Sweden)

    Gao Jin Sheng

    2016-01-01

    Full Text Available For image analysis in computer, the traditional approach is extracting and transcoding features after image segmentation. However, in this paper, we present a different way to analyze image. We adopt spatial logic technology to establish a reasoning system with corresponding semantic model, and prove its soundness and completeness, and then realize the image analysis in formal way. And it can be applied in artificial intelligence. This is a new attempt and also a challenging approach.

  10. Chromosome region-specific libraries for human genome analysis. Final progress report, 1 March 1991--28 February 1994

    Energy Technology Data Exchange (ETDEWEB)

    Kao, F.T.

    1994-04-01

    The objectives of this grant proposal include (1) development of a chromosome microdissection and PCR-mediated microcloning technology, (2) application of this microtechnology to the construction of region-specific libraries for human genome analysis. During this grant period, the authors have successfully developed this microtechnology and have applied it to the construction of microdissection libraries for the following chromosome regions: a whole chromosome 21 (21E), 2 region-specific libraries for the long arm of chromosome 2, 2q35-q37 (2Q1) and 2q33-q35 (2Q2), and 4 region-specific libraries for the entire short arm of chromosome 2, 2p23-p25 (2P1), 2p21-p23 (2P2), 2p14-p16 (wP3) and 2p11-p13 (2P4). In addition, 20--40 unique sequence microclones have been isolated and characterized for genomic studies. These region-specific libraries and the single-copy microclones from the library have been used as valuable resources for (1) isolating microsatellite probes in linkage analysis to further refine the disease locus; (2) isolating corresponding clones with large inserts, e.g. YAC, BAC, P1, cosmid and phage, to facilitate construction of contigs for high resolution physical mapping; and (3) isolating region-specific cDNA clones for use as candidate genes. These libraries are being deposited in the American Type Culture Collection (ATCC) for general distribution.

  11. Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases.

    Directory of Open Access Journals (Sweden)

    Xinyan Lu

    Full Text Available BACKGROUND: Array Comparative Genomic Hybridization (a-CGH is a powerful molecular cytogenetic tool to detect genomic imbalances and study disease mechanism and pathogenesis. We report our experience with the clinical implementation of this high resolution human genome analysis, referred to as Chromosomal Microarray Analysis (CMA. METHODS AND FINDINGS: CMA was performed clinically on 2513 postnatal samples from patients referred with a variety of clinical phenotypes. The initial 775 samples were studied using CMA array version 4 and the remaining 1738 samples were analyzed with CMA version 5 containing expanded genomic coverage. Overall, CMA identified clinically relevant genomic imbalances in 8.5% of patients: 7.6% using V4 and 8.9% using V5. Among 117 cases referred for additional investigation of a known cytogenetically detectable rearrangement, CMA identified the majority (92.5% of the genomic imbalances. Importantly, abnormal CMA findings were observed in 5.2% of patients (98/1872 with normal karyotypes/FISH results, and V5, with expanded genomic coverage, enabled a higher detection rate in this category than V4. For cases without cytogenetic results available, 8.0% (42/524 abnormal CMA results were detected; again, V5 demonstrated an increased ability to detect abnormality. Improved diagnostic potential of CMA is illustrated by 90 cases identified with 51 cryptic microdeletions and 39 predicted apparent reciprocal microduplications in 13 specific chromosomal regions associated with 11 known genomic disorders. In addition, CMA identified copy number variations (CNVs of uncertain significance in 262 probands; however, parental studies usually facilitated clinical interpretation. Of these, 217 were interpreted as familial variants and 11 were determined to be de novo; the remaining 34 await parental studies to resolve the clinical significance. CONCLUSIONS: This large set of clinical results demonstrates the significantly improved sensitivity

  12. Spreadsheet-like image analysis

    Science.gov (United States)

    Wilson, Paul

    1992-08-01

    This report describes the design of a new software system being built by the Army to support and augment automated nondestructive inspection (NDI) on-line equipment implemented by the Army for detection of defective manufactured items. The new system recalls and post-processes (off-line) the NDI data sets archived by the on-line equipment for the purpose of verifying the correctness of the inspection analysis paradigms, of developing better analysis paradigms and to gather statistics on the defects of the items inspected. The design of the system is similar to that of a spreadsheet, i.e., an array of cells which may be programmed to contain functions with arguments being data from other cells and whose resultant is the output of that cell's function. Unlike a spreadsheet, the arguments and the resultants of a cell may be a matrix such as a two-dimensional matrix of picture elements (pixels). Functions include matrix mathematics, neural networks and image processing as well as those ordinarily found in spreadsheets. The system employs all of the common environmental supports of the Macintosh computer, which is the hardware platform. The system allows the resultant of a cell to be displayed in any of multiple formats such as a matrix of numbers, text, an image, or a chart. Each cell is a window onto the resultant. Like a spreadsheet if the input value of any cell is changed its effect is cascaded into the resultants of all cells whose functions use that value directly or indirectly. The system encourages the user to play what-of games, as ordinary spreadsheets do.

  13. Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan

    OpenAIRE

    Thomas George H; Ye Ying; Ting Jason C; Ruczinski Ingo; Pevsner Jonathan

    2006-01-01

    Abstract Background A variety of diseases are caused by chromosomal abnormalities such as aneuploidies (having an abnormal number of chromosomes), microdeletions, microduplications, and uniparental disomy. High density single nucleotide polymorphism (SNP) microarrays provide information on chromosomal copy number changes, as well as genotype (heterozygosity and homozygosity). SNP array studies generate multiple types of data for each SNP site, some with more than 100,000 SNPs represented on e...

  14. Meta-analysis of results from quantitative trait loci mapping studies on pig chromosome 4.

    Science.gov (United States)

    Silva, K M; Bastiaansen, J W M; Knol, E F; Merks, J W M; Lopes, P S; Guimarães, S E F; van Arendonk, J A M

    2011-06-01

    Meta-analysis of results from multiple studies could lead to more precise quantitative trait loci (QTL) position estimates compared to the individual experiments. As the raw data from many different studies are not readily available, the use of results from published articles may be helpful. In this study, we performed a meta-analysis of QTL on chromosome 4 in pig, using data from 25 separate experiments. First, a meta-analysis was performed for individual traits: average daily gain and backfat thickness. Second, a meta-analysis was performed for the QTL of three traits affecting loin yield: loin eye area, carcass length and loin meat weight. Third, 78 QTL were selected from 20 traits that could be assigned to one of three broad categories: carcass, fatness or growth traits. For each analysis, the number of identified meta-QTL was smaller than the number of initial QTL. The reduction in the number of QTL ranged from 71% to 86% compared to the total number before the meta-analysis. In addition, the meta-analysis reduced the QTL confidence intervals by as much as 85% compared to individual QTL estimates. The reduction in the confidence interval was greater when a large number of independent QTL was included in the meta-analysis. Meta-QTL related to growth and fatness were found in the same region as the FAT1 region. Results indicate that the meta-analysis is an efficient strategy to estimate the number and refine the positions of QTL when QTL estimates are available from multiple populations and experiments. This strategy can be used to better target further studies such as the selection of candidate genes related to trait variation.

  15. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

    Science.gov (United States)

    Zody, Michael C; Garber, Manuel; Adams, David J; Sharpe, Ted; Harrow, Jennifer; Lupski, James R; Nicholson, Christine; Searle, Steven M; Wilming, Laurens; Young, Sarah K; Abouelleil, Amr; Allen, Nicole R; Bi, Weimin; Bloom, Toby; Borowsky, Mark L; Bugalter, Boris E; Butler, Jonathan; Chang, Jean L; Chen, Chao-Kung; Cook, April; Corum, Benjamin; Cuomo, Christina A; de Jong, Pieter J; DeCaprio, David; Dewar, Ken; FitzGerald, Michael; Gilbert, James; Gibson, Richard; Gnerre, Sante; Goldstein, Steven; Grafham, Darren V; Grocock, Russell; Hafez, Nabil; Hagopian, Daniel S; Hart, Elizabeth; Norman, Catherine Hosage; Humphray, Sean; Jaffe, David B; Jones, Matt; Kamal, Michael; Khodiyar, Varsha K; LaButti, Kurt; Laird, Gavin; Lehoczky, Jessica; Liu, Xiaohong; Lokyitsang, Tashi; Loveland, Jane; Lui, Annie; Macdonald, Pendexter; Major, John E; Matthews, Lucy; Mauceli, Evan; McCarroll, Steven A; Mihalev, Atanas H; Mudge, Jonathan; Nguyen, Cindy; Nicol, Robert; O'Leary, Sinéad B; Osoegawa, Kazutoyo; Schwartz, David C; Shaw-Smith, Charles; Stankiewicz, Pawel; Steward, Charles; Swarbreck, David; Venkataraman, Vijay; Whittaker, Charles A; Yang, Xiaoping; Zimmer, Andrew R; Bradley, Allan; Hubbard, Tim; Birren, Bruce W; Rogers, Jane; Lander, Eric S; Nusbaum, Chad

    2006-04-20

    Chromosome 17 is unusual among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second highest gene density in the genome. It is also enriched in segmental duplications, ranking third in density among the autosomes. Here we report a finished sequence for human chromosome 17, as well as a structural comparison with the finished sequence for mouse chromosome 11, the first finished mouse chromosome. Comparison of the orthologous regions reveals striking differences. In contrast to the typical pattern seen in mammalian evolution, the human sequence has undergone extensive intrachromosomal rearrangement, whereas the mouse sequence has been remarkably stable. Moreover, although the human sequence has a high density of segmental duplication, the mouse sequence has a very low density. Notably, these segmental duplications correspond closely to the sites of structural rearrangement, demonstrating a link between duplication and rearrangement. Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome. PMID:16625196

  16. Amplification, analysis and chromosome mapping of novel homeobox-containing and homeobox-flanking sequences in rice

    Institute of Scientific and Technical Information of China (English)

    刘国振; 严长杰; 翟文学; 何平; 杨江; 李小兵; 朱立煌

    1999-01-01

    Homeobox genes, widely distributed among animal and plant kingdoms, play an important role in developmental process. Several homeobox conserved fragments were amplified by PCR and the flanking regions were also obtained by an LM-PCR procedure. Sequencing and Southern analysis showed that they belong to a homeobox gene family of rice. Six homeobox-containing fragments were mapped on the molecular linkage map of rice. They were located on chromosomes 3, 4 and 7 respectively. It is noteworthy that there are 4 homeobox fragments located on rice chromosome 3 and the result is also consistent with the comparative genomics between rice and maize.

  17. Diagnostic Yield of Chromosomal Microarray Analysis in a Cohort of Patients with Autism Spectrum Disorders from a Highly Consanguineous Population

    Science.gov (United States)

    Al-Mamari, Watfa; Al-Saegh, Abeer; Al-Kindy, Adila; Bruwer, Zandre; Al-Murshedi, Fathiya; Al-Thihli, Khalid

    2015-01-01

    Autism Spectrum Disorders are a complicated group of disorders characterized with heterogeneous genetic etiologies. The genetic investigations for this group of disorders have expanded considerably over the past decade. In our study we designed a tired approach and studied the diagnostic yield of chromosomal microarray analysis on patients…

  18. Analysis of Dynamic Brain Imaging Data

    CERN Document Server

    Mitra, P

    1998-01-01

    Modern imaging techniques for probing brain function, including functional Magnetic Resonance Imaging, intrinsic and extrinsic contrast optical imaging, and magnetoencephalography, generate large data sets with complex content. In this paper we develop appropriate techniques of analysis and visualization of such imaging data, in order to separate the signal from the noise, as well as to characterize the signal. The techniques developed fall into the general category of multivariate time series analysis, and in particular we extensively use the multitaper framework of spectral analysis. We develop specific protocols for the analysis of fMRI, optical imaging and MEG data, and illustrate the techniques by applications to real data sets generated by these imaging modalities. In general, the analysis protocols involve two distinct stages: `noise' characterization and suppression, and `signal' characterization and visualization. An important general conclusion of our study is the utility of a frequency-based repres...

  19. [Effect of gametocidal chromosome 4S' on the phenotype segregation ratio in genetic analysis of common wheat lines].

    Science.gov (United States)

    Vdovichenko, Zh V; Antoniuk, M Z; Ternovskaia, T K

    2003-01-01

    Using experimental data on genetic analysis of introgressive lines for the character "hairy leaf sheath" controlled by the "cuckoo" chromosome 4S1, the algorithm for calculation of the theoretical segregation ratio in F2 was developed. Segregation distortion is caused by non-viability of the majority of gametes lacking the chromosome 4S1. The frequency of functioning gametes without the chromosome 4S1 is determined by the probability p versus the theoretically expected ratio 7 nonviable: 9 viable ones. Since segregation involves two characters, gamete viability and hairiness, the ratio 15 hairy: 1 hairless was used as a basis for search of the frequency p by maximum-likelihood method using 16 populations F2 from crossing the lines differing in the character studied. PMID:14650327

  20. High resolution chromosome analysis and fluorescence in situ hybridization in patients referred for Prader-Willi or Angelman syndrome

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-05-08

    Laboratory testing is helpful in the evaluation of patients suspected to have either Prader-Willi syndrome (PWS) or Angelman syndrome (AS) because most of the patients have recognizable cytogenetic deletions of 15q11q13. Maternal uniparental disomy of chromosome 15, identified by molecular genetic techniques, is found in about 20 to 25% of PWS patients. Paternal uniparental disomy of chromosome 15 is seen in 2 to 3% of AS patients. Thus, PWS and AS represent the first examples in humans of genetic imprinting or the differential expression of genetic information depending on the parental origin. Herein, I report our experience with FISH and high resolution chromosome analysis in patients referred to confirm or rule out PWS or AS. 10 refs., 1 tab.

  1. Digital-image processing and image analysis of glacier ice

    Science.gov (United States)

    Fitzpatrick, Joan J.

    2013-01-01

    This document provides a methodology for extracting grain statistics from 8-bit color and grayscale images of thin sections of glacier ice—a subset of physical properties measurements typically performed on ice cores. This type of analysis is most commonly used to characterize the evolution of ice-crystal size, shape, and intercrystalline spatial relations within a large body of ice sampled by deep ice-coring projects from which paleoclimate records will be developed. However, such information is equally useful for investigating the stress state and physical responses of ice to stresses within a glacier. The methods of analysis presented here go hand-in-hand with the analysis of ice fabrics (aggregate crystal orientations) and, when combined with fabric analysis, provide a powerful method for investigating the dynamic recrystallization and deformation behaviors of bodies of ice in motion. The procedures described in this document compose a step-by-step handbook for a specific image acquisition and data reduction system built in support of U.S. Geological Survey ice analysis projects, but the general methodology can be used with any combination of image processing and analysis software. The specific approaches in this document use the FoveaPro 4 plug-in toolset to Adobe Photoshop CS5 Extended but it can be carried out equally well, though somewhat less conveniently, with software such as the image processing toolbox in MATLAB, Image-Pro Plus, or ImageJ.

  2. Comparison of genomes of eight species of sections Linum and Adenolinum from the genus Linum based on chromosome banding, molecular markers and RAPD analysis.

    Science.gov (United States)

    Muravenko, Olga V; Yurkevich, Olga Yu; Bolsheva, Nadezhda L; Samatadze, Tatiana E; Nosova, Inna V; Zelenina, Daria A; Volkov, Alexander A; Popov, Konstantin V; Zelenin, Alexander V

    2009-03-01

    Karyotypes of species sects. Linum and Adenolinum have been studied using C/DAPI-banding, Ag-NOR staining, FISH with 5S and 26S rDNA and RAPD analysis. C/DAPI-banding patterns enabled identification of all homologous chromosome pairs in the studied karyotypes. The revealed high similarity between species L. grandiflorum (2n = 16) and L. decumbens by chromosome and molecular markers proved their close genome relationship and identified the chromosome number in L. decumbens as 2n = 16. The similarity found for C/DAPI-banding patterns between species with the same chromosome numbers corresponds with the results obtained by RAPD-analysis, showing clusterization of 16-, 18- and 30-chromosome species into three separate groups. 5S rDNA and 26S rDNA were co-localized in NOR-chromosome 1 in the genomes of all species investigated. In 30-chromosome species, there were three separate 5S rDNA sites in chromosomes 3, 8 and 13. In 16-chromosome species, a separate 5S rDNA site was also located in chromosome 3, whereas in 18-chromosome species it was found in the long arm of NOR-chromosome 1. Thus, the difference in localization of rDNA sites in species with 2n = 16, 2n = 30 and 2n = 18 confirms taxonomists opinion, who attributed these species to different sects. Linum and Adenolinum, respectively. The obtained results suggest that species with 2n = 16, 2n = 18 and 2n = 30 originated from a 16-chromosome ancestor. PMID:18500654

  3. Image registration with uncertainty analysis

    Science.gov (United States)

    Simonson, Katherine M.

    2011-03-22

    In an image registration method, edges are detected in a first image and a second image. A percentage of edge pixels in a subset of the second image that are also edges in the first image shifted by a translation is calculated. A best registration point is calculated based on a maximum percentage of edges matched. In a predefined search region, all registration points other than the best registration point are identified that are not significantly worse than the best registration point according to a predetermined statistical criterion.

  4. Ring chromosome 13

    DEFF Research Database (Denmark)

    Brandt, C A; Hertz, Jens Michael; Petersen, M B;

    1992-01-01

    A stillborn male child with anencephaly and multiple malformations was found to have the karyotype 46,XY,r(13) (p11q21.1). The breakpoint at 13q21.1, determined by high resolution banding, is the most proximal breakpoint ever reported in patients with ring chromosome 13. In situ hybridisation...... with the probe L1.26 confirmed the derivation from chromosome 13 and DNA polymorphism analysis showed maternal origin of the ring chromosome. Our results, together with a review of previous reports of cases with ring chromosome 13 with identified breakpoints, could neither support the theory of distinct clinical...

  5. Measurement of Nuchal Translucency Thickness for Detection of Chromosomal Abnormalities using First Trimester Ultrasound Fetal Images

    CERN Document Server

    Nirmala, S

    2010-01-01

    The Nuchal Translucency thickness measurement is made to identify the Down Syndrome in screening first trimester fetus and presented in this paper. The mean shift analysis and canny operators are utilized for segmenting the nuchal translucency region and the exact thickness has been estimated using Blob analysis. It is observed from the results that the fetus in the 14th week of Gestation is expected to have a nuchal translucency thickness of 1.87 plus or minus 0.25mm.

  6. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

    DEFF Research Database (Denmark)

    Purps, Josephine; Siegert, Sabine; Willuweit, Sascha;

    2014-01-01

    In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DY...

  7. Chromosome identification and gene mapping in potato by pachytene, trisomic and half-tetrad analysis.

    NARCIS (Netherlands)

    Wagenvoort, M.

    1993-01-01

    The research described in this thesis deals with chromosome identification and gene mapping. In contrast to results from literature, in this study only three chromosomes (1, 2 and 12) could unambiguously be identified in mitotic cells using conventional staining, and four (1, 2, 3 and 4) in case of

  8. Live embryo imaging to follow cell cycle and chromosomes stability after nuclear transfer.

    Science.gov (United States)

    Balbach, Sebastian T; Boiani, Michele

    2015-01-01

    Nuclear transfer (NT) into mouse oocytes yields a transcriptionally and functionally heterogeneous population of cloned embryos. Most studies of NT embryos consider only embryos at predefined key stages (e.g., morula or blastocyst), that is, after the bulk of reprogramming has taken place. These retrospective approaches are of limited use to elucidate mechanisms of reprogramming and to predict developmental success. Observing cloned embryo development using live embryo cinematography has the potential to reveal otherwise undetectable embryo features. However, light exposure necessary for live cell cinematography is highly toxic to cloned embryos. Here we describe a protocol for combined bright-field and fluorescence live-cell imaging of histone H2b-GFP expressing mouse embryos, to record cell divisions up to the blastocyst stage. This protocol, which can be adapted to observe other reporters such as Oct4-GFP or Nanog-GFP, allowed us to quantitatively analyze cleavage kinetics of cloned embryos. PMID:25287344

  9. Chromosome numbers and meiotic analysis in the pre-breeding of Brachiaria decumbens (Poaceae)

    Indian Academy of Sciences (India)

    Gléia Cristina Laverde Ricci; Alice Maria De Souza-Kaneshima; Mariana Ferrari Felismino; Andrea Beatriz Mendes-Bonato; Maria Suely Pagliarini; Cacilda Borges Do Valle

    2011-08-01

    A total of 44 accessions of Brachiaria decumbens were analysed for chromosome count and meiotic behaviour in order to identify potential progenitors for crosses. Among them, 15 accessions presented $2n = 18$; 27 accessions, $2n = 36$; and 2 accessions, $2n = 45$ chromosomes. Among the diploid accessions, the rate of meiotic abnormalities was low, ranging from 0.82% to 7.93%. In the 27 tetraploid accessions, the rate of meiotic abnormalities ranged from 18.41% to 65.83%. The most common meiotic abnormalities were related to irregular chromosome segregation, but chromosome stickiness and abnormal cytokinesis were observed in low frequency. All abnormalities can compromise pollen viability by generating unbalanced gametes. Based on the chromosome number and meiotic stability, the present study indicates the apomictic tetraploid accessions that can act as male genitor to produce interspecific hybrids with B. ruziziensis or intraspecific hybrids with recently artificially tetraploidized accessions.

  10. A 3D image analysis tool for SPECT imaging

    Science.gov (United States)

    Kontos, Despina; Wang, Qiang; Megalooikonomou, Vasileios; Maurer, Alan H.; Knight, Linda C.; Kantor, Steve; Fisher, Robert S.; Simonian, Hrair P.; Parkman, Henry P.

    2005-04-01

    We have developed semi-automated and fully-automated tools for the analysis of 3D single-photon emission computed tomography (SPECT) images. The focus is on the efficient boundary delineation of complex 3D structures that enables accurate measurement of their structural and physiologic properties. We employ intensity based thresholding algorithms for interactive and semi-automated analysis. We also explore fuzzy-connectedness concepts for fully automating the segmentation process. We apply the proposed tools to SPECT image data capturing variation of gastric accommodation and emptying. These image analysis tools were developed within the framework of a noninvasive scintigraphic test to measure simultaneously both gastric emptying and gastric volume after ingestion of a solid or a liquid meal. The clinical focus of the particular analysis was to probe associations between gastric accommodation/emptying and functional dyspepsia. Employing the proposed tools, we outline effectively the complex three dimensional gastric boundaries shown in the 3D SPECT images. We also perform accurate volume calculations in order to quantitatively assess the gastric mass variation. This analysis was performed both with the semi-automated and fully-automated tools. The results were validated against manual segmentation performed by a human expert. We believe that the development of an automated segmentation tool for SPECT imaging of the gastric volume variability will allow for other new applications of SPECT imaging where there is a need to evaluate complex organ function or tumor masses.

  11. Colour model analysis for microscopic image processing

    OpenAIRE

    García-Rojo Marcial; González Jesús; Déniz Oscar; González Roberto; Bueno Gloria

    2008-01-01

    Abstract This article presents a comparative study between different colour models (RGB, HSI and CIEL*a*b*) applied to a very large microscopic image analysis. Such analysis of different colour models is needed in order to carry out a successful detection and therefore a classification of different regions of interest (ROIs) within the image. This, in turn, allows both distinguishing possible ROIs and retrieving their proper colour for further ROI analysis. This analysis is not commonly done ...

  12. Discovering beautiful attributes for aesthetic image analysis

    OpenAIRE

    Marchesotti, Luca; Murray, Naila; Perronnin, Florent

    2014-01-01

    Aesthetic image analysis is the study and assessment of the aesthetic properties of images. Current computational approaches to aesthetic image analysis either provide accurate or interpretable results. To obtain both accuracy and interpretability by humans, we advocate the use of learned and nameable visual attributes as mid-level features. For this purpose, we propose to discover and learn the visual appearance of attributes automatically, using a recently introduced database, called AVA, w...

  13. Digital Image Analysis for Detechip Code Determination

    OpenAIRE

    Marcus Lyon; Wilson, Mark V.; Kerry A. Rouhier; David J. Symonsbergen; Kiran Bastola; Ishwor Thapa; Holmes, Andrea E.; Sharmin M. Sikich; Abby Jackson

    2012-01-01

    DETECHIP® is a molecular sensing array used for identification of a large variety of substances. Previous methodology for the analysis of DETECHIP® used human vision to distinguish color changes induced by the presence of the analyte of interest. This paper describes several analysis techniques using digital images of DETECHIP® . Both a digital camera and flatbed desktop photo scanner were used to obtain Jpeg images. Color information within these digital images was obt...

  14. Digital Image Analysis for Detechip Code Determination

    OpenAIRE

    Marcus Lyon; Wilson, Mark V.; Holmes, Andrea E.; Sharmin M. Sikich; Abby Jackson; Kerry A. Rouhier; David J. Symonsbergen; Kiran Bastola

    2012-01-01

    DETECHIP® is a molecular sensing array used for identification of a large variety of substances. Previous methodology for the analysis of DETECHIP® used human vision to distinguish color changes induced by the presence of the analyte of interest. This paper describes several analysis techniques using digital images of DETECHIP®. Both a digital camera and flatbed desktop photo scanner were used to obtain Jpeg images. Color information within these digital images was obtained through the me...

  15. Digital Image Analysis for DETCHIP® Code Determination

    OpenAIRE

    Lyon, Marcus; Wilson, Mark V.; Kerry A. Rouhier; David J. Symonsbergen; Bastola, Kiran; Thapa, Ishwor; Holmes, Andrea E.; Sharmin M. Sikich; Jackson, Abby

    2012-01-01

    DETECHIP® is a molecular sensing array used for identification of a large variety of substances. Previous methodology for the analysis of DETECHIP® used human vision to distinguish color changes induced by the presence of the analyte of interest. This paper describes several analysis techniques using digital images of DETECHIP®. Both a digital camera and flatbed desktop photo scanner were used to obtain Jpeg images. Color information within these digital images was obtained through the measur...

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

    Science.gov (United States)

    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

  17. Frequency and distribution analysis of chromosomal translocations induced by x-ray in human lymphocytes

    International Nuclear Information System (INIS)

    The characteristic of ionizing radiation suggests that induced chromosomal damage in the form of translocations would appear to be randomly distributed. However, the outcome of tests performed in vitro and in vivo (irradiated individuals) are contradictories. The most translocation-related chromosomes, as far as some studies reveal on one hand, appear to be less involved in accordance with others. These data, together with those related to molecular mechanisms involved in translocations production suggest that in G0 -irradiated cells, the frequency and distribution of this kind of chromosomal rearrangement, does not take place at random. They seem to be affected by in-nucleus chromosome distribution, by each chromosome's DNA length and functional features, by the efficiency of DNA repair mechanisms, and by inter individual differences. The objective of this study was to establish the frequency pattern of each human chromosome involved in radio-induced translocations, as well as to analyze the importance the chromosome length, the activity of DNA polymerase- dependant repair mechanisms, and inter individual differences within the scope of such distribution. To achieve the goals, peripheral blood lymphocytes from healthy donors were irradiated in presence and absence of 2'-3' dideoxithimidine (ddThd), a Β - DNA polymerase inhibitor, which takes part in the base repair mechanism (B E R). The results showed that: The presence of ddThd during the irradiation increase the basal frequency of radioinduced translocations in 60 %. This result suggests that ddThd repair synthesis inhibition can be in itself a valid methodology for radiation-induced bases damage assessment, damage which if not BER-repaired may result in translocation-leading double strand breaks. A statistically significant correlation between translocation frequency and chromosome length, in terms of percentage of genome, has been noticed both in (basal) irradiation and in irradiation with ddThd inhibitor

  18. Association Between Gene Polymorphisms on Chromosome 1 and Susceptibility to Pre-Eclampsia: An Updated Meta-Analysis

    OpenAIRE

    Zhang, Guixin; Zhao, Jinheng; Yi, Jianping; Luan, Yuanyuan; Wang, Qian

    2016-01-01

    Background This meta-analysis enabled us to obtain a precise estimation of the association between gene polymorphisms on chromosome 1 (MTHFR, AGT, F5, IL-10, LEPR) and the susceptibility to pre-eclampsia (PE) in order to reach a uniform conclusion. Material/Methods Web of Science, PubMed, EMBASE, Cochran Library (CENTRAL), and Chinese databases (Chinese National Knowledge Infrastructure-CNKI and Wan Fang) were electronically searched to select relevant studies for this meta-analysis. We selec...

  19. Prevalence of chromosomal abnormalities and timing of karyotype analysis in patients with recurrent implantation failure (RIF) following assisted reproduction

    OpenAIRE

    De Sutter, P.; Stadhouders, R.; Dutré, M.; Gerris, J.; Dhont, M.

    2012-01-01

    Aims: To analyze the prevalence and type of karyotype abnormalities in RIF patients and to evaluate the adequate timing for analysis and the presence of possible risk factors. Methods: 615 patients (317 women and 298 men) with RIF, having undergone at least 3 sequential failed IVF/ICSI cycles prior to karyotype analysis, were included in this study. Anomaly rates found were compared with published series. Results: Chromosomal abnormalities were diagnosed in 2.1% of patients (13/615): 8 female...

  20. Analysis of Y-chromosome STRs in Chile confirms an extensive introgression of European male lineages in urban populations.

    Science.gov (United States)

    Toscanini, Ulises; Brisighelli, Francesca; Moreno, Fabián; Pantoja-Astudillo, Jaime A; Morales, Eugenia Aguirre; Bustos, Patricio; Pardo-Seco, Jacobo; Salas, Antonio

    2016-03-01

    We analyzed the Y chromosome haplotypes (Yfiler) of 978 non-related Chilean males grouped in five sampling regions (Iquique, Santiago de Chile, Concepción, Temuco and Punta Arenas) covering main geo-political regions. Overall, 803 different haplotypes and 688 singletons were observed. Molecular diversity was moderately lower than in other neighboring countries (e.g. Argentina); and AMOVA analysis on Y-STR haplotypes showed that among variation within Chile accounted for only 0.25% of the total variation. Punta Arenas, in the southern cone, showed the lowest haplotype diversity, and discrimination capacity, and also the highest matching probability of the five Chilean samples, probably reflecting its more marked geographic isolation compared to the other regions. Multidimensional scaling (MDS) analysis based on RST genetic distances suggested a close proximity of Chilean Y-chromosome profiles to European ones. Consistently, haplogroups inferred from Y-STR profiles revealed that the Native American component constituted only 8% of all the haplotypes, and this component ranged from 5% in the Centre of the country to 9-10% in the South and 13% in the North, which is in good agreement with the distribution of Native American communities in these regions. AMOVA computed on inferred haplogroups confirmed the very low among variation observed in Chilean populations. The present project provides the first Chilean dataset to the international Y-chromosome STR Haplotype Reference Database (YHRD) and it is also the first reference database for Y-chromosome forensic casework of the country.

  1. Human peripheral blood lymphocytes for the analysis of chromosome aberrations in mutagen tests

    International Nuclear Information System (INIS)

    Studies on exposed individuals, and on cultured cells, have shown that the human peripheral blood lymphocyte is an extremely sensitive indicator of both in vivo and in vitro induced chromosome structural change. These changes in chromosome structure offer readily scored morphological evidence of damage to the genetic material. Although problems exist in the extrapolation from in vitro results to the in vivo situation, the lymphocyte offers several advantages as a test system. The types of chromosome damage which can be cytologically distinguished at metaphase can be divided into two main groups: chromosome type and chromatid type. The circulating lymphocyte is in the G/sub 0/ or G/sub 1/ phase of mitosis and exposure to ionising radiations and certain other mutagenic agents during this stage produces chromosome-type damage where the unit of breakage and reunion is the whole chromosome (i.e. both chromatids at the same locus). However, cells exposed to these agents while in the S or G/sub 2/ stages of the cell cycle, after the chromosome has divided into two sister chromatids, yield chromatid-type aberrations and only the single chromatid is involved in breakage or exchange. Other agents (e.g. some of the alkylating agents) will usually produce only chromatid-type aberrations in cells in cycle although the cells are exposed to the mutagen whilst in G/sub 1/

  2. Cytogenetic analysis of Aegilops chromosomes, potentially usable in triticale (X Triticosecale Witt.) breeding.

    Science.gov (United States)

    Kwiatek, M; Wiśniewska, H; Apolinarska, B

    2013-05-01

    Chromosome identification using fluorescence in situ hybridization (FISH) is widely used in cytogenetic research. It is a diagnostic tool helpful in chromosome identification. It can also be used to characterize alien introgressions, when exercised in a combination with genomic in situ hybridization (GISH). This work aims to find chromosome identification of Aegilops species and Aegilops × Secale amphiploids, which can be used in cereal breeding as a source of favourable agronomic traits. Four diploid and two tetraploid Aegilops species and three Aegilops × Secale hybrids were analysed using FISH with pSc119.2, pAs1, 5S rDNA and 25S rDNA clones to differentiate the U-, M-, S(sh)- and D-subgenome chromosomes of Aegilops genus. Additionally, GISH for chromosome categorization was carried out. Differences in the hybridization patterns allowed to identify all U-, M-, S(sh)- and D-subgenome chromosomes. Some differences in localization of the rDNA, pSc119.2 and pAs1 sequences between analogue subgenomes in diploid and tetraploid species and Aegilops × Secale hybrids were detected. The hybridization pattern of the M and S genome was more variable than that of the U and D genome. An importance of the cytogenetic markers in plant breeding and their possible role in chromosome structure, function and evolution is discussed. PMID:23378244

  3. Chromosomal Analysis of Couples with Repeated Spontaneous Abortions in Northeastern Iran

    Directory of Open Access Journals (Sweden)

    Saeedeh Ghazaey

    2015-04-01

    Full Text Available Background: Cytogenetic study of reproductive wastage is an important aspect in determining the genetic background of early embryogenesis. Approximately 15 to 20% of all pregnancies in humans are terminated as recurrent spontaneous abortions (RSAs. The aim of this study was to detect chromosome abnormalities in couples with RSAs and to compare our results with those reported previously. Materials and Methods: In this retrospective study, the pattern of chromosomal aberrations was evaluated during a six-year period from 2005 to 2011. The population under study was 728 couples who attended genetic counseling services for their RSAs at Pardis Clinical and Genetics Laboratory, Mashhad, Iran. Results: In this study, about 11.7% of couples were carriers of chromosomal aberrations. The majority of abnormalities were found in couples with history of abortion, without stillbirth or livebirth. Balanced reciprocal translocations, Robertsonian translocations, inversions and sex chromosome aneuploidy were seen in these cases. Balanced reciprocal translocations were the most frequent chromosomal anomalies (62.7% detected in current study. Conclusion: These findings suggest that chromosomal abnormalities can be one of the important causes of RSAs. In addition, cytogenetic study of families who experienced RSAs may prevent unnecessary treatment if RSA are caused by chromosomal abnormalities. The results of cytogenetic studies of RSA cases will provide a standard protocol for the genetic counselors in order to follow up and to help these families.

  4. Cytogenetic analysis of Aegilops chromosomes, potentially usable in triticale (X Triticosecale Witt.) breeding.

    Science.gov (United States)

    Kwiatek, M; Wiśniewska, H; Apolinarska, B

    2013-05-01

    Chromosome identification using fluorescence in situ hybridization (FISH) is widely used in cytogenetic research. It is a diagnostic tool helpful in chromosome identification. It can also be used to characterize alien introgressions, when exercised in a combination with genomic in situ hybridization (GISH). This work aims to find chromosome identification of Aegilops species and Aegilops × Secale amphiploids, which can be used in cereal breeding as a source of favourable agronomic traits. Four diploid and two tetraploid Aegilops species and three Aegilops × Secale hybrids were analysed using FISH with pSc119.2, pAs1, 5S rDNA and 25S rDNA clones to differentiate the U-, M-, S(sh)- and D-subgenome chromosomes of Aegilops genus. Additionally, GISH for chromosome categorization was carried out. Differences in the hybridization patterns allowed to identify all U-, M-, S(sh)- and D-subgenome chromosomes. Some differences in localization of the rDNA, pSc119.2 and pAs1 sequences between analogue subgenomes in diploid and tetraploid species and Aegilops × Secale hybrids were detected. The hybridization pattern of the M and S genome was more variable than that of the U and D genome. An importance of the cytogenetic markers in plant breeding and their possible role in chromosome structure, function and evolution is discussed.

  5. Multispectral Image Analysis for Astaxanthin Coating Classification

    DEFF Research Database (Denmark)

    Ljungqvist, Martin Georg; Ersbøll, Bjarne Kjær; Nielsen, Michael Engelbrecht;

    2012-01-01

    only with fish oil. In this study, multispectral image analysis of pellets captured reflection in 20 wavelengths (385–1050 nm). Linear discriminant analysis (LDA), principal component analysis, and support vector machine were used as statistical analysis. The features extracted from the multispectral...... images were pixel spectral values as well as using summary statistics such as the mean or median value of each pellet. Classification using LDA on pellet mean or median values showed overall good results. Multispectral imaging is a promising technique for noninvasive on-line quality food and feed...

  6. A chromosomal analysis of four species of Chilean Chrysomelinae (Coleoptera, Chrysomelidae

    Directory of Open Access Journals (Sweden)

    Eduard Petitpierre

    2012-10-01

    Full Text Available Four species of Chilean leaf beetles in the subfamily Chrysomelinae have been cytogenetically analyzed, Blaptea elguetai Petitpierre, 2011, Henicotherus porteri Bréthes, 1929 and Jolivetia obscura (Philippi, 1864 show 2n = 28 chromosomes and a 13 + Xyp male meioformula, and Pataya nitida (Philippi, 1864 has the highest number of 2n = 38 chromosomes. The karyotype of H. porteri is made of mostly small meta/submetacentric chromosomes, and that of Jolivetia obscura displays striking procentric blocks of heterochromatin at pachytene autosomic bivalents using conventional staining. These findings are discussed in relation to previous cytogenetic data and current taxonomy of the subfamily.

  7. [Fluorescence in situ hybridization with DNA probes derived from individual chromosomes and chromosome regions].

    Science.gov (United States)

    Bogomolov, A G; Karamysheva, T V; Rubtsov, N B

    2014-01-01

    A significant part of the eukaryotic genomes consists of repetitive DNA, which can form large clusters or distributed along euchromatic chromosome regions. Repeats located in chromosomal regions make a problem in analysis and identification of the chromosomal material with fluorescence in situ hybridization (FISH). In most cases, the identification of chromosome regions using FISH requires detection of the signal produced with unique sequences. The feasibility, advantages and disadvantages of traditional methods of suppression of repetitive DNA hybridization, methods of repeats-free probe construction and methods of chromosome-specific DNA sequences visualization using image processing of multicolor FISH results are considered in the paper. The efficiency of different techniques for DNA probe generation, different FISH protocols, and image processing of obtained microscopic images depends on the genomic size and structure of analyzing species. This problem was discussed and different approaches were considered for the analysis of the species with very large genome, rare species and species which specimens are too small in size to obtain the amount of genomic and Cot-1 DNA required for suppression of repetitive DNA hybridization.

  8. Solar Image Analysis and Visualization

    CERN Document Server

    Ireland, J

    2009-01-01

    This volume presents a selection of papers on the state of the art of image enhancement, automated feature detection, machine learning, and visualization tools in support of solar physics that focus on the challenges presented by new ground-based and space-based instrumentation. The articles and topics were inspired by the Third Solar Image Processing Workshop, held at Trinity College Dublin, Ireland but contributions from other experts have been included as well. This book is mainly aimed at researchers and graduate students working on image processing and compter vision in astronomy and solar physics.

  9. Natural user interfaces in medical image analysis cognitive analysis of brain and carotid artery images

    CERN Document Server

    Ogiela, Marek R

    2014-01-01

    This unique text/reference highlights a selection of practical applications of advanced image analysis methods for medical images. The book covers the complete methodology for processing, analysing and interpreting diagnostic results of sample CT images. The text also presents significant problems related to new approaches and paradigms in image understanding and semantic image analysis. To further engage the reader, example source code is provided for the implemented algorithms in the described solutions. Features: describes the most important methods and algorithms used for image analysis; e

  10. Chromosomal and Genetic Analysis of a Human Lung Adenocarcinoma Cell Line OM

    Institute of Scientific and Technical Information of China (English)

    Yong-Wu Li; Lin Bai; Lyu-Xia Dai; Xu He; Xian-Ping Zhou

    2016-01-01

    Background: Lung cancer has become the leading cause of death in many regions.Carcinogenesis is caused by the stepwise accumulation of genetic and chromosomal changes.The aim of this study was to investigate the chromosome and gene alterations in the human lung adenocarcinoma cell line OM.Methods: We used Giemsa banding and multiplex fluorescence in situ hybridization focusing on the human lung adenocarcinoma cell line OM to analyze its chromosome alterations.In addition, the gains and losses in the specific chromosome regions were identified by comparative genomic hybridization (CGH) and the amplifications of cancer-related genes were also detected by polymerase chain reaction (PCR).Results: We identified a large number of chromosomal numerical alterations on all chromosomes except chromosome X and 19.Chromosome 10 is the most frequently involved in translocations with six different interchromosomal translocations.CGH revealed the gains on chromosome regions of 3q25.3-28, 5p13, 12q22-23.24, and the losses on 3p25-26, 6p25, 6q26-27, 7q34-36, 8p22-23, 9p21-24, 10q25-26.3, 12p 13.31-13.33 and 17p 13.1-13.3.And PCR showed the amplification of genes: Membrane metalloendopeptidase (MME), sucrase-isomaltase (SI), butyrylcholinesterase (BCHE), and kininogen (KNG).Conclusions: The lung adenocarcinoma cell line OM exhibited multiple complex karyotypes, and chromosome 10 was frequently involved in chromosomal translocation, which may play key roles in tumorigenesis.We speculated that the oncogenes may be located at 3q25.3-28, 5p13, 12q22-23.24, while tumor suppressor genes may exist in 3p25-26, 6p25, 6q26-27, 7q34-36, 8p22-23, 9p21-24, 10q25-26.3, 12p 13.31-13.33, and 17p 13.1-13.3.Moreover, at least four genes (MME, SI, BCHE, and KNG) may be involved in the human lung adenocarcinoma cell line OM.

  11. Surface antigen expression in chronic lymphocytic leukemia: clustering analysis, interrelationships and effects of chromosomal abnormalities.

    Science.gov (United States)

    Hulkkonen, J; Vilpo, L; Hurme, M; Vilpo, J

    2002-02-01

    Chronic lymphocytic leukemia (CLL) is a phenotypically distinguishable form of B-lymphoid leukemias. The regularity of surface membrane antigen expression patterns, their interrelationships as well as the effects of the three frequent chromosomal aberrations, ie 11q deletion, 13q deletion and trisomy 12, were investigated in 35 classic CLL cases by flow cytometry. The two-way cluster analysis of 31 individual antigens revealed three expression patterns: (1) most cells in most cases positive (CD5, CD19, CD20, CD23, CD27, CD40, CD45, CD45RA); (2) most cells in most cases negative (CD10, CD14, CD34, CD122, CD154, mIgG); and (3) a mixed pattern with a variable number of positive cases and a variable percentage of positive cells in individual cases (CD11c, CD21, CD22, CD25, CD38, CD45RO, CD79b, CD80, CD95, CD124, CD126, CD130, FMC7, mIgD, mIgkappa, mIglambda, mIgM). The expressions of several antigens were strongly interdependent, even when antigens belonged to entirely different gene families. Such antigen pairs were: CD11c/CD21; CD19/CD45; CD19/CD79b; CD22/CD45RA; CD23/Igkappa; CD25/mIgM; CD27/CD45; CD45/CD79b; CD45RA/Igkappa. In contrast, the expression of some antigens was mutually exclusive, the best examples being CD45RA/CD45RO, CD38/CD80 and CD45RA/CD80. Deletion of chromosome arm 11q attenuated expression of splicing variant CD45RA, but enhanced CD45RO expression. In contrast, cases of trisomy 12 were associated with enhanced CD45RA and attenuated CD45RO expression. Similarly, trisomy 12 was associated with enhanced CD27 and mIgkappa expression. The variable levels of signaling surface membrane antigens, their interactions and interference by genetic aberrations are likely to affect the clinical progression and drug response of CLL. PMID:11840283

  12. Forensic analysis of polymorphism and regional stratification of Y-chromosomal microsatellites in Belarus.

    Science.gov (United States)

    Rebała, Krzysztof; Tsybovsky, Iosif S; Bogacheva, Anna V; Kotova, Svetlana A; Mikulich, Alexei I; Szczerkowska, Zofia

    2011-01-01

    Nine loci defining minimal haplotypes and four other Y-chromosomal short tandem repeats (Y-STRs) DYS437, DYS438, DYS439 and GATA H4.1 were analysed in 414 unrelated males residing in four regions of Belarus. Haplotypes of 328 males were further extended by 7 additional Y-STRs: DYS388, DYS426, DYS448, DYS456, DYS458, DYS460 and DYS635. The 13-locus haplotype diversity was 0.9978 and discrimination capacity was 78.7%, indicating presence of identical haplotypes among unrelated males. Seven additional Y-STRs enabled almost complete discrimination of undifferentiated 13-locus haplotypes, increasing haplotype diversity to 0.9998 and discrimination capacity to 97.9%. Analysis of molecular variance of minimal haplotypes excluded the use of a Y-STR database for Belarusians residing in northeastern Poland as representative for the Belarusian population in forensic practice, and revealed regional stratification within the country. However, four additional markers (DYS437, DYS438, DYS439 and GATA H4.1) were shown to eliminate the observed geographical substructure among Belarusian males. The results imply that in case of minimal and PowerPlex Y haplotypes, a separate frequency database should be used for northern Belarus to estimate Y-STR profile frequencies in forensic casework. In case of Yfiler haplotypes, regional stratification within Belarus may be neglected.

  13. Systematic Triple-Mutant Analysis Uncovers Functional Connectivity between Pathways Involved in Chromosome Regulation

    Directory of Open Access Journals (Sweden)

    James E. Haber

    2013-06-01

    Full Text Available Genetic interactions reveal the functional relationships between pairs of genes. In this study, we describe a method for the systematic generation and quantitation of triple mutants, termed triple-mutant analysis (TMA. We have used this approach to interrogate partially redundant pairs of genes in S. cerevisiae, including ASF1 and CAC1, two histone chaperones. After subjecting asf1Δ cac1Δ to TMA, we found that the Swi/Snf Rdh54 protein compensates for the absence of Asf1 and Cac1. Rdh54 more strongly associates with the chromatin apparatus and the pericentromeric region in the double mutant. Moreover, Asf1 is responsible for the synthetic lethality observed in cac1Δ strains lacking the HIRA-like proteins. A similar TMA was carried out after deleting both CLB5 and CLB6, cyclins that regulate DNA replication, revealing a strong functional connection to chromosome segregation. This approach can reveal functional redundancies that cannot be uncovered through traditional double-mutant analyses.

  14. Y-chromosomal STR analysis in the Pashtun population of Southern Afghanistan.

    Science.gov (United States)

    Achakzai, Niaz M; Rahman, Z; Shahzad, M S; Daud, S; Zar, M S; Israr, M; Husnain, T; Willuweit, Sascha; Roewer, Lutz

    2012-07-01

    Afghanistan is a landlocked country in the heart of Asia and since the dawn of humankind Afghanistan has faced centuries of turmoil, strife, conflict, warfare, distress, social unrest, difficult climate, harsh terrain and due to its unique geostrategic position in Eurasia which has historically attracted commerce and conflict. It is an important stop along the Silk Road, connecting the far eastern civilizations to the western world. A 5000-year history of constant invasion. Afghanistan has been repeatedly invaded and conquered by rulers and super powers, neighboring interference in this conflict-tattered land for centuries yet rarely leading to the conquest of this rugged and challenging terrain nation. Afghans are not only shepherds, farmers and nomads but also intense fighters and fierce warriors. Currently very limited genetic studies have been performed in Afghan populations. 17 Y chromosomal short tandem repeats (Y-STRs) were analyzed in 125 unrelated Pashtun (in hindi: Pathan) males residing in the Kandahar region of Southern Afghanistan. A total of 92 unique haplotypes were observed. The predominant haplotype reached a frequency of 9.6%. The haplotype diversity was 0.987 and the discrimination capacity 73.6%. Analysis of molecular variance (AMOVA) reveals a considerable regional stratification within the country as well as between different Pashtun (Pathan) groups from Afghanistan, Pakistan and India.

  15. Rapid molecular cytogenetic analysis of X-chromosomal microdeletions: Fluorescence in situ hybridization (FISH) for complex glycerol kinase deficiency

    Energy Technology Data Exchange (ETDEWEB)

    Worley, K.C.; Lindsay, E.A.; McCabe, E.R.B. [Baylor College of Medicine, Houston, TX (United States)] [and others

    1995-07-17

    Diagnosis of X-chromosomal microdeletions has relied upon the traditional methods of Southern blotting and DNA amplification, with carrier identification requiring time-consuming and unreliable dosage calculations. In this report, we describe rapid molecular cytogenetic identification of deleted DNA in affected males with the Xp21 contiguous gene syndrome (complex glycerol kinase deficiency, CGKD) and female carriers for this disorder. CGKD deletions involve the genes for glycerol kinase, Duchenne muscular dystrophy, and/or adrenal hypoplasia congenita. We report an improved method for diagnosis of deletions in individuals with CGKD and for identification of female carriers within their families using fluorescence in situ hybridization (FISH) with a cosmid marker (cosmid 35) within the glycerol kinase gene. When used in combination with an Xq control probe, affected males demonstrate a single signal from the control probe, while female carriers demonstrate a normal chromosome with two signals, as well as a deleted chromosome with a single signal from the control probe. FISH analysis for CGKD provides the advantages of speed and accuracy for evaluation of submicroscopic X-chromosome deletions, particularly in identification of female carriers. In addition to improving carrier evaluation, FISH will make prenatal diagnosis of CGKD more readily available. 17 refs., 2 figs.

  16. Digital Image Analysis for Detechip Code Determination

    Directory of Open Access Journals (Sweden)

    Marcus Lyon

    2012-09-01

    Full Text Available DETECHIP® is a molecular sensing array used for identification of a large variety of substances. Previous methodology for the analysis of DETECHIP® used human vision to distinguish color changes induced by the presence of the analyte of interest. This paper describes several analysis techniques using digital images of DETECHIP®. Both a digital camera and flatbed desktop photo scanner were used to obtain Jpeg images. Color information within these digital images was obtained through the measurement of redgreen-blue (RGB values using software such as GIMP, Photoshop and ImageJ. Several different techniques were used to evaluate these color changes. It was determined that the flatbed scanner produced in the clearest and more reproducible images. Furthermore, codes obtained using a macro written for use within ImageJ showed improved consistency versus pervious methods.

  17. Digital Image Analysis for Detechip Code Determination

    Directory of Open Access Journals (Sweden)

    Marcus Lyon

    2012-08-01

    Full Text Available DETECHIP® is a molecular sensing array used for identification of a large variety of substances. Previous methodology for the analysis of DETECHIP® used human vision to distinguish color changes induced by the presence of the analyte of interest. This paper describes several analysis techniques using digital images of DETECHIP® . Both a digital camera and flatbed desktop photo scanner were used to obtain Jpeg images. Color information within these digital images was obtained through the measurement of redgreen-blue (RGB values using software such as GIMP, Photoshop and ImageJ. Several different techniques were used to evaluate these color changes. It was determined that the flatbed scanner produced in the clearest and more reproducible images. Furthermore, codes obtained using a macro written for use within ImageJ showed improved consistency versus pervious methods.

  18. Analysis of chromosome translocation in the residents of Namie Town after the accident of Fukushima Daiichi Nuclear Power Plant

    International Nuclear Information System (INIS)

    The dose estimation by behavior survey of the residents carried out by Fukushima Prefecture after the accident reported that there are no residents who were exposed by over 1 mSv radiation. However, a lot of the parents are worrying about the health condition of their children in future. Our Hirosaki University accepted the request of the local government of this Namie-Town in Fukushima which wants to know whether children were exposed by radiological substances or not and started the inspection about the contamination and exposure level and dose estimation at an accident using chromosomal translocation analysis for 855 out of 3700 children whose age was under 18 years old at the time of accident. In order to estimate radiation dose using chromosome aberration in the accidents, there are four kinds of cytogenetic method; dicentric assay, a translocation assay, the PCC-ring assay and micronucleus test. A dicentric assay is used for the dose estimation in acute and external exposure cases, the chromosomal translocation method for dose assessment in chronic and old exposure and the PCC method for high dose exposure, respectively. In the case of the residents in Namie-Town, since about one year and ten months had already passed after the accident when implementation of this inspection was determined, the chromosomal translocation method was applied for the dose estimation of the initial exposure level. The main purpose of this translocation analysis using their own cells is to take away affairs of the residents including parents and children and also to reduce the uneasiness which is not wiped away by the health check due to a behavioral survey. In this inspection, after the contents and process of this analysis were explained in the Tsushima, Namie-Town temporarily constructed clinic, 3∼4 ml of whole 5 blood were taken from each children whose parents agreed with this analysis. The lymphocytic cells are isolated from the whole blood using CPT (Cell Preparation Tube

  19. Depth-based selective image reconstruction using spatiotemporal image analysis

    Science.gov (United States)

    Haga, Tetsuji; Sumi, Kazuhiko; Hashimoto, Manabu; Seki, Akinobu

    1999-03-01

    In industrial plants, a remote monitoring system which removes physical tour inspection is often considered desirable. However the image sequence given from the mobile inspection robot is hard to see because interested objects are often partially occluded by obstacles such as pillars or fences. Our aim is to improve the image sequence that increases the efficiency and reliability of remote visual inspection. We propose a new depth-based image processing technique, which removes the needless objects from the foreground and recovers the occluded background electronically. Our algorithm is based on spatiotemporal analysis that enables fine and dense depth estimation, depth-based precise segmentation, and accurate interpolation. We apply this technique to a real time sequence given from the mobile inspection robot. The resulted image sequence is satisfactory in that the operator can make correct visual inspection with less fatigue.

  20. 用染色体涂染技术分析五例染色体结构异常%Application of chromosome painting technique to analysis of structural aberration of human chromosomes

    Institute of Scientific and Technical Information of China (English)

    杨焕杰; 宋岩; 刘权章; 李钰; 傅松滨; 张贵寅; 李璞

    2001-01-01

    目的结合G-显带核型分析诊断染色体易位,并对G显带技术难以鉴定的微小易位进行分析。方法采用生物素标记的显微切割制备的X、Y、14q、10号染色体特异性探针,与患者外周血培养淋巴细胞中期染色体进行荧光原位杂交。结果室温存放近10年的标本、-80℃冻存标本及新鲜标本均可看到清晰的杂交信号,染色体结构异常很清楚。结论染色体涂染技术结合G显带核型分析,可以准确识别G显带技术难以鉴定的染色体微小易位。%Objective  This study was aimed at using chromosome painting technique to detect translocation, especially microtranslocations, on chromosomes in comparison with G-banding analysis. Methods  Chromosome painting technique was applied to analysis of metaphase chromosomes of patients for detecting translocations with biotin-labeled chromosomes X, Y, 14q, 10 specific probes. Results Fluorescence in situ hybridization FISH signals were shown clearly in slides even in specimen stored at room temperature for 10 years and at -80℃. Translocations were located precisely. Conclusion Microtranslocations, which are hard to analyze by G-banding, can be detected exactly using chromosome painting technique with G-band karyotype on metaphase chromosome.

  1. Quantum image classification using principal component analysis

    Directory of Open Access Journals (Sweden)

    Mateusz Ostaszewski

    2016-01-01

    Full Text Available We present a novel quantum algorithm for classification of images. The algorithm is constructed using principal component analysis and von Neuman quantum measurements. In order to apply the algorithm we present a new quantum representation of grayscale images.

  2. Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations

    Science.gov (United States)

    Dulik, Matthew C.; Owings, Amanda C.; Gaieski, Jill B.; Vilar, Miguel G.; Andre, Alestine; Lennie, Crystal; Mackenzie, Mary Adele; Kritsch, Ingrid; Snowshoe, Sharon; Wright, Ruth; Martin, James; Gibson, Nancy; Andrews, Thomas D.; Schurr, Theodore G.; Adhikarla, Syama; Adler, Christina J.; Balanovska, Elena; Balanovsky, Oleg; Bertranpetit, Jaume; Clarke, Andrew C.; Comas, David; Cooper, Alan; Der Sarkissian, Clio S. I.; GaneshPrasad, ArunKumar; Haak, Wolfgang; Haber, Marc; Hobbs, Angela; Javed, Asif; Jin, Li; Kaplan, Matthew E.; Li, Shilin; Martínez-Cruz, Begoña; Matisoo-Smith, Elizabeth A.; Melé, Marta; Merchant, Nirav C.; Mitchell, R. John; Parida, Laxmi; Pitchappan, Ramasamy; Platt, Daniel E.; Quintana-Murci, Lluis; Renfrew, Colin; Lacerda, Daniela R.; Royyuru, Ajay K.; Santos, Fabrício R.; Soodyall, Himla; Soria Hernanz, David F.; Swamikrishnan, Pandikumar; Tyler-Smith, Chris; Santhakumari, Arun Varatharajan; Vieira, Pedro Paulo; Wells, R. Spencer; Zalloua, Pierre A.; Ziegle, Janet S.

    2012-01-01

    For decades, the peopling of the Americas has been explored through the analysis of uniparentally inherited genetic systems in Native American populations and the comparison of these genetic data with current linguistic groupings. In northern North America, two language families predominate: Eskimo-Aleut and Na-Dene. Although the genetic evidence from nuclear and mtDNA loci suggest that speakers of these language families share a distinct biological origin, this model has not been examined using data from paternally inherited Y chromosomes. To test this hypothesis and elucidate the migration histories of Eskimoan- and Athapaskan-speaking populations, we analyzed Y-chromosomal data from Inuvialuit, Gwich’in, and Tłįchǫ populations living in the Northwest Territories of Canada. Over 100 biallelic markers and 19 chromosome short tandem repeats (STRs) were genotyped to produce a high-resolution dataset of Y chromosomes from these groups. Among these markers is an SNP discovered in the Inuvialuit that differentiates them from other Aboriginal and Native American populations. The data suggest that Canadian Eskimoan- and Athapaskan-speaking populations are genetically distinct from one another and that the formation of these groups was the result of two population expansions that occurred after the initial movement of people into the Americas. In addition, the population history of Athapaskan speakers is complex, with the Tłįchǫ being distinct from other Athapaskan groups. The high-resolution biallelic data also make clear that Y-chromosomal diversity among the first Native Americans was greater than previously recognized. PMID:22586127

  3. Examination of X chromosome markers in Rett syndrome: Exclusion mapping with a novel variation on multilocus linkage analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ellison, K.A.; Fill, C.P. (Baylor College of Medicine, Houston, TX (United States)); Terwililger, J.; Percy, A.K.; Zobhbi, H. (Columbia University, NY (United States)); DeGennaro, L.J.; Ott, J. (University of Massachusetts Medical School, Worcester (United States)); Anvret, M.; Martin-Gallardo, A. (National Institutes of Health, Bethesda, MD (United States))

    1992-02-01

    Rett syndrome is a neurologic disorder characterized by early normal development followed by regression, acquired deceleration of head growth, autism, ataxia, and sterotypic hand movements. The exclusive occurrence of the syndrome in females and the occurrence of a few familial cases with inheritance through maternal lines suggest that this disorder is most likely secondary to a mutation on the X chromosome. To address this hypothesis and to identify candidate regions for the Rett syndrome gene locus, genotypic analysis was performed in two families with maternally related affected half-sisters by using 63 DNA markers from the X chromosome. Nineteen of the loci studied were chosen for multipoint linkage analysis because they have been previously genetically mapped using a large number of meioses from reference families. Using the exclusion criterion of a lod score less than [minus]2, the authors were able to exclude the region between the Duchenne muscular dystrophy locus and the DXS456 locus. This region extends from Xp21.2 to Xq21-q23. The use of the multipoint linkage analysis approach outlined in this study should allow the exclusion of additional regions of the X chromosome as new markers are analyzed.

  4. A Robust Actin Filaments Image Analysis Framework.

    Science.gov (United States)

    Alioscha-Perez, Mitchel; Benadiba, Carine; Goossens, Katty; Kasas, Sandor; Dietler, Giovanni; Willaert, Ronnie; Sahli, Hichem

    2016-08-01

    The cytoskeleton is a highly dynamical protein network that plays a central role in numerous cellular physiological processes, and is traditionally divided into three components according to its chemical composition, i.e. actin, tubulin and intermediate filament cytoskeletons. Understanding the cytoskeleton dynamics is of prime importance to unveil mechanisms involved in cell adaptation to any stress type. Fluorescence imaging of cytoskeleton structures allows analyzing the impact of mechanical stimulation in the cytoskeleton, but it also imposes additional challenges in the image processing stage, such as the presence of imaging-related artifacts and heavy blurring introduced by (high-throughput) automated scans. However, although there exists a considerable number of image-based analytical tools to address the image processing and analysis, most of them are unfit to cope with the aforementioned challenges. Filamentous structures in images can be considered as a piecewise composition of quasi-straight segments (at least in some finer or coarser scale). Based on this observation, we propose a three-steps actin filaments extraction methodology: (i) first the input image is decomposed into a 'cartoon' part corresponding to the filament structures in the image, and a noise/texture part, (ii) on the 'cartoon' image, we apply a multi-scale line detector coupled with a (iii) quasi-straight filaments merging algorithm for fiber extraction. The proposed robust actin filaments image analysis framework allows extracting individual filaments in the presence of noise, artifacts and heavy blurring. Moreover, it provides numerous parameters such as filaments orientation, position and length, useful for further analysis. Cell image decomposition is relatively under-exploited in biological images processing, and our study shows the benefits it provides when addressing such tasks. Experimental validation was conducted using publicly available datasets, and in osteoblasts grown in

  5. A Robust Actin Filaments Image Analysis Framework

    Science.gov (United States)

    Alioscha-Perez, Mitchel; Benadiba, Carine; Goossens, Katty; Kasas, Sandor; Dietler, Giovanni; Willaert, Ronnie; Sahli, Hichem

    2016-01-01

    The cytoskeleton is a highly dynamical protein network that plays a central role in numerous cellular physiological processes, and is traditionally divided into three components according to its chemical composition, i.e. actin, tubulin and intermediate filament cytoskeletons. Understanding the cytoskeleton dynamics is of prime importance to unveil mechanisms involved in cell adaptation to any stress type. Fluorescence imaging of cytoskeleton structures allows analyzing the impact of mechanical stimulation in the cytoskeleton, but it also imposes additional challenges in the image processing stage, such as the presence of imaging-related artifacts and heavy blurring introduced by (high-throughput) automated scans. However, although there exists a considerable number of image-based analytical tools to address the image processing and analysis, most of them are unfit to cope with the aforementioned challenges. Filamentous structures in images can be considered as a piecewise composition of quasi-straight segments (at least in some finer or coarser scale). Based on this observation, we propose a three-steps actin filaments extraction methodology: (i) first the input image is decomposed into a ‘cartoon’ part corresponding to the filament structures in the image, and a noise/texture part, (ii) on the ‘cartoon’ image, we apply a multi-scale line detector coupled with a (iii) quasi-straight filaments merging algorithm for fiber extraction. The proposed robust actin filaments image analysis framework allows extracting individual filaments in the presence of noise, artifacts and heavy blurring. Moreover, it provides numerous parameters such as filaments orientation, position and length, useful for further analysis. Cell image decomposition is relatively under-exploited in biological images processing, and our study shows the benefits it provides when addressing such tasks. Experimental validation was conducted using publicly available datasets, and in osteoblasts

  6. Molecular cytogenetic analysis of human blastocysts andcytotrophoblasts by multi-color FISH and Spectra Imaging analyses

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Jingly F.; Ferlatte, Christy; Baumgartner, Adolf; Jung,Christine J.; Nguyen, Ha-Nam; Chu, Lisa W.; Pedersen, Roger A.; Fisher,Susan J.; Weier, Heinz-Ulrich G.

    2006-02-08

    Numerical chromosome aberrations in gametes typically lead to failed fertilization, spontaneous abortion or a chromosomally abnormal fetus. By means of preimplantation genetic diagnosis (PGD), we now can screen human embryos in vitro for aneuploidy before transferring the embryos to the uterus. PGD allows us to select unaffected embryos for transfer and increases the implantation rate in in vitro fertilization programs. Molecular cytogenetic analyses using multi-color fluorescence in situ hybridization (FISH) of blastomeres have become the major tool for preimplantation genetic screening of aneuploidy. However, current FISH technology can test for only a small number of chromosome abnormalities and hitherto failed to increase the pregnancy rates as expected. We are in the process of developing technologies to score all 24 chromosomes in single cells within a 3 day time limit, which we believe is vital to the clinical setting. Also, human placental cytotrophoblasts (CTBs) at the fetal-maternal interface acquire aneuploidies as they differentiate to an invasive phenotype. About 20-50% of invasive CTB cells from uncomplicated pregnancies were found aneuploidy, suggesting that the acquisition of aneuploidy is an important component of normal placentation, perhaps limiting the proliferative and invasive potential of CTBs. Since most invasive CTBs are interphase cells and possess extreme heterogeneity, we applied multi-color FISH and repeated hybridizations to investigate individual CTBs. In summary, this study demonstrates the strength of Spectral Imaging analysis and repeated hybridizations, which provides a basis for full karyotype analysis of single interphase cells.

  7. Analysis of unstable chromosome alterations frequency induced by neutron-gamma mixed field radiation

    International Nuclear Information System (INIS)

    Nowadays monitoring chromosome alterations in peripheral blood lymphocytes have been used to access the radiation absorbed dose in individuals exposed accidental or occupationally to gamma radiation. However there are not many studies based on the effects of mixed field neutron-gamma. The radiobiology of neutrons has great importance because in nuclear factories worldwide there are several hundred thousand individuals monitored as potentially receiving doses of neutron. In this paper it was observed the frequencies of unstable chromosome alterations induced by a gamma-neutron mixed field. Blood was obtained from one healthy donor and exposed to mixed field neutron-gamma sources 241AmBe (20 Ci) at the Neutron Calibration Laboratory (NCL-CRCN/NE-PE-Brazil). The chromosomes were observed at metaphase, following colcemid accumulation and 1000 well-spread metaphases were analyzed for the presence of chromosome alterations by two experienced scorers. The results suggest that there is the possibility of a directly proportional relationship between absorbed dose of neutron-gamma mixed field radiation and the frequency of unstable chromosome alterations analyzed in this paper. (author)

  8. Malware Analysis Using Visualized Image Matrices

    Directory of Open Access Journals (Sweden)

    KyoungSoo Han

    2014-01-01

    Full Text Available This paper proposes a novel malware visual analysis method that contains not only a visualization method to convert binary files into images, but also a similarity calculation method between these images. The proposed method generates RGB-colored pixels on image matrices using the opcode sequences extracted from malware samples and calculates the similarities for the image matrices. Particularly, our proposed methods are available for packed malware samples by applying them to the execution traces extracted through dynamic analysis. When the images are generated, we can reduce the overheads by extracting the opcode sequences only from the blocks that include the instructions related to staple behaviors such as functions and application programming interface (API calls. In addition, we propose a technique that generates a representative image for each malware family in order to reduce the number of comparisons for the classification of unknown samples and the colored pixel information in the image matrices is used to calculate the similarities between the images. Our experimental results show that the image matrices of malware can effectively be used to classify malware families both statically and dynamically with accuracy of 0.9896 and 0.9732, respectively.

  9. Image processing and analysis software development

    International Nuclear Information System (INIS)

    The work presented in this project is aimed at developing a software 'IMAGE GALLERY' to investigate various image processing and analysis techniques. The work was divided into two parts namely the image processing techniques and pattern recognition, which further comprised of character and face recognition. Various image enhancement techniques including negative imaging, contrast stretching, compression of dynamic, neon, diffuse, emboss etc. have been studied. Segmentation techniques including point detection, line detection, edge detection have been studied. Also some of the smoothing and sharpening filters have been investigated. All these imaging techniques have been implemented in a window based computer program written in Visual Basic Neural network techniques based on Perception model have been applied for face and character recognition. (author)

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

    International Nuclear Information System (INIS)

    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

  11. Demographic estimates from Y chromosome microsatellite polymorphisms: Analysis of a worldwide sample

    Directory of Open Access Journals (Sweden)

    Macpherson J

    2004-08-01

    Full Text Available Abstract Polymorphisms in microsatellites on the human Y chromosome have been used to estimate important demographic parameters of human history. We compare two coalescent-based statistical methods that give estimates for a number of demographic parameters using the seven Y chromosome polymorphisms in the HGDP-CEPH Cell Line Panel, a collection of samples from 52 worldwide populations. The estimates for the time to the most recent common ancestor vary according to the method used and the assumptions about the prior distributions of model parameters, but are generally consistent with other global Y chromosome studies. We explore the sensitivity of these results to assumptions about the prior distributions and the evolutionary models themselves.

  12. Principal component analysis of scintimammographic images.

    Science.gov (United States)

    Bonifazzi, Claudio; Cinti, Maria Nerina; Vincentis, Giuseppe De; Finos, Livio; Muzzioli, Valerio; Betti, Margherita; Nico, Lanconelli; Tartari, Agostino; Pani, Roberto

    2006-01-01

    The recent development of new gamma imagers based on scintillation array with high spatial resolution, has strongly improved the possibility of detecting sub-centimeter cancer in Scintimammography. However, Compton scattering contamination remains the main drawback since it limits the sensitivity of tumor detection. Principal component image analysis (PCA), recently introduced in scintimam nographic imaging, is a data reduction technique able to represent the radiation emitted from chest, breast healthy and damaged tissues as separated images. From these images a Scintimammography can be obtained where the Compton contamination is "removed". In the present paper we compared the PCA reconstructed images with the conventional scintimammographic images resulting from the photopeak (Ph) energy window. Data coming from a clinical trial were used. For both kinds of images the tumor presence was quantified by evaluating the t-student statistics for independent sample as a measure of the signal-to-noise ratio (SNR). Since the absence of Compton scattering, the PCA reconstructed images shows a better noise suppression and allows a more reliable diagnostics in comparison with the images obtained by the photopeak energy window, reducing the trend in producing false positive. PMID:17646004

  13. Morphometric Analysis of Recognized Genes for Autism Spectrum Disorders and Obesity in Relationship to the Distribution of Protein-Coding Genes on Human Chromosomes

    Directory of Open Access Journals (Sweden)

    Austen B. McGuire

    2016-05-01

    Full Text Available Mammalian chromosomes are comprised of complex chromatin architecture with the specific assembly and configuration of each chromosome influencing gene expression and function in yet undefined ways by varying degrees of heterochromatinization that result in Giemsa (G negative euchromatic (light bands and G-positive heterochromatic (dark bands. We carried out morphometric measurements of high-resolution chromosome ideograms for the first time to characterize the total euchromatic and heterochromatic chromosome band length, distribution and localization of 20,145 known protein-coding genes, 790 recognized autism spectrum disorder (ASD genes and 365 obesity genes. The individual lengths of G-negative euchromatin and G-positive heterochromatin chromosome bands were measured in millimeters and recorded from scaled and stacked digital images of 850-band high-resolution ideograms supplied by the International Society of Chromosome Nomenclature (ISCN 2013. Our overall measurements followed established banding patterns based on chromosome size. G-negative euchromatic band regions contained 60% of protein-coding genes while the remaining 40% were distributed across the four heterochromatic dark band sub-types. ASD genes were disproportionately overrepresented in the darker heterochromatic sub-bands, while the obesity gene distribution pattern did not significantly differ from protein-coding genes. Our study supports recent trends implicating genes located in heterochromatin regions playing a role in biological processes including neurodevelopment and function, specifically genes associated with ASD.

  14. Morphometric Analysis of Recognized Genes for Autism Spectrum Disorders and Obesity in Relationship to the Distribution of Protein-Coding Genes on Human Chromosomes.

    Science.gov (United States)

    McGuire, Austen B; Rafi, Syed K; Manzardo, Ann M; Butler, Merlin G

    2016-05-05

    Mammalian chromosomes are comprised of complex chromatin architecture with the specific assembly and configuration of each chromosome influencing gene expression and function in yet undefined ways by varying degrees of heterochromatinization that result in Giemsa (G) negative euchromatic (light) bands and G-positive heterochromatic (dark) bands. We carried out morphometric measurements of high-resolution chromosome ideograms for the first time to characterize the total euchromatic and heterochromatic chromosome band length, distribution and localization of 20,145 known protein-coding genes, 790 recognized autism spectrum disorder (ASD) genes and 365 obesity genes. The individual lengths of G-negative euchromatin and G-positive heterochromatin chromosome bands were measured in millimeters and recorded from scaled and stacked digital images of 850-band high-resolution ideograms supplied by the International Society of Chromosome Nomenclature (ISCN) 2013. Our overall measurements followed established banding patterns based on chromosome size. G-negative euchromatic band regions contained 60% of protein-coding genes while the remaining 40% were distributed across the four heterochromatic dark band sub-types. ASD genes were disproportionately overrepresented in the darker heterochromatic sub-bands, while the obesity gene distribution pattern did not significantly differ from protein-coding genes. Our study supports recent trends implicating genes located in heterochromatin regions playing a role in biological processes including neurodevelopment and function, specifically genes associated with ASD.

  15. Can Comprehensive Chromosome Screening Technology Improve IVF/ICSI Outcomes? A Meta-Analysis.

    Directory of Open Access Journals (Sweden)

    Minghao Chen

    Full Text Available To examine whether comprehensive chromosome screening (CCS for preimplantation genetic screening (PGS has an effect on improving in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI outcomes compared to traditional morphological methods.A literature search was conducted in PubMed, EMBASE, CNKI and ClinicalTrials.gov up to May 2015. Two reviewers independently evaluated titles and abstracts, extracted data and assessed quality. We included studies that compared the IVF/ICSI outcomes of CCS-based embryo selection with those of the traditional morphological method. Relative risk (RR values with corresponding 95% confidence intervals (CIs were calculated in RevMan 5.3, and subgroup analysis and Begg's test were used to assess heterogeneity and potential publication bias, respectively.Four RCTs and seven cohort studies were included. A meta-analysis of the outcomes showed that compared to morphological criteria, euploid embryos identified by CCS were more likely to be successfully implanted (RCT RR 1.32, 95% CI 1.18-1.47; cohort study RR 1.74, 95% CI 1.35-2.24. CCS-based PGS was also related to an increased clinical pregnancy rate (RCT RR 1.26, 95% CI 0.83-1.93; cohort study RR 1.48, 95% CI 1.20-1.83, an increased ongoing pregnancy rate (RCT RR 1.31, 95% CI 0.64-2.66; cohort study RR 1.61, 95% CI 1.30-2.00, and an increased live birth rate (RCT RR 1.26, 95% CI 1.05-1.50; cohort study RR 1.35, 95% CI 0.85-2.13 as well as a decreased miscarriage rate (RCT RR 0.53, 95% CI 0.24-1.15; cohort study RR 0.31, 95% CI 0.21-0.46 and a decreased multiple pregnancy rate (RCT RR 0.02, 95% CI 0.00-0.26; cohort study RR 0.19, 95% CI 0.07-0.51. The results of the subgroup analysis also showed a significantly increased implantation rate in the CCS group.The effectiveness of CCS-based PGS is comparable to that of traditional morphological methods, with better outcomes for women receiving IVF/ICSI technology. The transfer of both trophectoderm-biopsied and

  16. Chromosome Mapping of 18S Ribosomal RNA Genes in Eleven Hypostomus Species (Siluriformes, Loricariidae): Diversity Analysis of the Sites.

    Science.gov (United States)

    Rubert, Marceléia; da Rosa, Renata; Zawadzki, Claudio H; Mariotto, Sandra; Moreira-Filho, Orlando; Giuliano-Caetano, Lucia

    2016-08-01

    We investigated the chromosomal distribution of 18S ribosomal DNA (rDNA) in different populations of 11 species of Hypostomus collected in important Brazilian basins, namely South Atlantic, Upper Paraná, and Paraguay applying the fluorescence in situ hybridization (FISH). Hypostomus cochliodon, Hypostomus commersoni, Hypostomus hermanni, Hypostomus regani, Hypostomus albopunctatus, Hypostomus paulinus, Hypostomus aff. paulinus, Hypostomus iheringii, and Hypostomus mutucae presented multiple 18S rDNA sites while Hypostomus strigaticeps and Hypostomus nigromaculatus exhibited a single pair of chromosomes with 18S rDNA sites. The studied species presented variations in the number and position of these sites. The results accomplished were similar to those obtained by the analysis of AgNORs, revealing the same interspecific variability. Each species exhibited distinctive patterns of AgNOR and 18S rDNA distribution, which can be considered cytogenetic markers in each species of the genus and help improve the discussions on the phylogeny of the group.

  17. The Mouse Clock Locus: Sequence and Comparative Analysis of 204 Kb from Mouse Chromosome 5

    OpenAIRE

    Wilsbacher, Lisa D.; Sangoram, Ashvin M.; Antoch, Marina P.; Takahashi, Joseph S.

    2000-01-01

    The Clock gene encodes a basic helix-loop-helix (bHLH)–PAS transcription factor that regulates circadian rhythms in mice. We previously cloned Clock in mouse and human using a battery of behavioral and molecular techniques, including shotgun sequencing of two bacterial artificial chromosome (BAC) clones. Here we report the finished sequence of a 204-kb region from mouse chromosome 5. This region contains the complete loci for the Clock and Tpardl (pFT27) genes, as well as the 3′ partial locus...

  18. Inheritance of coronary artery disease in men: an analysis of the role of the Y chromosome

    OpenAIRE

    Charchar, Fadi J; Bloomer, Lisa D. S.; Barnes, Timothy A.; Cowley, Mark J.; Nelson, Christopher P.; Wang, Yanzhong,; Denniff, Matthew; Debiec, Radoslaw; Christofidou, Paraskevi; Nankervis, Scott; Dominiczak, Anna F; Bani-Mustafa, Ahmed; Balmforth, Anthony J.; Hall, Alistair S; Erdmann, Jeanette

    2012-01-01

    BackgroundA sexual dimorphism exists in the incidence and prevalence of coronary artery disease—men are more commonly affected than are age-matched women. We explored the role of the Y chromosome in coronary artery disease in the context of this sexual inequity.MethodsWe genotyped 11 markers of the male-specific region of the Y chromosome in 3233 biologically unrelated British men from three cohorts: the British Heart Foundation Family Heart Study (BHF-FHS), West of Scotland Coronary Preventi...

  19. Identification and Preliminary Analysis of Several Centromere-associated Bacterial Artificial Chromosome Clones from a Diploid Wheat Library

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Although the centromeres of some plants have been investigated previously, our knowledge of the wheat centromere is still very limited. To understand the structure and function of the wheat centromere, we used two centromeric repeats (RCS1 and CCS1-5ab) to obtain some centromere-associated bacterial artificial chromosome (BAC) clones in 32 RCS1-related BAC clones that had been screened out from a diploid wheat (Triticum boeoticum Boiss.; 2n=2x=14) BAC library. Southern hybridization results indicated that, of the 32 candidates,there were 28 RCS1-positive clones. Based on gel blot patterns, the frequency of RCS1 was approximately one copy every 69.4 kb in these 28 RCS1-positive BAC clones. More bands were detected when the same filter was probed with CCS1-5ab. Furthermore, the CCS1 bands covered all the bands detected by RCS1, which suggests that some CCS1 repeats were distributed together with RCS1. The frequency of CCS1 families was once every 35.8 kb, nearly twice that of RCS1. Fluorescence in situ hybridization (FISH) analysis indicated that the five BAC clones containing RCS1 and CCS1 sequences all detected signals at the centromeric regions in hexaploid wheat, but the signal intensities on the A-genome chromosomes were stronger than those on the B- and/or D-genome chromosomes. The FISH analysis among nine Triticeae cereals indicated that there were A-genomespecific (or rich) sequences dispersing on chromosome arms in the BAC clone TbBAC5. In addition, at the interphase cells, the centromeres of diploid species usually clustered at one pole and formed a ring-like allocation in the period before metaphase.

  20. 染色体核型异常患者全基因组芯片扫描结果分析%Analysis on the results of chromosomal microarray in patients with chromosome abnormality

    Institute of Scientific and Technical Information of China (English)

    姚如恩; 傅启华; 余永国

    2014-01-01

    目的:利用全基因组芯片扫描技术对染色体核型检测结果异常的患者样本进行重复检测分析,验证并确认患者染色体的具体核型。方法利用基因分型芯片技术对9例临床表型皆为智力落后合并多发畸形,且核型结果异常的样本进行检测分析,比较两种技术之间结果相符程度,通过芯片平台结果来验证染色体核型技术的准确性,同时分析其临床适用性。结果染色体核型结果和全基因组芯片分析技术的结果完全符合的为2例Turner综合征患者,均为嵌合型;3例染色体核型结果阳性患者,全基因组芯片分析结果为阴性,其中2例为随体增加,1例为染色体内倒位;4例涉及染色体片段大小不同的缺失和复制的患者,核型结果和全基因组芯片结果差异较大,并且核型检测结果与患者实际核型相差较大。结论染色体核型技术在用于以往认定的适应症如智力落后、多发畸形的检测中,检测的准确性相对全基因组芯片技术较低,在明确定位染色体缺失和复制大小及位置的能力上有明显的不足,但对于检测染色体平衡性结构性变化的作用不能被芯片所取代。%Objective To analyze the results of patients with chromosome abnormality by chromosomal microarray, and validate and depict patient′s karyotype.Methods Genotyping array was applied to assess in 9 patients with hypophrenia and deformity.The samples with karyotype analysis abnormality were determined.Comparison between karyotyping and microarray analysis was considered to validate the clinical utility of chromosomal microarray analysis. Results Two Turner syndrome patients had completely concordant results from karyotype analysis and chromosomal microarray.Three patients showed abnormal karyotyping results (2 patients with excess trabant and 1 patients with chromosomal inversion) were detected negative with chromosomal microarray

  1. Multispectral dual isotope and NMR image analysis

    International Nuclear Information System (INIS)

    Dual isotope scintigraphy and nuclear magnetic resonance imaging produce image data that is intrinsically multispectral. That is multiple images of the same anatomic region are generated with different gray scale distribution and morphologic content that is largely redundant. Image processing technology, originally developed by NASA for satellite imaging, is available for multispectral analysis. These methods have been applied to provide tissue characterization. Tissue specific information encoded in the grapy scale data from dual isotope and NMR studies may be extracted using multispectral pattern recognition methods. The authors used table lookup minimum distance, maximum likelihood and cluster analysis techniques with data sets from Ga-67 / Tc-99m, 1-131 labeled antibodies / Tc-99m, Tc-99m perfusion / Xe-133 ventilation, and NMR studies. The results show; tissue characteristic signatures exist in dual isotope and NMR imaging, and these spectral signatures are identifiable using multispectral image analysis and provide tissue classification maps with scatter diagrams that facilitate interpretation and assist in elucidating subtle changes

  2. Numerous transitions of sex chromosomes in Diptera.

    Directory of Open Access Journals (Sweden)

    Beatriz Vicoso

    2015-04-01

    Full Text Available Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot, but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes. Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa.

  3. Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2

    OpenAIRE

    Curk, Franck; Ancillo, Gema; Garcia-Lor, Andres; Luro, François; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Navarro, Luis; Ollitrault, Patrick

    2014-01-01

    Background The most economically important Citrus species originated by natural interspecific hybridization between four ancestral taxa (Citrus reticulata, Citrus maxima, Citrus medica, and Citrus micrantha) and from limited subsequent interspecific recombination as a result of apomixis and vegetative propagation. Such reticulate evolution coupled with vegetative propagation results in mosaic genomes with large chromosome fragments from the basic taxa in frequent interspecific heterozygosity....

  4. Array comparative genomic hybridization analysis of small supernumerary marker chromosomes in human infertility.

    Science.gov (United States)

    Guediche, N; Tosca, L; Kara Terki, A; Bas, C; Lecerf, L; Young, J; Briand-Suleau, A; Tou, B; Bouligand, J; Brisset, S; Misrahi, M; Guiochon-Mantel, A; Goossens, M; Tachdjian, G

    2012-01-01

    Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes that cannot be unambiguously identified by conventional banding cytogenetics. This study describes four patients with sSMC in relation with infertility. Patient 1 had primary infertility. His brother, fertile, carried the same sSMC (patient 2). Patient 3 presented polycystic ovary syndrome and patient 4 primary ovarian insufficiency. Cytogenetic studies, array comparative genomic hybridization (CGH) and sperm analyses were compared with cases previously reported. sSMC corresponded to the 15q11.2 region (patients 1 and 2), the centromeric chromosome 15 region (patient 3) and the 21p11.2 region (patient 4). Array CGH showed 3.6-Mb gain for patients 1 and 2 and 0.266-Mb gain for patient 4. Sperm fluorescent in-situ hybridization analyses found ratios of 0.37 and 0.30 of sperm nuclei with sSMC(15) for patients 1 and 2, respectively (P < 0.001). An increase of sperm nuclei with disomy X, Y and 18 was noted for patient 1 compared with control and patient 2 (P < 0.001). Among the genes mapped in the unbalanced chromosomal regions, POTE B and BAGE are related to the testis and ovary, respectively. The implication of sSMC in infertility could be due to duplication, but also to mechanical effects perturbing meiosis.

  5. Mutation screening and association analysis of six candidate genes for autism on chromosome 7q

    DEFF Research Database (Denmark)

    Bonora, Elena; Lamb, Janine A; Barnby, Gabrielle;

    2005-01-01

    Genetic studies have provided evidence for an autism susceptibility locus (AUTS1) on chromosome 7q. Screening for mutations in six genes mapping to 7q, CUTL1, SRPK2, SYPL, LAMB1, NRCAM and PTPRZ1 in 48 unrelated individuals with autism led to the identification of several new coding variants...

  6. Cytogenetic Mapping of Disease Resistance Genes and Analysis of Their Distribution Features on Chromosomes in Maize

    Institute of Scientific and Technical Information of China (English)

    LiLi-jia; SongYun-chun

    2003-01-01

    Cytogenetic maps of four clusters of disease resistance genes were generated by ISH of the two RFLP markers tightly linked to and flanking each of maize resistance genes and the cloned resistance genes from other plant species onto maize chromosomes, combining with data published before. These genes include Helminthosporium turcium Pass resistance genes Htl, Htnl and Ht2, Helminthosporium maydis Nisik resistance genes Rhml and Rhm2,maize dwarf mosaic virus resistance gene Mdml, wheat streak mosaic virus resistance gene Wsml, Helminthosporium carbonum ULLstrup resistance gene Hml and the cloned Xanthomonas oryzae pv. Oryzae resistance gene Xa21 of rice, Cladosporium fulvum resistance genes Cf-9 and Cf-2. 1 of tomato, and Pseudomonas syringae resistance gene RPS2 of Arabidopsis. Most of the tested disease resistance genes located on the four chromosomes, i. e. , chromosomesl, 3, 6 and 8, and they closely distributed at the interstitial regions of these chromosomal long arms with percentage distances ranging 31.44(±3.72)-72.40(±3. 25) except for genes Rhml, Rhm2, Mdml and Wsml which mapped on the satellites of the short arms of chromosome6. It showed that the tested RFLP markers and genes were duplicated or triplicated in maize genome. Homology and conservation of disease resistance genes among species, and relationship between distribution features and functions of the genes were discussed. The results provide important scientific basis for deeply understanding structure and function of disease resistance genes and breeding in maize.

  7. 40 CFR 798.5385 - In vivo mammalian bone marrow cytogenetics tests: Chromosomal analysis.

    Science.gov (United States)

    2010-07-01

    ... used. Examples of commonly used rodent species are rats, mice, and hamsters. (ii) Age. Healthy young adult animals shall be used. (iii) Number and sex. At least five female and five male animals per... aberrations also occur. (b) Definitions. (1) Chromosome-type aberrations are changes which result from...

  8. Mutation screening and association analysis of six candidate genes for autism on chromosome 7q

    DEFF Research Database (Denmark)

    Bonora, E.; Lamb, J.A.; Barnby, G.;

    2005-01-01

    Genetic studies have provided evidence for an autism susceptibility locus (AUTS1) on chromosome 7q. Screening for mutations in six genes mapping to 7q, CUTL1, SRPK2, SYPL, LAMB1, NRCAM and PTPRZ1 in 48 unrelated individuals with autism led to the identification of several new coding variants in t...

  9. Chromosome condensation and segmentation

    International Nuclear Information System (INIS)

    Some aspects of chromosome condensation in mammalians -humans especially- were studied by means of cytogenetic techniques of chromosome banding. Two further approaches were adopted: a study of normal condensation as early as prophase, and an analysis of chromosome segmentation induced by physical (temperature and γ-rays) or chemical agents (base analogues, antibiotics, ...) in order to show out the factors liable to affect condensation. Here 'segmentation' means an abnormal chromosome condensation appearing systematically and being reproducible. The study of normal condensation was made possible by the development of a technique based on cell synchronization by thymidine and giving prophasic and prometaphasic cells. Besides, the possibility of inducing R-banding segmentations on these cells by BrdU (5-bromodeoxyuridine) allowed a much finer analysis of karyotypes. Another technique was developed using 5-ACR (5-azacytidine), it allowed to induce a segmentation similar to the one obtained using BrdU and identify heterochromatic areas rich in G-C bases pairs

  10. A comparative analysis of Y chromosome and mtDNA phylogenies of the Hylobates gibbons

    Directory of Open Access Journals (Sweden)

    Chan Yi-Chiao

    2012-08-01

    Full Text Available Abstract Background The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. Comparison of phylogenies inferred from DNA sequences with differing inheritance patterns, such as mitochondrial, autosomal, and X and Y chromosomal loci, can provide more comprehensive inferences of the evolutionary histories of species. Gibbons, especially the genus Hylobates, are particularly intriguing as they consist of multiple closely related species which emerged rapidly and live in close geographic proximity. Our current understanding of relationships among Hylobates species is largely based on data from the maternally-inherited mitochondrial DNAs (mtDNAs. Results To infer the paternal histories of gibbon taxa, we sequenced multiple Y chromosomal loci from 26 gibbons representing 10 species. As expected, we find levels of sequence variation some five times lower than observed for the mitochondrial genome (mtgenome. Although our Y chromosome phylogenetic tree shows relatively low resolution compared to the mtgenome tree, our results are consistent with the monophyly of gibbon genera suggested by the mtgenome tree. In a comparison of the molecular dating of divergences and on the branching patterns of phylogeny trees between mtgenome and Y chromosome data, we found: 1 the inferred divergence estimates were more recent for the Y chromosome than for the mtgenome, 2 the species H. lar and H. pileatus are monophyletic in the mtgenome phylogeny, respectively, but a H. pileatus individual falls into the H. lar Y chromosome clade. Conclusions Based on the ~6.4 kb of Y chromosomal DNA sequence data generated for each of the 26 individuals in this study, we provide molecular inferences on gibbon and particularly on Hylobates evolution complementary to those from mtDNA data. Overall, our results illustrate the utility of

  11. Cytogenetic Mapping of Disease Resistance Genes and Analysis of Their Distribution Features on Chromosomes in Maize

    Institute of Scientific and Technical Information of China (English)

    Li Li-jia; Song Yun-chun

    2003-01-01

    Cytogenetic maps of four clusters of disease resistance genes were generated by ISH of the two RFLP markers tightly linked to and flanking each of maize resistance genes and the cloned resistance genes from other plant species onto maize chromosomes, combining with data published before. These genes include Helminthosporium turcium Pass resistance genes Ht1, Htn1 and Ht2, Helminthosporium maydis Nisik resistance genes Rhm1 and Rhm2, maize dwarf mosaic virus resistance gene Mdm1, wheat streak mosaic virus resistance gene Wsm1, Helminthosporium carbonum ULLstrup resistance gene Hml and the cloned Xanthomonas oryzae pv. Oryzae resistance gene Xa21 of rice, Cladosporium fulvum resistance genes Cf-9 and Cf-2.1 of tomato,and Pseudomonas syringae resistance gene RPS2 of Arabidopsis. Most of the tested disease resistance genes located on the four chromosomes, i.e., chromosomes1, 3, 6 and 8, and they closely distributed at the interstitial regions of these chromosomal long arms with percentage distances ranging 31.44(±3.72)-72.40(±3.25) except for genes Rhm1, Rhm2, Mdm1 and Wsm1 which mapped on the satellites of the short arms of chromosome6. It showed that the tested RFLP markers and genes were duplicated or triplicated in maize genome. Homology and conservation of disease resistance genes among species, and relationship between distribution features and functions of the genes were discussed. The results provide important scientific basis for deeply understanding structure and function of disease resistance genes and breeding in maize.

  12. Quantitative analysis of qualitative images

    Science.gov (United States)

    Hockney, David; Falco, Charles M.

    2005-03-01

    We show optical evidence that demonstrates artists as early as Jan van Eyck and Robert Campin (c1425) used optical projections as aids for producing their paintings. We also have found optical evidence within works by later artists, including Bermejo (c1475), Lotto (c1525), Caravaggio (c1600), de la Tour (c1650), Chardin (c1750) and Ingres (c1825), demonstrating a continuum in the use of optical projections by artists, along with an evolution in the sophistication of that use. However, even for paintings where we have been able to extract unambiguous, quantitative evidence of the direct use of optical projections for producing certain of the features, this does not mean that paintings are effectively photographs. Because the hand and mind of the artist are intimately involved in the creation process, understanding these complex images requires more than can be obtained from only applying the equations of geometrical optics.

  13. A one-step real-time multiplex PCR for screening Y-chromosomal microdeletions without downstream amplicon size analysis.

    Directory of Open Access Journals (Sweden)

    Viviana Kozina

    Full Text Available BACKGROUND: Y-chromosomal microdeletions (YCMD are one of the major genetic causes for non-obstructive azoospermia. Genetic testing for YCMD by multiplex polymerase chain reaction (PCR is an established method for quick and robust screening of deletions in the AZF regions of the Y-chromosome. Multiplex PCRs have the advantage of including a control gene in every reaction and significantly reducing the number of reactions needed to screen the relevant genomic markers. PRINCIPAL FINDINGS: The widely established "EAA/EMQN best practice guidelines for molecular diagnosis of Y-chromosomal microdeletions (2004" were used as a basis for designing a real-time multiplex PCR system, in which the YCMD can simply be identified by their melting points. For this reason, some AZF primers were substituted by primers for regions in their genomic proximity, and the ZFX/ZFY control primer was exchanged by the AMELX/AMELY control primer. Furthermore, we substituted the classical SybrGreen I dye by the novel and high-performing DNA-binding dye EvaGreen™ and put substantial effort in titrating the primer combinations in respect to optimal melting peak separation and peak size. SIGNIFICANCE: With these changes, we were able to develop a platform-independent and robust real-time based multiplex PCR, which makes the need for amplicon identification by electrophoretic sizing expendable. By using an open-source system for real-time PCR analysis, we further demonstrate the applicability of automated melting point and YCMD detection.

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

    Science.gov (United States)

    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.

  15. A feasibility assessment of automated FISH image and signal analysis to assist cervical cancer detection

    Science.gov (United States)

    Wang, Xingwei; Li, Yuhua; Liu, Hong; Li, Shibo; Zhang, Roy R.; Zheng, Bin

    2012-02-01

    Fluorescence in situ hybridization (FISH) technology provides a promising molecular imaging tool to detect cervical cancer. Since manual FISH analysis is difficult, time-consuming, and inconsistent, the automated FISH image scanning systems have been developed. Due to limited focal depth of scanned microscopic image, a FISH-probed specimen needs to be scanned in multiple layers that generate huge image data. To improve diagnostic efficiency of using automated FISH image analysis, we developed a computer-aided detection (CAD) scheme. In this experiment, four pap-smear specimen slides were scanned by a dual-detector fluorescence image scanning system that acquired two spectrum images simultaneously, which represent images of interphase cells and FISH-probed chromosome X. During image scanning, once detecting a cell signal, system captured nine image slides by automatically adjusting optical focus. Based on the sharpness index and maximum intensity measurement, cells and FISH signals distributed in 3-D space were projected into a 2-D con-focal image. CAD scheme was applied to each con-focal image to detect analyzable interphase cells using an adaptive multiple-threshold algorithm and detect FISH-probed signals using a top-hat transform. The ratio of abnormal cells was calculated to detect positive cases. In four scanned specimen slides, CAD generated 1676 con-focal images that depicted analyzable cells. FISH-probed signals were independently detected by our CAD algorithm and an observer. The Kappa coefficients for agreement between CAD and observer ranged from 0.69 to 1.0 in detecting/counting FISH signal spots. The study demonstrated the feasibility of applying automated FISH image and signal analysis to assist cyto-geneticists in detecting cervical cancers.

  16. Analysis of chromosomal aberrations, micronuclei and hematological disorders among workers of wireless communication instruments and cell phone (Mobile) users

    International Nuclear Information System (INIS)

    This study was carried out to investigate the hazardous effect of electromagnetic radiation (EMR) such as chromosomal aberration, disturbed micronucleus formation and hematological disorders that may detected among workers of wireless communication instruments and mobile phone users. Seven individuals ( 3 males and 4 females) of a central workers in the microwave unit of the wireless station and 7 users of Mobil phone (4 males and 3 females ) were volunteered to give blood samples. Chromosomes and micronucleus were prepared for cytogenetic analysis as well as blood film for differential count. The results obtained in the microwave group indicated that, the total summation of all types of aberrations (chromosomes and chromatid aberrations) had a frequency of 6. 14% for the exposed group, whereas, the frequency in the control group amounted to 1.57%. In Mobil phone users, the total summation of all types of aberrations(chromosome and chromatid aberrations) had a frequency of 4.43% for the exposed group and 1.71% for the control group. The incidence of the total number of micronuclei in the exposed microwave group was increased 4.3 folds as compared with those of the control group The incidence of the total number of micronuclei in the exposed mobile phone group was increased 2 fold as compared with those in the control group. On the other hand, normal ranges of total white blood cells counts were determined for mobile phone users but abnormalities in the differential counts of the different types of the white blood cells such as neutropenia, eosinophilia and lymphocytosis were observed in the individuals number 1,2,3,7 in microwave group

  17. Design Criteria For Networked Image Analysis System

    Science.gov (United States)

    Reader, Cliff; Nitteberg, Alan

    1982-01-01

    Image systems design is currently undergoing a metamorphosis from the conventional computing systems of the past into a new generation of special purpose designs. This change is motivated by several factors, notably among which is the increased opportunity for high performance with low cost offered by advances in semiconductor technology. Another key issue is a maturing in understanding of problems and the applicability of digital processing techniques. These factors allow the design of cost-effective systems that are functionally dedicated to specific applications and used in a utilitarian fashion. Following an overview of the above stated issues, the paper presents a top-down approach to the design of networked image analysis systems. The requirements for such a system are presented, with orientation toward the hospital environment. The three main areas are image data base management, viewing of image data and image data processing. This is followed by a survey of the current state of the art, covering image display systems, data base techniques, communications networks and software systems control. The paper concludes with a description of the functional subystems and architectural framework for networked image analysis in a production environment.

  18. Mathematical foundations of image processing and analysis

    CERN Document Server

    Pinoli, Jean-Charles

    2014-01-01

    Mathematical Imaging is currently a rapidly growing field in applied mathematics, with an increasing need for theoretical mathematics. This book, the second of two volumes, emphasizes the role of mathematics as a rigorous basis for imaging sciences. It provides a comprehensive and convenient overview of the key mathematical concepts, notions, tools and frameworks involved in the various fields of gray-tone and binary image processing and analysis, by proposing a large, but coherent, set of symbols and notations, a complete list of subjects and a detailed bibliography. It establishes a bridg

  19. Cancer detection by quantitative fluorescence image analysis.

    Science.gov (United States)

    Parry, W L; Hemstreet, G P

    1988-02-01

    Quantitative fluorescence image analysis is a rapidly evolving biophysical cytochemical technology with the potential for multiple clinical and basic research applications. We report the application of this technique for bladder cancer detection and discuss its potential usefulness as an adjunct to methods used currently by urologists for the diagnosis and management of bladder cancer. Quantitative fluorescence image analysis is a cytological method that incorporates 2 diagnostic techniques, quantitation of nuclear deoxyribonucleic acid and morphometric analysis, in a single semiautomated system to facilitate the identification of rare events, that is individual cancer cells. When compared to routine cytopathology for detection of bladder cancer in symptomatic patients, quantitative fluorescence image analysis demonstrated greater sensitivity (76 versus 33 per cent) for the detection of low grade transitional cell carcinoma. The specificity of quantitative fluorescence image analysis in a small control group was 94 per cent and with the manual method for quantitation of absolute nuclear fluorescence intensity in the screening of high risk asymptomatic subjects the specificity was 96.7 per cent. The more familiar flow cytometry is another fluorescence technique for measurement of nuclear deoxyribonucleic acid. However, rather than identifying individual cancer cells, flow cytometry identifies cellular pattern distributions, that is the ratio of normal to abnormal cells. Numerous studies by others have shown that flow cytometry is a sensitive method to monitor patients with diagnosed urological disease. Based upon results in separate quantitative fluorescence image analysis and flow cytometry studies, it appears that these 2 fluorescence techniques may be complementary tools for urological screening, diagnosis and management, and that they also may be useful separately or in combination to elucidate the oncogenic process, determine the biological potential of tumors

  20. Linkage analysis in a large Swedish family supports the presence of a susceptibility locus for adenoma and colorectal cancer on chromosome 9q22.32-31.1

    DEFF Research Database (Denmark)

    Skoglund, J; Djureinovic, T; Zhou, X-L;

    2006-01-01

    dominantly inherited colorectal cancer risk. Recently, a locus on chromosome 9q22.2-31.2 was identified by linkage analysis in sib pairs with colorectal cancer or adenoma. METHODS: Linkage analysis for the suggested locus on chromosome 9 was carried out in an extended Swedish family. This family had...... previously been investigated but following the identification of adenomas in several previously unaffected family members, these subjects were now considered to be gene carriers. RESULTS: In the present study, we found linkage of adenoma and colorectal cancer to chromosome 9q22.32-31.1 with a multipoint LOD...... score of 2.4. We were also able to define the region for this locus to 7.9 cM between the markers D9S280 and D9S277. CONCLUSIONS: Our result supports the presence of a susceptibility locus predisposing to adenoma and colorectal cancer in this chromosomal region....

  1. Experimental Researches on Carcinogenesis or Tumorigenicity of MDCK Canine Kidney Cell(CKC) Lines and Analysis of Their Chromosome Karyotypes

    Institute of Scientific and Technical Information of China (English)

    ZHANG De-li; FANG Fu-de; LI Liu-jin; XIA Geng-tian; HE Xu-yu; GAO Bu-xian; BAI Xiao-hong; HUANG Gao-sheng; LIU Shang-gao; YAN Long-fei

    2002-01-01

    The chromosomal number variations & structural aberrations of the MDCK cell line, primary feline or canine kidney cell(FKC or CKC) and Hela cell line were investigated and their karyotypes of conventional chromosome bands were analyzed. The carcinogenesis or tumorigenicity testing of these cell lines in about 232 nude mice and for colony formation in soft agarose and for haemagglutination under different concentration of plant lectins of these cells were carried out. Under the prerequisite that the incidence of cancer or tumor in negative-control nude mice inoculated subcutaneously with primary feline or canine kidney cell cultures purified in vitro at passage 3 was 0 (0/22) and 0 (0/10), respectively. The incidence of the progressively-growing malignant tumor(MT) in positive-control nude mice inoculated subcutaneously with Hela cell cultures of KB, X, or NM20/X strain was 10/10, 25/25 and 5/51, respectively. The results showed that the incidence of tumor in nude mice with tetrapioid YA strain of MDCK cell during 20 - 45 passages, with hypodiploid JB strain of MDCK cell on passage 25, with di-and hypoploid JC strain of MDCK cell during 2 - 15passages or with hypoploid M strain of MDCK cell during 9 - 27 passages was 28/58, 1/5, 4/18 and 0/31,respectively. The chromosomal analysis results showed that the ratio of difference in the rate of modal chromosome number between high (mcs + n) and lowest (mcs)passages was not more than 5 % - 15 % and the structure aberrations was generally 0 - 3%. These results proved that the genetic characteristics of chromosomal number of cell lines determines their tumorigenicity, but it is species-specific. MDCK line has tumorigenicity no matter what its chromosome karyotype is, at least it has very low tumorigenicity even when its modal chromosome number is hypoploid. The repeatedly frozen, thawed and split controls of tumorigenicity-positive cell lines(X strain of Hela, M strain of BHK-21, JA strain of Vero, YA strain of MDCK) have

  2. Ordered subset linkage analysis supports a susceptibility locus for age-related macular degeneration on chromosome 16p12

    Directory of Open Access Journals (Sweden)

    Weeks Daniel E

    2004-07-01

    Full Text Available Abstract Background Age-related macular degeneration (AMD is a complex disorder that is responsible for the majority of central vision loss in older adults living in developed countries. Phenotypic and genetic heterogeneity complicate the analysis of genome-wide scans for AMD susceptibility loci. The ordered subset analysis (OSA method is an approach for reducing heterogeneity, increasing statistical power for detecting linkage, and helping to define the most informative data set for follow-up analysis. OSA assesses the linkage evidence in subsets of potentially more homogeneous families by rank-ordering family-specific lod scores with respect to trait-associated covariates or phenotypic features. Here, we present results of incorporating five continuous covariates into our genome-wide linkage analysis of 389 microsatellite markers in 62 multiplex families: Body mass index (BMI, systolic (SBP and diastolic (DBP blood pressure, intraocular pressure (IOP, and pack-years of cigarette smoking. Chromosome-wide significance of increases in nonparametric multipoint lod scores in covariate-defined subsets relative to the overall sample was assessed by permutation. Results Using a correction for testing multiple covariates, statistically significant lod score increases were observed for two chromosomal regions: 14q13 with a lod score of 3.2 in 28 families with average IOP ≤ 15.5 (p = 0.002, and 6q14 with a lod score of 1.6 in eight families with average BMI ≥ 30.1 (p = 0.0004. On chromosome 16p12, nominally significant lod score increases (p ≤ 0.05, up to a lod score of 2.9 in 32 families, were observed with several covariate orderings. While less significant, this was the only region where linkage evidence was associated with multiple clinically meaningful covariates and the only nominally significant finding when analysis was restricted to advanced forms of AMD. Families with linkage to 16p12 had higher averages of SBP, IOP and BMI and were

  3. Objective facial photograph analysis using imaging software.

    Science.gov (United States)

    Pham, Annette M; Tollefson, Travis T

    2010-05-01

    Facial analysis is an integral part of the surgical planning process. Clinical photography has long been an invaluable tool in the surgeon's practice not only for accurate facial analysis but also for enhancing communication between the patient and surgeon, for evaluating postoperative results, for medicolegal documentation, and for educational and teaching opportunities. From 35-mm slide film to the digital technology of today, clinical photography has benefited greatly from technological advances. With the development of computer imaging software, objective facial analysis becomes easier to perform and less time consuming. Thus, while the original purpose of facial analysis remains the same, the process becomes much more efficient and allows for some objectivity. Although clinical judgment and artistry of technique is never compromised, the ability to perform objective facial photograph analysis using imaging software may become the standard in facial plastic surgery practices in the future. PMID:20511080

  4. Applications Of Binary Image Analysis Techniques

    Science.gov (United States)

    Tropf, H.; Enderle, E.; Kammerer, H. P.

    1983-10-01

    After discussing the conditions where binary image analysis techniques can be used, three new applications of the fast binary image analysis system S.A.M. (Sensorsystem for Automation and Measurement) are reported: (1) The human view direction is measured at TV frame rate while the subject's head is free movable. (2) Industrial parts hanging on a moving conveyor are classified prior to spray painting by robot. (3) In automotive wheel assembly, the eccentricity of the wheel is minimized by turning the tyre relative to the rim in order to balance the eccentricity of the components.

  5. AN OVERVIEW OF DOCUMENT IMAGE ANALYSIS SYSTEMS

    OpenAIRE

    Andrei Tigora

    2013-01-01

    This paper presents an overview of Document Image Analysis Systems, their composing modules, the approaches these modules use, as well as uses for these applications. One of the main goals is to present some of the most important technologies and methods behind the Document Image Analysis domain in order to evaluate the best approach when dealing with real-world documents. The other main goal is to ensure a foundation for those starting to build such complex software systems and to give an el...

  6. Chromosomal and Genetic Analysis of a Human Lung Adenocarcinoma Cell Line OM

    Directory of Open Access Journals (Sweden)

    Yong-Wu Li

    2016-01-01

    Conclusions: The lung adenocarcinoma cell line OM exhibited multiple complex karyotypes, and chromosome 10 was frequently involved in chromosomal translocation, which may play key roles in tumorigenesis. We speculated that the oncogenes may be located at 3q25.3-28, 5p13, 12q22-23.24, while tumor suppressor genes may exist in 3p25-26, 6p25, 6q26-27, 7q34-36, 8p22-23, 9p21-24, 10q25-26.3, 12p13.31-13.33, and 17p13.1-13.3. Moreover, at least four genes (MME, SI, BCHE, and KNG may be involved in the human lung adenocarcinoma cell line OM.

  7. Genetic, physical and functional analysis of the ataxia-telangiectasia locus on chromosome 11q22-23

    Energy Technology Data Exchange (ETDEWEB)

    Shiloh, Y.; Ziv, Y.; Savitski, K. [Tel Aviv Univ. (Israel)] [and others

    1994-09-01

    Ataxia-telangiectasia (A-T) is an autosomal recessive multisystem disorder featuring cerebellar degeneration, immunodeficiency, chromosomal instability, cancer susceptibility, and radiosensitivity. Four complementation groups have been observed in A-T. The two major groups, A and C, were localized to chromosome 11q22-23, and the other two, D and E, may map to the same chromosomal region. We developed an integrated system of positional and complementation cloning to identify the A-T gene(s). The A-T region was saturated with microsatellite markers by physically mapping markers generated at random by other labs and by identifying new polymorphic CA-repeats in YAC clones obtained from this region. According to recent linkage data based on these markers and linkage disequilibrium analysis in Moroccan Jewish A-T patients, the A-T(A) and A-T(C) mutations are contained within a 2 Mb interval between D11S1819 and D11S1960. This interval was cloned in YAC and cosmid contigs, and transcribed sequences were identified using the following methods: screening of cDNA libraries using cosmid clones; magnetic bead capture using YAC and cosmid clones; direct selection of cDNA clones using YAC clones immobilized on a solid matrix; and 3{prime} exon trapping. Preliminary results indicate that the A-T region is rich in transcribed sequences. Structural and functional analysis of these genes is being carried out by sequence analysis, by physical mapping using the cosmid contigs, and by testing their ability to complement the radiomimetic sensitivity of A-T cells.

  8. Chromosome analysis in 133 children with congenital mental retardation%133例智力低下患儿细胞遗传学研究

    Institute of Scientific and Technical Information of China (English)

    马宁; 杨晓; 朱丽娜; 王春枝

    2012-01-01

    Objective: To explore the chromosome karyotypes in children with mental retardation. Methods: The peripheral blood lymphocytes from 133 children with congenital mental retardation were cultured and analysed by the G -band technique. Results; Of the 133 cases, 74cases (55. 6% ) showed chromosome abnormalities. The number of autosomal abnormalities were found in 62 cases and Autosomal structural chromosome abnormalities were found in 9 cases, the number of sex chromosome abnormalities in 2 cases and sex chromosome structural abnormalities in leases. Conclusions; Chromosome abnormalities may be important cytogenetic factors for congenital mental retardation. Cytogenetic chromosome karyotypic analysis is an important method for congenital mental retardation child.%目的 探讨智力低下患儿与染色体异常的关系.方法 常规外周血染色体核型分析.结果 133例患儿中共检出染色体异常74例,异常检出率55.6%.其中常染色体数目异常62例,结构异常9例;性染色体数目异常2例,结构异常1例,结论 染色体异常是导致儿童智力低下的重要原因,对此类患儿进行染色体核型分析很有必要.

  9. Cladistic association analysis of Y chromosome effects on alcohol dependence and related personality traits

    OpenAIRE

    Kittles, Rick A.; Long, Jeffrey C.; Bergen, Andrew W; Eggert, Monica; Virkkunen, Matti; Linnoila, Markku; Goldman, David

    1999-01-01

    Association between Y chromosome haplotype variation and alcohol dependence and related personality traits was investigated in a large sample of psychiatrically diagnosed Finnish males. Haplotypes were constructed for 359 individuals using alleles at eight loci (seven microsatellite loci and a nucleotide substitution in the DYZ3 alphoid satellite locus). A cladogram linking the 102 observed haplotype configurations was constructed by using parsimony with a single-step mutation model. Then, a ...

  10. A collaborative study of the EDNAP group regarding Y-chromosome binary polymorphism analysis

    DEFF Research Database (Denmark)

    Brion, María; Dupuy, Berit M; Heinrich, Marielle;

    2005-01-01

    typing. A total of 535 samples from six different European populations were also analysed. In Galicia (NW Spain) and Belgium, the most frequent haplogroup was R1b*(xR1b1,R1b3df). Haplogroup F*(xK) is one of the most frequent in Austria and Denmark, while the lowest frequency appear in Belgium. Haplogroup...... frequencies found in this collaborative study were compared with previously published European Y-chromosome haplogroup data....

  11. Chromosome analysis of early embryonic mortality in layer and broiler chickens.

    Science.gov (United States)

    Thorne, M H; Collins, R K; Sheldon, B L

    1991-09-01

    1. Twenty-three lines of chickens, obtained from grandparent stocks of 4 Australian breeding companies, were analysed to determine the incidence of early embryonic mortality attributable to chromosome abnormalities. The lines included 10 layer strains, consisting of 6 White Leghorn, 2 New Hampshire and 2 Australorp lines, and 13 broiler lines. 2. A total of 10,730 eggs was examined after 3 d incubation; of these 9746 (90.8%) were fertile. Abortive embryonic development was observed in 1379 (14.1%) of the fertile eggs. This consisted of 952 (69.0%) dead and dying embryos, including 646 malformed and 427 (31.0%) membranes without embryos. 3. Early embryonic mortality was found to vary from 9.8 to 26.8% (average 16.4%) in broiler lines and from 8.0 to 27.9% (average 11.9%) in layer lines. 4. Among 898 abortive embryos analysed, 112 had abnormal chromosomes consisting of 27 haploids, 38 haploid-euploids, 24 triploids, 16 diploid-polyploids, 4 aneuploids, 2 tetraploids and 1 translocation. 5. In broilers and layers respectively, chromosome abnormalities were responsible for 4.4 to 28.1% (average 11.8%) and 7.4 to 25.0% (average 13.4%) of the early embryonic mortality. 6. The overall frequency of chromosome abnormalities in all fertile eggs varied from 0.7 to 3.7% for the broiler lines and 0.7 to 3.4% for the layer lines. PMID:1933445

  12. Linkage analysis of 19 French breast cancer families, with five chromosome 17q markers.

    OpenAIRE

    Mazoyer, S.; Lalle, P.; Narod, S A; Bignon, Y J; Courjal, F.; Jamot, B; Dutrillaux, B; Stoppa-Lyonnett, D; Sobol, H

    1993-01-01

    Nineteen French breast and breast-ovarian cancer families were tested for linkage with five chromosome 17q markers. The five breast-ovarian cancer families as a group give positive evidence for linkage, whereas the 14 breast cancer-only families do not. Heterogeneity of linkage of breast and breast-ovarian cancers is significant in France and supports the existence of more than one susceptibility gene.

  13. Generation and Analysis of Transposon Ac/Ds-Induced Chromosomal Rearrangements in Rice Plants.

    Science.gov (United States)

    Xuan, Yuan Hu; Peterson, Thomas; Han, Chang-Deok

    2016-01-01

    Closely-located transposable elements (TEs) have been known to induce chromosomal breakage and rearrangements via alternative transposition. To study genome rearrangements in rice, an Ac/Ds system has been employed. This system comprises an immobile Ac element expressed under the control of CaMV 35S promoter, and a modified Ds element. A starter line carried Ac and a single copy of Ds at the OsRLG5 (Oryza sativa receptor-like gene 5). To enhance the transpositional activity, seed-derived calli were cultured and regenerated into plants. Among 270 lines regenerated from the starter, one line was selected that contained a pair of inversely-oriented Ds elements at the OsRLG5 (Oryza sativa receptor-like gene 5). The selected line was again subjected to tissue culture to obtain a regenerant population. Among 300 regenerated plants, 107 (36 %) contained chromosomal rearrangements including deletions, duplications, and inversions of various sizes. From 34 plants, transposition mechanisms leading to such genomic rearrangements were analyzed. The rearrangements were induced by sister chromatid transposition (SCT), homologous recombination (HR), and single chromatid transposition (SLCT). Among them, 22 events (65 %) were found to be transmitted to the next generation. These results demonstrate a great potential of tissue culture regeneration and the Ac/Ds system in understanding alternative transposition mechanisms and in developing chromosome engineering in plants.

  14. Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data

    International Nuclear Information System (INIS)

    Chromosomal abnormalities have been associated with most human malignancies, with gains and losses on some genomic regions associated with particular entities. Of the 15429 cases collected for the Progenetix molecular-cytogenetic database, 5918 malignant epithelial neoplasias analyzed by chromosomal Comparative Genomic Hybridization (CGH) were selected for further evaluation. For the 22 clinico-pathological entities with more than 50 cases, summary profiles for genomic imbalances were generated from case specific data and analyzed. With large variation in overall genomic instability, recurring genomic gains and losses were prominent. Most entities showed frequent gains involving 8q2, while gains on 20q, 1q, 3q, 5p, 7q and 17q were frequent in different entities. Loss 'hot spots' included 3p, 4q, 13q, 17p and 18q among others. Related average imbalance patterns were found for clinically distinct entities, e.g. hepatocellular carcinomas (ca.) and ductal breast ca., as well as for histologically related entities (squamous cell ca. of different sites). Although considerable case-by-case variation of genomic profiles can be found by CGH in epithelial malignancies, a limited set of variously combined chromosomal imbalances may be typical for carcinogenesis. Focus on the respective regions should aid in target gene detection and pathway deduction

  15. Chromosome analysis of five Brazilian species of poison frogs (Anura: Dendrobatidae)

    Indian Academy of Sciences (India)

    Paula Camargo Rodrigues; Odair Aguiar; Flávia Serpieri; Albertina Pimentel Lima; Masao Uetanebaro; Shirlei Maria Recco-Pimentel

    2011-04-01

    Dendrobatid frogs have undergone an extensive systematic reorganization based on recent molecular findings. The present work describes karyotypes of the Brazilian species Adelphobates castaneoticus, A. quinquevittatus, Ameerega picta, A. galactonotus and Dendrobates tinctorius which were compared to each other and with previously described related species. All karyotypes consisted of $2n = 18$ chromosomes, except for A. picta which had $2n = 24$. The karyotypes of the Adelphobates and D. tinctorius species were highly similar to each other and to the other $2n = 18$ previously studied species, revealing conserved karyotypic characteristics in both genera. In recent phylogenetic studies, all Adelphobates species were grouped in a clade separated from the Dendrobates species. Thus, we hypothesized that their common karyotypic traits may have a distinct origin by chromosome rearrangements and mutations. In A. picta, with $2n = 24$, chromosome features of pairs from 1 to 8 are shared with other previously karyotyped species within this genus. Hence, the A. picta data reinforced that the C-banding pattern and the NOR location are species-specific traits in the genus Ameerega. Moreover, the Ameerega monophyletism proposed by previous phylogenetic studies indicates that the karyotypic differences among species in this genus result from a long divergence time.

  16. Generation and Analysis of Transposon Ac/Ds-Induced Chromosomal Rearrangements in Rice Plants.

    Science.gov (United States)

    Xuan, Yuan Hu; Peterson, Thomas; Han, Chang-Deok

    2016-01-01

    Closely-located transposable elements (TEs) have been known to induce chromosomal breakage and rearrangements via alternative transposition. To study genome rearrangements in rice, an Ac/Ds system has been employed. This system comprises an immobile Ac element expressed under the control of CaMV 35S promoter, and a modified Ds element. A starter line carried Ac and a single copy of Ds at the OsRLG5 (Oryza sativa receptor-like gene 5). To enhance the transpositional activity, seed-derived calli were cultured and regenerated into plants. Among 270 lines regenerated from the starter, one line was selected that contained a pair of inversely-oriented Ds elements at the OsRLG5 (Oryza sativa receptor-like gene 5). The selected line was again subjected to tissue culture to obtain a regenerant population. Among 300 regenerated plants, 107 (36 %) contained chromosomal rearrangements including deletions, duplications, and inversions of various sizes. From 34 plants, transposition mechanisms leading to such genomic rearrangements were analyzed. The rearrangements were induced by sister chromatid transposition (SCT), homologous recombination (HR), and single chromatid transposition (SLCT). Among them, 22 events (65 %) were found to be transmitted to the next generation. These results demonstrate a great potential of tissue culture regeneration and the Ac/Ds system in understanding alternative transposition mechanisms and in developing chromosome engineering in plants. PMID:27557685

  17. A time stamp comparative analysis of frequent chromosomal abnormalities in Romanian patients.

    Science.gov (United States)

    Suciu, Nicolae; Plaiasu, Vasilica

    2014-01-01

    Chromosome abnormalities represent the leading cause in many human genetic disorders. Gain or loss of genetic material can disrupt the normal expression of genes important in fetal development and result in abnormal phenotypes. Approximately 60% of first-trimester spontaneous abortions exhibit karyotype abnormalities. The majority of these abnormalities consist of numerical chromosomal changes, such as autosomal trisomy, monosomy X and polyploidy. In our current study, 411 cases were analyzed over a period of 5 years, which reflected the incidence of cytogenetic abnormalities in Romania. Down syndrome showed the highest frequency at 79%. At 2.6% structural chromosome abnormality syndromes and Turner syndrome followed suit. Next were the Edwards and Patau syndromes with an incidence of 1.2%. Klinefelter, Cri du chat and Wolf-Hirschhorn syndromes all had an incidence of 0.7%. Finally, the lowest frequencies were shown by Williams at 0.4% and only one case of Beckwith-Wiedemann syndrome with abnormal karyotype. The average maternal age at childbirth was 31.15 years (SD = 6.96) and the average paternal age was 33.41 years (SD = 7.17). PMID:23570267

  18. Genomewide clonal analysis of lethal mutations in the Drosophila melanogaster eye: comparison of the X chromosome and autosomes.

    Science.gov (United States)

    Call, Gerald B; Olson, John M; Chen, Jiong; Villarasa, Nikki; Ngo, Kathy T; Yabroff, Allison M; Cokus, Shawn; Pellegrini, Matteo; Bibikova, Elena; Bui, Chris; Cespedes, Albert; Chan, Cheryl; Chan, Stacy; Cheema, Amrita K; Chhabra, Akanksha; Chitsazzadeh, Vida; Do, Minh-Tu; Fang, Q Angela; Folick, Andrew; Goodstein, Gelsey L; Huang, Cheng R; Hung, Tony; Kim, Eunha; Kim, William; Kim, Yulee; Kohan, Emil; Kuoy, Edward; Kwak, Robert; Lee, Eric; Lee, JiEun; Lin, Henry; Liu, H-C Angela; Moroz, Tatiana; Prasad, Tharani; Prashad, Sacha L; Patananan, Alexander N; Rangel, Alma; Rosselli, Desiree; Sidhu, Sohrab; Sitz, Daniel; Taber, Chelsea E; Tan, Jingwen; Topp, Kasey; Tran, PhuongThao; Tran, Quynh-Minh; Unkovic, Mary; Wells, Maggie; Wickland, Jessica; Yackle, Kevin; Yavari, Amir; Zaretsky, Jesse M; Allen, Christopher M; Alli, Latifat; An, Ju; Anwar, Abbas; Arevalo, Sonia; Ayoub, Danny; Badal, Shawn S; Baghdanian, Armonde; Baghdanian, Arthur H; Baumann, Sara A; Becerra, Vivian N; Chan, Hei J; Chang, Aileen E; Cheng, Xibin A; Chin, Mabel; Chong, Fleurette; Crisostomo, Carlyn; Datta, Sanjit; Delosreyes, Angela; Diep, Francie; Ekanayake, Preethika; Engeln, Mark; Evers, Elizabeth; Farshidi, Farzin; Fischer, Katrina; Formanes, Arlene J; Gong, Jun; Gupta, Riju; Haas, Blake E; Hahm, Vicky; Hsieh, Michael; Hui, James Z; Iao, Mei L; Jin, Sophia D; Kim, Angela Y; Kim, Lydia S-H; King, Megan; Knudsen-Robbins, Chloe; Kohanchi, David; Kovshilovskaya, Bogdana; Ku, Amy; Kung, Raymond W; Landig, Mark E L; Latterman, Stephanie S; Lauw, Stephanie S; Lee, Daniel S; Lee, Joann S; Lei, Kai C; Leung, Lesley L; Lerner, Renata; Lin, Jian-ya; Lin, Kathleen; Lim, Bryon C; Lui, Crystal P Y; Liu, Tiffany Q; Luong, Vincent; Makshanoff, Jacob; Mei, An-Chi; Meza, Miguel; Mikhaeil, Yara A; Moarefi, Majid; Nguyen, Long H; Pai, Shekhar S; Pandya, Manish; Patel, Aadit R; Picard, Paul D; Safaee, Michael M; Salame, Carol; Sanchez, Christian; Sanchez, Nina; Seifert, Christina C; Shah, Abhishek; Shilgevorkyan, Oganes H; Singh, Inderroop; Soma, Vanessa; Song, Junia J; Srivastava, Neetika; StaAna, Jennifer L; Sun, Christie; Tan, Diane; Teruya, Alison S; Tikia, Robyn; Tran, Trinh; Travis, Emily G; Trinh, Jennifer D; Vo, Diane; Walsh, Thomas; Wong, Regan S; Wu, Katherine; Wu, Ya-Whey; Yang, Nkau X V; Yeranosian, Michael; Yu, James S; Zhou, Jennifer J; Zhu, Ran X; Abrams, Anna; Abramson, Amanda; Amado, Latiffe; Anderson, Jenny; Bashour, Keenan; Beyer, Elsa; Bookatz, Allen; Brewer, Sarah; Buu, Natalie; Calvillo, Stephanie; Cao, Joseph; Chan, Amy; Chan, Jenny; Chang, Aileen; Chang, Daniel; Chang, Yuli; Chen, YiBing; Choi, Joo; Chou, Jeyling; Dang, Peter; Datta, Sumit; Davarifar, Ardy; Deravanesian, Artemis; Desai, Poonam; Fabrikant, Jordan; Farnad, Shahbaz; Fu, Katherine; Garcia, Eddie; Garrone, Nick; Gasparyan, Srpouhi; Gayda, Phyllis; Go, Sherrylene; Goffstein, Chad; Gonzalez, Courtney; Guirguis, Mariam; Hassid, Ryan; Hermogeno, Brenda; Hong, Julie; Hong, Aria; Hovestreydt, Lindsay; Hu, Charles; Huff, Devon; Jamshidian, Farid; Jen, James; Kahen, Katrin; Kao, Linda; Kelley, Melissa; Kho, Thomas; Kim, Yein; Kim, Sarah; Kirkpatrick, Brian; Langenbacher, Adam; Laxamana, Santino; Lee, Janet; Lee, Chris; Lee, So-Youn; Lee, ToHang S; Lee, Toni; Lewis, Gemma; Lezcano, Sheila; Lin, Peter; Luu, Thanh; Luu, Julie; Marrs, Will; Marsh, Erin; Marshall, Jamie; Min, Sarah; Minasian, Tanya; Minye, Helena; Misra, Amit; Morimoto, Miles; Moshfegh, Yasaman; Murray, Jessica; Nguyen, Kha; Nguyen, Cynthia; Nodado, Ernesto; O'Donahue, Amanda; Onugha, Ndidi; Orjiakor, Nneka; Padhiar, Bhavin; Paul, Eric; Pavel-Dinu, Mara; Pavlenko, Alex; Paz, Edwin; Phaklides, Sarah; Pham, Lephong; Poulose, Preethi; Powell, Russell; Pusic, Aya; Ramola, Divi; Regalia, Kirsten; Ribbens, Meghann; Rifai, Bassel; Saakyan, Manyak; Saarikoski, Pamela; Segura, Miriam; Shadpour, Farnaz; Shemmassian, Aram; Singh, Ramnik; Singh, Vivek; Skinner, Emily; Solomin, Daniel; Soneji, Kosha; Spivey, Kristin; Stageberg, Erika; Stavchanskiy, Marina; Tekchandani, Leena; Thai, Leo; Thiyanaratnam, Jayantha; Tong, Maurine; Toor, Aneet; Tovar, Steve; Trangsrud, Kelly; Tsang, Wah-Yung; Uemura, Marc; Vollmer, Emily; Weiss, Emily; Wood, Damien; Wu, Joy; Wu, Sophia; Wu, Winston; Xu, Qing; Yamauchi, Yuki; Yarosh, Will; Yee, Laura; Yen, George; Banerjee, Utpal

    2007-10-01

    Using a large consortium of undergraduate students in an organized program at the University of California, Los Angeles (UCLA), we have undertaken a functional genomic screen in the Drosophila eye. In addition to the educational value of discovery-based learning, this article presents the first comprehensive genomewide analysis of essential genes involved in eye development. The data reveal the surprising result that the X chromosome has almost twice the frequency of essential genes involved in eye development as that found on the autosomes. PMID:17720911

  19. Curvelet based offline analysis of SEM images.

    Directory of Open Access Journals (Sweden)

    Syed Hamad Shirazi

    Full Text Available Manual offline analysis, of a scanning electron microscopy (SEM image, is a time consuming process and requires continuous human intervention and efforts. This paper presents an image processing based method for automated offline analyses of SEM images. To this end, our strategy relies on a two-stage process, viz. texture analysis and quantification. The method involves a preprocessing step, aimed at the noise removal, in order to avoid false edges. For texture analysis, the proposed method employs a state of the art Curvelet transform followed by segmentation through a combination of entropy filtering, thresholding and mathematical morphology (MM. The quantification is carried out by the application of a box-counting algorithm, for fractal dimension (FD calculations, with the ultimate goal of measuring the parameters, like surface area and perimeter. The perimeter is estimated indirectly by counting the boundary boxes of the filled shapes. The proposed method, when applied to a representative set of SEM images, not only showed better results in image segmentation but also exhibited a good accuracy in the calculation of surface area and perimeter. The proposed method outperforms the well-known Watershed segmentation algorithm.

  20. Principal Components Analysis In Medical Imaging

    Science.gov (United States)

    Weaver, J. B.; Huddleston, A. L.

    1986-06-01

    Principal components analysis, PCA, is basically a data reduction technique. PCA has been used in several problems in diagnostic radiology: processing radioisotope brain scans (Ref.1), automatic alignment of radionuclide images (Ref. 2), processing MRI images (Ref. 3,4), analyzing first-pass cardiac studies (Ref. 5) correcting for attenuation in bone mineral measurements (Ref. 6) and in dual energy x-ray imaging (Ref. 6,7). This paper will progress as follows; a brief introduction to the mathematics of PCA will be followed by two brief examples of how PCA has been used in the literature. Finally my own experience with PCA in dual-energy x-ray imaging will be given.

  1. Hyperspectral Image Analysis of Food Quality

    DEFF Research Database (Denmark)

    Arngren, Morten

    extensions to the analysis offood quality. This dissertation is concerned with hyperspectral image analysisused to assess the quality of single grain kernels. The focus is to highlight thebenefits and challenges of using hyperspectral imaging for food quality presentedin two research directions. Initially......Assessing the quality of food is a vital step in any food processing line to ensurethe best food quality and maximum profit for the farmer and food manufacturer.Traditional quality evaluation methods are often destructive and labourintensive procedures relying on wet chemistry or subjective human...... inspection.Near-infrared spectroscopy can address these issues by offering a fast and objectiveanalysis of the food quality. A natural extension to these single spectrumNIR systems is to include image information such that each pixel holds a NIRspectrum. This augmented image information offers several...

  2. Dynamic Chest Image Analysis: Model-Based Perfusion Analysis in Dynamic Pulmonary Imaging

    OpenAIRE

    Kiuru Aaro; Kormano Martti; Svedström Erkki; Liang Jianming; Järvi Timo

    2003-01-01

    The "Dynamic Chest Image Analysis" project aims to develop model-based computer analysis and visualization methods for showing focal and general abnormalities of lung ventilation and perfusion based on a sequence of digital chest fluoroscopy frames collected with the dynamic pulmonary imaging technique. We have proposed and evaluated a multiresolutional method with an explicit ventilation model for ventilation analysis. This paper presents a new model-based method for pulmonary perfusion ana...

  3. Familial transmission of a deletion of chromosome 21 derived from a translocation between chromosome 21 and an inverted chromosome 22.

    Science.gov (United States)

    Aviv, H; Lieber, C; Yenamandra, A; Desposito, F

    1997-06-27

    Chromosome analysis of a newborn boy with Down syndrome resulted in the identification of a family with an unusual derivative chromosome 22. The child has 46 chromosomes, including two chromosomes 21, one normal chromosome 22, and a derivative chromosome 22. Giemsa banding and fluorescent in situ hybridization (FISH) studies show that the derivative chromosome is chromosome 22 with evidence of both paracentric and pericentric inversions, joined to the long arm of chromosome 21 from 21q21.2 to qter. The rearrangement results in partial trisomy 21 extending from 21q21.2 to 21q terminus in the patient. The child's mother, brother, maternal aunt, and maternal grandmother are all carriers of the derivative chromosome. All have 45 chromosomes, with one normal chromosome 21, one normal chromosome 22, and the derivative chromosome 22. The rearrangement results in the absence of the short arm, the centromere, and the proximal long arm of chromosome 21 (del 21pter-21q21.2) in carriers. Carriers of the derivative chromosome in this family have normal physical appearance, mild learning disabilities and poor social adjustment. PMID:9182781

  4. PIXE analysis and imaging of papyrus documents

    Science.gov (United States)

    Lövestam, N. E. Göran; Swietlicki, Erik

    1990-01-01

    The analysis of antique papyrus documents using an external milliprobe is described. Missing characters of text in the documents were made visible by means of PIXE analysis and X-ray imaging of the areas studied. The contrast between the papyrus and the ink was further increased when the information contained in all the elements was taken into account simultaneously using a multivariate technique (partial least-squares regression).

  5. Affected kindred analysis of human X chromosome exomes to identify novel X-linked intellectual disability genes.

    Directory of Open Access Journals (Sweden)

    Tejasvi S Niranjan

    Full Text Available X-linked Intellectual Disability (XLID is a group of genetically heterogeneous disorders caused by mutations in genes on the X chromosome. Deleterious mutations in ~10% of X chromosome genes are implicated in causing XLID disorders in ~50% of known and suspected XLID families. The remaining XLID genes are expected to be rare and even private to individual families. To systematically identify these XLID genes, we sequenced the X chromosome exome (X-exome in 56 well-established XLID families (a single affected male from 30 families and two affected males from 26 families using an Agilent SureSelect X-exome kit and the Illumina HiSeq 2000 platform. To enrich for disease-causing mutations, we first utilized variant filters based on dbSNP, the male-restricted portions of the 1000 Genomes Project, or the Exome Variant Server datasets. However, these databases present limitations as automatic filters for enrichment of XLID genes. We therefore developed and optimized a strategy that uses a cohort of affected male kindred pairs and an additional small cohort of affected unrelated males to enrich for potentially pathological variants and to remove neutral variants. This strategy, which we refer to as Affected Kindred/Cross-Cohort Analysis, achieves a substantial enrichment for potentially pathological variants in known XLID genes compared to variant filters from public reference databases, and it has identified novel XLID candidate genes. We conclude that Affected Kindred/Cross-Cohort Analysis can effectively enrich for disease-causing genes in rare, Mendelian disorders, and that public reference databases can be used effectively, but cautiously, as automatic filters for X-linked disorders.

  6. Scanning transmission electron microscopy imaging and analysis

    CERN Document Server

    Pennycook, Stephen J

    2011-01-01

    Provides the first comprehensive treatment of the physics and applications of this mainstream technique for imaging and analysis at the atomic level Presents applications of STEM in condensed matter physics, materials science, catalysis, and nanoscience Suitable for graduate students learning microscopy, researchers wishing to utilize STEM, as well as for specialists in other areas of microscopy Edited and written by leading researchers and practitioners

  7. IMAGES AND SOCIAL REPRESENTATION: SEMIOTIC ANALYSIS CONTRIBUTIONS

    Directory of Open Access Journals (Sweden)

    Izabela Gonçalves Terra

    2016-09-01

    Full Text Available The common sense knowledge formation is object of study of the Social Representation Theory, which highlights the role of communication in the production of comprehension by the subjects. The visual images favor the socialization of meanings and are active elements in the formation of social representations. Given the expressive role of the images in the formation of representational contents, this paper aims to present a semiotics analysis method for researches on social representations. The semiotic analysis of images was selected as a theoretical and methodological basis, for offering the means required for guidance for an effective research method to identify the social representations of socially shared iconic signs. The analysis method was explored by means of analytical procedures, employed for the apprehension of social representations of the feminine in posters for Brazilian Ministry of Health campaigns, which allowed access to the network of meanings associated with the analyzed visual image. It should be emphasized that the relevance of the use of semiotic analysis to analyze social representations, which presents itself as a fertile perspective for further studies expanding the possibilities of exploitation of visual content.

  8. Good relationships between computational image analysis and radiological physics

    International Nuclear Information System (INIS)

    Good relationships between computational image analysis and radiological physics have been constructed for increasing the accuracy of medical diagnostic imaging and radiation therapy in radiological physics. Computational image analysis has been established based on applied mathematics, physics, and engineering. This review paper will introduce how computational image analysis is useful in radiation therapy with respect to radiological physics

  9. Web Based Distributed Coastal Image Analysis System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This project develops Web based distributed image analysis system processing the Moderate Resolution Imaging Spectroradiometer (MODIS) data to provide decision...

  10. Ultrasonic image analysis for beef tenderness

    Science.gov (United States)

    Park, Bosoon; Thane, Brian R.; Whittaker, A. D.

    1993-05-01

    Objective measurement of meat tenderness has been a topic of concern for palatability evaluation. In this study, a real-time ultrasonic B-mode imaging method was used for measuring beef palatability attributes such as juiciness, muscle fiber tenderness, connective tissue amount, overall tenderness, flavor intensity, and percent total collagen noninvasively. A temporal averaging image enhancement method was used for image analysis. Ultrasonic image intensity, fractal dimension, attenuation, and statistical gray-tone spatial-dependence matrix image texture measurement were analyzed. The contrast of the textural feature was the most correlated parameter with palatability attributes. The longitudinal scanning method was better for juiciness, muscle fiber tenderness, flavor intensity, and percent soluble collagen, whereas, the cross-sectional method was better for connective tissue, overall tenderness. The multivariate linear regression models were developed as a function of textural features and image intensity parameters. The determinant coefficients of regression models were for juiciness (R2 equals .97), for percent total collagen (R2 equals .88), for flavor intensity (R2 equals .75), for muscle fiber tenderness (R2 equals .55), and for overall tenderness (R2 equals .49), respectively.

  11. Analysis of chromosome 22 deletions in neurofibromatosis type 2-related tumors

    Energy Technology Data Exchange (ETDEWEB)

    Wolff, R.K.; Frazer, K.A.; Jackler, R.K.; Lanser, M.J.; Pitts, L.H.; Cox, D.R. (Univ. of California, San Francisco, CA (United States))

    1992-09-01

    The neurofibromatosis type 2 (NF2) gene has been hypothesized to be a recessive tumor suppressor, with mutations at the same locus on chromosome 22 that lead to NF2 also leading to sporadic tumors of the types seen in NF2. Flanking markers for this gene have previously been defined as D22S1 centromeric and D22S28 telomeric. Identification of subregions of this interval that are consistently rearranged in the NF2-related tumors would aid in better defining the disease locus. To this end, the authors have compared tumor and constitutional DNAs, isolated from 39 unrelated patients with sporadic and NF2-associated acoustic neuromas, meningiomas, schwannomas, and ependymomas, at eight polymorphic loci on chromosome 22. Two of the tumors studied revealed loss-of-heterozygosity patterns, which is consistent with the presence of chromosome 22 terminal deletions. By using additional polymorphic markers, the terminal deletion breakpoint found in one of the tumors, an acoustic neuroma from an NF2 patient, was mapped within the previously defined NF2 region. The breakpoint occurred between the haplotyped markers D22S41/D22S46 and D22S56. This finding redefines the proximal flanking marker and localizes the NF2 gene between markers D22S41/D22S46 and D22S28. In addition, the authors identified a sporadic acoustic neuroma that reveals a loss-of-heterozygosity pattern consistent with mitotic recombination or deletion and reduplication, which are mechanisms not previously seen in studies of these tumors. This finding, while inconsistent with models of tumorigenesis that invoke single deletions and their gene-dosage effects, lends further support to the recessive tumor-suppressor model. 33 refs., 2 figs., 1 tab.

  12. Identification of Chromosome Abnormalities in Subtelomeric Regions by Microarray Analysis: A Study of 5,380 Cases

    Science.gov (United States)

    Shao, Lina; Shaw, Chad A.; Lu, Xin-Yan; Sahoo, Trilochan; Bacino, Carlos A.; Lalani, Seema R.; Stankiewicz, Pawel; Yatsenko, Svetlana A.; Li, Yinfeng; Neill, Sarah; Pursley, Amber N.; Chinault, A. Craig; Patel, Ankita; Beaudet, Arthur L.; Lupski, James R.; Cheung, Sau W.

    2009-01-01

    Subtelomeric imbalances are a significant cause of congenital disorders. Screening for these abnormalities has traditionally utilized GTG-banding analysis, fluorescence in situ hybridization (FISH) assays, and multiplex ligation-dependent probe amplification. Microarray-based comparative genomic hybridization (array-CGH) is a relatively new technology that can identify microscopic and submicroscopic chromosomal imbalances. It has been proposed that an array with extended coverage at subtelomeric regions could characterize subtelomeric aberrations more efficiently in a single experiment. The targeted arrays for chromosome microarray analysis (CMA), developed by Baylor College of Medicine, have on average 12 BAC/PAC clones covering 10 Mb of each of the 41 subtelomeric regions. We screened 5,380 consecutive clinical patients using CMA. The most common reasons for referral included developmental delay (DD), and/or mental retardation (MR), dysmorphic features (DF), multiple congenital anomalies (MCA), seizure disorders (SD), and autistic, or other behavioral abnormalities. We found pathogenic rearrangements at subtelomeric regions in 236 patients (4.4%). Among these patients, 103 had a deletion, 58 had a duplication, 44 had an unbalanced translocation, and 31 had a complex rearrangement. The detection rates varied among patients with a normal karyotype analysis (2.98%), with an abnormal karyotype analysis (43.4%), and with an unavailable or no karyotype analysis (3.16%). Six patients out of 278 with a prior normal subtelomere-FISH analysis showed an abnormality including an interstitial deletion, two terminal deletions, two interstitial duplications, and a terminal duplication. In conclusion, genomic imbalances at subtelomeric regions contribute significantly to congenital disorders. Targeted array-CGH with extended coverage (up to 10 Mb) of subtelomeric regions will enhance the detection of subtelomeric imbalances, especially for submicroscopic imbalances. PMID

  13. Image analysis for ophthalmological diagnosis image processing of Corvis ST images using Matlab

    CERN Document Server

    Koprowski, Robert

    2016-01-01

    This monograph focuses on the use of analysis and processing methods for images from the Corvis® ST tonometer. The presented analysis is associated with the quantitative, repeatable and fully automatic evaluation of the response of the eye, eyeball and cornea to an air-puff. All the described algorithms were practically implemented in MATLAB®. The monograph also describes and provides the full source code designed to perform the discussed calculations. As a result, this monograph is intended for scientists, graduate students and students of computer science and bioengineering as well as doctors wishing to expand their knowledge of modern diagnostic methods assisted by various image analysis and processing methods.

  14. Digital image sequence processing, compression, and analysis

    CERN Document Server

    Reed, Todd R

    2004-01-01

    IntroductionTodd R. ReedCONTENT-BASED IMAGE SEQUENCE REPRESENTATIONPedro M. Q. Aguiar, Radu S. Jasinschi, José M. F. Moura, andCharnchai PluempitiwiriyawejTHE COMPUTATION OF MOTIONChristoph Stiller, Sören Kammel, Jan Horn, and Thao DangMOTION ANALYSIS AND DISPLACEMENT ESTIMATION IN THE FREQUENCY DOMAINLuca Lucchese and Guido Maria CortelazzoQUALITY OF SERVICE ASSESSMENT IN NEW GENERATION WIRELESS VIDEO COMMUNICATIONSGaetano GiuntaERROR CONCEALMENT IN DIGITAL VIDEOFrancesco G.B. De NataleIMAGE SEQUENCE RESTORATION: A WIDER PERSPECTIVEAnil KokaramVIDEO SUMMARIZATIONCuneyt M. Taskiran and Edward

  15. Recent Advances in Morphological Cell Image Analysis

    Directory of Open Access Journals (Sweden)

    Shengyong Chen

    2012-01-01

    Full Text Available This paper summarizes the recent advances in image processing methods for morphological cell analysis. The topic of morphological analysis has received much attention with the increasing demands in both bioinformatics and biomedical applications. Among many factors that affect the diagnosis of a disease, morphological cell analysis and statistics have made great contributions to results and effects for a doctor. Morphological cell analysis finds the cellar shape, cellar regularity, classification, statistics, diagnosis, and so forth. In the last 20 years, about 1000 publications have reported the use of morphological cell analysis in biomedical research. Relevant solutions encompass a rather wide application area, such as cell clumps segmentation, morphological characteristics extraction, 3D reconstruction, abnormal cells identification, and statistical analysis. These reports are summarized in this paper to enable easy referral to suitable methods for practical solutions. Representative contributions and future research trends are also addressed.

  16. High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosomal analysis

    DEFF Research Database (Denmark)

    Bosch, Elena; Calafell, Francesc; Rosser, Zoë H;

    2003-01-01

    that precedes the split between European and Native American populations, it is possible to assign chromosomes in an admixed population to either continental source. On this basis, 58+/-6% of these Y chromosomes have been assigned to a European origin. The high proportion of European Y chromosomes contrasts...

  17. cDNA cloning, mRNA distribution and heterogeneity, chromosomal location, and RFLP analysis of human osteopontin (OPN)

    DEFF Research Database (Denmark)

    Young, M F; Kerr, J M; Termine, J D;

    1990-01-01

    of the Arg-Gly-Asp (RGD) cell attachment site. Chromosomal mapping of the osteopontin gene (OPN) using human-rodent cell hybrids demonstrated a location on chromosome 4 in the human genome. In situ hybridization of metaphase chromosomes using radiolabeled OP1a as a probe indicated that the gene is located...

  18. Autonomous Image Analysis for Future Mars Missions

    Science.gov (United States)

    Gulick, V. C.; Morris, R. L.; Ruzon, M. A.; Bandari, E.; Roush, T. L.

    1999-01-01

    To explore high priority landing sites and to prepare for eventual human exploration, future Mars missions will involve rovers capable of traversing tens of kilometers. However, the current process by which scientists interact with a rover does not scale to such distances. Specifically, numerous command cycles are required to complete even simple tasks, such as, pointing the spectrometer at a variety of nearby rocks. In addition, the time required by scientists to interpret image data before new commands can be given and the limited amount of data that can be downlinked during a given command cycle constrain rover mobility and achievement of science goals. Experience with rover tests on Earth supports these concerns. As a result, traverses to science sites as identified in orbital images would require numerous science command cycles over a period of many weeks, months or even years, perhaps exceeding rover design life and other constraints. Autonomous onboard science analysis can address these problems in two ways. First, it will allow the rover to preferentially transmit "interesting" images, defined as those likely to have higher science content. Second, the rover will be able to anticipate future commands. For example, a rover might autonomously acquire and return spectra of "interesting" rocks along with a high-resolution image of those rocks in addition to returning the context images in which they were detected. Such approaches, coupled with appropriate navigational software, help to address both the data volume and command cycle bottlenecks that limit both rover mobility and science yield. We are developing fast, autonomous algorithms to enable such intelligent on-board decision making by spacecraft. Autonomous algorithms developed to date have the ability to identify rocks and layers in a scene, locate the horizon, and compress multi-spectral image data. We are currently investigating the possibility of reconstructing a 3D surface from a sequence of images

  19. Cladistic association analysis of Y chromosome effects on alcohol dependence and related personality traits.

    Science.gov (United States)

    Kittles, R A; Long, J C; Bergen, A W; Eggert, M; Virkkunen, M; Linnoila, M; Goldman, D

    1999-03-30

    Association between Y chromosome haplotype variation and alcohol dependence and related personality traits was investigated in a large sample of psychiatrically diagnosed Finnish males. Haplotypes were constructed for 359 individuals using alleles at eight loci (seven microsatellite loci and a nucleotide substitution in the DYZ3 alphoid satellite locus). A cladogram linking the 102 observed haplotype configurations was constructed by using parsimony with a single-step mutation model. Then, a series of contingency tables nested according to the cladogram hierarchy were used to test for association between Y haplotype and alcohol dependence. Finally, using only alcohol-dependent subjects, we tested for association between Y haplotype and personality variables postulated to define subtypes of alcoholism-antisocial personality disorder, novelty seeking, harm avoidance, and reward dependence. Significant association with alcohol dependence was observed at three Y haplotype clades, with significance levels of P = 0.002, P = 0.020, and P = 0.010. Within alcohol-dependent subjects, no relationship was revealed between Y haplotype and antisocial personality disorder, novelty seeking, harm avoidance, or reward dependence. These results demonstrate, by using a fully objective association design, that differences among Y chromosomes contribute to variation in vulnerability to alcohol dependence. However, they do not demonstrate an association between Y haplotype and the personality variables thought to underlie the subtypes of alcoholism.

  20. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

    Science.gov (United States)

    Purps, Josephine; Siegert, Sabine; Willuweit, Sascha; Nagy, Marion; Alves, Cíntia; Salazar, Renato; Angustia, Sheila M.T.; Santos, Lorna H.; Anslinger, Katja; Bayer, Birgit; Ayub, Qasim; Wei, Wei; Xue, Yali; Tyler-Smith, Chris; Bafalluy, Miriam Baeta; Martínez-Jarreta, Begoña; Egyed, Balazs; Balitzki, Beate; Tschumi, Sibylle; Ballard, David; Court, Denise Syndercombe; Barrantes, Xinia; Bäßler, Gerhard; Wiest, Tina; Berger, Burkhard; Niederstätter, Harald; Parson, Walther; Davis, Carey; Budowle, Bruce; Burri, Helen; Borer, Urs; Koller, Christoph; Carvalho, Elizeu F.; Domingues, Patricia M.; Chamoun, Wafaa Takash; Coble, Michael D.; Hill, Carolyn R.; Corach, Daniel; Caputo, Mariela; D’Amato, Maria E.; Davison, Sean; Decorte, Ronny; Larmuseau, Maarten H.D.; Ottoni, Claudio; Rickards, Olga; Lu, Di; Jiang, Chengtao; Dobosz, Tadeusz; Jonkisz, Anna; Frank, William E.; Furac, Ivana; Gehrig, Christian; Castella, Vincent; Grskovic, Branka; Haas, Cordula; Wobst, Jana; Hadzic, Gavrilo; Drobnic, Katja; Honda, Katsuya; Hou, Yiping; Zhou, Di; Li, Yan; Hu, Shengping; Chen, Shenglan; Immel, Uta-Dorothee; Lessig, Rüdiger; Jakovski, Zlatko; Ilievska, Tanja; Klann, Anja E.; García, Cristina Cano; de Knijff, Peter; Kraaijenbrink, Thirsa; Kondili, Aikaterini; Miniati, Penelope; Vouropoulou, Maria; Kovacevic, Lejla; Marjanovic, Damir; Lindner, Iris; Mansour, Issam; Al-Azem, Mouayyad; Andari, Ansar El; Marino, Miguel; Furfuro, Sandra; Locarno, Laura; Martín, Pablo; Luque, Gracia M.; Alonso, Antonio; Miranda, Luís Souto; Moreira, Helena; Mizuno, Natsuko; Iwashima, Yasuki; Neto, Rodrigo S. Moura; Nogueira, Tatiana L.S.; Silva, Rosane; Nastainczyk-Wulf, Marina; Edelmann, Jeanett; Kohl, Michael; Nie, Shengjie; Wang, Xianping; Cheng, Baowen; Núñez, Carolina; Pancorbo, Marian Martínez de; Olofsson, Jill K.; Morling, Niels; Onofri, Valerio; Tagliabracci, Adriano; Pamjav, Horolma; Volgyi, Antonia; Barany, Gusztav; Pawlowski, Ryszard; Maciejewska, Agnieszka; Pelotti, Susi; Pepinski, Witold; Abreu-Glowacka, Monica; Phillips, Christopher; Cárdenas, Jorge; Rey-Gonzalez, Danel; Salas, Antonio; Brisighelli, Francesca; Capelli, Cristian; Toscanini, Ulises; Piccinini, Andrea; Piglionica, Marilidia; Baldassarra, Stefania L.; Ploski, Rafal; Konarzewska, Magdalena; Jastrzebska, Emila; Robino, Carlo; Sajantila, Antti; Palo, Jukka U.; Guevara, Evelyn; Salvador, Jazelyn; Ungria, Maria Corazon De; Rodriguez, Jae Joseph Russell; Schmidt, Ulrike; Schlauderer, Nicola; Saukko, Pekka; Schneider, Peter M.; Sirker, Miriam; Shin, Kyoung-Jin; Oh, Yu Na; Skitsa, Iulia; Ampati, Alexandra; Smith, Tobi-Gail; Calvit, Lina Solis de; Stenzl, Vlastimil; Capal, Thomas; Tillmar, Andreas; Nilsson, Helena; Turrina, Stefania; De Leo, Domenico; Verzeletti, Andrea; Cortellini, Venusia; Wetton, Jon H.; Gwynne, Gareth M.; Jobling, Mark A.; Whittle, Martin R.; Sumita, Denilce R.; Wolańska-Nowak, Paulina; Yong, Rita Y.Y.; Krawczak, Michael; Nothnagel, Michael; Roewer, Lutz

    2014-01-01

    In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent. PMID:24854874

  1. A microarray system for Y chromosomal and mitochondrial single nucleotide polymorphism analysis in chimpanzee populations.

    Science.gov (United States)

    Andrés, Olga; Rönn, Ann-Charlotte; Bonhomme, Maxime; Kellermann, Thomas; Crouau-Roy, Brigitte; Doxiadis, Gaby; Verschoor, Ernst J; Goossens, Benoît; Domingo-Roura, Xavier; Bruford, Michael W; Bosch, Montserrat; Syvänen, Ann-Christine

    2008-05-01

    Chimpanzee populations are diminishing as a consequence of human activities, and as a result this species is now endangered. In the context of conservation programmes, genetic data can add vital information, for instance on the genetic diversity and structure of threatened populations. Single nucleotide polymorphisms (SNP) are biallelic markers that are widely used in human molecular studies and can be implemented in efficient microarray systems. This technology offers the potential of robust, multiplexed SNP genotyping at low reagent cost in other organisms than humans, but it is not commonly used yet in wild population studies. Here, we describe the characterization of new SNPs in Y-chromosomal intronic regions in chimpanzees and also identify SNPs from mitochondrial genes, with the aim of developing a microarray system that permits the simultaneous study of both paternal and maternal lineages. Our system consists of 42 SNPs for the Y chromosome and 45 SNPs for the mitochondrial genome. We demonstrate the applicability of this microarray in a captive population where genotypes accurately reflected its large pedigree. Two wild-living populations were also analysed and the results show that the microarray will be a useful tool alongside microsatellite markers, since it supplies complementary information about population structure and ecology. SNP genotyping using microarray technology, therefore, is a promising approach and may become an essential tool in conservation genetics to help in the management and study of captive and wild-living populations. Moreover, microarrays that combine SNPs from different genomic regions could replace microsatellite typing in the future. PMID:21585830

  2. Cladistic association analysis of Y chromosome effects on alcohol dependence and related personality traits

    Science.gov (United States)

    Kittles, Rick A.; Long, Jeffrey C.; Bergen, Andrew W.; Eggert, Monica; Virkkunen, Matti; Linnoila, Markku; Goldman, David

    1999-01-01

    Association between Y chromosome haplotype variation and alcohol dependence and related personality traits was investigated in a large sample of psychiatrically diagnosed Finnish males. Haplotypes were constructed for 359 individuals using alleles at eight loci (seven microsatellite loci and a nucleotide substitution in the DYZ3 alphoid satellite locus). A cladogram linking the 102 observed haplotype configurations was constructed by using parsimony with a single-step mutation model. Then, a series of contingency tables nested according to the cladogram hierarchy were used to test for association between Y haplotype and alcohol dependence. Finally, using only alcohol-dependent subjects, we tested for association between Y haplotype and personality variables postulated to define subtypes of alcoholism—antisocial personality disorder, novelty seeking, harm avoidance, and reward dependence. Significant association with alcohol dependence was observed at three Y haplotype clades, with significance levels of P = 0.002, P = 0.020, and P = 0.010. Within alcohol-dependent subjects, no relationship was revealed between Y haplotype and antisocial personality disorder, novelty seeking, harm avoidance, or reward dependence. These results demonstrate, by using a fully objective association design, that differences among Y chromosomes contribute to variation in vulnerability to alcohol dependence. However, they do not demonstrate an association between Y haplotype and the personality variables thought to underlie the subtypes of alcoholism. PMID:10097188

  3. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

    Science.gov (United States)

    Purps, Josephine; Siegert, Sabine; Willuweit, Sascha; Nagy, Marion; Alves, Cíntia; Salazar, Renato; Angustia, Sheila M T; Santos, Lorna H; Anslinger, Katja; Bayer, Birgit; Ayub, Qasim; Wei, Wei; Xue, Yali; Tyler-Smith, Chris; Bafalluy, Miriam Baeta; Martínez-Jarreta, Begoña; Egyed, Balazs; Balitzki, Beate; Tschumi, Sibylle; Ballard, David; Court, Denise Syndercombe; Barrantes, Xinia; Bäßler, Gerhard; Wiest, Tina; Berger, Burkhard; Niederstätter, Harald; Parson, Walther; Davis, Carey; Budowle, Bruce; Burri, Helen; Borer, Urs; Koller, Christoph; Carvalho, Elizeu F; Domingues, Patricia M; Chamoun, Wafaa Takash; Coble, Michael D; Hill, Carolyn R; Corach, Daniel; Caputo, Mariela; D'Amato, Maria E; Davison, Sean; Decorte, Ronny; Larmuseau, Maarten H D; Ottoni, Claudio; Rickards, Olga; Lu, Di; Jiang, Chengtao; Dobosz, Tadeusz; Jonkisz, Anna; Frank, William E; Furac, Ivana; Gehrig, Christian; Castella, Vincent; Grskovic, Branka; Haas, Cordula; Wobst, Jana; Hadzic, Gavrilo; Drobnic, Katja; Honda, Katsuya; Hou, Yiping; Zhou, Di; Li, Yan; Hu, Shengping; Chen, Shenglan; Immel, Uta-Dorothee; Lessig, Rüdiger; Jakovski, Zlatko; Ilievska, Tanja; Klann, Anja E; García, Cristina Cano; de Knijff, Peter; Kraaijenbrink, Thirsa; Kondili, Aikaterini; Miniati, Penelope; Vouropoulou, Maria; Kovacevic, Lejla; Marjanovic, Damir; Lindner, Iris; Mansour, Issam; Al-Azem, Mouayyad; Andari, Ansar El; Marino, Miguel; Furfuro, Sandra; Locarno, Laura; Martín, Pablo; Luque, Gracia M; Alonso, Antonio; Miranda, Luís Souto; Moreira, Helena; Mizuno, Natsuko; Iwashima, Yasuki; Neto, Rodrigo S Moura; Nogueira, Tatiana L S; Silva, Rosane; Nastainczyk-Wulf, Marina; Edelmann, Jeanett; Kohl, Michael; Nie, Shengjie; Wang, Xianping; Cheng, Baowen; Núñez, Carolina; Pancorbo, Marian Martínez de; Olofsson, Jill K; Morling, Niels; Onofri, Valerio; Tagliabracci, Adriano; Pamjav, Horolma; Volgyi, Antonia; Barany, Gusztav; Pawlowski, Ryszard; Maciejewska, Agnieszka; Pelotti, Susi; Pepinski, Witold; Abreu-Glowacka, Monica; Phillips, Christopher; Cárdenas, Jorge; Rey-Gonzalez, Danel; Salas, Antonio; Brisighelli, Francesca; Capelli, Cristian; Toscanini, Ulises; Piccinini, Andrea; Piglionica, Marilidia; Baldassarra, Stefania L; Ploski, Rafal; Konarzewska, Magdalena; Jastrzebska, Emila; Robino, Carlo; Sajantila, Antti; Palo, Jukka U; Guevara, Evelyn; Salvador, Jazelyn; Ungria, Maria Corazon De; Rodriguez, Jae Joseph Russell; Schmidt, Ulrike; Schlauderer, Nicola; Saukko, Pekka; Schneider, Peter M; Sirker, Miriam; Shin, Kyoung-Jin; Oh, Yu Na; Skitsa, Iulia; Ampati, Alexandra; Smith, Tobi-Gail; Calvit, Lina Solis de; Stenzl, Vlastimil; Capal, Thomas; Tillmar, Andreas; Nilsson, Helena; Turrina, Stefania; De Leo, Domenico; Verzeletti, Andrea; Cortellini, Venusia; Wetton, Jon H; Gwynne, Gareth M; Jobling, Mark A; Whittle, Martin R; Sumita, Denilce R; Wolańska-Nowak, Paulina; Yong, Rita Y Y; Krawczak, Michael; Nothnagel, Michael; Roewer, Lutz

    2014-09-01

    In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent. PMID:24854874

  4. Quantitative Analysis in Nuclear Medicine Imaging

    CERN Document Server

    2006-01-01

    This book provides a review of image analysis techniques as they are applied in the field of diagnostic and therapeutic nuclear medicine. Driven in part by the remarkable increase in computing power and its ready and inexpensive availability, this is a relatively new yet rapidly expanding field. Likewise, although the use of radionuclides for diagnosis and therapy has origins dating back almost to the discovery of natural radioactivity itself, radionuclide therapy and, in particular, targeted radionuclide therapy has only recently emerged as a promising approach for therapy of cancer and, to a lesser extent, other diseases. As effort has, therefore, been made to place the reviews provided in this book in a broader context. The effort to do this is reflected by the inclusion of introductory chapters that address basic principles of nuclear medicine imaging, followed by overview of issues that are closely related to quantitative nuclear imaging and its potential role in diagnostic and therapeutic applications. ...

  5. 羊水细胞染色体分析在产前的应用%Amniotic fluid cel chromosome analysis in prenatal application

    Institute of Scientific and Technical Information of China (English)

    王亚群; 童克婷

    2013-01-01

    Objective Study amniotic fluid cel chromosome usefulness in clinical prenatal diagnosis and in the diagnosis of chromosomal disorders. Methods Puncture indications of second trimester amniotic fluid cel culture and chromosome analysis detected abnormal karyotype types and statistics. Results 474 cases were successfuly cultured amniotic fluid detection of abnormal karyotype 22 cases, autosomal abnormal number of 15 cases, the sex chromosome abnormalities, six cases of chromosome structural abnormalities, abnormal detection rate of 4.64%, chromosome polymorphismThe karyotype 22 cases. A conclusion Second trimester amniotic fluid chromosome chromosome-risk pregnant woman is an important means of prenatal diagnosis.%  目的研究羊水细胞染色体检查在临床产前诊断中的实用性和在染色体疾病诊断中的意义.方法对孕中期有穿刺指征的孕妇羊水细胞培养并进行染色体分析,检出异常核型及类型并统计.结果在成功培养的474例羊水中,检出异常核型22例,其中常染色体数目异常15例,性染色体数目异常1例,染色体结构异常6例,异常检出率为4.64%,染色体多态性核型22例.结论孕中期对染色体高危孕妇进行羊水染色体检查是产前诊断的重要手段.

  6. Karyotype analysis of the Russian wheat aphid, Diuraphis noxia (Kurdjumov) (Hemiptera: Aphididae) reveals a large X chromosome with rRNA and histone gene families.

    Science.gov (United States)

    Novotná, Jana; Havelka, Jan; Starý, Petr; Koutecký, Petr; Vítková, Magda

    2011-03-01

    The Russsian wheat aphid (RWA), Diuraphis noxia (Kurdjumov), is a worldwide pest of cereals. Despite its economic importance, little is known about its genome. Here we investigated physical genomic features in RWA by karyotype analysis using differential staining with AgNO(3), CMA(3), and DAPI, by chromosomal localization of ribosomal DNA (rDNA), H3 and H4 histone genes, and the "arthropod" telomeric sequence (TTAGG)(n) using fluorescence in situ hybridization (FISH), and by measuring the RWA genome size using flow cytometry. The female karyotype, 2n = 10, is composed of four autosome pairs and a pair of X chromosomes, whereas the male karyotype, 2n = 9, has a single X. The X chromosome is the largest element in the karyotype. All three molecular markers used, i.e., 18S rRNA and both H3 and H4 probes are co-localized at one end of the X chromosome. The FISH probes revealed that the AgNO(3)-positive bridge between two prometaphase X chromosomes of females, which is believed to be responsible for the elimination of one X chromosome in aphid oocytes determined to undergo male development, contains clusters of both histone genes, in addition to an rDNA cluster. Interestingly, RWA lacks the (TTAGG)(n) telomeric sequence in its genome, in contrast to several previously investigated aphid species. Additionally, we compared female and male genome sizes. The female genome size is 2C = 0.86 pg, whereas the male genome size is 2C = 0.70 pg. The difference between the DNA content in the two genders suggests that the RWA X chromosome occupies about 35% of the female haploid genome (1C = 0.43 pg), which makes it one of the largest sex chromosomes in the animal kingdom.

  7. Liver Ultrasound Image Analysis using Enhancement Techniques

    Directory of Open Access Journals (Sweden)

    Smriti Sahu, Maheedhar Dubey, Mohammad Imroze Khan

    2012-12-01

    Full Text Available Liver cancer is the sixth most common malignanttumour and the third most common cause ofcancer-related deaths worldwide. Chronic Liverdamage affects up to 20% of our population. It hasmany causes - viral infections (Hepatitis B and C,toxins, genetic, metabolic and autoimmune diseases.The rate of liver cancer in Australia has increasedfour-fold in the past 20 years. For detection andqualitative diagnosis of liver diseases, Ultrasound(US image is an easy-to-use and minimally invasiveimaging modality. Medical images are oftendeteriorated by noise due to various sources ofinterferences and other phenomena known asSpeckle noise. Therefore it is required to apply somedigital image processing techniques for smoothingor suppression of speckle noise in ultrasoundimages. This paper attempts to undertake the studythree types of the image enhancement techniquesincluding, Shock Filter, Contrast Limited AdaptiveHistogram Equalization (CLAHE and Spatialfilter. These smoothing techniques are comparedusing performance matrices Peak Signal to NoiseRatio (PSNR and Mean Square Error (MSE. Ithas been observed that the Spatial high pass filtergives the better performance than others for liverultrasound image analysis.

  8. The synthesis and analysis of color images

    Science.gov (United States)

    Wandell, Brian A.

    1987-01-01

    A method is described for performing the synthesis and analysis of digital color images. The method is based on two principles. First, image data are represented with respect to the separate physical factors, surface reflectance and the spectral power distribution of the ambient light, that give rise to the perceived color of an object. Second, the encoding is made efficiently by using a basis expansion for the surface spectral reflectance and spectral power distribution of the ambient light that takes advantage of the high degree of correlation across the visible wavelengths normally found in such functions. Within this framework, the same basic methods can be used to synthesize image data for color display monitors and printed materials, and to analyze image data into estimates of the spectral power distribution and surface spectral reflectances. The method can be applied to a variety of tasks. Examples of applications include the color balancing of color images, and the identification of material surface spectral reflectance when the lighting cannot be completely controlled.

  9. Scalable histopathological image analysis via active learning.

    Science.gov (United States)

    Zhu, Yan; Zhang, Shaoting; Liu, Wei; Metaxas, Dimitris N

    2014-01-01

    Training an effective and scalable system for medical image analysis usually requires a large amount of labeled data, which incurs a tremendous annotation burden for pathologists. Recent progress in active learning can alleviate this issue, leading to a great reduction on the labeling cost without sacrificing the predicting accuracy too much. However, most existing active learning methods disregard the "structured information" that may exist in medical images (e.g., data from individual patients), and make a simplifying assumption that unlabeled data is independently and identically distributed. Both may not be suitable for real-world medical images. In this paper, we propose a novel batch-mode active learning method which explores and leverages such structured information in annotations of medical images to enforce diversity among the selected data, therefore maximizing the information gain. We formulate the active learning problem as an adaptive submodular function maximization problem subject to a partition matroid constraint, and further present an efficient greedy algorithm to achieve a good solution with a theoretically proven bound. We demonstrate the efficacy of our algorithm on thousands of histopathological images of breast microscopic tissues. PMID:25320821

  10. BioImage Suite: An integrated medical image analysis suite: An update

    OpenAIRE

    Papademetris, Xenophon; Jackowski, Marcel P; Rajeevan, Nallakkandi; DiStasio, Marcello; Okuda, Hirohito; Constable, R. Todd; Staib, Lawrence H.

    2006-01-01

    BioImage Suite is an NIH-supported medical image analysis software suite developed at Yale. It leverages both the Visualization Toolkit (VTK) and the Insight Toolkit (ITK) and it includes many additional algorithms for image analysis especially in the areas of segmentation, registration, diffusion weighted image processing and fMRI analysis. BioImage Suite has a user-friendly user interface developed in the Tcl scripting language. A final beta version is freely available for download 1

  11. Pain related inflammation analysis using infrared images

    Science.gov (United States)

    Bhowmik, Mrinal Kanti; Bardhan, Shawli; Das, Kakali; Bhattacharjee, Debotosh; Nath, Satyabrata

    2016-05-01

    Medical Infrared Thermography (MIT) offers a potential non-invasive, non-contact and radiation free imaging modality for assessment of abnormal inflammation having pain in the human body. The assessment of inflammation mainly depends on the emission of heat from the skin surface. Arthritis is a disease of joint damage that generates inflammation in one or more anatomical joints of the body. Osteoarthritis (OA) is the most frequent appearing form of arthritis, and rheumatoid arthritis (RA) is the most threatening form of them. In this study, the inflammatory analysis has been performed on the infrared images of patients suffering from RA and OA. For the analysis, a dataset of 30 bilateral knee thermograms has been captured from the patient of RA and OA by following a thermogram acquisition standard. The thermograms are pre-processed, and areas of interest are extracted for further processing. The investigation of the spread of inflammation is performed along with the statistical analysis of the pre-processed thermograms. The objectives of the study include: i) Generation of a novel thermogram acquisition standard for inflammatory pain disease ii) Analysis of the spread of the inflammation related to RA and OA using K-means clustering. iii) First and second order statistical analysis of pre-processed thermograms. The conclusion reflects that, in most of the cases, RA oriented inflammation affects bilateral knees whereas inflammation related to OA present in the unilateral knee. Also due to the spread of inflammation in OA, contralateral asymmetries are detected through the statistical analysis.

  12. Analysis of root-knot nematode and fusarium wilt disease resistance in cotton (Gossypium spp.) using chromosome substitution lines from two alien species.

    Science.gov (United States)

    Ulloa, M; Wang, C; Saha, S; Hutmacher, R B; Stelly, D M; Jenkins, J N; Burke, J; Roberts, P A

    2016-04-01

    Chromosome substitution (CS) lines in plants are a powerful genetic resource for analyzing the contribution of chromosome segments to phenotypic variance. In this study, a series of interspecific cotton (Gossypium spp.) CS lines were used to identify a new germplasm resource, and to validate chromosomal regions and favorable alleles associated with nematode or fungal disease resistance traits. The CS lines were developed in the G. hirsutum L. TM-1 background with chromosome or chromosome segment substitutions from G. barbadense L. Pima 3-79 or G. tomentosum. Root-knot nematode (Meloidogyne incognita) and fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) (races 1 and 4) resistance alleles and quantitative trait loci (QTL) previously placed on cotton chromosomes using SSR markers in two interspecific recombinant inbred line populations were chosen for testing. Phenotypic responses of increased resistance or susceptibility in controlled inoculation and infested field assays confirmed the resistance QTLs, based on substitution with the positive or negative allele for resistance. Lines CS-B22Lo, CS-B04, and CS-B18 showed high resistance to nematode root-galling, confirming QTLs on chromosomes 4 and 22 (long arm) with resistance alleles from Pima 3-79. Line CS-B16 had less fusarium race 1-induced vascular root staining and higher percent survival than the TM-1 parent, confirming a major resistance QTL on chromosome 16. Lines CS-B(17-11) and CS-B17 had high fusarium race 4 vascular symptoms and low survival due to susceptible alleles introgressed from Pima 3-79, confirming the localization on chromosome 17 of an identified QTL with resistance alleles from TM1 and other resistant lines. Analyses validated regions on chromosomes 11, 16, and 17 harboring nematode and fusarium wilt resistance genes and demonstrated the value of CS lines as both a germplasm resource for breeding programs and as a powerful genetic analysis tool for determining QTL effects for disease

  13. Analysis of root-knot nematode and fusarium wilt disease resistance in cotton (Gossypium spp.) using chromosome substitution lines from two alien species.

    Science.gov (United States)

    Ulloa, M; Wang, C; Saha, S; Hutmacher, R B; Stelly, D M; Jenkins, J N; Burke, J; Roberts, P A

    2016-04-01

    Chromosome substitution (CS) lines in plants are a powerful genetic resource for analyzing the contribution of chromosome segments to phenotypic variance. In this study, a series of interspecific cotton (Gossypium spp.) CS lines were used to identify a new germplasm resource, and to validate chromosomal regions and favorable alleles associated with nematode or fungal disease resistance traits. The CS lines were developed in the G. hirsutum L. TM-1 background with chromosome or chromosome segment substitutions from G. barbadense L. Pima 3-79 or G. tomentosum. Root-knot nematode (Meloidogyne incognita) and fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) (races 1 and 4) resistance alleles and quantitative trait loci (QTL) previously placed on cotton chromosomes using SSR markers in two interspecific recombinant inbred line populations were chosen for testing. Phenotypic responses of increased resistance or susceptibility in controlled inoculation and infested field assays confirmed the resistance QTLs, based on substitution with the positive or negative allele for resistance. Lines CS-B22Lo, CS-B04, and CS-B18 showed high resistance to nematode root-galling, confirming QTLs on chromosomes 4 and 22 (long arm) with resistance alleles from Pima 3-79. Line CS-B16 had less fusarium race 1-induced vascular root staining and higher percent survival than the TM-1 parent, confirming a major resistance QTL on chromosome 16. Lines CS-B(17-11) and CS-B17 had high fusarium race 4 vascular symptoms and low survival due to susceptible alleles introgressed from Pima 3-79, confirming the localization on chromosome 17 of an identified QTL with resistance alleles from TM1 and other resistant lines. Analyses validated regions on chromosomes 11, 16, and 17 harboring nematode and fusarium wilt resistance genes and demonstrated the value of CS lines as both a germplasm resource for breeding programs and as a powerful genetic analysis tool for determining QTL effects for disease

  14. Novel data set for retrospective biodosimetry using both conventional and FISH chromosome analysis after high accidental overexposure

    Energy Technology Data Exchange (ETDEWEB)

    Sevan' kaev, A.V.; Khvostunov, I.K.; Mikhailova, G.F.; Golub, E.V.; Potetnya, O.I.; Shepel, N.N.; Nugis, V.Yu.; Nadejina, N.M

    2000-05-15

    Blood samples of ten Chernobyl and one non-Chernobyl victims were analysed both by conventional cytogenetics and by fluorescence in situ hybridization (FISH) using a cocktail of chromosomes 2, 3 and 8. The analysed group comprised men acutely irradiated mainly in 1986 and aged 26-47 years at the time of first blood sampling. All of them displayed acute radiation syndrome of varying severity. Chromosome analysis of the earliest blood samples was carried out by conventional scoring of unstable aberrations with the number of metaphases analysed per individual ranging from 35 to 300. Estimated individual doses ranged from 0.85 to 9.8 G y. After a 10 year delay, i.e. in 1996, blood samples were analysed both by conventional scoring of unstable aberrations and by FISH measurements of stable ones. Usually about 500 metaphases per individual were scored. Estimated by the FISH-method individual translocation (tc + ti) frequencies ranged from 2.2 to 116.8 per 100 cells full genome equivalent. Based on three different published dicentric dose response, in vitro curves individual doses were calculated from the earliest dicentric frequencies. A dose response curve for truly persisting translocations (tc + ti) was estimated over the range 1-10 Gy.

  15. Characterisation of mycelial morphology using image analysis.

    Science.gov (United States)

    Paul, G C; Thomas, C R

    1998-01-01

    Image analysis is now well established in quantifying and characterising microorganisms from fermentation samples. In filamentous fermentations it has become an invaluable tool for characterising complex mycelial morphologies, although it is not yet used extensively in industry. Recent method developments include characterisation of spore germination from the inoculum stage and of the subsequent dispersed and pellet forms. Further methods include characterising vacuolation and simple structural differentiation of mycelia, also from submerged cultures. Image analysis can provide better understanding of the development of mycelial morphology, of the physiological states of the microorganisms in the fermenter, and of their interactions with the fermentation conditions. This understanding should lead to improved design and operation of mycelial fermentations. PMID:9468800

  16. Morphological Analysis of Cryogenic Spray Images

    OpenAIRE

    Ganu, Hrishikesh V.; Raghunandan, B. N.

    2008-01-01

    This study gives the development of a new technique for analyzing images of Cryogenic sprays, to estimate the drop-size distribution. It has a sound mathematical basis, in the form of Mathematical Morphology, and we have tried to build up a formulation for a granulometry, starting from the elementary operations of Dilation and Erosion. An axiomatic foundation for granulometry has also been discussed. We have taken an actual LN2 spray photograph for analysis, to illustrate the use of Morpholog...

  17. Machine learning for medical images analysis.

    Science.gov (United States)

    Criminisi, A

    2016-10-01

    This article discusses the application of machine learning for the analysis of medical images. Specifically: (i) We show how a special type of learning models can be thought of as automatically optimized, hierarchically-structured, rule-based algorithms, and (ii) We discuss how the issue of collecting large labelled datasets applies to both conventional algorithms as well as machine learning techniques. The size of the training database is a function of model complexity rather than a characteristic of machine learning methods.

  18. Nuclear Image Analysis Study of Neuroendocrine Tumors

    OpenAIRE

    Park, Meeja; Baek, Taehwa; Baek, Jongho; Son, Hyunjin; Kang, Dongwook; Kim, Jooheon; Lee, Hyekyung

    2012-01-01

    Background There is a subjective disagreement about nuclear chromatin in the field of pathology. Objective values of red, green, and blue (RGB) light intensities for nuclear chromatin can be obtained through a quantitative analysis using digital images. Methods We examined 10 cases of well differentiated neuroendocrine tumors of the rectum, small cell lung carcinomas, and moderately differentiated squamous cell lung carcinomas respectively. For each case, we selected 30 representative cells a...

  19. Cytogenetic analysis of mechanism of formation of radiation-induced chromosome exchanges. [Crepis capillaris, x radiation

    Energy Technology Data Exchange (ETDEWEB)

    Azatyan, R.A.; Akif' ev, A.P.; Shavel' zon, R.A.; Voskanyan, A.Z.; Zakaryan, M.S.

    1977-01-01

    An unusual spectrum of aberrations, characterized by a sharp exchange deficiency, was demonstrated in germinating seeds of Crepis capillaris L. synchronized with 2'-deoxy-5-fluorouridine at the start of the S phase following exposure to 100 R x-rays. The modification of the cytogenetic effect of x-radiation of dry crepis seeds (10 and 15 kR) by 5-aminouracil consisted of a higher yield of aberrations without decrease in share of exchanges of the chromosome type. The obtained data are consistent with the hypothesis that exchange aberrations occur due to interaction between spontaneous single-stranded DNA defects limited to identical or similar repeated nucleotide sequences The exchange interactions are blocked when the cells move into the stage of DNA synthesis.

  20. Genetic analysis of 17 Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic minority group.

    Science.gov (United States)

    Yi, Zhou; Jun, Wang; XingBo, Song; XiaoJun, Lu; Liu, Ding; BinWu, Ying

    2010-03-01

    We have co-amplified and analyzed 17 Y-chromosomal STRs loci (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, DYS439, DYS437, DYS448, DYS456, DYS458, DYS635, YGATA-H4 and DYS385a/b) in 132 healthy unrelated autochthonous male individuals of Chinese Tibetan ethnic group residing in Lassa area of China. The gene diversity values for the Y-STRs loci ranged from a minimum 0.206 for DYS391 locus to a maximum of 0.912 for DYS385a/b locus in the populations. A total of 123 haplotypes were identified, among which 115 were unique and 8 occurred more than once. The overall haplotype diversity for 17 Y-STRs loci was 0.998. Research results will be valuable for forensic use in the regions and for Chinese population genetic study. PMID:20116321

  1. Y chromosome comparative analysis of Rondônia with other Brazilian populations.

    Science.gov (United States)

    Nunes, Adriana C S; Silva, Dayse A; Teixeira, Marco A D; Nunes, Dorisvalder D; Lopes, Claudia M S; Netto, Ovídio R Tucunduva; Gusmão, Leonor; Carvalho, Elizeu F; Moura, Maria Manuela F

    2011-05-01

    In the present study, a Brazilian population, located in the Rondônia state, was genetically characterized for a set of Y chromosome specific STRs included in the Applied Biosystems kit (AmpFℓSTR®Yfiler™), which allows the simultaneous amplification of 16 markers: DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS438, DYS439, DYS437, DYS448, DYS456, DYS458, DYS635 and GATA H4. The studied population from Rondônia state, in the North of Brazil, included individuals with admixed Native American, African and European ancestry. When comparing Rondônia with other Brazilian populations no significant genetic distances were found. In the comparison with other worldwide populations, although a predominant male European influence could be detected, there were significant differences with some populations from Central and South America and Africa. PMID:21269865

  2. Image analysis of blood platelets adhesion.

    Science.gov (United States)

    Krízová, P; Rysavá, J; Vanícková, M; Cieslar, P; Dyr, J E

    2003-01-01

    Adhesion of blood platelets is one of the major events in haemostatic and thrombotic processes. We studied adhesion of blood platelets on fibrinogen and fibrin dimer sorbed on solid support material (glass, polystyrene). Adhesion was carried on under static and dynamic conditions and measured as percentage of the surface covered with platelets. Within a range of platelet counts in normal and in thrombocytopenic blood we observed a very significant decrease in platelet adhesion on fibrin dimer with bounded active thrombin with decreasing platelet count. Our results show the imperative use of platelet poor blood preparations as control samples in experiments with thrombocytopenic blood. Experiments carried on adhesive surfaces sorbed on polystyrene showed lower relative inaccuracy than on glass. Markedly different behaviour of platelets adhered on the same adhesive surface, which differed only in support material (glass or polystyrene) suggest that adhesion and mainly spreading of platelets depends on physical quality of the surface. While on polystyrene there were no significant differences between fibrin dimer and fibrinogen, adhesion measured on glass support material markedly differed between fibrin dimer and fibrinogen. We compared two methods of thresholding in image analysis of adhered platelets. Results obtained by image analysis of spreaded platelets showed higher relative inaccuracy than results obtained by image analysis of platelets centres and aggregates.

  3. Construction and analysis of tree models for chromosomal classification of diffuse large B-cell lymphomas

    Institute of Scientific and Technical Information of China (English)

    Hui-Yong Jiang; Zhong-Xi Huang; Xue-Feng Zhang; Richard Desper; Tong Zhao

    2007-01-01

    AIM: To construct tree models for classification of diffuse large B-cell lymphomas (DLBCL) by chromosome copy numbers, to compare them with cDNA microarray classification, and to explore models of multi-gene, multi-step and multi-pathway processes of DLBCL tumorigenesis.METHODS: Maximum-weight branching and distance based models were constructed based on the comparative genomic hybridization (CGH) data of 123 DLBCL samples using the established methods and software of Desper et al. A maximum likelihood tree model was also used to analyze the data. By comparing with the results reported in literature, values of tree models in the classification of DLBCL were elucidated.RESULTS: Both the branching and the distance-based trees classified DLBCL into three groups. We combined the classification methods of the two models and classified DLBCL into three categories according to their characteristics. The first group was marked by +Xq, +Xp, -17p and +13q; the second group by +3q, +18q and +18p; and the third group was marked by -6q and +6p. This chromosomal classification was consistent with cDNA classification. It indicated that -6q and +3q were two main events in the tumorigenesis of lymphoma.CONCLUSION: Tree models of lymphoma established from CGH data can be used in the classification of DLBCL. These models can suggest multi-gene, multi-step and multi-pathway processes of tumorigenesis.Two pathways, -6q preceding +6q and +3q preceding +18q, may be important in understanding tumorigenesis of DLBCL. The pathway, -6q preceding +6q, may have a close relationship with the tumorigenesis of non-GCB DLBCL.

  4. Autoregressive higher-order hidden Markov models: exploiting local chromosomal dependencies in the analysis of tumor expression profiles.

    Directory of Open Access Journals (Sweden)

    Michael Seifert

    Full Text Available Changes in gene expression programs play a central role in cancer. Chromosomal aberrations such as deletions, duplications and translocations of DNA segments can lead to highly significant positive correlations of gene expression levels of neighboring genes. This should be utilized to improve the analysis of tumor expression profiles. Here, we develop a novel model class of autoregressive higher-order Hidden Markov Models (HMMs that carefully exploit local data-dependent chromosomal dependencies to improve the identification of differentially expressed genes in tumor. Autoregressive higher-order HMMs overcome generally existing limitations of standard first-order HMMs in the modeling of dependencies between genes in close chromosomal proximity by the simultaneous usage of higher-order state-transitions and autoregressive emissions as novel model features. We apply autoregressive higher-order HMMs to the analysis of breast cancer and glioma gene expression data and perform in-depth model evaluation studies. We find that autoregressive higher-order HMMs clearly improve the identification of overexpressed genes with underlying gene copy number duplications in breast cancer in comparison to mixture models, standard first- and higher-order HMMs, and other related methods. The performance benefit is attributed to the simultaneous usage of higher-order state-transitions in combination with autoregressive emissions. This benefit could not be reached by using each of these two features independently. We also find that autoregressive higher-order HMMs are better able to identify differentially expressed genes in tumors independent of the underlying gene copy number status in comparison to the majority of related methods. This is further supported by the identification of well-known and of previously unreported hotspots of differential expression in glioblastomas demonstrating the efficacy of autoregressive higher-order HMMs for the analysis of individual

  5. Laser microdissection-based analysis of the Y sex chromosome of the Antarctic fish Chionodraco hamatus (Notothenioidei, Channichthyidae

    Directory of Open Access Journals (Sweden)

    Ennio Cocca

    2015-02-01

    Full Text Available Microdissection, DOP-PCR amplification and microcloning were used to study the large Y chromosome of Chionodraco hamatus, an Antarctic fish belonging to the Notothenioidei, the dominant component of the Southern Ocean fauna. The species has evolved a multiple sex chromosome system with digametic males showing an X1YX2 karyotype and females an X1X1X2X2 karyotype. Fluorescence in situ hybridization, performed with a painting probe made from microdissected Y chromosomes, allowed a deeper insight on the chromosomal rearrangement, which underpinned the fusion event that generated the Y. Then, we used a DNA library established by microdissection and microcloning of the whole Y chromosome of Ch. hamatus for searching sex-linked sequences. One clone provided preliminary information on the presence on the Y chromosome of the CHD1 gene homologue, which is sex-linked in birds but in no other vertebrates. Several clones from the Y-chromosome mini-library contained microsatellites and transposable elements, one of which mapped to the q arm putative fusion region of the Y chromosome. The findings confirm that interspersed repetitive sequences might have fostered chromosome rearrangements and the emergence of the Y chromosome in Ch. hamatus. Detection of the CHD1 gene in the Y sex-determining region could be a classical example of convergent evolution in action.

  6. Reticle defect sizing of optical proximity correction defects using SEM imaging and image analysis techniques

    Science.gov (United States)

    Zurbrick, Larry S.; Wang, Lantian; Konicek, Paul; Laird, Ellen R.

    2000-07-01

    Sizing of programmed defects on optical proximity correction (OPC) feature sis addressed using high resolution scanning electron microscope (SEM) images and image analysis techniques. A comparison and analysis of different sizing methods is made. This paper addresses the issues of OPC defect definition and discusses the experimental measurement results obtained by SEM in combination with image analysis techniques.

  7. An integrated approach of comparative genomics and heritability analysis of pig and human on obesity trait: evidence for candidate genes on human chromosome 2

    Science.gov (United States)

    2012-01-01

    Background Traditional candidate gene approach has been widely used for the study of complex diseases including obesity. However, this approach is largely limited by its dependence on existing knowledge of presumed biology of the phenotype under investigation. Our combined strategy of comparative genomics and chromosomal heritability estimate analysis of obesity traits, subscapular skinfold thickness and back-fat thickness in Korean cohorts and pig (Sus scrofa), may overcome the limitations of candidate gene analysis and allow us to better understand genetic predisposition to human obesity. Results We found common genes including FTO, the fat mass and obesity associated gene, identified from significant SNPs by association studies of each trait. These common genes were related to blood pressure and arterial stiffness (P = 1.65E-05) and type 2 diabetes (P = 0.00578). Through the estimation of variance of genetic component (heritability) for each chromosome by SNPs, we observed a significant positive correlation (r = 0.479) between genetic contributions of human and pig to obesity traits. Furthermore, we noted that human chromosome 2 (syntenic to pig chromosomes 3 and 15) was most important in explaining the phenotypic variance for obesity. Conclusions Obesity genetics still awaits further discovery. Navigating syntenic regions suggests obesity candidate genes on chromosome 2 that are previously known to be associated with obesity-related diseases: MRPL33, PARD3B, ERBB4, STK39, and ZNF385B. PMID:23253381

  8. An integrated approach of comparative genomics and heritability analysis of pig and human on obesity trait: evidence for candidate genes on human chromosome 2

    Directory of Open Access Journals (Sweden)

    Kim Jaemin

    2012-12-01

    Full Text Available Abstract Background Traditional candidate gene approach has been widely used for the study of complex diseases including obesity. However, this approach is largely limited by its dependence on existing knowledge of presumed biology of the phenotype under investigation. Our combined strategy of comparative genomics and chromosomal heritability estimate analysis of obesity traits, subscapular skinfold thickness and back-fat thickness in Korean cohorts and pig (Sus scrofa, may overcome the limitations of candidate gene analysis and allow us to better understand genetic predisposition to human obesity. Results We found common genes including FTO, the fat mass and obesity associated gene, identified from significant SNPs by association studies of each trait. These common genes were related to blood pressure and arterial stiffness (P = 1.65E-05 and type 2 diabetes (P = 0.00578. Through the estimation of variance of genetic component (heritability for each chromosome by SNPs, we observed a significant positive correlation (r = 0.479 between genetic contributions of human and pig to obesity traits. Furthermore, we noted that human chromosome 2 (syntenic to pig chromosomes 3 and 15 was most important in explaining the phenotypic variance for obesity. Conclusions Obesity genetics still awaits further discovery. Navigating syntenic regions suggests obesity candidate genes on chromosome 2 that are previously known to be associated with obesity-related diseases: MRPL33, PARD3B, ERBB4, STK39, and ZNF385B.

  9. Multispectral laser imaging for advanced food analysis

    Science.gov (United States)

    Senni, L.; Burrascano, P.; Ricci, M.

    2016-07-01

    A hardware-software apparatus for food inspection capable of realizing multispectral NIR laser imaging at four different wavelengths is herein discussed. The system was designed to operate in a through-transmission configuration to detect the presence of unwanted foreign bodies inside samples, whether packed or unpacked. A modified Lock-In technique was employed to counterbalance the significant signal intensity attenuation due to transmission across the sample and to extract the multispectral information more efficiently. The NIR laser wavelengths used to acquire the multispectral images can be varied to deal with different materials and to focus on specific aspects. In the present work the wavelengths were selected after a preliminary analysis to enhance the image contrast between foreign bodies and food in the sample, thus identifying the location and nature of the defects. Experimental results obtained from several specimens, with and without packaging, are presented and the multispectral image processing as well as the achievable spatial resolution of the system are discussed.

  10. Remote Sensing Digital Image Analysis An Introduction

    CERN Document Server

    Richards, John A

    2013-01-01

    Remote Sensing Digital Image Analysis provides the non-specialist with a treatment of the quantitative analysis of satellite and aircraft derived remotely sensed data. Since the first edition of the book there have been significant developments in the algorithms used for the processing and analysis of remote sensing imagery; nevertheless many of the fundamentals have substantially remained the same.  This new edition presents material that has retained value since those early days, along with new techniques that can be incorporated into an operational framework for the analysis of remote sensing data. The book is designed as a teaching text for the senior undergraduate and postgraduate student, and as a fundamental treatment for those engaged in research using digital image processing in remote sensing.  The presentation level is for the mathematical non-specialist.  Since the very great number of operational users of remote sensing come from the earth sciences communities, the text is pitched at a leve...

  11. Nursing image: an evolutionary concept analysis.

    Science.gov (United States)

    Rezaei-Adaryani, Morteza; Salsali, Mahvash; Mohammadi, Eesa

    2012-12-01

    A long-term challenge to the nursing profession is the concept of image. In this study, we used the Rodgers' evolutionary concept analysis approach to analyze the concept of nursing image (NI). The aim of this concept analysis was to clarify the attributes, antecedents, consequences, and implications associated with the concept. We performed an integrative internet-based literature review to retrieve English literature published from 1980-2011. Findings showed that NI is a multidimensional, all-inclusive, paradoxical, dynamic, and complex concept. The media, invisibility, clothing style, nurses' behaviors, gender issues, and professional organizations are the most important antecedents of the concept. We found that NI is pivotal in staff recruitment and nursing shortage, resource allocation to nursing, nurses' job performance, workload, burnout and job dissatisfaction, violence against nurses, public trust, and salaries available to nurses. An in-depth understanding of the NI concept would assist nurses to eliminate negative stereotypes and build a more professional image for the nurse and the profession. PMID:23343236

  12. Simple Low Level Features for Image Analysis

    Science.gov (United States)

    Falcoz, Paolo

    As human beings, we perceive the world around us mainly through our eyes, and give what we see the status of “reality”; as such we historically tried to create ways of recording this reality so we could augment or extend our memory. From early attempts in photography like the image produced in 1826 by the French inventor Nicéphore Niépce (Figure 2.1) to the latest high definition camcorders, the number of recorded pieces of reality increased exponentially, posing the problem of managing all that information. Most of the raw video material produced today has lost its memory augmentation function, as it will hardly ever be viewed by any human; pervasive CCTVs are an example. They generate an enormous amount of data each day, but there is not enough “human processing power” to view them. Therefore the need for effective automatic image analysis tools is great, and a lot effort has been put in it, both from the academia and the industry. In this chapter, a review of some of the most important image analysis tools are presented.

  13. Characterization of X chromosome inactivation using integrated analysis of whole-exome and mRNA sequencing.

    Directory of Open Access Journals (Sweden)

    Szabolcs Szelinger

    Full Text Available In females, X chromosome inactivation (XCI is an epigenetic, gene dosage compensatory mechanism by inactivation of one copy of X in cells. Random XCI of one of the parental chromosomes results in an approximately equal proportion of cells expressing alleles from either the maternally or paternally inherited active X, and is defined by the XCI ratio. Skewed XCI ratio is suggestive of non-random inactivation, which can play an important role in X-linked genetic conditions. Current methods rely on indirect, semi-quantitative DNA methylation-based assay to estimate XCI ratio. Here we report a direct approach to estimate XCI ratio by integrated, family-trio based whole-exome and mRNA sequencing using phase-by-transmission of alleles coupled with allele-specific expression analysis. We applied this method to in silico data and to a clinical patient with mild cognitive impairment but no clear diagnosis or understanding molecular mechanism underlying the phenotype. Simulation showed that phased and unphased heterozygous allele expression can be used to estimate XCI ratio. Segregation analysis of the patient's exome uncovered a de novo, interstitial, 1.7 Mb deletion on Xp22.31 that originated on the paternally inherited X and previously been associated with heterogeneous, neurological phenotype. Phased, allelic expression data suggested an 83∶20 moderately skewed XCI that favored the expression of the maternally inherited, cytogenetically normal X and suggested that the deleterious affect of the de novo event on the paternal copy may be offset by skewed XCI that favors expression of the wild-type X. This study shows the utility of integrated sequencing approach in XCI ratio estimation.

  14. [Imaging Mass Spectrometry in Histopathologic Analysis].

    Science.gov (United States)

    Yamazaki, Fumiyoshi; Seto, Mitsutoshi

    2015-04-01

    Matrix-assisted laser desorption/ionization (MALDI)-imaging mass spectrometry (IMS) enables visualization of the distribution of a range of biomolecules by integrating biochemical information from mass spectrometry with positional information from microscopy. IMS identifies a target molecule. In addition, IMS enables global analysis of biomolecules containing unknown molecules by detecting the ratio of the molecular weight to electric charge without any target, which makes it possible to identify novel molecules. IMS generates data on the distribution of lipids and small molecules in tissues, which is difficult to visualize with either conventional counter-staining or immunohistochemistry. In this review, we firstly introduce the principle of imaging mass spectrometry and recent advances in the sample preparation method. Secondly, we present findings regarding biological samples, especially pathological ones. Finally, we discuss the limitations and problems of the IMS technique and clinical application, such as in drug development. PMID:26536781

  15. PAMS photo image retrieval prototype alternatives analysis

    Energy Technology Data Exchange (ETDEWEB)

    Conner, M.L.

    1996-04-30

    Photography and Audiovisual Services uses a system called the Photography and Audiovisual Management System (PAMS) to perform order entry and billing services. The PAMS system utilizes Revelation Technologies database management software, AREV. Work is currently in progress to link the PAMS AREV system to a Microsoft SQL Server database engine to provide photograph indexing and query capabilities. The link between AREV and SQLServer will use a technique called ``bonding.`` This photograph imaging subsystem will interface to the PAMS system and handle the image capture and retrieval portions of the project. The intent of this alternatives analysis is to examine the software and hardware alternatives available to meet the requirements for this project, and identify a cost-effective solution.

  16. Covariance of Lucky Images: Performance analysis

    Science.gov (United States)

    Cagigal, Manuel P.; Valle, Pedro J.; Cagigas, Miguel A.; Villó-Pérez, Isidro; Colodro-Conde, Carlos; Ginski, C.; Mugrauer, M.; Seeliger, M.

    2016-09-01

    The covariance of ground-based Lucky Images (COELI) is a robust and easy-to-use algorithm that allows us to detect faint companions surrounding a host star. In this paper we analyze the relevance of the number of processed frames, the frames quality, the atmosphere conditions and the detection noise on the companion detectability. This analysis has been carried out using both experimental and computer simulated imaging data. Although the technique allows us the detection of faint companions, the camera detection noise and the use of a limited number of frames reduce the minimum detectable companion intensity to around 1000 times fainter than that of the host star when placed at an angular distance corresponding to the few first Airy rings. The reachable contrast could be even larger when detecting companions with the assistance of an adaptive optics system.

  17. Motion as a phenotype: the use of live-cell imaging and machine visual screening to characterize transcription-dependent chromosome dynamics

    Directory of Open Access Journals (Sweden)

    Silver Pamela A

    2006-04-01

    the analysis of chromosome motion a machine visual screening approach that used unbiased visual data rather than segmented geometric data. This novel analytical approach will allow for high-throughput study of processes that can be monitored via alterations in chromosome motion and connectivity with the nuclear periphery.

  18. Introgression of tomato chromosomes into the potato genome: an analysis through molecular marker and in situ hybridisation techniques.

    OpenAIRE

    Calderé, F.G.

    1998-01-01

    Transfer of alien chromosomes and genes across intergeneric boundaries can be useful not only for the introgression of desirable characters but also for fundamental genetic studies. The successful demonstration of hybridisation of potato ( Solanum tuberosum ) and tomato ( Lycopersicon esculentum ) through protoplast fusion in 1978, created the potential for introgressing chromosomes and genes from one genus into the other. However, real prospects of adding tomato chromosomes into the potato g...

  19. Similarity analysis between chromosomes of Homo sapiens and monkeys with correlation coefficient, rank correlation coefficient and cosine similarity measures

    OpenAIRE

    Chinta Someswara Rao; S. Viswanadha Raju

    2016-01-01

    In this paper, we consider correlation coefficient, rank correlation coefficient and cosine similarity measures for evaluating similarity between Homo sapiens and monkeys. We used DNA chromosomes of genome wide genes to determine the correlation between the chromosomal content and evolutionary relationship. The similarity among the H. sapiens and monkeys is measured for a total of 210 chromosomes related to 10 species. The similarity measures of these different species show the relationship b...

  20. A device for extraction, manipulation and stretching of DNA from single human chromosomes

    DEFF Research Database (Denmark)

    Rasmussen, Kristian Hagsted; Marie, Rodolphe; Moresco, Jacob Lange;

    2011-01-01

    by time-lapse imaging; pressure-driven flow was then used to shunt the chromosomal DNA package into a nanoslit. A long linear DNA strand (>1.3 Mbp) was seen to stretch out from the DNA package and along the length of the nanoslit. Delivery of DNA in its native metaphase chromosome package as well...... as the microfluidic environment prevented DNA from shearing and will be important for preparing ultra-long lengths of DNA for nanofluidic analysis....

  1. ANALYSIS ON GENETIC POLYMORPHISM OF 6 STR LOCI ON CHROMOSOME 12 IN CHINESE HAN POPULATION

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Objective To analyze the genetic polymorphism of 6 STR loci (D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613) on chromosome 12 in Chinese Han population. Methods EDTA-blood specimens were collected from 153 unrelated individuals of Chinese Han population in Shaanxi province. Allele and genotype frequencies for the 6 STR loci were estimated and statistical parameters of polymorphism were calculated. Results 8 alleles and 18 genotypes, 10 alleles and 17 genotypes, 9 alleles and 15 genotypes, 12alleles and 29 genotypes, 12 alleles and 31 genotypes, 8 alleles and 11 genotypes were observed at D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613, respectively. No deviations of the observed allele frequency from Hardy-weinberg equilibrium expectations were found for any of these loci. The Heterozygotes of these 6 loci were 78.89%, 66.10%, 54.95%, 79.10%, 71.98% and 59.48%, respectively. It indicated the high genetic polymorphism of the loci in Chinese Han population. Conclusion The 6 STR loci belonged to the genetic marker system of high discriminutesation and high information in Chinese Han population and can be used in the study of gene-related diseases.

  2. Loss of Heterozygosity Analysis on the Long Arm of Chromosome 7 in Gastric Carcinoma

    Institute of Scientific and Technical Information of China (English)

    JinlianLi; ShijuanMai; BingjianFeng; QishengFeng; LixiHuang; XingiuanYu; ZhizhongPan; YouqingZhon; JianchuanXia

    2004-01-01

    OBJECTIVE In order to define the common deleted region related to primary gastric carcinomas in Chinese, the frequency of loss of heterozygosit (LOH) on human chromosome 7q and its clinical significance were investigated. METHODS A set of 9 microsatellite markers on 7q with an average genetic distance of 10cM were used to identify LOH by multi-PCR amplification of matched tumor and non-tumor DNAs from 70 patients with primary gastric carcinoma. The PCR products were separated by electrophoresis in polyacrylamide gels and analysed for LOH by using Genescan and Genotyper software. RESULTS The total frequency of LOH at any locus on 7q was 34.3% (24/70) in the tumors. Compared to non-tumor DNA, LOH at D7S486 and D7S798 loci were higher, 24.0%(12/50) and 19.2%(5/26), respectively. The total frequency of LOH on 7q was markedly higher with an increase in the clinical stage (P<0.05). The frequency of LOH at D7S486 in cases with lymph node metastasis was significanty higher than in cases without lymph node metastasis, P=0.015. CONCLUSION The higher incidence of LOH at D7S486 and D7S798 inprimary gastric carcinoma compared to normal tissue suggests that the potential tumor suppressor genes (TSGs) involved in the progression of gastric carcinoma might be nearby these 2 loci.

  3. Human Y-chromosome SNP characterization by multiplex amplified product-length polymorphism analysis.

    Science.gov (United States)

    Medina, Laura Smeldy Jurado; Muzzio, Marina; Schwab, Marisol; Costantino, María Leticia Bravi; Barreto, Guillermo; Bailliet, Graciela

    2014-09-01

    We designed an allele-specific amplification protocol to optimize Y-chromosome SNP typing, which is an unavoidable step for defining the phylogenetic status of paternal lineages. It allows the simultaneous highly specific definition of up to six mutations in a single reaction by amplification fragment length polymorphism (AFLP) without the need of specialized equipment, at a considerably lower cost than that based on single-base primer extension (SNaPshot™) technology or PCR-RFLP systems, requiring as little as 0.5 ng DNA and compatible with the small fragments characteristic of low-quality DNA. By designation of two primers recognizing the derived and ancestral state for each SNP, which can be differentiated by size by the addition of a noncomplementary nucleotide tail, we could define major Y clades E, F, K, R, Q, and subhaplogroups R1, R1a, R1b, R1b1b, R1b1c, J1, J2, G1, G2, I1, Q1a3, and Q1a3a1 through amplification fragments that ranged between 60 and 158bp. PMID:24846779

  4. Sequence analysis, chromosomal location, and developmental expression of the mouse preproendothelin-1 gene

    Energy Technology Data Exchange (ETDEWEB)

    Maemura, Koji; Kurihara, Hiroki; Kurihara, Yukiko [Univ. of Tokyo (Japan)] [and others

    1996-01-15

    Recent studies have designated endothelins (ETs) as morphogenetic factors in embryonic development. In the present study, we cloned and characterized the mouse preproendothelin-1 (preproET-1) gene (Edn1) and examined its expression in reference to development. Edn1 comprises five exons, and the open reading frame encodes the 202-amino-acid preproET-1. The sequences and structural organization of Edn1 are highly homologous to those of other species, especially in the terminal 200-bp sequence of the 3{prime}-noncoding region. Interspecific backcross mapping located Edn1 in the central region of chromosomal 13, where a mouse mutation, congenital hydrocephalus (ch), is also mapped. The highest expression of Edn1 mRNA is detected in the lung in adult mice, whereas Edn1 is predominantly expressed in the epithelium and mesenchyme of the pharyngeal arches and in the endothelium of the large arteries. Edn1 expression and ET-1 peptide levels in the lung progressively increase during the perinatal stage, whereas the expression of Edn3, a gene encoding ET-3, reciprocally decreases. These results suggest that Edn1 expression is developmentally regulated in different tissues and organs in mice in a spatial- and temporal-specific manner. 36 refs., 7 figs.

  5. Image analysis software and sample preparation demands

    Science.gov (United States)

    Roth, Karl n.; Wenzelides, Knut; Wolf, Guenter; Hufnagl, Peter

    1990-11-01

    Image analysis offers the opportunity to analyse many processes in medicine, biology and engeneering in a quantitative manner. Experience shows that it is only by awareness of preparation methods and attention to software design that full benefit can be reaped from a picture processing system in the fields of cytology and histology. Some examples of special stains for automated analysis are given here and the effectiveness of commercially available software packages is investigated. The application of picture processing and development of related special hardware and software has been increasing within the last years. As PC-based picture processing systems can be purchased at reasonable costs more and more users are confronted with these problems. Experience shows that the quality of commercially available software packages differ and the requirements on the sample preparation needed for successful problem solutions are often underestimated. But as always, sample preparation is still the key to success in automated image analysis for cells and tissues. Hence, a problem solution requires the permanent interaction between sample preparation methods and algorithm development.

  6. Bone feature analysis using image processing techniques.

    Science.gov (United States)

    Liu, Z Q; Austin, T; Thomas, C D; Clement, J G

    1996-01-01

    In order to establish the correlation between bone structure and age, and information about age-related bone changes, it is necessary to study microstructural features of human bone. Traditionally, in bone biology and forensic science, the analysis if bone cross-sections has been carried out manually. Such a process is known to be slow, inefficient and prone to human error. Consequently, the results obtained so far have been unreliable. In this paper we present a new approach to quantitative analysis of cross-sections of human bones using digital image processing techniques. We demonstrate that such a system is able to extract various bone features consistently and is capable of providing more reliable data and statistics for bones. Consequently, we will be able to correlate features of bone microstructure with age and possibly also with age related bone diseases such as osteoporosis. The development of knowledge-based computer vision-systems for automated bone image analysis can now be considered feasible.

  7. Chromosome Microarray.

    Science.gov (United States)

    Anderson, Sharon

    2016-01-01

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

  8. Genome-wide analysis of host-chromosome binding sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1

    Directory of Open Access Journals (Sweden)

    Wang Pu

    2010-10-01

    Full Text Available Abstract The Epstein-Barr Virus (EBV Nuclear Antigen 1 (EBNA1 protein is required for the establishment of EBV latent infection in proliferating B-lymphocytes. EBNA1 is a multifunctional DNA-binding protein that stimulates DNA replication at the viral origin of plasmid replication (OriP, regulates transcription of viral and cellular genes, and tethers the viral episome to the cellular chromosome. EBNA1 also provides a survival function to B-lymphocytes, potentially through its ability to alter cellular gene expression. To better understand these various functions of EBNA1, we performed a genome-wide analysis of the viral and cellular DNA sites associated with EBNA1 protein in a latently infected Burkitt lymphoma B-cell line. Chromatin-immunoprecipitation (ChIP combined with massively parallel deep-sequencing (ChIP-Seq was used to identify cellular sites bound by EBNA1. Sites identified by ChIP-Seq were validated by conventional real-time PCR, and ChIP-Seq provided quantitative, high-resolution detection of the known EBNA1 binding sites on the EBV genome at OriP and Qp. We identified at least one cluster of unusually high-affinity EBNA1 binding sites on chromosome 11, between the divergent FAM55 D and FAM55B genes. A consensus for all cellular EBNA1 binding sites is distinct from those derived from the known viral binding sites, suggesting that some of these sites are indirectly bound by EBNA1. EBNA1 also bound close to the transcriptional start sites of a large number of cellular genes, including HDAC3, CDC7, and MAP3K1, which we show are positively regulated by EBNA1. EBNA1 binding sites were enriched in some repetitive elements, especially LINE 1 retrotransposons, and had weak correlations with histone modifications and ORC binding. We conclude that EBNA1 can interact with a large number of cellular genes and chromosomal loci in latently infected cells, but that these sites are likely to represent a complex ensemble of direct and indirect EBNA

  9. Biological dosimetry of ionizing radiation by chromosomal aberration analysis; Dosimetria biologica de las radiaciones ionizantes mediante el analisis de aberraciones cromosomicas

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez-Castano, S.; Silva, A.; Navlet, J.

    1990-07-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical, and cytogenetic data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable. In this case, the study ol chromosomal aberrations, normally dicentric chromosomes, in peripheral lymphocytes can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using dicentric chromosomes analysis, X-rays at 300 kVp, 114 rad/min and temperature 37 degree celsius has been produced. Experimental data is fitted to model Y ={alpha} + {beta}{sub 1}D + {beta}{sub 2}D 2 , where Y is the number of dicentrics per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 14 refs.

  10. Analysis of image quality based on perceptual preference

    Science.gov (United States)

    Xue, Liqin; Hua, Yuning; Zhao, Guangzhou; Qi, Yaping

    2007-11-01

    This paper deals with image quality analysis considering the impact of psychological factors involved in assessment. The attributes of image quality requirement were partitioned according to the visual perception characteristics and the preference of image quality were obtained by the factor analysis method. The features of image quality which support the subjective preference were identified, The adequacy of image is evidenced to be the top requirement issues to the display image quality improvement. The approach will be beneficial to the research of the image quality subjective quantitative assessment method.

  11. 4p16.3 microdeletions and microduplications detected by chromosomal microarray analysis: New insights into mechanisms and critical regions.

    Science.gov (United States)

    Bi, Weimin; Cheung, Sau-Wai; Breman, Amy M; Bacino, Carlos A

    2016-10-01

    Deletions in the 4p16.3 region cause Wolf-Hirschhorn syndrome, a well known contiguous microdeletion syndrome with the critical region for common phenotype mapped in WHSCR2. Recently, duplications in 4p16.3 were reported in three patients with developmental delay and dysmorphic features. Through chromosomal microarray analysis, we identified 156 patients with a deletion (n = 109) or duplication (n = 47) in 4p16.3 out of approximately 60,000 patients analyzed by Baylor Miraca Genetics Laboratories. Seventy-five of the postnatally detected deletions encompassed the entire critical region, 32 (43%) of which were associated with other chromosome rearrangements, including six patients (8%) that had a duplication adjacent to the terminal deletion. Our data indicate that Wolf-Hirschhorn syndrome deletions with an adjacent duplication occur at a higher frequency than previously appreciated. Pure deletions (n = 14) or duplications (n = 15) without other copy number changes distal to or inside the WHSCR2 were identified for mapping of critical regions. Our data suggest that deletion of the segment from 0.6 to 0.9 Mb from the terminus of 4p causes a seizure phenotype and duplications of a region distal to the previously defined smallest region of overlap for 4p16.3 microduplication syndrome are associated with neurodevelopmental problems. We detected seven Wolf-Hirschhorn syndrome deletions and one 4p16.3 duplication prenatally; all of the seven are either >8 Mb in size and/or associated with large duplications. In conclusion, our study provides deeper insight into the molecular mechanisms, the critical regions and effective prenatal diagnosis for 4p16.3 deletions/ duplications. © 2016 Wiley Periodicals, Inc.

  12. New Lesions Detected by Single Nucleotide Polymorphism Array–Based Chromosomal Analysis Have Important Clinical Impact in Acute Myeloid Leukemia

    Science.gov (United States)

    Tiu, Ramon V.; Gondek, Lukasz P.; O'Keefe, Christine L.; Huh, Jungwon; Sekeres, Mikkael A.; Elson, Paul; McDevitt, Michael A.; Wang, Xiao Fei; Levis, Mark J.; Karp, Judith E.; Advani, Anjali S.; Maciejewski, Jaroslaw P.

    2009-01-01

    Purpose Cytogenetics is the primary outcome predictor in acute myeloid leukemia (AML). Metaphase cytogenetics (MC) detects an abnormal karyotype in only half of patients with AML, however. Single nucleotide polymorphism arrays (SNP-A) can detect acquired somatic uniparental disomy (UPD) and other cryptic defects, even in samples deemed normal by MC. We hypothesized that SNP-A will improve detection of chromosomal defects in AML and that this would enhance the prognostic value of MC. Patients and Methods We performed 250K and 6.0 SNP-A analyses on 140 patients with primary (p) and secondary (s) AML and correlated the results with clinical outcomes and Flt-3/nucleophosmin (NPM-1) status. Results SNP-A is more sensitive than MC in detecting unbalanced lesions (pAML, 65% v 39%, P = .002; and sAML, 78% v 51%, P = .003). Acquired somatic UPD, not detectable by MC, was common in our AML cohort (29% in pAML and 35% in sAML). Patients with SNP-A lesions including acquired somatic UPD exhibited worse overall survival (OS) and event-free survival (EFS) in pAML with normal MC and in pAML/sAML with abnormal MC. SNP-A improved the predictive value of Flt-3 internal tandem duplication/NPM-1 status, with inferior survival seen in patients with additional SNP-A defects. Multivariate analyses confirmed the independent predictive value of SNP-A defects for OS (hazard ratio [HR] = 2.52; 95% CI, 1.29 to 5.22; P = .006) and EFS (HR = 1.72; 95% CI, 1.12 to 3.48; P = .04). Conclusion SNP-A analysis allows enhanced detection of chromosomal abnormalities and provides important prognostic impact in AML. PMID:19770377

  13. Digital image analysis of palaeoenvironmental records and applications

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Environmental change signals in geological or biological records are commonly reflected on their reflecting or transmitting images. These environmental signals can be extracted through digital image analysis. The analysis principle involves section line selection, color value reading and calculating environmental proxy index along the section lines, layer identification, auto-chronology and investigation of structure evolution of growth bands. On detailed illustrations of the image technique, this note provides image analyzing procedures of coral, tree-ring and stalagmite records. The environmental implications of the proxy index from image analysis are accordingly given through application demonstration of the image technique.

  14. Etching and image analysis of the microstructure in marble

    DEFF Research Database (Denmark)

    Alm, Ditte; Brix, Susanne; Howe-Rasmussen, Helle;

    2005-01-01

    of grains exposed on that surface are measured on the microscope images using image analysis by the program Adobe Photoshop 7.0 with Image Processing Toolkit 4.0. The parameters measured by the program on microscope images of thin sections of two marble types are used for calculation of the coefficient...

  15. Retrospective analysis of fetal sex chromosome abnormalities%胎儿性染色体异常的回顾性分析

    Institute of Scientific and Technical Information of China (English)

    欧德明; 董兴盛; 江陵; 陆林苑; 王德刚

    2015-01-01

    Objective To investigate the incidence of fetal sex chromosomal abnormalities, the distribution of various sex chromosome abnormal karyotypes and the outcomes of pregnancy, in order to provide more evidences for genetic counseling. Methods The cytogenetic analysis results of 8 864 pregnant women underwent prenatal diagnosis in Zhongshan Fraternity Hospital Prenatal Diagnosis Centre during 2009~2013 were retrospectively analyzed. The results of fetal sex chromosome abnormalities and pregnancy outcomes were summarized. Results Among the 57 cases(0. 64 %) with sex chromosomal abnormalities, there were 53 cases were chromosome number abnormalities(0. 60 %), 37 cases were simple type, 16 cases were mosaicism, in which 29 cases were Turner syndrome, 4 cases were XYY syndrome, 11 cases were XXX syndrome,9 cases were XXY syndrome, and 4 cases were chromosomal structural abnormalities ( 0. 05 %) . Conclusion Invasive prenatal diagnosis has an important role for determining fetal sex chromosome abnormalities, and serological screening and B-ultrasound has an important value for fetal sex chromosome abnormalities. The pregnancy outcome and ethical issues related guidelines of fetal sex chromosomal abnormalities need to be developed.%目的 探讨胎儿性染色体异常的发生率、常见分布情况及妊娠结局,为遗传咨询提供更多信息. 方法 回顾性分析2009~2013年中山市博爱医院产前诊断中心8 864 例孕妇产前诊断的染色体检验结果,总结性染色体异常发生情况及妊娠结局. 结果 共检出性染色体异常胎儿57例(0. 64 %). 性染色体异常中,染色体数目异常53例(0. 60%),单纯型37例,嵌合型16例,其中Turner综合征29例,XYY综合征4例,XXX综合征11例,XXY综合征9例;性染色体结构异常4例( 0. 05 %). 结论 介入性产前诊断对确定胎儿性染色体异常具有重要作用. 性染色体异常胎儿的妊娠结局及伦理问题需要国家层面制定相关指南.

  16. Comparative Analysis of Various Image Fusion Techniques For Biomedical Images: A Review

    Directory of Open Access Journals (Sweden)

    Nayera Nahvi,

    2014-05-01

    Full Text Available Image Fusion is a process of combining the relevant information from a set of images, into a single image, wherein the resultant fused image will be more informative and complete than any of the input images. This paper discusses implementation of DWT technique on different images to make a fused image having more information content. As DWT is the latest technique for image fusion as compared to simple image fusion and pyramid based image fusion, so we are going to implement DWT as the image fusion technique in our paper. Other methods such as Principal Component Analysis (PCA based fusion, Intensity hue Saturation (IHS Transform based fusion and high pass filtering methods are also discussed. A new algorithm is proposed using Discrete Wavelet transform and different fusion techniques including pixel averaging, min-max and max-min methods for medical image fusion. KEYWORDS:

  17. Prevalence of chromosomal abnormalities and timing of karyotype analysis in patients with recurrent implantation failure (RIF) following assisted reproduction

    Science.gov (United States)

    De Sutter, P.; Stadhouders, R.; Dutré, M.; Gerris, J.; Dhont, M.

    2012-01-01

    Aims: To analyze the prevalence and type of karyotype abnormalities in RIF patients and to evaluate the adequate timing for analysis and the presence of possible risk factors. Methods: 615 patients (317 women and 298 men) with RIF, having undergone at least 3 sequential failed IVF/ICSI cycles prior to karyotype analysis, were included in this study. Anomaly rates found were compared with published series. Results: Chromosomal abnormalities were diagnosed in 2.1% of patients (13/615): 8 females (2.5%) and 5 males (1.7%) which is significantly higher for the females than in unselected newborns (0.8%) and normo-ovulatory women (0.6%) but lower than in women with high-order implantation failure (10.8%). No significant differences were found with couples at the start of IVF/ICSI (2.0%). Karyotyping all patients prior to IVF/ICSI results in a higher cost than selecting RIF patients. Two subgroups showed an increased prevalence of abnormalities: secondary infertile women with a history of only miscarriages (9.1%) and women with female infertility (6.0%). Conclusion: A karyotype analysis is indicated in all women with RIF. Nulliparous women with a history of miscarriage and women with documented infertility are at greater risk of CA and are to be advised to undergo karyotyping. PMID:24753890

  18. Localization, by linkage analysis, of the cystinuria type III gene to chromosome 19q13.1

    Energy Technology Data Exchange (ETDEWEB)

    Bisceglia, L.; Totaro, A.; Melchionda, S. [and others

    1997-03-01

    Cystinuria is an autosomal recessive aminoaciduria in which three urinary phenotypes (I, II, and III) have been described. An amino acid transporter gene, SLC3A1 (formerly rBAT), was found to be responsible for this disorder. Mutational and linkage analysis demonstrated the presence of genetic heterogeneity in which the SLC3A1 gene is responsible for type I cystinuria but not for type II or type III. In this study, we report the identification of the cystinuria type III locus on the long arm of chromosome 19 (19q13.1), obtained after a genomewide search. Pairwise linkage analysis in a series of type III or type II families previously excluded from linkage to the cystinuria type I locus (SLC3A1 gene) revealed a significant maximum LOD score (Z{sub max}) of 13.11 at a maximum recombination fraction ({theta}{sub max}) of .00, with marker D19S225. Multipoint linkage analysis performed with the use of additional markers from the region placed the cystinuria type III locus between D19S414 and D19S220. Preliminary data on type II families also seem to place the disease locus for this rare type of cystinuria at 19q13.1 (significant Z{sub max} = 3.11 at {theta}{sub max} of .00, with marker D19S225). 33 refs., 2 figs., 1 tab.

  19. The Scientific Image in Behavior Analysis.

    Science.gov (United States)

    Keenan, Mickey

    2016-05-01

    Throughout the history of science, the scientific image has played a significant role in communication. With recent developments in computing technology, there has been an increase in the kinds of opportunities now available for scientists to communicate in more sophisticated ways. Within behavior analysis, though, we are only just beginning to appreciate the importance of going beyond the printing press to elucidate basic principles of behavior. The aim of this manuscript is to stimulate appreciation of both the role of the scientific image and the opportunities provided by a quick response code (QR code) for enhancing the functionality of the printed page. I discuss the limitations of imagery in behavior analysis ("Introduction"), and I show examples of what can be done with animations and multimedia for teaching philosophical issues that arise when teaching about private events ("Private Events 1 and 2"). Animations are also useful for bypassing ethical issues when showing examples of challenging behavior ("Challenging Behavior"). Each of these topics can be accessed only by scanning the QR code provided. This contingency has been arranged to help the reader embrace this new technology. In so doing, I hope to show its potential for going beyond the limitations of the printing press. PMID:27606187

  20. From Pixels to Geographic Objects in Remote Sensing Image Analysis

    NARCIS (Netherlands)

    Addink, E.A.; Van Coillie, Frieke M.B.; Jong, Steven M. de

    2012-01-01

    Traditional image analysis methods are mostly pixel-based and use the spectral differences of landscape elements at the Earth surface to classify these elements or to extract element properties from the Earth Observation image. Geographic object-based image analysis (GEOBIA) has received considerabl

  1. Image analysis and platform development for automated phenotyping in cytomics

    NARCIS (Netherlands)

    Yan, Kuan

    2013-01-01

    This thesis is dedicated to the empirical study of image analysis in HT/HC screen study. Often a HT/HC screening produces extensive amounts that cannot be manually analyzed. Thus, an automated image analysis solution is prior to an objective understanding of the raw image data. Compared to general a

  2. Chromosomal instability in Streptomyces avermitilis: major deletion in the central region and stable circularized chromosome

    Directory of Open Access Journals (Sweden)

    Wen Ying

    2010-07-01

    Full Text Available Abstract Background The chromosome of Streptomyces has been shown to be unstable, frequently undergoing gross chromosomal rearrangements. However, the mechanisms underlying this phenomenon remain unclear, with previous studies focused on two chromosomal ends as targets for rearrangements. Here we investigated chromosomal instability of Streptomyces avermitilis, an important producer of avermectins, and characterized four gross chromosomal rearrangement events, including a major deletion in the central region. The present findings provide a valuable contribution to the mechanistic study of genetic instability in Streptomyces. Results Thirty randomly-selected "bald" mutants derived from the wild-type strain all contained gross chromosomal rearrangements of various types. One of the bald mutants, SA1-8, had the same linear chromosomal structure as the high avermectin-producing mutant 76-9. Chromosomes of both strains displayed at least three independent chromosomal rearrangements, including chromosomal arm replacement to form new 88-kb terminal inverted repeats (TIRs, and two major deletions. One of the deletions eliminated the 36-kb central region of the chromosome, but surprisingly did not affect viability of the cells. The other deletion (74-kb was internal to the right chromosomal arm. The chromosome of another bald mutant, SA1-6, was circularized with deletions at both ends. No obvious homology was found in all fusion sequences. Generational stability analysis showed that the chromosomal structure of SA1-8 and SA1-6 was stable. Conclusions Various chromosomal rearrangements, including chromosomal arm replacement, interstitial deletions and chromosomal circularization, occurred in S. avermitilis by non-homologous recombination. The finding of an inner deletion involving in the central region of S. avermitilis chromosome suggests that the entire Streptomyces chromosome may be the target for rearrangements, which are not limited, as previously

  3. A comparative chromosome analysis of Thai wild boar (Sus scrofa jubatus and relationship to domestic pig (S. s. domestica by conventional staining, G-banding and high-resolution technique

    Directory of Open Access Journals (Sweden)

    Pornnarong Siripiyasing

    2007-01-01

    Full Text Available This research is the first comparative chromosome analysis report of Thai wild boar (Sus scrofa jubatus and its relationship to domestic pig (S. s. domestica by conventional staining, G-banding and high-resolution technique. Blood samples of the Thai wild boar were taken from two males and two females kept in Nakhon Ratchasima Zoo. After standard whole blood lymphocyte culture at 37 oC for 72 hr. in the presence of colchicine, the metaphase spreads were performed on microscopic slides and airdried. Conventional staining, G-banding and high-resolution technique were applied to stain the chromosomes. The results showed that the number of diploid chromosomes of Thai wild boar was 2n (diploid = 38, and the fundamental numbers (NF were 62 in the male and female. The type of autosomes were 12 metacentric, 14 submetacentric, 4 acrocentric and 6 telocentric chromosomes, with X and Y chromosomes being metacentric chromosomes. We found that chromosomes 1, 5, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, X and Y had the same Gbanding and high-resolution technique patterns as those of domestic pig chromosomes. Chromosomes 2, 3, 4, 6, 9 and 15 are similar to those of domestic pig chromosomes. These results show the evolutionary relationship between the Thai wild boar and the domestic pig.

  4. Analysis of image quality metric for ROI using image restoration techniques

    Directory of Open Access Journals (Sweden)

    Syed Amma Sheik

    2014-03-01

    Full Text Available Analysis of an image plays vital role in the image processing field, which leads to the inventions of applications in the area of telemedicine, remote sensing via satellites and other spacecrafts, radar, sonar and acoustic image processing etc. This concept is a key factor in research field. One of the common image analysis is use of Region of Interest (ROI image, which is an effortless way of analyzing images. This paper proposes a method to analyze the Image Quality Metric (IQM for a ROI based color image. IQM is accomplished by the use of the three image restoration algorithms such as Blind deconvolution algorithm, Wiener Filtering algorithm and Lucy – Richardson algorithm. Keywords: Blind Deconvolution, Lucy Richardson, Point Spread Function, Region of Interest, Image Quality Metric, Wiener Filter.

  5. Chromosomal differences between European and North American Atlantic salmon discovered by linkage mapping and supported by fluorescence in situ hybridization analysis

    Directory of Open Access Journals (Sweden)

    Brenna-Hansen Silje

    2012-08-01

    Full Text Available Abstract Background Geographical isolation has generated a distinct difference between Atlantic salmon of European and North American Atlantic origin. The European Atlantic salmon generally has 29 pairs of chromosomes and 74 chromosome arms whereas it has been reported that the North American Atlantic salmon has 27 chromosome pairs and an NF of 72. In order to predict the major chromosomal rearrangements causing these differences, we constructed a dense linkage map for Atlantic salmon of North American origin and compared it with the well-developed map for European Atlantic salmon. Results The presented male and female genetic maps for the North American subspecies of Atlantic salmon, contains 3,662 SNPs located on 27 linkage groups. The total lengths of the female and male linkage maps were 2,153 cM and 968 cM respectively, with males characteristically showing recombination only at the telomeres. We compared these maps with recently published SNP maps from European Atlantic salmon, and predicted three chromosomal reorganization events that we then tested using fluorescence in situ hybridization (FISH analysis. The proposed rearrangements, which define the differences in the karyotypes of the North American Atlantic salmon relative to the European Atlantic salmon, include the translocation of the p arm of ssa01 to ssa23 and polymorphic fusions: ssa26 with ssa28, and ssa08 with ssa29. Conclusions This study identified major chromosomal differences between European and North American Atlantic salmon. However, while gross structural differences were significant, the order of genetic markers at the fine-resolution scale was remarkably conserved. This is a good indication that information from the International Cooperation to Sequence the Atlantic salmon Genome, which is sequencing a European Atlantic salmon, can be transferred to Atlantic salmon from North America.

  6. Image sequence analysis in nuclear medicine: (1) Parametric imaging using statistical modelling

    International Nuclear Information System (INIS)

    This is a review of parametric imaging methods on Nuclear Medicine. A Parametric Image is an image in which each pixel value is a function of the value of the same pixel of an image sequence. The Local Model Method is the fitting of each pixel time activity curve by a model which parameter values form the Parametric Images. The Global Model Method is the modelling of the changes between two images. It is applied to image comparison. For both methods, the different models, the identification criterion, the optimization methods and the statistical properties of the images are discussed. The analysis of one or more Parametric Images is performed using 1D or 2D histograms. The statistically significant Parametric Images, (Images of significant Variances, Amplitudes and Differences) are also proposed

  7. Using grid technologies to face medical image analysis challenges

    OpenAIRE

    Montagnat, Johan; Breton, Vincent; Magnin, Isabelle

    2003-01-01

    International audience The availability of digital imagers inside hospitals and their ever growing inspection capabilities have established digital medical images as a key component of many pathologies diagnosis, follow-up and treatment. To face the growing image analysis requirements, automated medical image processing algorithms have been developed over the two past decades. In parallel, medical image databases have been set up in health centers. Some attempts have been made to cross dat...

  8. High frequency of submicroscopic chromosomal imbalances in patients with syndromic craniosynostosis detected by a combined approach of microsatellite segregation analysis, multiplex ligation-dependent probe amplification and array-based comparative genome hybridisation.

    NARCIS (Netherlands)

    Jehee, F.S.; Krepischi-Santos, A.C.; Rocha, K.M.; Cavalcanti, D.P.; Kim, C.A.; Bertola, D.R.; Alonso, L.G.; D'Angelo, C.S.; Mazzeu, J.F.; Froyen, G.; Lugtenberg, D.; Vianna-Morgante, A.M.; Rosenberg, C.; Passos-Bueno, M.R.

    2008-01-01

    We present the first comprehensive study, to our knowledge, on genomic chromosomal analysis in syndromic craniosynostosis. In total, 45 patients with craniosynostotic disorders were screened with a variety of methods including conventional karyotype, microsatellite segregation analysis, subtelomeric

  9. Assignment of human sprouty 4 gene to chromosome segment 5q32∼33 and analysis of its pattern of expression

    Indian Academy of Sciences (India)

    Hua Liu; Jin-Zhong Chen; Shao-Hua Gu; Jian-Liang Dai; En-Pang Zhao; Lu Huang; Wang-Xiang Xu; Yi Xie; Yu-Min Mao

    2003-04-01

    The human sprouty 4 (SPYR4) gene was localized to chromosome band 5q32∼33 by screening the Stanford radiation hybrid G3 panel using a SPRY4-specific primer pair for PCR. Northern blot analysis revealed two different mRNAs (5 kb and 2 kb) in liver, skeletal muscle, heart, lung, kidney, spleen, placenta and small intestine. Reverse transcriptase-PCR analysis showed that SPYR4 was expressed in all tested tissues to different levels.

  10. Prenatal diagnosis of familial dysautonomia by analysis of linked CA-repeat polymorphisms on chromosome 9q31-q33

    Energy Technology Data Exchange (ETDEWEB)

    Eng, C.M.; Desnick, R.J. [Mount Sinai School of Medicine, New York, NY (United States); Slaugenhaupt, S.A.; Gusella, J.F. [Harvard Medical School, Boston, MA (United States)] [and others

    1995-11-20

    Familial dysautonomia (FD) is an autosomal recessive sensory neuropathy that affects about 1 in 3,700 individuals of Ashkenazi Jewish ancestry. The underlying biochemical and genetic defects are unknown, thereby precluding prenatal diagnosis in at-risk families. Recently, the FD gene (DYS) was mapped with strong linkage disequilibrium to polymorphic markers in the chromosome 9 region q31-q33. In this report, the use of these markers for the prenatal diagnosis of FD by linkage analysis in families with a previously affected child was evaluated. Genomic DNA from appropriate family members was analyzed to construct haplotypes using informative CA repeat polymorphisms closely linked to and flanking the FD locus. The calculation of risk for the prenatal diagnoses was performed by linkage analysis. All seven FD families were informative for the closely linked polymorphic markers and fetal diagnoses were made in eight pregnancies. Six fetal diagnoses were predicted with >98% accuracy, while two with recombinations were predicted with at least 88% and 92% accuracy. Use of these closely linked markers permitted the reliable prenatal diagnosis of FD in families with a previously affected child. 14 refs., 3 figs.

  11. Blind Analysis of CT Image Noise Using Residual Denoised Images

    CERN Document Server

    Roychowdhury, Sohini; Alessio, Adam

    2016-01-01

    CT protocol design and quality control would benefit from automated tools to estimate the quality of generated CT images. These tools could be used to identify erroneous CT acquisitions or refine protocols to achieve certain signal to noise characteristics. This paper investigates blind estimation methods to determine global signal strength and noise levels in chest CT images. Methods: We propose novel performance metrics corresponding to the accuracy of noise and signal estimation. We implement and evaluate the noise estimation performance of six spatial- and frequency- based methods, derived from conventional image filtering algorithms. Algorithms were tested on patient data sets from whole-body repeat CT acquisitions performed with a higher and lower dose technique over the same scan region. Results: The proposed performance metrics can evaluate the relative tradeoff of filter parameters and noise estimation performance. The proposed automated methods tend to underestimate CT image noise at low-flux levels...

  12. Blind Analysis of CT Image Noise Using Residual Denoised Images

    OpenAIRE

    Roychowdhury, Sohini; Hollraft, Nathan; Alessio, Adam

    2016-01-01

    CT protocol design and quality control would benefit from automated tools to estimate the quality of generated CT images. These tools could be used to identify erroneous CT acquisitions or refine protocols to achieve certain signal to noise characteristics. This paper investigates blind estimation methods to determine global signal strength and noise levels in chest CT images. Methods: We propose novel performance metrics corresponding to the accuracy of noise and signal estimation. We implem...

  13. Automative Multi Classifier Framework for Medical Image Analysis

    Directory of Open Access Journals (Sweden)

    R. Edbert Rajan

    2015-04-01

    Full Text Available Medical image processing is the technique used to create images of the human body for medical purposes. Nowadays, medical image processing plays a major role and a challenging solution for the critical stage in the medical line. Several researches have done in this area to enhance the techniques for medical image processing. However, due to some demerits met by some advanced technologies, there are still many aspects that need further development. Existing study evaluate the efficacy of the medical image analysis with the level-set shape along with fractal texture and intensity features to discriminate PF (Posterior Fossa tumor from other tissues in the brain image. To develop the medical image analysis and disease diagnosis, to devise an automotive subjective optimality model for segmentation of images based on different sets of selected features from the unsupervised learning model of extracted features. After segmentation, classification of images is done. The classification is processed by adapting the multiple classifier frameworks in the previous work based on the mutual information coefficient of the selected features underwent for image segmentation procedures. In this study, to enhance the classification strategy, we plan to implement enhanced multi classifier framework for the analysis of medical images and disease diagnosis. The performance parameter used for the analysis of the proposed enhanced multi classifier framework for medical image analysis is Multiple Class intensity, image quality, time consumption.

  14. Analysis of positional candidate genes in the AAA1 susceptibility locus for abdominal aortic aneurysms on chromosome 19

    Directory of Open Access Journals (Sweden)

    Ferrell Robert E

    2011-01-01

    Full Text Available Abstract Background Abdominal aortic aneurysm (AAA is a complex disorder with multiple genetic risk factors. Using affected relative pair linkage analysis, we previously identified an AAA susceptibility locus on chromosome 19q13. This locus has been designated as the AAA1 susceptibility locus in the Online Mendelian Inheritance in Man (OMIM database. Methods Nine candidate genes were selected from the AAA1 locus based on their function, as well as mRNA expression levels in the aorta. A sample of 394 cases and 419 controls was genotyped for 41 SNPs located in or around the selected nine candidate genes using the Illumina GoldenGate platform. Single marker and haplotype analyses were performed. Three genes (CEBPG, PEPD and CD22 were selected for DNA sequencing based on the association study results, and exonic regions were analyzed. Immunohistochemical staining of aortic tissue sections from AAA and control individuals was carried out for the CD22 and PEPD proteins with specific antibodies. Results Several SNPs were nominally associated with AAA (p CEBPG, peptidase D (PEPD, and CD22. Haplotype analysis found a nominally associated 5-SNP haplotype in the CEBPG/PEPD locus, as well as a nominally associated 2-SNP haplotype in the CD22 locus. DNA sequencing of the coding regions revealed no variation in CEBPG. Seven sequence variants were identified in PEPD, including three not present in the NCBI SNP (dbSNP database. Sequencing of all 14 exons of CD22 identified 20 sequence variants, five of which were in the coding region and six were in the 3'-untranslated region. Five variants were not present in dbSNP. Immunohistochemical staining for CD22 revealed protein expression in lymphocytes present in the aneurysmal aortic wall only and no detectable expression in control aorta. PEPD protein was expressed in fibroblasts and myofibroblasts in the media-adventitia border in both aneurysmal and non-aneurysmal tissue samples. Conclusions Association testing

  15. Sequencing and association analysis of the type 1 diabetes – linked region on chromosome 10p12-q11

    Directory of Open Access Journals (Sweden)

    Barratt Bryan J

    2007-05-01

    Full Text Available Abstract Background In an effort to locate susceptibility genes for type 1 diabetes (T1D several genome-wide linkage scans have been undertaken. A chromosomal region designated IDDM10 retained genome-wide significance in a combined analysis of the main linkage scans. Here, we studied sequence polymorphisms in 23 Mb on chromosome 10p12-q11, including the putative IDDM10 region, to identify genes associated with T1D. Results Initially, we resequenced the functional candidate genes, CREM and SDF1, located in this region, genotyped 13 tag single nucleotide polymorphisms (SNPs and found no association with T1D. We then undertook analysis of the whole 23 Mb region. We constructed and sequenced a contig tile path from two bacterial artificial clone libraries. By comparison with a clone library from an unrelated person used in the Human Genome Project, we identified 12,058 SNPs. We genotyped 303 SNPs and 25 polymorphic microsatellite markers in 765 multiplex T1D families and followed up 22 associated polymorphisms in up to 2,857 families. We found nominal evidence of association in six loci (P = 0.05 – 0.0026, located near the PAPD1 gene. Therefore, we resequenced 38.8 kb in this region, found 147 SNPs and genotyped 84 of them in the T1D families. We also tested 13 polymorphisms in the PAPD1 gene and in five other loci in 1,612 T1D patients and 1,828 controls from the UK. Overall, only the D10S193 microsatellite marker located 28 kb downstream of PAPD1 showed nominal evidence of association in both T1D families and in the case-control sample (P = 0.037 and 0.03, respectively. Conclusion We conclude that polymorphisms in the CREM and SDF1 genes have no major effect on T1D. The weak T1D association that we detected in the association scan near the PAPD1 gene may be either false or due to a small genuine effect, and cannot explain linkage at the IDDM10 region.

  16. MORPHOLOGICAL GRANULOMETRIC ANALYSIS OF SEDIMENT IMAGES

    Directory of Open Access Journals (Sweden)

    Yoganand Balagurunathan

    2011-05-01

    Full Text Available Sediments are routinely analyzed in terms of the sizing characteristics of the grains of which they are composed. Via sieving methods, the grains are separated and a weight-based size distribution constructed. Various moment parameters are computed from the size distribution and these serve as sediment characteristics. This paper examines the feasibility of a fully electronic granularity analysis using digital image processing. The study uses a random model of three-dimensional grains in conjunction with the morphological method of granulometric size distributions. The random model is constructed to simulate sand, silt, and clay particle distributions. Owing to the impossibility of perfectly sifting small grains so that they do not touch, the model is used in both disjoint and non-disjoint modes, and watershed segmentation is applied in the non-disjoint model. The image-based granulometric size distributions are transformed so that they take into account the necessity to view sediment fractions at different magnifications and in different frames. Gray-scale granulometric moments are then computed using both ordinary and reconstructive granulometries. The resulting moments are then compared to moments found from real grains in seven different sediments using standard weight-based size distributions.

  17. Image processing and analysis with graphs theory and practice

    CERN Document Server

    Lézoray, Olivier

    2012-01-01

    Covering the theoretical aspects of image processing and analysis through the use of graphs in the representation and analysis of objects, Image Processing and Analysis with Graphs: Theory and Practice also demonstrates how these concepts are indispensible for the design of cutting-edge solutions for real-world applications. Explores new applications in computational photography, image and video processing, computer graphics, recognition, medical and biomedical imaging With the explosive growth in image production, in everything from digital photographs to medical scans, there has been a drast

  18. Some selected quantitative methods of thermal image analysis in Matlab.

    Science.gov (United States)

    Koprowski, Robert

    2016-05-01

    The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of ​​the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image.

  19. Similarity analysis between chromosomes of Homo sapiens and monkeys with correlation coefficient, rank correlation coefficient and cosine similarity measures.

    Science.gov (United States)

    Someswara Rao, Chinta; Viswanadha Raju, S

    2016-03-01

    In this paper, we consider correlation coefficient, rank correlation coefficient and cosine similarity measures for evaluating similarity between Homo sapiens and monkeys. We used DNA chromosomes of genome wide genes to determine the correlation between the chromosomal content and evolutionary relationship. The similarity among the H. sapiens and monkeys is measured for a total of 210 chromosomes related to 10 species. The similarity measures of these different species show the relationship between the H. sapiens and monkey. This similarity will be helpful at theft identification, maternity identification, disease identification, etc. PMID:26981409

  20. Dynamic Chest Image Analysis: Model-Based Perfusion Analysis in Dynamic Pulmonary Imaging

    Science.gov (United States)

    Liang, Jianming; Järvi, Timo; Kiuru, Aaro; Kormano, Martti; Svedström, Erkki

    2003-12-01

    The "Dynamic Chest Image Analysis" project aims to develop model-based computer analysis and visualization methods for showing focal and general abnormalities of lung ventilation and perfusion based on a sequence of digital chest fluoroscopy frames collected with the dynamic pulmonary imaging technique. We have proposed and evaluated a multiresolutional method with an explicit ventilation model for ventilation analysis. This paper presents a new model-based method for pulmonary perfusion analysis. According to perfusion properties, we first devise a novel mathematical function to form a perfusion model. A simple yet accurate approach is further introduced to extract cardiac systolic and diastolic phases from the heart, so that this cardiac information may be utilized to accelerate the perfusion analysis and improve its sensitivity in detecting pulmonary perfusion abnormalities. This makes perfusion analysis not only fast but also robust in computation; consequently, perfusion analysis becomes computationally feasible without using contrast media. Our clinical case studies with 52 patients show that this technique is effective for pulmonary embolism even without using contrast media, demonstrating consistent correlations with computed tomography (CT) and nuclear medicine (NM) studies. This fluoroscopical examination takes only about 2 seconds for perfusion study with only low radiation dose to patient, involving no preparation, no radioactive isotopes, and no contrast media.

  1. Dynamic Chest Image Analysis: Model-Based Perfusion Analysis in Dynamic Pulmonary Imaging

    Directory of Open Access Journals (Sweden)

    Kiuru Aaro

    2003-01-01

    Full Text Available The "Dynamic Chest Image Analysis" project aims to develop model-based computer analysis and visualization methods for showing focal and general abnormalities of lung ventilation and perfusion based on a sequence of digital chest fluoroscopy frames collected with the dynamic pulmonary imaging technique. We have proposed and evaluated a multiresolutional method with an explicit ventilation model for ventilation analysis. This paper presents a new model-based method for pulmonary perfusion analysis. According to perfusion properties, we first devise a novel mathematical function to form a perfusion model. A simple yet accurate approach is further introduced to extract cardiac systolic and diastolic phases from the heart, so that this cardiac information may be utilized to accelerate the perfusion analysis and improve its sensitivity in detecting pulmonary perfusion abnormalities. This makes perfusion analysis not only fast but also robust in computation; consequently, perfusion analysis becomes computationally feasible without using contrast media. Our clinical case studies with 52 patients show that this technique is effective for pulmonary embolism even without using contrast media, demonstrating consistent correlations with computed tomography (CT and nuclear medicine (NM studies. This fluoroscopical examination takes only about 2 seconds for perfusion study with only low radiation dose to patient, involving no preparation, no radioactive isotopes, and no contrast media.

  2. Performance Analysis of Noise Reduction Technologies in Brain MRI Image

    Directory of Open Access Journals (Sweden)

    Sheela.V.K

    2016-02-01

    Full Text Available Rapid advancement in icon-based analysis for the treatment of diseases which are affected on internal organs of human body drives medical imaging processing into an important technique among various methods of psychoanalysis. Among all the available imaging modalities magnetic resonance imaging techniques are extensively used for the analysis and discussion of diseases in soft tissue. MRI image provides insight into the anatomical structure within the body. Accuracy of the construction of the target within the body depends upon the overall imaging process. The quality of MRI image determines the effectiveness in feature extraction, analysis, recognition and quantitative measurements. The primary factors which decrease the visibility of the structure are blurring effect and noises. This leads to the need of removal of noise from MRI images as a function of the preprocessing technique in image processing; usually noise filters are employed for this function. In this paper analyzes the operation of different noise filters.

  3. CHROMOSOMAL ABNORMALITIES IN PATIENTS WITH RECURRENT MISCARRIAGE

    Directory of Open Access Journals (Sweden)

    Daniela Mierla

    2012-06-01

    Full Text Available Chromosomal abnormalities are involved in the etiology of recurrent spontaneous pregnancy loss and sub-fertility. The purpose of this study was to determine the frequency and contribution of chromosomal abnormalities in recurrent miscarriages. The results obtained and literature review are helpful in understanding the importance of cytogenetics analysis of female infertility. To investigate the distribution of chromosomal abnormalities in the Romanian population with recurrent miscarriage, karyotype analysis by G-banding was performed from peripheral blood in 967 women infertility. Results: Chromosomal abnormalities were found to 79 women (8,17%. The percentage of chromosomal abnormalities in the studied population correlates with the data in the literature. Chromosomal abnormalities could play the important role in etiology of infertility and are more frequently detected in this group of patients compared to general population. In the infertile couples balanced chromosomal abnormalities are the main cause of spontaneous abortions.

  4. Applications of Digital Image Analysis in Experimental Mechanics

    OpenAIRE

    Lyngbye, J. : Ph.D.

    1992-01-01

    The present thesis "Application of Digital Image Analysis in Experimental Mechanics" has been prepared as a part of Janus Lyngbyes Ph.D. study during the period December 1988 to June 1992 at the Department of Building technology and Structural Engineering, University of Aalborg, Denmark. In this thesis attention will be focused on optimal use and analysis of the information of digital images. This is realized during investigation and application of parametric methods in digital image analysis...

  5. Imaging biomarkers in multiple Sclerosis: From image analysis to population imaging.

    Science.gov (United States)

    Barillot, Christian; Edan, Gilles; Commowick, Olivier

    2016-10-01

    The production of imaging data in medicine increases more rapidly than the capacity of computing models to extract information from it. The grand challenges of better understanding the brain, offering better care for neurological disorders, and stimulating new drug design will not be achieved without significant advances in computational neuroscience. The road to success is to develop a new, generic, computational methodology and to confront and validate this methodology on relevant diseases with adapted computational infrastructures. This new concept sustains the need to build new research paradigms to better understand the natural history of the pathology at the early phase; to better aggregate data that will provide the most complete representation of the pathology in order to better correlate imaging with other relevant features such as clinical, biological or genetic data. In this context, one of the major challenges of neuroimaging in clinical neurosciences is to detect quantitative signs of pathological evolution as early as possible to prevent disease progression, evaluate therapeutic protocols or even better understand and model the natural history of a given neurological pathology. Many diseases encompass brain alterations often not visible on conventional MRI sequences, especially in normal appearing brain tissues (NABT). MRI has often a low specificity for differentiating between possible pathological changes which could help in discriminating between the different pathological stages or grades. The objective of medical image analysis procedures is to define new quantitative neuroimaging biomarkers to track the evolution of the pathology at different levels. This paper illustrates this issue in one acute neuro-inflammatory pathology: Multiple Sclerosis (MS). It exhibits the current medical image analysis approaches and explains how this field of research will evolve in the next decade to integrate larger scale of information at the temporal, cellular

  6. Live imaging of X chromosome reactivation dynamics in early mouse development can discriminate naïve from primed pluripotent stem cells.

    Science.gov (United States)

    Kobayashi, Shin; Hosoi, Yusuke; Shiura, Hirosuke; Yamagata, Kazuo; Takahashi, Saori; Fujihara, Yoshitaka; Kohda, Takashi; Okabe, Masaru; Ishino, Fumitoshi

    2016-08-15

    Pluripotent stem cells can be classified into two distinct states, naïve and primed, which show different degrees of potency. One difficulty in stem cell research is the inability to distinguish these states in live cells. Studies on female mice have shown that reactivation of inactive X chromosomes occurs in the naïve state, while one of the X chromosomes is inactivated in the primed state. Therefore, we aimed to distinguish the two states by monitoring X chromosome reactivation. Thus far, X chromosome reactivation has been analysed using fixed cells; here, we inserted different fluorescent reporter gene cassettes (mCherry and eGFP) into each X chromosome. Using these knock-in 'Momiji' mice, we detected X chromosome reactivation accurately in live embryos, and confirmed that the pluripotent states of embryos were stable ex vivo, as represented by embryonic and epiblast stem cells in terms of X chromosome reactivation. Thus, Momiji mice provide a simple and accurate method for identifying stem cell status based on X chromosome reactivation.

  7. Introgression of tomato chromosomes into the potato genome: an analysis through molecular marker and in situ hybridisation techniques.

    NARCIS (Netherlands)

    Calderé, F.G.

    1998-01-01

    Transfer of alien chromosomes and genes across intergeneric boundaries can be useful not only for the introgression of desirable characters but also for fundamental genetic studies. The successful demonstration of hybridisation of potato ( Solanum tuberosum ) and tomato ( Lycopersicon esculentum ) t

  8. Meta-Analysis of Results from Quantitative Trait Loci Mapping Studies on Pig Chromosome 4

    NARCIS (Netherlands)

    Moraes Silva, De K.M.; Bastiaansen, J.W.M.; Knol, E.F.; Merks, J.W.M.; Lopes, P.S.; Guimaraes, R.M.; Arendonk, van J.A.M.

    2011-01-01

    Meta-analysis of results from multiple studies could lead to more precise quantitative trait loci (QTL) position estimates compared to the individual experiments. As the raw data from many different studies are not readily available, the use of results from published articles may be helpful. In this

  9. Cluster analysis of European Y-chromosomal STR haplotypes using the discrete Laplace method

    DEFF Research Database (Denmark)

    Andersen, Mikkel Meyer; Eriksen, Poul Svante; Morling, Niels

    2014-01-01

    method can be used for cluster analysis to further validate the discrete Laplace method. A very important practical fact is that the calculations can be performed on a normal computer. We identified two sub-clusters of the Eastern and Western European Y-STR haplotypes similar to results of previous...

  10. The promoter analysis of the human C17orf25 gene, a novel chromosome 17p13.3 gene

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The human C17orf25 gene (Accession No. AF177342) is one of thirteen genes cloned from a regiondisplaying a high score of loss of heterozygosity within chromosome 17p13.3 in human hepatocellular car-cinoma in China[1]. To unveil the underlying mechanisms for the transcription regulation of this gene andunderstand its implication to the hepatocellular carcinogenesis, we looked into the relevant aspects by bothbioinformatic and experimental executions. We found: 1, The abundant expression of the C17orf25 genewas evident in all the cell lines and tissue samples tested, showing little hepatoma-selectivity; 2, Its tran-scription starts at a single site, locating at -60 from the translation initiation codon; 3, A 58 bp fragmentcontaining the transcription start, extending from -112 to -55, represents the minimal promoter; 4, Theconsensus sequence within this fragment recognized by SP1 contributes predominantly to the activity of theminimal promoter; 5, The bioinformatic analysis suggests that the C17orf25 gene may encode a protein inthe family of the glyoxalase. Our data has provided some deep insight into both function and regulation ofthe C17orf25 gene in the context of the normal liver and hepatocellular carcinoma.

  11. [The retrospective cytogenetic dosimetry using the results of conventional chromosomal analysis in Chernobyl clean-up workers].

    Science.gov (United States)

    Maznik, N A; Vinnikov, V A

    2005-01-01

    The paper presents the results of the cohortal biodosimetry carried out in 435 Chernobyl clean-up workers, who were surveyed with the conventional cytogenetic technique in terms from several days to 10 years after the end of their duties in the Chernobyl accident exclusive zone. An empirical model of the aberrant cell dynamics was utilized for the calculation of mean initial yields of dicentrics and centric rings in groups with different terms and duration of staying in the Chernobyl zone. Corresponding protracted irradiation doses estimated from aberration levels ranged from 79 to 670 mGy. The probabilistic distribution of the radiation doses was constructed by the applying the Bayesian analysis to initial individual chromosome exchange yields extrapolated to the exposure termination moment. This distribution was characterized by the mean dose about 460 mGy and maximum of probability density in the interval of 50-300 mGy. For the late somatic risk assessment in clean-up workers the probabilistic distribution of equivalentally-acute radiation doses was proposed; that had the mean value about 270 mGy, modal classes of 250-350 mGy and 99.8% of the probability density concentrated within the dose range from 0 to 1000 mGy. PMID:16454338

  12. Molecular cloning, expression analysis and chromosomal mapping of salt-responsive cDNAs in rice ( Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    李子银; 张劲松; 陈受宜

    1999-01-01

    By using differential display PCR (DD-PCR) technique, two salt-inducible and one salt-repressed cDNA fragments were isolated from rice. The three eDNA fragments were characterized respectively as partial sequence of rice S-adenosylmethionine deearboxylase (SAMDC) gene, a new member of translation elongation factor 1A gene (named REF1A ), and a novel gene whose function is unknown (named SRG1). The full-length cDNA of SAMDC gene (named SAMDC1) was further isolated by RT-PCR approach and the deduced polypeptide was found to be homologous to SAMDC proteins of other plants, yeast and human. Northern hybridization revealed that expression of SAMDC1 and REF1A was induced, while SRG1 was dramatically repressed, by salinity stress. Southern blot analysis demonstrated that SAMDC1 and SRG1 were present as a single copy gene in rice genome, whereas rice REF1A gene was organized as a gene family. The REF1A, SAMDC1, and SRG1 genes were located on chromosome 3, 4, and 6 respectively by RFLP mapping approach using ZYQ

  13. A Comparative Analysis of B Chromosomes and Genetic Diversity in Maize (Zea mays L.) Landraces from Southwest China

    Institute of Scientific and Technical Information of China (English)

    YAO Qi-lun; YANG Ke-cheng; PAN Guang-tang; RONG Ting-zhao

    2007-01-01

    The number of B chromosomes (Bs) in 54 maize landraces from Southwest China was tested by means of cytological observations. Nine landraces with Bs were observed. A map, showing the geographic distribution of the landraces with Bs, was plotted. It was found that southeastern Sichuan Province in China was the main distribution area of the landraces with Bs in Southwest China. In order to obtain information on relationships between Bs and genetic variation, genetic diversity both among and within 11 landraces was evaluated. For each SSR marker, the number of alleles ranged from 3 to 12 with an average of 7.86, which revealed a high level of genetic diversity among maize landraces in Southwest China.Based on SSRs data, higher genetic variation was found in the landraces with 2B, and the genetic distance between the landraces with and without Bs was higher. The results together with the principal component analysis (PCA) supported the hypothesis that maize landraces in Southwest China were first introduced to the middle part of southwest Sichuan, China. At the same time, the effect of Bs on genetic variation was discussed.

  14. Potential chromosomal introgression barriers revealed by linkage analysis in a hybrid of Pinus massoniana and P. hwangshanensis

    Directory of Open Access Journals (Sweden)

    Yin Tongming

    2010-02-01

    Full Text Available Abstract Background Exploring the genetic mechanisms underlying speciation is a hot topic in modern genetics and evolutionary studies. Distortion of marker transmission ratio is frequently ascribed to selection against alleles that cause hybrid incompatibility. The natural introgression between P. massoniana and P. hwangshanensis and their distribution ranges lead to the emergence of the two species as desirable organisms to study the genetic mechanisms for speciation. Results Using seeds sampled from trees at different elevations, we consistently detected sharp decreases in seed germination rates of trees in the hybrid zone, which might be due largely to the hybrid incompatibility. A genetic map was established using 192 megagametophytes from a single tree in the hybrid zone of the two species. Segregation distortion analysis revealed that the percentage of significant-segregation-distortion (SSD markers was extremely high, accounting for more than 25% of the segregating markers. The extension range, the distortion direction, and the distortion intensity of SSD markers also varied dramatically on different linkage groups. Conclusions In this study, we display the potential chromosomal introgression barriers between P. massoniana and P. hwangshanensis. Our study provides a valuable platform for conducting genome-wide association of hybrid incompatible QTLs and/or candidate genes with marker transmission ratio distortion in the hybrid.

  15. Image pattern recognition supporting interactive analysis and graphical visualization

    Science.gov (United States)

    Coggins, James M.

    1992-01-01

    Image Pattern Recognition attempts to infer properties of the world from image data. Such capabilities are crucial for making measurements from satellite or telescope images related to Earth and space science problems. Such measurements can be the required product itself, or the measurements can be used as input to a computer graphics system for visualization purposes. At present, the field of image pattern recognition lacks a unified scientific structure for developing and evaluating image pattern recognition applications. The overall goal of this project is to begin developing such a structure. This report summarizes results of a 3-year research effort in image pattern recognition addressing the following three principal aims: (1) to create a software foundation for the research and identify image pattern recognition problems in Earth and space science; (2) to develop image measurement operations based on Artificial Visual Systems; and (3) to develop multiscale image descriptions for use in interactive image analysis.

  16. Molecular analysis of chromosome 21 in a patient with a phenotype of down syndrome and apparently normal karyotype

    Energy Technology Data Exchange (ETDEWEB)

    Ahlbom, B.E.; Wadelius, C.; Zech, L.; Anneren, G. [Uppsala Univ. (Sweden)] [and others

    1996-06-28

    Down syndrome (DS) is caused in most cases by the presence of an extra chromosome 21. It has been shown that the DS phenotype is produced by duplication of only a small part of the long arm of chromosome 21, the 21q22 region, including and distal to locus D21S55. We present molecular investigations on a woman with clinically typical DS but apparently normal chromosomes. Her parents were consanguineous and she had a sister with a DS phenotype, who died at the age of 15 days. Repeated cytogenetic investigations (G-banding and high resolution banding) on the patient and her parents showed apparently normal chromosomes. Autoradiographs of quantitative Southern blots of DNAs from the patient, her parents, trisomy 21 patients, and normal controls were analyzed after hybridization with unique DNA sequences regionally mapped on chromosome 21. Sequences D21S59, D21S1, D21S11, D21S8, D21S17, D21S55, ERG, D21S15, D21S112, and COL6A1 were all found in two copies. Fluorescent in situ hybridization with a chromosome 21-specific genomic library showed no abnormalities and only two copies of chromosome 21 were detected. Nineteen markers from the critical region studied with polymerase chain reaction amplification of di- and tetranucleotide repeats did not indicate any partial trisomy 21. From his study we conclude that the patient does not have any partial submicroscopic trisomy for any segment of chromosome 21. It seems reasonable to assume that she suffers from an autosomal recessive disorder which is phenotypically indistinguishable from DS. 23 refs., 6 figs., 3 tabs.

  17. Recent Male-Mediated Gene Flow over a Linguistic Barrier in Iberia, Suggested by Analysis of a Y-Chromosomal DNA Polymorphism

    Science.gov (United States)

    Hurles, Matthew E.; Veitia, Reiner; Arroyo, Eduardo; Armenteros, Manuel; Bertranpetit, Jaume; Pérez-Lezaun, Anna; Bosch, Elena; Shlumukova, Maria; Cambon-Thomsen, Anne; McElreavey, Ken; López de Munain, Adolfo; Röhl, Arne; Wilson, Ian J.; Singh, Lalji; Pandya, Arpita; Santos, Fabrício R.; Tyler-Smith, Chris; Jobling, Mark A.

    1999-01-01

    Summary We have examined the worldwide distribution of a Y-chromosomal base-substitution polymorphism, the T/C transition at SRY-2627, where the T allele defines haplogroup 22; sequencing of primate homologues shows that the ancestral state cannot be determined unambiguously but is probably the C allele. Of 1,191 human Y chromosomes analyzed, 33 belong to haplogroup 22. Twenty-nine come from Iberia, and the highest frequencies are in Basques (11%; n=117) and Catalans (22%; n=32). Microsatellite and minisatellite (MSY1) diversity analysis shows that non-Iberian haplogroup-22 chromosomes are not significantly different from Iberian ones. The simplest interpretation of these data is that haplogroup 22 arose in Iberia and that non-Iberian cases reflect Iberian emigrants. Several different methods were used to date the origin of the polymorphism: microsatellite data gave ages of 1,650, 2,700, 3,100, or 3,450 years, and MSY1 gave ages of 1,000, 2,300, or 2,650 years, although 95% confidence intervals on all of these figures are wide. The age of the split between Basque and Catalan haplogroup-22 chromosomes was calculated as only 20% of the age of the lineage as a whole. This study thus provides evidence for direct or indirect gene flow over the substantial linguistic barrier between the Indo-European and non–Indo-European–speaking populations of the Catalans and the Basques, during the past few thousand years. PMID:10521311

  18. Three modality image registration of brain SPECT/CT and MR images for quantitative analysis of dopamine transporter imaging

    Science.gov (United States)

    Yamaguchi, Yuzuho; Takeda, Yuta; Hara, Takeshi; Zhou, Xiangrong; Matsusako, Masaki; Tanaka, Yuki; Hosoya, Kazuhiko; Nihei, Tsutomu; Katafuchi, Tetsuro; Fujita, Hiroshi

    2016-03-01

    Important features in Parkinson's disease (PD) are degenerations and losses of dopamine neurons in corpus striatum. 123I-FP-CIT can visualize activities of the dopamine neurons. The activity radio of background to corpus striatum is used for diagnosis of PD and Dementia with Lewy Bodies (DLB). The specific activity can be observed in the corpus striatum on SPECT images, but the location and the shape of the corpus striatum on SPECT images only are often lost because of the low uptake. In contrast, MR images can visualize the locations of the corpus striatum. The purpose of this study was to realize a quantitative image analysis for the SPECT images by using image registration technique with brain MR images that can determine the region of corpus striatum. In this study, the image fusion technique was used to fuse SPECT and MR images by intervening CT image taken by SPECT/CT. The mutual information (MI) for image registration between CT and MR images was used for the registration. Six SPECT/CT and four MR scans of phantom materials are taken by changing the direction. As the results of the image registrations, 16 of 24 combinations were registered within 1.3mm. By applying the approach to 32 clinical SPECT/CT and MR cases, all of the cases were registered within 0.86mm. In conclusions, our registration method has a potential in superimposing MR images on SPECT images.

  19. Medical Image Analysis by Cognitive Information Systems - a Review.

    Science.gov (United States)

    Ogiela, Lidia; Takizawa, Makoto

    2016-10-01

    This publication presents a review of medical image analysis systems. The paradigms of cognitive information systems will be presented by examples of medical image analysis systems. The semantic processes present as it is applied to different types of medical images. Cognitive information systems were defined on the basis of methods for the semantic analysis and interpretation of information - medical images - applied to cognitive meaning of medical images contained in analyzed data sets. Semantic analysis was proposed to analyzed the meaning of data. Meaning is included in information, for example in medical images. Medical image analysis will be presented and discussed as they are applied to various types of medical images, presented selected human organs, with different pathologies. Those images were analyzed using different classes of cognitive information systems. Cognitive information systems dedicated to medical image analysis was also defined for the decision supporting tasks. This process is very important for example in diagnostic and therapy processes, in the selection of semantic aspects/features, from analyzed data sets. Those features allow to create a new way of analysis.

  20. Link Graph Analysis for Adult Images Classification

    CERN Document Server

    Kharitonov, Evgeny; Muchnik, Ilya; Romanenko, Fedor; Belyaev, Dmitry; Kotlyarov, Dmitry

    2010-01-01

    In order to protect an image search engine's users from undesirable results adult images' classifier should be built. The information about links from websites to images is employed to create such a classifier. These links are represented as a bipartite website-image graph. Each vertex is equipped with scores of adultness and decentness. The scores for image vertexes are initialized with zero, those for website vertexes are initialized according to a text-based website classifier. An iterative algorithm that propagates scores within a website-image graph is described. The scores obtained are used to classify images by choosing an appropriate threshold. The experiments on Internet-scale data have shown that the algorithm under consideration increases classification recall by 17% in comparison with a simple algorithm which classifies an image as adult if it is connected with at least one adult site (at the same precision level).

  1. Dynamic chest image analysis: model-based pulmonary perfusion analysis with pyramid images

    Science.gov (United States)

    Liang, Jianming; Haapanen, Arto; Jaervi, Timo; Kiuru, Aaro J.; Kormano, Martti; Svedstrom, Erkki; Virkki, Raimo

    1998-07-01

    The aim of the study 'Dynamic Chest Image Analysis' is to develop computer analysis and visualization methods for showing focal and general abnormalities of lung ventilation and perfusion based on a sequence of digital chest fluoroscopy frames collected at different phases of the respiratory/cardiac cycles in a short period of time. We have proposed a framework for ventilation study with an explicit ventilation model based on pyramid images. In this paper, we extend the framework to pulmonary perfusion study. A perfusion model and the truncated pyramid are introduced. The perfusion model aims at extracting accurate, geographic perfusion parameters, and the truncated pyramid helps in understanding perfusion at multiple resolutions and speeding up the convergence process in optimization. Three cases are included to illustrate the experimental results.

  2. Image Retrieval: Theoretical Analysis and Empirical User Studies on Accessing Information in Images.

    Science.gov (United States)

    Ornager, Susanne

    1997-01-01

    Discusses indexing and retrieval for effective searches of digitized images. Reports on an empirical study about criteria for analysis and indexing digitized images, and the different types of user queries done in newspaper image archives in Denmark. Concludes that it is necessary that the indexing represent both a factual and an expressional…

  3. Temporal Analysis of Image-Rivalry Suppression

    OpenAIRE

    Rishi Bhardwaj; Robert P. O'shea

    2012-01-01

    During binocular rivalry, perception alternates between two different images presented one to each eye. At any moment, one image is visible, dominant, while the other is invisible, suppressed. Alternations in perception during rivalry could involve competition between eyes, eye-rivalry, or between images, image-rivalry, or both. We measured response criteria, sensitivities, and thresholds to brief contrast increments to one of the rival stimuli in conventional rivalry displays and in a displa...

  4. Link Graph Analysis for Adult Images Classification

    OpenAIRE

    Kharitonov, E.; Slesarev, A.; Muchnik, I.; Romanenko, F.; Belyaev, D.; Kotlyarov, D.

    2010-01-01

    In order to protect an image search engine’s users from undesirable results adult images’ classifier should be built. The information about links from websites to images is employed to create such a classifier. These links are represented as a bipartite website-image graph. Each vertex is equipped with scores of adultness and decentness. The scores for image vertexes are initialized with zero, those for website vertexes are initialized according to a text-based website classifier. An iterativ...

  5. Machine learning approaches in medical image analysis

    DEFF Research Database (Denmark)

    de Bruijne, Marleen

    2016-01-01

    Machine learning approaches are increasingly successful in image-based diagnosis, disease prognosis, and risk assessment. This paper highlights new research directions and discusses three main challenges related to machine learning in medical imaging: coping with variation in imaging protocols......, learning from weak labels, and interpretation and evaluation of results....

  6. Principal component analysis of psoriasis lesions images

    DEFF Research Database (Denmark)

    Maletti, Gabriela Mariel; Ersbøll, Bjarne Kjær

    2003-01-01

    A set of RGB images of psoriasis lesions is used. By visual examination of these images, there seem to be no common pattern that could be used to find and align the lesions within and between sessions. It is expected that the principal components of the original images could be useful during future...

  7. CAPER 3.0: A Scalable Cloud-Based System for Data-Intensive Analysis of Chromosome-Centric Human Proteome Project Data Sets.

    Science.gov (United States)

    Yang, Shuai; Zhang, Xinlei; Diao, Lihong; Guo, Feifei; Wang, Dan; Liu, Zhongyang; Li, Honglei; Zheng, Junjie; Pan, Jingshan; Nice, Edouard C; Li, Dong; He, Fuchu

    2015-09-01

    The Chromosome-centric Human Proteome Project (C-HPP) aims to catalog genome-encoded proteins using a chromosome-by-chromosome strategy. As the C-HPP proceeds, the increasing requirement for data-intensive analysis of the MS/MS data poses a challenge to the proteomic community, especially small laboratories lacking computational infrastructure. To address this challenge, we have updated the previous CAPER browser into a higher version, CAPER 3.0, which is a scalable cloud-based system for data-intensive analysis of C-HPP data sets. CAPER 3.0 uses cloud computing technology to facilitate MS/MS-based peptide identification. In particular, it can use both public and private cloud, facilitating the analysis of C-HPP data sets. CAPER 3.0 provides a graphical user interface (GUI) to help users transfer data, configure jobs, track progress, and visualize the results comprehensively. These features enable users without programming expertise to easily conduct data-intensive analysis using CAPER 3.0. Here, we illustrate the usage of CAPER 3.0 with four specific mass spectral data-intensive problems: detecting novel peptides, identifying single amino acid variants (SAVs) derived from known missense mutations, identifying sample-specific SAVs, and identifying exon-skipping events. CAPER 3.0 is available at http://prodigy.bprc.ac.cn/caper3.

  8. Automatic quantitative analysis of cardiac MR perfusion images

    NARCIS (Netherlands)

    Breeuwer, Marcel; Spreeuwers, Luuk; Quist, Marcel

    2001-01-01

    Magnetic Resonance Imaging (MRI) is a powerful technique for imaging cardiovascular diseases. The introduction of cardiovascular MRI into clinical practice is however hampered by the lack of efficient and accurate image analysis methods. This paper focuses on the evaluation of blood perfusion in the

  9. Towards automatic quantitative analysis of cardiac MR perfusion images

    NARCIS (Netherlands)

    Breeuwer, M.; Quist, M.; Spreeuwers, L.J.; Paetsch, I.; Al-Saadi, N.; Nagel, E.

    2001-01-01

    Magnetic Resonance Imaging (MRI) is a powerful technique for imaging cardiovascular diseases. The introduction of cardiovascular MRI into clinical practice is however hampered by the lack of efficient and reliable automatic image analysis methods. This paper focuses on the automatic evaluation of th

  10. Mesh Processing in Medical-Image Analysis-a Tutorial

    DEFF Research Database (Denmark)

    Levine, Joshua A.; Paulsen, Rasmus Reinhold; Zhang, Yongjie

    2012-01-01

    Medical-image analysis requires an understanding of sophisticated scanning modalities, constructing geometric models, building meshes to represent domains, and downstream biological applications. These four steps form an image-to-mesh pipeline. For research in this field to progress, the imaging...

  11. Analysis of Digital Images Using Morphlogical Operations

    Directory of Open Access Journals (Sweden)

    Suresha M

    2013-03-01

    Full Text Available The main aim of this study is to transform the digital images into different forms. Image processingtechniques are used with wide varieties of applications. The requirement is different for differentapplications. This study is mainly focused on how to transform the image using mathematical morphologyso that it can be suitable for the respective applications.Mathematical morphology has been chosen to explain how images are used to illustrate mathematical settheoretic operations, suchas union, intersection by means of morphological operations like dilation anderosion.These techniques are implemented in MATLAB using image processing algorithms. MATLAB is anexcellent tool to accomplish these tasks

  12. Present Status and Prospects for Biological Dosimetry using Chromosome Aberration Analysis (invited paper)

    Energy Technology Data Exchange (ETDEWEB)

    Jin, C.Z.; Liu, X.L.; Zhang, Z.Y.; Luo, Y.S

    1998-07-01

    Biological dosimetry of radiation exposures was performed in 21 persons who received an overexposure to radiation in several radiation accidents during 1980-1996 in China. Based on the frequencies of dicentrics and rings the individual dose was estimated. Long-term follow-up studies have been carried out on five of the moderate and high dose exposed victims. The automated karyotype analysis system and the FISH technique have been established. The application of FISH for a dose-response relationship for translocations after irradiation with {sup 60}Co {gamma} rays has been performed. (author)

  13. Image analysis for dental bone quality assessment using CBCT imaging

    Science.gov (United States)

    Suprijanto; Epsilawati, L.; Hajarini, M. S.; Juliastuti, E.; Susanti, H.

    2016-03-01

    Cone beam computerized tomography (CBCT) is one of X-ray imaging modalities that are applied in dentistry. Its modality can visualize the oral region in 3D and in a high resolution. CBCT jaw image has potential information for the assessment of bone quality that often used for pre-operative implant planning. We propose comparison method based on normalized histogram (NH) on the region of inter-dental septum and premolar teeth. Furthermore, the NH characteristic from normal and abnormal bone condition are compared and analyzed. Four test parameters are proposed, i.e. the difference between teeth and bone average intensity (s), the ratio between bone and teeth average intensity (n) of NH, the difference between teeth and bone peak value (Δp) of NH, and the ratio between teeth and bone of NH range (r). The results showed that n, s, and Δp have potential to be the classification parameters of dental calcium density.

  14. Analysis of verification image using electronic portal imaging devices (EPID)

    Energy Technology Data Exchange (ETDEWEB)

    Inoue, Shinichi; Matsumoto, Mitsuhiro; Hasegawa, Hironori; Satoh, Kazuhiko; Sakurai, Kuniaki; Kawagoe, Yasumitsu; Kusumi, Yoshimi [Osaka Univ., Suita (Japan). Hospital

    1999-05-01

    We studied the evaluation of patient set-up error by verification image using electronic portal imaging devices (EPID). We analyzed which cleared 3 mm in our hospital for visual by using a distance measurement function. The body parts examined included the head and neck, thorax, pelvis and abdomen. The items that were evaluated included shell, Pb block, multi-leaf collimator and landmark. Patient set-up error was 10.4%, with that for the pelvis especially poor. The visual false rate was 17.9%. The result for the abdomen was poor because of the absence of landmark. We showed a decrease in patient set-up error by using EPID and improvement of radiotherapy. (author)

  15. CMOS Image Sensor with On-Chip Image Compression: A Review and Performance Analysis

    Directory of Open Access Journals (Sweden)

    Milin Zhang

    2010-01-01

    Full Text Available Demand for high-resolution, low-power sensing devices with integrated image processing capabilities, especially compression capability, is increasing. CMOS technology enables the integration of image sensing and image processing, making it possible to improve the overall system performance. This paper reviews the current state of the art in CMOS image sensors featuring on-chip image compression. Firstly, typical sensing systems consisting of separate image-capturing unit and image-compression processing unit are reviewed, followed by systems that integrate focal-plane compression. The paper also provides a thorough review of a new design paradigm, in which image compression is performed during the image-capture phase prior to storage, referred to as compressive acquisition. High-performance sensor systems reported in recent years are also introduced. Performance analysis and comparison of the reported designs using different design paradigm are presented at the end.

  16. Cloning of the Full-Length Rhesus Cytomegalovirus Genome as an Infectious and Self-Excisable Bacterial Artificial Chromosome for Analysis of Viral Pathogenesis

    OpenAIRE

    Chang, W. L. William; Peter A Barry

    2003-01-01

    Rigorous investigation of many functions encoded by cytomegaloviruses (CMVs) requires analysis in the context of virus-host interactions. To facilitate the construction of rhesus CMV (RhCMV) mutants for in vivo studies, a bacterial artificial chromosome (BAC) containing an enhanced green fluorescent protein (EGFP) cassette was engineered into the intergenic region between unique short 1 (US1) and US2 of the full-length viral genome by Cre/lox-mediated recombination. Infectious virions were re...

  17. Waardenburg syndrome (WS): the analysis of a single family with a WS1 mutation showing linkage to RFLP markers on human chromosome 2q.

    OpenAIRE

    Asher, J H; Morell, R; Friedman, T B

    1991-01-01

    Waardenburg syndrome type I (WS1; MIM 19350) is caused by a pleiotropic, autosomal dominant mutation with variable penetrance and expressivity. Of individuals with this mutation, 20%-25% are hearing impaired. A multilocus linkage analysis of RFLP data from a single WS1 family with 11 affected individuals indicates that the WS1 mutation in this family is linked to the following four marker loci located on the long arm of chromosome 2: ALPP (alkaline phosphatase, placental), FN1 (fibronectin 1)...

  18. Development of a two-parameter slit-scan flow cytometer for screening of normal and aberrant chromosomes: application to a karyotype of Sus scrofa domestica (pig)

    Science.gov (United States)

    Hausmann, Michael; Doelle, Juergen; Arnold, Armin; Stepanow, Boris; Wickert, Burkhard; Boscher, Jeannine; Popescu, Paul C.; Cremer, Christoph

    1992-07-01

    Laser fluorescence activated slit-scan flow cytometry offers an approach to a fast, quantitative characterization of chromosomes due to morphological features. It can be applied for screening of chromosomal abnormalities. We give a preliminary report on the development of the Heidelberg slit-scan flow cytometer. Time-resolved measurement of the fluorescence intensity along the chromosome axis can be registered simultaneously for two parameters when the chromosome axis can be registered simultaneously for two parameters when the chromosome passes perpendicularly through a narrowly focused laser beam combined by a detection slit in the image plane. So far automated data analysis has been performed off-line on a PC. In its final performance, the Heidelberg slit-scan flow cytometer will achieve on-line data analysis that allows an electro-acoustical sorting of chromosomes of interest. Interest is high in the agriculture field to study chromosome aberrations that influence the size of litters in pig (Sus scrofa domestica) breeding. Slit-scan measurements have been performed to characterize chromosomes of pigs; we present results for chromosome 1 and a translocation chromosome 6/15.

  19. Stable Chromosome Condensation Revealed by Chromosome Conformation Capture.

    Science.gov (United States)

    Eagen, Kyle P; Hartl, Tom A; Kornberg, Roger D

    2015-11-01

    Chemical cross-linking and DNA sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to 10-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes. PMID:26544940

  20. The Effects of X Chromosome Loss on Neuroanatomical and Cognitive Phenotypes During Adolescence: a Multi-modal Structural MRI and Diffusion Tensor Imaging Study.

    Science.gov (United States)

    Xie, Sheng; Zhang, Zhixin; Zhao, Qiuling; Zhang, Jiaying; Zhong, Suyu; Bi, Yanchao; He, Yong; Pan, Hui; Gong, Gaolang

    2015-09-01

    The absence of all or part of one X chromosome in female humans causes Turner's syndrome (TS), providing a unique "knockout model" to investigate the role of the X chromosome in neuroanatomy and cognition. Previous studies have demonstrated TS-associated brain differences; however, it remains largely unknown 1) how the brain structures are affected by the type of X chromosome loss and 2) how X chromosome loss influences the brain-cognition relationship. Here, we addressed these by investigating gray matter morphology and white matter connectivity using a multimodal MRI dataset from 34 adolescent TS patients (13 mosaic and 21 nonmosaic) and 21 controls. Intriguingly, the 2 TS groups exhibited significant differences in surface area in the right angular gyrus and in white matter integrity of the left tapetum of corpus callosum; these data support a link between these brain phenotypes and the type of X chromosome loss in TS. We further showed that the X chromosome modulates specific brain-cognition relationships: thickness and surface area in multiple cortical regions are positively correlated with working-memory performance in controls but negatively in TS. These findings provide novel insights into the X chromosome effect on neuroanatomical and cognitive phenotypes and highlight the role of genetic factors in brain-cognition relationships. PMID:24770708

  1. Automated analysis of protein subcellular location in time series images

    OpenAIRE

    Hu, Yanhua; Osuna-Highley, Elvira; Hua, Juchang; Nowicki, Theodore Scott; Stolz, Robert; McKayle, Camille; Murphy, Robert F.

    2010-01-01

    Motivation: Image analysis, machine learning and statistical modeling have become well established for the automatic recognition and comparison of the subcellular locations of proteins in microscope images. By using a comprehensive set of features describing static images, major subcellular patterns can be distinguished with near perfect accuracy. We now extend this work to time series images, which contain both spatial and temporal information. The goal is to use temporal features to improve...

  2. Application of the Alkaline Comet Assay and the Analysis of Structural Chromosome Aberrations in Assessment of Genetic Damage After Accidental Exposure to Ionising Radiation

    International Nuclear Information System (INIS)

    Full text: Living with the effects of low-level ionising radiation is one of the normal hazards of life. However, the effects of lower doses may not show up for years after exposure and are due to various changes in DNA molecules and chromosomes. Radiation-induced mutations seem to be brought about by the deletion of small pieces of chromosomes during the process of chromosome breakage and repair. Since chromosome damage is most likely to happen in dividing cells, ionising radiation usually cause cancer in those parts of the body where cells are actively dividing. Ionising radiation kills rapidly dividing cells, blood lymphocytes among them. People are exposed to high doses of ionising radiation when radiation accidents occur. The cytogenetical consequences of accidental exposure to gamma-radiation (radiation dose 221 mSv) were investigated by using alkaline Comet assay and the analysis of structural chromosomal aberrations (CA). Blood samples were repeatedly collected during one-year period after the accident. By using the Comet assay immediately after accidental exposure a high level of DNA damage was recorded. Although this level was decreasing over a one-year period, it was still elevated compared to normal values of DNA damage for unexposed persons. Immediately after the accident prevalence of CA (dicentrics, acentrics) over chromatid aberrations was recorded. However, one year afterwards only a few chromatid breaks were recorded. Our results confirmed usefulness of the alkaline Comet assay as a simple and sensitive technique for the biomonitoring of DNA damages, especially in the cases of accidental exposure to ionising radiation. (author)

  3. Chromosome karyotype analysis of 3 901 cases and its clinical significance%3901例外周血染色体分析及临床意义

    Institute of Scientific and Technical Information of China (English)

    王翔; 李旭; 陈葳; 杨文方; 赵明刚

    2012-01-01

    To study the abnormal detection of chromosome and the relationship between abnormal karyotype of chromosome and diseases. Methods A total of 3 901 peripheral blood samples were enrolled. Karyotype was analyzed by chromosome cultivation, G-banding in all cases and C -banding or FISH in some cases if necessary. Results There were 484 cases of abnormal karyotypes with the rate of 12.41% , among which 293 cases were males and 191 cases were females. Among cases of abnormal karyotypes, 179 cases were abnormal karyotypes of euchromosome ( 4. 59% ), 168 were abnormal karyptypes of sex chromosome ( 4. 31% ) and 137 with chromosome polymorphism ( 3.51% ). Eleven cases of balanced chromosomal translocation were identified as the first reported karyotypes in the world by State Key Laboratory of Medical Genetics. A significant association between the kinds of abnormal karyotype and clinical manifestations was found ( r = 0. 013 , P = 0. 000 ). Conclusion It is important and necessary to make chromosomal analysis for patients with abnormal pregnancy history, mental retardation and disorder of sex development.%目的 研究染色体异常检出的情况及其与疾病的关系.方法 对3 901例待检者抽取外周血,采用染色体培养、G显带、C显带,必要时行荧光原位杂交技术进行核心分析.结果 3 901例受检者中共检出染色体异常核型484例,异常检出率为12.41%,异常核型中男性293例,女性191例;异常核型中常染色体异常179例,占受检者的4.59%;性染色体异常168例,占4.31%,多态性137例,占3.51%.平衡易位核型中11例为世界首报.染色体异常检出类型与临床表现有显著性相关(r=0.013,P=0.000).结论 对不良孕产史、智力低下、性分化异常的患者进行染色体核型分析具有重要的临床意义.

  4. Association Between Gene Polymorphisms on Chromosome 1 and Susceptibility to Pre-Eclampsia: An Updated Meta-Analysis.

    Science.gov (United States)

    Zhang, Guixin; Zhao, Jinheng; Yi, Jianping; Luan, Yuanyuan; Wang, Qian

    2016-01-01

    BACKGROUND This meta-analysis enabled us to obtain a precise estimation of the association between gene polymorphisms on chromosome 1 (MTHFR, AGT, F5, IL-10, LEPR) and the susceptibility to pre-eclampsia (PE) in order to reach a uniform conclusion. MATERIAL AND METHODS Web of Science, PubMed, EMBASE, Cochran Library (CENTRAL), and Chinese databases (Chinese National Knowledge Infrastructure-CNKI and Wan Fang) were electronically searched to select relevant studies for this meta-analysis. We selected 95 case-control studies investigating 5 genes (MTHFR, AGT, F5, IL-10, and LEPR) with 8 SNPs. Odds ratios (OR) with their 95% confidence intervals (CI) were used for estimating the association. RESULTS A total of 16 646 PE patients and 28 901 normal-pregnancy patients were included in this meta-analysis. The overall results suggested that rs1801133 of MTHFR (OR=1.17, 95% CI: 1.05-1.13) and rs6025 of F5 (OR=1.53, 95%CI: 1.07-2.20) are significantly associated with PE, whereas rs1801131 of MTHFR, rs699 and rs4762 of AGT, rs1800896 and rs1800871 of IL-10, and rs1137101 of LEPR have no significant association with PE. Subgroup analysis by ethnicity revealed that, except for MTHFR rs1801133 and F5 rs6025 in Caucasians, which were significantly associated with an increased risk of PE, none of these SNPs were significantly associated with PE. As suggested by a symmetric funnel plot in conjunction with the Egger's test, there was no significant publication bias in MTHFR rs1801133 (P=0.318) and rs1801131 (P=0.204), F5 rs6025 (P=0.511), LEPR rs1137101 (P=0.511), AGT rs4762 (P=0.215) and rs699 (P=0.482), IL-10 rs1800871 (P=0.955), and rs1800896 (P=0.144). CONCLUSIONS This meta-analysis provides evidence that MTHFR rs1801133 and F5 rs6025 are associated with an increased risk of PE, especially in Caucasians. However, we do not have sufficient evidence to conclude there is a significant association between other gene polymorphisms and PE. PMID:27348238

  5. Analysis of engineering drawings and raster map images

    CERN Document Server

    Henderson, Thomas C

    2013-01-01

    Presents up-to-date methods and algorithms for the automated analysis of engineering drawings and digital cartographic maps Discusses automatic engineering drawing and map analysis techniques Covers detailed accounts of the use of unsupervised segmentation algorithms to map images

  6. Radiation-induced chromosomal instability in human mammary epithelial cells

    Science.gov (United States)

    Durante, M.; Grossi, G. F.; Yang, T. C.

    1996-01-01

    Karyotypes of human cells surviving X- and alpha-irradiation have been studied. Human mammary epithelial cells of the immortal, non-tumorigenic cell line H184B5 F5-1 M/10 were irradiated and surviving clones isolated and expanded in culture. Cytogenetic analysis was performed using dedicated software with an image analyzer. We have found that both high- and low-LET radiation induced chromosomal instability in long-term cultures, but with different characteristics. Complex chromosomal rearrangements were observed after X-rays, while chromosome loss predominated after alpha-particles. Deletions were observed in both cases. In clones derived from cells exposed to alpha-particles, some cells showed extensive chromosome breaking and double minutes. Genomic instability was correlated to delayed reproductive death and neoplastic transformation. These results indicate that chromosomal instability is a radiation-quality-dependent effect which could determine late genetic effects, and should therefore be carefully considered in the evaluation of risk for space missions.

  7. Antenna trajectory error analysis in backprojection-based SAR images

    Science.gov (United States)

    Wang, Ling; Yazıcı, Birsen; Yanik, H. Cagri

    2014-06-01

    We present an analysis of the positioning errors in Backprojection (BP)-based Synthetic Aperture Radar (SAR) images due to antenna trajectory errors for a monostatic SAR traversing a straight linear trajectory. Our analysis is developed using microlocal analysis, which can provide an explicit quantitative relationship between the trajectory error and the positioning error in BP-based SAR images. The analysis is applicable to arbitrary trajectory errors in the antenna and can be extended to arbitrary imaging geometries. We present numerical simulations to demonstrate our analysis.

  8. Dynamics of chromosome segregation in Escherichia coli

    DEFF Research Database (Denmark)

    Nielsen, Henrik Jørck

    2007-01-01

    Since the 1960’es the conformation and segregation of the chromosome in Escherichia coli has been a subject of interest for many scientists. However, after 40 years of research, we still know incredibly little about how the chromosome is organized inside the cell, how it manages to duplicate...... method enabled us to start the analysis on the distribution of various chromosomal loci inside slowly growing cells. With the actual counting and measuring no longer being any problem we could easily analyze 14 loci distributed on the E.coli chromosome. More than 15.000 cells were analyzed in total...... the new system, which is based on the pMT1 par system from Yersenia pestis, we labeled loci on opposite sides of the E.coli chromosome simultaneously and were able to show that the E.coli chromosome is organized with one chromosomal arm in each cell half. This astounding result is described in Paper III...

  9. New approaches in intelligent image analysis techniques, methodologies and applications

    CERN Document Server

    Nakamatsu, Kazumi

    2016-01-01

    This book presents an Introduction and 11 independent chapters, which are devoted to various new approaches of intelligent image processing and analysis. The book also presents new methods, algorithms and applied systems for intelligent image processing, on the following basic topics: Methods for Hierarchical Image Decomposition; Intelligent Digital Signal Processing and Feature Extraction; Data Clustering and Visualization via Echo State Networks; Clustering of Natural Images in Automatic Image Annotation Systems; Control System for Remote Sensing Image Processing; Tissue Segmentation of MR Brain Images Sequence; Kidney Cysts Segmentation in CT Images; Audio Visual Attention Models in Mobile Robots Navigation; Local Adaptive Image Processing; Learning Techniques for Intelligent Access Control; Resolution Improvement in Acoustic Maps. Each chapter is self-contained with its own references. Some of the chapters are devoted to the theoretical aspects while the others are presenting the practical aspects and the...

  10. IMAGE ANALYSIS FOR MODELLING SHEAR BEHAVIOUR

    Directory of Open Access Journals (Sweden)

    Philippe Lopez

    2011-05-01

    Full Text Available Through laboratory research performed over the past ten years, many of the critical links between fracture characteristics and hydromechanical and mechanical behaviour have been made for individual fractures. One of the remaining challenges at the laboratory scale is to directly link fracture morphology of shear behaviour with changes in stress and shear direction. A series of laboratory experiments were performed on cement mortar replicas of a granite sample with a natural fracture perpendicular to the axis of the core. Results show that there is a strong relationship between the fracture's geometry and its mechanical behaviour under shear stress and the resulting damage. Image analysis, geostatistical, stereological and directional data techniques are applied in combination to experimental data. The results highlight the role of geometric characteristics of the fracture surfaces (surface roughness, size, shape, locations and orientations of asperities to be damaged in shear behaviour. A notable improvement in shear understanding is that shear behaviour is controlled by the apparent dip in the shear direction of elementary facets forming the fracture.

  11. Automatic target recognition in SAR images using multilinear analysis

    OpenAIRE

    Porgès, Tristan; Favier, Gérard

    2011-01-01

    International audience Multilinear analysis provides a powerful mathematical framework for analyzing synthetic aperture radar (SAR) images resulting from the interaction of multiple factors like sky luminosity and viewing angles, while preserving their original shape. In this paper, we propose a multilinear principal component analysis (MPCA) algorithm for target recognition in SAR images. First, we form a high order tensor with the training image set and we apply the higher-order singular...

  12. ANALYSIS OF SST IMAGES BY WEIGHTED ENSEMBLE TRANSFORM KALMAN FILTER

    OpenAIRE

    Sai, Gorthi; Beyou, Sébastien; Memin, Etienne

    2011-01-01

    International audience This paper presents a novel, efficient scheme for the analysis of Sea Surface Temperature (SST) ocean images. We consider the estimation of the velocity fields and vorticity values from a sequence of oceanic images. The contribution of this paper lies in proposing a novel, robust and simple approach based onWeighted Ensemble Transform Kalman filter (WETKF) data assimilation technique for the analysis of real SST images, that may contain coast regions or large areas o...

  13. Facial Image Analysis Based on Local Binary Patterns: A Survey

    NARCIS (Netherlands)

    Huang, D.; Shan, C.; Ardebilian, M.; Chen, L.

    2011-01-01

    Facial image analysis, including face detection, face recognition,facial expression analysis, facial demographic classification, and so on, is an important and interesting research topic in the computervision and image processing area, which has many important applications such as human-computer

  14. Chromosomal variations in the primate Alouatta seniculus seniculus.

    Science.gov (United States)

    Yunis, E J; Torres de Caballero, O M; Ramírez, C; Ramírez, Z E

    1976-01-01

    Chromosome analysis in 23 specimens of Alouatta s. seniculus trapped in different localities of Colombia were examined with the C- and Q-banding techniques. The chromosome numbers (2n=44) showed variations from 2n = 43 to 2n = 45 involving three and five microchromosomes, respectively. Two specimens also showed a structural chromosome variation involving a pericentric inversion of the chromosome No. 13. Chromosome measurements revealed an X chromosome with a value significantly smaller to that established for the standard mammalian X chromosome. PMID:817992

  15. Dynamic infrared imaging in identification of breast cancer tissue with combined image processing and frequency analysis.

    Science.gov (United States)

    Joro, R; Lääperi, A-L; Soimakallio, S; Järvenpää, R; Kuukasjärvi, T; Toivonen, T; Saaristo, R; Dastidar, P

    2008-01-01

    Five combinations of image-processing algorithms were applied to dynamic infrared (IR) images of six breast cancer patients preoperatively to establish optimal enhancement of cancer tissue before frequency analysis. mid-wave photovoltaic (PV) IR cameras with 320x254 and 640x512 pixels were used. The signal-to-noise ratio and the specificity for breast cancer were evaluated with the image-processing combinations from the image series of each patient. Before image processing and frequency analysis the effect of patient movement was minimized with a stabilization program developed and tested in the study by stabilizing image slices using surface markers set as measurement points on the skin of the imaged breast. A mathematical equation for superiority value was developed for comparison of the key ratios of the image-processing combinations. The ability of each combination to locate the mammography finding of breast cancer in each patient was compared. Our results show that data collected with a 640x512-pixel mid-wave PV camera applying image-processing methods optimizing signal-to-noise ratio, morphological image processing and linear image restoration before frequency analysis possess the greatest superiority value, showing the cancer area most clearly also in the match centre of the mammography estimation. PMID:18666012

  16. Multimodal digital color imaging system for facial skin lesion analysis

    Science.gov (United States)

    Bae, Youngwoo; Lee, Youn-Heum; Jung, Byungjo

    2008-02-01

    In dermatology, various digital imaging modalities have been used as an important tool to quantitatively evaluate the treatment effect of skin lesions. Cross-polarization color image was used to evaluate skin chromophores (melanin and hemoglobin) information and parallel-polarization image to evaluate skin texture information. In addition, UV-A induced fluorescent image has been widely used to evaluate various skin conditions such as sebum, keratosis, sun damages, and vitiligo. In order to maximize the evaluation efficacy of various skin lesions, it is necessary to integrate various imaging modalities into an imaging system. In this study, we propose a multimodal digital color imaging system, which provides four different digital color images of standard color image, parallel and cross-polarization color image, and UV-A induced fluorescent color image. Herein, we describe the imaging system and present the examples of image analysis. By analyzing the color information and morphological features of facial skin lesions, we are able to comparably and simultaneously evaluate various skin lesions. In conclusion, we are sure that the multimodal color imaging system can be utilized as an important assistant tool in dermatology.

  17. Identification and Phylogenetic Analysis of a CC-NBS-LRR Encoding Gene Assigned on Chromosome 7B of Wheat

    Directory of Open Access Journals (Sweden)

    Xiangqi Zhang

    2013-07-01

    Full Text Available Hexaploid wheat displays limited genetic variation. As a direct A and B genome donor of hexaploid wheat, tetraploid wheat represents an important gene pool for cultivated bread wheat. Many disease resistant genes express conserved domains of the nucleotide-binding site and leucine-rich repeats (NBS-LRR. In this study, we isolated a CC-NBS-LRR gene locating on chromosome 7B from durum wheat variety Italy 363, and designated it TdRGA-7Ba. Its open reading frame was 4014 bp, encoding a 1337 amino acid protein with a complete NBS domain and 18 LRR repeats, sharing 44.7% identity with the PM3B protein. TdRGA-7Ba expression was continuously seen at low levels and was highest in leaves. TdRGA-7Ba has another allele TdRGA-7Bb with a 4 bp deletion at position +1892 in other cultivars of tetraploid wheat. In Ae. speltoides, as a B genome progenitor, both TdRGA-7Ba and TdRGA-7Bb were detected. In all six species of hexaploid wheats (AABBDD, only TdRGA-7Bb existed. Phylogenic analysis showed that all TdRGA-7Bb type genes were grouped in one sub-branch. We speculate that TdRGA-7Bb was derived from a TdRGA-7Ba mutation, and it happened in Ae. speltoides. Both types of TdRGA-7B participated in tetraploid wheat formation. However, only the TdRGA-7Bb was retained in hexaploid wheat.

  18. Analysis of 24 Y chromosomal STR haplotypes in a Chinese Han population sample from Henan Province, Central China.

    Science.gov (United States)

    Shi, Meisen; Liu, Yaju; Zhang, Juntao; Bai, Rufeng; Lv, Xiaojiao; Ma, Shuhua

    2015-07-01

    We analyzed haplotypes for 24 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) and 7 additional STRs (DYS388, DYS444, DYS447, DYS449, DYS522 and DYS527a/b) in 1100 unrelated Chinese Han individuals from Henan Province using AGCU Y24 STR kit systems. The calculated average gene diversity (GD) values ranged from 0.4105 to 0.9647 for the DYS388 and DYS385a/b loci, respectively. The discriminatory capacity (DC) was 72.91% with 802 observed haplotypes using 17 Yfiler loci, by the addition of 7 Y-STRs to the Yfiler system, the DC was increased to 79.09% while showing 870 observed haplotypes. Among the additional 7 Y-STRs, DYS449, DYS527a/b, DYS444 and DYS522 were major contributors to enhancing discrimination. In the analysis of molecular variance, the Henan Han population clustered with Han origin populations and showed significant differences from other Non-Han populations. In the present study, we report 24 Y-STR population data in Henan Han population, and we emphasize the need for adding additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory capacity in a population with low genetic diversity. PMID:25864156

  19. BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in upland cotton.

    Directory of Open Access Journals (Sweden)

    Ramesh Buyyarapu

    Full Text Available Although new and emerging next-generation sequencing (NGS technologies have reduced sequencing costs significantly, much work remains to implement them for de novo sequencing of complex and highly repetitive genomes such as the tetraploid genome of Upland cotton (Gossypium hirsutum L.. Herein we report the results from implementing a novel, hybrid Sanger/454-based BAC-pool sequencing strategy using minimum tiling path (MTP BACs from Ctg-3301 and Ctg-465, two large genomic segments in A12 and D12 homoeologous chromosomes (Ctg. To enable generation of longer contig sequences in assembly, we implemented a hybrid assembly method to process ~35x data from 454 technology and 2.8-3x data from Sanger method. Hybrid assemblies offered higher sequence coverage and better sequence assemblies. Homology studies revealed the presence of retrotransposon regions like Copia and Gypsy elements in these contigs and also helped in identifying new genomic SSRs. Unigenes were anchored to the sequences in Ctg-3301 and Ctg-465 to support the physical map. Gene density, gene structure and protein sequence information derived from protein prediction programs were used to obtain the functional annotation of these genes. Comparative analysis of both contigs with Arabidopsis genome exhibited synteny and microcollinearity with a conserved gene order in both genomes. This study provides insight about use of MTP-based BAC-pool sequencing approach for sequencing complex polyploid genomes with limited constraints in generating better sequence assemblies to build reference scaffold sequences. Combining the utilities of MTP-based BAC-pool sequencing with current longer and short read NGS technologies in multiplexed format would provide a new direction to cost-effectively and precisely sequence complex plant genomes.

  20. PIZZARO: Forensic analysis and restoration of image and video data.

    Science.gov (United States)

    Kamenicky, Jan; Bartos, Michal; Flusser, Jan; Mahdian, Babak; Kotera, Jan; Novozamsky, Adam; Saic, Stanislav; Sroubek, Filip; Sorel, Michal; Zita, Ales; Zitova, Barbara; Sima, Zdenek; Svarc, Petr; Horinek, Jan

    2016-07-01

    This paper introduces a set of methods for image and video forensic analysis. They were designed to help to assess image and video credibility and origin and to restore and increase image quality by diminishing unwanted blur, noise, and other possible artifacts. The motivation came from the best practices used in the criminal investigation utilizing images and/or videos. The determination of the image source, the verification of the image content, and image restoration were identified as the most important issues of which automation can facilitate criminalists work. Novel theoretical results complemented with existing approaches (LCD re-capture detection and denoising) were implemented in the PIZZARO software tool, which consists of the image processing functionality as well as of reporting and archiving functions to ensure the repeatability of image analysis procedures and thus fulfills formal aspects of the image/video analysis work. Comparison of new proposed methods with the state of the art approaches is shown. Real use cases are presented, which illustrate the functionality of the developed methods and demonstrate their applicability in different situations. The use cases as well as the method design were solved in tight cooperation of scientists from the Institute of Criminalistics, National Drug Headquarters of the Criminal Police and Investigation Service of the Police of the Czech Republic, and image processing experts from the Czech Academy of Sciences.

  1. PIZZARO: Forensic analysis and restoration of image and video data.

    Science.gov (United States)

    Kamenicky, Jan; Bartos, Michal; Flusser, Jan; Mahdian, Babak; Kotera, Jan; Novozamsky, Adam; Saic, Stanislav; Sroubek, Filip; Sorel, Michal; Zita, Ales; Zitova, Barbara; Sima, Zdenek; Svarc, Petr; Horinek, Jan

    2016-07-01

    This paper introduces a set of methods for image and video forensic analysis. They were designed to help to assess image and video credibility and origin and to restore and increase image quality by diminishing unwanted blur, noise, and other possible artifacts. The motivation came from the best practices used in the criminal investigation utilizing images and/or videos. The determination of the image source, the verification of the image content, and image restoration were identified as the most important issues of which automation can facilitate criminalists work. Novel theoretical results complemented with existing approaches (LCD re-capture detection and denoising) were implemented in the PIZZARO software tool, which consists of the image processing functionality as well as of reporting and archiving functions to ensure the repeatability of image analysis procedures and thus fulfills formal aspects of the image/video analysis work. Comparison of new proposed methods with the state of the art approaches is shown. Real use cases are presented, which illustrate the functionality of the developed methods and demonstrate their applicability in different situations. The use cases as well as the method design were solved in tight cooperation of scientists from the Institute of Criminalistics, National Drug Headquarters of the Criminal Police and Investigation Service of the Police of the Czech Republic, and image processing experts from the Czech Academy of Sciences. PMID:27182830

  2. An application of image processing techniques in computed tomography image analysis

    DEFF Research Database (Denmark)

    McEvoy, Fintan

    2007-01-01

    An estimate of the thickness of subcutaneous adipose tissue at differing positions around the body was required in a study examining body composition. To eliminate human error associated with the manual placement of markers for measurements and to facilitate the collection of data from a large...... number of animals and image slices, automation of the process was desirable. The open-source and free image analysis program ImageJ was used. A macro procedure was created that provided the required functionality. The macro performs a number of basic image processing procedures. These include an initial...... process designed to remove the scanning table from the image and to center the animal in the image. This is followed by placement of a vertical line segment from the mid point of the upper border of the image to the image center. Measurements are made between automatically detected outer and inner...

  3. On Texture and Geometry in Image Analysis

    DEFF Research Database (Denmark)

    Gustafsson, David Karl John

    2009-01-01

    -out of the captured scene will also change. At large viewing distances, the sky occupies a large region in the image and buildings, trees and lawns appear as uniformly colored regions. The following questions are addressed: How much of the visual appearance in terms of geometry and texture of an image can...

  4. Construction and analysis of an hn-cDNA library derived from the p-arm of pig chromosome 12.

    Science.gov (United States)

    Anderson Dear, D V; Miller, J R

    1996-09-01

    Our aim is to find unidentified genes on specific pig chromosomes or chromosome fragments. Our approach has involved the construction of a heterogeneous nuclear complementary (hn-c) DNA library of the p-arm of pig Chromosome (Chr) 12, the only pig chromosome present in the pig x hamster hybrid cell line 8990. Total RNA was extracted from the cells and first-strand synthesis of hn-cDNA carried out with random and oligo dT primers. Pig hn-cDNA was isolated by amplification of first-strand synthesized hn-cDNA with primers specific for Short Interspersed Repeat Elements (SINEs) via the polymerase chain reaction (PCR). Hn-cDNAs were size selected and cloned in E. coli XL-1 blue cells with PCR-Script as the vector. The library consisted of 6000 clones. Clone inserts were amplified by PCR with vector-specific primers, and randomly picked inserts greater than 600 bp were sequenced. Homology searches were carried out with the FASTA search program on the GenEmbl database. Thirty clones were sequenced, and of these three showed strong homologies to GenEmbl sequences: (1) to sheep, mouse, human, and rat mammary gland factor (MGF); (2) to MLN-50, a gene that is amplified in human familial breast cancer and is present on human Chr 17; the latter is homologous to pig chromosome 12; (3) to a family of unassigned overlapping human ESTs. Of the other sequenced clones, seven were over 80% homologous with pig SINE sequences; three were over 75% homologous to human LINE sequences; six displayed open reading frames over a mean distance equivalent to 50 amino acids, although these showed no significant similarities with sequences in the databases. Using this approach, we have been able to identify several new genes on the p-arm of pig Chr 12. This is the first report of gene isolation from a library derived from a pig chromosome fragment. PMID:8703117

  5. Cytogenetic analysis and chromosomal characteristics of the polymorphic 18S rDNA of Haliotis discus hannai from Fujian, China.

    Science.gov (United States)

    Wang, Haishan; Luo, Xuan; You, Weiwei; Dong, Yunwei; Ke, Caihuan

    2015-01-01

    We report on novel chromosomal characteristics of Haliotis discus hannai from a breeding population at Fujian, China. The karyotypes of H. discus hannai we obtained from an abalone farm include a common type 2n = 36 = 10M + 8SM (82%) and two rare types 2n = 36 = 11M + 7SM (14%) and 2n = 36 = 10M + 7SM + 1ST (4%). The results of silver staining showed that the NORs of H. discus hannai were usually located terminally on the long arms of chromosome pairs 14 and 17, NORs were also sometimes located terminally on the short arms of other chromosomes, either metacentric or submetacentric pairs. The number of Ag-nucleoli ranged from 2 to 8, and the mean number was 3.61 ± 0.93. Among the scored interphase cells, 41% had 3 detectable nucleoli and 37% had 4 nucleoli. The 18S rDNA FISH result is the first report of the location of 18S rDNA genes in H. discus hannai. The 18S rDNA locations were highly polymorphic in this species. Copies of the gene were observed in the terminal of long or/and short arms of submetacentric or/and metacentric chromosomes. Using FISH with probe for vertebrate-like telomeric sequences (CCCTAA)3 displayed positive green FITC signals at telomere regions of all analyzed chromosome types. We found about 7% of chromosomes had breaks in prophase. A special form of nucleolus not previously described from H. discus hannai was observed in some interphase cells. It consists of many small silver-stained nucleoli gathered together to form a larger nucleolus and may correspond to prenucleolar bodies.

  6. Cytogenetic analysis and chromosomal characteristics of the polymorphic 18S rDNA of Haliotis discus hannai from Fujian, China.

    Directory of Open Access Journals (Sweden)

    Haishan Wang

    Full Text Available We report on novel chromosomal characteristics of Haliotis discus hannai from a breeding population at Fujian, China. The karyotypes of H. discus hannai we obtained from an abalone farm include a common type 2n = 36 = 10M + 8SM (82% and two rare types 2n = 36 = 11M + 7SM (14% and 2n = 36 = 10M + 7SM + 1ST (4%. The results of silver staining showed that the NORs of H. discus hannai were usually located terminally on the long arms of chromosome pairs 14 and 17, NORs were also sometimes located terminally on the short arms of other chromosomes, either metacentric or submetacentric pairs. The number of Ag-nucleoli ranged from 2 to 8, and the mean number was 3.61 ± 0.93. Among the scored interphase cells, 41% had 3 detectable nucleoli and 37% had 4 nucleoli. The 18S rDNA FISH result is the first report of the location of 18S rDNA genes in H. discus hannai. The 18S rDNA locations were highly polymorphic in this species. Copies of the gene were observed in the terminal of long or/and short arms of submetacentric or/and metacentric chromosomes. Using FISH with probe for vertebrate-like telomeric sequences (CCCTAA3 displayed positive green FITC signals at telomere regions of all analyzed chromosome types. We found about 7% of chromosomes had breaks in prophase. A special form of nucleolus not previously described from H. discus hannai was observed in some interphase cells. It consists of many small silver-stained nucleoli gathered together to form a larger nucleolus and may correspond to prenucleolar bodies.

  7. Fine genetic mapping of the Batten disease locus (CLN3) by haplotype analysis and demonstration of allelic association with chromosome 16p microsatellite loci

    Energy Technology Data Exchange (ETDEWEB)

    Mitchison, H.M.; McKay, T.R. [Univ. College London Medical School (United Kingdom); Thompson, A.D.; Mulley, J.C.; Kozman, H.M.; Richards, R.I.; Callen, D.F. [Women and Children`s Hospital, Adelaide (Australia); Stallings, R.L.; Doggett, N.A. [Los Alamos National Lab., NM (United States); Attwood, J. [Galton Lab., London (United Kingdom)] [and others

    1993-05-01

    Batten disease, juvenile onset neuronal ceroid lipofuscinosis, is an autosomal recessive neurodegenerative disorder characterized by accumulation of autofluorescent lipopigment in neurons and other cell types. The disease locus (CLN3) has previously been assigned to chromosome 16p. The genetic localization of CLN3 has been refined by analyzing 70 families using a high-resolution map of 15 marker loci encompassing the CLN3 region on 16p. Crossovers in three maternal meioses allowed localization of CLN3 to the interval between D16S297 and D16S57. Within that interval alleles at three highly polymorphic dinucleotide repeat loci (D16S288, D16S298, D16S299) were found to be in strong linkage disequilibrium with CLN3. Analysis of haplotypes suggests that a majority of CLN3 chromosomes have arisen from a single founder mutation. 15 refs., 2 figs., 5 tabs.

  8. Interpretation of medical images by model guided analysis

    International Nuclear Information System (INIS)

    Progress in the development of digital pictorial information systems stimulates a growing interest in the use of image analysis techniques in medicine. Especially when precise quantitative information is required the use of fast and reproducable computer analysis may be more appropriate than relying on visual judgement only. Such quantitative information can be valuable, for instance, in diagnostics or in irradiation therapy planning. As medical images are mostly recorded in a prescribed way, human anatomy guarantees a common image structure for each particular type of exam. In this thesis it is investigated how to make use of this a priori knowledge to guide image analysis. For that purpose models are developed which are suited to capture common image structure. The first part of this study is devoted to an analysis of nuclear medicine images of myocardial perfusion. In ch. 2 a model of these images is designed in order to represent characteristic image properties. It is shown that for these relatively simple images a compact symbolic description can be achieved, without significant loss of diagnostically importance of several image properties. Possibilities for automatic interpretation of more complex images is investigated in the following chapters. The central topic is segmentation of organs. Two methods are proposed and tested on a set of abdominal X-ray CT scans. Ch. 3 describes a serial approach based on a semantic network and the use of search areas. Relational constraints are used to guide the image processing and to classify detected image segments. In teh ch.'s 4 and 5 a more general parallel approach is utilized, based on a markov random field image model. A stochastic model used to represent prior knowledge about the spatial arrangement of organs is implemented as an external field. (author). 66 refs.; 27 figs.; 6 tabs

  9. Angelman syndrome: Validation of molecular cytogenetic analysis of chromosome 15q11-q13 for deletion detection

    Energy Technology Data Exchange (ETDEWEB)

    White, L.; Knoll, J.H.M. [Harvard Medical School, Boston, MA (United States)

    1995-03-13

    In a series of 18 individuals comprising parents of Angelman syndrome (AS) patients and AS patients with large deletions, microdeletions, and no deletions, we utilized fluorescence in situ hybridization (FISH) with genomic phage clones for loci D15S63 and GABRB3 for deletion detection of chromosome 15q11-q13. Utilization of probes at these loci allows detection of common large deletions and permits discrimination of less common small deletions. In all individuals the molecular cytogenetic data were concordant with the DNA deletion analyses. FISH provides an accurate method of deletion detection for chromosome 15q11-q13. 23 refs., 2 figs., 1 tab.

  10. Analysis of Pregerminated Barley Using Hyperspectral Image Analysis

    DEFF Research Database (Denmark)

    Arngren, Morten; Hansen, Per Waaben; Eriksen, Birger;

    2011-01-01

    imaging system in a mathematical modeling framework to identify pregerminated barley at an early stage of approximately 12 h of pregermination. Our model only assigns pregermination as the cause for a single kernel’s lack of germination and is unable to identify dormancy, kernel damage etc. The analysis...... is based on more than 750 Rosalina barley kernels being pregerminated at 8 different durations between 0 and 60 h based on the BRF method. Regerminating the kernels reveals a grouping of the pregerminated kernels into three categories: normal, delayed and limited germination. Our model employs a supervised...... classification framework based on a set of extracted features insensitive to the kernel orientation. An out-of-sample classification error of 32% (CI95%: 29–35%) is obtained for single kernels when grouped into the three categories, and an error of 3% (CI95%: 0–15%) is achieved on a bulk kernel level. The model...

  11. Methods for processing and analysis functional and anatomical brain images: computerized tomography, emission tomography and nuclear resonance imaging

    International Nuclear Information System (INIS)

    The various methods for brain image processing and analysis are presented and compared. The following topics are developed: the physical basis of brain image comparison (nature and formation of signals intrinsic performance of the methods image characteristics); mathematical methods for image processing and analysis (filtering, functional parameter extraction, morphological analysis, robotics and artificial intelligence); methods for anatomical localization (neuro-anatomy atlas, proportional stereotaxic atlas, numerized atlas); methodology of cerebral image superposition (normalization, retiming); image networks

  12. Meiosis and chromosome painting of sex chromosome systems in Ceboidea.

    Science.gov (United States)

    Mudry, M D; Rahn, I M; Solari, A J

    2001-06-01

    The identity of the chromosomes involved in the multiple sex system of Alouatta caraya (Aca) and the possible distribution of this system among other Ceboidea were investigated by chromosome painting of mitotic cells from five species and by analysis of meiosis at pachytene in two species. The identity of the autosome #7 (X2) involved in the multiple system of Aca and its breakage points were demonstrated by both meiosis and chromosome painting. These features are identical to those described by Consigliere et al. [1996] in Alouatta seniculus sara (Assa) and Alouatta seniculus arctoidea (Asar). This multiple system was absent in the other four Ceboidea species studied here. However, data from the literature strongly suggest the presence of this multiple in other members of this genus. The presence of this multiple system among several species and subspecies that show high levels of chromosome rearrangements may suggest a special selective value of this multiple. The meiotic features of the sex systems of Aca and Cebus apella paraguayanus (Cap) are strikingly different at pachytene, as the latter system is similar to the sex pair of man and other primates. The relatively large genetic distances between species presently showing this multiple system suggest that its origin is not recent. Other members of the same genus should be investigated at meiosis and by chromosome painting in order to know the extent and distribution of this complex sex-chromosome system. PMID:11376445

  13. Analysis of Factors Affecting Positron Emission Mammography (PEM) Image Formation

    International Nuclear Information System (INIS)

    Image reconstruction for positron emission mammography (PEM) with the breast positioned between two parallel, planar detectors is usually performed by backprojection to image planes. Three important factors affecting PEM image reconstruction by backprojection are investigated: (1) image uniformity (flood) corrections, (2) image sampling (pixel size) and (3) count allocation methods. An analytic expression for uniformity correction is developed that incorporates factors for spatial-dependent detector sensitivity and geometric effects from acceptance angle limits on coincidence events. There is good agreement between experimental floods from a PEM system with a pixellated detector and numerical simulations. The analytic uniformity corrections are successfully applied to image reconstruction of compressed breast phantoms and reduce the necessity for flood scans at different image planes. Experimental and simulated compressed breast phantom studies show that lesion contrast is improved when the image pixel size is half of, rather than equal to, the detector pixel size, though this occurs at the expense of some additional image noise. In PEM reconstruction counts usually are allocated to the pixel in the image plane intersected by the line of response (LOR) between the centers of the detection pixels. An alternate count allocation method is investigated that distributes counts to image pixels in proportion to the area of the tube of response (TOR) connecting the detection pixels that they overlay in the image plane. This TOR method eliminates some image artifacts that occur with the LOR method and increases tumor signal-to-noise ratios at the expense of a slight decrease in tumor contrast. Analysis of image uniformity, image sampling and count allocation methods in PEM image reconstruction points to ways of improving image formation. Further work is required to optimize image reconstruction parameters for particular detection or quantitation tasks

  14. Multivariate image analysis for quality inspection in fish feed production

    DEFF Research Database (Denmark)

    Ljungqvist, Martin Georg

    . The colour appearance of fish products is important for customers. Salmonid fish get their red colour from a natural pigment called astaxanthin. To ensure a similar red colour of fish in aquaculture astaxanthin is used as an additive coated on the feed pellets. Astaxanthin can either be of natural origin...... are: pellet size, type and concentration level of astaxanthin in pellet coating, as well as astaxanthin type detected in salmonid fish. Methods used are three different devices for multi- and hyper-spectral imaging, together with shape analysis and multi-variate statistical analysis. The results...... of the work demonstrate a high potential of image analysis and spectral imaging for assessing the product quality of fish feed pellets, astaxanthin and fish meat. We show how image analysis can be used to inspect the pellet size, and how spectral imaging can be used to inspect the surface quality...

  15. Quantitative methods for the analysis of electron microscope images

    DEFF Research Database (Denmark)

    Skands, Peter Ulrik Vallø

    1996-01-01

    The topic of this thesis is an general introduction to quantitative methods for the analysis of digital microscope images. The images presented are primarily been acquired from Scanning Electron Microscopes (SEM) and interfermeter microscopes (IFM). The topic is approached though several examples...... foundation of the thesis fall in the areas of: 1) Mathematical Morphology; 2) Distance transforms and applications; and 3) Fractal geometry. Image analysis opens in general the possibility of a quantitative and statistical well founded measurement of digital microscope images. Herein lies also the conditions...

  16. Theoretical analysis of radiographic images by nonstationary Poisson processes

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, K.; Uchida, S. (Gifu Univ. (Japan)); Yamada, I.

    1980-12-01

    This paper deals with the noise analysis of radiographic images obtained in the usual fluorescent screen-film system. The theory of nonstationary Poisson processes is applied to the analysis of the radiographic images containing the object information. The ensemble averages, the autocorrelation functions, and the Wiener spectrum densities of the light-energy distribution at the fluorescent screen and of the film optical-density distribution are obtained. The detection characteristics of the system are evaluated theoretically. Numerical examples one-dimensional image are shown and the results are compared with those obtained under the assumption that the object image is related to the background noise by the additive process.

  17. Theoretical Analysis of Radiographic Images by Nonstationary Poisson Processes

    Science.gov (United States)

    Tanaka, Kazuo; Yamada, Isao; Uchida, Suguru

    1980-12-01

    This paper deals with the noise analysis of radiographic images obtained in the usual fluorescent screen-film system. The theory of nonstationary Poisson processes is applied to the analysis of the radiographic images containing the object information. The ensemble averages, the autocorrelation functions, and the Wiener spectrum densities of the light-energy distribution at the fluorescent screen and of the film optical-density distribution are obtained. The detection characteristics of the system are evaluated theoretically. Numerical examples of the one-dimensional image are shown and the results are compared with those obtained under the assumption that the object image is related to the background noise by the additive process.

  18. IMAGE ANALYSIS BASED ON EDGE DETECTION TECHNIQUES

    Institute of Scientific and Technical Information of China (English)

    纳瑟; 刘重庆

    2002-01-01

    A method that incorporates edge detection technique, Markov Random field (MRF), watershed segmentation and merging techniques was presented for performing image segmentation and edge detection tasks. It first applies edge detection technique to obtain a Difference In Strength (DIS) map. An initial segmented result is obtained based on K-means clustering technique and the minimum distance. Then the region process is modeled by MRF to obtain an image that contains different intensity regions. The gradient values are calculated and then the watershed technique is used. DIS calculation is used for each pixel to define all the edges (weak or strong) in the image. The DIS map is obtained. This help as priority knowledge to know the possibility of the region segmentation by the next step (MRF), which gives an image that has all the edges and regions information. In MRF model,gray level l, at pixel location i, in an image X, depends on the gray levels of neighboring pixels. The segmentation results are improved by using watershed algorithm. After all pixels of the segmented regions are processed, a map of primitive region with edges is generated. The edge map is obtained using a merge process based on averaged intensity mean values. A common edge detectors that work on (MRF) segmented image are used and the results are compared. The segmentation and edge detection result is one closed boundary per actual region in the image.

  19. GSK-3 inhibitors induce chromosome instability

    Directory of Open Access Journals (Sweden)

    Staples Oliver D

    2007-08-01

    Full Text Available Abstract Background Several mechanisms operate during mitosis to ensure accurate chromosome segregation. However, during tumour evolution these mechanisms go awry resulting in chromosome instability. While several lines of evidence suggest that mutations in adenomatous polyposis coli (APC may promote chromosome instability, at least in colon cancer, the underlying mechanisms remain unclear. Here, we turn our attention to GSK-3 – a protein kinase, which in concert with APC, targets β-catenin for proteolysis – and ask whether GSK-3 is required for accurate chromosome segregation. Results To probe the role of GSK-3 in mitosis, we inhibited GSK-3 kinase activity in cells using a panel of small molecule inhibitors, including SB-415286, AR-A014418, 1-Azakenpaullone and CHIR99021. Analysis of synchronised HeLa cells shows that GSK-3 inhibitors do not prevent G1/S progression or cell division. They do, however, significantly delay mitotic exit, largely because inhibitor-treated cells have difficulty aligning all their chromosomes. Although bipolar spindles form and the majority of chromosomes biorient, one or more chromosomes often remain mono-oriented near the spindle poles. Despite a prolonged mitotic delay, anaphase frequently initiates without the last chromosome aligning, resulting in chromosome non-disjunction. To rule out the possibility of "off-target" effects, we also used RNA interference to selectively repress GSK-3β. Cells deficient for GSK-3β exhibit a similar chromosome alignment defect, with chromosomes clustered near the spindle poles. GSK-3β repression also results in cells accumulating micronuclei, a hallmark of chromosome missegregation. Conclusion Thus, not only do our observations indicate a role for GSK-3 in accurate chromosome segregation, but they also raise the possibility that, if used as therapeutic agents, GSK-3 inhibitors may induce unwanted side effects by inducing chromosome instability.

  20. Digital image processing and analysis human and computer vision applications with CVIPtools

    CERN Document Server

    Umbaugh, Scott E

    2010-01-01

    Section I Introduction to Digital Image Processing and AnalysisDigital Image Processing and AnalysisOverviewImage Analysis and Computer VisionImage Processing and Human VisionKey PointsExercisesReferencesFurther ReadingComputer Imaging SystemsImaging Systems OverviewImage Formation and SensingCVIPtools SoftwareImage RepresentationKey PointsExercisesSupplementary ExercisesReferencesFurther ReadingSection II Digital Image Analysis and Computer VisionIntroduction to Digital Image AnalysisIntroductionPreprocessingBinary Image AnalysisKey PointsExercisesSupplementary ExercisesReferencesFurther Read

  1. Clinical analysis of 41 Neonates with Chromosomal Disorder%新生儿染色体病41例临床分析

    Institute of Scientific and Technical Information of China (English)

    韦露明; 高宗燕; 钟丹妮

    2012-01-01

    目的 探讨新生儿期常见染色体病核型、临床表现及预防措施.方法 对2005年1月~2010年12月在某院住院的41例染色体病患儿母亲围生期并发症、高危因素、患儿临床表现、染色体核型进行回顾性分析.结果 41例中孕母有围生期并发症及高危因素者共17例.21-三体综合征29例,18三体综合征1例,猫叫综合征2例,Tumer综合征1例,其他各型染色体核型异常8例.所有患儿均有特殊外貌和(或)体征,26例合并其他畸形或疾病,1例新生儿期夭折,1例9月大时死亡.结论 新生儿期根据特殊外貌体征和染色体核型分析可诊断染色体病,高龄初产与染色体病存在着相关性.%OBJECTIVE To explore the phototypes of the common chromosomal disorder, clinical characteristics and strategies of prevention. METHODS The maternal perinatal complication, clinical manifestation, chromosomal phenotype of 41 neonates with chromosomal disorders were selected from the First Affiliated Hospital of Guangxi Medical University, and they were retrospectively analyzed in our study. RESULTS Among 41 cases, 17 cases had perinatal complication and risk factors. Of 41 cases, 29 cases had trisomy 21 syndrome, 1 case had trisomy 18 syndrome, 2 cases had cir du chat syndrome, 1 case had turner syndrome, and 8 cases had other abnormal phenotypes. All the cases had characteristic appearances or signs, 16 cases were accompanied with other abnormalities or disease. One case died in neonatal period, and one died at 9 months old. CONCLUSION Chromosomal disorder can be diagnosed according to characteristic appearance, signs and Chromosomal analysis. Elderly primipara is related to Chromosomal disorder.

  2. Exploiting multi-context analysis in semantic image classification

    Institute of Scientific and Technical Information of China (English)

    TIAN Yong-hong; HUANG Tie-jun; GAO Wen

    2005-01-01

    As the popularity of digital images is rapidly increasing on the Internet, research on technologies for semantic image classification has become an important research topic. However, the well-known content-based image classification methods do not overcome the so-called semantic gap problem in which low-level visual features cannot represent the high-level semantic content of images. Image classification using visual and textual information often performs poorly since the extracted textual features are often too limited to accurately represent the images. In this paper, we propose a semantic image classification approach using multi-context analysis. For a given image, we model the relevant textual information as its multi-modal context, and regard the related images connected by hyperlinks as its link context. Two kinds of context analysis models, i.e., cross-modal correlation analysis and link-based correlation model, are used to capture the correlation among different modals of features and the topical dependency among images induced by the link structure. We propose a new collective classification model called relational support vector classifier (RSVC) based on the well-known Support Vector Machines (SVMs) and the link-based correlation model. Experiments showed that the proposed approach significantly improved classification accuracy over that of SVM classifiers using visual and/or textual features.

  3. Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis chromosome 20

    Directory of Open Access Journals (Sweden)

    Schäffer Alejandro A

    2008-11-01

    Full Text Available Abstract Background Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequencing, mapping tools such as radiation hybrid DNA panels remain useful aids for sequence assembly, focused resequencing efforts, and for building physical maps of species that have not yet been sequenced. For placement of specific, individual genes or markers on a map, low-throughput methods remain commonplace. Typically, PCR amplification of DNA from each panel cell line is followed by gel electrophoresis and scoring of each clone for the presence or absence of PCR product. To improve sensitivity and efficiency of radiation hybrid panel analysis in comparison to gel-based methods, we adapted fluorescence-based real-time PCR and dissociation curve analysis for use as a novel scoring method. Results As proof of principle for this dissociation curve method, we generated new maps of river buffalo (Bubalus bubalis chromosome 20 by both dissociation curve analysis and conventional marker scoring. We also obtained sequence data to augment dissociation curve results. Few genes have been previously mapped to buffalo chromosome 20, and sequence detail is limited, so 65 markers were screened from the orthologous chromosome of domestic cattle. Thirty bovine markers (46% were suitable as cross-species markers for dissociation curve analysis in the buffalo radiation hybrid panel under a standard protocol, compared to 25 markers suitable for conventional typing. Computational analysis placed 27 markers on a chromosome map generated by the new method, while the gel-based approach produced only 20 mapped markers. Among 19 markers common to both maps, the marker order on the map was maintained perfectly. Conclusion Dissociation curve

  4. Pattern recognition software and techniques for biological image analysis.

    Directory of Open Access Journals (Sweden)

    Lior Shamir

    Full Text Available The increasing prevalence of automated image acquisition systems is enabling new types of microscopy experiments that generate large image datasets. However, there is a perceived lack of robust image analysis systems required to process these diverse datasets. Most automated image analysis systems are tailored for specific types of microscopy, contrast methods, probes, and even cell types. This imposes significant constraints on experimental design, limiting their application to the narrow set of imaging methods for which they were designed. One of the approaches to address these limitations is pattern recognition, which was originally developed for remote sensing, and is increasingly being applied to the biology domain. This approach relies on training a computer to recognize patterns in images rather than developing algorithms or tuning parameters for specific image processing tasks. The generality of this approach promises to enable data mining in extensive image repositories, and provide objective and quantitative imaging assays for routine use. Here, we provide a brief overview of the technologies behind pattern recognition and its use in computer vision for biological and biomedical imaging. We list available software tools that can be used by biologists and suggest practical experimental considerations to make the best use of pattern recognition techniques for imaging assays.

  5. Introducing PLIA: Planetary Laboratory for Image Analysis

    Science.gov (United States)

    Peralta, J.; Hueso, R.; Barrado, N.; Sánchez-Lavega, A.

    2005-08-01

    We present a graphical software tool developed under IDL software to navigate, process and analyze planetary images. The software has a complete Graphical User Interface and is cross-platform. It can also run under the IDL Virtual Machine without the need to own an IDL license. The set of tools included allow image navigation (orientation, centring and automatic limb determination), dynamical and photometric atmospheric measurements (winds and cloud albedos), cylindrical and polar projections, as well as image treatment under several procedures. Being written in IDL, it is modular and easy to modify and grow for adding new capabilities. We show several examples of the software capabilities with Galileo-Venus observations: Image navigation, photometrical corrections, wind profiles obtained by cloud tracking, cylindrical projections and cloud photometric measurements. Acknowledgements: This work has been funded by Spanish MCYT PNAYA2003-03216, fondos FEDER and Grupos UPV 15946/2004. R. Hueso acknowledges a post-doc fellowship from Gobierno Vasco.

  6. Systematic mutation analysis of KIAA0767 and KIAA1646 in chromosome 22q-linked periodic catatonia

    Directory of Open Access Journals (Sweden)

    Gawlik Micha

    2005-10-01

    Full Text Available Abstract Background Periodic catatonia is a familial subtype of schizophrenia characterized by hyperkinetic and akinetic episodes, followed by a catatonic residual syndrome. The phenotype has been evaluated in two independent genome-wide linkage scans with evidence for a major locus on chromosome 15q15, and a second independent locus on chromosome 22qtel. Methods In the positional and brain-expressed candidate genes KIAA0767 and KIAA1646, we searched for variants in the complete exons and adjacent splice-junctions as well as in parts of the 5'- and 3'-untranslated regions by means of a systematic mutation screening in individuals from chromosome 22q-linked pedigrees. Results The mutation scan revealed 24 single nucleotide polymorphisms, among them two rare codon variants (KIAA0767: S159I; KIAA1646: V338G. However, both were neither found segregating with the disease in the respective pedigree nor found at a significant frequency in a case-control association sample. Conclusion Starting from linkage signals at chromosome22qtel in periodic catatonia, we screened two positional brain-expressed candidate genes for genetic variation. Our study excludes genetic variations in the coding and putative promoter regions of KIAA0767 and KIAA1646 as causative factors for periodic catatonia.

  7. Analysis of IFT74 as a candidate gene for chromosome 9p-linked ALS-FTD

    Directory of Open Access Journals (Sweden)

    Rogaeva Ekaterina

    2006-12-01

    Full Text Available Abstract Background A new locus for amyotrophic lateral sclerosis – frontotemporal dementia (ALS-FTD has recently been ascribed to chromosome 9p. Methods We identified chromosome 9p segregating haplotypes within two families with ALS-FTD (F476 and F2 and undertook mutational screening of candidate genes within this locus. Results Candidate gene sequencing at this locus revealed the presence of a disease segregating stop mutation (Q342X in the intraflagellar transport 74 (IFT74 gene in family 476 (F476, but no mutation was detected within IFT74 in family 2 (F2. While neither family was sufficiently informative to definitively implicate or exclude IFT74 mutations as a cause of chromosome 9-linked ALS-FTD, the nature of the mutation observed within F476 (predicted to truncate the protein by 258 amino acids led us to sequence the open reading frame of this gene in a large number of ALS and FTD cases (n = 420. An additional sequence variant (G58D was found in a case of sporadic semantic dementia. I55L sequence variants were found in three other unrelated affected individuals, but this was also found in a single individual among 800 Human Diversity Gene Panel samples. Conclusion Confirmation of the pathogenicity of IFT74 sequence variants will require screening of other chromosome 9p-linked families.

  8. Relationship of Extreme Chromosomal Instability with Long-term Survival in a Retrospective Analysis of Primary Breast Cancer

    DEFF Research Database (Denmark)

    Roylance, Rebecca; Endesfelder, David; Gorman, Patricia;

    2011-01-01

    Background: Chromosomal instability (CIN) is thought to be associated with poor prognosis in solid tumors; however, evidence from preclinical and mouse tumor models suggest that CIN may paradoxically enhance or impair cancer cell fitness. Breast cancer prognostic expression signature sets, which ...

  9. CHROMOSOMAL ABNORMALITIES IN PATIENTS WITH RECURRENT MISCARRIAGE

    OpenAIRE

    Daniela Mierla; Viorica Radoi; Veronica Stoian

    2012-01-01

    Chromosomal abnormalities are involved in the etiology of recurrent spontaneous pregnancy loss and sub-fertility. The purpose of this study was to determine the frequency and contribution of chromosomal abnormalities in recurrent miscarriages. The results obtained and literature review are helpful in understanding the importance of cytogenetics analysis of female infertility. To investigate the distribution of chromosomal abnormalities in the Romanian population with recurrent miscarriage, ka...

  10. Plasmid Characterization and Chromosome Analysis of Two netF+ Clostridium perfringens Isolates Associated with Foal and Canine Necrotizing Enteritis.

    Science.gov (United States)

    Mehdizadeh Gohari, Iman; Kropinski, Andrew M; Weese, Scott J; Parreira, Valeria R; Whitehead, Ashley E; Boerlin, Patrick; Prescott, John F

    2016-01-01

    The recent discovery of a novel beta-pore-forming toxin, NetF, which is strongly associated with canine and foal necrotizing enteritis should improve our understanding of the role of type A Clostridium perfringens associated disease in these animals. The current study presents the complete genome sequence of two netF-positive strains, JFP55 and JFP838, which were recovered from cases of foal necrotizing enteritis and canine hemorrhagic gastroenteritis, respectively. Genome sequencing was done using Single Molecule, Real-Time (SMRT) technology-PacBio and Illumina Hiseq2000. The JFP55 and JFP838 genomes include a single 3.34 Mb and 3.53 Mb chromosome, respectively, and both genomes include five circular plasmids. Plasmid annotation revealed that three plasmids were shared by the two newly sequenced genomes, including a NetF/NetE toxins-encoding tcp-conjugative plasmid, a CPE/CPB2 toxins-encoding tcp-conjugative plasmid and a putative bacteriocin-encoding plasmid. The putative beta-pore-forming toxin genes, netF, netE and netG, were located in unique pathogenicity loci on tcp-conjugative plasmids. The C. perfringens JFP55 chromosome carries 2,825 protein-coding genes whereas the chromosome of JFP838 contains 3,014 protein-encoding genes. Comparison of these two chromosomes with three available reference C. perfringens chromosome sequences identified 48 (~247 kb) and 81 (~430 kb) regions unique to JFP55 and JFP838, respectively. Some of these divergent genomic regions in both chromosomes are phage- and plasmid-related segments. Sixteen of these unique chromosomal regions (~69 kb) were shared between the two isolates. Five of these shared regions formed a mosaic of plasmid-integrated segments, suggesting that these elements were acquired early in a clonal lineage of netF-positive C. perfringens strains. These results provide significant insight into the basis of canine and foal necrotizing enteritis and are the first to demonstrate that netF resides on a large and

  11. Diagnostic imaging analysis of the impacted mesiodens

    International Nuclear Information System (INIS)

    The research was performed to predict the three dimensional relationship between the impacted mesiodens and the maxillary central incisors and the proximity with the anatomic structures by comparing their panoramic images with the CT images. Among the patients visiting Seoul National University Dental Hospital from April 2003 to July 2007, those with mesiodens were selected (154 mesiodens of 120 patients). The numbers, shapes, orientation and positional relationship of mesiodens with maxillary central incisors were investigated in the panoramic images. The proximity with the anatomical structures and complications were investigated in the CT images as well. The sex ratio (M : F) was 2.28 : 1 and the mean number of mesiodens per one patient was 1.28. Conical shape was 84.4% and inverted orientation was 51.9%. There were more cases of anatomical structures encroachment, especially on the nasal floor and nasopalatine duct, when the mesiodens was not superimposed with the central incisor. There were, however, many cases of the nasopalatine duct encroachment when the mesiodens was superimpoised with the apical 1/3 of central incisor (52.6%). Delayed eruption (55.6%), crown rotation (66.7%) and crown resorption (100%) were observed when the mesiodens was superimposed with the crown of the central incisor. It is possible to predict three dimensional relationship between the impacted mesiodens and the maxillary central incisors in the panoramic images, but more details should be confirmed by the CT images when necessary.

  12. Chromosomal mapping of specific DNA gains and losses in solid tumors using comparative genomic hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Schrock, E.; Manoir, S. du; Speicher, M. [National Center for Human Genome Research, Bethesda, MD (United States)] [and others

    1994-09-01

    Comparative genomic hybridization (CGH) is a new molecular cytogenetic technique that is based on two color FISH and quantitative digital imaging microscopy. CGH is used to comprehensively survey tumor genomes for copy number changes and to determine the map position of amplification sites on normal reference chromosomes. CGH was used to analyze 107 different solid tumors, including 16 low grade astrocytomas, 15 recurrent astrocytic tumors, 13 high grade astrocytomas, 13 small cell lung cancers (SCLC), 14 breast cancer samples (7 diploid and 7 aneupoid tumors), 18 chromophobe renal cell carcinomas and 5 seminomas. Tumor DNA was extracted from frozen tissue, autopic material and formalin fixed, paraffin-embedded tissue samples. Our results revealed tumor specific gains and losses of certain chromosomes or chromosomal subregions (e.g., chromosomes 7 and 10 in glioblastomas, chromosomes 3 and 5 in SCLC). Numerous DNA-amplifications were mapped on reference metaphase and prometaphase chromosomes. The frequent amplification of the EGFR gene (malignant gliomas), protooncogenes of the myc family (SCLC) and of c-myc, int-2 and c-erbB2 (breast cancer) was confirmed. Many additional amplification sites, however, were mapped that were not described before. The results of CGH analysis were independently confirmed by means of cytogenetic banding analysis, interphase cytogenetics with region specific DNA-clones, Southern-Blot analysis, DNA-cytometry and studies of loss of heterozygosity.

  13. Image Analysis of Defocused Single-molecule Images for Three-dimensional Molecule Orientation Studies

    OpenAIRE

    Patra, D; Gregor, I.; Enderlein, J.

    2004-01-01

    An efficient algorithm for pattern matching has been developed based on least-squares analysis of fitting a discrete set of master patterns against measured images. This algorithm has been applied to determine three-dimensional molecule orientations in defocused single-molecule images. The developed algorithm exploits the excellent agreement between electrodynamic calculations of single-molecule emission and experimentally measured images. The procedure is found to be reliable and simple and ...

  14. Digital Image Analysis for DETCHIP(®) Code Determination.

    Science.gov (United States)

    Lyon, Marcus; Wilson, Mark V; Rouhier, Kerry A; Symonsbergen, David J; Bastola, Kiran; Thapa, Ishwor; Holmes, Andrea E; Sikich, Sharmin M; Jackson, Abby

    2012-08-01

    DETECHIP(®) is a molecular sensing array used for identification of a large variety of substances. Previous methodology for the analysis of DETECHIP(®) used human vision to distinguish color changes induced by the presence of the analyte of interest. This paper describes several analysis techniques using digital images of DETECHIP(®). Both a digital camera and flatbed desktop photo scanner were used to obtain Jpeg images. Color information within these digital images was obtained through the measurement of red-green-blue (RGB) values using software such as GIMP, Photoshop and ImageJ. Several different techniques were used to evaluate these color changes. It was determined that the flatbed scanner produced in the clearest and more reproducible images. Furthermore, codes obtained using a macro written for use within ImageJ showed improved consistency versus pervious methods. PMID:25267940

  15. [POSSIBILITIES AND LIMITATIONS ANALYSIS OF SCREENING IN PREGNANT WOMEN FOR DOWN SYNDROME AND OTHER COMMON CHROMOSOMAL DISORDERS OVER A PERIOD OF TWO YEARS].

    Science.gov (United States)

    Hachmerian M; Angelova L; Ivanov St; Kovachev E

    2016-01-01

    Maternal biochemical screening and the new non-invasive prenatal screening tests as well as prenatal diagnostic tests as tools to fight serious chromosomal diseases have their possibilities and limitations. The article presents analysis of the results in 7 201 pregnant women: 4426 first trimester and 2775 second trimester biochemical screening, together with 994 calculated integrated risks performed in the Laboratory of medical genetics in 2013 and 2014 year. A matter of mass screening in both periods is the criterion of efficiency--financially justified reasons on the basis of comparison "sensitivity" of different approaches. First trimester screening revealed 5 (71.42%) cases of chromosomal disease and 1 (14.28%) case with large congenital anomaly. From second trimester biochemical screening 3 (60%) cases were revealed. Chromosomal pathology in pregnant women with calculated integrated risk was found in 7 (70%) cases. From a total of 22 screened pregnant women with prenatal or postnatal verified diagnosis of Down syndrome, Edvards, Patau or Turner, highest detection rate is found in first trimester screening--6 of 7 (85.7%). Contingent approach is most widely used in Europe and we confidently recommend it. PMID:27514138

  16. Collinearity of homoeologous group 3 chromosomes in the genus Hordeum and Secale cereale as revealed by 3H-derived FISH analysis.

    Science.gov (United States)

    Aliyeva-Schnorr, Lala; Stein, Nils; Houben, Andreas

    2016-05-01

    Crop wild relatives are considered as important genetic resources of allelic diversity for domesticated crop species. Their utilization in breeding programs, however, is often limited due to crossing barriers and genome incompatibilities. Wild relatives of barley possess attractive properties and hence allelic diversity for adapting barley better to changing environmental conditions. Therefore, gaining a better knowledge about genomic synteny between cultivated barley and wild relatives of the same genus is an important task. To visualize genomic collinearity in related species, 22 genomic single-copy and 14 complementary DNA (cDNA) chromosome 3H-specific probes were mapped to the chromosomes of Hordeum bulbosum, Hordeum marinum, Hordeum pubiflorum, Hordeum murinum, and Secale cereale by fluorescent in situ hybridization (FISH). Most probes showed reliable signals confirming homoeology between cultivated barley and related species. Differences in order and position of FISH markers demonstrated sequence movements or small-scale chromosomal rearrangements within genus Hordeum and confirmed interchromosomal rearrangements between barley and rye. Comparison between repeat-free genomic and cDNA probes showed that gene-containing single-copy genomic DNA (gDNA) probes are performing more reliably for FISH-based analysis of synteny.

  17. Morphological Analysis on Chromosome of Polygonatum odoratum (Mill.) Druce%关玉竹染色体形态学研究

    Institute of Scientific and Technical Information of China (English)

    吴杰; 赵鑫; 李艳辉; 刘宇; 李鑫龙; 宁伟

    2009-01-01

    Objective To study the karyomorphology of Polygonatum odoratum (Mill.) Druce.from Changbai mountain.Methods Conventional pressed slice method was employed.Results The chromosomal number of S.chinensis was 2n = 20,the karyotype belonged to "2B" and was formulated as K(2n) = 2X = 2st + 8sm + 10m,the asymmetry index was K%=61.71%.Conclusion Detailed analysis was consequently displayed on symmetrical degree,chromosomal type and compositions of P.odoratum.The chromosomal morphostructure of P.odoratum was reported for the first time.%目的 对长白山地区分布的关玉竹体细胞染色体计数,对其进行核形态学研究.方法 采用常规压片法.结果 关玉竹的染色体数目为2n = 20,核型公式为K(2n) = 2X = 2sm(2SAT) + 8sm + 10m,属"2B"类型,核型不对称系数为61.71%.结论 基于观察结果分析了关玉竹染色体对称程度、类型及染色体组成.关玉竹染色体的随体结构为首次报道.

  18. Anima: Modular workflow system for comprehensive image data analysis

    Directory of Open Access Journals (Sweden)

    Ville eRantanen

    2014-07-01

    Full Text Available Modern microscopes produce vast amounts of image data, and computational methods are needed to analyze and interpret these data. Furthermore, a single image analysis project may require tens or hundreds of analysis steps starting from data import and preprocessing to segmentation and statistical analysis; and ending with visualization and reporting. To manage such large-scale image data analysis projects, we present here a modular workflow system called Anima. Anima is designed for comprehensive and efficient image data analysis, and it contains several features that are crucial in high-throughput image data analysis: programming language independence, batch processing, easily customized data processing, interoperability with other software via application programming interfaces, and advanced multivariate statistical analysis. The utility of Anima is shown with two case studies focusing on testing different algorithms developed in different imaging platforms and an automated prediction of alive/dead C. elegans worms by integrating several analysis environmens. Anima is fully open source and available with documentation at http://www.anduril.org/anima

  19. Geopositioning Precision Analysis of Multiple Image Triangulation Using Lro Nac Lunar Images

    Science.gov (United States)

    Di, K.; Xu, B.; Liu, B.; Jia, M.; Liu, Z.

    2016-06-01

    This paper presents an empirical analysis of the geopositioning precision of multiple image triangulation using Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) images at the Chang'e-3(CE-3) landing site. Nine LROC NAC images are selected for comparative analysis of geopositioning precision. Rigorous sensor models of the images are established based on collinearity equations with interior and exterior orientation elements retrieved from the corresponding SPICE kernels. Rational polynomial coefficients (RPCs) of each image are derived by least squares fitting using vast number of virtual control points generated according to rigorous sensor models. Experiments of different combinations of images are performed for comparisons. The results demonstrate that the plane coordinates can achieve a precision of 0.54 m to 2.54 m, with a height precision of 0.71 m to 8.16 m when only two images are used for three-dimensional triangulation. There is a general trend that the geopositioning precision, especially the height precision, is improved with the convergent angle of the two images increasing from several degrees to about 50°. However, the image matching precision should also be taken into consideration when choosing image pairs for triangulation. The precisions of using all the 9 images are 0.60 m, 0.50 m, 1.23 m in along-track, cross-track, and height directions, which are better than most combinations of two or more images. However, triangulation with selected fewer images could produce better precision than that using all the images.

  20. Texture analysis for the segmentation of sugar cane multispectral images

    OpenAIRE

    Solano, Agustin; Schneider, Gerardo; Kemerer, Alejandra; Hadad, Alejandro Javier

    2014-01-01

    In this paper is presented an analysis of the impact of texture features for segmentation of multispectral aerial images of sugar cane. Currently there are no precise techniques to estimate objectively areas of fallen cane and this causes significant losses in crop productivity and industrialization. For the real-ization of this work was made an image dataset. To build this dataset was im-plemented a software from which were obtained labeled regions in the images related to this agronomic phe...

  1. Basic research planning in mathematical pattern recognition and image analysis

    Science.gov (United States)

    Bryant, J.; Guseman, L. F., Jr.

    1981-01-01

    Fundamental problems encountered while attempting to develop automated techniques for applications of remote sensing are discussed under the following categories: (1) geometric and radiometric preprocessing; (2) spatial, spectral, temporal, syntactic, and ancillary digital image representation; (3) image partitioning, proportion estimation, and error models in object scene interference; (4) parallel processing and image data structures; and (5) continuing studies in polarization; computer architectures and parallel processing; and the applicability of "expert systems" to interactive analysis.

  2. An Ultrasound Image Despeckling Approach Based on Principle Component Analysis

    OpenAIRE

    Jawad F. Al-Asad; Ali M. Reza; Udomchai Techavipoo

    2014-01-01

    An approach based on principle component analysis (PCA) to filter out multiplicative noise from ultrasound images is presented in this paper. An image with speckle noise is segmented into small dyadic lengths, depending on the original size of the image, and the global covariance matrix is found. A projection matrix is then formed by selecting the maximum eigenvectors of the global covariance matrix. This projection matrix is used to filter speckle noise by projecting each segment into the si...

  3. Chromosome assortment in Saccharum.

    Science.gov (United States)

    Al-Janabi, S M; Honeycutt, R J; Sobral, B W

    1994-12-01

    Recent work has revealed random chromosome pairing and assortment in Saccharum spontaneum L., the most widely distributed, and morphologically and cytologically variable of the species of Saccharum. This conclusion was based on the analysis of a segregating population from across between S. spontaneum 'SES 208' and a spontaneously-doubled haploid of itself, derived from anther culture. To determine whether polysomic inheritance is common in Saccharum and whether it is observed in a typical biparental cross, we studied chromosome pairing and assortment in 44 progeny of a cross between euploid, meiotically regular, 2n=80 forms of Saccharum officinarum 'LA Purple' and Saccharum robustum ' Mol 5829'. Papuan 2n=80 forms of S. robustum have been suggested as the immediate progenitor species for cultivated sugarcane (S. officinarum). A total of 738 loci in LA Purple and 720 loci in Mol 5829 were amplified and typed in the progeny by arbitrarily primed PCR using 45 primers. Fifty and 33 single-dose polymorphisms were identified in the S. officinarum and S. robustum genomes, respectively (χ 2 at 98%). Linkage analysis of single-dose polymorphisms in both genomes revealed linkages in repulsion and coupling phases. In the S. officinarum genome, a map hypothesis gave 7 linkage groups with 17 linked and 33 unlinked markers. Four of 13 pairwise linkages were in repulsion phase and 9 were in coupling phase. In the S. robustum genome, a map hypothesis gave 5 linkage groups, defined by 12 markers, with 21 markers unlinked, and 2 of 9 pairwise linkages were in repulsion phase. Therefore, complete polysomic inheritance was not observed in either species, suggesting that chromosomal behavior is different from that observed by linkage analysis of over 500 markers in the S. spontaneum map. Implications of this finding for evolution and breeding are discussed.

  4. Uncooled LWIR imaging: applications and market analysis

    Science.gov (United States)

    Takasawa, Satomi

    2015-05-01

    The evolution of infrared (IR) imaging sensor technology for defense market has played an important role in developing commercial market, as dual use of the technology has expanded. In particular, technologies of both reduction in pixel pitch and vacuum package have drastically evolved in the area of uncooled Long-Wave IR (LWIR; 8-14 μm wavelength region) imaging sensor, increasing opportunity to create new applications. From the macroscopic point of view, the uncooled LWIR imaging market is divided into two areas. One is a high-end market where uncooled LWIR imaging sensor with sensitivity as close to that of cooled one as possible is required, while the other is a low-end market which is promoted by miniaturization and reduction in price. Especially, in the latter case, approaches towards consumer market have recently appeared, such as applications of uncooled LWIR imaging sensors to night visions for automobiles and smart phones. The appearance of such a kind of commodity surely changes existing business models. Further technological innovation is necessary for creating consumer market, and there will be a room for other companies treating components and materials such as lens materials and getter materials and so on to enter into the consumer market.

  5. Automatic analysis of a skull fracture based on image content

    Science.gov (United States)

    Shao, Hong; Zhao, Hong

    2003-09-01

    Automatic analysis based on image content is a hotspot with bright future of medical image diagnosis technology research. Analysis of the fracture of skull can help doctors diagnose. In this paper, a new approach is proposed to automatically detect the fracture of skull based on CT image content. First region growing method, whose seeds and growing rules are chosen by k-means clustering dynamically, is applied for image automatic segmentation. The segmented region boundary is found by boundary tracing. Then the shape of the boundary is analyzed, and the circularity measure is taken as description parameter. At last the rules for computer automatic diagnosis of the fracture of the skull are reasoned by entropy function. This method is used to analyze the images from the third ventricles below layer to cerebral cortex top layer. Experimental result shows that the recognition rate is 100% for the 100 images, which are chosen from medical image database randomly and are not included in the training examples. This method integrates color and shape feature, and isn't affected by image size and position. This research achieves high recognition rate and sets a basis for automatic analysis of brain image.

  6. Co-regulation analysis of closely linked genes identifies a highly recurrent gain on chromosome 17q25.3 in prostate cancer

    International Nuclear Information System (INIS)

    Transcriptional profiling of prostate cancer (PC) has unveiled new markers of neoplasia and allowed insights into mechanisms underlying this disease. Genomewide analyses have also identified new chromosomal abnormalities associated with PC. The combination of both classes of data for the same sample cohort might provide better criteria for identifying relevant factors involved in neoplasia. Here we describe transcriptional signatures identifying distinct normal and tumoral prostate tissue compartments, and the inference and demonstration of a new, highly recurrent copy number gain on chromosome 17q25.3. We have applied transcriptional profiling to tumoral and non-tumoral prostate samples with relatively homogeneous epithelial representations as well as pure stromal tissue from peripheral prostate and cultured cell lines, followed by quantitative RT-PCR validations and immunohistochemical analysis. In addition, we have performed in silico colocalization analysis of co-regulated genes and validation by fluorescent in situ hybridization (FISH). The transcriptomic analysis has allowed us to identify signatures corresponding to non-tumoral luminal and tumoral epithelium, basal epithelial cells, and prostate stromal tissue. In addition, in silico analysis of co-regulated expression of physically linked genes has allowed us to predict the occurrence of a copy number gain at chromosomal region 17q25.3. This computational inference was validated by fluorescent in situ hybridization, which showed gains in this region in over 65% of primary and metastatic tumoral samples. Our approach permits to directly link gene copy number variations with transcript co-regulation in association with neoplastic states. Therefore, transcriptomic studies of carefully selected samples can unveil new diagnostic markers and transcriptional signatures highly specific of PC, and lead to the discovery of novel genomic abnormalities that may provide additional insights into the causes and mechanisms

  7. Co-regulation analysis of closely linked genes identifies a highly recurrent gain on chromosome 17q25.3 in prostate cancer

    Directory of Open Access Journals (Sweden)

    Martínez-A Carlos

    2008-10-01

    Full Text Available Abstract Background Transcriptional profiling of prostate cancer (PC has unveiled new markers of neoplasia and allowed insights into mechanisms underlying this disease. Genomewide analyses have also identified new chromosomal abnormalities associated with PC. The combination of both classes of data for the same sample cohort might provide better criteria for identifying relevant factors involved in neoplasia. Here we describe transcriptional signatures identifying distinct normal and tumoral prostate tissue compartments, and the inference and demonstration of a new, highly recurrent copy number gain on chromosome 17q25.3. Methods We have applied transcriptional profiling to tumoral and non-tumoral prostate samples with relatively homogeneous epithelial representations as well as pure stromal tissue from peripheral prostate and cultured cell lines, followed by quantitative RT-PCR validations and immunohistochemical analysis. In addition, we have performed in silico colocalization analysis of co-regulated genes and validation by fluorescent in situ hybridization (FISH. Results The transcriptomic analysis has allowed us to identify signatures corresponding to non-tumoral luminal and tumoral epithelium, basal epithelial cells, and prostate stromal tissue. In addition, in silico analysis of co-regulated expression of physically linked genes has allowed us to predict the occurrence of a copy number gain at chromosomal region 17q25.3. This computational inference was validated by fluorescent in situ hybridization, which showed gains in this region in over 65% of primary and metastatic tumoral samples. Conclusion Our approach permits to directly link gene copy number variations with transcript co-regulation in association with neoplastic states. Therefore, transcriptomic studies of carefully selected samples can unveil new diagnostic markers and transcriptional signatures highly specific of PC, and lead to the discovery of novel genomic abnormalities

  8. Occupancy Analysis of Sports Arenas Using Thermal Imaging

    DEFF Research Database (Denmark)

    Gade, Rikke; Jørgensen, Anders; Moeslund, Thomas B.

    2012-01-01

    This paper presents a system for automatic analysis of the occupancy of sports arenas. By using a thermal camera for image capturing the number of persons and their location on the court are found without violating any privacy issues. The images are binarised with an automatic threshold method...

  9. Spinal X-ray image analysis in scoliosis

    NARCIS (Netherlands)

    Sardjono, Tri Arief

    2007-01-01

    In this thesis new image analysis methods are discussed to determine the curvature of scoliotic patients characterised by the Cobb angle and to enhance the vertebral parts based on features from a frontal X-ray image. Chapter 1 provides some background information on scoliosis, how to diagnose it, t

  10. Four challenges in medical image analysis from an industrial perspective.

    Science.gov (United States)

    Weese, Jürgen; Lorenz, Cristian

    2016-10-01

    Today's medical imaging systems produce a huge amount of images containing a wealth of information. However, the information is hidden in the data and image analysis algorithms are needed to extract it, to make it readily available for medical decisions and to enable an efficient work flow. Advances in medical image analysis over the past 20 years mean there are now many algorithms and ideas available that allow to address medical image analysis tasks in commercial solutions with sufficient performance in terms of accuracy, reliability and speed. At the same time new challenges have arisen. Firstly, there is a need for more generic image analysis technologies that can be efficiently adapted for a specific clinical task. Secondly, efficient approaches for ground truth generation are needed to match the increasing demands regarding validation and machine learning. Thirdly, algorithms for analyzing heterogeneous image data are needed. Finally, anatomical and organ models play a crucial role in many applications, and algorithms to construct patient-specific models from medical images with a minimum of user interaction are needed. These challenges are complementary to the on-going need for more accurate, more reliable and faster algorithms, and dedicated algorithmic solutions for specific applications.

  11. Direct identification of pure penicillium species using image analysis

    DEFF Research Database (Denmark)

    Dørge, Thorsten Carlheim; Carstensen, Jens Michael; Frisvad, Jens Christian

    2000-01-01

    recording. Isolates of nine different species of the genus Penicillium have been selected for the purpose. After incubation for 7 days, the fungal colonies are digitized using a very accurate digital camera. Prior to the image analysis each image is corrected for self-illumination, thereby gaining a set...

  12. ANALYSIS OF MULAN’S IMAGE

    Directory of Open Access Journals (Sweden)

    Chen Chongjie

    2010-05-01

    Full Text Available Mulan is an ancient Chinese heroine. The story shows that she is the same as other women,having personal life, but also has a heart that loves her country and her parents. She always thinksabout her family, society, dan country. This article was based on library research, using Mulan poemdan a folklore entitled Mulan Pergi Berperang as media to analyze Mulan’s image. It can be said thateventhough at that time there was no gender perspective concept, Mulan had been able to replace herfather to go to war. She gave a lot of contributions for her country, society, and family. Analysisrepresents that Mulan has three images, as a heroine, as a daughter for her family, and self-image orleader for the women. Having good character and spirit to love country, people, and family make herequal to men. And, it makes her respected by people in each generation.

  13. Optical image acquisition system for colony analysis

    Science.gov (United States)

    Wang, Weixing; Jin, Wenbiao

    2006-02-01

    For counting of both colonies and plaques, there is a large number of applications including food, dairy, beverages, hygiene, environmental monitoring, water, toxicology, sterility testing, AMES testing, pharmaceuticals, paints, sterile fluids and fungal contamination. Recently, many researchers and developers have made efforts for this kind of systems. By investigation, some existing systems have some problems since they belong to a new technology product. One of the main problems is image acquisition. In order to acquire colony images with good quality, an illumination box was constructed as: the box includes front lightning and back lightning, which can be selected by users based on properties of colony dishes. With the illumination box, lightning can be uniform; colony dish can be put in the same place every time, which make image processing easy. A digital camera in the top of the box connected to a PC computer with a USB cable, all the camera functions are controlled by the computer.

  14. Electron Microscopy and Image Analysis for Selected Materials

    Science.gov (United States)

    Williams, George

    1999-01-01

    This particular project was completed in collaboration with the metallurgical diagnostics facility. The objective of this research had four major components. First, we required training in the operation of the environmental scanning electron microscope (ESEM) for imaging of selected materials including biological specimens. The types of materials range from cyanobacteria and diatoms to cloth, metals, sand, composites and other materials. Second, to obtain training in surface elemental analysis technology using energy dispersive x-ray (EDX) analysis, and in the preparation of x-ray maps of these same materials. Third, to provide training for the staff of the metallurgical diagnostics and failure analysis team in the area of image processing and image analysis technology using NIH Image software. Finally, we were to assist in the sample preparation, observing, imaging, and elemental analysis for Mr. Richard Hoover, one of NASA MSFC's solar physicists and Marshall's principal scientist for the agency-wide virtual Astrobiology Institute. These materials have been collected from various places around the world including the Fox Tunnel in Alaska, Siberia, Antarctica, ice core samples from near Lake Vostoc, thermal vents in the ocean floor, hot springs and many others. We were successful in our efforts to obtain high quality, high resolution images of various materials including selected biological ones. Surface analyses (EDX) and x-ray maps were easily prepared with this technology. We also discovered and used some applications for NIH Image software in the metallurgical diagnostics facility.

  15. Determination of fish gender using fractal analysis of ultrasound images

    DEFF Research Database (Denmark)

    McEvoy, Fintan J.; Tomkiewicz, Jonna; Støttrup, Josianne;

    2009-01-01

    The gender of cod Gadus morhua can be determined by considering the complexity in their gonadal ultrasonographic appearance. The fractal dimension (DB) can be used to describe this feature in images. B-mode gonadal ultrasound images in 32 cod, where gender was known, were collected. Fractal...... by subjective analysis alone. The mean (and standard deviation) of the fractal dimension DB for male fish was 1.554 (0.073) while for female fish it was 1.468 (0.061); the difference was statistically significant (P=0.001). The area under the ROC curve was 0.84 indicating the value of fractal analysis in gender...... result. Fractal analysis is useful for gender determination in cod. This or a similar form of analysis may have wide application in veterinary imaging as a tool for quantification of complexity in images...

  16. Analysis Operator Learning and Its Application to Image Reconstruction

    CERN Document Server

    Hawe, Simon; Diepold, Klaus

    2012-01-01

    Exploiting a priori known structural information lies at the core of many image reconstruction methods that can be stated as inverse problems. The synthesis model, which assumes that images can be decomposed into a linear combination of very few atoms of some dictionary, is now a well established tool for the design of image reconstruction algorithms. An interesting alternative is the analysis model, where the signal is multiplied by an analysis operator and the outcome is assumed to be the sparse. This approach has only recently gained increasing interest. The quality of reconstruction methods based on an analysis model severely depends on the right choice of the suitable operator. In this work, we present an algorithm for learning an analysis operator from training images. Our method is based on an $\\ell_p$-norm minimization on the set of full rank matrices with normalized columns. We carefully introduce the employed conjugate gradient method on manifolds, and explain the underlying geometry of the constrai...

  17. Porosity determination on pyrocarbon using automatic quantitative image analysis

    International Nuclear Information System (INIS)

    Methods of porosity determination are reviewed and applied to the measurement of the porosity of pyrocarbon. Specifically, the mathematical basis of stereology and the procedures involved in quantitative image analysis are detailed

  18. Segmentation and learning in the quantitative analysis of microscopy images

    Science.gov (United States)

    Ruggiero, Christy; Ross, Amy; Porter, Reid

    2015-02-01

    In material science and bio-medical domains the quantity and quality of microscopy images is rapidly increasing and there is a great need to automatically detect, delineate and quantify particles, grains, cells, neurons and other functional "objects" within these images. These are challenging problems for image processing because of the variability in object appearance that inevitably arises in real world image acquisition and analysis. One of the most promising (and practical) ways to address these challenges is interactive image segmentation. These algorithms are designed to incorporate input from a human operator to tailor the segmentation method to the image at hand. Interactive image segmentation is now a key tool in a wide range of applications in microscopy and elsewhere. Historically, interactive image segmentation algorithms have tailored segmentation on an image-by-image basis, and information derived from operator input is not transferred between images. But recently there has been increasing interest to use machine learning in segmentation to provide interactive tools that accumulate and learn from the operator input over longer periods of time. These new learning algorithms reduce the need for operator input over time, and can potentially provide a more dynamic balance between customization and automation for different applications. This paper reviews the state of the art in this area, provides a unified view of these algorithms, and compares the segmentation performance of various design choices.

  19. Image analysis on the archimedes palimpsest

    OpenAIRE

    Tonazzini, Anna; Bedini, Luigi; Salerno, Emanuele

    2004-01-01

    Image processing procedures developed at ISTI-CNR have been applied to recover some of the hidden writing in the Archimedes palimpsest, an ancient manuscript in which faint remnants of several treatises by the great philosopher and mathematician are partially hidden under a more recent text.

  20. Wound Image Analysis Using Contour Evolution

    Directory of Open Access Journals (Sweden)

    K. Sundeep Kumar

    2014-05-01

    Full Text Available The aim of the algorithm described in this paper is to segment wound images from the normal and classify them according to the types of the wound. The segmentation of wounds extravagates color representation, which has been followed by an algorithm of grayscale segmentation based on the stack mathematical approach. Accurate classification of wounds and analyzing wound healing process is a critical task for patient care and health cost reduction at hospital. The tissue uniformity and flatness leads to a simplified approach but requires multispectral imaging for enhanced wound delineation. Contour Evolution method which uses multispectral imaging replaces more complex tools such as, SVM supervised classification, as no training step is required. In Contour Evolution, classification can be done by clustering color information, with differential quantization algorithm, the color centroids of small squares taken from segmented part of the wound image in (C1,C2 plane. Where C1, C2 are two chrominance components. Wound healing is identified by measuring the size of the wound through various means like contact and noncontact methods of wound. The wound tissues proportion is also estimated by a qualitative visual assessment based on the red-yellow-black code. Moreover, involving all the spectral response of the tissue and not only RGB components provides a higher discrimination for separating healed epithelial tissue from granulation tissue.