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Sample records for hybridization cgh analysis

  1. Cluster Analysis of Comparative Genomic Hybridization (CGH Data Using Self-Organizing Maps: Application to Prostate Carcinomas

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    Torsten Mattfeldt

    2001-01-01

    Full Text Available Comparative genomic hybridization (CGH is a modern genetic method which enables a genome‐wide survey of chromosomal imbalances. For each chromosome region, one obtains the information whether there is a loss or gain of genetic material, or whether there is no change at that region. Usually it is not possible to evaluate all 46 chromosomes of a metaphase, therefore several (up to 20 or more metaphases are analyzed per individual, and expressed as average. Mostly one does not study one individual alone but groups of 20–30 individuals. Therefore, large amounts of data quickly accumulate which must be put into a logical order. In this paper we present the application of a self‐organizing map (Genecluster as a tool for cluster analysis of data from pT2N0 prostate cancer cases studied by CGH. Self‐organizing maps are artificial neural networks with the capability to form clusters on the basis of an unsupervised learning rule, i.e., in our examples it gets the CGH data as only information (no clinical data. We studied a group of 40 recent cases without follow‐up, an older group of 20 cases with follow‐up, and the data set obtained by pooling both groups. In all groups good clusterings were found in the sense that clinically similar cases were placed into the same clusters on the basis of the genetic information only. The data indicate that losses on chromosome arms 6q, 8p and 13q are all frequent in pT2N0 prostatic cancer, but the loss on 8p has probably the largest prognostic importance.

  2. Genetic characterization of dogs via chromosomal analysis and array-based comparative genomic hybridization (aCGH).

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    Müller, M H; Reimann-Berg, N; Bullerdiek, J; Murua Escobar, H

    2012-01-01

    The results of cytogenetic and molecular cytogenetic investigations revealed similarities in genetic background and biological behaviour between tumours and genetic diseases of humans and dogs. These findings classify the dog a good and accepted model for human cancers such as osteosarcomas, mammary carcinomas, oral melanomas and others. With the appearance of new studies and advances in canine genome sequencing, the number of known homologies in diseases between these species raised and still is expected to increase. In this context, array-based comparative genomic hybridization (aCGH) provides a novel tool to rapidly characterize numerical aberrations in canine tumours or to detect copy number aberrations between different breeds. As it is possible to spot probes covering the whole genome on each chip to discover copy number aberrations of all chromosomes simultaneously, this method is time-saving and cost-effective - considering the relation of costs and the amount of data obtained. Complemented with traditional methods like karyotyping and fluorescence in situ hybridization (FISH) analyses, the aCGH is able to provide new insights into the underlying causes of canine carcinogenesis.

  3. Identification and characterization of a de novo partial trisomy 10p by comparative genomic hybridization (CGH).

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    Benzacken, B; Lapierre, J M; Siffroi, J P; Chalvon, A; Tachdjian, G

    1998-10-01

    We report the characterization of a de novo unbalanced chromosome rearrangement by comparative genomic hybridization (CGH) in a 15-day-old child with hypotonia and dysmorphia. We describe the combined use of CGH and fluorescence in situ hybridization (FISH) to identify the origin of the additional chromosomal material on the short arm of chromosome 6. Investigation with FISH revealed that the excess material was not derived from chromosome 6. Identification of unknown unbalanced aberrations that could not be identified by traditional cytogenetics procedures is possible by CGH analysis. Visual analysis of digital images from CGH-metaphase spreads revealed a predominantly green signal on the telomeric region of chromosome 10p. After quantitative digital ratio imaging of 10 CGH-metaphase spreads, a region of gain was found in the chromosome band 10p14-pter. The CGH finding was confirmed by FISH analysis, using a whole chromosome 10 paint probe. These results show the usefulness of CGH for a rapid characterization of de novo unbalanced translocation, unidentifiable by karyotype alone.

  4. A web server for mining Comparative Genomic Hybridization (CGH) data

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    Liu, Jun; Ranka, Sanjay; Kahveci, Tamer

    2007-11-01

    Advances in cytogenetics and molecular biology has established that chromosomal alterations are critical in the pathogenesis of human cancer. Recurrent chromosomal alterations provide cytological and molecular markers for the diagnosis and prognosis of disease. They also facilitate the identification of genes that are important in carcinogenesis, which in the future may help in the development of targeted therapy. A large amount of publicly available cancer genetic data is now available and it is growing. There is a need for public domain tools that allow users to analyze their data and visualize the results. This chapter describes a web based software tool that will allow researchers to analyze and visualize Comparative Genomic Hybridization (CGH) datasets. It employs novel data mining methodologies for clustering and classification of CGH datasets as well as algorithms for identifying important markers (small set of genomic intervals with aberrations) that are potentially cancer signatures. The developed software will help in understanding the relationships between genomic aberrations and cancer types.

  5. Insertional translocation detected using FISH confirmation of array-comparative genomic hybridization (aCGH) results.

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    Kang, Sung-Hae L; Shaw, Chad; Ou, Zhishuo; Eng, Patricia A; Cooper, M Lance; Pursley, Amber N; Sahoo, Trilochan; Bacino, Carlos A; Chinault, A Craig; Stankiewicz, Pawel; Patel, Ankita; Lupski, James R; Cheung, Sau Wai

    2010-05-01

    Insertional translocations (ITs) are rare events that require at least three breaks in the chromosomes involved and thus qualify as complex chromosomal rearrangements (CCR). In the current study, we identified 40 ITs from approximately 18,000 clinical cases (1:500) using array-comparative genomic hybridization (aCGH) in conjunction with fluorescence in situ hybridization (FISH) confirmation of the aCGH findings, and parental follow-up studies. Both submicroscopic and microscopically visible IT events were detected. They were divided into three major categories: (1) simple intrachromosomal and interchromosomal IT resulting in pure segmental trisomy, (2) complex IT involving more than one abnormality, (3) deletion inherited from a parent with a balanced IT resulting in pure segmental monosomy. Of the cases in which follow-up parental studies were available, over half showed inheritance from an apparently unaffected parent carrying the same unbalanced rearrangement detected in the propositi, thus decreasing the likelihood that these IT events are clinically relevant. Nevertheless, we identified six cases in which small submicroscopic events were detected involving known disease-associated genes/genomic segments and are likely to be pathogenic. We recommend that copy number gains detected by clinical aCGH analysis should be confirmed using FISH analysis whenever possible in order to determine the physical location of the duplicated segment. We hypothesize that the increased use of aCGH in the clinic will demonstrate that IT occurs more frequently than previously considered but can identify genomic rearrangements with unclear clinical significance.

  6. ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.

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    Ramón Díaz-Uriarte

    Full Text Available BACKGROUND: Copy number alterations (CNAs in genomic DNA have been associated with complex human diseases, including cancer. One of the most common techniques to detect CNAs is array-based comparative genomic hybridization (aCGH. The availability of aCGH platforms and the need for identification of CNAs has resulted in a wealth of methodological studies. METHODOLOGY/PRINCIPAL FINDINGS: ADaCGH is an R package and a web-based application for the analysis of aCGH data. It implements eight methods for detection of CNAs, gains and losses of genomic DNA, including all of the best performing ones from two recent reviews (CBS, GLAD, CGHseg, HMM. For improved speed, we use parallel computing (via MPI. Additional information (GO terms, PubMed citations, KEGG and Reactome pathways is available for individual genes, and for sets of genes with altered copy numbers. CONCLUSIONS/SIGNIFICANCE: ADACGH represents a qualitative increase in the standards of these types of applications: a all of the best performing algorithms are included, not just one or two; b we do not limit ourselves to providing a thin layer of CGI on top of existing BioConductor packages, but instead carefully use parallelization, examining different schemes, and are able to achieve significant decreases in user waiting time (factors up to 45x; c we have added functionality not currently available in some methods, to adapt to recent recommendations (e.g., merging of segmentation results in wavelet-based and CGHseg algorithms; d we incorporate redundancy, fault-tolerance and checkpointing, which are unique among web-based, parallelized applications; e all of the code is available under open source licenses, allowing to build upon, copy, and adapt our code for other software projects.

  7. Whole genome amplification for CGH analysis: Linker-adapter PCR as the method of choice for difficult and limited samples.

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    Pirker, Christine; Raidl, Maria; Steiner, Elisabeth; Elbling, Leonilla; Holzmann, Klaus; Spiegl-Kreinecker, Sabine; Aubele, Michaela; Grasl-Kraupp, Bettina; Marosi, Christine; Micksche, Michael; Berger, Walter

    2004-09-01

    Comparative genomic hybridization (CGH) is a powerful method to investigate chromosomal imbalances in tumor cells. However, DNA quantity and quality can be limiting factors for successful CGH analysis. The aim of this study was to investigate the applicability of degenerate oligonucleotide-primed PCR (DOP-PCR) and a recently developed linker-adapter-mediated PCR (LA-PCR) for whole genome amplification for use in CGH, especially for difficult source material. We comparatively analyzed DNA of variable quality derived from different cell/tissue types. Additionally, dilution experiments down to the DNA content of a single cell were performed. FISH and/or classical cytogenetic analyses were used as controls. In the case of high quality DNA samples, both methods were equally suitable for CGH. When analyzing very small amounts of these DNA samples (equivalent to one or a few human diploid cells), DOP-PCR-CGH, but not LA-PCR-CGH, frequently produced false-positive signals (e.g., gains in 1p and 16p, and losses in chromosome 4q). In case of formalin-fixed paraffin-embedded tissues, success rates by LA-PCR-CGH were significantly higher as compared to DOP-PCR-CGH. DNA of minor quality frequently could be analyzed correctly by LA-PCR-CGH, but was prone to give false-positive and/or false-negative results by DOP-PCR-CGH. LA-PCR is superior to DOP-PCR for amplification of DNA for CGH analysis, especially in the case of very limited or partly degraded source material. Copyright 2004 Wiley-Liss, Inc

  8. Analysis of Array-CGH Data Using the R and Bioconductor Software Suite

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    Winfried A. Hofmann

    2009-01-01

    Full Text Available Background. Array-based comparative genomic hybridization (array-CGH is an emerging high-resolution and high-throughput molecular genetic technique that allows genome-wide screening for chromosome alterations. DNA copy number alterations (CNAs are a hallmark of somatic mutations in tumor genomes and congenital abnormalities that lead to diseases such as mental retardation. However, accurate identification of amplified or deleted regions requires a sequence of different computational analysis steps of the microarray data. Results. We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection, and comparative analysis of array-CGH data which allows the accurate and sensitive detection of CNAs. Conclusion. The implemented option for the determination of minimal altered regions (MARs from a series of tumor samples is a step forward in the identification of new tumor suppressor genes or oncogenes.

  9. aCGH-MAS: Analysis of aCGH by means of Multiagent System

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    Benito, Rocío; Bajo, Javier; Rodríguez, Ana Eugenia; Abáigar, María

    2015-01-01

    There are currently different techniques, such as CGH arrays, to study genetic variations in patients. CGH arrays analyze gains and losses in different regions in the chromosome. Regions with gains or losses in pathologies are important for selecting relevant genes or CNVs (copy-number variations) associated with the variations detected within chromosomes. Information corresponding to mutations, genes, proteins, variations, CNVs, and diseases can be found in different databases and it would be of interest to incorporate information of different sources to extract relevant information. This work proposes a multiagent system to manage the information of aCGH arrays, with the aim of providing an intuitive and extensible system to analyze and interpret the results. The agent roles integrate statistical techniques to select relevant variations and visualization techniques for the interpretation of the final results and to extract relevant information from different sources of information by applying a CBR system. PMID:25874203

  10. A model-based circular binary segmentation algorithm for the analysis of array CGH data

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    Tu Shih-Hsin

    2011-10-01

    Full Text Available Abstract Background Circular Binary Segmentation (CBS is a permutation-based algorithm for array Comparative Genomic Hybridization (aCGH data analysis. CBS accurately segments data by detecting change-points using a maximal-t test; but extensive computational burden is involved for evaluating the significance of change-points using permutations. A recent implementation utilizing a hybrid method and early stopping rules (hybrid CBS to improve the performance in speed was subsequently proposed. However, a time analysis revealed that a major portion of computation time of the hybrid CBS was still spent on permutation. In addition, what the hybrid method provides is an approximation of the significance upper bound or lower bound, not an approximation of the significance of change-points itself. Results We developed a novel model-based algorithm, extreme-value based CBS (eCBS, which limits permutations and provides robust results without loss of accuracy. Thousands of aCGH data under null hypothesis were simulated in advance based on a variety of non-normal assumptions, and the corresponding maximal-t distribution was modeled by the Generalized Extreme Value (GEV distribution. The modeling results, which associate characteristics of aCGH data to the GEV parameters, constitute lookup tables (eXtreme model. Using the eXtreme model, the significance of change-points could be evaluated in a constant time complexity through a table lookup process. Conclusions A novel algorithm, eCBS, was developed in this study. The current implementation of eCBS consistently outperforms the hybrid CBS 4× to 20× in computation time without loss of accuracy. Source codes, supplementary materials, supplementary figures, and supplementary tables can be found at http://ntumaps.cgm.ntu.edu.tw/eCBSsupplementary.

  11. CGHPRO – A comprehensive data analysis tool for array CGH

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    Lenzner Steffen

    2005-04-01

    Full Text Available Abstract Background Array CGH (Comparative Genomic Hybridisation is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances. It is based on the co-hybridisation of differentially labelled test and reference DNA onto arrays of genomic BAC clones, cDNAs or oligonucleotides, and after correction for various intervening variables, loss or gain in the test DNA can be indicated from spots showing aberrant signal intensity ratios. Now that this technique is no longer confined to highly specialized laboratories and is entering the realm of clinical application, there is a need for a user-friendly software package that facilitates estimates of DNA dosage from raw signal intensities obtained by array CGH experiments, and which does not depend on a sophisticated computational environment. Results We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection and comparative analysis of array-CGH data. CGHPRO is a stand-alone JAVA application that guides the user through the whole process of data analysis. The import option for image analysis data covers several data formats, but users can also customize their own data formats. Several graphical representation tools assist in the selection of the appropriate normalization method. Intensity ratios of each clone can be plotted in a size-dependent manner along the chromosome ideograms. The interactive graphical interface offers the chance to explore the characteristics of each clone, such as the involvement of the clones sequence in segmental duplications. Circular Binary Segmentation and unsupervised Hidden Markov Model algorithms facilitate objective detection of chromosomal breakpoints. The storage of all essential data in a back-end database allows the simultaneously comparative analysis of different cases. The various display options facilitate also the definition of shortest regions of overlap and simplify the

  12. Parsimonious higher-order hidden Markov models for improved array-CGH analysis with applications to Arabidopsis thaliana.

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    Michael Seifert

    2012-01-01

    Full Text Available Array-based comparative genomic hybridization (Array-CGH is an important technology in molecular biology for the detection of DNA copy number polymorphisms between closely related genomes. Hidden Markov Models (HMMs are popular tools for the analysis of Array-CGH data, but current methods are only based on first-order HMMs having constrained abilities to model spatial dependencies between measurements of closely adjacent chromosomal regions. Here, we develop parsimonious higher-order HMMs enabling the interpolation between a mixture model ignoring spatial dependencies and a higher-order HMM exhaustively modeling spatial dependencies. We apply parsimonious higher-order HMMs to the analysis of Array-CGH data of the accessions C24 and Col-0 of the model plant Arabidopsis thaliana. We compare these models against first-order HMMs and other existing methods using a reference of known deletions and sequence deviations. We find that parsimonious higher-order HMMs clearly improve the identification of these polymorphisms. Moreover, we perform a functional analysis of identified polymorphisms revealing novel details of genomic differences between C24 and Col-0. Additional model evaluations are done on widely considered Array-CGH data of human cell lines indicating that parsimonious HMMs are also well-suited for the analysis of non-plant specific data. All these results indicate that parsimonious higher-order HMMs are useful for Array-CGH analyses. An implementation of parsimonious higher-order HMMs is available as part of the open source Java library Jstacs (www.jstacs.de/index.php/PHHMM.

  13. Parsimonious higher-order hidden Markov models for improved array-CGH analysis with applications to Arabidopsis thaliana.

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    Seifert, Michael; Gohr, André; Strickert, Marc; Grosse, Ivo

    2012-01-01

    Array-based comparative genomic hybridization (Array-CGH) is an important technology in molecular biology for the detection of DNA copy number polymorphisms between closely related genomes. Hidden Markov Models (HMMs) are popular tools for the analysis of Array-CGH data, but current methods are only based on first-order HMMs having constrained abilities to model spatial dependencies between measurements of closely adjacent chromosomal regions. Here, we develop parsimonious higher-order HMMs enabling the interpolation between a mixture model ignoring spatial dependencies and a higher-order HMM exhaustively modeling spatial dependencies. We apply parsimonious higher-order HMMs to the analysis of Array-CGH data of the accessions C24 and Col-0 of the model plant Arabidopsis thaliana. We compare these models against first-order HMMs and other existing methods using a reference of known deletions and sequence deviations. We find that parsimonious higher-order HMMs clearly improve the identification of these polymorphisms. Moreover, we perform a functional analysis of identified polymorphisms revealing novel details of genomic differences between C24 and Col-0. Additional model evaluations are done on widely considered Array-CGH data of human cell lines indicating that parsimonious HMMs are also well-suited for the analysis of non-plant specific data. All these results indicate that parsimonious higher-order HMMs are useful for Array-CGH analyses. An implementation of parsimonious higher-order HMMs is available as part of the open source Java library Jstacs (www.jstacs.de/index.php/PHHMM).

  14. Improved analysis of bacterial CGH data beyond the log-ratio paradigm

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    Aakra Ågot

    2009-03-01

    Full Text Available Abstract Background Existing methods for analyzing bacterial CGH data from two-color arrays are based on log-ratios only, a paradigm inherited from expression studies. We propose an alternative approach, where microarray signals are used in a different way and sequence identity is predicted using a supervised learning approach. Results A data set containing 32 hybridizations of sequenced versus sequenced genomes have been used to test and compare methods. A ROC-analysis has been performed to illustrate the ability to rank probes with respect to Present/Absent calls. Classification into Present and Absent is compared with that of a gaussian mixture model. Conclusion The results indicate our proposed method is an improvement of existing methods with respect to ranking and classification of probes, especially for multi-genome arrays.

  15. Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH

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    Bejjani Bassem A

    2010-06-01

    Full Text Available Abstract Background Microarray-based comparative genomic hybridization (aCGH is a powerful diagnostic tool for the detection of DNA copy number gains and losses associated with chromosome abnormalities, many of which are below the resolution of conventional chromosome analysis. It has been presumed that whole-genome oligonucleotide (oligo arrays identify more clinically significant copy-number abnormalities than whole-genome bacterial artificial chromosome (BAC arrays, yet this has not been systematically studied in a clinical diagnostic setting. Results To determine the difference in detection rate between similarly designed BAC and oligo arrays, we developed whole-genome BAC and oligonucleotide microarrays and validated them in a side-by-side comparison of 466 consecutive clinical specimens submitted to our laboratory for aCGH. Of the 466 cases studied, 67 (14.3% had a copy-number imbalance of potential clinical significance detectable by the whole-genome BAC array, and 73 (15.6% had a copy-number imbalance of potential clinical significance detectable by the whole-genome oligo array. However, because both platforms identified copy number variants of unclear clinical significance, we designed a systematic method for the interpretation of copy number alterations and tested an additional 3,443 cases by BAC array and 3,096 cases by oligo array. Of those cases tested on the BAC array, 17.6% were found to have a copy-number abnormality of potential clinical significance, whereas the detection rate increased to 22.5% for the cases tested by oligo array. In addition, we validated the oligo array for detection of mosaicism and found that it could routinely detect mosaicism at levels of 30% and greater. Conclusions Although BAC arrays have faster turnaround times, the increased detection rate of oligo arrays makes them attractive for clinical cytogenetic testing.

  16. Aneuploidy analysis of non-pronuclear embryos from IVF with use of array CGH: a case report.

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    Lixin, Deng; Zhifeng, Xiang; Cong, He; Jinzhou, Zhang; Hongbin, Xie

    2014-06-01

    By using array comparative genomic hybridization (array CGH), to analyze the aneuploidy of the single blastomeres from non-pronuclear embryos on cleavage-stage in IVF cycle. Four non-pronuclear embryos were got from an IVF cycle, and the each single cell was biopsied from the four cleavage-stage embryos on the third day after the insemination which was investigated by using array CGH. After the biopsy, all the embryos continued to cleave, and lately entered the morula stage on the fifth day, just one embryo 3 was developed to early blastocyst stage on the sixth day. The four blastomere 24 chromosomes showed one X monomer and three normal XY diploids; the autosome chromosomes of blastomeres were abnormally gained or lost at different chromosome from four embryos, such as Embryo 1 : 49,X (-1, -5, -11, -19, -20, -21, -Y, +3, +6, +7, +8, +10, +13, +14, +16, +17, +18); Embryo 2 : 44,XY (-12, -15); Embryo 3: 47,XY (-3, -8, -9, -21, +7, +17, +18, +19, +20); Embryo 4 : 54,XY (+4, +7, +10, +12, +13, +16, +17, +22). With the use of the array CGH, the aneuploidy analysis could review the abnormal chromosomes of single blastomere from the non-pronuclear embryos, which can harbor the risk of abnormal sex chromosome and autosome chromosomes.

  17. Model-based clustering of array CGH data

    National Research Council Canada - National Science Library

    Shah, Sohrab P; Cheung, K-John; Johnson, Nathalie A; Alain, Guillaume; Gascoyne, Randy D; Horsman, Douglas E; Ng, Raymond T; Murphy, Kevin P

    2009-01-01

    Motivation: Analysis of array comparative genomic hybridization (aCGH) data for recurrent DNA copy number alterations from a cohort of patients can yield distinct sets of molecular signatures or profiles...

  18. High-resolution SNP array analysis of patients with developmental disorder and normal array CGH results

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    Siggberg Linda

    2012-09-01

    Full Text Available Abstract Background Diagnostic analysis of patients with developmental disorders has improved over recent years largely due to the use of microarray technology. Array methods that facilitate copy number analysis have enabled the diagnosis of up to 20% more patients with previously normal karyotyping results. A substantial number of patients remain undiagnosed, however. Methods and Results Using the Genome-Wide Human SNP array 6.0, we analyzed 35 patients with a developmental disorder of unknown cause and normal array comparative genomic hybridization (array CGH results, in order to characterize previously undefined genomic aberrations. We detected no seemingly pathogenic copy number aberrations. Most of the vast amount of data produced by the array was polymorphic and non-informative. Filtering of this data, based on copy number variant (CNV population frequencies as well as phenotypically relevant genes, enabled pinpointing regions of allelic homozygosity that included candidate genes correlating to the phenotypic features in four patients, but results could not be confirmed. Conclusions In this study, the use of an ultra high-resolution SNP array did not contribute to further diagnose patients with developmental disorders of unknown cause. The statistical power of these results is limited by the small size of the patient cohort, and interpretation of these negative results can only be applied to the patients studied here. We present the results of our study and the recurrence of clustered allelic homozygosity present in this material, as detected by the SNP 6.0 array.

  19. [Genomic abnormalities in children with mental retardation and autism: the use of comparative genomic hybridization in situ (HRCGH) and molecular karyotyping with DNA-microchips (array CGH)].

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    Vorsanova, S G; Iurov, I Iu; Kurinnaia, O S; Voinova, V Iu; Iurov, Iu B

    2013-01-01

    Genomic abnormalities occur with high frequency in children with mental retardation and autistic spectrum disorders (ADS). Molecular karyotyping using DNA microarrays is a new technology for diagnosis of genomic and chromosomal abnormalities in autism implemented in the fields of biological psychiatry and medical genetics. We carried out a comparative analysis of the frequency and spectrum of genome abnormalities in children with mental retardation and autism of unknown etiology using high-resolution comparative genomic methods for hybridization (HRCGH) and molecular karyotyping (array CGH). In a study of 100 children with autism, learning difficulties and congenital malformations by HRCGH, we identified genomic rearrangements in 46% of cases. Using array CGH we examined 50 children with autism. In 44 cases out of 50 (88%), different genomic abnormalities and genomic variations (CNV - copy number variations) were identified. Unbalanced genomic rearrangements, including deletions and duplications, were found in 23 cases out of 44 (52%). These data suggest that genomic abnormalities which are not detectable by common methods of chromosome analysis are often discovered by molecular cytogenetic techniques in children autism spectrum disorders. In addition, 54 children with idiopathic mental retardation and congenital malformations (31 boys and 23 girls) without autism spectrum disorders were examined using molecular karyotyping and microarray containing an increased number of DNA samples for genomic loci of chromosome X. Deletions and duplications affecting different regions of the chromosome X were detected in 11 out of 54 children (20.4%).

  20. Characterization of genomic alterations in radiation-associated breast cancer among childhood cancer survivors, using comparative genomic hybridization (CGH arrays.

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    Xiaohong R Yang

    Full Text Available Ionizing radiation is an established risk factor for breast cancer. Epidemiologic studies of radiation-exposed cohorts have been primarily descriptive; molecular events responsible for the development of radiation-associated breast cancer have not been elucidated. In this study, we used array comparative genomic hybridization (array-CGH to characterize genome-wide copy number changes in breast tumors collected in the Childhood Cancer Survivor Study (CCSS. Array-CGH data were obtained from 32 cases who developed a second primary breast cancer following chest irradiation at early ages for the treatment of their first cancers, mostly Hodgkin lymphoma. The majority of these cases developed breast cancer before age 45 (91%, n = 29, had invasive ductal tumors (81%, n = 26, estrogen receptor (ER-positive staining (68%, n = 19 out of 28, and high proliferation as indicated by high Ki-67 staining (77%, n = 17 out of 22. Genomic regions with low-copy number gains and losses and high-level amplifications were similar to what has been reported in sporadic breast tumors, however, the frequency of amplifications of the 17q12 region containing human epidermal growth factor receptor 2 (HER2 was much higher among CCSS cases (38%, n = 12. Our findings suggest that second primary breast cancers in CCSS were enriched for an "amplifier" genomic subgroup with highly proliferative breast tumors. Future investigation in a larger irradiated cohort will be needed to confirm our findings.

  1. A hybrid Gerchberg-Saxton-like algorithm for DOE and CGH calculation

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    Wang, Haichao; Yue, Weirui; Song, Qiang; Liu, Jingdan; Situ, Guohai

    2017-02-01

    The Gerchberg-Saxton (GS) algorithm is widely used in various disciplines of modern sciences and technologies where phase retrieval is required. However, this legendary algorithm most likely stagnates after a few iterations. Many efforts have been taken to improve this situation. Here we propose to introduce the strategy of gradient descent and weighting technique to the GS algorithm, and demonstrate it using two examples: design of a diffractive optical element (DOE) to achieve off-axis illumination in lithographic tools, and design of a computer generated hologram (CGH) for holographic display. Both numerical simulation and optical experiments are carried out for demonstration.

  2. Genomic analysis of clonal eosinophils by CGH arrays reveals new genetic regions involved in chronic eosinophilia.

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    Arefi, Maryam; Robledo, Cristina; Peñarrubia, María J; García de Coca, Alfonso; Cordero, Miguel; Hernández-Rivas, Jesús M; García, Juan Luis

    2014-11-01

    To assess the presence of genetic imbalances in patients with myeloproliferative neoplasms (MPNs), 38 patients with chronic eosinophilia were studied by array comparative genomic hybridization (aCGH): seven had chronic myelogenous leukaemia (CML), BCR-ABL1 positive, nine patients had myeloproliferative neoplasia Ph- (MPN-Ph-), three had a myeloid neoplasm associated with a PDGFRA rearrangement, and the remaining two cases were Lymphoproliferative T neoplasms associated with eosinophilia. In addition, 17 patients had a secondary eosinophilia and were used as controls. Eosinophilic enrichment was carried out in all cases. Genomic imbalances were found in 76% of all MPN patients. Losses on 20q were the most frequent genetic abnormality in MPNs (32%), affected the three types of MPN studied. This study also found losses at 11q13.3 in 26% of patients with MPN-Ph- and in 19p13.11 in two of the three patients with an MPN associated with a PDGFRA rearrangement. In addition, 29% of patients with CML had losses on 8q24. In summary, aCGH revealed clonality in eosinophils in most MPNs, suggesting that it could be a useful technique for defining clonality in these diseases. The presence of genetic losses in new regions could provide new insights into the knowledge of these MPN associated with eosinophilia. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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

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    Baudis Michael

    2007-12-01

    Full Text Available Abstract Background Chromosomal abnormalities have been associated with most human malignancies, with gains and losses on some genomic regions associated with particular entities. Methods 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. Results 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. Conclusion 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.

  4. Cytogenetic analysis from DNA by comparative genomic hybridization.

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    Tachdjian, G; Aboura, A; Lapierre, J M; Viguié, F

    2000-01-01

    Comparative genomic hybridization (CGH) is a modified in situ hybridization technique which allows detection and mapping of DNA sequence copy differences between two genomes in a single experiment. In CGH analysis, two differentially labelled genomic DNA (study and reference) are co-hybridized to normal metaphase spreads. Chromosomal locations of copy number changes in the DNA segments of the study genome are revealed by a variable fluorescence intensity ratio along each target chromosome. Since its development, CGH has been applied mostly as a research tool in the field of cancer cytogenetics to identify genetic changes in many previously unknown regions. CGH may also have a role in clinical cytogenetics for detection and identification of unbalanced chromosomal abnormalities.

  5. Comparative genomic hybridization analysis of benign and invasive male breast neoplasms

    DEFF Research Database (Denmark)

    Ojopi, Elida Paula Benquique; Cavalli, Luciane Regina; Cavalieri, Luciane Mara Bogline

    2002-01-01

    Comparative genomic hybridization (CGH) analysis was performed for the identification of chromosomal imbalances in two benign gynecomastias and one malignant breast carcinoma derived from patients with male breast disease and compared with cytogenetic analysis in two of the three cases. CGH analy...

  6. High-Resolution Analysis of Gene Copy Number Alterations in Human Prostate Cancer Using CGH on cDNA Microarrays: Impact of Copy Number on Gene Expression

    Directory of Open Access Journals (Sweden)

    Maija Wolf

    2004-05-01

    Full Text Available Identification of target genes for genetic rearrangements in prostate cancer and the impact of copy number changes on gene expression are currently not well understood. Here, we applied high-resolution comparative genomic hybridization (CGH on cDNA microarrays for analysis of prostate cancer cell lines. CGH microarrays identified most of the alterations detected by classical chromosomal CGH, as well as a number of previously unreported alterations. Specific recurrent regions of gain (28 and loss (18 were found, their boundaries defined with sub-megabasepair accuracy. The most common changes included copy number decreases at 13% and gains at iq and 5p. Refined mapping identified several sites, such as at 13q (33-44, 49-51, 74-76 Mbp from the p-telomere, which matched with minimal regions of loss seen in extensive loss of heterozygosity mapping studies of large numbers of tumors. Previously unreported recurrent changes were found at 2p, 2q, 3p, 17q (losses, at 3q, 5p, 6p (gains. Integration of genomic and transcriptomic data revealed the role of individual candidate target genes for genomic alterations as well as a highly significant (P < .0001 overall association between copy number levels and the percentage of differentially expressed genes. Across the genome, the overall impact of copy number on gene expression levels was, to a large extent, attributable to low-level gains and losses of copy number, corresponding to common deletions and gains of often large chromosomal regions.

  7. An Xq22.3 duplication detected by comparative genomic hybridization microarray (Array-CGH) defines a new locus (FGS5) for FG syndrome.

    Science.gov (United States)

    Jehee, Fernanda Sarquis; Rosenberg, Carla; Krepischi-Santos, Ana Cristina; Kok, Fernando; Knijnenburg, Jeroen; Froyen, Guy; Vianna-Morgante, Angela M; Opitz, John M; Passos-Bueno, Maria Rita

    2005-12-15

    FG syndrome is an X-linked multiple congenital anomalies (MCA) syndrome. It has been mapped to four distinct loci FGS1-4, through linkage analysis (Xq13, Xp22.3, and Xp11.4-p11.3) and based on the breakpoints of an X chromosome inversion (Xq11:Xq28), but so far no gene has been identified. We describe a boy with FG syndrome who has an inherited duplication at band Xq22.3 detected by comparative genomic hybridization microarray (Array-CGH). These duplication maps outside all four loci described so far for FG syndrome, representing therefore a new locus, which we propose to be called FGS5. MID2, a gene closely related to MID1, which is known to be mutated in Opitz G/BBB syndrome, maps within the duplicated segment of our patient. Since FG and Opitz G/BBB syndromes share many manifestations we considered MID2 a candidate gene for FG syndrome. We also discuss the involvement of other potential genes within the duplicated segment and its relationship with clinical symptoms of our patient, as well as the laboratory abnormalities found in his mother, a carrier of the duplication.

  8. Detection and precise mapping of germline rearrangements in BRCA1, BRCA2, MSH2, and MLH1 using zoom-in array comparative genomic hybridization (aCGH)

    DEFF Research Database (Denmark)

    Staaf, Johan; Törngren, Therese; Rambech, Eva

    2008-01-01

    Disease-predisposing germline mutations in cancer susceptibility genes may consist of large genomic rearrangements that are challenging to detect and characterize using standard PCR-based mutation screening methods. Here, we describe a custom-made zoom-in microarray comparative genomic...... hybridization (CGH) platform of 60mer oligonucleotides. The 4 x 44 K array format provides high-resolution coverage (200-300 bp) of 400-700 kb genomic regions surrounding six cancer susceptibility genes. We evaluate its performance to accurately detect and precisely map earlier described or novel large germline...

  9. Asterias: A Parallelized Web-based Suite for the Analysis of Expression and aCGH Data

    Directory of Open Access Journals (Sweden)

    Ramón Díaz-Uriarte

    2007-01-01

    Full Text Available The analysis of expression and CGH arrays plays a central role in the study of complex diseases, especially cancer, including finding markers for early diagnosis and prognosis, choosing an optimal therapy, or increasing our understanding of cancer development and metastasis. Asterias (http://www.asterias.info is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI and run on a server with 60 CPUs for computation; compared to a desktop or server-based but not parallelized application, parallelization provides speed ups of factors up to 50. Most of our applications allow the user to obtain additional information for user-selected genes (chromosomal location, PubMed ids, Gene Ontology terms, etc. by using clickable links in tables and/or fi gures. Our tools include: normalization of expression and aCGH data (DNMAD; converting between different types of gene/clone and protein identifi ers (IDconverter/IDClight; fi ltering and imputation (preP; finding differentially expressed genes related to patient class and survival data (Pomelo II; searching for models of class prediction (Tnasas; using random forests to search for minimal models for class prediction or for large subsets of genes with predictive capacity (GeneSrF; searching for molecular signatures and predictive genes with survival data (SignS; detecting regions of genomic DNA gain or loss (ADaCGH. The capability to send results between different applications, access to additional functional information, and parallelized computation make our suite unique and exploit features only available to web-based applications.

  10. Array-based comparative genomic hybridization is more informative than conventional karyotyping and fluorescence in situ hybridization in the analysis of first-trimester spontaneous abortion

    Directory of Open Access Journals (Sweden)

    Gao Jinsong

    2012-07-01

    Full Text Available Abstract Background Array-based comparative genomic hybridization (aCGH is a new technique for detecting submicroscopic deletions and duplications, and can overcome many of the limitations associated with classic cytogenetic analysis. However, its clinical use in spontaneous abortion needs comprehensive evaluation. We used aCGH to investigate chromosomal imbalances in 100 spontaneous abortions and compared the results with G-banding karyotyping and fluorescence in situ hybridization (FISH. Inconsistent results were verified by quantitative fluorescence PCR. Results Abnormalities were detected in 61 cases. aCGH achieved the highest detection rate (93.4%, 57/61 compared with traditional karyotyping (77%, 47/61 and FISH analysis (68.9%, 42/61. aCGH identified all chromosome abnormalities reported by traditional karyotyping and interphase FISH analysis, with the exception of four triploids. It also detected three additional aneuploidy cases in 37 specimens with ‘normal’ karyotypes, one mosaicism and 10 abnormalities in 14 specimens that failed to grow in vitro. Conclusions aCGH analysis circumvents many limitations in traditional karyotyping or FISH. The accuracy and efficiency of aCGH in spontaneous abortions highlights its clinical usefulness for the future. As aborted tissues have the potential to be contaminated with maternal cells, the threshold value of detection in aCGH should be lowered to avoid false negatives.

  11. Medical applications of array CGH and the transformation of clinical cytogenetics.

    Science.gov (United States)

    Shaffer, L G; Bejjani, B A

    2006-01-01

    Microarray-based comparative genomic hybridization (array CGH) merges molecular diagnostics with traditional chromosome analysis and is transforming the field of cytogenetics. Prospective studies of individuals with developmental delay and dysmorphic features have demonstrated that array CGH has the ability to detect any genomic imbalance including deletions, duplications, aneuploidies and amplifications. Detection rates for chromosome abnormalities with array CGH range from 5-17% in individuals with normal results from prior routine cytogenetic testing. In addition, copy number variants (CNVs) were identified in all studies. These CNVs may include large-scale variation and can confound the diagnostic interpretations. Although cytogeneticists will require additional training and laboratories must become appropriately equipped, array CGH holds the promise of being the initial diagnostic tool in the identification of visible and submicroscopic chromosome abnormalities in mental retardation and other developmental disabilities.

  12. PanCGH: a genotype-calling algorithm for pangenome CGH data.

    NARCIS (Netherlands)

    Bayjanov, J.; Wels, M.W.W.; Starrenburg, M.; Hylckama Vlieg, J.E. van; Siezen, R.J.; Molenaar, D.

    2009-01-01

    MOTIVATION: Pangenome arrays contain DNA oligomers targeting several sequenced reference genomes from the same species. In microbiology, these can be employed to investigate the often high genetic variability within a species by comparative genome hybridization (CGH). The biological interpretation o

  13. Copy number analysis of the low-copy repeats at the primate NPHP1 locus by array comparative genomic hybridization.

    Science.gov (United States)

    Yuan, Bo; Liu, Pengfei; Rogers, Jeffrey; Lupski, James R

    2016-06-01

    Array comparative genomic hybridization (aCGH) has been widely used to detect copy number variants (CNVs) in both research and clinical settings. A customizable aCGH platform may greatly facilitate copy number analyses in genomic regions with higher-order complexity, such as low-copy repeats (LCRs). Here we present the aCGH analyses focusing on the 45 kb LCRs [1] at the NPHP1 region with diverse copy numbers in humans. Also, the interspecies aCGH analysis comparing human and nonhuman primates revealed dynamic copy number transitions of the human 45 kb LCR orthologues during primate evolution and therefore shed light on the origin of complexity at this locus. The original aCGH data are available at GEO under GSE73962.

  14. Genome-wide microarray expression and genomic alterations by array-CGH analysis in neuroblastoma stem-like cells.

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    Raquel Ordóñez

    Full Text Available Neuroblastoma has a very diverse clinical behaviour: from spontaneous regression to a very aggressive malignant progression and resistance to chemotherapy. This heterogeneous clinical behaviour might be due to the existence of Cancer Stem Cells (CSC, a subpopulation within the tumor with stem-like cell properties: a significant proliferation capacity, a unique self-renewal capacity, and therefore, a higher ability to form new tumors. We enriched the CSC-like cell population content of two commercial neuroblastoma cell lines by the use of conditioned cell culture media for neurospheres, and compared genomic gains and losses and genome expression by array-CGH and microarray analysis, respectively (in CSC-like versus standard tumor cells culture. Despite the array-CGH did not show significant differences between standard and CSC-like in both analyzed cell lines, the microarray expression analysis highlighted some of the most relevant biological processes and molecular functions that might be responsible for the CSC-like phenotype. Some signalling pathways detected seem to be involved in self-renewal of normal tissues (Wnt, Notch, Hh and TGF-β and contribute to CSC phenotype. We focused on the aberrant activation of TGF-β and Hh signalling pathways, confirming the inhibition of repressors of TGF-β pathway, as SMAD6 and SMAD7 by RT-qPCR. The analysis of the Sonic Hedgehog pathway showed overexpression of PTCH1, GLI1 and SMO. We found overexpression of CD133 and CD15 in SIMA neurospheres, confirming that this cell line was particularly enriched in stem-like cells. This work shows a cross-talk among different pathways in neuroblastoma and its importance in CSC-like cells.

  15. A predictive factor of the quality of microarray comparative genomic hybridization analysis for formalin-fixed paraffin-embedded archival tissue.

    Science.gov (United States)

    Nakao, Kenjiro; Oikawa, Masahiro; Arai, Junichi; Mussazhanova, Zhanna; Kondo, Hisayoshi; Shichijo, Kazuko; Nakashima, Masahiro; Hayashi, Tomayoshi; Yoshiura, Koh-Ichiro; Hatachi, Toshiko; Nagayasu, Takeshi

    2013-09-01

    Utilizing formalin-fixed paraffin-embedded (FFPE) archival tissue, the most common form of tissue preservation in routine practice, for cytogenetic analysis using microarray comparative genomic hybridization (aCGH) remains challenging. We searched for a predictive factor of the performance of FFPE DNA in aCGH analysis. DNA was extracted from 63 FFPE archival tissue samples of various tissue types (31 breast cancers, 24 lung cancers, and 8 thyroid tumors), followed by aCGH analysis using high-density oligonucleotide microarrays. Tumor DNA from matched frozen samples and from FFPE samples after whole-genome amplification were also analyzed in 2 and 4 case, respectively. The derivative log ratio spread (DLRSpread) was used to assess the overall quality of each aCGH result. The DLRSpread correlated significantly with the double-stranded DNA ratio of tumor DNA, storage time, and the degree of labeling with Cy5 (Parchival tissue samples can be utilized for aCGH analysis.

  16. Significance of genome-wide analysis of copy number alterations and UPD in myelodysplastic syndromes using combined CGH - SNP arrays.

    Science.gov (United States)

    Ahmad, Ausaf; Iqbal, M Anwar

    2012-01-01

    Genetic information is an extremely valuable data source in characterizing the personal nature of cancer. Chromosome instability is a hallmark of most cancer cells. Chromosomal abnormalities are correlated with poor prognosis, disease classification, risk stratification, and treatment selection. Copy number alterations (CNAs) are an important molecular signature in cancer initiation, development, and progression. Recent application of whole-genome tools to characterize normal and cancer genomes provides the powerful molecular cytogenetic means to enumerate the multiple somatic, genetic and epigenetic alterations that occur in cancer. Combined array comparative genomic hybridization (aCGH) with single nucleotide polymorphism (SNP) array is a useful technique allowing detection of CNAs and loss of heterozygosity (LOH) or uni-parental disomy (UPD) together in a single experiment. It also provides allelic information on deletions, duplications, and amplifications. UPD can result in an abnormal phenotype when the chromosomes involved are imprinted. Myelodysplastic syndromes (MDS) are the most common clonal stem cell hematologic malignancy characterized by ineffective hematopoiesis, which leads to rapid progression into acute myeloid leukemia. UPD that occurs without concurrent changes in the gene copy number is a common chromosomal defect in hematologic malignancies, especially in MDS. Approximately 40-50% of MDS patients do not have karyotypic abnormalities that are detectable using classical metaphase cytogenetic techniques (MC) because of inherent limitations of MC, low resolution and the requirement of having dividing cells. In this review, we highlight advances in the clinical application of microarray technology in MDS and discuss the clinical potential of microarray.

  17. Integrated high-resolution array CGH and SKY analysis of homozygous deletions and other genomic alterations present in malignant mesothelioma cell lines.

    Science.gov (United States)

    Klorin, Geula; Rozenblum, Ester; Glebov, Oleg; Walker, Robert L; Park, Yoonsoo; Meltzer, Paul S; Kirsch, Ilan R; Kaye, Frederic J; Roschke, Anna V

    2013-05-01

    High-resolution oligonucleotide array comparative genomic hybridization (aCGH) and spectral karyotyping (SKY) were applied to a panel of malignant mesothelioma (MMt) cell lines. SKY has not been applied to MMt before, and complete karyotypes are reported based on the integration of SKY and aCGH results. A whole genome search for homozygous deletions (HDs) produced the largest set of recurrent and non-recurrent HDs for MMt (52 recurrent HDs in 10 genomic regions; 36 non-recurrent HDs). For the first time, LINGO2, RBFOX1/A2BP1, RPL29, DUSP7, and CCSER1/FAM190A were found to be homozygously deleted in MMt, and some of these genes could be new tumor suppressor genes for MMt. Integration of SKY and aCGH data allowed reconstruction of chromosomal rearrangements that led to the formation of HDs. Our data imply that only with acquisition of structural and/or numerical karyotypic instability can MMt cells attain a complete loss of tumor suppressor genes located in 9p21.3, which is the most frequently homozygously deleted region. Tetraploidization is a late event in the karyotypic progression of MMt cells, after HDs in the 9p21.3 region have already been acquired.

  18. arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

    Directory of Open Access Journals (Sweden)

    Moreau Yves

    2005-05-01

    Full Text Available Abstract Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH. One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.

  19. Spatial normalization of array-CGH data

    Directory of Open Access Journals (Sweden)

    Brennetot Caroline

    2006-05-01

    Full Text Available Abstract Background Array-based comparative genomic hybridization (array-CGH is a recently developed technique for analyzing changes in DNA copy number. As in all microarray analyses, normalization is required to correct for experimental artifacts while preserving the true biological signal. We investigated various sources of systematic variation in array-CGH data and identified two distinct types of spatial effect of no biological relevance as the predominant experimental artifacts: continuous spatial gradients and local spatial bias. Local spatial bias affects a large proportion of arrays, and has not previously been considered in array-CGH experiments. Results We show that existing normalization techniques do not correct these spatial effects properly. We therefore developed an automatic method for the spatial normalization of array-CGH data. This method makes it possible to delineate and to eliminate and/or correct areas affected by spatial bias. It is based on the combination of a spatial segmentation algorithm called NEM (Neighborhood Expectation Maximization and spatial trend estimation. We defined quality criteria for array-CGH data, demonstrating significant improvements in data quality with our method for three data sets coming from two different platforms (198, 175 and 26 BAC-arrays. Conclusion We have designed an automatic algorithm for the spatial normalization of BAC CGH-array data, preventing the misinterpretation of experimental artifacts as biologically relevant outliers in the genomic profile. This algorithm is implemented in the R package MANOR (Micro-Array NORmalization, which is described at http://bioinfo.curie.fr/projects/manor and available from the Bioconductor site http://www.bioconductor.org. It can also be tested on the CAPweb bioinformatics platform at http://bioinfo.curie.fr/CAPweb.

  20. aCGH Analysis to Estimate Genetic Variations among Domesticated Chickens

    Directory of Open Access Journals (Sweden)

    Tomoyoshi Komiyama

    2016-01-01

    Full Text Available Chickens have been familiar to humans since ancient times and have been used not only for culinary purposes but also for cultural purposes including ritual ceremonies and traditional entertainment. The various chicken breeds developed for these purposes often display distinct morphological and/or behavioural traits. For example, the Japanese Shamo is larger and more aggressive than other domesticated chickens, reflecting its role as a fighting cock breed, whereas Japanese Naganakidori breeds, which have long-crowing behaviour, were bred instead for their entertaining and aesthetic qualities. However, the genetic backgrounds of these distinct morphological and behavioural traits remain unclear. Therefore, the question arises as to which genomic regions in these chickens were acted upon by selective pressures through breeding. We compared the entire genomes of six chicken breeds domesticated for various cultural purposes by utilizing array comparative genomic hybridization. From these analyses, we identified 782 regions that underwent insertions, deletions, or mutations, representing man-made selection pressure in these chickens. Furthermore, we found that a number of genes diversified in domesticated chickens bred for cultural or entertainment purposes were different from those diversified in chickens bred for food, such as broilers and layers.

  1. Molecular karyotyping: array CGH quality criteria for constitutional genetic diagnosis.

    Science.gov (United States)

    Vermeesch, Joris R; Melotte, Cindy; Froyen, Guy; Van Vooren, Steven; Dutta, Binita; Maas, Nicole; Vermeulen, Stefan; Menten, Björn; Speleman, Frank; De Moor, Bart; Van Hummelen, Paul; Marynen, Peter; Fryns, Jean-Pierre; Devriendt, Koen

    2005-03-01

    Array CGH (comparative genomic hybridization) enables the identification of chromosomal copy number changes. The availability of clone sets covering the human genome opens the possibility for the widespread use of array CGH for both research and diagnostic purposes. In this manuscript we report on the parameters that were critical for successful implementation of the technology, assess quality criteria, and discuss the potential benefits and pitfalls of the technology for improved pre- and postnatal constitutional genetic diagnosis. We propose to name the genome-wide array CGH "molecular karyotyping," in analogy with conventional karyotyping that uses staining methods to visualize chromosomes.

  2. Application of the cghRA framework to the genomic characterization of Diffuse Large B-Cell Lymphoma.

    Science.gov (United States)

    Mareschal, Sylvain; Ruminy, Philippe; Alcantara, Marion; Villenet, Céline; Figeac, Martin; Dubois, Sydney; Bertrand, Philippe; Bouzelfen, Abdelilah; Viailly, Pierre-Julien; Penther, Dominique; Tilly, Hervé; Bastard, Christian; Jardin, Fabrice

    2017-05-08

    Although sequencing-based technologies are becoming the new reference in genome analysis, comparative genomic hybridization arrays (aCGH) still constitute a simple and reliable approach for copy number analysis. The most powerful algorithms to analyse such data have been freely provided by the scientific community for many years, but combining them is a complex scripting task. The cghRA framework combines a user-friendly graphical interface and a powerful objectoriented command-line interface to handle a full aCGH analysis, as is illustrated in an original series of 107 Diffuse Large B-Cell Lymphomas. New algorithms for copy-number calling, polymorphism detection and minimal common region (MCR) prioritization were also developed and validated. While their performances will only be demonstrated with aCGH, these algorithms could actually prove useful to any copy-number analysis, whatever the technique used. R package and source for Linux, MS Windows and MacOS are freely available at http://bioinformatics.ovsa.fr/cghRA . mareschal@ovsa.fr. Supplementary data are available at Bioinformatics online.

  3. Interspecies comparative genome hybridization and interspecies representational difference analysis reveal gross DNA differences between humans and great apes.

    Science.gov (United States)

    Toder, R; Xia, Y; Bausch, E

    1998-09-01

    Comparative chromosome G-/R-banding, comparative gene mapping and chromosome painting techniques have demonstrated that only few chromosomal rearrangements occurred during great ape and human evolution. Interspecies comparative genome hybridization (CGH), used here in this study, between human, gorilla and pygmy chimpanzee revealed species-specific regions in all three species. In contrast to the human, a far more complex distribution of species-specific blocks was detected with CGH in gorilla and pygmy chimpanzee. Most of these blocks coincide with already described heterochromatic regions on gorilla and chimpanzee chromosomes. Representational difference analysis (RDA) was used to subtract the complex genome of gorilla against human in order to enrich gorilla-specific DNA sequences. Gorilla-specific clones isolated with this technique revealed a 32-bp repeat unit. These clones were mapped by fluorescence in situ hybridization (FISH) to the telomeric regions of gorilla chromosomes that had been shown by interspecies CGH to contain species-specific sequences.

  4. CGH, cDNA and Tissue Microarray Analyses Implicate FGFR2 Amplification in a Small Subset of Breast Tumors

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    Mervi Heiskanen

    2001-01-01

    Full Text Available Multiple regions of the genome are often amplified during breast cancer development and progression, as evidenced in a number of published studies by comparative genomic hybridization (CGH. However, only relatively few target genes for such amplifications have been identified. Here, we indicate how small‐scale commercially available cDNA and CGH microarray formats combined with the tissue microarray technology enable rapid identification of putative amplification target genes as well as analysis of their clinical significance. According to CGH, the SUM‐52 breast cancer cell line harbors several high‐level DNA amplification sites, including the 10q26 chromosomal region where the fibroblast growth factor receptor 2 (FGFR2 gene has been localized. High level amplification of FGFR2 in SUM‐52 was identified using CGH analysis on a microarray of BAC clones. A cDNA microarray survey of 588 genes showed >40‐fold overexpression of FGFR2. Finally, a tissue microarray based FISH analysis of 750 uncultured primary breast cancers demonstrated in vivo amplification of the FGFR2 gene in about 1% of the tumors. In conclusion, three consecutive microarray (CGH, cDNA and tissue experiments revealed high‐level amplification and overexpression of the FGFR2 in a breast cancer cell line, but only a low frequency of involvement in primary breast tumors. Applied to a genomic scale with larger arrays, this strategy should facilitate identification of the most important target genes for cytogenetic rearrangements, such as DNA amplification sites detected by conventional CGH. Figures on http://www.esacp.org/acp/2001/22‐4/heiskanen.htm

  5. A New Normalizing Algorithm for BAC CGH Arrays with Quality Control Metrics

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    Jeffrey C. Miecznikowski

    2011-01-01

    Full Text Available The main focus in pin-tip (or print-tip microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose “SmoothArray”, a new method to preprocess comparative genomic hybridization (CGH bacterial artificial chromosome (BAC arrays and we show the effects on a cancer dataset. As part of our R software package “aCGHplus,” this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.

  6. Development of a novel ozone- and photo-stable HyPer5 red fluorescent dye for array CGH and microarray gene expression analysis with consistent performance irrespective of environmental conditions

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    Kille Peter

    2008-11-01

    Full Text Available Abstract Background Array-based comparative genomic hybridization (CGH and gene expression profiling have become vital techniques for identifying molecular defects underlying genetic diseases. Regardless of the microarray platform, cyanine dyes (Cy3 and Cy5 are one of the most widely used fluorescent dye pairs for microarray analysis owing to their brightness and ease of incorporation, enabling high level of assay sensitivity. However, combining both dyes on arrays can become problematic during summer months when ozone levels rise to near 25 parts per billion (ppb. Under such conditions, Cy5 is known to rapidly degrade leading to loss of signal from either "homebrew" or commercial arrays. Cy5 can also suffer disproportionately from dye photobleaching resulting in distortion of (Cy5/Cy3 ratios used in copy number analysis. Our laboratory has been active in fluorescent dye research to find a suitable alternative to Cy5 that is stable to ozone and resistant to photo-bleaching. Here, we report on the development of such a dye, called HyPer5, and describe its' exceptional ozone and photostable properties on microarrays. Results Our results show HyPer5 signal to be stable to high ozone levels. Repeated exposure of mouse arrays hybridized with HyPer5-labeled cDNA to 300 ppb ozone at 5, 10 and 15 minute intervals resulted in no signal loss from the dye. In comparison, Cy5 arrays showed a dramatic 80% decrease in total signal during the same interval. Photobleaching experiments show HyPer5 to be resistant to light induced damage with 3- fold improvement in dye stability over Cy5. In high resolution array CGH experiments, HyPer5 is demonstrated to detect chromosomal aberrations at loci 2p21-16.3 and 15q26.3-26.2 from three patient sample using bacterial artificial chromosome (BAC arrays. The photostability of HyPer5 is further documented by repeat array scanning without loss of detection. Additionally, HyPer5 arrays are shown to preserve sensitivity and

  7. Estimation of tumor heterogeneity using CGH array data

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    Li Shengting

    2009-01-01

    Full Text Available Abstract Background Array-based comparative genomic hybridization (CGH is a commonly-used approach to detect DNA copy number variation in whole genome-wide screens. Several statistical methods have been proposed to define genomic segments with different copy numbers in cancer tumors. However, most tumors are heterogeneous and show variation in DNA copy numbers across tumor cells. The challenge is to reveal the copy number profiles of the subpopulations in a tumor and to estimate the percentage of each subpopulation. Results We describe a relation between experimental data and exact DNA copy number and develop a statistical method to reveal the heterogeneity of tumors containing a mixture of different-stage cells. Furthermore, we validate the method on simulated data and apply the method to 29 pairs of breast primary tumors and their matched lymph node metastases. Conclusion We demonstrate a new method for CGH array analysis that allows a tumor sample to be classified according to its heterogeneity. The method gives an interpretable series of copy number profiles, one for each major subpopulation in a tumor. The profiles facilitate identification of copy number alterations in cancer development.

  8. Stochastic segmentation models for array-based comparative genomic hybridization data analysis.

    Science.gov (United States)

    Lai, Tze Leung; Xing, Haipeng; Zhang, Nancy

    2008-04-01

    Array-based comparative genomic hybridization (array-CGH) is a high throughput, high resolution technique for studying the genetics of cancer. Analysis of array-CGH data typically involves estimation of the underlying chromosome copy numbers from the log fluorescence ratios and segmenting the chromosome into regions with the same copy number at each location. We propose for the analysis of array-CGH data, a new stochastic segmentation model and an associated estimation procedure that has attractive statistical and computational properties. An important benefit of this Bayesian segmentation model is that it yields explicit formulas for posterior means, which can be used to estimate the signal directly without performing segmentation. Other quantities relating to the posterior distribution that are useful for providing confidence assessments of any given segmentation can also be estimated by using our method. We propose an approximation method whose computation time is linear in sequence length which makes our method practically applicable to the new higher density arrays. Simulation studies and applications to real array-CGH data illustrate the advantages of the proposed approach.

  9. Analysis of Chinese women with primary ovarian insufficiency by high resolution array-comparative genomic hybridization

    Institute of Scientific and Technical Information of China (English)

    LIAO Can; FU Fang; YANG Xin; SUN Yi-min; LI Dong-zhi

    2011-01-01

    Background Primary ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 years. The etiology of primary ovarian insufficiency in human female patients is still unclear. The purpose of this study is to investigate the potential genetic causes in primary amenorrhea patients by high resolution array based comparative genomic hybridization (array-CGH) analysis.Methods Following the standard karyotyping analysis, genomic DNA from whole blood of 15 primary amenorrhea patients and 15 normal control women was hybridized with Affymetrix cytogenetic 2.7M arrays following the standard protocol. Copy number variations identified by array-CGH were confirmed by real time polymerase chain reaction.Results All the 30 samples were negative by conventional karyotyping analysis. Microdeletions on chromosome 17q21.31-q21.32 with approximately 1.3 Mb were identified in four patients by high resolution array-CGH analysis. This included the female reproductive secretory pathway related factor N-ethylmaleimide-sensitive factor (NSF) gene.Conclusions The results of the present study suggest that there may be critical regions regulating primary ovarian insufficiency in women with a 17q21.31-q21.32 microdeletion. This effect might be due to the loss of function of the NSF gene/genes within the deleted region or to effects on contiguous genes.

  10. Array CGH improves detection of mutations in the GALC gene associated with Krabbe disease

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    Tanner Alice K

    2012-06-01

    Full Text Available Abstract Background Krabbe disease is an autosomal recessive lysosomal storage disorder caused by mutations in the GALC gene. The most common mutation in the Caucasian population is a 30-kb deletion of exons 11 through 17. There are few other reports of intragenic GALC deletions or duplications, due in part to difficulties detecting them. Methods and results We used gene-targeted array comparative genomic hybridization (CGH to analyze the GALC gene in individuals with Krabbe disease in whom sequence analysis with 30-kb deletion analysis identified only one mutation. In our sample of 33 cases, traditional approaches failed to identify two pathogenic mutations in five (15.2% individuals with confirmed Krabbe disease. The addition of array CGH deletion/duplication analysis to the genetic testing strategy led to the identification of a second pathogenic mutation in three (9.1% of these five individuals. In all three cases, the deletion or duplication identified through array CGH was a novel GALC mutation, including the only reported duplication in the GALC gene, which would have been missed by traditional testing methodologies. We report these three cases in detail. The second mutation remains unknown in the remaining two individuals (6.1%, despite our full battery of testing. Conclusions Analysis of the GALC gene using array CGH deletion/duplication testing increased the two-mutation detection rate from 84.8% to 93.9% in affected individuals. Better mutation detection rates are important for improving molecular diagnosis of Krabbe disease, as well as for providing prenatal and carrier testing in family members.

  11. Comparative genomic hybridization in clinical cytogenetics

    Energy Technology Data Exchange (ETDEWEB)

    Bryndorf, T.; Kirchhoff, M.; Rose, H. [and others

    1995-11-01

    We report the results of applying comparative genomic hybridization (CGH) in a cytogenetic service laboratory for (1) determination of the origin of extra and missing chromosomal material in intricate cases of unbalanced aberrations and (2) detection of common prenatal numerical chromosome aberrations. A total of 11 fetal samples were analyzed. Seven cases of complex unbalanced aberrations that could not be identified reliably by conventional cytogenetics were successfully resolved by CGH analysis. CGH results were validated by using FISH with chromosome-specific probes. Four cases representing common prenatal numerical aberrations (trisomy 21, 18, and 13 and monosomy X) were also successfully diagnosed by CGH. We conclude that CGH is a powerful adjunct to traditional cytogenetic techniques that makes it possible to solve clinical cases of intricate unbalanced aberrations in a single hybridization. CGH may also be a useful adjunct to screen for euchromatic involvement in marker chromosomes. Further technical development may render CGH applicable for routine aberration screening. 16 refs., 4 figs., 2 tabs.

  12. Clinical applications of BAC array-CGH to the study of diffuse large B-cell lymphomas.

    Science.gov (United States)

    Robledo, Cristina; García, Juan Luis; Hernández, Jesús M

    2013-01-01

    BAC array-CGH is a powerful method to identify DNA copy number changes (gains, amplifications and deletions) on a genome-wide scale, and to map these changes to genomic sequence. It is based on the analysis of genomic DNA isolated from test and reference cell populations, the differential labelling with fluorescent dyes and the co-hybridization with a genomic array. BAC array-CGH has proven to be a specific, sensitive, and reliable technique, with considerable advantages compared to other methods used for the analysis of DNA copy number changes. The application of genome scanning technologies and the recent advances in bioinformatics tools that enable us to perform a robust and highly sensitive analysis of array-CGH data, useful not only for genome scanning of tumor cells but also in the identification of novel cancer related genes, oncogenes and suppressor genes. Cytogenetic analysis provides essential information for diagnosis and prognosis in patients with hematologic malignancies such as lymphomas. However, the chromosomal interpretation in non-Hodgkin lymphoma (NHL) is sometimes inconclusive. Copy number aberrations identified by BAC array-CGH analyses could be a complementary methodology to chromosomal analysis. In NHL the genomic imbalances might have a prognostic rather than a diagnostic value. In fact, the diagnosis of NHL is based on pathological and molecular cytogenetics data. Furthermore genetic variations and their association with specific types of lymphoma development, and elucidation of the variable genetic pathways leading to lymphoma development, are important directions for future cancer research. Array-CGH, along with FISH and PCR, will be used for routine diagnostic purposes in near future.

  13. Evaluation of somatic genomic imbalances in thyroid carcinomas of follicular origin by CGH-based approaches.

    Science.gov (United States)

    Baldan, Federica; Mio, Catia; Allegri, Lorenzo; Passon, Nadia; Lepore, Saverio M; Russo, Diego; Damante, Giuseppe

    2017-09-07

    Application of distinct technologies of cancer genome analysis has provided important information for the molecular characterization of several human neoplasia, including follicular cell-derived thyroid carcinoma. Among them, comparative genomic hybridization (CGH)-based procedures have been extensively applied to evaluate genomic imbalances present in these tumours, obtaining data leading to an increase in the understanding of their complexity and diversity. In this review, after a brief overview of the most commonly used CGH-based technichs, we will describe the major results deriving from the most influential studies in the literature which used this approach to investigate the genomic aberrations of thyroid cancer cells. In most studies a small number of patients have been analyzed. Deletions and duplications at different chromosomal regions were detected in all investigated cohorts. A higher number of genomic imbalances has been detected in anaplastic or poorly differentiated thyroid carcinomas compared to well differentiated ones. Limitations in the interpretation of the results, as well the potential impact in the clinical practice are discussed. Though a quite heterogeneous picture arises from results so far available, CGH array, combined with other methodologies as well as an accurate clinical management, may offer novel opportunities for a better stratification of thyroid cancer patients.

  14. Implementation of High Resolution Whole Genome Array CGH in the Prenatal Clinical Setting: Advantages, Challenges, and Review of the Literature

    Directory of Open Access Journals (Sweden)

    Paola Evangelidou

    2013-01-01

    Full Text Available Array Comparative Genomic Hybridization analysis is replacing postnatal chromosomal analysis in cases of intellectual disabilities, and it has been postulated that it might also become the first-tier test in prenatal diagnosis. In this study, array CGH was applied in 64 prenatal samples with whole genome oligonucleotide arrays (BlueGnome, Ltd. on DNA extracted from chorionic villi, amniotic fluid, foetal blood, and skin samples. Results were confirmed with Fluorescence In Situ Hybridization or Real-Time PCR. Fifty-three cases had normal karyotype and abnormal ultrasound findings, and seven samples had balanced rearrangements, five of which also had ultrasound findings. The value of array CGH in the characterization of previously known aberrations in five samples is also presented. Seventeen out of 64 samples carried copy number alterations giving a detection rate of 26.5%. Ten of these represent benign or variables of unknown significance, giving a diagnostic capacity of the method to be 10.9%. If karyotype is performed the additional diagnostic capacity of the method is 5.1% (3/59. This study indicates the ability of array CGH to identify chromosomal abnormalities which cannot be detected during routine prenatal cytogenetic analysis, therefore increasing the overall detection rate. In addition a thorough review of the literature is presented.

  15. Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties

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    Penttilä Merja

    2010-07-01

    Full Text Available Abstract Background Trichoderma reesei is the main industrial producer of cellulases and hemicellulases that are used to depolymerize biomass in a variety of biotechnical applications. Many of the production strains currently in use have been generated by classical mutagenesis. In this study we characterized genomic alterations in high-producing mutants of T. reesei by high-resolution array comparative genomic hybridization (aCGH. Our aim was to obtain genome-wide information which could be utilized for better understanding of the mechanisms underlying efficient cellulase production, and would enable targeted genetic engineering for improved production of proteins in general. Results We carried out an aCGH analysis of four high-producing strains (QM9123, QM9414, NG14 and Rut-C30 using the natural isolate QM6a as a reference. In QM9123 and QM9414 we detected a total of 44 previously undocumented mutation sites including deletions, chromosomal translocation breakpoints and single nucleotide mutations. In NG14 and Rut-C30 we detected 126 mutations of which 17 were new mutations not documented previously. Among these new mutations are the first chromosomal translocation breakpoints identified in NG14 and Rut-C30. We studied the effects of two deletions identified in Rut-C30 (a deletion of 85 kb in the scaffold 15 and a deletion in a gene encoding a transcription factor on cellulase production by constructing knock-out strains in the QM6a background. Neither the 85 kb deletion nor the deletion of the transcription factor affected cellulase production. Conclusions aCGH analysis identified dozens of mutations in each strain analyzed. The resolution was at the level of single nucleotide mutation. High-density aCGH is a powerful tool for genome-wide analysis of organisms with small genomes e.g. fungi, especially in studies where a large set of interesting strains is analyzed.

  16. Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization

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    Moerman Donald G

    2008-10-01

    Full Text Available Abstract Background Microarray comparative genomic hybridization (CGH is currently one of the most powerful techniques to measure DNA copy number in large genomes. In humans, microarray CGH is widely used to assess copy number variants in healthy individuals and copy number aberrations associated with various diseases, syndromes and disease susceptibility. In model organisms such as Caenorhabditis elegans (C. elegans the technique has been applied to detect mutations, primarily deletions, in strains of interest. Although various constraints on oligonucleotide properties have been suggested to minimize non-specific hybridization and improve the data quality, there have been few experimental validations for CGH experiments. For genomic regions where strict design filters would limit the coverage it would also be useful to quantify the expected loss in data quality associated with relaxed design criteria. Results We have quantified the effects of filtering various oligonucleotide properties by measuring the resolving power for detecting deletions in the human and C. elegans genomes using NimbleGen microarrays. Approximately twice as many oligonucleotides are typically required to be affected by a deletion in human DNA samples in order to achieve the same statistical confidence as one would observe for a deletion in C. elegans. Surprisingly, the ability to detect deletions strongly depends on the oligonucleotide 15-mer count, which is defined as the sum of the genomic frequency of all the constituent 15-mers within the oligonucleotide. A similarity level above 80% to non-target sequences over the length of the probe produces significant cross-hybridization. We recommend the use of a fairly large melting temperature window of up to 10°C, the elimination of repeat sequences, the elimination of homopolymers longer than 5 nucleotides, and a threshold of -1 kcal/mol on the oligonucleotide self-folding energy. We observed very little difference in data

  17. Genomic profiling of plasmablastic lymphoma using array comparative genomic hybridization (aCGH: revealing significant overlapping genomic lesions with diffuse large B-cell lymphoma

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    Lu Xin-Yan

    2009-11-01

    Full Text Available Abstract Background Plasmablastic lymphoma (PL is a subtype of diffuse large B-cell lymphoma (DLBCL. Studies have suggested that tumors with PL morphology represent a group of neoplasms with clinopathologic characteristics corresponding to different entities including extramedullary plasmablastic tumors associated with plasma cell myeloma (PCM. The goal of the current study was to evaluate the genetic similarities and differences among PL, DLBCL (AIDS-related and non AIDS-related and PCM using array-based comparative genomic hybridization. Results Examination of genomic data in PL revealed that the most frequent segmental gain (> 40% include: 1p36.11-1p36.33, 1p34.1-1p36.13, 1q21.1-1q23.1, 7q11.2-7q11.23, 11q12-11q13.2 and 22q12.2-22q13.3. This correlated with segmental gains occurring in high frequency in DLBCL (AIDS-related and non AIDS-related cases. There were some segmental gains and some segmental loss that occurred in PL but not in the other types of lymphoma suggesting that these foci may contain genes responsible for the differentiation of this lymphoma. Additionally, some segmental gains and some segmental loss occurred only in PL and AIDS associated DLBCL suggesting that these foci may be associated with HIV infection. Furthermore, some segmental gains and some segmental loss occurred only in PL and PCM suggesting that these lesions may be related to plasmacytic differentiation. Conclusion To the best of our knowledge, the current study represents the first genomic exploration of PL. The genomic aberration pattern of PL appears to be more similar to that of DLBCL (AIDS-related or non AIDS-related than to PCM. Our findings suggest that PL may remain best classified as a subtype of DLBCL at least at the genome level.

  18. A hidden Markov model-based algorithm for identifying tumour subtype using array CGH data

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    Zhang Ke

    2011-12-01

    Full Text Available Abstract Background The recent advancement in array CGH (aCGH research has significantly improved tumor identification using DNA copy number data. A number of unsupervised learning methods have been proposed for clustering aCGH samples. Two of the major challenges for developing aCGH sample clustering are the high spatial correlation between aCGH markers and the low computing efficiency. A mixture hidden Markov model based algorithm was developed to address these two challenges. Results The hidden Markov model (HMM was used to model the spatial correlation between aCGH markers. A fast clustering algorithm was implemented and real data analysis on glioma aCGH data has shown that it converges to the optimal cluster rapidly and the computation time is proportional to the sample size. Simulation results showed that this HMM based clustering (HMMC method has a substantially lower error rate than NMF clustering. The HMMC results for glioma data were significantly associated with clinical outcomes. Conclusions We have developed a fast clustering algorithm to identify tumor subtypes based on DNA copy number aberrations. The performance of the proposed HMMC method has been evaluated using both simulated and real aCGH data. The software for HMMC in both R and C++ is available in ND INBRE website http://ndinbre.org/programs/bioinformatics.php.

  19. Risk assessment models in genetics clinic for array comparative genomic hybridization: Clinical information can be used to predict the likelihood of an abnormal result in patients.

    Science.gov (United States)

    Marano, Rachel M; Mercurio, Laura; Kanter, Rebecca; Doyle, Richard; Abuelo, Dianne; Morrow, Eric M; Shur, Natasha

    2013-03-01

    Array comparative genomic hybridization (aCGH) testing can diagnose chromosomal microdeletions and duplications too small to be detected by conventional cytogenetic techniques. We need to consider which patients are more likely to receive a diagnosis from aCGH testing versus patients that have lower likelihood and may benefit from broader genome wide scanning. We retrospectively reviewed charts of a population of 200 patients, 117 boys and 83 girls, who underwent aCGH testing in Genetics Clinic at Rhode Island hospital between 1 January/2008 and 31 December 2010. Data collected included sex, age at initial clinical presentation, aCGH result, history of seizures, autism, dysmorphic features, global developmental delay/intellectual disability, hypotonia and failure to thrive. aCGH analysis revealed abnormal results in 34 (17%) and variants of unknown significance in 24 (12%). Patients with three or more clinical diagnoses had a 25.0% incidence of abnormal aCGH findings, while patients with two or fewer clinical diagnoses had a 12.5% incidence of abnormal aCGH findings. Currently, we provide families with a range of 10-30% of a diagnosis with aCGH testing. With increased clinical complexity, patients have an increased probability of having an abnormal aCGH result. With this, we can provide individualized risk estimates for each patient.

  20. Array-CGH testing in spontaneous abortions with normal karyotypes

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    Cleide L. Borovik

    2008-01-01

    Full Text Available In about 50% of first trimester spontaneous abortion the cause remains undetermined after standard cytogenetic investigation. We evaluated the usefulness of array-CGH in diagnosing chromosome abnormalities in products of conception from first trimester spontaneous abortions. Cell culture was carried out in short- and long-term cultures of 54 specimens and cytogenetic analysis was successful in 49 of them. Cytogenetic abnormalities (numerical and structural were detected in 22 (44.89% specimens. Subsequent, array-CGH based on large insert clones spaced at ~1 Mb intervals over the whole genome was used in 17 cases with normal G-banding karyotype. This revealed chromosome aneuplodies in three additional cases, giving a final total of 51% cases in which an abnormal karyotype was detected. In keeping with other recently published works, this study shows that array-CGH detects abnormalities in a further ~10% of spontaneous abortion specimens considered to be normal using standard cytogenetic methods. As such, array-CGH technique may present a suitable complementary test to cytogenetic analysis in cases with a normal karyotype.

  1. Comparative genomic hybridization: technical development and cytogenetic aspects for routine use in clinical laboratories.

    Science.gov (United States)

    Lapierre, J M; Cacheux, V; Da Silva, F; Collot, N; Hervy, N; Wiss, J; Tachdjian, G

    1998-01-01

    Comparative genomic hybridization (CGH) offers a new global approach for detection of chromosomal material imbalances of the entire genome in a single experiment without cell culture. In this paper, we discuss the technical development and the cytogenetic aspects of CGH in a clinical laboratory. Based only on the visual inspection of CGH metaphase spreads, the correct identification of numerical and structural anomalies are reported. No commercial image analysis software was required in these experiments. We have demonstrated that this new technology can be set up easily for routine use in a clinical cytogenetics laboratory.

  2. High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues.

    Science.gov (United States)

    van Essen, Hendrik F; Ylstra, Bauke

    2012-01-01

    We describe protocols to acquire high-quality DNA from formalin-fixed, paraffin-embedded (FFPE) tissues for the use in array comparative genome hybridization (CGH). Formalin fixation combined with paraffin embedding is routine procedure for solid malignancies in the diagnostic practice of the pathologist. As a consequence, large archives of FFPE tissues are available in pathology institutes across the globe. This archival material is for many research questions an invaluable resource, with long-term clinical follow-up and survival data available. FFPE is, thus, highly attractive for large genomics studies, including experiments requiring samples for test/learning and validation. Most larger array CGH studies have, therefore, made use of FFPE material and show that CNAs have tumor- and tissue-specific traits (Chin et al. Cancer Cell 10: 529-541, 2006; Fridlyand et al. BMC Cancer 6: 96, 2006; Weiss et al. Oncogene 22: 1872-1879, 2003; Jong et al. Oncogene 26: 1499-1506, 2007). The protocols described are tailored to array CGH of FFPE solid malignancies: from sectioning FFPE blocks to specific cynosures for pathological revisions of sections, DNA isolation, quality testing, and amplification. The protocols are technical in character and elaborate up to the labeling of isolated DNA while further processes and interpretation and data analysis are beyond the scope.

  3. Array CGH demonstrates characteristic aberration signatures in human papillary thyroid carcinomas governed by RET/PTC.

    Science.gov (United States)

    Unger, K; Malisch, E; Thomas, G; Braselmann, H; Walch, A; Jackl, G; Lewis, P; Lengfelder, E; Bogdanova, T; Wienberg, J; Zitzelsberger, H

    2008-07-31

    The aim of this study is to investigate additional genetic alterations in papillary thyroid carcinomas (PTCs) with known RET/PTC rearrangements. We applied array-based comparative genomic hybridization (array CGH) to 33 PTC (20 PTC from adults, 13 post-Chernobyl PTC from children) with known RET/PTC status. Principal component analysis and hierarchical cluster analysis identified cases with similar aberration patterns. Significant deviations between tumour-groups were obtained by statistical testing (Fisher's exact test in combination with Benjamini-Hochberg FDR-controlling procedure). FISH analysis on FFPE sections was applied to validate the array CGH data. Deletions were found more frequently in RET/PTC-positive and RET/PTC-negative tumours than amplifications. Specific aberration signatures were identified that discriminated between RET/PTC-positive and RET/PTC-negative cases (aberrations on chromosomes 1p, 3q, 4p, 7p, 9p/q, 10q, 12q, 13q and 21q). In addition, childhood and adult RET/PTC-positive cases differ significantly for a deletion on the distal part of chromosome 1p. There are additional alterations in RET/PTC-positive tumours, which may act as modifiers of RET activation. In contrast, alterations in RET/PTC-negative tumours indicate alternative routes of tumour development. The data presented serve as a starting point for further studies on gene expression and function of genes identified in this study.

  4. Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer

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    Kenter Gemma G

    2007-02-01

    Full Text Available Abstract Background Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH and microsatellite marker analysis for the detection of loss of heterozygosity (LOH. Currently, high throughput methods such as array comparative genomic hybridization (array CGH, single nucleotide polymorphism array (SNP array and gene expression arrays are available to study genome-wide alterations. Integration of these 3 platforms allows detection of genomic alterations at high resolution and investigation of an association between copy number changes and expression. Results Genome-wide copy number and genotype analysis of 10 cervical cancer cell lines by array CGH and SNP array showed highly complex large-scale alterations. A comparison between array CGH and SNP array revealed that the overall concordance in detection of the same areas with copy number alterations (CNA was above 90%. The use of SNP arrays demonstrated that about 75% of LOH events would not have been found by methods which screen for copy number changes, such as array CGH, since these were LOH events without CNA. Regions frequently targeted by CNA, as determined by array CGH, such as amplification of 5p and 20q, and loss of 8p were confirmed by fluorescent in situ hybridization (FISH. Genome-wide, we did not find a correlation between copy-number and gene expression. At chromosome arm 5p however, 22% of the genes were significantly upregulated in cell lines with amplifications as compared to cell lines without amplifications, as measured by gene expression arrays. For 3 genes, SKP2, ANKH and TRIO, expression differences were confirmed by quantitative real-time PCR (qRT-PCR. Conclusion This study showed that copy number data retrieved from either array CGH or SNP array are comparable and that the integration of genome-wide LOH, copy number and gene

  5. Array comparative genomic hybridization-based characterization of genetic alterations in pulmonary neuroendocrine tumors

    OpenAIRE

    Voortman, Johannes; Lee, Jih-Hsiang; Killian, Jonathan Keith; Suuriniemi, Miia; Wang, Yonghong; Lucchi, Marco; Smith, William I; Meltzer, Paul; Wang, Yisong; Giaccone, Giuseppe

    2010-01-01

    The goal of this study was to characterize and classify pulmonary neuroendocrine tumors based on array comparative genomic hybridization (aCGH). Using aCGH, we performed karyotype analysis of 33 small cell lung cancer (SCLC) tumors, 13 SCLC cell lines, 19 bronchial carcinoids, and 9 gastrointestinal carcinoids. In contrast to the relatively conserved karyotypes of carcinoid tumors, the karyotypes of SCLC tumors and cell lines were highly aberrant. High copy number (CN) gains were detected in ...

  6. Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing.

    Science.gov (United States)

    Wiszniewska, Joanna; Bi, Weimin; Shaw, Chad; Stankiewicz, Pawel; Kang, Sung-Hae L; Pursley, Amber N; Lalani, Seema; Hixson, Patricia; Gambin, Tomasz; Tsai, Chun-hui; Bock, Hans-Georg; Descartes, Maria; Probst, Frank J; Scaglia, Fernando; Beaudet, Arthur L; Lupski, James R; Eng, Christine; Cheung, Sau Wai; Bacino, Carlos; Patel, Ankita

    2014-01-01

    In clinical diagnostics, both array comparative genomic hybridization (array CGH) and single nucleotide polymorphism (SNP) genotyping have proven to be powerful genomic technologies utilized for the evaluation of developmental delay, multiple congenital anomalies, and neuropsychiatric disorders. Differences in the ability to resolve genomic changes between these arrays may constitute an implementation challenge for clinicians: which platform (SNP vs array CGH) might best detect the underlying genetic cause for the disease in the patient? While only SNP arrays enable the detection of copy number neutral regions of absence of heterozygosity (AOH), they have limited ability to detect single-exon copy number variants (CNVs) due to the distribution of SNPs across the genome. To provide comprehensive clinical testing for both CNVs and copy-neutral AOH, we enhanced our custom-designed high-resolution oligonucleotide array that has exon-targeted coverage of 1860 genes with 60,000 SNP probes, referred to as Chromosomal Microarray Analysis - Comprehensive (CMA-COMP). Of the 3240 cases evaluated by this array, clinically significant CNVs were detected in 445 cases including 21 cases with exonic events. In addition, 162 cases (5.0%) showed at least one AOH region >10 Mb. We demonstrate that even though this array has a lower density of SNP probes than other commercially available SNP arrays, it reliably detected AOH events >10 Mb as well as exonic CNVs beyond the detection limitations of SNP genotyping. Thus, combining SNP probes and exon-targeted array CGH into one platform provides clinically useful genetic screening in an efficient manner.

  7. Chromosomal aberrations in bladder cancer: fresh versus formalin fixed paraffin embedded tissue and targeted FISH versus wide microarray-based CGH analysis.

    Directory of Open Access Journals (Sweden)

    Elena Panzeri

    Full Text Available Bladder carcinogenesis is believed to follow two alternative pathways driven by the loss of chromosome 9 and the gain of chromosome 7, albeit other nonrandom copy number alterations (CNAs were identified. However, confirmation studies are needed since many aspects of this model remain unclear and considerable heterogeneity among cases has emerged. One of the purposes of this study was to evaluate the performance of a targeted test (UroVysion assay widely used for the detection of Transitional Cell Carcinoma (TCC of the bladder, in two different types of material derived from the same tumor. We compared the results of UroVysion test performed on Freshly Isolated interphasic Nuclei (FIN and on Formalin Fixed Paraffin Embedded (FFPE tissues from 22 TCCs and we didn't find substantial differences. A second goal was to assess the concordance between array-CGH profiles and the targeted chromosomal profiles of UroVysion assay on an additional set of 10 TCCs, in order to evaluate whether UroVysion is an adequately sensitive method for the identification of selected aneuploidies and nonrandom CNAs in TCCs. Our results confirmed the importance of global genomic screening methods, that is array based CGH, to comprehensively determine the genomic profiles of large series of TCCs tumors. However, this technique has yet some limitations, such as not being able to detect low level mosaicism, or not detecting any change in the number of copies for a kind of compensatory effect due to the presence of high cellular heterogeneity. Thus, it is still advisable to use complementary techniques such as array-CGH and FISH, as the former is able to detect alterations at the genome level not excluding any chromosome, but the latter is able to maintain the individual data at the level of single cells, even if it focuses on few genomic regions.

  8. True 3q chromosomal amplification in squamous cell lung carcinoma by FISH and aCGH molecular analysis: impact on targeted drugs.

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    Matteo Brunelli

    Full Text Available Squamous lung carcinoma lacks specific "ad hoc" therapies. Amplification of chromosome 3q is the most common genomic aberration and this region harbours genes having role as novel targets for therapeutics. There is no standard definition on how to score and report 3q amplification. False versus true 3q chromosomal amplification in squamous cell lung carcinoma may have tremendous impact on trials involving drugs which target DNA zones mapping on 3q. Forty squamous lung carcinomas were analyzed by FISH to assess chromosome 3q amplification. aCGH was performed as gold-standard to avoid false positive amplifications. Three clustered patterns of fluorescent signals were observed. Eight cases out of 40 (20% showed ≥8 3q signals. Twenty out of 40 (50% showed from 3 to 7 signals. The remaining showed two fluorescent signals (30%. When corrected by whole chromosome 3 signals, only cases with ≥8 signals maintained a LSI 3q/CEP3 ratio >2. Only the cases showing 3q amplification by aCGH (+3q25.3-3q27.3 showed ≥8 fluorescent signals at FISH evidencing a 3q/3 ratio >2. The remaining cases showed flat genomic portrait at aCGH on chromosome 3. We concluded that: 1 absolute copy number of 3q chromosomal region may harbour false positive interpretation of 3q amplification in squamous cell carcinoma; 2 a case results truly "amplified for chromosome 3q" when showing ≥8 fluorescent 3q signals; 3 trials involving drugs targeting loci on chromosome 3q in squamous lung carcinoma therapy have to consider false versus true 3q chromosomal amplification.

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

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    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.

  10. Reliable single cell array CGH for clinical samples.

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    Zbigniew T Czyż

    Full Text Available BACKGROUND: Disseminated cancer cells (DCCs and circulating tumor cells (CTCs are extremely rare, but comprise the precursors cells of distant metastases or therapy resistant cells. The detailed molecular analysis of these cells may help to identify key events of cancer cell dissemination, metastatic colony formation and systemic therapy escape. METHODOLOGY/PRINCIPAL FINDINGS: Using the Ampli1™ whole genome amplification (WGA technology and high-resolution oligonucleotide aCGH microarrays we optimized conditions for the analysis of structural copy number changes. The protocol presented here enables reliable detection of numerical genomic alterations as small as 0.1 Mb in a single cell. Analysis of single cells from well-characterized cell lines and single normal cells confirmed the stringent quantitative nature of the amplification and hybridization protocol. Importantly, fixation and staining procedures used to detect DCCs showed no significant impact on the outcome of the analysis, proving the clinical usability of our method. In a proof-of-principle study we tracked the chromosomal changes of single DCCs over a full course of high-dose chemotherapy treatment by isolating and analyzing DCCs of an individual breast cancer patient at four different time points. CONCLUSIONS/SIGNIFICANCE: The protocol enables detailed genome analysis of DCCs and thereby assessment of the clonal evolution during the natural course of the disease and under selection pressures. The results from an exemplary patient provide evidence that DCCs surviving selective therapeutic conditions may be recruited from a pool of genomically less advanced cells, which display a stable subset of specific genomic alterations.

  11. Array CGH in patients with learning disability (mental retardation) and congenital anomalies: updated systematic review and meta-analysis of 19 studies and 13,926 subjects.

    Science.gov (United States)

    Sagoo, Gurdeep S; Butterworth, Adam S; Sanderson, Simon; Shaw-Smith, Charles; Higgins, Julian P T; Burton, Hilary

    2009-03-01

    Array-based comparative genomic hybridization is being increasingly used in patients with learning disability (mental retardation) and congenital anomalies. In this article, we update our previous meta-analysis evaluating the diagnostic and false-positive yields of this technology. An updated systematic review and meta-analysis was conducted investigating patients with learning disability and congenital anomalies in whom conventional cytogenetic analyses have proven negative. Nineteen studies (13,926 patients) were included of which 12 studies (13,464 patients) were published since our previous analysis. The overall diagnostic yield of causal abnormalities was 10% (95% confidence interval: 8-12%). The overall number needed to test to identify an extra causal abnormality was 10 (95% confidence interval: 8-13). The overall false-positive yield of noncausal abnormalities was 7% (95% confidence interval: 5-10%). This updated meta-analysis provides new evidence to support the use of array-based comparative genomic hybridization in investigating patients with learning disability and congenital anomalies in whom conventional cytogenetic tests have proven negative. However, given that this technology also identifies false positives at a similar rate to causal variants, caution in clinical practice should be advised.

  12. Comprehensive embryo analysis of advanced maternal age-related aneuploidies and mosaicism by short comparative genomic hybridization.

    Science.gov (United States)

    Rius, Mariona; Daina, Gemma; Obradors, Albert; Ramos, Laia; Velilla, Esther; Fernández, Sílvia; Martínez-Passarell, Olga; Benet, Jordi; Navarro, Joaquima

    2011-01-01

    The short comparative genomic hybridization (short-CGH) method was used to perform a comprehensive cytogenetic study of isolated blastomeres from advanced maternal age embryos, discarded after fluorescent in situ hybridization (FISH) preimplantation genetic screening (PGS), detecting aneuploidies (38.5% of which corresponded to chromosomes not screened by 9-chromosome FISH), structural aberrations (31.8%), and mosaicism (77.3%). The short-CGH method was subsequently applied in one PGS, achieving a twin pregnancy.

  13. Analysis of comparative genomic hybridization and loss of heterozygosity in 43 primary gastric carcinomas

    Institute of Scientific and Technical Information of China (English)

    王琦; 王柏秋; 关新元; 高慧; 程慧; 张岂凡; 黄承斌; 李璞; 傅松滨

    2003-01-01

    Objective To investigate common chromosomal changes and the LOH frequency of microsatellite loci in primary gastric cancer samples in order to locate the deleted regions in which human gastric cancer related genes might exist.Methods Comparative genomic hybridization (CGH) was used to define global chromosomal aberrations in 43 primary gastric tumors. Based on the results of CGH, analysis of loss of heterozygosity (LOH) was performed in chromosome 19 in which the loss was first discovered in the gastric cancers. The PCR-based approach was used to investigate 22 loci, which are spaced at 1.1-10.9 cM intervals throughout chromosome 19. The amplified PCR fragments were subjected to electrophoresis in PAGE gel and analyzed with GenescanTM and GenotyperTM. Results CGH analysis revealed gains in chromosome 3p(8/43), 8q(8/43), 20 [20 (9/43), 20p(7/43), 20q(4/43)], 12q(16/43), 13q(12/43) and losses in 19 [19 (15/43)], 7 [17 (8/43), 17p (10/43)], 16 (10/43) and 1p (11/43). Among the 43 evaluated samples, the most frequent LOH was detected at locus D19S571 (27.81%). Conclusions The tumorigenesis of gastric cancer includes several chromosomal changes. The aberration of chromosome 19 was the first common change founded in gastric cancer. The region near the D19S571 might harbor potential genes related to the tumorigenesis of gastric cancer.

  14. Hybrid methods for cybersecurity analysis :

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Warren Leon,; Dunlavy, Daniel M.

    2014-01-01

    Early 2010 saw a signi cant change in adversarial techniques aimed at network intrusion: a shift from malware delivered via email attachments toward the use of hidden, embedded hyperlinks to initiate sequences of downloads and interactions with web sites and network servers containing malicious software. Enterprise security groups were well poised and experienced in defending the former attacks, but the new types of attacks were larger in number, more challenging to detect, dynamic in nature, and required the development of new technologies and analytic capabilities. The Hybrid LDRD project was aimed at delivering new capabilities in large-scale data modeling and analysis to enterprise security operators and analysts and understanding the challenges of detection and prevention of emerging cybersecurity threats. Leveraging previous LDRD research e orts and capabilities in large-scale relational data analysis, large-scale discrete data analysis and visualization, and streaming data analysis, new modeling and analysis capabilities were quickly brought to bear on the problems in email phishing and spear phishing attacks in the Sandia enterprise security operational groups at the onset of the Hybrid project. As part of this project, a software development and deployment framework was created within the security analyst work ow tool sets to facilitate the delivery and testing of new capabilities as they became available, and machine learning algorithms were developed to address the challenge of dynamic threats. Furthermore, researchers from the Hybrid project were embedded in the security analyst groups for almost a full year, engaged in daily operational activities and routines, creating an atmosphere of trust and collaboration between the researchers and security personnel. The Hybrid project has altered the way that research ideas can be incorporated into the production environments of Sandias enterprise security groups, reducing time to deployment from months and

  15. Symbolic Algorithmic Analysis of Rectangular Hybrid Systems

    Institute of Scientific and Technical Information of China (English)

    Hai-Bin Zhang; Zhen-Hua Duan

    2009-01-01

    This paper investigates symbolic algorithmic analysis of rectangular hybrid systems. To deal with the symbolic reachability problem, a restricted constraint system called hybrid zone is formalized for the representation and manipulation of rectangular automata state-spaces. Hybrid zones are proved to be closed over symbolic reachability operations of rectangular hybrid systems. They are also applied to model-checking procedures for verifying some important classes of timed computation tree logic formulas. To represent hybrid zones, a data structure called difference constraint matrix is defined.These enable us to deal with the symbolic algorithmic analysis of rectangular hybrid systems in an efficient way.

  16. BAC CGH-array identified specific small-scale genomic imbalances in diploid DMBA-induced rat mammary tumors

    Directory of Open Access Journals (Sweden)

    Samuelson Emma

    2012-08-01

    Full Text Available Abstract Background Development of breast cancer is a multistage process influenced by hormonal and environmental factors as well as by genetic background. The search for genes underlying this malignancy has recently been highly productive, but the etiology behind this complex disease is still not understood. In studies using animal cancer models, heterogeneity of the genetic background and environmental factors is reduced and thus analysis and identification of genetic aberrations in tumors may become easier. To identify chromosomal regions potentially involved in the initiation and progression of mammary cancer, in the present work we subjected a subset of experimental mammary tumors to cytogenetic and molecular genetic analysis. Methods Mammary tumors were induced with DMBA (7,12-dimethylbenz[a]anthrazene in female rats from the susceptible SPRD-Cu3 strain and from crosses and backcrosses between this strain and the resistant WKY strain. We first produced a general overview of chromosomal aberrations in the tumors using conventional kartyotyping (G-banding and Comparative Genome Hybridization (CGH analyses. Particular chromosomal changes were then analyzed in more details using an in-house developed BAC (bacterial artificial chromosome CGH-array platform. Results Tumors appeared to be diploid by conventional karyotyping, however several sub-microscopic chromosome gains or losses in the tumor material were identified by BAC CGH-array analysis. An oncogenetic tree analysis based on the BAC CGH-array data suggested gain of rat chromosome (RNO band 12q11, loss of RNO5q32 or RNO6q21 as the earliest events in the development of these mammary tumors. Conclusions Some of the identified changes appear to be more specific for DMBA-induced mammary tumors and some are similar to those previously reported in ACI rat model for estradiol-induced mammary tumors. The later group of changes is more interesting, since they may represent anomalies that involve

  17. A patient with limb girdle muscular dystrophy carries a TRIM32 deletion, detected by a novel CGH array, in compound heterozygosis with a nonsense mutation.

    Science.gov (United States)

    Neri, M; Selvatici, R; Scotton, C; Trabanelli, C; Armaroli, A; De Grandis, D; Levy, N; Gualandi, F; Ferlini, A

    2013-06-01

    Limb girdle muscular dystrophy 2H is a rare autosomal recessive muscular dystrophy, clinically highly variable, caused by mutations in the TRIM32 gene. Here we describe a 35-years-old who experienced progressive muscle weakness. The muscle biopsy revealed an unspecific pattern of atrophic and hypertrophic fibers; the immunohistochemistry for several proteins was normal. Comparative genomic hybridization (CGH) analysis showed a heterozygous deletion of the entire TRIM32 gene. On the other allele we identified the R316X nonsense mutation. The genetic diagnosis of LGMD2H in this case was reached by using a novel high throughput diagnostic tool.

  18. Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis.

    Science.gov (United States)

    Hosein, Abdel Nasser; Song, Sarah; McCart Reed, Amy E; Jayanthan, Janani; Reid, Lynne E; Kutasovic, Jamie R; Cummings, Margaret C; Waddell, Nic; Lakhani, Sunil R; Chenevix-Trench, Georgia; Simpson, Peter T

    2013-06-01

    Pathology archives contain vast resources of clinical material in the form of formalin-fixed paraffin-embedded (FFPE) tissue samples. Owing to the methods of tissue fixation and storage, the integrity of DNA and RNA available from FFPE tissue is compromized, which means obtaining informative data regarding epigenetic, genomic, and expression alterations can be challenging. Here, we have investigated the utility of repairing damaged DNA derived from FFPE tumors prior to single-nucleotide polymorphism (SNP) arrays for whole-genome DNA copy number analysis. DNA was extracted from FFPE samples spanning five decades, involving tumor material obtained from surgical specimens and postmortems. Various aspects of the protocol were assessed, including the method of DNA extraction, the role of Quality Control quantitative PCR (qPCR) in predicting sample success, and the effect of DNA restoration on assay performance, data quality, and the prediction of copy number aberrations (CNAs). DNA that had undergone the repair process yielded higher SNP call rates, reduced log R ratio variance, and improved calling of CNAs compared with matched FFPE DNA not subjected to repair. Reproducible mapping of genomic break points and detection of focal CNAs representing high-level gains and homozygous deletions (HD) were possible, even on autopsy material obtained in 1974. For example, DNA amplifications at the ERBB2 and EGFR gene loci and a HD mapping to 13q14.2 were validated using immunohistochemistry, in situ hybridization, and qPCR. The power of SNP arrays lies in the detection of allele-specific aberrations; however, this aspect of the analysis remains challenging, particularly in the distinction between loss of heterozygosity (LOH) and copy neutral LOH. In summary, attempting to repair DNA that is damaged during fixation and storage may be a useful pretreatment step for genomic studies of large archival FFPE cohorts with long-term follow-up or for understanding rare cancer types, where

  19. Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization.

    Science.gov (United States)

    Oikawa, Masahiro; Yoshiura, Koh-ichiro; Kondo, Hisayoshi; Miura, Shiro; Nagayasu, Takeshi; Nakashima, Masahiro

    2011-12-07

    It has been postulated that ionizing radiation induces breast cancers among atomic bomb (A-bomb) survivors. We have reported a higher incidence of HER2 and C-MYC oncogene amplification in breast cancers from A-bomb survivors. The purpose of this study was to clarify the effect of A-bomb radiation exposure on genomic instability (GIN), which is an important hallmark of carcinogenesis, in archival formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer by using microarray-comparative genomic hybridization (aCGH). Tumor DNA was extracted from FFPE tissues of invasive ductal cancers from 15 survivors who were exposed at 1.5 km or less from the hypocenter and 13 calendar year-matched non-exposed patients followed by aCGH analysis using a high-density oligonucleotide microarray. The total length of copy number aberrations (CNA) was used as an indicator of GIN, and correlation with clinicopathological factors were statistically tested. The mean of the derivative log ratio spread (DLRSpread), which estimates the noise by calculating the spread of log ratio differences between consecutive probes for all chromosomes, was 0.54 (range, 0.26 to 1.05). The concordance of results between aCGH and fluorescence in situ hybridization (FISH) for HER2 gene amplification was 88%. The incidence of HER2 amplification and histological grade was significantly higher in the A-bomb survivors than control group (P = 0.04, respectively). The total length of CNA tended to be larger in the A-bomb survivors (P = 0.15). Correlation analysis of CNA and clinicopathological factors revealed that DLRSpread was negatively correlated with that significantly (P = 0.034, r = -0.40). Multivariate analysis with covariance revealed that the exposure to A-bomb was a significant (P = 0.005) independent factor which was associated with larger total length of CNA of breast cancers. Thus, archival FFPE tissues from A-bomb survivors are useful for genome-wide aCGH analysis. Our results suggested that A

  20. Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Oikawa Masahiro

    2011-12-01

    Full Text Available Abstract Background It has been postulated that ionizing radiation induces breast cancers among atomic bomb (A-bomb survivors. We have reported a higher incidence of HER2 and C-MYC oncogene amplification in breast cancers from A-bomb survivors. The purpose of this study was to clarify the effect of A-bomb radiation exposure on genomic instability (GIN, which is an important hallmark of carcinogenesis, in archival formalin-fixed paraffin-embedded (FFPE tissues of breast cancer by using microarray-comparative genomic hybridization (aCGH. Methods Tumor DNA was extracted from FFPE tissues of invasive ductal cancers from 15 survivors who were exposed at 1.5 km or less from the hypocenter and 13 calendar year-matched non-exposed patients followed by aCGH analysis using a high-density oligonucleotide microarray. The total length of copy number aberrations (CNA was used as an indicator of GIN, and correlation with clinicopathological factors were statistically tested. Results The mean of the derivative log ratio spread (DLRSpread, which estimates the noise by calculating the spread of log ratio differences between consecutive probes for all chromosomes, was 0.54 (range, 0.26 to 1.05. The concordance of results between aCGH and fluorescence in situ hybridization (FISH for HER2 gene amplification was 88%. The incidence of HER2 amplification and histological grade was significantly higher in the A-bomb survivors than control group (P = 0.04, respectively. The total length of CNA tended to be larger in the A-bomb survivors (P = 0.15. Correlation analysis of CNA and clinicopathological factors revealed that DLRSpread was negatively correlated with that significantly (P = 0.034, r = -0.40. Multivariate analysis with covariance revealed that the exposure to A-bomb was a significant (P = 0.005 independent factor which was associated with larger total length of CNA of breast cancers. Conclusions Thus, archival FFPE tissues from A-bomb survivors are useful for

  1. Modeling and analysis using hybrid Petri nets

    CERN Document Server

    Ghomri, Latéfa

    2007-01-01

    This paper is devoted to the use of hybrid Petri nets (PNs) for modeling and control of hybrid dynamic systems (HDS). Modeling, analysis and control of HDS attract ever more of researchers' attention and several works have been devoted to these topics. We consider in this paper the extensions of the PN formalism (initially conceived for modeling and analysis of discrete event systems) in the direction of hybrid modeling. We present, first, the continuous PN models. These models are obtained from discrete PNs by the fluidification of the markings. They constitute the first steps in the extension of PNs toward hybrid modeling. Then, we present two hybrid PN models, which differ in the class of HDS they can deal with. The first one is used for deterministic HDS modeling, whereas the second one can deal with HDS with nondeterministic behavior. Keywords: Hybrid dynamic systems; D-elementary hybrid Petri nets; Hybrid automata; Controller synthesis

  2. Detection of chromosomal abnormalities by comparative genomic hybridization.

    Science.gov (United States)

    Lapierre, Jean-Michel; Tachdjian, Gérard

    2005-04-01

    Comparative genomic hybridization (CGH) is a modified in-situ hybridization technique. In this type of analysis, two differentially labeled genomic DNAs (study and reference) are cohybridized to normal metaphase spreads or to microarray. Chromosomal locations of copy number changes in the DNA segments of the study genome are revealed by a variable fluorescence intensity ratio along each target chromosome. Thus, CGH allows detection and mapping of DNA sequence copy differences between two genomes in a single experiment. Since its development, comparative genomic hybridization has been applied mostly as a research tool in the field of cancer cytogenetics to identify genetic changes in many previously unknown regions. It is also a powerful tool for detection and identification of unbalanced chromosomal abnormalities in prenatal, postnatal and preimplantation diagnostics. The development of comparative genomic hybridization and increase in resolution analysis by using the microarray-based technique offer new information on chromosomal pathologies and thus better management of patients.

  3. Microdeletion and microduplication analysis of chinese conotruncal defects patients with targeted array comparative genomic hybridization.

    Directory of Open Access Journals (Sweden)

    Xiaohui Gong

    Full Text Available OBJECTIVE: The current study aimed to develop a reliable targeted array comparative genomic hybridization (aCGH to detect microdeletions and microduplications in congenital conotruncal defects (CTDs, especially on 22q11.2 region, and for some other chromosomal aberrations, such as 5p15-5p, 7q11.23 and 4p16.3. METHODS: Twenty-seven patients with CTDs, including 12 pulmonary atresia (PA, 10 double-outlet right ventricle (DORV, 3 transposition of great arteries (TGA, 1 tetralogy of Fallot (TOF and one ventricular septal defect (VSD, were enrolled in this study and screened for pathogenic copy number variations (CNVs, using Agilent 8 x 15K targeted aCGH. Real-time quantitative polymerase chain reaction (qPCR was performed to test the molecular results of targeted aCGH. RESULTS: Four of 27 patients (14.8% had 22q11.2 CNVs, 1 microdeletion and 3 microduplications. qPCR test confirmed the microdeletion and microduplication detected by the targeted aCGH. CONCLUSION: Chromosomal abnormalities were a well-known cause of multiple congenital anomalies (MCA. This aCGH using arrays with high-density coverage in the targeted regions can detect genomic imbalances including 22q11.2 and other 10 kinds CNVs effectively and quickly. This approach has the potential to be applied to detect aneuploidy and common microdeletion/microduplication syndromes on a single microarray.

  4. Comparative genomic hybridization: Detection of segmental aneusomies

    Energy Technology Data Exchange (ETDEWEB)

    Cronin, J.E.; Magrane, G.G.; Gray, J.W. [Univ. of California, San Francisco, CA (United States)] [and others

    1994-09-01

    Comparative genomic hybridization (CGH) has been used successfully to detect whole chromosome and segmental aneusomies. However, its sensitivity for detection of segmental aneusomies is still not well known. We present here an analysis of CGH sensitivity with emphasis on detection of abnormalities commonly found during pre-and neo-natal diagnosis. CGH is performed by hybridizing green and red fluorescing test and normal DNA samples, respectively, to normal metaphase spreads and measuring green:red fluorescence ratios along all chromosomes. The ratios are normalized such that 2 copies of a normal chromosome region in the test sample gives a ratio of 1.0. Alterations in test vs. control gene copy number range from 1.5 [trisomy] to 0.5 [monosomy]. Clinical samples analyzed included Wolf Hirschhorn (4p-), Cri du Chat (5p-) and DiGeorge (22q-). In addition, 7 cell lines with chromosome 21 segmental aneusomies were analyzed. These included 3 with terminal duplications, 1 with a terminal deletion, 1 with an interstitial deletion and 2 with interstitial amplifications. The DiGeorge deletion was the only deletion not deleted by CGH. This is not surprising as standard G banding does not routinely detect this 1-2 megabase deletion. The 4p- and 5p- monosomies were detected and breakpoints correctly assigned prospectively. Proximal alterations involving 21q22.11 are unambiguously defined. Specifically, two interstitial aneusomies involving this region are detected. Studies involving late prophase chromosome normal spreads gave identical breakpoints. Thus, analysis of extended chromosomes did not improve the sensitivity of the technique. Taken together, these data suggest that CGH can detect segmental aneusomies greater than 8 megabases in extent. Smaller aneusomies can, at times, be detected. Work is now underway to modify the analysis software to increase sensitivity and to decrease the amount of material needed for analysis.

  5. aCGH detects partial tetrasomy of 12p in blood from Pallister-Killian syndrome cases without invasive skin biopsy.

    Science.gov (United States)

    Theisen, Aaron; Rosenfeld, Jill A; Farrell, Sandra A; Harris, Catharine J; Wetzel, Heather H; Torchia, Beth A; Bejjani, Bassem A; Ballif, Blake C; Shaffer, Lisa G

    2009-05-01

    Pallister-Killian syndrome (PKS) is a genetic disorder characterized by mental retardation, seizures, streaks of hypo- or hyperpigmentation and dysmorphic features. PKS is associated with tissue-limited mosaic partial tetrasomy of 12p, usually caused by an isochromosome 12p. The mosaicism is usually detected in cultured skin fibroblasts or amniotic cells and rarely in phytohemagluttinin-stimulated lymphocytes, which suggests stimulation of T-lymphocytes may distort the percentage of abnormal cells. We recently reported on the identification by microarray-based comparative genomic hybridization (aCGH) of a previously unsuspected case of partial tetrasomy of 12p caused by an isochromosome 12p. Here we report on seven additional individuals with partial tetrasomy of 12p characterized by our laboratory. All individuals were referred for mental retardation/developmental delay and/or dysmorphic features. In each case, aCGH using genomic DNA extracted from whole peripheral blood detected copy-number gain for all clones for the short arm of chromosome 12. In all but one case, FISH on metaphases from cultured lymphocytes did not detect the copy-number gain; in the remaining case, metaphase FISH on cultured lymphocytes showed an isochromosome in 10% of cells. However, interphase FISH using probes to 12p on peripheral blood smears showed additional hybridization signals in 18-70% of cells. Microarray and FISH analysis on cultured skin biopsies from four individuals confirmed the presence of an isochromosome 12p. Our results demonstrate the usefulness of aCGH with genomic DNA from whole peripheral blood to detect chromosome abnormalities that are not present in stimulated blood cultures and would otherwise require invasive skin biopsies for identification.

  6. Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies

    Directory of Open Access Journals (Sweden)

    Iourov Ivan Y

    2012-12-01

    Full Text Available Abstract Background Array comparative genomic hybridization (CGH has been repeatedly shown to be a successful tool for the identification of genomic variations in a clinical population. During the last decade, the implementation of array CGH has resulted in the identification of new causative submicroscopic chromosome imbalances and copy number variations (CNVs in neuropsychiatric (neurobehavioral diseases. Currently, array-CGH-based technologies have become an integral part of molecular diagnosis and research in individuals with neuropsychiatric disorders and children with intellectual disability (mental retardation and congenital anomalies. Here, we introduce the Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies analyzed by BAC array CGH and a novel bioinformatic strategy. Results Among 54 individuals highly selected according to clinical criteria and molecular and cytogenetic data (from 2426 patients evaluated cytogenetically and molecularly between November 2007 and May 2012, chromosomal imbalances were detected in 26 individuals (48%. In two patients (4%, a previously undescribed condition was observed. The latter has been designated as meiotic (constitutional genomic instability resulted in multiple submicroscopic rearrangements (including CNVs. Using bioinformatic strategy, we were able to identify clinically relevant CNVs in 15 individuals (28%. Selected cases were confirmed by molecular cytogenetic and molecular genetic methods. Eight out of 26 chromosomal imbalances (31% have not been previously reported. Among them, three cases were co-occurrence of subtle chromosome 9 and 21 deletions. Conclusions We conducted an array CGH study of Russian patients suffering from intellectual disability, autism, epilepsy and congenital anomalies. In total, phenotypic manifestations of clinically relevant genomic variations were found to result from genomic rearrangements affecting 1247 disease

  7. Stochastic Reachability Analysis of Hybrid Systems

    CERN Document Server

    Bujorianu, Luminita Manuela

    2012-01-01

    Stochastic reachability analysis (SRA) is a method of analyzing the behavior of control systems which mix discrete and continuous dynamics. For probabilistic discrete systems it has been shown to be a practical verification method but for stochastic hybrid systems it can be rather more. As a verification technique SRA can assess the safety and performance of, for example, autonomous systems, robot and aircraft path planning and multi-agent coordination but it can also be used for the adaptive control of such systems. Stochastic Reachability Analysis of Hybrid Systems is a self-contained and accessible introduction to this novel topic in the analysis and development of stochastic hybrid systems. Beginning with the relevant aspects of Markov models and introducing stochastic hybrid systems, the book then moves on to coverage of reachability analysis for stochastic hybrid systems. Following this build up, the core of the text first formally defines the concept of reachability in the stochastic framework and then...

  8. Comparative genomic hybridization: practical guidelines.

    NARCIS (Netherlands)

    Jeuken, J.W.M.; Sprenger, S.H.; Wesseling, P.

    2002-01-01

    Comparative genomic hybridization (CGH) is a technique used to identify copy number changes throughout a genome. Until now, hundreds of CGH studies have been published reporting chromosomal imbalances in a large variety of human neoplasms. Additionally, technical improvements of specific steps in a

  9. Array-CGH and quantitative PCR genetic analysis in a case with bilateral hypoplasia of pulmonary arteries and lungs and simultaneous unilateral renal agenesis.

    Science.gov (United States)

    Hussein, Kais; Steinemann, Doris; Scholz, Henrike; Menkhaus, Ralf; Feist, Henning; Kreipe, Hans

    2010-08-18

    We describe the clinical course and have characterised anatomically and genetically a unique case of a newborn with bilateral hypoplasia of pulmonary arteries, consecutive extremely hypoplastic lung tissue and associated unilateral renal agenesis. Intrauterine oxygenation by the placenta seemed to have allowed normotrophic body maturity but immediately after delivery, in the third trimester, progressive hypoxemia developed and the newborn succumbed to acute respiratory failure. Genetic analysis by array-based comparative genomic hybridisation and quantitative PCR revealed duplication of 1p21, which, however, might not be the disease causing aberration. This case might represent an extreme form of previously reported, rare cases with simultaneous dysorganogenesis of lungs and kidneys.

  10. FISH and array-CGH analysis of a complex chromosome 3 aberration suggests that loss of CNTN4 and CRBN contributes to mental retardation in 3pter deletions.

    Science.gov (United States)

    Dijkhuizen, Trijnie; van Essen, Ton; van der Vlies, Pieter; Verheij, Joke B G M; Sikkema-Raddatz, Birgit; van der Veen, Anneke Y; Gerssen-Schoorl, Klasien B J; Buys, Charles H C M; Kok, Klaas

    2006-11-15

    Imbalances of 3p telomeric sequences cause 3p- and trisomy 3p syndrome, respectively, showing distinct, but also shared clinical features. No causative genes have been identified in trisomy 3p patients, but for the 3p- syndrome, there is growing evidence that monosomy for one or more of four genes at 3pter, CHL1, CNTN4, CRBN, and MEGAP/srGAP3, may play a causative role. We describe here an analysis of a complex chromosome 3p aberration in a severely mentally retarded patient that revealed two adjacent segments with different copy number gains and a distal deletion. The deletion in this patient included the loci for CHL1, CNTN4, and CRBN, and narrowed the critical segment associated with the 3p- syndrome to 1.5 Mb, including the loci for CNTN4 and CRBN. We speculate that the deletion contributes more to this patient's phenotype than the gains that were observed. We suggest that 3p- syndrome associated features are primarily caused by loss of CNTN4 and CRBN, with loss of CHL1 probably having an additional detrimental effect on the cognitive functioning of the present patient.

  11. A multi-sample based method for identifying common CNVs in normal human genomic structure using high-resolution aCGH data.

    Directory of Open Access Journals (Sweden)

    Chihyun Park

    Full Text Available BACKGROUND: It is difficult to identify copy number variations (CNV in normal human genomic data due to noise and non-linear relationships between different genomic regions and signal intensity. A high-resolution array comparative genomic hybridization (aCGH containing 42 million probes, which is very large compared to previous arrays, was recently published. Most existing CNV detection algorithms do not work well because of noise associated with the large amount of input data and because most of the current methods were not designed to analyze normal human samples. Normal human genome analysis often requires a joint approach across multiple samples. However, the majority of existing methods can only identify CNVs from a single sample. METHODOLOGY AND PRINCIPAL FINDINGS: We developed a multi-sample-based genomic variations detector (MGVD that uses segmentation to identify common breakpoints across multiple samples and a k-means-based clustering strategy. Unlike previous methods, MGVD simultaneously considers multiple samples with different genomic intensities and identifies CNVs and CNV zones (CNVZs; CNVZ is a more precise measure of the location of a genomic variant than the CNV region (CNVR. CONCLUSIONS AND SIGNIFICANCE: We designed a specialized algorithm to detect common CNVs from extremely high-resolution multi-sample aCGH data. MGVD showed high sensitivity and a low false discovery rate for a simulated data set, and outperformed most current methods when real, high-resolution HapMap datasets were analyzed. MGVD also had the fastest runtime compared to the other algorithms evaluated when actual, high-resolution aCGH data were analyzed. The CNVZs identified by MGVD can be used in association studies for revealing relationships between phenotypes and genomic aberrations. Our algorithm was developed with standard C++ and is available in Linux and MS Windows format in the STL library. It is freely available at: http://embio.yonsei.ac.kr/~Park/mgvd.php.

  12. Genomic alterations detected by comparative genomic hybridization in ovarian endometriomas

    Directory of Open Access Journals (Sweden)

    L.C. Veiga-Castelli

    2010-08-01

    Full Text Available Endometriosis is a complex and multifactorial disease. Chromosomal imbalance screening in endometriotic tissue can be used to detect hot-spot regions in the search for a possible genetic marker for endometriosis. The objective of the present study was to detect chromosomal imbalances by comparative genomic hybridization (CGH in ectopic tissue samples from ovarian endometriomas and eutopic tissue from the same patients. We evaluated 10 ovarian endometriotic tissues and 10 eutopic endometrial tissues by metaphase CGH. CGH was prepared with normal and test DNA enzymatically digested, ligated to adaptors and amplified by PCR. A second PCR was performed for DNA labeling. Equal amounts of both normal and test-labeled DNA were hybridized in human normal metaphases. The Isis FISH Imaging System V 5.0 software was used for chromosome analysis. In both eutopic and ectopic groups, 4/10 samples presented chromosomal alterations, mainly chromosomal gains. CGH identified 11q12.3-q13.1, 17p11.1-p12, 17q25.3-qter, and 19p as critical regions. Genomic imbalances in 11q, 17p, 17q, and 19p were detected in normal eutopic and/or ectopic endometrium from women with ovarian endometriosis. These regions contain genes such as POLR2G, MXRA7 and UBA52 involved in biological processes that may lead to the establishment and maintenance of endometriotic implants. This genomic imbalance may affect genes in which dysregulation impacts both eutopic and ectopic endometrium.

  13. límites organizacionales del CGH

    Directory of Open Access Journals (Sweden)

    Carlos Chávez Becker

    2005-01-01

    Full Text Available El presente trabajo se centra en el análisis de los mecanismos que el Consejo General de Huelga empleó para tomar decisiones, su esquema de representación y su forma de operación política con el fin de establecer algunas relaciones significativas entre tales elementos analíticos y los resultados obtenidos por la organización al término del conflicto en febrero de 2000. La principal intención es evaluar al CGH como la organización de los estudiantes en términos de su actuar político a la luz de los costos y beneficios que representó su actividad.

  14. Chromosomal Localization of DNA Amplifications in Neuroblastoma Tumors Using cDNA Microarray Comparative Genomic Hybridization

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    Ben Beheshti

    2003-01-01

    Full Text Available Conventional comparative genomic hybridization (CGH profiling of neuroblastomas has identified many genomic aberrations, although the limited resolution has precluded a precise localization of sequences of interest within amplicons. To map high copy number genomic gains in clinically matched stage IV neuroblastomas, CGH analysis using a 19,200-feature cDNA microarray was used. A dedicated (freely available algorithm was developed for rapid in silico determination of chromosomal localizations of microarray cDNA targets, and for generation of an ideogram-type profile of copy number changes. Using these methodologies, novel gene amplifications undetectable by chromosome CGH were identified, and larger MYCN amplicon sizes (in one tumor up to 6 Mb than those previously reported in neuroblastoma were identified. The genes HPCAL1, LPIN1/KIAA0188, NAG, and NSE1/LOC151354 were found to be coamplified with MYCN. To determine whether stage IV primary tumors could be further subclassified based on their genomic copy number profiles, hierarchical clustering was performed. Cluster analysis of microarray CGH data identified three groups: 1 no amplifications evident, 2 a small MYCN amplicon as the only detectable imbalance, and 3 a large MYCN amplicon with additional gene amplifications. Application of CGH to cDNA microarray targets will help to determine both the variation of amplicon size and help better define amplification-dependent and independent pathways of progression in neuroblastoma.

  15. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis

    NARCIS (Netherlands)

    Greshock, J; Naylor, TL; Margolin, A; Diskin, S; Cleaver, SH; Futreal, PA; deJong, PJ; Zhao, SY; Liebman, M; Weber, BL

    2004-01-01

    Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for disease-gene discovery in cancer and developmental disorders as well as numerous other applications. However, w

  16. DNA copy number changes in high-grade malignant peripheral nerve sheath tumors by array CGH

    Directory of Open Access Journals (Sweden)

    Bjerkehagen Bodil

    2008-06-01

    Full Text Available Abstract Background Malignant peripheral nerve sheath tumors (MPNSTs are rare and highly aggressive soft tissue tumors showing complex chromosomal aberrations. In order to identify recurrent chromosomal regions of gain and loss, and thereby novel gene targets of potential importance for MPNST development and/or progression, we have analyzed DNA copy number changes in seven high-grade MPNSTs using microarray-based comparative genomic hybridization (array CGH. Results Considerable more gains than losses were observed, and the most frequent minimal recurrent regions of gain included 1q24.1-q24.2, 1q24.3-q25.1, 8p23.1-p12, 9q34.11-q34.13 and 17q23.2-q25.3, all gained in five of seven samples. The 17q23.2-q25.3 region was gained in all five patients with poor outcome and not in the two patients with disease-free survival. cDNA microarray analysis and quantitative real-time reverse transcription PCR were used to investigate expression of genes located within these regions. The gene lysyl oxidase-like 2 (LOXL2 was identified as a candidate target for the 8p23.1-p12 gain. Within 17q, the genes topoisomerase II-α (TOP2A, ets variant gene 4 (E1A enhancer binding protein, E1AF (ETV4 and baculoviral IAP repeat-containing 5 (survivin (BIRC5 showed increased expression in all samples compared to two benign tumors. Increased expression of these genes has previously been associated with poor survival in other malignancies, and for TOP2A, in MPNSTs as well. In addition, we have analyzed the expression of five micro RNAs located within the 17q23.2-q25.3 region, but none of them showed high expression levels compared to the benign tumors. Conclusion Our study shows the potential of using DNA copy number changes obtained by array CGH to predict the prognosis of MPNST patients. Although no clear correlations between the expression level and patient outcome were observed, the genes TOP2A, ETV4 and BIRC5 are interesting candidate targets for the 17q gain associated

  17. Approximate Dynamic Programming for Fast Denoising of aCGH Data

    CERN Document Server

    Miller, Gary L; Schwartz, Russell; Tsourakakis, Charalampos E

    2010-01-01

    DNA sequence copy number is the number of copies of DNA at a region of a genome. Identifying genomic regions whose DNA copy number deviates from the normal is a crucial task in understanding cancer evolution. Array-based comparative genomic hybridization (aCGH) is a high-throughput technique for identifying DNA gain or loss. Due to the high level of noise in microarray data, however, interpretation of aCGH output is a difficult and error-prone task. In this paper, we adopt a recent formulation of the denoising aCGH data problem as a regularized least squares problem and propose an approximation algorithm within $\\epsilon$ additive error, where \\epsilon is an arbitrarily small positive constant. Specifically, we show that for n probes, we can approximate the optimal value of our function within additive \\epsilon with an algorithm that runs in $\\tilde{O}(n^{1.5} \\log{(\\frac{U}{\\epsilon}))}$ time, where U is the maximum value over the regularization term and the probes. The basis of our algorithm is the definiti...

  18. Prenatal Diagnosis of a Fetus with de novo Supernumerary Ring Chromosome 16 Characterized by Array Comparative Genomic Hybridization

    Directory of Open Access Journals (Sweden)

    Pietro Cignini

    2011-09-01

    Full Text Available A fetus with de novo ring chromosome 16 is presented. At 20 weeks' gestation, ultrasound examination demonstrated bilateral clubfoot, bilateral renal pyelectasis, hypoplasia of the corpus callosum, and transposition of the great vessel. Amniocentesis was performed. Chromosome analysis identified a ring chromosome 16 [47,XY,r(16] and array comparative genomic hybridization (a-CGH demonstrated that the ring included the euchromatic portion 16p11.2. Postmortem examination confirmed prenatal findings. This is the first case of de novo ring chromosome 16 diagnosed prenatally with a new phenotypic pattern and also reinforces the importance of offering amniocentesis with a-CGH if fetal anomalies are detected.

  19. Identification of genome-wide copy number variations among diverse pig breeds by array CGH

    Directory of Open Access Journals (Sweden)

    Li Yan

    2012-12-01

    Full Text Available Abstract Background Recent studies have shown that copy number variation (CNV in mammalian genomes contributes to phenotypic diversity, including health and disease status. In domestic pigs, CNV has been catalogued by several reports, but the extent of CNV and the phenotypic effects are far from clear. The goal of this study was to identify CNV regions (CNVRs in pigs based on array comparative genome hybridization (aCGH. Results Here a custom-made tiling oligo-nucleotide array was used with a median probe spacing of 2506 bp for screening 12 pigs including 3 Chinese native pigs (one Chinese Erhualian, one Tongcheng and one Yangxin pig, 5 European pigs (one Large White, one Pietrain, one White Duroc and two Landrace pigs, 2 synthetic pigs (Chinese new line DIV pigs and 2 crossbred pigs (Landrace × DIV pigs with a Duroc pig as the reference. Two hundred and fifty-nine CNVRs across chromosomes 1–18 and X were identified, with an average size of 65.07 kb and a median size of 98.74 kb, covering 16.85 Mb or 0.74% of the whole genome. Concerning copy number status, 93 (35.91% CNVRs were called as gains, 140 (54.05% were called as losses and the remaining 26 (10.04% were called as both gains and losses. Of all detected CNVRs, 171 (66.02% and 34 (13.13% CNVRs directly overlapped with Sus scrofa duplicated sequences and pig QTLs, respectively. The CNVRs encompassed 372 full length Ensembl transcripts. Two CNVRs identified by aCGH were validated using real-time quantitative PCR (qPCR. Conclusions Using 720 K array CGH (aCGH we described a map of porcine CNVs which facilitated the identification of structural variations for important phenotypes and the assessment of the genetic diversity of pigs.

  20. Programmable CGH on photochromic material using DMD

    Science.gov (United States)

    Alata, Romain; Pariani, Giorgio; Zamkotsian, Frederic; Lanzoni, Patrick; Bianco, Andrea; Bertarelli, Chiara

    2016-07-01

    Computer Generated Holograms (CGHs) are useful for wavefront shaping and complex optics testing, including aspherical and free-form optics. Today, CGHs are recorded directly with a laser or intermediates masks but allows only recording binary CGHs; binary CGHs are efficient but can reconstruct only pixilated images. We propose to use a Digital Micro-mirror Device (DMD) for writing binary CGHs as well as grayscale CGHs, able to reconstruct fulfilled images. DMD is actually studied at LAM, for generating programmable slit masks in multi-object spectrographs. It is composed of 2048x1080 individually controllable micro-mirrors, with a pitch of 13.68 μm. This is a real-time reconfigurable mask, perfect for recording CGHs. A first setup has been developed for hologram recording, where the DMD is enlightened with a collimated beam and illuminates a photosensible plate through an Offner relay, with a magnification of 1:1. Our set up resolution is 2-3 μm, leading to a CGH resolution equal to the DMD micro mirror size. In order to write and erase CGHs during test procedure or on request, we use a photochromic plate called PUR-GD71-50-ST developed at Politecnico di Milano. It is opaque at rest, and becomes transparent when it is illuminated with visible light, between 500 and 700 nm; then it can be erased by a UV flash. We choose to code the CGHs in equally spaced levels, so called stepped CGH. We recorded up to 1000x1000 pixels CGHs with a contrast greater than 50, knowing that the material is able to reach an ultimate contrast of 1000. A second bench has also been developed, dedicated to the reconstruction of the recorded images with a 632.8nm He-Ne laser beam. Very faithful reconstructions have been obtained. Thanks to our recording and reconstruction set-ups, we have been able to successfully record binary and stepped CGHs, and reconstruct them with a high fidelity, revealing the potential of this method for generating programmable/rewritable stepped CGHs on

  1. Array CGH characterization of an unbalanced X-autosome translocation associated with Xq27.2-qter deletion, 11q24.3-qter duplication and Xq22.3-q27.1 duplication in a girl with primary amenorrhea and mental retardation.

    Science.gov (United States)

    Chen, Chih-Ping; Lin, Shuan-Pei; Chern, Schu-Rern; Kuo, Yu-Ling; Wu, Peih-Shan; Chen, Yu-Ting; Lee, Meng-Shan; Wang, Wayseen

    2014-02-01

    We present array comparative genomic hybridization (aCGH) characterization of an unbalanced X-autosome translocation with an Xq interstitial segmental duplication in a 16-year-old girl with primary ovarian failure, mental retardation, attention deficit disorder, learning difficulty and facial dysmorphism. aCGH analysis revealed an Xq27.2-q28 deletion, an 11q24.3-q25 duplication, and an inverted duplication of Xq22.3-q27.1. The karyotype was 46,X,der(X)t(X;11)(q27.2;q24.3) dup(X)(q27.1q22.3). We discuss the genotype-phenotype correlation in this case. Our case provides evidence for an association of primary amenorrhea and mental retardation with concomitant unbalanced X-autosome translocation and X chromosome rearrangement.

  2. Analysis and design of hybrid control systems

    Energy Technology Data Exchange (ETDEWEB)

    Malmborg, J.

    1998-05-01

    Different aspects of hybrid control systems are treated: analysis, simulation, design and implementation. A systematic methodology using extended Lyapunov theory for design of hybrid systems is developed. The methodology is based on conventional control designs in separate regions together with a switching strategy. Dynamics are not well defined if the control design methods lead to fast mode switching. The dynamics depend on the salient features of the implementation of the mode switches. A theorem for the stability of second order switching together with the resulting dynamics is derived. The dynamics on an intersection of two sliding sets are defined for two relays working on different time scales. The current simulation packages have problems modeling and simulating hybrid systems. It is shown how fast mode switches can be found before or during simulation. The necessary analysis work is a very small overhead for a modern simulation tool. To get some experience from practical problems with hybrid control the switching strategy is implemented in two different software environments. In one of them a time-optimal controller is added to an existing PID controller on a commercial control system. Successful experiments with this hybrid controller shows the practical use of the method 78 refs, 51 figs, 2 tabs

  3. Array comparative genomic hybridization profiling analysis reveals deoxyribonucleic acid copy number variations associated with premature ovarian failure.

    Science.gov (United States)

    Aboura, Azzedine; Dupas, Claire; Tachdjian, Gérard; Portnoï, Marie-France; Bourcigaux, Nathalie; Dewailly, Didier; Frydman, René; Fauser, Bart; Ronci-Chaix, Nathalie; Donadille, Bruno; Bouchard, Philippe; Christin-Maitre, Sophie

    2009-11-01

    Premature ovarian failure (POF) is defined by amenorrhea of at least 4- to 6-month duration, occurring before 40 yr of age, with two FSH levels in the postmenopausal range. Its etiology remains unknown in more than 80% of cases. Standard karyotypes, having a resolution of 5-10 Mb, have identified critical chromosomal regions, mainly located on the long arm of the X chromosome. Array comparative genomic hybridization (a-CGH) analysis is able to detect submicroscopic chromosomal rearrangements with a higher genomic resolution. We searched for copy number variations (CNVs), using a-CGH analysis with a resolution of approximately 0.7 Mb, in a cohort of patients with POF. We prospectively included 99 women. Our study included a conventional karyotype and DNA microarrays comprising 4500 bacterial artificial chromosome clones spread on the entire genome. Thirty-one CNVs have been observed, three on the X chromosome and 28 on autosomal chromosomes. Data have been compared to control populations obtained from the Database of Genomic Variants (http://projects.tcag.ca/variation). Eight statistically significantly different CNVs have been identified in chromosomal regions 1p21.1, 5p14.3, 5q13.2, 6p25.3, 14q32.33, 16p11.2, 17q12, and Xq28. We report the first study of CNV analysis in a large cohort of Caucasian POF patients. In the eight statistically significant CNVs we report, we found five genes involved in reproduction, thus representing potential candidate genes in POF. The current study along with emerging information regarding CNVs, as well as data on their potential association with human diseases, emphasizes the importance of assessing CNVs in cohorts of POF women.

  4. Bundled Hybrid Offset Riser Global Strength Analysis

    Institute of Scientific and Technical Information of China (English)

    William C.Webster; Zhuang Kang; Wenzhou Liang; Youwei Kang; Liping Sun

    2011-01-01

    Bundled hybrid offset riser(BHOR)global strength analysis,which is more complex than single line offset riser global strength analysis,was carried out in this paper.At first,the equivalent theory is used to deal with BHOR,and then its global strength in manifold cases was analyzed,along with the use of a three-dimensional nonlinear time domain finite element program.So the max bending stress,max circumferential stress,and max axial stress in the BHOR bundle main section(BMS)were obtained,and the values of these three stresses in each riser were obtained through the "stress distribution method".Finally,the Max Von Mises stress in each riser was given and a check was made whether or not they met the demand.This paper provides a reference for strength analysis of the bundled hybrid offset riser and some other bundled pipelines.

  5. Distinct molecular signatures in pediatric infratentorial glioblastomas defined by aCGH.

    Science.gov (United States)

    Sharma, S; Free, A; Mei, Y; Peiper, S C; Wang, Z; Cowell, J K

    2010-10-01

    Glioblastomas (GBM) are rare in children, but reportedly have more varied outcome which suggests differences in tumor etiology compared to typical GBM of adults. To investigate this we performed high resolution array comparative genomic hybridization (aCGH) analysis on three pediatric infratentorial GBM, ages 3.5, 7 and 14 years. Two of these tumors occurred in the brainstem and one in the spinal cord. While histologically typical, one brainstem tumor showed mainly pleomorphic astrocytic cells, whereas the other brainstem and spinal tumors showed a GFAP positive small cell component. Whole chromosomal gains (#1 and #2) and loss (#20) were seen only in the pleomorphic brainstem GBM, which also showed a high level of segmental genomic copy number changes. Segmental loss involving chromosome 8 was seen in all three tumors (Chr8;133039446-136869494, Chr8;pter-3581577, and Chr8;pter-30480019 respectively), whereas loss involving chromosome 16 was seen in only 2 cases with small cell components (Chr16;31827239-qter and Chr16;pter-29754532). Segmental gain of chromosome 7 was shared only between the 2 brainstem cases (Chr7;17187166-qter and Chr7;69824947-qter). Chromosome 17 showed segmental gain of 17q in the backdrop of loss of 17p only in case 1. Segmental gain of chromosome 1q was seen only in case 2. The spinal GBM showed a relatively stable karyotype with a unique loss of Chr19;32848902-qter. None of the frequent losses, gains and amplifications known to occur in adult GBM were identified, suggesting that pediatric infratentorial glioblastomas show a molecular karyotype that was more characteristic of pediatric embryonal tumors than adult GBM.

  6. Analysis of hybrid viscous damper by real time hybrid simulations

    DEFF Research Database (Denmark)

    Brodersen, Mark Laier; Ou, Ge; Høgsberg, Jan Becker

    2016-01-01

    Results from real time hybrid simulations are compared to full numerical simulations for a hybrid viscous damper, composed of a viscous dashpot in series with an active actuator and a load cell. By controlling the actuator displacement via filtered integral force feedback the damping performance...... of the hybrid viscous damper is improved, while for pure integral force feedback the damper stroke is instead increased. In the real time hybrid simulations viscous damping is emulated by a bang-bang controlled Magneto-Rheological (MR) damper. The controller activates high-frequency modes and generates drift...... in the actuator displacement, and only a fraction of the measured damper force can therefore be used as input to the investigated integral force feedback in the real time hybrid simulations....

  7. Analysis of fuel cell hybrid locomotives

    Science.gov (United States)

    Miller, Arnold R.; Peters, John; Smith, Brian E.; Velev, Omourtag A.

    Led by Vehicle Projects LLC, an international industry-government consortium is developing a 109 t, 1.2 MW road-switcher locomotive for commercial and military railway applications. As part of the feasibility and conceptual-design analysis, a study has been made of the potential benefits of a hybrid power plant in which fuel cells comprise the prime mover and a battery or flywheel provides auxiliary power. The potential benefits of a hybrid power plant are: (i) enhancement of transient power and hence tractive effort; (ii) regenerative braking; (iii) reduction of capital cost. Generally, the tractive effort of a locomotive at low speed is limited by wheel adhesion and not by available power. Enhanced transient power is therefore unlikely to benefit a switcher locomotive, but could assist applications that require high acceleration, e.g. subway trains with all axles powered. In most cases, the value of regeneration in locomotives is minimal. For low-speed applications such as switchers, the available kinetic energy and the effectiveness of traction motors as generators are both minimal. For high-speed heavy applications such as freight, the ability of the auxiliary power device to absorb a significant portion of the available kinetic energy is low. Moreover, the hybrid power plant suffers a double efficiency penalty, namely, losses occur in both absorbing and then releasing energy from the auxiliary device, which result in a net storage efficiency of no more than 50% for present battery technology. Capital cost in some applications may be reduced. Based on an observed locomotive duty cycle, a cost model shows that a hybrid power plant for a switcher may indeed reduce capital cost. Offsetting this potential benefit are the increased complexity, weight and volume of the power plant, as well as 20-40% increased fuel consumption that results from lower efficiency. Based on this analysis, the consortium has decided to develop a pure fuel cell road-switcher locomotive

  8. 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.

  9. Analysis of hybrid solar systems

    Science.gov (United States)

    Swisher, J.

    1980-10-01

    The TRNSYS simulation program was used to evaluate the performance of active charge/passive discharge solar systems with water as the working fluid. TRNSYS simulations are used to evaluate the heating performance and cooling augmentation provided by systems in several climates. The results of the simulations are used to develop a simplified analysis tool similar to the F-chart and Phi-bar procedures used for active systems. This tool, currently in a preliminary stage, should provide the designer with quantitative performance estimates for comparison with other passive, active, and nonsolar heating and cooling designs.

  10. Gene expression profiles in squamous cell cervical carcinoma using array-based comparative genomic hybridization analysis.

    Science.gov (United States)

    Choi, Y-W; Bae, S M; Kim, Y-W; Lee, H N; Kim, Y W; Park, T C; Ro, D Y; Shin, J C; Shin, S J; Seo, J-S; Ahn, W S

    2007-01-01

    Our aim was to identify novel genomic regions of interest and provide highly dynamic range information on correlation between squamous cell cervical carcinoma and its related gene expression patterns by a genome-wide array-based comparative genomic hybridization (array-CGH). We analyzed 15 cases of cervical cancer from KangNam St Mary's Hospital of the Catholic University of Korea. Microdissection assay was performed to obtain DNA samples from paraffin-embedded cervical tissues of cancer as well as of the adjacent normal tissues. The bacterial artificial chromosome (BAC) array used in this study consisted of 1440 human BACs and the space among the clones was 2.08 Mb. All the 15 cases of cervical cancer showed the differential changes of the cervical cancer-associated genetic alterations. The analysis limit of average gains and losses was 53%. A significant positive correlation was found in 8q24.3, 1p36.32, 3q27.1, 7p21.1, 11q13.1, and 3p14.2 changes through the cervical carcinogenesis. The regions of high level of gain were 1p36.33-1p36.32, 8q24.3, 16p13.3, 1p36.33, 3q27.1, and 7p21.1. And the regions of homozygous loss were 2q12.1, 22q11.21, 3p14.2, 6q24.3, 7p15.2, and 11q25. In the high level of gain regions, GSDMDC1, RECQL4, TP73, ABCF3, ALG3, HDAC9, ESRRA, and RPS6KA4 were significantly correlated with cervical cancer. The genes encoded by frequently lost clones were PTPRG, GRM7, ZDHHC3, EXOSC7, LRP1B, and NR3C2. Therefore, array-CGH analyses showed that specific genomic alterations were maintained in cervical cancer that were critical to the malignant phenotype and may give a chance to find out possible target genes present in the gained or lost clones.

  11. Probabilistic Analysis Methods for Hybrid Ventilation

    DEFF Research Database (Denmark)

    Brohus, Henrik; Frier, Christian; Heiselberg, Per

    This paper discusses a general approach for the application of probabilistic analysis methods in the design of ventilation systems. The aims and scope of probabilistic versus deterministic methods are addressed with special emphasis on hybrid ventilation systems. A preliminary application of stoc...... of stochastic differential equations is presented comprising a general heat balance for an arbitrary number of loads and zones in a building to determine the thermal behaviour under random conditions....

  12. Multiple Break-Points Detection in Array CGH Data via the Cross-Entropy Method.

    Science.gov (United States)

    Priyadarshana, W J R M; Sofronov, Georgy

    2015-01-01

    Array comparative genome hybridization (aCGH) is a widely used methodology to detect copy number variations of a genome in high resolution. Knowing the number of break-points and their corresponding locations in genomic sequences serves different biological needs. Primarily, it helps to identify disease-causing genes that have functional importance in characterizing genome wide diseases. For human autosomes the normal copy number is two, whereas at the sites of oncogenes it increases (gain of DNA) and at the tumour suppressor genes it decreases (loss of DNA). The majority of the current detection methods are deterministic in their set-up and use dynamic programming or different smoothing techniques to obtain the estimates of copy number variations. These approaches limit the search space of the problem due to different assumptions considered in the methods and do not represent the true nature of the uncertainty associated with the unknown break-points in genomic sequences. We propose the Cross-Entropy method, which is a model-based stochastic optimization technique as an exact search method, to estimate both the number and locations of the break-points in aCGH data. We model the continuous scale log-ratio data obtained by the aCGH technique as a multiple break-point problem. The proposed methodology is compared with well established publicly available methods using both artificially generated data and real data. Results show that the proposed procedure is an effective way of estimating number and especially the locations of break-points with high level of precision. Availability: The methods described in this article are implemented in the new R package breakpoint and it is available from the Comprehensive R Archive Network at http://CRAN.R-project.org/package=breakpoint.

  13. Sustainable process design & analysis of hybrid separations

    DEFF Research Database (Denmark)

    Kumar Tula, Anjan; Befort, Bridgette; Garg, Nipun

    2016-01-01

    Distillation is an energy intensive operation in chemical process industries. There are around 40,000 distillation columns in operation in the US, requiring approximately 40% of the total energy consumption in US chemical process industries. However, analysis of separations by distillation has...... shown that more than 50% of energy is spent in purifying the last 5-10% of the distillate product. Membrane modules on the other hand can achieve high purity separations at lower energy costs, but if the flux is high, it requires large membrane area. A hybrid scheme where distillation and membrane...... modules are combined such that each operates at its highest efficiency, has the potential for significant energy reduction without significant increase of capital costs. This paper presents a method for sustainable design of hybrid distillation-membrane schemes with guaranteed reduction of energy...

  14. Exome sequencing of germline DNA from non-BRCA1/2 familial breast cancer cases selected on the basis of aCGH tumor profiling.

    Directory of Open Access Journals (Sweden)

    Florentine S Hilbers

    Full Text Available The bulk of familial breast cancer risk (∼70% cannot be explained by mutations in the known predisposition genes, primarily BRCA1 and BRCA2. Underlying genetic heterogeneity in these cases is the probable explanation for the failure of all attempts to identify further high-risk alleles. While exome sequencing of non-BRCA1/2 breast cancer cases is a promising strategy to detect new high-risk genes, rational approaches to the rigorous pre-selection of cases are needed to reduce heterogeneity. We selected six families in which the tumours of multiple cases showed a specific genomic profile on array comparative genomic hybridization (aCGH. Linkage analysis in these families revealed a region on chromosome 4 with a LOD score of 2.49 under homogeneity. We then analysed the germline DNA of two patients from each family using exome sequencing. Initially focusing on the linkage region, no potentially pathogenic variants could be identified in more than one family. Variants outside the linkage region were then analysed, and we detected multiple possibly pathogenic variants in genes that encode DNA integrity maintenance proteins. However, further analysis led to the rejection of all variants due to poor co-segregation or a relatively high allele frequency in a control population. We concluded that using CGH results to focus on a sub-set of families for sequencing analysis did not enable us to identify a common genetic change responsible for the aggregation of breast cancer in these families. Our data also support the emerging view that non-BRCA1/2 hereditary breast cancer families have a very heterogeneous genetic basis.

  15. Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons

    Directory of Open Access Journals (Sweden)

    De Paepe Anne

    2004-02-01

    Full Text Available Abstract Background Activation of proto-oncogenes by DNA amplification is an important mechanism in the development and maintenance of cancer cells. Until recently, identification of the targeted genes relied on labour intensive and time consuming positional cloning methods. In this study, we outline a straightforward and efficient strategy for fast and comprehensive cloning of amplified and overexpressed genes. Results As a proof of principle, we analyzed neuroblastoma cell line IMR-32, with at least two amplification sites along the short arm of chromosome 2. In a first step, overexpressed cDNA clones were isolated using a PCR based subtractive cloning method. Subsequent deposition of these clones on a custom microarray and hybridization with IMR-32 DNA, resulted in the identification of clones that were overexpressed due to gene amplification. Using this approach, amplification of all previously reported amplified genes in this cell line was detected. Furthermore, four additional clones were found to be amplified, including the TEM8 gene on 2p13.3, two anonymous transcripts, and a fusion transcript, resulting from 2p13.3 and 2p24.3 fused sequences. Conclusions The combinatorial strategy of subtractive cDNA cloning and array CGH analysis allows comprehensive amplicon dissection, which opens perspectives for improved identification of hitherto unknown targeted oncogenes in cancer cells.

  16. 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.

  17. Sentiment Analysis Using Hybrid Approach: A Survey

    Directory of Open Access Journals (Sweden)

    Chauhan Ashish P

    2015-01-01

    Full Text Available Sentiment analysis is the process of identifying people’s attitude and emotional state’s from language. The main objective is realized by identifying a set of potential features in the review and extracting opinion expressions about those features by exploiting their associations. Opinion mining, also known as Sentiment analysis, plays an important role in this process. It is the study of emotions i.e. Sentiments, Expressionsthat are stated in natural language. Natural language techniques are applied to extract emotions from unstructured data. There are several techniques which can be used to analysis such type of data. Here, we are categorizing these techniques broadly as ”supervised learning”, ”unsupervised learning” and ”hybrid techniques”. The objective of this paper is to provide the overview of Sentiment Analysis, their challenges and a comparative analysis of it’s techniques in the field of Natural Language Processing

  18. Partial biochemical and biological characterization of purified chicken growth hormone (cGH). Isolation of cGH charge variants and evidence that cGH is phosphorylated.

    Science.gov (United States)

    Arámburo, C; Carranza, M; Sanchez, R; Perera, G

    1989-11-01

    Chicken growth hormone (cGH) was purified from frozen pituitary glands obtained from recently sacrificed broilers. Glands were homogenized in a protease inhibitor solution (0.5 mM PMSF, 50 KIU/ml aprotinin, pH 7.2); extract was taken to pH 9.0 with calcium hydroxide and the supernatant was differentially precipitated with 20% (fraction A) and 50% (fraction B) ammonium sulfate. cGH (fraction B-DE-1) was obtained in pure form from fraction B after DEAE-cellulose chromatography at pH 8.6, with a yield of 2.9 mg/g tissue. Three charge variants of cGH (Rf = 0.23, 0.30, and 0.35) could be isolated by electroelution after semipreparative nondenaturing polyacrylamide gel electrophoresis of fraction B-DE-1. These charge variants showed the same apparent molecular weight (26,300 Da) by sodium dodecyl sulfate polyacrylamide gel electrophoresis under reducing conditions. Isoelectric focusing of fraction B-DE-1 revealed two major components (pI = 7.2 and 7.4) and four minor bands (pI = 6.2, 6.7, 7.1, and 7.5). It was found that fraction B-DE-1 contained a significant amount of esterified phosphate (1 nmol PO4/3.5 nmol protein) similar to that reported previously for ovine GH. The functional integrity of the cGH obtained here was characterized by two heterologous and one homologous bioassays. High activity was shown by fraction B-DE-1 in the tibia assay (1.76 UI/mg) and in the liver ornithine decarboxylase assay (sixfold over control), both made in hypophysectomized rats; and it also stimulated lipolysis (138 and 215% at 10 and 100 ng/ml, respectively) on chicken abdominal adipose tissue explants.

  19. Design Considerations for Array CGH to OligonucleotideArrays

    Energy Technology Data Exchange (ETDEWEB)

    Baldocchi, R.A.; Glynne, R.J.; Chin, K.; Kowbel, D.; Collins, C.; Mack, D.H.; Gray, J.W.

    2005-03-04

    Background: Representational oligonucleotide microarray analysis has been developed for detection of single nucleotide polymorphisms and/or for genome copy number changes. In this process, the intensity of hybridization to oligonucleotides arrays is increased by hybridizing a polymerase chain reaction (PCR)-amplified representation of reduced genomic complexity. However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome. Methods: In an effort to identify aspects of oligonucleotide hybridization affecting signal intensity, we explored the importance of the PCR product strand to which each oligonucleotide is homologous and the sequence of the array oligonucleotides. We accomplished this by hybridizing multiple PCR-amplified products to oligonucleotide arrays carrying two sense and two antisense 50-mer oligonucleotides for each PCR amplicon. Results: In some cases, hybridization intensity depended more strongly on the PCR amplicon strand (i.e., sense vs. antisense) than on the detection oligonucleotide sequence. In other cases, the oligonucleotide sequence seemed to dominate. Conclusion: Oligonucleotide arrays for analysis of DNA copy number or for single nucleotide polymorphism content should be designed to carry probes to sense and antisense strands of each PCR amplicon to ensure sufficient hybridization and signal intensity.

  20. The Utility of Chromosomal Microarray Analysis in Developmental and Behavioral Pediatrics

    Science.gov (United States)

    Beaudet, Arthur L.

    2013-01-01

    Chromosomal microarray analysis (CMA) has emerged as a powerful new tool to identify genomic abnormalities associated with a wide range of developmental disabilities including congenital malformations, cognitive impairment, and behavioral abnormalities. CMA includes array comparative genomic hybridization (CGH) and single nucleotide polymorphism…

  1. Supernumerary marker chromosomes derived from chromosome 6: cytogenetic, molecular cytogenetic, and array CGH characterization.

    Science.gov (United States)

    Huang, Bing; Pearle, Phyllis; Rauen, Katherine A; Cotter, Philip D

    2012-07-01

    Supernumerary marker chromosomes (SMC) are relatively common in prenatal diagnosis. As the clinical outcomes vary greatly, a better understanding of the karyotype-phenotype correlation for different SMCs will be important for genetic counseling. We present two cases of prenatally detected de novo, small SMCs. The markers were present in 80% of amniocyte colonies in Case 1 and 38% of the colonies in Case 2. The SMCs were determined to be derived from chromosome 6 during postnatal confirmation studies. Although the sizes and the chromosomal origin of the SMCs in these two cases appeared to be similar, the clinical outcomes varied. The clinical manifestations observed in Case 1 included small for gestational age, feeding difficulty at birth, hydronephrosis, deviated septum and dysmorphic features, while the phenotype is apparently normal in Case 2. Array comparative genomic hybridization (CGH) was performed and showed increase in dosage for approximately 26 Mb of genetic material from the proximal short and long arms of chromosome 6 in Case 1. Results of array CGH were uninformative in Case 2, either due to mosaicism or lack of detectable euchromatin. The difference in the clinical presentation in these two patients may have resulted from the difference in the actual gene contents of the marker chromosomes and/or the differential distribution of the mosaicism.

  2. Detection of clinically relevant exonic copy-number changes by array CGH.

    Science.gov (United States)

    Boone, Philip M; Bacino, Carlos A; Shaw, Chad A; Eng, Patricia A; Hixson, Patricia M; Pursley, Amber N; Kang, Sung-Hae L; Yang, Yaping; Wiszniewska, Joanna; Nowakowska, Beata A; del Gaudio, Daniela; Xia, Zhilian; Simpson-Patel, Gayle; Immken, LaDonna L; Gibson, James B; Tsai, Anne C-H; Bowers, Jennifer A; Reimschisel, Tyler E; Schaaf, Christian P; Potocki, Lorraine; Scaglia, Fernando; Gambin, Tomasz; Sykulski, Maciej; Bartnik, Magdalena; Derwinska, Katarzyna; Wisniowiecka-Kowalnik, Barbara; Lalani, Seema R; Probst, Frank J; Bi, Weimin; Beaudet, Arthur L; Patel, Ankita; Lupski, James R; Cheung, Sau Wai; Stankiewicz, Pawel

    2010-12-01

    Array comparative genomic hybridization (aCGH) is a powerful tool for the molecular elucidation and diagnosis of disorders resulting from genomic copy-number variation (CNV). However, intragenic deletions or duplications--those including genomic intervals of a size smaller than a gene--have remained beyond the detection limit of most clinical aCGH analyses. Increasing array probe number improves genomic resolution, although higher cost may limit implementation, and enhanced detection of benign CNV can confound clinical interpretation. We designed an array with exonic coverage of selected disease and candidate genes and used it clinically to identify losses or gains throughout the genome involving at least one exon and as small as several hundred base pairs in size. In some patients, the detected copy-number change occurs within a gene known to be causative of the observed clinical phenotype, demonstrating the ability of this array to detect clinically relevant CNVs with subkilobase resolution. In summary, we demonstrate the utility of a custom-designed, exon-targeted oligonucleotide array to detect intragenic copy-number changes in patients with various clinical phenotypes.

  3. 基于微阵列芯片的比较基因组杂交技术在临床实验室产前诊断中的应用%Prenatal diagnosis by array-based comparative genomic hybridization in the clinical laboratory setting

    Institute of Scientific and Technical Information of China (English)

    Amy M. BREMAN; 毕为民; 张秀慧

    2009-01-01

    Array-based comparative genomic hybridization (array CGH), a method used to detect gains or losses of genetic material, has recently been applied to prenatal diagnosis of genomic imbalance in the clinical laboratory setting. This new and exciting diagnostic tool represents a major technological step forward in cytogenetic testing and addresses many of the limitations of current cytogenetic methods.Conventional chromosome analysis, the current gold standard in prenatal diagnosis, focuses primarily on the detection of common aneuploidies and is limited by its capacity to detect only those copy number changes that are large enough to be microscopically visible (typically 5-6 Mb in size at the 500 band level). In contrast, array CGH analysis simultaneously evaluates regions across the entire genome and al-lows for detection of unbalanced structural and numerical chromosome abnormalities of less than one hun-dred kb. Array CGH analysis also overcomes some of the limitations of chromosome analysis, such as the requirement for cell culture and longer reporting time, by using direct uncultured fetal specimens. With many diagnostic laboratories now embracing this technology, the past year has seen tremendous growth in the use of array CGH analysis for prenatal diagnosis. This review aims to summarize array CGH methodology and its current applications in prenatal diagnosis.

  4. Effect of bone decalcification procedures on DNA in situ hybridization and comparative genomic hybridization. EDTA is highly preferable to a routinely used acid decalcifier

    NARCIS (Netherlands)

    J.C. Alers (Janneke); P-J. Krijtenburg (Pieter-Jaap); K.J. Vissers (Kees); H. van Dekken (Herman)

    1999-01-01

    textabstractDecalcification is routinely performed for histological studies of bone-containing tissue. Although DNA in situ hybridization (ISH) and comparative genomic hybridization (CGH) have been successfully employed on archival material, little has been reported on

  5. PHOTOPROBER® Biotin: An Alternative Method for Labeling Archival DNA for Comparative Genomic Hybridization

    Directory of Open Access Journals (Sweden)

    Dirk Korinth

    2004-01-01

    Full Text Available Comparative genomic hybridization (CGH represents a powerful method for screening the entire genome of solid tumors for chromosomal imbalances. Particularly it enabled the molecular cytogenetic analysis of archival, formalin‐fixed, paraffin‐embedded (FFPE tissue. A well‐known dilemma, however, is the poor DNA quality of this material with fragment sizes below 1000 bp. Nick translation, the conventionally used enzymatic DNA labeling method in CGH, leads to even shorter fragments often below a critical limit for successful analysis. In this study we report the alternative application of non‐enzymatic, PHOTOPROBE® biotin labeling for conjugation of the hapten to the DNA prior to in situ hybridization and fluorescence detection. We analyzed 51 FFPE tumor samples mainly from the upper respiratory tract by both labeling methods. In 19 cases, both approaches were successful. The comparison of hybridized metaphases showed a distinct higher fluorescence signal of the PHOTOPROBE® samples sometimes with a discrete cytoplasm background which however did not interfere with specificity and sensitivity of the detected chromosomal imbalances. For further 32 cases characterized by an average DNA fragment size below 1000 bp, PHOTOPROBE® biotin was the only successful labeling technique thus offering a new option for CGH analysis of highly degraded DNA from archival material.

  6. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.

    Science.gov (United States)

    Park, Hansoo; Kim, Jong-Il; Ju, Young Seok; Gokcumen, Omer; Mills, Ryan E; Kim, Sheehyun; Lee, Seungbok; Suh, Dongwhan; Hong, Dongwan; Kang, Hyunseok Peter; Yoo, Yun Joo; Shin, Jong-Yeon; Kim, Hyun-Jin; Yavartanoo, Maryam; Chang, Young Wha; Ha, Jung-Sook; Chong, Wilson; Hwang, Ga-Ram; Darvishi, Katayoon; Kim, Hyeran; Yang, Song Ju; Yang, Kap-Seok; Kim, Hyungtae; Hurles, Matthew E; Scherer, Stephen W; Carter, Nigel P; Tyler-Smith, Chris; Lee, Charles; Seo, Jeong-Sun

    2010-05-01

    Copy number variants (CNVs) account for the majority of human genomic diversity in terms of base coverage. Here, we have developed and applied a new method to combine high-resolution array comparative genomic hybridization (CGH) data with whole-genome DNA sequencing data to obtain a comprehensive catalog of common CNVs in Asian individuals. The genomes of 30 individuals from three Asian populations (Korean, Chinese and Japanese) were interrogated with an ultra-high-resolution array CGH platform containing 24 million probes. Whole-genome sequencing data from a reference genome (NA10851, with 28.3x coverage) and two Asian genomes (AK1, with 27.8x coverage and AK2, with 32.0x coverage) were used to transform the relative copy number information obtained from array CGH experiments into absolute copy number values. We discovered 5,177 CNVs, of which 3,547 were putative Asian-specific CNVs. These common CNVs in Asian populations will be a useful resource for subsequent genetic studies in these populations, and the new method of calling absolute CNVs will be essential for applying CNV data to personalized medicine.

  7. Formalin-fixed paraffin-embedded clinical tissues show spurious copy number changes in array-CGH profiles.

    Science.gov (United States)

    Mc Sherry, E A; Mc Goldrick, A; Kay, E W; Hopkins, A M; Gallagher, W M; Dervan, P A

    2007-11-01

    Formalin-fixed paraffin-embedded (FFPE) archival clinical specimens are invaluable in discovery of prognostic and therapeutic targets for diseases such as cancer. However, the suitability of FFPE-derived genetic material for array-based comparative genomic hybridization (array-CGH) studies is underexplored. In this study, genetic profiles of matched FFPE and fresh-frozen specimens were examined to investigate DNA integrity differences between these sample types and determine the impact this may have on genetic profiles. Genomic DNA was extracted from three patient-matched FFPE and fresh-frozen clinical tissue samples. T47D breast cancer control cells were also grown in culture and processed to yield a fresh T47D sample, a fresh-frozen T47D sample and a FFPE T47D sample. DNA was extracted from all the samples; array-CGH conducted and genetic profiles of matched samples were then compared. A loss of high molecular weight DNA was observed in the FFPE clinical tissues and FFPE T47D samples. A dramatic increase in absolute number of genetic alterations was observed in all FFPE tissues relative to matched fresh-frozen counterparts. In future, alternative fixation and tissue-processing procedures, and/or new DNA extraction and CGH profiling protocols, may be implemented, enabling identification of changes involved in disease progression using stored clinical specimens.

  8. Genome-Wide Screening of Cytogenetic Abnormalities in Multiple Myeloma Patients Using Array-CGH Technique: A Czech Multicenter Experience

    Directory of Open Access Journals (Sweden)

    Jan Smetana

    2014-01-01

    Full Text Available Characteristic recurrent copy number aberrations (CNAs play a key role in multiple myeloma (MM pathogenesis and have important prognostic significance for MM patients. Array-based comparative genomic hybridization (aCGH provides a powerful tool for genome-wide classification of CNAs and thus should be implemented into MM routine diagnostics. We demonstrate the possibility of effective utilization of oligonucleotide-based aCGH in 91 MM patients. Chromosomal aberrations associated with effect on the prognosis of MM were initially evaluated by I-FISH and were found in 93.4% (85/91. Incidence of hyperdiploidy was 49.5% (45/91; del(13(q14 was detected in 57.1% (52/91; gain(1(q21 occurred in 58.2% (53/91; del(17(p13 was observed in 15.4% (14/91; and t(4;14(p16;q32 was found in 18.6% (16/86. Genome-wide screening using Agilent 44K aCGH microarrays revealed copy number alterations in 100% (91/91. Most common deletions were found at 13q (58.9%, 1p (39.6%, and 8p (31.1%, whereas gain of whole 1q was the most often duplicated region (50.6%. Furthermore, frequent homozygous deletions of genes playing important role in myeloma biology such as TRAF3, BIRC1/BIRC2, RB1, or CDKN2C were observed. Taken together, we demonstrated the utilization of aCGH technique in clinical diagnostics as powerful tool for identification of unbalanced genomic abnormalities with prognostic significance for MM patients.

  9. Kinematic Analysis of a Hybrid Structure

    Directory of Open Access Journals (Sweden)

    Q.J. Duan

    2012-11-01

    Full Text Available This paper presents a kinematic analysis and simulation of a hybrid structure applied to the new design cable-suspended feed structure (CSFS for the next generation of large spherical radio telescopes. First, considering the requirement that feeds should be tilted from 40° to 60° and that the tracking precision in steady state is 4mm, a novel design of the feed supporting structure including a cable-cabin structure, an AB axis structure and a Stewart platform is performed. Next, kinematic analysis and the simulation of the CSFS are done. Simulations have been developed in combination with the 50m CSFS model, which demonstrate the effectiveness and feasibility of the proposed three-level cable-suspended feed system.

  10. Genomic characterization of some Iranian children with idiopathic mental retardation using array comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Farkhondeh Behjati

    2013-01-01

    Full Text Available Background: Mental retardation (MR has a prevalence of 1-3% and genetic causes are present in more than 50% of patients. Chromosomal abnormalities are one of the most common genetic causes of MR and are responsible for 4-28% of mental retardation. However, the smallest loss or gain of material visible by standard cytogenetic is about 4 Mb and for smaller abnormalities, molecular cytogenetic techniques such as array comparative genomic hybridization (array CGH should be used. It has been shown that 15-25% of idiopathic MR (IMR has submicroscopic rearrangements detectable by array CGH. In this project, the genomic abnormalities were investigated in 32 MR patients using this technique. Materials and Methods: Patients with IMR with dysmorphism were investigated in this study. Karyotype analysis, fragile X and metabolic tests were first carried out on the patients. The copy number variation was then assessed in a total of 32 patients with normal results for the mentioned tests using whole genome oligo array CGH. Multiple ligation probe amplification was carried out as a confirmation test. Results: In total, 19% of the patients showed genomic abnormalities. This is reduced to 12.5% once the two patients with abnormal karyotypes (upon re-evaluation are removed. Conclusion: The array CGH technique increased the detection rate of genomic imbalances in our patients by 12.5%. It is an accurate and reliable method for the determination of genomic imbalances in patients with IMR and dysmorphism.

  11. 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.

  12. Analysis of the genome content of Lactococcus garvieae by genomic interspecies microarray hybridization

    Directory of Open Access Journals (Sweden)

    Gibello Alicia

    2010-03-01

    Full Text Available Abstract Background Lactococcus garvieae is a bacterial pathogen that affects different animal species in addition to humans. Despite the widespread distribution and emerging clinical significance of L. garvieae in both veterinary and human medicine, there is almost a complete lack of knowledge about the genetic content of this microorganism. In the present study, the genomic content of L. garvieae CECT 4531 was analysed using bioinformatics tools and microarray-based comparative genomic hybridization (CGH experiments. Lactococcus lactis subsp. lactis IL1403 and Streptococcus pneumoniae TIGR4 were used as reference microorganisms. Results The combination and integration of in silico analyses and in vitro CGH experiments, performed in comparison with the reference microorganisms, allowed establishment of an inter-species hybridization framework with a detection threshold based on a sequence similarity of ≥ 70%. With this threshold value, 267 genes were identified as having an analogue in L. garvieae, most of which (n = 258 have been documented for the first time in this pathogen. Most of the genes are related to ribosomal, sugar metabolism or energy conversion systems. Some of the identified genes, such as als and mycA, could be involved in the pathogenesis of L. garvieae infections. Conclusions In this study, we identified 267 genes that were potentially present in L. garvieae CECT 4531. Some of the identified genes could be involved in the pathogenesis of L. garvieae infections. These results provide the first insight into the genome content of L. garvieae.

  13. [Middle ear salivary gland choristoma related to branchio-oto-renal syndrome diagnosed by array-CGH].

    Science.gov (United States)

    Amrhein, P; Sittel, C; Spaich, C; Kohlhase, J; Boppert, R; Kohlhof, P; Koitschev, A

    2014-05-01

    Branchio-oto-renal (BOR) syndrome is characterized by ear malformations associated with sensorineural or mixed hearing loss. In addition, preauricular tags, preauricular pits, branchial cleft fistulas and cysts, as well as renal dysplasia are seen. A genetic mutation on chromosome 8, either autosomal dominantly inherited or occuring as a spontaneous mutation, is the cause in the majority of cases. Using array-based comparative genomic hybridization (CGH), it is possible to detect even the smallest genetic changes. Salivary gland choristoma in the middle ear is very rare. Surgical removal and histological clarification are required.

  14. Increased nuchal translucency with normal karyotype: a follow-up study of 100 cases supplemented with CGH and MLPA analyses

    DEFF Research Database (Denmark)

    Schou, K V; Kirchhoff, M; Nygaard, U;

    2009-01-01

    OBJECTIVE: To evaluate whether high-resolution comparative genomic hybridization (HR-CGH) and subtelomeric and syndrome-specific multiplex ligation-dependent probe amplification (MLPA) would detect minor chromosomal aberrations in fetuses with increased nuchal translucency thickness (NT) and norm...... disease, which supports the current approach of repeated ultrasound examinations in these high-risk pregnancies....... and subtelomeric regions. Pregnancy outcome was followed up. RESULTS: Among 80 liveborn children who were followed up, three (4%) had syndromes involving mental retardation, including a case of Sotos syndrome caused by a de novo mutation. 15% of fetuses were lost during pregnancy due to abnormalities...

  15. Multivariate analysis applied to tomato hybrid production.

    Science.gov (United States)

    Balasch, S; Nuez, F; Palomares, G; Cuartero, J

    1984-11-01

    Twenty characters were measured on 60 tomato varieties cultivated in the open-air and in polyethylene plastic-house. Data were analyzed by means of principal components, factorial discriminant methods, Mahalanobis D(2) distances and principal coordinate techniques. Factorial discriminant and Mahalanobis D(2) distances methods, both of which require collecting data plant by plant, lead to similar conclusions as the principal components method that only requires taking data by plots. Characters that make up the principal components in both environments studied are the same, although the relative importance of each one of them varies within the principal components. By combining information supplied by multivariate analysis with the inheritance mode of characters, crossings among cultivars can be experimented with that will produce heterotic hybrids showing characters within previously established limits.

  16. Whole genome amplification and its impact on CGH array profiles

    Directory of Open Access Journals (Sweden)

    Meldrum Cliff

    2008-07-01

    Full Text Available Abstract Background Some array comparative genomic hybridisation (array CGH platforms require a minimum of micrograms of DNA for the generation of reliable and reproducible data. For studies where there are limited amounts of genetic material, whole genome amplification (WGA is an attractive method for generating sufficient quantities of genomic material from miniscule amounts of starting material. A range of WGA methods are available and the multiple displacement amplification (MDA approach has been shown to be highly accurate, although amplification bias has been reported. In the current study, WGA was used to amplify DNA extracted from whole blood. In total, six array CGH experiments were performed to investigate whether the use of whole genome amplified DNA (wgaDNA produces reliable and reproducible results. Four experiments were conducted on amplified DNA compared to unamplified DNA and two experiments on unamplified DNA compared to unamplified DNA. Findings All the experiments involving wgaDNA resulted in a high proportion of losses and gains of genomic material. Previously, amplification bias has been overcome by using amplified DNA in both the test and reference DNA. Our data suggests that this approach may not be effective, as the gains and losses introduced by WGA appears to be random and are not reproducible between different experiments using the same DNA. Conclusion In light of these findings, the use of both amplified test and reference DNA on CGH arrays may not provide an accurate representation of copy number variation in the DNA.

  17. Impact of hybrid GSI analysis using ETR ensembles

    Indian Academy of Sciences (India)

    V S Prasad; C J Johny

    2016-04-01

    Performance of a hybrid assimilation system combining 3D Var based NGFS (NCMRWF Global ForecastSystem) with ETR (Ensemble Transform with Rescaling) based Global Ensemble Forecast (GEFS) ofresolution T-190L28 is investigated. The experiment is conducted for a period of one week in June 2013and forecast skills over different spatial domains are compared with respect to mean analysis state.Rainfall forecast is verified over Indian region against combined observations of IMD and NCMRWF.Hybrid assimilation produced marginal improvements in overall forecast skill in comparison with 3DVar. Hybrid experiment made significant improvement in wind forecasts in all the regions on verificationagainst mean analysis. The verification of forecasts with radiosonde observations also show improvementin wind forecasts with the hybrid assimilation. On verification against observations, hybrid experimentshows more improvement in temperature and wind forecasts at upper levels. Both hybrid and operational3D Var failed in prediction of extreme rainfall event over Uttarakhand on 17 June, 2013.

  18. CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens

    Directory of Open Access Journals (Sweden)

    MacKinnon Ruth N

    2012-02-01

    Full Text Available Abstract Background The analysis of nucleic acids is limited by the availability of archival specimens and the quality and amount of the extracted material. Archived cytogenetic preparations are stored in many laboratories and are a potential source of total genomic DNA for array karyotyping and other applications. Array CGH using DNA from fixed cytogenetic preparations has been described, but it is not known whether it can be used for SNP arrays. Diagnostic bone marrow specimens taken during the assessment of hematological malignancies are also a potential source of DNA, but it is generally assumed that DNA must be extracted, or the specimen frozen, within a day or two of collection, to obtain DNA suitable for further analysis. We have assessed DNA extracted from these materials for both SNP array and array CGH. Results We show that both SNP array and array CGH can be performed on genomic DNA extracted from cytogenetic specimens stored in Carnoy's fixative, and from bone marrow which has been stored unfrozen, at 4°C, for at least 36 days. We describe a procedure for extracting a usable concentration of total genomic DNA from cytogenetic suspensions of low cellularity. Conclusions The ability to use these archival specimens for DNA-based analysis increases the potential for retrospective genetic analysis of clinical specimens. Fixed cytogenetic preparations and long-term refrigerated bone marrow both provide DNA suitable for array karyotyping, and may be suitable for a wider range of analytical procedures.

  19. Correlation between localization, age, and chromosomal imbalances in ependymal tumours as detected by CGH.

    Science.gov (United States)

    Jeuken, Judith W M; Sprenger, Sandra H E; Gilhuis, Job; Teepen, Hans L J M; Grotenhuis, Andre J; Wesseling, Pieter

    2002-06-01

    Ependymal tumours (ETs) are gliomas that arise from the ependymal lining of the cerebral ventricles and from the remnants of the central canal of the spinal cord. Both clinical and genetic studies suggest that distinct genetic subtypes of ETs exist, the subtypes being correlated with patient age and/or tumour site. In the present study, the tumour genome of 20 ETs (15 adult and five paediatric cases) was screened for chromosomal imbalances by comparative genomic hybridization (CGH). The most frequently detected imbalances were -22q (75%), -10q (65%), -21 (50%), -16p (50%), -1p (45%), +4q (45%), -10p (45%), -2q (40%), -6 (40%), -19 (40%), -2p (35%), -3p (35%), and -16q (35%). Comparison of the chromosomal imbalances detected in ETs with those previously reported in oligodendroglial and astrocytic tumours revealed that in this respect ETs show similarities to these other gliomas. By combining these results with those of a recent study of Zheng et al. and Hirose et al., it was found that although ETs from different sites and from adult and paediatric patients show overlap at the CGH level, some chromosomal imbalances occur predominantly in a certain category. In adult patients, spinal ETs relatively often showed +2, +7, +12, and -14q; infratentorial ETs -22; and supratentorial ETs -9. In addition, in posterior fossa ETs, -6 and +9 were much more frequent in adults than in children. It is concluded that the genetic background of ETs is complex and partly determined by tumour site, histopathological subtype, and age of the patient.

  20. The communication of secondary variants: interviews with parents whose children have undergone array-CGH testing.

    Science.gov (United States)

    Christenhusz, G M; Devriendt, K; Peeters, H; Van Esch, H; Dierickx, K

    2014-09-01

    Children with unexplained developmental disabilities or congenital anomalies are increasingly being referred for genetic diagnostic testing using array-comparative genomic hybridisation (array-CGH) and next-generation sequencing (NGS) technologies. Their parents will have to deal with the secondary variants that will inevitably arise. We conducted 16 prospective semi-structured interviews with native Dutch-speaking parents whose children had undergone clinical array-CGH testing. The interviews explored the parents' experiences, expectations and opinions, specifically regarding the communication of results. Concrete examples of 'unexpected results' were provided to help guide the discussion, differing in severity, treatability, time of onset, level of risk, and carrier status. Data was analysed using content and narrative analysis methodologies. Parental motivations for and against the disclosure of unexpected results cluster around four main themes: actionability; knowledge; context; and characteristics of the result. Most parents wished to know all types of results. Disclosure was framed within a holistic, contextual, family-wide view. Genetic counselling should aim to integrate explorations of the motivations of parents surrounding the disclosure of results with good clinical care. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  1. Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons

    NARCIS (Netherlands)

    van Hijum, Sacha A. F. T.; Baerends, Richard J. S.; Zomer, Aldert L.; Karsens, Harma A.; Martin-Requena, Victoria; Trelles, Oswaldo; Kok, Jan; Kuipers, Oscar P.

    2008-01-01

    Background: Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. Since prokaryotes in general have less conserved genome sequences than eukaryotes, sequence divergences between the genes in the genomes used for an aCGH experiment

  2. DNA copy number aberrations in breast cancer by array comparative genomic hybridization

    DEFF Research Database (Denmark)

    Li, J.; Wang, K.; Li, S.;

    2009-01-01

    Array comparative genomic hybridization (CGH) has been popularly used for analyzing DNA copy number variations in diseases like cancer. In this study, we investigated 82 sporadic samples from 49 breast cancer patients using 1-Mb resolution bacterial artificial chromosome CGH arrays. A number of h...

  3. De Novo Identification of Single Nucleotide Mutations in Caenorhabditis elegans Using Array Comparative Genomic Hybridization

    Science.gov (United States)

    Maydan, Jason S.; Okada, H. Mark; Flibotte, Stephane; Edgley, Mark L.; Moerman, Donald G.

    2009-01-01

    Array comparative genomic hybridization (aCGH) has been used primarily to detect copy-number variants between two genomes. Here we report using aCGH to detect single nucleotide mutations on oligonucleotide microarrays with overlapping 50-mer probes. This technique represents a powerful method for rapidly detecting novel homozygous single nucleotide mutations in any organism with a sequenced reference genome. PMID:19189945

  4. Analysis of Hybrid Hydrogen Systems: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Dean, J.; Braun, R.; Munoz, D.; Penev, M.; Kinchin, C.

    2010-01-01

    Report on biomass pathways for hydrogen production and how they can be hybridized to support renewable electricity generation. Two hybrid systems were studied in detail for process feasibility and economic performance. The best-performing system was estimated to produce hydrogen at costs ($1.67/kg) within Department of Energy targets ($2.10/kg) for central biomass-derived hydrogen production while also providing value-added energy services to the electric grid.

  5. Clinical and cytogenetic features of a patient with partial trisomy 8q and partial monosomy 13q delineated by array comparative genomic hybridization.

    Science.gov (United States)

    Sohn, Young Bae; Yun, Jun No; Park, Sang-Jin; Park, Moon Sung; Kim, Sung Hwan; Lee, Jang Hoon

    2013-01-01

    Partial trisomy 8q is rare and has distinctive clinical features, including severe mental retardation, growth impairment, dysmorphic facial appearances, cleft palate, congenital heart disease, and urogenital anomalies. Partial monosomy 13q is a rare genetic disorder displaying a variety of phenotypic characteristics including mental retardation, dysmorphic facial features, and congenital anomalies. Here, we describe for the first time clinical observations and cytogenetic analysis of a patient with a concomitant occurrence of partial trisomy of 8q (8q21.3→qter) and partial monosomy 13q(13q34→qter). The patient was a female neonate with facial dysmorphia, agenesis of the corpus callosum, cleft palate, and congenital heart disease. G-band standard karyotype was 46,XX,add(13)(q34). To determine the origin of additional genomic gain in chromosome 13, array comparative genomic hybridization (CGH) was performed. Array CGH showed a 56.8 Mb sized gain on chromosome 8q and a 0.28 Mb sized loss on chromosome 13q. Therefore, the final karyotype of the patient was defined as 46,XX, der(13)t(8;13)(q21.3;q34). In conclusion, we described the clinical and cytogenetic analysis of the patient with concomitant occurrence of partial trisomy 8q and partial monosomy 13q delineated by array CGH. This report suggests that the array CGH would be a valuable diagnostic tool for identifying the origin of small additional genetic materials.

  6. Characterization of genetic rearrangements in esophageal squamous carcinoma cell lines by a combination of M-FISH and array-CGH: further confirmation of some split genomic regions in primary tumors

    Directory of Open Access Journals (Sweden)

    Hao Jia-Jie

    2012-08-01

    Full Text Available Abstract Background Chromosomal and genomic aberrations are common features of human cancers. However, chromosomal numerical and structural aberrations, breakpoints and disrupted genes have yet to be identified in esophageal squamous cell carcinoma (ESCC. Methods Using multiplex-fluorescence in situ hybridization (M-FISH and oligo array-based comparative hybridization (array-CGH, we identified aberrations and breakpoints in six ESCC cell lines. Furthermore, we detected recurrent breakpoints in primary tumors by dual-color FISH. Results M-FISH and array-CGH results revealed complex numerical and structural aberrations. Frequent gains occurred at 3q26.33-qter, 5p14.1-p11, 7pter-p12.3, 8q24.13-q24.21, 9q31.1-qter, 11p13-p11, 11q11-q13.4, 17q23.3-qter, 18pter-p11, 19 and 20q13.32-qter. Losses were frequent at 18q21.1-qter. Breakpoints that clustered within 1 or 2 Mb were identified, including 9p21.3, 11q13.3-q13.4, 15q25.3 and 3q28. By dual-color FISH, we observed that several recurrent breakpoint regions in cell lines were also present in ESCC tumors. In particular, breakpoints clustered at 11q13.3-q13.4 were identified in 43.3% (58/134 of ESCC tumors. Both 11q13.3-q13.4 splitting and amplification were significantly correlated with lymph node metastasis (LNM (P = 0.004 and 0.022 and advanced stages (P = 0.004 and 0.039. Multivariate logistic regression analysis revealed that only 11q13.3-q13.4 splitting was an independent predictor for LNM (P = 0.026. Conclusions The combination of M-FISH and array-CGH helps produce more accurate karyotypes. Our data provide significant, detailed information for appropriate uses of these ESCC cell lines for cytogenetic and molecular biological studies. The aberrations and breakpoints detected in both the cell lines and primary tumors will contribute to identify affected genes involved in the development and progression of ESCC.

  7. A Theoretical Analysis of Why Hybrid Ensembles Work

    Directory of Open Access Journals (Sweden)

    Kuo-Wei Hsu

    2017-01-01

    Full Text Available Inspired by the group decision making process, ensembles or combinations of classifiers have been found favorable in a wide variety of application domains. Some researchers propose to use the mixture of two different types of classification algorithms to create a hybrid ensemble. Why does such an ensemble work? The question remains. Following the concept of diversity, which is one of the fundamental elements of the success of ensembles, we conduct a theoretical analysis of why hybrid ensembles work, connecting using different algorithms to accuracy gain. We also conduct experiments on classification performance of hybrid ensembles of classifiers created by decision tree and naïve Bayes classification algorithms, each of which is a top data mining algorithm and often used to create non-hybrid ensembles. Therefore, through this paper, we provide a complement to the theoretical foundation of creating and using hybrid ensembles.

  8. Methods for high throughput validation of amplified fragment pools of BAC DNA for constructing high resolution CGH arrays

    Directory of Open Access Journals (Sweden)

    Malloff Chad A

    2004-01-01

    Full Text Available Abstract Background The recent development of array based comparative genomic hybridization (CGH technology provides improved resolution for detection of genomic DNA copy number alterations. In array CGH, generating spotting solution is a multi-step process where bacterial artificial chromosome (BAC clones are converted to replenishable PCR amplified fragments pools (AFP for use as spotting solution in a microarray format on glass substrate. With completion of the human and mouse genome sequencing, large BAC clone sets providing complete genome coverage are available for construction of whole genome BAC arrays. Currently, Southern hybridization, fluorescent in-situ hybridization (FISH, and BAC end sequencing methods are commonly used to identify the initial BAC clone but not the end product used for spotting arrays. The AFP sequencing technique described in this study is a novel method designed to verify the identity of array spotting solution in a high throughput manner. Results We show here that Southern hybridization, FISH, and AFP sequencing can be used to verify the identity of final spotting solutions using less than 10% of the AFP product. Single pass AFP sequencing identified over half of the 960 AFPs analyzed. Moreover, using two vector primers approximately 90% of the AFP spotting solutions can be identified. Conclusions In this feasibility study we demonstrate that current methods for identifying initial BAC clones can be adapted to verify the identity of AFP spotting solutions used in printing arrays. Of these methods, AFP sequencing proves to be the most efficient for large scale identification of spotting solution in a high throughput manner.

  9. Mars Hybrid Propulsion System Trajectory Analysis. Part II; Cargo Missions

    Science.gov (United States)

    Chai, Patrick R.; Merrill, Raymond G.; Qu, Min

    2015-01-01

    NASA's Human Spaceflight Architecture Team is developing a reusable hybrid transportation architecture in which both chemical and electric propulsion systems are used to send crew and cargo to Mars destinations such as Phobos, Deimos, the surface of Mars, and other orbits around Mars. By combining chemical and electrical propulsion into a single spaceship and applying each where it is more effective, the hybrid architecture enables a series of Mars trajectories that are more fuel-efficient than an all chemical architecture without significant increases in flight times. This paper shows the feasibility of the hybrid transportation architecture to pre-deploy cargo to Mars and Phobos in support of the Evolvable Mars Campaign crew missions. The analysis shows that the hybrid propulsion stage is able to deliver all of the current manifested payload to Phobos and Mars through the first three crew missions. The conjunction class trajectory also allows the hybrid propulsion stage to return to Earth in a timely fashion so it can be reused for additional cargo deployment. The 1,100 days total trip time allows the hybrid propulsion stage to deliver cargo to Mars every other Earth-Mars transit opportunity. For the first two Mars surface mission in the Evolvable Mars Campaign, the short trip time allows the hybrid propulsion stage to be reused for three round-trip journeys to Mars, which matches the hybrid propulsion stage's designed lifetime for three round-trip crew missions to the Martian sphere of influence.

  10. CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss

    Directory of Open Access Journals (Sweden)

    Mark A. van de Wiel

    2007-01-01

    Full Text Available An algorithm to reduce multi-sample array CGH data from thousands of clones to tens or hundreds of clone regions is introduced. This reduction of the data is performed such that little information is lost, which is possible due to the high dependencies between neighboring clones. The algorithm is explained using a small example. The potential beneficial effects of the algorithm for downstream analysis are illustrated by re-analysis of previously published colorectal cancer data. Using multiple testing corrections suitable for these data, we provide statistical evidence for genomic differences on several clone regions between MSI+ and CIN+ tumors. The algorithm, named CGHregions, is available as an easy-to-use script in R.

  11. Array CGH on unstimulated blood does not detect all cases of Pallister-Killian syndrome: a skin biopsy should remain the diagnostic gold standard.

    Science.gov (United States)

    Hodge, Jennelle C; Hulshizer, Rachael L; Seger, Pam; St Antoine, Angelique; Bair, Jennifer; Kirmani, Salman

    2012-03-01

    A child whose features are consistent with Pallister-Killian syndrome (PKS) did not have detectable tetrasomy 12p due to an additional isochromosome 12p in an unstimulated blood specimen by interphase FISH or array CGH analysis. The diagnosis of PKS was made through these methods solely in a skin biopsy specimen. To determine the sensitivity of our array CGH platform to tetrasomy 12p mosaicism, dilutions of DNA from both the child's skin fibroblasts and a PKS cell line were analyzed. Tetrasomy 12p at 10% mosaicism was identifiable but 5% was below the limit of detection. This result suggests through extrapolation that the tetrasomy 12p is present in <10% of cells in our patient's blood, confirming the tissue-limited mosaicism of PKS. Multiple recent studies show that array CGH provides greater sensitivity than chromosome analysis to detect mosaic abnormalities including that of tetrasomy 12p in blood specimens. However, our case demonstrates that the biology of PKS precludes the exclusive use of array CGH on blood for diagnosis. A tissue sample should continue to be the diagnostic gold standard for PKS.

  12. Genomic analysis by oligonucleotide array Comparative Genomic Hybridization utilizing formalin-fixed, paraffin-embedded tissues.

    Science.gov (United States)

    Savage, Stephanie J; Hostetter, Galen

    2011-01-01

    Formalin fixation has been used to preserve tissues for more than a hundred years, and there are currently more than 300 million archival samples in the United States alone. The application of genomic protocols such as high-density oligonucleotide array Comparative Genomic Hybridization (aCGH) to formalin-fixed, paraffin-embedded (FFPE) tissues, therefore, opens an untapped resource of available tissues for research and facilitates utilization of existing clinical data in a research sample set. However, formalin fixation results in cross-linking of proteins and DNA, typically leading to such a significant degradation of DNA template that little is available for use in molecular applications. Here, we describe a protocol to circumvent formalin fixation artifact by utilizing enzymatic reactions to obtain quality DNA from a wide range of FFPE tissues for successful genome-wide discovery of gene dosage alterations in archival clinical samples.

  13. Using Array-Based Comparative Genomic Hybridization to Diagnose Pallister-Killian Syndrome.

    Science.gov (United States)

    Lee, Mi Na; Lee, Jiwon; Yu, Hee Joon; Lee, Jeehun; Kim, Sun Hee

    2017-01-01

    Pallister-Killian syndrome (PKS) is a rare multisystem disorder characterized by isochromosome 12p and tissue-limited mosaic tetrasomy 12p. In this study, we diagnosed three pediatric patients who were suspicious of having PKS using array-based comparative genomic hybridization (array CGH) and FISH analyses performed on peripheral lymphocytes. Patients 1 and 2 presented with craniofacial dysmorphic features, hypotonia, and a developmental delay. Array CGH revealed two to three copies of 12p in patient 1 and three copies in patient 2. FISH analysis showed trisomy or tetrasomy 12p. Patient 3, who had clinical features comparable to those of patients 1 and 2, was diagnosed by using FISH analysis alone. Here, we report three patients with mosaic tetrasomy 12p. There have been only reported cases diagnosed by chromosome analysis and FISH analysis on skin fibroblast or amniotic fluid. To our knowledge, patient 1 was the first case diagnosed by using array CGH performed on peripheral lymphocytes in Korea.

  14. New techniques for emulsion analysis in a hybrid experiment

    Energy Technology Data Exchange (ETDEWEB)

    Kodama, K. (Aichi University of Education, Kariya 448 (Japan)); Ushida, N. (Aichi University of Education, Kariya 448 (Japan)); Mokhtarani, A. (University of California (Davis), Davis, CA 95616 (United States)); Paolone, V.S. (University of California (Davis), Davis, CA 95616 (United States)); Volk, J.T. (University of California (Davis), Davis, CA 95616 (United States)); Wilcox, J.O. (University of California (Davis), Davis, CA 95616 (United States)); Yager, P.M. (University of California (Davis), Davis, CA 95616 (United States)); Edelstein, R.M. (Carnegie-Mellon University, Pittsburgh, PA 15213 (United States)); Freyberger, A.P. (Carnegie-Mellon University, Pittsburgh, PA 15213 (United States)); Gibaut, D.B. (Carnegie-Mellon University, Pittsburgh, PA 15213 (United States)); Lipton, R.J. (Carnegie-Mellon University, Pittsburgh, PA 15213 (United States)); Nichols, W.R. (Carnegie-Mellon University, Pittsburgh, PA 15213 (United States)); Potter, D.M. (Carnegie-Mellon Univers

    1994-08-01

    A new method, called graphic scanning, was developed by the Nagoya University Group for emulsion analysis in a hybrid experiment. This method enhances both speed and reliability of emulsion analysis. Details of the application of this technique to the analysis of Fermilab experiment E653 are described. ((orig.))

  15. Analysis of nuclear and organellar DNA in somatic hybrids between solanaceous species.

    NARCIS (Netherlands)

    Wolters, A.M.A.

    1994-01-01

    This thesis describes an analysis of the possibilities and limitations of somatic hybridization of solanaceous species. Emphasis was laid on the elucidation of the interactions between nuclei, chloroplasts and mitochondria in the obtained somatic hybrids. Hybridization experiments between tomato ( L

  16. STUDY OF ECONOMIC AND FINANCIAL VIABILITY OF A CENTRAL GENERATING HYDROELECTRIC (CGH

    Directory of Open Access Journals (Sweden)

    Bruno Santos Lopes Candido

    2012-11-01

    Full Text Available The article discusses the evaluation of a Central Hydroelectric Generator (CGH, as an investment. The objective is to project the cash flow of the project and evaluate outcomes to ensure important information for decision-making through technical analysis of investment projects. The work begins with literature on the subject and subsequent case study. To develop this study was carried out data collection on construction and identification of key variables related to energy market in Brazil. Later techniques were used for evaluating investment projects, regarding their financial feasibility. An interview with a business sector, and research and consulting firms. The result was positive and showed that the project is a viable investment thus adding value to shareholders compared to other investment alternatives in the financial market.

  17. Study of improved ray tracing parallel algorithm for CGH of 3D objects on GPU

    Science.gov (United States)

    Cong, Bin; Jiang, Xiaoyu; Yao, Jun; Zhao, Kai

    2014-11-01

    An improved parallel algorithm for holograms of three-dimensional objects was presented. According to the physical characteristics and mathematical properties of the original ray tracing algorithm for computer generated holograms (CGH), using transform approximation and numerical analysis methods, we extract parts of ray tracing algorithm which satisfy parallelization features and implement them on graphics processing unit (GPU). Meanwhile, through proper design of parallel numerical procedure, we did parallel programming to the two-dimensional slices of three-dimensional object with CUDA. According to the experiments, an effective method of dealing with occlusion problem in ray tracing is proposed, as well as generating the holograms of 3D objects with additive property. Our results indicate that the improved algorithm can effectively shorten the computing time. Due to the different sizes of spatial object points and hologram pixels, the speed has increased 20 to 70 times comparing with original ray tracing algorithm.

  18. Hybrid Dynamic Network Data Envelopment Analysis

    Directory of Open Access Journals (Sweden)

    Ling Li

    2015-01-01

    Full Text Available Conventional DEA models make no hypothesis concerning the internal operations in a static situation. To open the “black box” and work with dynamic assessment issues synchronously, we put forward a hybrid model for evaluating the relative efficiencies of a set of DMUs over an observed time period with a composite of network DEA and dynamic DEA. We vertically deal with intermediate products between divisions with assignable inputs in the network structure and, horizontally, we extend network structure by means of a dynamic pattern with unrelated activities between two succeeding periods. The hybrid dynamic network DEA model proposed in this paper enables us to (i pry into the internal operations of DEA by another network structure, (ii obtain dynamic change of period efficiency, and (iii gain the overall dynamic efficiency of DMUs over the entire observed periods. We finally illustrate the calculation procedure of the proposed approach by a numerical example.

  19. Analysis of Synchronization for Coupled Hybrid Systems

    DEFF Research Database (Denmark)

    Li, Zheng; Wisniewski, Rafal

    2006-01-01

    In the control systems with coupled multi-subsystem, the subsystems might be synchronized (i.e. all the subsystems have the same operation states), which results in negative influence to the whole system. For example, in the supermarket refrigeration systems, the synchronized switch of each...... subsystem will cause low efficiency, inferior control performance and a high wear on the compressor. This paper takes the supermarket refrigeration systems as an example to analyze the synchronization and its coupling strengths of coupled hybrid systems, which may provide a base for further research...

  20. Intragenic rearrangements in X-linked intellectual deficiency: results of a-CGH in a series of 54 patients and identification of TRPC5 and KLHL15 as potential XLID genes.

    Science.gov (United States)

    Mignon-Ravix, Cécile; Cacciagli, Pierre; Choucair, Nancy; Popovici, Cornel; Missirian, Chantal; Milh, Mathieu; Mégarbané, André; Busa, Tiffany; Julia, Sophie; Girard, Nadine; Badens, Catherine; Sigaudy, Sabine; Philip, Nicole; Villard, Laurent

    2014-08-01

    High-resolution array comparative genomic hybridization (a-CGH) enables the detection of intragenic rearrangements, such as single exon deletion or duplication. This approach can lead to the identification of new disease genes. We report on the analysis of 54 male patients presenting with intellectual deficiency (ID) and a family history suggesting X-linked (XL) inheritance or maternal skewed X-chromosome inactivation (XCI), using a home-made X-chromosome-specific microarray covering the whole human X-chromosome at high resolution. The majority of patients had whole genome array-CGH prior to the selection and we did not include large rearrangements such as MECP2 and FMR1 duplications. We identified four rearrangements considered as causative or potentially pathogenic, corresponding to a detection rate of 8%. Two CNVs affected known XLID genes and were therefore considered as causative (IL1RAPL1 and OPHN1 intragenic deletions). Two new CNVs were considered as potentially pathogenic as they affected interesting candidates for ID. The first CNV is a deletion of the first exon of the TRPC5 gene, encoding a cation channel implicated in dendrite growth and patterning, in a child presenting with ID and an autism spectrum disorder (ASD). The second CNV is a partial deletion of KLHL15, in a patient with severe ID, epilepsy, and anomalies of cortical development. In both cases, in spite of strong arguments for clinical relevance, we were not able at this stage to confirm pathogenicity of the mutations, and the causality of the variants identified in XLID remains to be confirmed.

  1. Application of Array-Based Comparative Genomic Hybridization to Pediatric Neurologic Diseases

    OpenAIRE

    2013-01-01

    Purpose Array comparative genomic hybridization (array-CGH) is a technique used to analyze quantitative increase or decrease of chromosomes by competitive DNA hybridization of patients and controls. This study aimed to evaluate the benefits and yield of array-CGH in comparison with conventional karyotyping in pediatric neurology patients. Materials and Methods We included 87 patients from the pediatric neurology clinic with at least one of the following features: developmental delay, mental r...

  2. Design and fabrication of CGH for 600mm diameter SiC primary mirror surface figure testing

    Science.gov (United States)

    Pang, Zhihai; Ma, Zhen; Fan, Xuewu; Zou, Gangyi

    2016-09-01

    Computer-generated hologram (CGH) is an effective way to compensate wavefront aberration in null test of aspheric surfaces and freeform surfaces. Our strategies of CGH design for 600mm diameter SiC primary mirror surface figure testing are presented, and an experiment demonstrating the compensation test results of CGH is reported. We design a CGH including two sections on the same substrate in order to align the CGH to the incident wavefront: main section for compensating wavefront in null test, alignment section for adjusting the relative position between CGH and interferometer. In order to isolate different orders of diffraction, we used power carrier to make different orders of diffraction come to focus at different position along the axis to avoid ghost reflections. We measured the 600mm diameter SiC primary mirror using this CGH, and the surface test result is 0.033λ rms.

  3. Characteristics of Highly Polymorphic Segmental Copy-Number Variations Observed in Japanese by BAC-Array-CGH

    Science.gov (United States)

    Takahashi, Norio; Satoh, Yasunari; Sasaki, Keiko; Shimoichi, Yuko; Sugita, Keiko; Katayama, Hiroaki

    2011-01-01

    Segmental copy-number variations (CNVs) may contribute to genetic variation in humans. Reports of the existence and characteristics of CNVs in a large Japanese cohort are quite limited. We report the data from a large Japanese population. We conducted population screening for 213 unrelated Japanese individuals using comparative genomic hybridization based on a bacterial artificial chromosome microarray (BAC-aCGH). We summarize the data by focusing on highly polymorphic CNVs in ≥5.0% of the individual, since they may be informative for demonstrating the relationships between genotypes and their phenotypes. We found a total of 680 CNVs at 16 different BAC-regions in the genome. The majority of the polymorphic CNVs presented on BAC-clones that overlapped with regions of segmental duplication, and the majority of the polymorphic CNVs observed in this population had been previously reported in other publications. Some of the CNVs contained genes which might be related to phenotypic heterogeneity among individuals. PMID:21197411

  4. Hybrid energy system cost analysis: San Nicolas Island, California

    Energy Technology Data Exchange (ETDEWEB)

    Olsen, T.L.; McKenna, E.

    1996-07-01

    This report analyzes the local wind resource and evaluates the costs and benefits of supplementing the current diesel-powered energy system on San Nicolas Island, California (SNI), with wind turbines. In Section 2.0 the SNI site, naval operations, and current energy system are described, as are the data collection and analysis procedures. Section 3.0 summarizes the wind resource data and analyses that were presented in NREL/TP 442-20231. Sections 4.0 and 5.0 present the conceptual design and cost analysis of a hybrid wind and diesel energy system on SNI, with conclusions following in Section 6. Appendix A presents summary pages of the hybrid system spreadsheet model, and Appendix B contains input and output files for the HYBRID2 program.

  5. Hybrid Ventilation with Innovative Heat Recovery—A System Analysis

    Directory of Open Access Journals (Sweden)

    Bengt Hellström

    2013-02-01

    Full Text Available One of the most important factors when low energy houses are built is to have good heat recovery on the ventilation system. However, standard ventilation units use a considerable amount of electricity. This article discusses the consequences on a system level of using hybrid ventilation with heat recovery. The simulation program TRNSYS was used in order to investigate a ventilation system with heat recovery. The system also includes a ground source storage and waste water heat recovery system. The result of the analysis shows that the annual energy gain from ground source storage is limited. However, this is partly a consequence of the fact that the well functioning hybrid ventilation system leaves little room for improvements. The analysis shows that the hybrid ventilation system has potential to be an attractive solution for low energy buildings with a very low need for electrical energy.

  6. Buckling analysis of a ring stiffened hybrid composite cylinder

    Science.gov (United States)

    Potluri, Rakesh; Eswara Kumar, A.; Navuri, Karteek; Nagaraju, M.; Mojeswara Rao, Duduku

    2016-09-01

    This study aims to understand the response of the ring stiffened cylinders made up of hybrid composites subjected to buckling loads by using the concepts of Design of Experiments (DOE) and optimization by using Finite Element Method (FEM) simulation software Ansys workbench V15. Carbon epoxy and E-glass epoxy composites were used in the hybrid composite. This hybrid composite was analyzed by using different layup angles. Central composite design (CCD) was used to perform design of experiments (D.O.E) and kriging method was used to generate a response surface. The response surface optimization (RSO) was performed by using the method of the multi-objective genetic algorithm (MOGA). After optimization, the best candidate was chosen and applied to the ring stiffened cylinder and eigenvalue buckling analysis was performed to understand the buckling behavior. Best laminate candidates with high buckling strength have been identified. A generalized procedure of the laminate optimization and analysis have been shown.

  7. Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins

    Science.gov (United States)

    2012-01-01

    Background Interspecific hybrids between S. cerevisiae × S. kudriavzevii have frequently been detected in wine and beer fermentations. Significant physiological differences among parental and hybrid strains under different stress conditions have been evidenced. In this study, we used comparative genome hybridization analysis to evaluate the genome composition of different S. cerevisiae × S. kudriavzevii natural hybrids isolated from wine and beer fermentations to infer their evolutionary origins and to figure out the potential role of common S. kudriavzevii gene fraction present in these hybrids. Results Comparative genomic hybridization (CGH) and ploidy analyses carried out in this study confirmed the presence of individual and differential chromosomal composition patterns for most S. cerevisiae × S. kudriavzevii hybrids from beer and wine. All hybrids share a common set of depleted S. cerevisiae genes, which also are depleted or absent in the wine strains studied so far, and the presence a common set of S. kudriavzevii genes, which may be associated with their capability to grow at low temperatures. Finally, a maximum parsimony analysis of chromosomal rearrangement events, occurred in the hybrid genomes, indicated the presence of two main groups of wine hybrids and different divergent lineages of brewing strains. Conclusion Our data suggest that wine and beer S. cerevisiae × S. kudriavzevii hybrids have been originated by different rare-mating events involving a diploid wine S. cerevisiae and a haploid or diploid European S. kudriavzevii strains. Hybrids maintain several S. kudriavzevii genes involved in cold adaptation as well as those related to S. kudriavzevii mitochondrial functions. PMID:22906207

  8. Mars Hybrid Propulsion System Trajectory Analysis. Part I; Crew Missions

    Science.gov (United States)

    Chai, Patrick R.; Merrill, Raymond G.; Qu, Min

    2015-01-01

    NASAs Human spaceflight Architecture team is developing a reusable hybrid transportation architecture in which both chemical and electric propulsion systems are used to send crew and cargo to Mars destinations such as Phobos, Deimos, the surface of Mars, and other orbits around Mars. By combining chemical and electrical propulsion into a single space- ship and applying each where it is more effective, the hybrid architecture enables a series of Mars trajectories that are more fuel-efficient than an all chemical architecture without significant increases in flight times. This paper provides the analysis of the interplanetary segments of the three Evolvable Mars Campaign crew missions to Mars using the hybrid transportation architecture. The trajectory analysis provides departure and arrival dates and propellant needs for the three crew missions that are used by the campaign analysis team for campaign build-up and logistics aggregation analysis. Sensitivity analyses were performed to investigate the impact of mass growth, departure window, and propulsion system performance on the hybrid transportation architecture. The results and system analysis from this paper contribute to analyses of the other human spaceflight architecture team tasks and feed into the definition of the Evolvable Mars Campaign.

  9. Modelling and analysis of real-time and hybrid systems

    Energy Technology Data Exchange (ETDEWEB)

    Olivero, A.

    1994-09-29

    This work deals with the modelling and analysis of real-time and hybrid systems. We first present the timed-graphs as model for the real-time systems and we recall the basic notions of the analysis of real-time systems. We describe the temporal properties on the timed-graphs using TCTL formulas. We consider two methods for property verification: in one hand we study the symbolic model-checking (based on backward analysis) and in the other hand we propose a verification method derived of the construction of the simulation graph (based on forward analysis). Both methods have been implemented within the KRONOS verification tool. Their application for the automatic verification on several real-time systems confirms the practical interest of our approach. In a second part we study the hybrid systems, systems combining discrete components with continuous ones. As in the general case the analysis of this king of systems is not decidable, we identify two sub-classes of hybrid systems and we give a construction based method for the generation of a timed-graph from an element into the sub-classes. We prove that in one case the timed-graph obtained is bi-similar with the considered system and that there exists a simulation in the other case. These relationships allow the application of the described technics on the hybrid systems into the defined sub-classes. (authors). 60 refs., 43 figs., 8 tabs., 2 annexes.

  10. Genome sequence of Cronobacter sakazakii BAA-894 and comparative genomic hybridization analysis with other Cronobacter species.

    Directory of Open Access Journals (Sweden)

    Eva Kucerova

    Full Text Available BACKGROUND: The genus Cronobacter (formerly called Enterobacter sakazakii is composed of five species; C. sakazakii, C. malonaticus, C. turicensis, C. muytjensii, and C. dublinensis. The genus includes opportunistic human pathogens, and the first three species have been associated with neonatal infections. The most severe diseases are caused in neonates and include fatal necrotizing enterocolitis and meningitis. The genetic basis of the diversity within the genus is unknown, and few virulence traits have been identified. METHODOLOGY/PRINCIPAL FINDINGS: We report here the first sequence of a member of this genus, C. sakazakii strain BAA-894. The genome of Cronobacter sakazakii strain BAA-894 comprises a 4.4 Mb chromosome (57% GC content and two plasmids; 31 kb (51% GC and 131 kb (56% GC. The genome was used to construct a 387,000 probe oligonucleotide tiling DNA microarray covering the whole genome. Comparative genomic hybridization (CGH was undertaken on five other C. sakazakii strains, and representatives of the four other Cronobacter species. Among 4,382 annotated genes inspected in this study, about 55% of genes were common to all C. sakazakii strains and 43% were common to all Cronobacter strains, with 10-17% absence of genes. CONCLUSIONS/SIGNIFICANCE: CGH highlighted 15 clusters of genes in C. sakazakii BAA-894 that were divergent or absent in more than half of the tested strains; six of these are of probable prophage origin. Putative virulence factors were identified in these prophage and in other variable regions. A number of genes unique to Cronobacter species associated with neonatal infections (C. sakazakii, C. malonaticus and C. turicensis were identified. These included a copper and silver resistance system known to be linked to invasion of the blood-brain barrier by neonatal meningitic strains of Escherichia coli. In addition, genes encoding for multidrug efflux pumps and adhesins were identified that were unique to C. sakazakii

  11. Hybrid reliability model for fatigue reliability analysis of steel bridges

    Institute of Scientific and Technical Information of China (English)

    曹珊珊; 雷俊卿

    2016-01-01

    A kind of hybrid reliability model is presented to solve the fatigue reliability problems of steel bridges. The cumulative damage model is one kind of the models used in fatigue reliability analysis. The parameter characteristics of the model can be described as probabilistic and interval. The two-stage hybrid reliability model is given with a theoretical foundation and a solving algorithm to solve the hybrid reliability problems. The theoretical foundation is established by the consistency relationships of interval reliability model and probability reliability model with normally distributed variables in theory. The solving process is combined with the definition of interval reliability index and the probabilistic algorithm. With the consideration of the parameter characteristics of theS−N curve, the cumulative damage model with hybrid variables is given based on the standards from different countries. Lastly, a case of steel structure in the Neville Island Bridge is analyzed to verify the applicability of the hybrid reliability model in fatigue reliability analysis based on the AASHTO.

  12. The hebridological analysis of productivity traits in pea hybrids

    Directory of Open Access Journals (Sweden)

    Світлана Володимирівна Коблай

    2015-09-01

    Full Text Available To study the nature of inheritance of quantitative traits that influence productivity of pea hybrids were obtained first and second generations for which sample and varieties with different leaf morphotype are served as parental form. As the results of hybridological analysis it is determined the degree of domination and revealed the heterosis combinations

  13. Nuclear-Renewable Hybrid Energy System Market Analysis Plans

    Energy Technology Data Exchange (ETDEWEB)

    Ruth, Mark

    2016-06-09

    This presentation describes nuclear-renewable hybrid energy systems (N-R HESs), states their potential benefits, provides figures for the four tightly coupled N-R HESs that NREL is currently analyzing, and outlines the analysis process that is underway.

  14. Array comparative genomic hybridization-based characterization of genetic alterations in pulmonary neuroendocrine tumors.

    Science.gov (United States)

    Voortman, Johannes; Lee, Jih-Hsiang; Killian, Jonathan Keith; Suuriniemi, Miia; Wang, Yonghong; Lucchi, Marco; Smith, William I; Meltzer, Paul; Wang, Yisong; Giaccone, Giuseppe

    2010-07-20

    The goal of this study was to characterize and classify pulmonary neuroendocrine tumors based on array comparative genomic hybridization (aCGH). Using aCGH, we performed karyotype analysis of 33 small cell lung cancer (SCLC) tumors, 13 SCLC cell lines, 19 bronchial carcinoids, and 9 gastrointestinal carcinoids. In contrast to the relatively conserved karyotypes of carcinoid tumors, the karyotypes of SCLC tumors and cell lines were highly aberrant. High copy number (CN) gains were detected in SCLC tumors and cell lines in cytogenetic bands encoding JAK2, FGFR1, and MYC family members. In some of those samples, the CN of these genes exceeded 100, suggesting that they could represent driver alterations and potential drug targets in subgroups of SCLC patients. In SCLC tumors, as well as bronchial carcinoids and carcinoids of gastrointestinal origin, recurrent CN alterations were observed in 203 genes, including the RB1 gene and 59 microRNAs of which 51 locate in the DLK1-DIO3 domain. These findings suggest the existence of partially shared CN alterations in these tumor types. In contrast, CN alterations of the TP53 gene and the MYC family members were predominantly observed in SCLC. Furthermore, we demonstrated that the aCGH profile of SCLC cell lines highly resembles that of clinical SCLC specimens. Finally, by analyzing potential drug targets, we provide a genomics-based rationale for targeting the AKT-mTOR and apoptosis pathways in SCLC.

  15. Use of Virtual Medium in Designing of the CGH Wave Front Generator for Aspheric Testing

    Institute of Scientific and Technical Information of China (English)

    KANG Guo-guo; XIE Jing-hui; LIU Yi

    2007-01-01

    Design method and procedures of computer-generated hologram (CGH) used for aspheric test are introduced in detail.For CGH phase calculation,virtual medium which has zero refractive index at given wavelength is used to model ideal aspheric wavefront.Reflective Fresnel zones located in a ring area concentric to the CGH structure is designed to reduce or eliminate alignment errors.Substrate figure error,pattern distortion,etching and duty cycle variations that influence the reconstructed wavefront are quantitatively analyzed in theory and corresponding error equations are obtained to guide the tolerance distribution during CGH fabricating.A design example is given and the uncertainty of measurement achieves λ/20.

  16. Validation of a hybrid life-cycle inventory analysis method.

    Science.gov (United States)

    Crawford, Robert H

    2008-08-01

    The life-cycle inventory analysis step of a life-cycle assessment (LCA) may currently suffer from several limitations, mainly concerned with the use of incomplete and unreliable data sources and methods of assessment. Many past LCA studies have used traditional inventory analysis methods, namely process analysis and input-output analysis. More recently, hybrid inventory analysis methods have been developed, combining these two traditional methods in an attempt to minimise their limitations. In light of recent improvements, these hybrid methods need to be compared and validated, as these too have been considered to have several limitations. This paper evaluates a recently developed hybrid inventory analysis method which aims to improve the limitations of previous methods. It was found that the truncation associated with process analysis can be up to 87%, reflecting the considerable shortcomings in the quantity of process data currently available. Capital inputs were found to account for up to 22% of the total inputs to a particular product. These findings suggest that current best-practice methods are sufficiently accurate for most typical applications, but this is heavily dependent upon data quality and availability. The use of input-output data assists in improving the system boundary completeness of life-cycle inventories. However, the use of input-output analysis alone does not always provide an accurate model for replacing process data. Further improvements in the quantity of process data currently available are needed to increase the reliability of life-cycle inventories.

  17. Predictive diagnostic value for the clinical features accompanying intellectual disability in children with pathogenic copy number variations: a multivariate analysis

    Science.gov (United States)

    2014-01-01

    Background Array comparative genomic hybridization (a-CGH) has become the first-tier investigation in patients with unexplained developmental delay/intellectual disability (DD/ID). Although the costs are progressively decreasing, a-CGH is still an expensive and labour-intensive technique: for this reason a definition of the categories of patients that can benefit the most of the analysis is needed. Aim of the study was to retrospectively analyze the clinical features of children with DD/ID attending the outpatient clinic of the Mother & Child Department of the University Hospital of Modena subjected to a-CGH, to verify by uni- and multivariate analysis the independent predictors of pathogenic CNVs. Methods 116 patients were included in the study. Data relative to the CNVs and to the patients’ clinical features were analyzed for genotype/phenotype correlations. Results and conclusions 27 patients (23.3%) presented pathogenic CNVs (21 deletions, 3 duplications and 3 cases with both duplications and deletions). Univariate analysis showed a significant association of the pathogenic CNVs with the early onset of symptoms (before 1 yr of age) and the presence of malformations and dysmorphisms. Logistic regression analysis showed a significant independent predictive value for diagnosing a pathogenic CNV for malformations (P = 0.002) and dysmorphisms (P = 0.023), suggesting that those features should address a-CGH analysis as a high-priority test for diagnosis. PMID:24775911

  18. A recurrent copy number variation of the NEB triplicate region: only revealed by the targeted nemaline myopathy CGH array.

    Science.gov (United States)

    Kiiski, Kirsi; Lehtokari, Vilma-Lotta; Löytynoja, Ari; Ahlstén, Liina; Laitila, Jenni; Wallgren-Pettersson, Carina; Pelin, Katarina

    2016-04-01

    Recently, new large variants have been identified in the nebulin gene (NEB) causing nemaline myopathy (NM). NM constitutes a heterogeneous group of disorders among the congenital myopathies, and disease-causing variants in NEB are a main cause of the recessively inherited form of NM. NEB consists of 183 exons and it includes homologous sequences such as a 32-kb triplicate region (TRI), where eight exons are repeated three times (exons 82-89, 90-97, 98-105). In human, the normal copy number of NEB TRI is six (three copies in each allele). Recently, we described a custom NM-CGH microarray designed to detect copy number variations (CNVs) in the known NM genes. The array has now been updated to include all the currently known 10 NM genes. The NM-CGH array is superior in detecting CNVs, especially of the NEB TRI, that is not included in the exome capture kits. To date, we have studied 266 samples from 196 NM families using the NM-CGH microarray, and identified a novel recurrent NEB TRI variation in 13% (26/196) of the families and in 10% of the controls (6/60). An analysis of the breakpoints revealed adjacent repeat elements, which are known to predispose for rearrangements such as CNVs. The control CNV samples deviate only one copy from the normal six copies, whereas the NM samples include CNVs of up to four additional copies. Based on this study, NEB seems to tolerate deviations of one TRI copy, whereas addition of two or more copies might be pathogenic.

  19. Hybrid vehicle assessment. Phase 1: Petroleum savings analysis

    Science.gov (United States)

    Levin, R.; Liddle, S.; Deshpande, G.; Trummel, M.; Vivian, H. C.

    1984-01-01

    The results of a comprehensive analysis of near term electric hybrid vehicles are presented, with emphasis on their potential to save significant amounts of petroleum on a national scale in the 1990s. Performance requirements and expected annual usage patterns of these vehicles are first modeled. The projected U.S. fleet composition is estimated, and conceptual hybrid vehicle designs are conceived and analyzed for petroleum use when driven in the expected annual patterns. These petroleum consumption estimates are then compared to similar estimates for projected 1990 conventional vehicles having the same performance and driven in the same patterns. Results are presented in the form of three utility functions and comparisons of sevral conceptual designs are made. The Hybrid Vehicle (HV) design and assessment techniques are discussed and a general method is explained for selecting the optimum energy management strategy for any vehicle mission battery combination. Conclusions and recommendations are presented, and development recommendations are identified.

  20. Proteomic Analysis of Pachytene Spermatocytes of Sterile Hybrid Male Mice.

    Science.gov (United States)

    Wang, Lu; Guo, Yueshuai; Liu, Wenjing; Zhao, Weidong; Song, Gendi; Zhou, Tao; Huang, Hefeng; Guo, Xuejiang; Sun, Fei

    2016-09-01

    Incompatibilities in interspecific hybrids, such as reduced hybrid fertility and lethality, are common features resulting from reproductive isolation that lead to speciation. Subspecies crosses of house mice produce offspring in which one sex is infertile or absent, yet the molecular mechanisms of hybrid sterility are poorly understood. In this study, we observed extensive asynapsis of chromosomes and disturbance of the sex body in pachytene spermatocytes of sterile F1 males (PWK/Ph female × C57BL/6J male). We report the high-confidence identification of 4005 proteins in the pachytene spermatocytes of fertile F1 males (PWK/Ph male × C57BL/6J female) and sterile F1 males (PWK/Ph female × C57BL/6J male), of which 215 were upregulated and 381 were downregulated. Bioinformatics analysis of the proteome led to the identification of 43 and 59 proteins known to be essential for male meiosis and spermatogenesis in mice, respectively. Characterization of the proteome of pachytene spermatocytes associated with hybrid male sterility provides an inventory of proteins that is useful for understanding meiosis and the mechanisms of hybrid male infertility.

  1. Intelligent Hybrid Cluster Based Classification Algorithm for Social Network Analysis

    Directory of Open Access Journals (Sweden)

    S. Muthurajkumar

    2014-05-01

    Full Text Available In this paper, we propose an hybrid clustering based classification algorithm based on mean approach to effectively classify to mine the ordered sequences (paths from weblog data in order to perform social network analysis. In the system proposed in this work for social pattern analysis, the sequences of human activities are typically analyzed by switching behaviors, which are likely to produce overlapping clusters. In this proposed system, a robust Modified Boosting algorithm is proposed to hybrid clustering based classification for clustering the data. This work is useful to provide connection between the aggregated features from the network data and traditional indices used in social network analysis. Experimental results show that the proposed algorithm improves the decision results from data clustering when combined with the proposed classification algorithm and hence it is proved that of provides better classification accuracy when tested with Weblog dataset. In addition, this algorithm improves the predictive performance especially for multiclass datasets which can increases the accuracy.

  2. Hybrid Expert Systems In Image Analysis

    Science.gov (United States)

    Dixon, Mark J.; Gregory, Paul J.

    1987-04-01

    Vision systems capable of inspecting industrial components and assemblies have a large potential market if they can be easily programmed and produced quickly. Currently, vision application software written in conventional high-level languages such as C or Pascal are produced by experts in program design, image analysis, and process control. Applications written this way are difficult to maintain and modify. Unless other similar inspection problems can be found, the final program is essentially one-off redundant code. A general-purpose vision system targeted for the Visual Machines Ltd. C-VAS 3000 image processing workstation, is described which will make writing image analysis software accessible to the non-expert both in programming computers and image analysis. A significant reduction in the effort required to produce vision systems, will be gained through a graphically-driven interactive application generator. Finally, an Expert System will be layered on top to guide the naive user through the process of generating an application.

  3. DNA hybridization sensing for cytogenetic analysis

    DEFF Research Database (Denmark)

    Kwasny, Dorota; Dapra, Johannes; Brøgger, Anna Line;

    2013-01-01

    Cytogenetic analysis focuses on studying the cell structure, mainly in respect to chromosome content and their structure. Chromosome abnormalities, such as translocations may cause various genetic disorders, but are also associated with heametological malignancies. Chromosome translocations...... for cheaper detection a label-free approach has been investigated using electrochemical impedance spectroscopy as a sensing method. We present here our recent results in regards to DNA sensing on metallic and conductive polymer electrodes for translocation detection. Our sensors are inexpensive and can...... be successfully applied in cytogenetic analysis as a replacement of standard techniques....

  4. Exome sequencing and arrayCGH detection of gene sequence and copy number variation between ILS and ISS mouse strains.

    Science.gov (United States)

    Dumas, Laura; Dickens, C Michael; Anderson, Nathan; Davis, Jonathan; Bennett, Beth; Radcliffe, Richard A; Sikela, James M

    2014-06-01

    It has been well documented that genetic factors can influence predisposition to develop alcoholism. While the underlying genomic changes may be of several types, two of the most common and disease associated are copy number variations (CNVs) and sequence alterations of protein coding regions. The goal of this study was to identify CNVs and single-nucleotide polymorphisms that occur in gene coding regions that may play a role in influencing the risk of an individual developing alcoholism. Toward this end, two mouse strains were used that have been selectively bred based on their differential sensitivity to alcohol: the Inbred long sleep (ILS) and Inbred short sleep (ISS) mouse strains. Differences in initial response to alcohol have been linked to risk for alcoholism, and the ILS/ISS strains are used to investigate the genetics of initial sensitivity to alcohol. Array comparative genomic hybridization (arrayCGH) and exome sequencing were conducted to identify CNVs and gene coding sequence differences, respectively, between ILS and ISS mice. Mouse arrayCGH was performed using catalog Agilent 1 × 244 k mouse arrays. Subsequently, exome sequencing was carried out using an Illumina HiSeq 2000 instrument. ArrayCGH detected 74 CNVs that were strain-specific (38 ILS/36 ISS), including several ISS-specific deletions that contained genes implicated in brain function and neurotransmitter release. Among several interesting coding variations detected by exome sequencing was the gain of a premature stop codon in the alpha-amylase 2B (AMY2B) gene specifically in the ILS strain. In total, exome sequencing detected 2,597 and 1,768 strain-specific exonic gene variants in the ILS and ISS mice, respectively. This study represents the most comprehensive and detailed genomic comparison of ILS and ISS mouse strains to date. The two complementary genome-wide approaches identified strain-specific CNVs and gene coding sequence variations that should provide strong candidates to

  5. Analysis of Linear Hybrid Systems in CLP

    DEFF Research Database (Denmark)

    Banda, Gourinath; Gallagher, John Patrick

    2009-01-01

    notation for specifying real-time systems. The main contributions are (i) a technique for capturing the reachable states of the continuously changing state variables of the LHA as CLP constraints; (ii) a way of representing events in the LHA as constraints in CLP, along with a product construction...... and argue that we contribute to the general field of using static analysis tools for verification...

  6. Fuel cell hybrid taxi life cycle analysis

    Energy Technology Data Exchange (ETDEWEB)

    Baptista, Patricia, E-mail: patricia.baptista@ist.utl.pt [IDMEC-Instituto Superior Tecnico, Universidade Tecnica de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisboa (Portugal); Ribau, Joao; Bravo, Joao; Silva, Carla [IDMEC-Instituto Superior Tecnico, Universidade Tecnica de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisboa (Portugal); Adcock, Paul; Kells, Ashley [Intelligent Energy, Charnwood Building, HolywellPark, Ashby Road, Loughborough, LE11 3GR (United Kingdom)

    2011-09-15

    A small fleet of classic London Taxis (Black cabs) equipped with hydrogen fuel cell power systems is being prepared for demonstration during the 2012 London Olympics. This paper presents a Life Cycle Analysis for these vehicles in terms of energy consumption and CO{sub 2} emissions, focusing on the impacts of alternative vehicle technologies for the Taxi, combining the fuel life cycle (Tank-to-Wheel and Well-to-Tank) and vehicle materials Cradle-to-Grave. An internal combustion engine diesel taxi was used as the reference vehicle for the currently available technology. This is compared to battery and fuel cell vehicle configurations. Accordingly, the following energy pathways are compared: diesel, electricity and hydrogen (derived from natural gas steam reforming). Full Life Cycle Analysis, using the PCO-CENEX drive cycle, (derived from actual London Taxi drive cycles) shows that the fuel cell powered vehicle configurations have lower energy consumption (4.34 MJ/km) and CO{sub 2} emissions (235 g/km) than both the ICE Diesel (9.54 MJ/km and 738 g/km) and the battery electric vehicle (5.81 MJ/km and 269 g/km). - Highlights: > A Life Cycle Analysis of alternative vehicle technologies for the London Taxi was performed. > The hydrogen powered vehicles have the lowest energy consumption and CO{sub 2} emissions results. > A hydrogen powered solution can be a sustainable alternative in a full life cycle framework.

  7. Hybrid vehicle assessment. Phase I. Petroleum savings analysis

    Energy Technology Data Exchange (ETDEWEB)

    Levin, R.; Liddle, S.; Deshpande, G.; Trummel, M.; Vivian, H.

    1984-03-01

    This report presents the results of a comprehensive analysis of near-term electric-hybrid vehicles. Its purpose was to estimate their potential to save significant amounts of petroleum on a national scale in the 1990s. Performance requirements and expected annual usage patterns of these vehicles were first modeled. The projected US fleet composition was estimated, and conceptual hybrid vehicle designs were conceived and analyzed for petroleum use when driven in the expected annual patterns. These petroleum consumption estimates were then compared to similar estimates for projected 1990 conventional vehicles having the same performance and driven in the same patterns. Results are presented in the form of three utility functions and comparisons of several conceptual designs are made. The Hybrid Vehicle (HV) design and assessment techniques are discussed and a general method is explained for selecting the optimum energy management strategy for any vehicle-mission-battery combination. A discussion of lessons learned during the construction and test of the General Electric Hybrid Test Vehicle is also presented. Conclusions and recommendations are presented, and development recommendations are identified.

  8. Performance Analysis of a Hybrid Power Cutting System for Roadheader

    Directory of Open Access Journals (Sweden)

    Yang Yang

    2017-01-01

    Full Text Available An electrohydraulic hybrid power cutting transmission system for roadheader under specific working condition was proposed in this paper. The overall model for the new system composed of an electric motor model, a hydraulic pump-motor model, a torsional planetary set model, and a hybrid power train model was established. The working mode characteristics were simulated under the conditions of taking the effect of cutting picks into account. The advantages of new hybrid power cutting system about the dynamic response under shock load were investigated compared with the traditional cutting system. The results illustrated that the hybrid power system had an obvious cushioning in terms of the dynamic load of cutting electric motor and planetary gear set. Besides, the hydraulic motor could provide an auxiliary power to improve the performance of the electric motor. With further analysis, a dynamic load was found to have a high relation to the stiffness and damping of coupling in the transmission train. The results could be a useful guide for the design of cutting transmission of roadheader.

  9. The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH

    Directory of Open Access Journals (Sweden)

    Oga Atsunori

    2008-12-01

    Full Text Available Abstract Background The treatment strategy usually depends on the disease state in the individual patient. However, it is difficult to estimate the disease state before treatment in many patients. The purpose of this study was to develop a BAC (bacterial artificial chromosome mini-array allowing for the estimation of node metastasis, liver metastasis, peritoneal dissemination and the depth of tumor invasion in gastric cancers. Methods Initially, the DNA copy number aberrations (DCNAs were analyzed by array-based comparative genomic hybridization (aCGH in 83 gastric adenocarcinomas as a training-sample set. Next, two independent analytical methods were applied to the aCGH data to identify the BAC clones with DNA copy number aberrations that were linked with the disease states. One of the methods, a decision-tree model classifier, identified 6, 4, 4, 4, and 7 clones for estimating lymph node metastasis, liver metastasis, peritoneal dissemination, depth of tumor invasion, and histological type, respectively. In the other method, a clone-by-clone comparison of the frequency of the DNA copy number aberrations selected 26 clones to estimate the disease states. Results By spotting these 50 clones together with 26 frequently or rarely involved clones and 62 reference clones, a mini-array was made to estimate the above parameters, and the diagnostic performance of the mini-array was evaluated for an independent set of 30 gastric cancers (blinded – sample set. In comparison to the clinicopathological features, the overall accuracy was 66.7% for node metastasis, 86.7% for liver metastasis, 86.7% for peritoneal dissemination, and 96.7% for depth of tumor invasion. The intratumoral heterogeneity barely affected the diagnostic performance of the mini-array. Conclusion These results suggest that the mini-array makes it possible to determine an optimal treatment for each of the patients with gastric adenocarcinoma.

  10. Novel Genomic Aberrations in Testicular Germ Cell Tumors by Array-CGH, and Associated Gene Expression Changes

    Directory of Open Access Journals (Sweden)

    Rolf I. Skotheim

    2006-01-01

    Full Text Available Introduction: Testicular germ cell tumors of adolescent and young adult men (TGCTs generally have near triploid and complex karyotypes. The actual genes driving the tumorigenesis remain essentially to be identified. Materials and Methods: To determine the detailed DNA copy number changes, and investigate their impact on gene expression levels, we performed an integrated microarray profiling of TGCT genomes and transcriptomes. We analyzed 17 TGCTs, three precursor lesions, and the embryonal carcinoma cell lines, NTERA2 and 2102Ep, by comparative genomic hybridization microarrays (array-CGH, and integrated the data with transcriptome profiles of the same samples. Results: The gain of chromosome arm 12p was, as expected, the most common aberration, and we found CCND2, CD9, GAPD, GDF3, NANOG, and TEAD4 to be the therein most highly over-expressed genes. Additional frequent genomic aberrations revealed some shorter chromosomal segments, which are novel to TGCT, as well as known aberrations for which we here refined boundaries. These include gains from 7p15.2 and 21q22.2, and losses of 4p16.3 and 22q13.3. Integration of DNA copy number information to gene expression profiles identified that BRCC3, FOS, MLLT11, NES, and RAC1 may act as novel oncogenes in TGCT. Similarly, DDX26, ERCC5, FZD4, NME4, OPTN, and RB1 were both lost and under-expressed genes, and are thus putative TGCT suppressor genes. Conclusion: This first genome-wide integrated array-CGH and gene expression profiling of TGCT provides novel insights into the genome biology underlying testicular tumorigenesis.

  11. Dance in mental health nursing: a hybrid concept analysis.

    Science.gov (United States)

    Ravelin, Teija; Kylmä, Jari; Korhonen, Teija

    2006-04-01

    The aim of this concept analysis is to describe the defining attributes and consequences of the concept of dance and to define it in a mental health nursing context using hybrid concept analysis. Dance is a human resource learned from culture. Dance implies body movements, steps, expression, and interaction. The outcomes of dance are mostly functional, including a client's physical and emotional health, well-being, ability to cooperate with other people in activities of daily life, and meeting role expectations within family and community. Based on the findings of this concept analysis, dance can be used as a nursing intervention.

  12. A hybrid monkey search algorithm for clustering analysis.

    Science.gov (United States)

    Chen, Xin; Zhou, Yongquan; Luo, Qifang

    2014-01-01

    Clustering is a popular data analysis and data mining technique. The k-means clustering algorithm is one of the most commonly used methods. However, it highly depends on the initial solution and is easy to fall into local optimum solution. In view of the disadvantages of the k-means method, this paper proposed a hybrid monkey algorithm based on search operator of artificial bee colony algorithm for clustering analysis and experiment on synthetic and real life datasets to show that the algorithm has a good performance than that of the basic monkey algorithm for clustering analysis.

  13. A Hybrid Monkey Search Algorithm for Clustering Analysis

    Directory of Open Access Journals (Sweden)

    Xin Chen

    2014-01-01

    Full Text Available Clustering is a popular data analysis and data mining technique. The k-means clustering algorithm is one of the most commonly used methods. However, it highly depends on the initial solution and is easy to fall into local optimum solution. In view of the disadvantages of the k-means method, this paper proposed a hybrid monkey algorithm based on search operator of artificial bee colony algorithm for clustering analysis and experiment on synthetic and real life datasets to show that the algorithm has a good performance than that of the basic monkey algorithm for clustering analysis.

  14. A hybrid transfinite element approach for nonlinear transient thermal analysis

    Science.gov (United States)

    Tamma, Kumar K.; Railkar, Sudhir B.

    1987-01-01

    A new computational approach for transient nonlinear thermal analysis of structures is proposed. It is a hybrid approach which combines the modeling versatility of contemporary finite elements in conjunction with transform methods and classical Bubnov-Galerkin schemes. The present study is limited to nonlinearities due to temperature-dependent thermophysical properties. Numerical test cases attest to the basic capabilities and therein validate the transfinite element approach by means of comparisons with conventional finite element schemes and/or available solutions.

  15. From amplification to gene in thyroid cancer: A high-resolution mapped bacterial-artificial-chromosome resource for cancer chromosome aberrations guides gene discovery after comparative genome hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Chen, X.N.; Gonsky, R.; Korenberg, J.R. [UCLA School of Medicine, Los Angeles, CA (United States). Cedars-Sinai Research Inst.; Knauf, J.A.; Fagin, J.A. [Univ. of Cincinnati, OH (United States). Div. of Endocrinology/Metabolism; Wang, M.; Lai, E.H. [Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Pharmacology; Chissoe, S. [Washington Univ. School of Medicine, St. Louis, MO (United States). Genome Sequencing

    1998-08-01

    Chromosome rearrangements associated with neoplasms provide a rich resource for definition of the pathways of tumorigenesis. The power of comparative genome hybridization (CGH) to identify novel genes depends on the existence of suitable markers, which are lacking throughout most of the genome. The authors now report a general approach that translates CGH data into higher-resolution genomic-clone data that are then used to define the genes located in aneuploid regions. They used CGH to study 33 thyroid-tumor DNAs and two tumor-cell-line DNAs. The results revealed amplifications of chromosome band 2p21, with less-intense amplification on 2p13, 19q13.1, and 1p36 and with least-intense amplification on 1p34, 1q42, 5q31, 5q33-34, 9q32-34, and 14q32. To define the 2p21 region amplified, a dense array of 373 FISH-mapped chromosome 2 bacterial artificial chromosomes (BACs) was constructed, and 87 of these were hybridized to a tumor-cell line. Four BACs carried genomic DNA that was amplified in these cells. The maximum amplified region was narrowed to 3--6 Mb by multicolor FISH with the flanking BACs, and the minimum amplicon size was defined by a contig of 420 kb. Sequence analysis of the amplified BAC 1D9 revealed a fragment of the gene, encoding protein kinase C epsilon (PKC{epsilon}), that was then shown to be amplified and rearranged in tumor cells. In summary, CGH combined with a dense mapped resource of BACs and large-scale sequencing has led directly to the definition of PKC{epsilon} as a previously unmapped candidate gene involved in thyroid tumorigenesis.

  16. Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples.

    Science.gov (United States)

    Hostetter, Galen; Kim, Su Young; Savage, Stephanie; Gooden, Gerald C; Barrett, Michael; Zhang, Jian; Alla, Lalitamba; Watanabe, April; Einspahr, Janine; Prasad, Anil; Nickoloff, Brian J; Carpten, John; Trent, Jeffrey; Alberts, David; Bittner, Michael

    2010-01-01

    Genomic technologies, such as array comparative genomic hybridization (aCGH), increasingly offer definitive gene dosage profiles in clinical samples. Historically, copy number profiling was limited to large fresh-frozen tumors where intact DNA could be readily extracted. Genomic analyses of pre-neoplastic tumors and diagnostic biopsies are often limited to DNA processed by formalin-fixation and paraffin-embedding (FFPE). We present specialized protocols for DNA extraction and processing from FFPE tissues utilizing DNase processing to generate randomly fragmented DNA. The protocols are applied to FFPE clinical samples of varied tumor types, from multiple institutions and of varied block age. Direct comparative analyses with regression coefficient were calculated on split-sample (portion fresh/portion FFPE) of colorectal tumor samples. We show equal detection of a homozygous loss of SMAD4 at the exon-level in the SW480 cell line and gene-specific alterations in the split tumor samples. aCGH application to a set of archival FFPE samples of skin squamous cell carcinomas detected a novel hemizygous deletion in INPP5A on 10q26.3. Finally we present data on derivative of log ratio, a particular sensitive detector of measurement variance, for 216 sequential hybridizations to assess protocol reliability over a wide range of FFPE samples.

  17. Identification of novel genomic aberrations in AML-M5 in a level of array CGH.

    Directory of Open Access Journals (Sweden)

    Rui Zhang

    Full Text Available To assess the possible existence of unbalanced chromosomal abnormalities and delineate the characterization of copy number alterations (CNAs of acute myeloid leukemia-M5 (AML-M5, R-banding karyotype, oligonucelotide array CGH and FISH were performed in 24 patients with AML-M5. A total of 117 CNAs with size ranging from 0.004 to 146.263 Mb was recognized in 12 of 24 cases, involving all chromosomes other than chromosome 1, 4, X and Y. Cryptic CNAs with size less than 5 Mb accounted for 59.8% of all the CNAs. 12 recurrent chromosomal alterations were mapped. Seven out of them were described in the previous AML studies and five were new candidate AML-M5 associated CNAs, including gains of 3q26.2-qter and 13q31.3 as well as losses of 2q24.2, 8p12 and 14q32. Amplication of 3q26.2-qter was the sole large recurrent chromosomal anomaly and the pathogenic mechanism in AML-M5 was possibly different from the classical recurrent 3q21q26 abnormality in AML. As a tumor suppressor gene, FOXN3, was singled out from the small recurrent CNA of 14q32, however, it is proved that deletion of FOXN3 is a common marker of myeloid leukemia rather than a specific marker for AML-M5 subtype. Moreover, the concurrent amplication of MLL and deletion of CDKN2A were noted and it might be associated with AML-M5. The number of CNA did not show a significant association with clinico-biological parameters and CR number of the 22 patients received chemotherapy. This study provided the evidence that array CGH served as a complementary platform for routine cytogenetic analysis to identify those cryptic alterations in the patients with AML-M5. As a subtype of AML, AML-M5 carries both common recurrent CNAs and unique CNAs, which may harbor novel oncogenes or tumor suppressor genes. Clarifying the role of these genes will contribute to the understanding of leukemogenic network of AML-M5.

  18. Genome-wide screening for genetic alterations in esophageal cancer by aCGH identifies 11q13 amplification oncogenes associated with nodal metastasis.

    Directory of Open Access Journals (Sweden)

    Jianming Ying

    Full Text Available BACKGROUND: Esophageal squamous cell carcinoma (ESCC is highly prevalent in China and other Asian countries, as a major cause of cancer-related mortality. ESCC displays complex chromosomal abnormalities, including multiple structural and numerical aberrations. Chromosomal abnormalities, such as recurrent amplifications and homozygous deletions, directly contribute to tumorigenesis through altering the expression of key oncogenes and tumor suppressor genes. METHODOLOGY/PRINCIPLE FINDINGS: To understand the role of genetic alterations in ESCC pathogenesis and identify critical amplification/deletion targets, we performed genome-wide 1-Mb array comparative genomic hybridization (aCGH analysis for 10 commonly used ESCC cell lines. Recurrent chromosomal gains were frequently detected on 3q26-27, 5p15-14, 8p12, 8p22-24, 11q13, 13q21-31, 18p11 and 20q11-13, with frequent losses also found on 8p23-22, 11q22, 14q32 and 18q11-23. Gain of 11q13.3-13.4 was the most frequent alteration in ESCC. Within this region, CCND1 oncogene was identified with high level of amplification and overexpression in ESCC, while FGF19 and SHANK2 was also remarkably over-expressed. Moreover, a high concordance (91.5% of gene amplification and protein overexpression of CCND1 was observed in primary ESCC tumors. CCND1 amplification/overexpression was also significantly correlated with the lymph node metastasis of ESCC. CONCLUSION: These findings suggest that genomic gain of 11q13 is the major mechanism contributing to the amplification. Novel oncogenes identified within the 11q13 amplicon including FGF19 and SHANK2 may play important roles in ESCC tumorigenesis.

  19. High-resolution array CGH profiling identifies Na/K transporting ATPase interacting 2 (NKAIN2 as a predisposing candidate gene in neuroblastoma.

    Directory of Open Access Journals (Sweden)

    Paolo Romania

    Full Text Available Neuroblastoma (NB, the most common solid cancer in early childhood, usually occurs sporadically but also its familial occurance is known in 1-2% of NB patients. Germline mutations in the ALK and PHOX2B genes have been found in a subset of familial NBs. However, because some individuals harbouring mutations in these genes do not develop this tumor, additional genetic alterations appear to be required for NB pathogenesis. Herein, we studied an Italian family with three NB patients, two siblings and a first cousin, carrying an ALK germline-activating mutation R1192P, that was inherited from their unaffected mothers and with no mutations in the PHOX2B gene. A comparison between somatic and germline DNA copy number changes in the two affected siblings by a high resolution array-based Comparative Genomic Hybridization (CGH analysis revealed a germline gain at NKAIN2 (Na/K transporting ATPase interacting 2 locus in one of the sibling, that was inherited from the parent who does not carry the ALK mutation. Surprisingly, NKAIN2 was expressed at high levels also in the affected sibling that lacks the genomic gain at this locus, clearly suggesting the existance of other regulatory mechanisms. High levels of NKAIN2 were detected in the MYCN-amplified NB cell lines and in the most aggressive NB lesions as well as in the peripheral blood of a large cohort of NB patients. Consistent with a role of NKAIN2 in NB development, NKAIN2 was down-regulated during all-trans retinoic acid differentiation in two NB cell lines. Taken together, these data indicate a potential role of NKAIN2 gene in NB growth and differentiation.

  20. Performance analysis of a hybrid fingerprint extracted from optical coherence tomography fingertip scans

    CSIR Research Space (South Africa)

    Darlow, Luke N

    2016-06-01

    Full Text Available International Conference on Biometrics (ICB), 13-16 June 2016, Halmstad, Sweden Performance analysis of a hybrid fingerprint extracted from optical coherence tomography fingertip scans Darlow LN Connan J Singh A ABSTRACT: The Hybrid fingerprint is a...

  1. Analysis/design of strip reinforced random composites (strip hybrids)

    Science.gov (United States)

    Chamis, C. C.; Sinclair, J. H.

    1978-01-01

    Advanced analysis methods and composite mechanics were applied to a strip-reinforced random composite square panel with fixed ends to illustrate the use of these methods for the a priori assessment of the composite panel when subjected to complex loading conditions. The panel was assumed to be of E-glass random composite. The strips were assumed to be of three advanced unidirectional composites to cover a range of low, intermediate, and high modulus stiffness. The panels were assumed to be subjected to complex loadings to assess their adequacy as load-carrying members in auto body, aircraft engine nacelle and windmill blade applications. The results show that strip hybrid panels can be several times more structurally efficient than the random composite base materials. Some of the results are presented in graphical form and procedures are described for use of these graphs as guides for preliminary design of strip hybrids.

  2. Analysis/design of strip reinforced random composites /strip hybrids/

    Science.gov (United States)

    Chamis, C. C.; Sinclair, J. H.

    1978-01-01

    Results are described which were obtained by applying advanced analysis methods and composite mechanics to a strip-reinforced random composite square panel with fixed ends. This was done in order to illustrate the use of these methods for the apriori assessment of the composite panel when subjected to complex loading conditions. The panel was assumed to be of E-Glass/Random Composite. The strips were assumed to be of three advanced unidirectional composites to cover a range of low, intermediate, and high modulus stiffness. The panels were assumed to be subjected to complex loadings to assess their adequacy as load-carrying members in auto body, aircraft engine nacelle, and windmill blade applications. The results show that strip hybrid panels can be several times more structurally efficient than the random composite base materials. Some of the results are presented in graphical form and procedures are described for use of these graphs as guides for preliminary design of strip hybrids.

  3. Accuracy Analysis and Calibration of Gantry Hybrid Machine Tool

    Institute of Scientific and Technical Information of China (English)

    唐晓强; 李铁民; 尹文生; 汪劲松

    2003-01-01

    The kinematic accuracy is a key factor in the design of parallel or hybrid machine tools. This analysis improved the accuracy of a 4-DOF (degree of freedom) gantry hybrid machine tool based on a 3-DOF planar parallel manipulator by compensating for various positioning errors. The machine tool architecture was described with the inverse kinematic solution. The control parameter error model was used to analyze the accuracy of the 3-DOF planar parallel manipulator and to develop a kinematic calibration method. The experimental results prove that the calibration method reduces the cutter nose errors from ±0.50 mm to ±0.03 mm for a horizontal movement of 600 mm by compensating for errors in the slider home position, the guide way distance and the extensible strut home position. The calibration method will be useful for similar types of parallel kinematic machines.

  4. Plug-In Hybrid Vehicle Analysis (Milestone Report)

    Energy Technology Data Exchange (ETDEWEB)

    Markel, T.; Brooker, A.; Gonder, J.; O' Keefe, M.; Simpson, A.; Thornton, M.

    2006-11-01

    NREL's plug-in hybrid electric vehicle (PHEV) analysis activities made great strides in FY06 to objectively assess PHEV technology, support the larger U.S. Department of Energy PHEV assessment effort, and share technical knowledge with the vehicle research community and vehicle manufacturers. This report provides research papers and presentations developed in FY06 to support these efforts. The report focuses on the areas of fuel economy reporting methods, cost and consumption benefit analysis, real-world performance expectations, and energy management strategies.

  5. Hybrid Information Flow Analysis for Programs with Arrays

    Directory of Open Access Journals (Sweden)

    Gergö Barany

    2016-07-01

    Full Text Available Information flow analysis checks whether certain pieces of (confidential data may affect the results of computations in unwanted ways and thus leak information. Dynamic information flow analysis adds instrumentation code to the target software to track flows at run time and raise alarms if a flow policy is violated; hybrid analyses combine this with preliminary static analysis. Using a subset of C as the target language, we extend previous work on hybrid information flow analysis that handled pointers to scalars. Our extended formulation handles arrays, pointers to array elements, and pointer arithmetic. Information flow through arrays of pointers is tracked precisely while arrays of non-pointer types are summarized efficiently. A prototype of our approach is implemented using the Frama-C program analysis and transformation framework. Work on a full machine-checked proof of the correctness of our approach using Isabelle/HOL is well underway; we present the existing parts and sketch the rest of the correctness argument.

  6. Association of cGH EcoRV Gene with Production in Tolaki Chicken

    Directory of Open Access Journals (Sweden)

    Muhammad Amrullah Pagala

    2017-02-01

    Full Text Available cGH (Chicken Growth Hormone gene plays a crucial role in production responses of chicken. The objective of the research was to investigate the association of cGH gene with production in Tolaki chicken. Tolaki chicken is native chickens from Southeast Sulawesi Province of Indonesian. cGH gene was genotyped in 58 Tolaki chicken with PCR-RFLP. PCR was used to amplify genomic DNA for GH gene (399 bp. The amplicon was cutted by EcoRV and produced three genotypes: AA, AG, and GG and two alleles: A and G allele. The study showed the association of GH gene polymorphism with Production traits. GG genotype have better production (daily weight gain and feed conversion than AG genotype in Tolaki chicken, providing evidence that GH gene might be an important candidate gene for production traits.

  7. Electric and Hybrid Vehicle System Research and Development Project: Hybrid Vehicle Potential Assessment. Volume VI. Cost analysis

    Energy Technology Data Exchange (ETDEWEB)

    Hardy, K.S.

    1979-09-30

    The purpose of the cost analysis is to determine the economic feasibility of a variety of hybrid vehicles with respect to conventional vehicles specifically designed for the same duty cycle defined by the mission analysis. Several different hybrid configurations including parallel, parallel-flywheel, and series vehicles were evaluated. The ramifications of incorporating examples of advanced batteries, these being the advanced lead-acid, nickel-zinc, and sodium sulfur were also investigated. Vehicles were specifically designed with these batteries and for the driving cycles specified by the mission. Simulated operation on the missions yielded the energy consumption (petroleum and/or electricity) over the driving cycles. It was concluded that: in the event that gasoline prices reach $2.50 to $3.00/gal, hybrid vehicles in many applications will become economically competitive with conventional vehicles without subsidization; in some commercial applications hybrid vehicles could be economically competitive, when the gasoline price ranges from $1.20 to $1.50/gal. The cost per kWh per cycle of the advanced batteries is much more important economically than the specific energy; the series hybrid vehicles were found to be more expensive in comparison to the parallel or parallel-flywheel hybrids when designed as passenger vehicles; and hybrid vehicles designed for private use could become economically competitive and displace up to 50% of the fuel normally used on that mission if subsidies of $500 to $2000 were supplied to the owner/operator. (LCL)

  8. Analysis of a Hybrid Wing Body Center Section Test Article

    Science.gov (United States)

    Wu, Hsi-Yung T.; Shaw, Peter; Przekop, Adam

    2013-01-01

    The hybrid wing body center section test article is an all-composite structure made of crown, floor, keel, bulkhead, and rib panels utilizing the Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) design concept. The primary goal of this test article is to prove that PRSEUS components are capable of carrying combined loads that are representative of a hybrid wing body pressure cabin design regime. This paper summarizes the analytical approach, analysis results, and failure predictions of the test article. A global finite element model of composite panels, metallic fittings, mechanical fasteners, and the Combined Loads Test System (COLTS) test fixture was used to conduct linear structural strength and stability analyses to validate the specimen under the most critical combination of bending and pressure loading conditions found in the hybrid wing body pressure cabin. Local detail analyses were also performed at locations with high stress concentrations, at Tee-cap noodle interfaces with surrounding laminates, and at fastener locations with high bearing/bypass loads. Failure predictions for different composite and metallic failure modes were made, and nonlinear analyses were also performed to study the structural response of the test article under combined bending and pressure loading. This large-scale specimen test will be conducted at the COLTS facility at the NASA Langley Research Center.

  9. Comparative genomic hybridization analysis detects frequent over-representation of DNA sequences at 3q, 7p, 8q and 18q in head and neck carcinomas

    DEFF Research Database (Denmark)

    Bergamo, N A; Rogatto, S R; Poli-Frederico, R C;

    2000-01-01

    Comparative genomic hybridization (CGH) was used to identify chromosomal imbalances in 19 samples of squamous cell carcinoma of the head and neck (HNSCC). The chromosome arms most often over-represented were 3q (48%), 8q (42%), and 7p (32%); in many cases, these changes were observed at high copy...... and 2q material were detected in patients exhibiting a clinical history of recurrence and/or metastasis followed by terminal disease. This association suggests that gain of 1q and 2q may be a new marker of head and neck tumors with a refractory clinical response....

  10. From hybridization theory to microarray data analysis: performance evaluation

    Directory of Open Access Journals (Sweden)

    Berger Fabrice

    2011-12-01

    Full Text Available Abstract Background Several preprocessing methods are available for the analysis of Affymetrix Genechips arrays. The most popular algorithms analyze the measured fluorescence intensities with statistical methods. Here we focus on a novel algorithm, AffyILM, available from Bioconductor, which relies on inputs from hybridization thermodynamics and uses an extended Langmuir isotherm model to compute transcript concentrations. These concentrations are then employed in the statistical analysis. We compared the performance of AffyILM and other traditional methods both in the old and in the newest generation of GeneChips. Results Tissue mixture and Latin Square datasets (provided by Affymetrix were used to assess the performances of the differential expression analysis depending on the preprocessing strategy. A correlation analysis conducted on the tissue mixture data reveals that the median-polish algorithm allows to best summarize AffyILM concentrations computed at the probe-level. Those correlation results are equivalent to the best correlations observed using popular preprocessing methods relying on intensity values. The performances of each tested preprocessing algorithm were quantified using the Latin Square HG-U133A dataset, thanks to the comparison of differential analysis results with the list of spiked genes. The figures of merit generated illustrates that the performances associated to AffyILM(medianpolish, inferred from the present statistical analysis, are comparable to the best performing strategies previously reported. Conclusions Converting probe intensities to estimates of target concentrations prior to the statistical analysis, AffyILM(medianpolish is one of the best performing strategy currently available. Using hybridization theory, probe-level estimates of target concentrations should be identically distributed. In the future, a probe-level multivariate analysis of the concentrations should be compared to the univariate analysis of

  11. Analysis of Non-binary Hybrid LDPC Codes

    CERN Document Server

    Sassatelli, Lucile

    2008-01-01

    In this paper, we analyse asymptotically a new class of LDPC codes called Non-binary Hybrid LDPC codes, which has been recently introduced. We use density evolution techniques to derive a stability condition for hybrid LDPC codes, and prove their threshold behavior. We study this stability condition to conclude on asymptotic advantages of hybrid LDPC codes compared to their non-hybrid counterparts.

  12. Chromosomal imbalances detected in primary bone tumors by comparative genomic hybridization and interphase fluorescence in situ hybridization

    OpenAIRE

    Baruffi Marcelo Razera; Engel Edgard Edward; Squire Jeremy Andrew; Tone Luis Gonzaga; Rogatto Silvia Regina

    2003-01-01

    We applied a combination of comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH), to characterize the genetic aberrations in three osteosarcomas (OS) and one Ewing's sarcoma. CGH identified recurrent chromosomal losses at 10p14-pter and gains at 8q22.3-24.1 in OS. Interphase FISH allowed to confirm 8q gain in two cases. A high amplification level of 11q12-qter was detected in one OS. The Ewing's sarcoma showed gain at 1p32-36.1 as the sole chromosome alteratio...

  13. Analysis of high velocity impact on hybrid composite fan blades

    Science.gov (United States)

    Chamis, C. C.; Sinclair, J. H.

    1979-01-01

    This paper describes recent developments in the analysis of high velocity impact of composite blades using a computerized capability which consists of coupling a composites mechanics code with the direct-time integration features of NASTRAN. The application of the capability to determine the linear dynamic response of an intraply hybrid composite aircraft engine fan blade is described in detail. The predicted results agree with measured data. The results also show that the impact stresses reach sufficiently high magnitudes to cause failures in the impact region at early times of the impact event.

  14. Analysis and Design of Hybrid Excitation Permanent Magnet Synchronous Generators

    Institute of Scientific and Technical Information of China (English)

    JIN Wan-bing; ZHANG Dong; AN Zhong-liang; TAN Ren-yuan

    2006-01-01

    On the basis of a conventional permanent magnet (PM) synchronous generator's construction,a novel kind of Hybrid Excitation Permanent Magnet Synchronous Generator (HEPMSG) is introduced by inserting exciting winding in the stator or rotor.Firstly,the construction of HEPMSG is improved with the addition of PM excitation on the ferromagnetic pole,and its working principle and design method are studied in detail.Then,an appropriate exciting current control system is presented considering the characteristics of HEPMSG.Finally,a prototype is made,and test results confirm the analysis and design.

  15. Flow cytometry-based DNA hybridization and polymorphism analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cai, H.; Kommander, K.; White, P.S.; Nolan, J.P.

    1998-07-01

    Functional analysis of the humane genome, including the quantification of differential gene expression and the identification of polymorphic sites and disease genes, is an important element of the Human Genome Project. Current methods of analysis are mainly gel-based assays that are not well-suited to rapid genome-scale analyses. To analyze DNA sequence on a large scale, robust and high throughput assays are needed. The authors are developing a suite of microsphere-based approaches employing fluorescence detection to screen and analyze genomic sequence. The approaches include competitive DNA hybridization to measure DNA or RNA targets in unknown samples, and oligo ligation or extension assays to analyze single-nucleotide polymorphisms. Apart from the advances of sensitivity, simplicity, and low sample consumption, these flow cytometric approaches have the potential for high throughput multiplexed analysis using multicolored microspheres and automated sample handling.

  16. Submicroscopic deletions of 11q24-25 in individuals without Jacobsen syndrome: re-examination of the critical region by high-resolution array-CGH

    Directory of Open Access Journals (Sweden)

    VanAllen Margot I

    2008-11-01

    Full Text Available Abstract Background Jacobsen syndrome is a rare contiguous gene disorder that results from a terminal deletion of the long arm of chromosome 11. It is typically characterized by intellectual disability, a variety of physical anomalies and a distinctive facial appearance. The 11q deletion has traditionally been identified by routine chromosome analysis. Array-based comparative genomic hybridization (array-CGH has offered new opportunities to identify and refine chromosomal abnormalities in regions known to be associated with clinical syndromes. Results Using the 1 Mb BAC array (Spectral Genomics, we screened 70 chromosomally normal children with idiopathic intellectual disability (ID and congenital abnormalities, and identified five cases with submicroscopic abnormalities believed to contribute to their phenotypes. Here, we provide detailed molecular cytogenetic descriptions and clinical presentation of two unrelated subjects with de novo submicroscopic deletions within chromosome bands 11q24-25. In subject 1 the chromosome rearrangement consisted of a 6.18 Mb deletion (from 128.25–134.43 Mb and an adjacent 5.04 Mb duplication (from 123.15–128.19 Mb, while in subject 2, a 4.74 Mb interstitial deletion was found (from 124.29–129.03 Mb. Higher resolution array analysis (385 K Nimblegen was used to refine all breakpoints. Deletions of the 11q24-25 region are known to be associated with Jacobsen syndrome (JBS: OMIM 147791. However, neither of the subjects had the typical features of JBS (trigonocephaly, platelet disorder, heart abnormalities. Both subjects had ID, dysmorphic features and additional phenotypic abnormalities: subject 1 had a kidney abnormality, bilateral preauricular pits, pectus excavatum, mild to moderate conductive hearing loss and behavioral concerns; subject 2 had macrocephaly, an abnormal MRI with delayed myelination, fifth finger shortening and squaring of all fingertips, and sensorineural hearing loss. Conclusion Two

  17. Analysis of plug-in hybrid electric vehicle utility factors

    Science.gov (United States)

    Bradley, Thomas H.; Quinn, Casey W.

    Plug-in hybrid electric vehicles (PHEVs) are hybrid electric vehicles that can be fueled from both conventional liquid fuels and grid electricity. To represent the total contribution of both of these fuels to the operation, energy use, and environmental impacts of PHEVs, researchers have developed the concept of the utility factor. As standardized in documents such as SAE J1711 and SAE J2841, the utility factor represents the proportion of vehicle distance travelled that can be allocated to a vehicle test condition so as to represent the real-world driving habits of a vehicle fleet. These standards must be used with care so that the results are understood within the context of the assumptions implicit in the standardized utility factors. This study analyzes and derives alternatives to the standard utility factors from the 2001 National Highway Transportation Survey, so as to understand the sensitivity of PHEV performance to assumptions regarding charging frequency, vehicle characteristics, driver characteristics, and means of defining the utility factor. Through analysis of these alternative utility factors, this study identifies areas where analysis, design, and policy development for PHEVs can be improved by alternative utility factor calculations.

  18. Hybrid Analysis Approach for Stochastic Response of Offshore Jacket Platforms

    Institute of Scientific and Technical Information of China (English)

    金伟良; 郑忠双; 李海波; 张立

    2000-01-01

    The dynamic response of offshore platforms is more serious in hostile sea environment than in shallow sea. In this paper, a hybrid solution combined with analytical and numerical method is proposed to compute the stochastic response of fixed offshore platforms to random waves, considering wave-structure interaction and non-linear drag force. The simulation program includes two steps: the first step is the eigenanalysis aspects associated the structure and the second step is response estimation based on spectral equations. The eigenanalysis could be done through conventional finite element method conveniently and its natural frequency and mode shapes obtained. In the second part of the process, the solution of the offshore structural response is obtained by iteration of a series of coupled spectral equations. Considering the third-order term in the drag force, the evaluation of the three-fold convolution should be demanded for nonlinear stochastic response analysis. To demonstrate this method, a numerical analysis is carried out for both linear and non-linear platform motions. The final response spectra have the typical two peaks in agreement with reality, indicating that the hybrid method is effective and can be applied to offshore engineering.

  19. Phenotype in patients with intellectual disability and pathological results in array CGH.

    Science.gov (United States)

    Caballero Pérez, V; López Pisón, F J; Miramar Gallart, M D; González Álvarez, A; García Jiménez, M C; García Iñiguez, J P; Orden Rueda, C; Gil Hernández, I; Fuertes Rodrigo, C; Fernando Martínez, R; Rodríguez Valle, A; Alcaine Villarroya, M J

    2016-05-06

    Global developmental delay (GDD) and intellectual disability (ID) are frequent reasons for consultation in paediatric neurology departments. Nowadays, array comparative genomic hybridisation (array-CGH) is one of the most widely used techniques for diagnosing these disorders. Our purpose was to determine the phenotypic features associated with pathological results in this genetic test. We conducted a blind study of the epidemiological, clinical, anthropometric, and morphological features of 80 patients with unexplained ID to determine which features were associated with pathological results in array-CGH. Pathological results were found in 27.5% of the patients. Factors associated with pathological results in array-CGH were a family history of GDD/ID (OR = 12.1), congenital malformations (OR = 5.33), having more than 3 facial dysmorphic features (OR = 20.9), and hypotonia (OR = 3.25). Our findings are consistent with those reported by other published series. We therefore conclude that the probability of having pathological results in array-CGH increases with the presence of any of the features mentioned above in patients with ID/GDD. Copyright © 2016 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

  20. Copy Number Variation Analysis by Array Analysis of Single Cells Following Whole Genome Amplification.

    Science.gov (United States)

    Dimitriadou, Eftychia; Zamani Esteki, Masoud; Vermeesch, Joris Robert

    2015-01-01

    Whole genome amplification is required to ensure the availability of sufficient material for copy number variation analysis of a genome deriving from an individual cell. Here, we describe the protocols we use for copy number variation analysis of non-fixed single cells by array-based approaches following single-cell isolation and whole genome amplification. We are focusing on two alternative protocols, an isothermal and a PCR-based whole genome amplification method, followed by either comparative genome hybridization (aCGH) or SNP array analysis, respectively.

  1. Analysis of Network Parameters Influencing Performance of Hybrid Multimedia Networks

    Directory of Open Access Journals (Sweden)

    Dominik Kovac

    2013-10-01

    Full Text Available Multimedia networks is an emerging subject that currently attracts the attention of research and industrial communities. This environment provides new entertainment services and business opportunities merged with all well-known network services like VoIP calls or file transfers. Such a heterogeneous system has to be able satisfy all network and end-user requirements which are increasing constantly. Therefore the simulation tools enabling deep analysis in order to find the key performance indicators and factors which influence the overall quality for specific network service the most are highly needed. This paper provides a study on the network parameters like communication technology, routing protocol, QoS mechanism, etc. and their effect on the performance of hybrid multimedia network. The analysis was performed in OPNET Modeler environment and the most interesting results are discussed at the end of this paper

  2. Performance Analysis of Hybrid Electric Vehicle over Different Driving Cycles

    Science.gov (United States)

    Panday, Aishwarya; Bansal, Hari Om

    2017-02-01

    Article aims to find the nature and response of a hybrid vehicle on various standard driving cycles. Road profile parameters play an important role in determining the fuel efficiency. Typical parameters of road profile can be reduced to a useful smaller set using principal component analysis and independent component analysis. Resultant data set obtained after size reduction may result in more appropriate and important parameter cluster. With reduced parameter set fuel economies over various driving cycles, are ranked using TOPSIS and VIKOR multi-criteria decision making methods. The ranking trend is then compared with the fuel economies achieved after driving the vehicle over respective roads. Control strategy responsible for power split is optimized using genetic algorithm. 1RC battery model and modified SOC estimation method are considered for the simulation and improved results compared with the default are obtained.

  3. BIOMETRIC ANALYSIS OF THE ARTIFICIAL HYBRIDIZATION BETWEEN Pangasius djambal BLEEKER, 1846 AND Pangasianodon hypophthalmus SAUVAGE, 1878

    Directory of Open Access Journals (Sweden)

    Rudhy Gustiano

    2016-10-01

    Full Text Available It is really important, since the possible use of these pangasiid hybrids in aquaculture faces the problem of potential impact on wild population. Therefore, it is urgently needed to provide quick identification tools in the field. This study investigated morphological characters of Pangasius djambal and Pangasianodon hypophthalmus and their hybrids. A detailed morphological analysis using 32 morphometric measurements and five meristic counts was done on the hybridization of P. djambal and P. hypophthalmus. Morphometric analysis and meristic counts showed that the reciprocal hybrids have intermediate characters except for gill raker number in which lower than that of parental species. In general, the hybrids have tendency to be like P. hypophthalmus rather than P. djambal. The only typical character of P. djambal appeared on hybrids is teeth shape, both vomerine and palatine. It is clearly defined that the true hybrids have seven pelvic fin rays.

  4. Streptococcus thermophilus core genome: comparative genome hybridization study of 47 strains.

    Science.gov (United States)

    Rasmussen, Thomas Bovbjerg; Danielsen, Morten; Valina, Ondrej; Garrigues, Christel; Johansen, Eric; Pedersen, Martin Bastian

    2008-08-01

    A DNA microarray platform based on 2,200 genes from publicly available sequences was designed for Streptococcus thermophilus. We determined how single-nucleotide polymorphisms in the 65- to 75-mer oligonucleotide probe sequences affect the hybridization signals. The microarrays were then used for comparative genome hybridization (CGH) of 47 dairy S. thermophilus strains. An analysis of the exopolysaccharide genes in each strain confirmed previous findings that this class of genes is indeed highly variable. A phylogenetic tree based on the CGH data showed similar distances for most strains, indicating frequent recombination or gene transfer within S. thermophilus. By comparing genome sizes estimated from the microarrays and pulsed-field gel electrophoresis, the amount of unknown DNA in each strain was estimated. A core genome comprised of 1,271 genes detected in all 47 strains was identified. Likewise, a set of noncore genes detected in only some strains was identified. The concept of an industrial core genome is proposed. This is comprised of the genes in the core genome plus genes that are necessary in an applied industrial context.

  5. Identification of cryptic microaberrations in osteosarcoma by high-definition oligonucleotide array comparative genomic hybridization.

    Science.gov (United States)

    Selvarajah, Shamini; Yoshimoto, Maisa; Maire, Georges; Paderova, Jana; Bayani, Jane; Squire, Jeremy A; Zielenska, Maria

    2007-11-01

    Osteosarcoma (OS) is an aggressive bone tumor characterized by complex abnormal karyotypes and a high level of genomic instability. Using high-resolution array comparative genomic hybridization (aCGH), a novel class of localized copy number variations called microaberrations has been detected. These genomic anomalies typically involve DNA imbalances affecting 700 kb to 1 Mb DNA, and are often associated with some type of genetic syndromes. Because the origin of instability in OS is poorly understood, we used aCGH to determine whether microaberrations were a characteristic of four OS cell lines: U-2 OS, HOS, MG-63, and SAOS-2. TP53 is mutated in SAOS-2, a line in which 17 microaberrations were found. In contrast, U-2 OS, which has a wild-type TP53, had only six such anomalies, the lowest incidence. A 500-kb microaberration within a region of gain at 5p15.33 in SAOS-2 was confirmed by fluorescence in situ hybridization. Significantly, this genomic location is close to the TERT gene, a region of gain in all four cell lines. To our knowledge, this is the first systematic analysis of the incidence of microaberrations in OS. The high levels of these anomalies detected suggest that the instability processes in OS that lead to a highly abnormal karyotypes may also be associated with acquisition of genomic microaberrations.

  6. Fatigue Life Analysis of Tapered Hybrid Composite Flexbeams

    Science.gov (United States)

    Murri, Gretchen B.; Schaff, Jeffery R.; Dobyns, Alan L.

    2002-01-01

    Nonlinear-tapered flexbeam laminates from a full-size composite helicopter rotor hub flexbeam were tested under combined constant axial tension and cyclic bending loads. The two different graphite/glass hybrid configurations tested under cyclic loading failed by delamination in the tapered region. A 2-D finite element model was developed which closely approximated the flexbeam geometry, boundary conditions, and loading. The analysis results from two geometrically nonlinear finite element codes, ANSYS and ABAQUS, are presented and compared. Strain energy release rates (G) obtained from the above codes using the virtual crack closure technique (VCCT) at a resin crack location in the flexbeams are presented for both hybrid material types. These results compare well with each other and suggest that the initial delamination growth from the resin crack toward the thick region of the flexbeam is strongly mode II. The peak calculated G values were used with material characterization data to calculate fatigue life curves and compared with test data. A curve relating maximum surface strain to number of loading cycles at delamination onset compared reasonably well with the test results.

  7. Regulatory pathway analysis by high-throughput in situ hybridization.

    Directory of Open Access Journals (Sweden)

    Axel Visel

    2007-10-01

    Full Text Available Automated in situ hybridization enables the construction of comprehensive atlases of gene expression patterns in mammals. Such atlases can become Web-searchable digital expression maps of individual genes and thus offer an entryway to elucidate genetic interactions and signaling pathways. Towards this end, an atlas housing approximately 1,000 spatial gene expression patterns of the midgestation mouse embryo was generated. Patterns were textually annotated using a controlled vocabulary comprising >90 anatomical features. Hierarchical clustering of annotations was carried out using distance scores calculated from the similarity between pairs of patterns across all anatomical structures. This process ordered hundreds of complex expression patterns into a matrix that reflects the embryonic architecture and the relatedness of patterns of expression. Clustering yielded 12 distinct groups of expression patterns. Because of the similarity of expression patterns within a group, members of each group may be components of regulatory cascades. We focused on the group containing Pax6, an evolutionary conserved transcriptional master mediator of development. Seventeen of the 82 genes in this group showed a change of expression in the developing neocortex of Pax6-deficient embryos. Electromobility shift assays were used to test for the presence of Pax6-paired domain binding sites. This led to the identification of 12 genes not previously known as potential targets of Pax6 regulation. These findings suggest that cluster analysis of annotated gene expression patterns obtained by automated in situ hybridization is a novel approach for identifying components of signaling cascades.

  8. Comparative genomic hybridization analysis of genetic aberrations associated with development of esophageal squamous cell carcinoma in Henan, China

    Institute of Scientific and Technical Information of China (English)

    Yan-Ru Qin; Li-Dong Wang; Zong-Min Fan; Dora Kwong; Xin-Yuan Guan

    2008-01-01

    AIM: To characterize cytogenetic alterations in esophageal squamous cell carcinoma (ESCC) and its metastasis.METHODS: A total of 37 cases of primary ESCC and 15 pairs of primary ESCC tumors and their matched metastatic lymph nodes cases were enrolled from Linzhou, the high incidence area for ESCC in Henan, northern China. The comparative genomic hybridization (CGH) was applied to determine the chromosomal aberrations on the DNA extracted from the frozen ESCC and metastatic lymph node samples from these patients.RESULTS: CGH showed chromosomal aberrations in all the cases. In 37 cases of primary ESCC, chromosomal profile of DNA copy number was characterized by frequently detected gains at 8q (29/37, 78%), 3q (24/37, 65%), 5p (19/37, 51%); and frequently detected losses at 3p (21/37, 57%), 8p and 9q (14/37, 38%). In 15 pairs of primary ESCC tumors and their matched metastatic lymph node cases, the majority of the chromosomal aberrations in both primary tumor and metastatic lymph node lesions were consistent with the primary ESCC cases, but new candidate regions of interest were also detected. The most significant finding is the gains of chromosome 6p with a minimum high-level amplification region at 6pl2-6ql2 in 7 metastatic lymph nodes but only in 2 corresponding primary tumors (P = 0.05) and 20p with a minimum high-level amplification region at 20pl2 in 11 metastatic lymph nodes but only in 5 corresponding primary tumors (P < 0.05). Another interesting finding is the loss of chromosome 10p and 10q in 8 and 7 metastatic lymph nodes but only in 2 corresponding primary tumors (P < 0.05).CONCLUSION: Using the CGH technique to detect chromosomal aberrations in both the primary tumor and its metastatic lymph nodes of ESCC, gains of 8q, 3q and 5p and loss of 3p, 8p, 9q and 13q were specifically implicated in ESCC in Linzhou population. Gains of 6p and 20p and loss of 10pq may contribute to the lymph node metastasis of ESCC. These findings suggest that the gains and losses

  9. Genome-wide detection of copy number variations among diverse horse breeds by array CGH.

    Science.gov (United States)

    Wang, Wei; Wang, Shenyuan; Hou, Chenglin; Xing, Yanping; Cao, Junwei; Wu, Kaifeng; Liu, Chunxia; Zhang, Dong; Zhang, Li; Zhang, Yanru; Zhou, Huanmin

    2014-01-01

    Recent studies have found that copy number variations (CNVs) are widespread in human and animal genomes. CNVs are a significant source of genetic variation, and have been shown to be associated with phenotypic diversity. However, the effect of CNVs on genetic variation in horses is not well understood. In the present study, CNVs in 6 different breeds of mare horses, Mongolia horse, Abaga horse, Hequ horse and Kazakh horse (all plateau breeds) and Debao pony and Thoroughbred, were determined using aCGH. In total, seven hundred CNVs were identified ranging in size from 6.1 Kb to 0.57 Mb across all autosomes, with an average size of 43.08 Kb and a median size of 15.11 Kb. By merging overlapping CNVs, we found a total of three hundred and fifty-three CNV regions (CNVRs). The length of the CNVRs ranged from 6.1 Kb to 1.45 Mb with average and median sizes of 38.49 Kb and 13.1 Kb. Collectively, 13.59 Mb of copy number variation was identified among the horses investigated and accounted for approximately 0.61% of the horse genome sequence. Five hundred and eighteen annotated genes were affected by CNVs, which corresponded to about 2.26% of all horse genes. Through the gene ontology (GO), genetic pathway analysis and comparison of CNV genes among different breeds, we found evidence that CNVs involving 7 genes may be related to the adaptation to severe environment of these plateau horses. This study is the first report of copy number variations in Chinese horses, which indicates that CNVs are ubiquitous in the horse genome and influence many biological processes of the horse. These results will be helpful not only in mapping the horse whole-genome CNVs, but also to further research for the adaption to the high altitude severe environment for plateau horses.

  10. Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds.

    Directory of Open Access Journals (Sweden)

    Jiying Wang

    Full Text Available Copy number variations (CNVs are important forms of genomic variation, and have attracted extensive attentions in humans as well as domestic animals. In the study, using a custom-designed 2.1 M array comparative genomic hybridization (aCGH, genome-wide CNVs were identified among 12 individuals from diverse pig breeds, including one Asian wild population, six Chinese indigenous breeds and two modern commercial breeds (Yorkshire and Landrace, with one individual of the other modern commercial breed, Duroc, as the reference. A total of 1,344 CNV regions (CNVRs were identified, covering 47.79 Mb (∼1.70% of the pig genome. The length of these CNVRs ranged from 3.37 Kb to 1,319.0 Kb with a mean of 35.56 Kb and a median of 11.11 Kb. Compared with similar studies reported, most of the CNVRs (74.18% were firstly identified in present study. In order to confirm these CNVRs, 21 CNVRs were randomly chosen to be validated by quantitative real time PCR (qPCR and a high rate (85.71% of confirmation was obtained. Functional annotation of CNVRs suggested that the identified CNVRs have important function, and may play an important role in phenotypic and production traits difference among various breeds. Our results are essential complementary to the CNV map in the pig genome, which will provide abundant genetic markers to investigate association studies between various phenotypes and CNVs in pigs.

  11. Array-CGH and clinical characterization in a patient with subtelomeric 6p deletion without ocular dysgenesis.

    Science.gov (United States)

    Piccione, Maria; Antona, R; Salzano, E; Cavani, S; Malacarne, M; Morreale Bubella, R; Pierluigi, M; Viaggi, C D; Corsello, Giovanni

    2012-01-01

    Subtelomeric terminal 6p deletion has been recognized as a clinically identifiable syndrome including facial dysmorphism, malformation of the anterior eye chamber, hearing loss, heart defects, and developmental delay. Genotype-phenotype correlations of previously published patients have strongly suggested anterior eye segment anomalies as one of the major malformations of the syndrome if the critical 6p25 region contains the FOXC 1 gene. In addition, the presence in this region of one or more genes involved in hearing loss has been hypothesized. We report a patient with a 47,XYY karyotype and submicroscopic terminal 6p deletion. Further characterization of the deletion with array comparative genome hybridization also revealed a cryptic microduplication on chromosome 19. The patient showed dysmorphic features, neuromotor retardation, and profound language impairment, in absence of hearing loss and structural eye anomalies. As far as we know this is the first reported terminal 6p25.1 deletion case without eye dysgenesis precisely characterized by array-CGH. Our result suggests that the genes in this region may not be obvious candidates for hearing loss and demonstrate the need for further elucidation of the function of the genes involved in eye developmental processes.

  12. Screening of 50 cypriot patients with autism spectrum disorders or autistic features using 400K custom array-CGH.

    Science.gov (United States)

    Kousoulidou, Ludmila; Moutafi, Maria; Nicolaides, Paola; Hadjiloizou, Stavros; Christofi, Christos; Paradesiotou, Anna; Anastasiadou, Violetta; Sismani, Carolina; Patsalis, Philippos C

    2013-01-01

    Autism spectrum disorders (ASDs) comprise a distinct entity of neurodevelopmental disorders with a strong genetic component. Despite the identification of several candidate genes and causative genomic copy number variations (CNVs), the majority of ASD cases still remain unresolved. We have applied microarray-based comparative genomic hybridization (array-CGH) using Agilent 400K custom array in the first Cyprus population screening for identification of ASD-associated CNVs. A cohort of 50 ASD patients (G1), their parents (G2), 50 ethnically matched normal controls (G3), and 80 normal individuals having children with various developmental and neurological conditions (G4) were tested. As a result, 14 patients were found to carry 20 potentially causative aberrations, two of which were de novo. Comparison of the four population groups revealed an increased rate of rare disease-associated variants in normal parents of children with autism. The above data provided additional evidence, supporting the complexity of ASD aetiology in comparison to other developmental disorders involving cognitive impairment. Furthermore, we have demonstrated the rationale of a more targeted approach combining accurate clinical description with high-resolution population-oriented genomic screening for defining the role of CNVs in autism and identifying meaningful associations on the molecular level.

  13. Characteristics of Highly Polymorphic Segmental Copy-Number Variations Observed in Japanese by BAC-Array-CGH

    Directory of Open Access Journals (Sweden)

    Norio Takahashi

    2011-01-01

    Full Text Available Segmental copy-number variations (CNVs may contribute to genetic variation in humans. Reports of the existence and characteristics of CNVs in a large Japanese cohort are quite limited. We report the data from a large Japanese population. We conducted population screening for 213 unrelated Japanese individuals using comparative genomic hybridization based on a bacterial artificial chromosome microarray (BAC-aCGH. We summarize the data by focusing on highly polymorphic CNVs in ≥5.0% of the individual, since they may be informative for demonstrating the relationships between genotypes and their phenotypes. We found a total of 680 CNVs at 16 different BAC-regions in the genome. The majority of the polymorphic CNVs presented on BAC-clones that overlapped with regions of segmental duplication, and the majority of the polymorphic CNVs observed in this population had been previously reported in other publications. Some of the CNVs contained genes which might be related to phenotypic heterogeneity among individuals.

  14. Copy-Number Variations Observed in a Japanese Population by BAC Array CGH: Summary of Relatively Rare CNVs

    Directory of Open Access Journals (Sweden)

    Yasunari Satoh

    2012-01-01

    Full Text Available Copy-number variations (CNVs may contribute to genetic variation in humans. Reports regarding existence and characteristics of CNVs in a large apparently healthy Japanese cohort are quite limited. We report the data from a screening of 213 unrelated Japanese individuals using comparative genomic hybridization based on a bacterial artificial chromosome microarray (BAC aCGH. In a previous paper, we summarized the data by focusing on highly polymorphic CNVs (in ≥5.0 % of the individuals. However, rare variations have recently received attention from scientists who espouse a hypothesis called “common disease and rare variants.” Here, we report CNVs identified in fewer than 10 individuals in our study population. We found a total of 126 CNVs at 52 different BAC regions in the genome. The CNVs observed at 27 of the 52 BAC-regions were found in only one unrelated individual. The majority of CNVs found in this study were not identified in the Japanese who were examined in the other studies. Family studies were conducted, and the results demonstrated that the CNVs were inherited from one parent in the families.

  15. Screening of 50 Cypriot Patients with Autism Spectrum Disorders or Autistic Features Using 400K Custom Array-CGH

    Directory of Open Access Journals (Sweden)

    Ludmila Kousoulidou

    2013-01-01

    Full Text Available Autism spectrum disorders (ASDs comprise a distinct entity of neurodevelopmental disorders with a strong genetic component. Despite the identification of several candidate genes and causative genomic copy number variations (CNVs, the majority of ASD cases still remain unresolved. We have applied microarray-based comparative genomic hybridization (array-CGH using Agilent 400K custom array in the first Cyprus population screening for identification of ASD-associated CNVs. A cohort of 50 ASD patients (G1, their parents (G2, 50 ethnically matched normal controls (G3, and 80 normal individuals having children with various developmental and neurological conditions (G4 were tested. As a result, 14 patients were found to carry 20 potentially causative aberrations, two of which were de novo. Comparison of the four population groups revealed an increased rate of rare disease-associated variants in normal parents of children with autism. The above data provided additional evidence, supporting the complexity of ASD aetiology in comparison to other developmental disorders involving cognitive impairment. Furthermore, we have demonstrated the rationale of a more targeted approach combining accurate clinical description with high-resolution population-oriented genomic screening for defining the role of CNVs in autism and identifying meaningful associations on the molecular level.

  16. Design, analysis and modeling of a novel hybrid powertrain system based on hybridized automated manual transmission

    Science.gov (United States)

    Wu, Guang; Dong, Zuomin

    2017-09-01

    Hybrid electric vehicles are widely accepted as a promising short to mid-term technical solution due to noticeably improved efficiency and lower emissions at competitive costs. In recent years, various hybrid powertrain systems were proposed and implemented based on different types of conventional transmission. Power-split system, including Toyota Hybrid System and Ford Hybrid System, are well-known examples. However, their relatively low torque capacity, and the drive of alternative and more advanced designs encouraged other innovative hybrid system designs. In this work, a new type of hybrid powertrain system based hybridized automated manual transmission (HAMT) is proposed. By using the concept of torque gap filler (TGF), this new hybrid powertrain type has the potential to overcome issue of torque gap during gearshift. The HAMT design (patent pending) is described in details, from gear layout and design of gear ratios (EV mode and HEV mode) to torque paths at different gears. As an analytical tool, mutli-body model of vehicle equipped with this HAMT was built to analyze powertrain dynamics at various steady and transient modes. A gearshift was decomposed and analyzed based basic modes. Furthermore, a Simulink-SimDriveline hybrid vehicle model was built for the new transmission, driveline and vehicle modular. Control strategy has also been built to harmonically coordinate different powertrain components to realize TGF function. A vehicle launch simulation test has been completed under 30% of accelerator pedal position to reveal details during gearshift. Simulation results showed that this HAMT can eliminate most torque gap that has been persistent issue of traditional AMT, improving both drivability and performance. This work demonstrated a new type of transmission that features high torque capacity, high efficiency and improved drivability.

  17. Modeling and Analysis of Hybrid Dynamic Systems Using Hybrid Petri Nets

    OpenAIRE

    GHOMRI Latefa; Alla, Hassane

    2008-01-01

    Some extensions of PNs permitting HDS modeling were presented here. The first models to be presented are continuous PNs. This model may be used for modeling either a continuous system or a discrete system. In this case, it is an approximation that is often satisfactory. Hybrid PNs combine in the same formalism a discrete PN and a continuous PN. Two hybrid PN models were considered in this chapter. The first, called the hybrid PN, has a deterministic behavior; this means that we can predict th...

  18. Local analysis of hybrid systems on polyhedral sets with state-dependent switching

    Directory of Open Access Journals (Sweden)

    Leth John

    2014-06-01

    Full Text Available This paper deals with stability analysis of hybrid systems. Various stability concepts related to hybrid systems are introduced. The paper advocates a local analysis. It involves the equivalence relation generated by reset maps of a hybrid system. To establish a tangible method for stability analysis, we introduce the notion of a chart, which locally reduces the complexity of the hybrid system. In a chart, a hybrid system is particularly simple and can be analyzed with the use of methods borrowed from the theory of differential inclusions. Thus, the main contribution of this paper is to show how stability of a hybrid system can be reduced to a specialization of the well established stability theory of differential inclusions. A number of examples illustrate the concepts introduced in the paper.

  19. Performance Analysis of a Hybrid District Heating System

    DEFF Research Database (Denmark)

    Mikulandric, Robert; Krajačić, Goran; Duic, Neven

    2015-01-01

    Hybridisation of district heating systems can contribute to more efficient heat generation through cogeneration power plants or through the share increase of renewable energy sources in total energy consumption while reducing negative aspects of particular energy source utilisation. In this work......, the performance of a hybrid district energy system for a small town in Croatia has been analysed. Mathematical model for process analysis and optimisation algorithm for optimal system configuration has been developed and described. The main goal of the system optimisation is to reduce heat production costs....... Several energy sources for heat production have been considered in 8 different simulation cases. Simulation results show that the heat production costs could be reduced with introduction of different energy systems into an existing district heating system. Renewable energy based district heating systems...

  20. Second Year Analysis of a Hybrid Schedule High School

    Directory of Open Access Journals (Sweden)

    James B. Schreiber

    2001-11-01

    Full Text Available The current study examined two independent sophomore cohorts from a mid-western high school that had implemented a multi-schedule system (i.e., traditional, block, hybrid. The purpose of the study was to examine differences among the schedule types, gender, and GPA group on a state mandated standardized test. Analysis of covariance was used to examine the differences. Results indicate that a significant difference among schedule types was observed for only one cohort and for only one test (mathematics-computation. Results also indicate that schedule type did not significantly interact with gender or GPA group. The authors conclude that for these cohorts the type of schedule does not negatively or positively influence achievement.

  1. Seedling test and genetic analysis of white poplar hybrid clones

    Institute of Scientific and Technical Information of China (English)

    LI Bo; JIANG Xi-bing; ZHANG You-hui; ZHANG Zhi-yi; LI Shan-wen; AN Xin-min

    2008-01-01

    Cross breeding strategies are very efficient for gaining new and superior genotypes. Ninety-eight new white poplar hybrid clones produced from 12 cross combinations within the Section Leuce Duby were studied using genetic analysis and seedling tests. We exploited the wide variation that exists in this population and found that the differences among diameter at breast height (DBH), root collar diameter (RCD) and height (H) were statistically extremely significant. The repeatability of clones of these measured traits ranged from 0.947-0.967, which indicated that these Waits were strongly controlled by genetic factors. Based on multiple comparisons, a total of 25 clones showed better performance in growth than the conlrol cultivar. These 25 clones were from six different cross combinations, which can guarantee a larger genetic background for future new clone promotion projects. This study provides a simple overview on these clones and can guide us to carry out subsequent selection plans.

  2. ANALYSIS OF A TRANSPORT PROCESS USING HYBRID PETRI NETS

    Directory of Open Access Journals (Sweden)

    Elisabeta Mihaela CIORTEA

    2013-05-01

    Full Text Available Purpose of the paper is to analyze the Petri net model, to describe the transport process, part of amanufacturing system and its dynamics.A hibrid Petri net model is built to describe the dinamics of the transport process manufacturingsystem. Mathematical formulation of the dinamycs processes a detailed description. Based on this model, theanalysis of the transport process is designed to be able to execute a production plan and resolve any conflictsthat may arise in the system.In the analysis dinamics known two stages: in the continuous variables are discrete hybrid system in thehibrid discrete variables are used as safety control with very well defined responsibilities.In terms of the chosen model, analyze transport process is designed to help execute a production planand resolve conflicts that may arise in the process, and then the ones in the system

  3. Comparative genomic and in situ hybridization of germ cell tumors of the infantile testis

    NARCIS (Netherlands)

    Mostert, M; Rosenberg, C; Stoop, H; Schuyer, M; Timmer, A; Oosterhuis, W; Looijenga, L

    2000-01-01

    Chromosomal information on germ cell tumors of the infantile testis, ie, teratomas and yolk sac tumors, is limited and controversial. We studied two teratomas and four yolk sac tumors using comparative genomic hybridization (CGH) and in situ hybridization. No chromosomal anomalies were found in the

  4. Application of Microarray-Based Comparative Genomic Hybridization in Prenatal and Postnatal Settings: Three Case Reports

    Directory of Open Access Journals (Sweden)

    Jing Liu

    2011-01-01

    Full Text Available Microarray-based comparative genomic hybridization (array CGH is a newly emerged molecular cytogenetic technique for rapid evaluation of the entire genome with sub-megabase resolution. It allows for the comprehensive investigation of thousands and millions of genomic loci at once and therefore enables the efficient detection of DNA copy number variations (a.k.a, cryptic genomic imbalances. The development and the clinical application of array CGH have revolutionized the diagnostic process in patients and has provided a clue to many unidentified or unexplained diseases which are suspected to have a genetic cause. In this paper, we present three clinical cases in both prenatal and postnatal settings. Among all, array CGH played a major discovery role to reveal the cryptic and/or complex nature of chromosome arrangements. By identifying the genetic causes responsible for the clinical observation in patients, array CGH has provided accurate diagnosis and appropriate clinical management in a timely and efficient manner.

  5. Limit Cycle Analysis in a Class of Hybrid Systems

    Directory of Open Access Journals (Sweden)

    Antonio Favela-Contreras

    2016-01-01

    Full Text Available Hybrid systems are those that inherently combine discrete and continuous dynamics. This paper considers the hybrid system model to be an extension of the discrete automata associating a continuous evolution with each discrete state. This model is called the hybrid automaton. In this work, we achieve a mathematical formulation of the steady state and we show a way to obtain the initial conditions region to reach a specific limit cycle for a class of uncoupled and coupled continuous-linear hybrid systems. The continuous-linear term is used in the sense of the system theory and, in this sense, continuous-linear hybrid automata will be defined. Thus, some properties and theorems that govern the hybrid automata dynamic behavior to evaluate a limit cycle existence have been established; this content is explained under a theoretical framework.

  6. Improved Aerodynamic Analysis for Hybrid Wing Body Conceptual Design Optimization

    Science.gov (United States)

    Gern, Frank H.

    2012-01-01

    This paper provides an overview of ongoing efforts to develop, evaluate, and validate different tools for improved aerodynamic modeling and systems analysis of Hybrid Wing Body (HWB) aircraft configurations. Results are being presented for the evaluation of different aerodynamic tools including panel methods, enhanced panel methods with viscous drag prediction, and computational fluid dynamics. Emphasis is placed on proper prediction of aerodynamic loads for structural sizing as well as viscous drag prediction to develop drag polars for HWB conceptual design optimization. Data from transonic wind tunnel tests at the Arnold Engineering Development Center s 16-Foot Transonic Tunnel was used as a reference data set in order to evaluate the accuracy of the aerodynamic tools. Triangularized surface data and Vehicle Sketch Pad (VSP) models of an X-48B 2% scale wind tunnel model were used to generate input and model files for the different analysis tools. In support of ongoing HWB scaling studies within the NASA Environmentally Responsible Aviation (ERA) program, an improved finite element based structural analysis and weight estimation tool for HWB center bodies is currently under development. Aerodynamic results from these analyses are used to provide additional aerodynamic validation data.

  7. 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)

  8. BIOMETRIC ANALYSIS OF THE ARTIFICIAL HYBRIDIZATION BETWEEN Pangasius djambal BLEEKER, 1846 AND Pangasianodon hypophthalmus SAUVAGE, 1878

    OpenAIRE

    Rudhy Gustiano

    2016-01-01

    It is really important, since the possible use of these pangasiid hybrids in aquaculture faces the problem of potential impact on wild population. Therefore, it is urgently needed to provide quick identification tools in the field. This study investigated morphological characters of Pangasius djambal and Pangasianodon hypophthalmus and their hybrids. A detailed morphological analysis using 32 morphometric measurements and five meristic counts was done on the hybridization of P. djambal and P....

  9. Analysis on Dry Matter Production Characteristics of Super Hybrid Rice

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Six middle-season indica hybrid rice combinations,including five super hybrid rice combinations with the high yield about 10.5 t/ha and a check hybrid rice combination Shanyou 63 with a yield potential about 9.5 t/ha,were used as materials to study the dry matter production characteristics.The super hybrid rice showed a high ability in dry matter production and accumulation and its yield enhanced with the increase of dry matter accumulation.The advantage period of dry matter production in the super hybrid rice was mainly at the middle and late growth stages compared with the check.The grain yield had no significant correlation with the dry matter accumulation before the elongation stage while had a significantly positive correlation with the dry matter accumulation from the elongation to maturity stages in super hybrid rice.There were more dry matter in vegetative organs at the heading stage in the super hybrid rice but its contribution to yield (apparent conversion percentage) was averagely 4.3 percent points lower than that in the check.For crop growth rate (CGR),the comparative advantage of super hybrid rice was at the middle and late stages,especially after flowering.Moreover,as the rising of leaf area index (LAI) and leaf area duration (LAD),CGR enhanced.The total LAD and the mean of LAD per day of super hybrid rice was about 14.79% and 10.31% higher than those of the check,respectively.The results indicate that the high yield of super hybrid rice mostly comes from the products of photosynthesis after heading,which is shown by the increased CGR at middle and later stages.It is suggested that LAD character might be used to better explain the advantage in the dry matter production of super hybrid rice than LAI.

  10. Simultaneous thermal analysis and thermodilatometry of hybrid fiber reinforced UHPC

    Science.gov (United States)

    Scheinherrová, Lenka; Fořt, Jan; Pavlík, Zbyšek; Černý, Robert

    2017-07-01

    Development of concrete technology and the availability of variety of materials such as silica fume, mineral microfillers and high-range water-reducing admixtures make possible to produce Ultra-High Performance Concrete (UHPC) with compressive strength higher than 160 MPa. However, UHPC is prone to spall under high temperatures what limits its use for special applications only, such as offshore and marine structures, industrial floors, security barriers etc. The spalling is caused by the thermal stresses due to the temperature gradient during heating, and by the splitting force owing to the release of water vapour. Hybrid fibre reinforcement based on combination of steel and polymer fibres is generally accepted by concrete community as a functional solution preventing spalling. In this way, Ultra-High Performance Fibre Reinforced Concrete (UHPFRC) is produced possessing high mechanical strength, durability and resistance to water and salt ingress. Since UHPFRC find use in construction industry in tunnel linings, precast tunnel segments, and high-rise buildings, its behaviour during the high-temperature exposure and its residual parameters are of the particular importance. On this account, Simultaneous Thermal Analysis (STA) and Thermodilatometry Analysis (TDA) were done in the paper to identify the structural and chemical changes in UHPFRC during its high-temperature load. Based on the experimental results, several physical and chemical processes that studied material underwent at high-temperatures were recognized. The obtained data revealed changes in the composition of the studied material and allowed identification of critical temperatures for material damage.

  11. Analysis of SMA Hybrid Composite Structures using Commercial Codes

    Science.gov (United States)

    Turner, Travis L.; Patel, Hemant D.

    2004-01-01

    A thermomechanical model for shape memory alloy (SMA) actuators and SMA hybrid composite (SMAHC) structures has been recently implemented in the commercial finite element codes MSC.Nastran and ABAQUS. The model may be easily implemented in any code that has the capability for analysis of laminated composite structures with temperature dependent material properties. The model is also relatively easy to use and requires input of only fundamental engineering properties. A brief description of the model is presented, followed by discussion of implementation and usage in the commercial codes. Results are presented from static and dynamic analysis of SMAHC beams of two types; a beam clamped at each end and a cantilevered beam. Nonlinear static (post-buckling) and random response analyses are demonstrated for the first specimen. Static deflection (shape) control is demonstrated for the cantilevered beam. Approaches for modeling SMAHC material systems with embedded SMA in ribbon and small round wire product forms are demonstrated and compared. The results from the commercial codes are compared to those from a research code as validation of the commercial implementations; excellent correlation is achieved in all cases.

  12. Mulibrey nanism: Two novel mutations in a child identified by Array CGH and DNA sequencing.

    Science.gov (United States)

    Mozzillo, Enza; Cozzolino, Carla; Genesio, Rita; Melis, Daniela; Frisso, Giulia; Orrico, Ada; Lombardo, Barbara; Fattorusso, Valentina; Discepolo, Valentina; Della Casa, Roberto; Simonelli, Francesca; Nitsch, Lucio; Salvatore, Francesco; Franzese, Adriana

    2016-08-01

    In childhood, several rare genetic diseases have overlapping symptoms and signs, including those regarding growth alterations, thus the differential diagnosis is sometimes difficult. The proband, aged 3 years, was suspected to have Silver-Russel syndrome because of intrauterine growth retardation, postnatal growth retardation, typical facial dysmorphic features, macrocephaly, body asymmetry, and bilateral fifth finger clinodactyly. Other features were left atrial and ventricular enlargement and patent foramen ovale. Total X-ray skeleton showed hypoplasia of the twelfth rib bilaterally and of the coccyx, slender long bones with thick cortex, and narrow medullary channels. The genetic investigation did not confirm Silver-Russel syndrome. At the age of 5 the patient developed an additional sign: hepatomegaly. Array CGH revealed a 147 kb deletion (involving TRIM 37 and SKA2 genes) on one allele of chromosome 17, inherited from his mother. These results suggested Mulibrey nanism. The clinical features were found to fit this hypothesis. Sequencing of the TRIM 37 gene showed a single base change at a splicing locus, inherited from his father that provoked a truncated protein. The combined use of Array CGH and DNA sequencing confirmed diagnosis of Mulibrey nanism. The large deletion involving the SKA2 gene, along with the increased frequency of malignant tumours in mulibrey patients, suggests closed monitoring for cancer of our patient and his mother. Array CGH should be performed as first tier test in all infants with multiple anomalies. The clinician should reconsider the clinical features when the genetics suggests this. © 2016 Wiley Periodicals, Inc.

  13. X chromosome array-CGH for the identification of novel X-linked mental retardation genes.

    Science.gov (United States)

    Bauters, Marijke; Van Esch, Hilde; Marynen, Peter; Froyen, Guy

    2005-01-01

    Array-CGH technology for the detection of submicroscopic copy number changes in the genome has recently been developed for the identification of novel disease-associated genes. It has been estimated that submicroscopic genomic deletions or duplications will be present in 5-7% of patients with idiopathic mental retardation (MR). Since 30% more males than females are diagnosed with MR, we have developed a full coverage X chromosome array-CGH with a theoretical resolution of 82 kb, for the detection of copy number alterations in patients with suspected X-linked mental retardation (XLMR). First, we have validated the genomic location of X-derived clones through male versus female hybridisations. Next, we validated our array for efficient and reproducible detection of known alterations in XLMR patients. In all cases, we were able to detect the deletions and duplications in males as well as females. Due to the high resolution of our X-array, the boundaries of the genomic aberrations could clearly be identified making genotype-phenotype studies more reliable. Here, we describe the production and validation of a full coverage X-array-CGH, which will allow for fast and easy screening of submicroscopic copy number alterations in XLMR patients with the aim to identify novel MR genes or mechanisms involved in a deranged cognitive development.

  14. Prenatal diagnosis and array comparative genomic hybridization characterization of interstitial deletions of 8q23.3-q24.11 and 8q24.13 associated with Langer-Giedion syndrome, Cornelia de Lange syndrome and haploinsufficiency of TRPS1, RAD21 and EXT1.

    Science.gov (United States)

    Chen, Chih-Ping; Lin, Ming-Huei; Chen, Yi-Yung; Chern, Schu-Rern; Chen, Yen-Ni; Wu, Peih-Shan; Pan, Chen-Wen; Lee, Meng-Shan; Wang, Wayseen

    2015-10-01

    The aim of this research was to present prenatal diagnosis of Langer-Giedion syndrome (LGS/TRPS type II) and Cornelia de Lange syndrome-4 (CDLS4). A 36-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Conventional cytogenetic analysis of amniocentesis revealed an interstitial deletion of chromosome 8q or del(8)(q23.3q24.13). Level II prenatal ultrasound examination revealed craniofacial dysmorphism. The pregnancy was terminated, and a malformed fetus was delivered with characteristic craniofacial dysmorphism of LGS/TRPS type II and CDLS4. Whole-genome array comparative genomic hybridization (aCGH) on the DNA extracted from cultured amniocytes was performed. The analysis by aCGH revealed a result of arr 8q23.3q24.11 (116,087,006-118,969,399)×1, 8q24.13 (123,086,851-124,470,847)×1 (NCBI build 37) with a 2.88-Mb deletion of 8q23.3-q24.11 encompassing six OMIM genes, TRPS1, EIF3H, RAD21, SLC30A8, MED30, and EXT1, and a 1.383-Mb deletion of 8q24.13 encompassing four OMIM genes, ZHX2, DERL1, ZHX1, and ATAD2. In the present case, the conventional cytogenetic analysis of cultured amniocytes revealed del(8)(q23.3q24.13), whereas aCGH analysis of cultured amniocytes showed the deletions of 8q23.3-q24.11 and 8q24.13 with the presence of the segment 8q24.12. Therefore, aCGH provides the advantage of better understanding of the nature of interstitial deletion and genotype-phenotype correlation in this case. Copyright © 2015. Published by Elsevier B.V.

  15. Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins

    Directory of Open Access Journals (Sweden)

    Peris David

    2012-08-01

    Full Text Available Abstract Background Interspecific hybrids between S. cerevisiae × S. kudriavzevii have frequently been detected in wine and beer fermentations. Significant physiological differences among parental and hybrid strains under different stress conditions have been evidenced. In this study, we used comparative genome hybridization analysis to evaluate the genome composition of different S. cerevisiae × S. kudriavzevii natural hybrids isolated from wine and beer fermentations to infer their evolutionary origins and to figure out the potential role of common S. kudriavzevii gene fraction present in these hybrids. Results Comparative genomic hybridization (CGH and ploidy analyses carried out in this study confirmed the presence of individual and differential chromosomal composition patterns for most S. cerevisiae × S. kudriavzevii hybrids from beer and wine. All hybrids share a common set of depleted S. cerevisiae genes, which also are depleted or absent in the wine strains studied so far, and the presence a common set of S. kudriavzevii genes, which may be associated with their capability to grow at low temperatures. Finally, a maximum parsimony analysis of chromosomal rearrangement events, occurred in the hybrid genomes, indicated the presence of two main groups of wine hybrids and different divergent lineages of brewing strains. Conclusion Our data suggest that wine and beer S. cerevisiae × S. kudriavzevii hybrids have been originated by different rare-mating events involving a diploid wine S. cerevisiae and a haploid or diploid European S. kudriavzevii strains. Hybrids maintain several S. kudriavzevii genes involved in cold adaptation as well as those related to S. kudriavzevii mitochondrial functions.

  16. User-interfaces for hybrid systems: Analysis and design through hybrid reachability

    Science.gov (United States)

    Oishi, Meeko Mitsuko Karen

    Hybrid systems combine discrete state dynamics, which model mode switching, with continuous state dynamics, which model the physical processes themselves. Applications of hybrid system theory to automated systems have traditionally assumed that the controller itself is an automaton which runs in parallel with the system under control. We model human interaction with hybrid systems, which involves the user; the automation's discrete mode-logic, and the underlying continuous dynamics of the physical system. Often in safety-critical systems, user-interfaces display a reduced set of information about the entire system, however must still provide adequate information and must not confuse the user. We present (1) a method of designing a discrete event system abstraction of the hybrid system, in order to verify or design user-interfaces for hybrid human-automation systems, and (2) the relationship between user-interfaces and discrete observability properties. Using a hybrid computational tool for reachability, we find the largest region in which the system can always remain---this is the safe region of operation. By implementing a controller which arises from this computation, we mathematically guarantee that this safe region is invariant. Assigning discrete states to the computed invariant regions, we create a discrete event system from this hybrid system with safety restrictions. This abstraction can then be used in existing interface verification and design methods. A user-interface, modeled as a discrete system, must, not only be reduced (extraneous information has been eliminated), but also "immediately observable". We derive conditions for immediate observability, in which the current state can be constructed from the current output and last occurring event. Based on finite state machine state-reduction techniques, we synthesize an output for remote user-interfaces which fulfills this property. Aircraft are prime examples of complex, safety-critical systems. In

  17. Computational analysis on plug-in hybrid electric motorcycle chassis

    Science.gov (United States)

    Teoh, S. J.; Bakar, R. A.; Gan, L. M.

    2013-12-01

    Plug-in hybrid electric motorcycle (PHEM) is an alternative to promote sustainability lower emissions. However, the PHEM overall system packaging is constrained by limited space in a motorcycle chassis. In this paper, a chassis applying the concept of a Chopper is analysed to apply in PHEM. The chassis 3dimensional (3D) modelling is built with CAD software. The PHEM power-train components and drive-train mechanisms are intergraded into the 3D modelling to ensure the chassis provides sufficient space. Besides that, a human dummy model is built into the 3D modelling to ensure the rider?s ergonomics and comfort. The chassis 3D model then undergoes stress-strain simulation. The simulation predicts the stress distribution, displacement and factor of safety (FOS). The data are used to identify the critical point, thus suggesting the chassis design is applicable or need to redesign/ modify to meet the require strength. Critical points mean highest stress which might cause the chassis to fail. This point occurs at the joints at triple tree and bracket rear absorber for a motorcycle chassis. As a conclusion, computational analysis predicts the stress distribution and guideline to develop a safe prototype chassis.

  18. Hybrid pairwise likelihood analysis of animal behavior experiments.

    Science.gov (United States)

    Cattelan, Manuela; Varin, Cristiano

    2013-12-01

    The study of the determinants of fights between animals is an important issue in understanding animal behavior. For this purpose, tournament experiments among a set of animals are often used by zoologists. The results of these tournament experiments are naturally analyzed by paired comparison models. Proper statistical analysis of these models is complicated by the presence of dependence between the outcomes of fights because the same animal is involved in different contests. This paper discusses two different model specifications to account for between-fights dependence. Models are fitted through the hybrid pairwise likelihood method that iterates between optimal estimating equations for the regression parameters and pairwise likelihood inference for the association parameters. This approach requires the specification of means and covariances only. For this reason, the method can be applied also when the computation of the joint distribution is difficult or inconvenient. The proposed methodology is investigated by simulation studies and applied to real data about adult male Cape Dwarf Chameleons. © 2013, The International Biometric Society.

  19. Performance analysis of switching based hybrid FSO/RF transmission

    KAUST Repository

    Usman, Muneer

    2014-09-01

    Hybrid free space optical (FSO)/ radio frequency (RF) systems have emerged as a promising solution for high data rate wireless back haul.We present and analyze a switching based transmission scheme for hybrid FSO/RF system. Specifically, either FSO or RF link will be active at a certain time instance, with FSO link enjoying a higher priority. Analytical expressions have been obtained for the outage probability, average bit error rate and ergodic capacity for the resulting system. Numerical examples are presented to compare the performance of the hybrid scheme with FSO only scenario.

  20. Metaphase FISH on a Chip: Miniaturized Microfluidic Device for Fluorescence in situ Hybridization

    DEFF Research Database (Denmark)

    Vedarethinam, Indumathi; Shah, Pranjul Jaykumar; Dimaki, Maria;

    2010-01-01

    Fluorescence in situ Hybridization (FISH) is a major cytogenetic technique for clinical genetic diagnosis of both inherited and acquired chromosomal abnormalities. Although FISH techniques have evolved and are often used together with other cytogenetic methods like CGH, PRINS and PNA-FISH, the pr......Fluorescence in situ Hybridization (FISH) is a major cytogenetic technique for clinical genetic diagnosis of both inherited and acquired chromosomal abnormalities. Although FISH techniques have evolved and are often used together with other cytogenetic methods like CGH, PRINS and PNA...

  1. Genetic analysis of agro-morphological traits in promising hybrids of sunflower (Helianthus annuus L.

    Directory of Open Access Journals (Sweden)

    Maryam GOLABADI

    2015-11-01

    Full Text Available The main objective underlying sunflower breeding programs is to develop high-yielding productive F1 hybrid cultivars. This study was conducted to investigate the genetic control of some agro-morphological traits of new sunflower F1 hybrids. For this purpose, fourteen inbred lines of sunflower were crossed with three male sterile inbred lines. Their hybrids (14 hybrids were then evaluated against three control cultivars. The data thus obtained were analyzed using the nested model (North Carolina Design І as a completely randomized block design (CRBD with four replications. Analysis of variance showed that the hybrids were significantly different in all the traits studied, except for head and stem diameters. From among the hybrids evaluated, Cms19 × Rn1-81 was found to have the highest seed yield and oil content. Cluster analysis classified the hybrids into four different groups. Genetic analysis showed that days to maturity, seed weight, and oil content (% were under the additive gene action. Breeding strategies based on selection could be suggested for the improvement of these traits. Head angle, head diameter, seed yield, and oil yield were under the dominance gene action; breeding based on hybridization methods is, therefore, proposed for these traits. Finally, both additive and dominance gene actions were observed to play important roles in the genetic control of plant height and stem diameter.

  2. Comparative genomic in situ hybridization analysis on the ...

    African Journals Online (AJOL)

    AJL

    2012-04-10

    Apr 10, 2012 ... different parents/ancestors/genomes in hybrid plants to be distinguished ... sequences in common between the two species. Therefore, cGISH ... genomic organization and genome evolution in plants. (Zoller et al., 2001).

  3. Synchronizability Analysis of Harmonious Unification Hybrid Preferential Model

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The harmonious unification hybrid preferential model uses the dr ratio to adjust the proportion of deterministic preferential attachment and random preferential attachment, enriched the only deterministic preferential network model,

  4. SIMS: a hybrid method for rapid conformational analysis.

    Directory of Open Access Journals (Sweden)

    Bryant Gipson

    Full Text Available Proteins are at the root of many biological functions, often performing complex tasks as the result of large changes in their structure. Describing the exact details of these conformational changes, however, remains a central challenge for computational biology due the enormous computational requirements of the problem. This has engendered the development of a rich variety of useful methods designed to answer specific questions at different levels of spatial, temporal, and energetic resolution. These methods fall largely into two classes: physically accurate, but computationally demanding methods and fast, approximate methods. We introduce here a new hybrid modeling tool, the Structured Intuitive Move Selector (sims, designed to bridge the divide between these two classes, while allowing the benefits of both to be seamlessly integrated into a single framework. This is achieved by applying a modern motion planning algorithm, borrowed from the field of robotics, in tandem with a well-established protein modeling library. sims can combine precise energy calculations with approximate or specialized conformational sampling routines to produce rapid, yet accurate, analysis of the large-scale conformational variability of protein systems. Several key advancements are shown, including the abstract use of generically defined moves (conformational sampling methods and an expansive probabilistic conformational exploration. We present three example problems that sims is applied to and demonstrate a rapid solution for each. These include the automatic determination of "active" residues for the hinge-based system Cyanovirin-N, exploring conformational changes involving long-range coordinated motion between non-sequential residues in Ribose-Binding Protein, and the rapid discovery of a transient conformational state of Maltose-Binding Protein, previously only determined by Molecular Dynamics. For all cases we provide energetic validations using well

  5. Design and Analysis of the AlNiCo Hybrid Magnet in EMS Maglev Vehicles

    Directory of Open Access Journals (Sweden)

    Lv Chao

    2017-01-01

    Full Text Available In order to solve the problem of hybrid electromagnet lock orbit, we design a new type of AlNiCo-NdFeB hybrid levitation electromagnet. The theoretical analysis has be carried on and mathematical model is established for AlNiCo-NdFeB hybrid levitation electromagnet. Through two dimensional simulation, the electromagnetic characteristics of the suspended electromagnet are analyzed in the 3 typical operating conditions , which are in heavy load at gap 8mm, in full load at gap 16mm and in no-load at gap 3mm. And it’s compared with the traditional electromagnetic magnet and NdFeB hybrid electromagnet. Calculation and analysis show that the new hybrid levitation electromagnet can effectively solve the problems of the electromagnet lock orbit, at the same time, have a good dynamic performance and suspension regulation performance.

  6. Site-specific analysis of hybrid geothermal/fossil power plants

    Energy Technology Data Exchange (ETDEWEB)

    1977-06-01

    A preliminary economic analysis of a hybrid geothermal/coal power plant has been completed for four geothermal Resource areas: Roosevelt Hot Springs, Coso Hot Springs, East Mesa and Long Valley. A hybrid plant would be economically viable at Roosevelt Hot Springs and somewhat less so at Coso Hot Springs. East Mesa and Long Valley show no economic promise. A well-designed hybrid plant could use geothermal energy for boiler feedwater heating, auxiliary power, auxiliary heating, and cooling water. Construction and operation of a hybrid plant at either Roosevelt Hot Springs or Coso Hot Springs is recommended. Brown University provided the theoretical basis for the hybrid study. A modified version of the Lawrence Berkeley Livermore GEOTHM Program is the major analytical tool used in the analysis. The Intermountain Power Project is the reference all coal-fired plant. Costing methods followed recommendations issued by the Energy research and Development Administration.

  7. Evaluation of new NS maize hybrids using biplot analysis

    Directory of Open Access Journals (Sweden)

    Stojaković Milisav

    2012-01-01

    Full Text Available The study analyzed two-year results of a testing of 20 new maize hybrids from FAO MG 600 as compared to a standard. Data on the hybrids NS6683, NS6686, NS281633, and NS396432 are discussed in the paper in greater detail. In order to study grain yield, grain moisture, root and stalk lodging, and resistance to pests and diseases, field trials using a RCB design with four replicates were conducted in six locations in 2009 and five locations in 2010. The results were presented in the form of GGE biplots in order to rank hybrids relative to the standard while taking into account the genotype x environment interaction and to identify the highest-yielding genotypes in different environments. It was determined that the new NS hybrids had higher grain yield than the standard by 0.883 to 1.720 tha-1, lower grain moisture by 0.85 to 2.54%, better tolerance to root and stalk lodging, and pest and disease resistance on a par to the standard. The study identified so-called ideal locations for particular hybrids, which may be of use when determining which areas the hybrids are best suited for.

  8. Genetic molecular analysis of Coffea arabica (Rubiaceae hybrids using SRAP markers

    Directory of Open Access Journals (Sweden)

    Manoj Kumar Mishra

    2011-06-01

    Full Text Available In Coffea arabica (arabica coffee, the phenotypic as well as genetic variability has been found low because of the narrow genetic basis and self fertile nature of the species. Because of high similarity in phenotypic appearance among the majority of arabica collections, selection of parental lines for inter-varietals hybridization and identification of resultant hybrids at an early stage of plant growth is difficult. DNA markers are known to be reliable in identifying closely related cultivars and hybrids. Sequence Related Amplified Polymorphism (SRAP is a new molecular marker technology developed based on PCR. In this paper, sixty arabica-hybrid progenies belonging to six crosses were analyzed using 31 highly polymorphic SRAP markers. The analysis revealed seven types of SRAP marker profiles which are useful in discriminating the parents and hybrids. The number of bands amplified per primer pair ranges from 6.13 to 8.58 with average number of seven bands. Among six hybrid combinations, percentage of bands shared between hybrids and their parents ranged from 66.29% to 85.71% with polymorphic bands varied from 27.64% to 60.0%. Percentage of hybrid specific fragments obtained in various hybrid combinations ranged from 0.71% to 10.86% and ascribed to the consequence of meiotic recombination. Based on the similarity index calculation, it was observed that F1 hybrids share maximum number of bands with the female parent compared to male parent. The results obtained in the present study revealed the effectiveness of SRAP technique in cultivar identification and hybrid analysis in this coffee species. Rev. Biol. Trop. 59 (2: 607-617. Epub 2011 June 01.

  9. Comparative Genomic Hybridization Selection of Blastocysts for Repeated Implantation Failure Treatment: A Pilot Study

    Science.gov (United States)

    Greco, Ermanno; Bono, Sara; Ruberti, Alessandra; Lobascio, Anna Maria; Greco, Pierfrancesco; Biricik, Anil; Spizzichino, Letizia; Greco, Alessia; Tesarik, Jan; Minasi, Maria Giulia; Fiorentino, Francesco

    2014-01-01

    The aim of this study is to determine if the use of preimplantation genetic screening (PGS) by array comparative genomic hybridization (array CGH) and transfer of a single euploid blastocyst in patients with repeated implantation failure (RIF) can improve clinical results. Three patient groups are compared: 43 couples with RIF for whom embryos were selected by array CGH (group RIF-PGS), 33 couples with the same history for whom array CGH was not performed (group RIF NO PGS), and 45 good prognosis infertile couples with array CGH selected embryos (group NO RIF PGS). A single euploid blastocyst was transferred in groups RIF-PGS and NO RIF PGS. Array CGH was not performed in group RIF NO PGS in which 1-2 blastocysts were transferred. One monoembryonic sac with heartbeat was found in 28 patients of group RIF PGS and 31 patients of group NO RIF PGS showing similar clinical pregnancy and implantation rates (68.3% and 70.5%, resp.). In contrast, an embryonic sac with heartbeat was only detected in 7 (21.2%) patients of group RIF NO PGS. In conclusion, PGS by array CGH with single euploid blastocyst transfer appears to be a successful strategy for patients with multiple failed IVF attempts. PMID:24779011

  10. Hybrid-Electric and All-Electric Rotorcraft Analysis and Tool Development Project

    Data.gov (United States)

    National Aeronautics and Space Administration — During this Phase I effort ESAero will draw upon its knowledge of hybrid-electric propulsion system design and analysis for fixed wing aircraft to investigate the...

  11. Tiling array-CGH for the assessment of genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs

    Directory of Open Access Journals (Sweden)

    Ringnér Markus

    2008-07-01

    Full Text Available Abstract Background Today, no objective criteria exist to differentiate between individual primary tumors and intra- or intermammary dissemination respectively, in patients diagnosed with two or more synchronous breast cancers. To elucidate whether these tumors most likely arise through clonal expansion, or whether they represent individual primary tumors is of tumor biological interest and may have clinical implications. In this respect, high resolution genomic profiling may provide a more reliable approach than conventional histopathological and tumor biological factors. Methods 32 K tiling microarray-based comparative genomic hybridization (aCGH was used to explore the genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs, and was compared with histopathological and tumor biological parameters. Results Based on global copy number profiles and unsupervised hierarchical clustering, five of ten (p = 1.9 × 10-5 unilateral tumor pairs displayed similar genomic profiles within the pair, while only one of eight bilateral tumor pairs (p = 0.29 displayed pair-wise genomic similarities. DNA index, histological type and presence of vessel invasion correlated with the genomic analyses. Conclusion Synchronous unilateral tumor pairs are often genomically similar, while synchronous bilateral tumors most often represent individual primary tumors. However, two independent unilateral primary tumors can develop synchronously and contralateral tumor spread can occur. The presence of an intraductal component is not informative when establishing the independence of two tumors, while vessel invasion, the presence of which was found in clustering tumor pairs but not in tumor pairs that did not cluster together, supports the clustering outcome. Our data suggest that genomically similar unilateral tumor pairs may represent a more aggressive disease that requires the addition of more severe treatment modalities, and

  12. BAC array CGH in patients with Velocardiofacial syndrome-like features reveals genomic aberrations on chromosome region 1q21.1

    Directory of Open Access Journals (Sweden)

    Estivill Xavier

    2009-12-01

    Full Text Available Abstract Background Microdeletion of the chromosome 22q11.2 region is the most common genetic aberration among patients with velocardiofacial syndrome (VCFS but a subset of subjects do not show alterations of this chromosome region. Methods We analyzed 18 patients with VCFS-like features by comparative genomic hybridisation (aCGH array and performed a face-to-face slide hybridization with two different arrays: a whole genome and a chromosome 22-specific BAC array. Putative rearrangements were confirmed by FISH and MLPA assays. Results One patient carried a combination of rearrangements on 1q21.1, consisting in a microduplication of 212 kb and a close microdeletion of 1.15 Mb, previously reported in patients with variable phenotypes, including mental retardation, congenital heart defects (CHD and schizophrenia. While 326 control samples were negative for both 1q21.1 rearrangements, one of 73 patients carried the same 212-kb microduplication, reciprocal to TAR microdeletion syndrome. Also, we detected four copy number variants (CNVs inherited from one parent (a 744-kb duplication on 10q11.22; a 160 kb duplication and deletion on 22q11.21 in two cases; and a gain of 140 kb on 22q13.2, not present in control subjects, raising the potential role of these CNVs in the VCFS-like phenotype. Conclusions Our results confirmed aCGH as a successful strategy in order to characterize additional submicroscopic aberrations in patients with VCF-like features that fail to show alterations in 22q11.2 region. We report a 212-kb microduplication on 1q21.1, detected in two patients, which may contribute to CHD.

  13. A generalized hybrid transfinite element computational approach for nonlinear/linear unified thermal/structural analysis

    Science.gov (United States)

    Tamma, Kumar K.; Railkar, Sudhir B.

    1987-01-01

    The present paper describes the development of a new hybrid computational approach for applicability for nonlinear/linear thermal structural analysis. The proposed transfinite element approach is a hybrid scheme as it combines the modeling versatility of contemporary finite elements in conjunction with transform methods and the classical Bubnov-Galerkin schemes. Applicability of the proposed formulations for nonlinear analysis is also developed. Several test cases are presented to include nonlinear/linear unified thermal-stress and thermal-stress wave propagations. Comparative results validate the fundamental capablities of the proposed hybrid transfinite element methodology.

  14. In situ hybridization analysis of isodicentric X-chromosomes with short arm fusion

    DEFF Research Database (Denmark)

    Koch, J E; Kølvraa, S; Hertz, Jens Michael;

    1990-01-01

    We present here an alternative approach to the study of mosaic cell lines containing dicentric chromosomes. The approach is based on chromosome-specific non-radioactive in situ hybridization with centromere (alpha satellite DNA) probes. The hybridization analysis may be used as an alternative...... it for the analysis of two cases of isodicentric X-chromosomes. The approach is expected to be generally applicable, so that it may be applied to the scoring of other types of chromosomal mosaicism as well....

  15. Parallel Hybrid Gas-Electric Geared Turbofan Engine Conceptual Design and Benefits Analysis

    Science.gov (United States)

    Lents, Charles; Hardin, Larry; Rheaume, Jonathan; Kohlman, Lee

    2016-01-01

    The conceptual design of a parallel gas-electric hybrid propulsion system for a conventional single aisle twin engine tube and wing vehicle has been developed. The study baseline vehicle and engine technology are discussed, followed by results of the hybrid propulsion system sizing and performance analysis. The weights analysis for the electric energy storage & conversion system and thermal management system is described. Finally, the potential system benefits are assessed.

  16. 微阵列比较基因组杂交技术在自然流产遗传学分析中的应用%Application of array-based comparative genomic hybridization technique in genetic analysis of ;patients with spontaneous abortion

    Institute of Scientific and Technical Information of China (English)

    楚艳; 吴东; 侯巧芳; 霍晓东; 高越; 王涛; 王红丹; 杨艳丽; 廖世秀

    2016-01-01

    目的:探讨微阵列比较基因组杂交(array-CGH)技术在自然流产组织染色体分析中的应用,为自然流产的遗传咨询和临床诊治提供指导。方法选取2013年11月至2016年1月在河南省人民医院就诊的自然流产患者382例,收集流产绒毛或胎儿组织,采用array-CGH技术对流产绒毛或胎儿组织的全基因组拷贝数进行检测,并同时行细胞培养和传统G显带染色体核型分析,比较G显带染色体核型分析及array-CGH的结果。结果 array-CGH技术成功获得结果382例,检测成功率为100.0%(382/382),染色体异常检出率为46.6%(178/382);染色体核型分析技术成功获得结果281例,检测成功率为73.6%(281/382),染色体异常检出率为40.2%(113/281);array-CGH均高于染色体核型分析技术。array-CGH检测出的178例染色体异常中,染色体数目异常163例(91.6%,163/178);染色体结构异常15例(8.4%,15/178),其中10例同时出现了染色体微重复和微缺失的流产胚胎中有4例被证实父母一方为染色体平衡易位携带者。染色体核型分析检出的113例染色体异常中,染色体数目异常108例(95.6%,108/113),染色体结构异常5例(4.4%,5/113)。两种方法的结果不一致有3例,其中2例为三倍体、1例为性染色体低比例嵌合,array-CGH均漏检为正常。结论 array-CGH技术用于自然流产胚胎组织的染色体分析成功率高,对标本的取材要求远低于传统染色体核型分析技术,且分辨率高、准确快速,可以作为流产组织遗传学诊断的一线技术。%Objective To investigate the value of array-based comparative genomic hybridization (array-CGH) technique for the detection of chromosomal analysis of miscarried embryo, and to provide genetic counseling for couples with spontaneous abortion. Methods Totally 382 patients who underwent miscarriage were enrolled in this study. All

  17. Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila

    Directory of Open Access Journals (Sweden)

    Kulathinal Rob J

    2010-04-01

    Full Text Available Abstract Background Genome-wide analysis of sequence divergence among species offers profound insights into the evolutionary processes that shape lineages. When full-genome sequencing is not feasible for a broad comparative study, we propose the use of array-based comparative genomic hybridization (aCGH in order to identify orthologous genes with high sequence divergence. Here we discuss experimental design, statistical power, success rate, sources of variation and potential confounding factors. We used a spotted PCR product microarray platform from Drosophila melanogaster to assess sequence divergence on a gene-by-gene basis in three fully sequenced heterologous species (D. sechellia, D. simulans, and D. yakuba. Because complete genome assemblies are available for these species this study presents a powerful test for the use of aCGH as a tool to measure sequence divergence. Results We found a consistent and linear relationship between hybridization ratio and sequence divergence of the sample to the platform species. At higher levels of sequence divergence (D. melanogaster ~84% of features had significantly less hybridization to the array in the heterologous species than the platform species, and thus could be identified as "diverged". At lower levels of divergence (≥ 97% identity, only 13% of genes were identified as diverged. While ~40% of the variation in hybridization ratio can be accounted for by variation in sequence identity of the heterologous sample relative to D. melanogaster, other individual characteristics of the DNA sequences, such as GC content, also contribute to variation in hybridization ratio, as does technical variation. Conclusions Here we demonstrate that aCGH can accurately be used as a proxy to estimate genome-wide divergence, thus providing an efficient way to evaluate how evolutionary processes and genomic architecture can shape species diversity in non-model systems. Given the increased number of species for which

  18. GeoNeoLogical novel and other hybrimedia experiments: or how to use hybrid methods such as Hybrid Discourse Analysis (HDA within a knowledge base

    Directory of Open Access Journals (Sweden)

    Andrade, Pedro

    2016-07-01

    Full Text Available In this essay I will present some results of the project Public Communication of Art, which developed a seminal theory and methodology intended to cope with hybridity and new media literacy in our globalized and inter/transcultural world. Some of the methods used blend vision with touch and are called ‘hybrid methods’ or ‘hybrimethods’. Examples of these are, for instance, a Multitouch Interactive Table, a Multitouch Questionnaire, Trichotomies Game and GeoNeoLogic Novel, this last one being a hybrid novel activated by fusion of vision, touch and GPS coordinates. Another hybrimethod is a sort of discursive analysis, named Hybrid Discourse Analysis (HDA, which uses ‘semantic-logical networks’ organized by concepts and ‘relation-concepts’. HDA is here articulated with Critical Sociology and applied to the analysis of a text on Magic Realism, which is also a hybrid genre within the social field of literature.

  19. Multi-channel Hybrid Access Femtocells: A Stochastic Geometric Analysis

    CERN Document Server

    Zhong, Yi

    2011-01-01

    For two-tier networks consisting of macrocells and femtocells, the channel access mechanism can be configured to be open access, closed access, or hybrid access. Hybrid access arises as a compromise between open and closed access mechanisms, in which a fraction of available spectrum resource is shared to nonsubscribers while the remaining reserved for subscribers. This paper focuses on a hybrid access mechanism for multi-channel femtocells which employ orthogonal spectrum access schemes. Considering a randomized channel assignment strategy, we analyze the performance in the downlink. Using stochastic geometry as technical tools, we derive the distributions of signal-to-interference-plus-noise ratios, and mean achievable rates, of both nonsubscribers and subscribers. The established expressions are amenable to numerical evaluation, and shed key insights into the performance tradeoff between subscribers and nonsubscribers. The analytical results are corroborated by numerical simulations.

  20. Analysis of advanced solar hybrid desiccant cooling systems for buildings

    Energy Technology Data Exchange (ETDEWEB)

    Schlepp, D.; Schultz, K.

    1984-10-01

    This report describes an assessment of the energy savings possible from developing hybrid desiccant/vapor-compression air conditioning systems. Recent advances in dehumidifier design for solar desiccant cooling systems have resulted in a dehumidifier with a low pressure drop and high efficiency in heat and mass transfer. A recent study on hybrid desiccant/vapor compression systems showed a 30%-80% savings in resource energy when compared with the best conventional systems with vapor compression. A system consisting of a dehumidifier with vapor compression subsystems in series was found to be the simplest and best overall performer.

  1. Phenotypic and Genotypic Analysis of Newly Obtained Interspecific Hybrids in the Campanula Genus

    Science.gov (United States)

    Röper, Anna-Catharina; Orabi, Jihad; Lütken, Henrik; Christensen, Brian; Thonning Skou, Anne-Marie; Müller, Renate

    2015-01-01

    Interspecific hybridisation creates new phenotypes within several ornamental plant species including the Campanula genus. We have employed phenotypic and genotypic methods to analyse and evaluate interspecific hybridisation among cultivars of four Campanula species, i.e. C. cochleariifolia, C. isophylla, C. medium and C. formanekiana. Hybrids were analysed using amplified fragment length polymorphism (AFLP), flow cytometry and biometrical measurements. Results of correlation matrices demonstrated heterogeneous phenotypes for the parental species, which confirmed our basic premise for new phenotypes of interspecific hybrids. AFLP assays confirmed the hybridity and identified self-pollinated plants. Limitation of flow cytometry analysis detection was observed while detecting the hybridity status of two closely related parents, e.g. C. cochleariiafolia × C. isophylla. Phenotypic characteristics such as shoot habitus and flower colour were strongly influenced by one of the parental species in most crosses. Rooting analysis revealed that inferior rooting quality occurred more often in interspecific hybrids than in the parental species. Only interspecific hybrid lines of C. formanekiana ‘White’ × C. medium ‘Pink’ showed a high rooting level. Phenotype analyses demonstrated a separation from the interspecific hybrid lines of C. formanekiana ‘White’ × C. medium ‘Pink’ to the other clustered hybrids of C. formanekiana and C. medium. In our study we demonstrated that the use of correlation matrices is a suitable tool for identifying suitable cross material. This study presents a comprehensive overview for analysing newly obtained interspecific hybrids. The chosen methods can be used as guidance for analyses for further interspecific hybrids in Campanula, as well as in other ornamental species. PMID:26352688

  2. De novo complex intra chromosomal rearrangement after ICSI: characterisation by BACs micro array-CGH

    Science.gov (United States)

    Kasakyan, Serdar; Lohmann, Laurence; Aboura, Azeddine; Quimsiyeh, Mazin; Menezo, Yves; Tachdjian, Gerard; Benkhalifa, Moncef

    2008-01-01

    Background In routine Assisted Reproductive Technology (ART) men with severe oligozoospermia or azoospermia should be informed about the risk of de novo congenital or chromosomal abnormalities in ICSI program. Also the benefits of preimplantation or prenatal genetic diagnosis practice need to be explained to the couple. Methods From a routine ICSI attempt, using ejaculated sperm from male with severe oligozoospermia and having normal karyotype, a 30 years old pregnant woman was referred to prenatal diagnosis in the 17th week for bichorionic biamniotic twin gestation. Amniocentesis was performed because of the detection of an increased foetal nuchal translucency for one of the fetus by the sonographic examination during the 12th week of gestation (WG). Chromosome and DNA studies of the fetus were realized on cultured amniocytes Results Conventional, molecular cytogenetic and microarray CGH experiments allowed us to conclude that the fetus had a de novo pericentromeric inversion associated with a duplication of the 9p22.1-p24 chromosomal region, 46,XY,invdup(9)(p22.1p24) [arrCGH 9p22.1p24 (RP11-130C19 → RP11-87O1)x3]. As containing the critical 9p22 region, our case is in coincidence with the general phenotype features of the partial trisomy 9p syndrome with major growth retardation, microcephaly and microretrognathia. Conclusion This de novo complex chromosome rearrangement illustrates the possible risk of chromosome or gene defects in ICSI program and the contribution of array-CGH for mapping rapidly de novo chromosomal imbalance. PMID:19105807

  3. De novo complex intra chromosomal rearrangement after ICSI: characterisation by BACs micro array-CGH.

    Science.gov (United States)

    Kasakyan, Serdar; Lohmann, Laurence; Aboura, Azeddine; Quimsiyeh, Mazin; Menezo, Yves; Tachdjian, Gerard; Benkhalifa, Moncef

    2008-12-23

    In routine Assisted Reproductive Technology (ART) men with severe oligozoospermia or azoospermia should be informed about the risk of de novo congenital or chromosomal abnormalities in ICSI program. Also the benefits of preimplantation or prenatal genetic diagnosis practice need to be explained to the couple. From a routine ICSI attempt, using ejaculated sperm from male with severe oligozoospermia and having normal karyotype, a 30 years old pregnant woman was referred to prenatal diagnosis in the 17th week for bichorionic biamniotic twin gestation. Amniocentesis was performed because of the detection of an increased foetal nuchal translucency for one of the fetus by the sonographic examination during the 12th week of gestation (WG). Chromosome and DNA studies of the fetus were realized on cultured amniocytes Conventional, molecular cytogenetic and microarray CGH experiments allowed us to conclude that the fetus had a de novo pericentromeric inversion associated with a duplication of the 9p22.1-p24 chromosomal region, 46,XY,invdup(9)(p22.1p24) [arrCGH 9p22.1p24 (RP11-130C19 --> RP11-87O1)x3]. As containing the critical 9p22 region, our case is in coincidence with the general phenotype features of the partial trisomy 9p syndrome with major growth retardation, microcephaly and microretrognathia. This de novo complex chromosome rearrangement illustrates the possible risk of chromosome or gene defects in ICSI program and the contribution of array-CGH for mapping rapidly de novo chromosomal imbalance.

  4. De novo complex intra chromosomal rearrangement after ICSI: characterisation by BACs micro array-CGH

    Directory of Open Access Journals (Sweden)

    Quimsiyeh Mazin

    2008-12-01

    Full Text Available Abstract Background In routine Assisted Reproductive Technology (ART men with severe oligozoospermia or azoospermia should be informed about the risk of de novo congenital or chromosomal abnormalities in ICSI program. Also the benefits of preimplantation or prenatal genetic diagnosis practice need to be explained to the couple. Methods From a routine ICSI attempt, using ejaculated sperm from male with severe oligozoospermia and having normal karyotype, a 30 years old pregnant woman was referred to prenatal diagnosis in the 17th week for bichorionic biamniotic twin gestation. Amniocentesis was performed because of the detection of an increased foetal nuchal translucency for one of the fetus by the sonographic examination during the 12th week of gestation (WG. Chromosome and DNA studies of the fetus were realized on cultured amniocytes Results Conventional, molecular cytogenetic and microarray CGH experiments allowed us to conclude that the fetus had a de novo pericentromeric inversion associated with a duplication of the 9p22.1-p24 chromosomal region, 46,XY,invdup(9(p22.1p24 [arrCGH 9p22.1p24 (RP11-130C19 → RP11-87O1x3]. As containing the critical 9p22 region, our case is in coincidence with the general phenotype features of the partial trisomy 9p syndrome with major growth retardation, microcephaly and microretrognathia. Conclusion This de novo complex chromosome rearrangement illustrates the possible risk of chromosome or gene defects in ICSI program and the contribution of array-CGH for mapping rapidly de novo chromosomal imbalance.

  5. Genetic analysis of hybridization and introgression between wild mongoose and brown lemurs

    Directory of Open Access Journals (Sweden)

    Nievergelt Caroline M

    2009-02-01

    Full Text Available Abstract Background Hybrid zones generally represent areas of secondary contact after speciation. The nature of the interaction between genes of individuals in a hybrid zone is of interest in the study of evolutionary processes. In this study, data from nuclear microsatellites and mitochondrial DNA sequences were used to genetically characterize hybridization between wild mongoose lemurs (Eulemur mongoz and brown lemurs (E. fulvus at Anjamena in west Madagascar. Results Two segments of mtDNA have been sequenced and 12 microsatellite loci screened in 162 brown lemurs and mongoose lemurs. Among the mongoose lemur population at Anjamena, we identified two F1 hybrids (one also having the mtDNA haplotype of E. fulvus and six other individuals with putative introgressed alleles in their genotype. Principal component analysis groups both hybrids as intermediate between E. mongoz and E. fulvus and admixture analyses revealed an admixed genotype for both animals. Paternity testing proved one F1 hybrid to be fertile. Of the eight brown lemurs genotyped, all have either putative introgressed microsatellite alleles and/or the mtDNA haplotype of E. mongoz. Conclusion Introgression is bidirectional for the two species, with an indication that it is more frequent in brown lemurs than in mongoose lemurs. We conclude that this hybridization occurs because mongoose lemurs have expanded their range relatively recently. Introgressive hybridization may play an important role in the unique lemur radiation, as has already been shown in other rapidly evolving animals.

  6. Ray analysis of a class of hybrid cylindrical aircraft wings

    OpenAIRE

    Jha, RM; Bokhari, SA; Sudhakan, V; Mahapatra, PR

    1988-01-01

    A new approach to the modelling of aircraft wings, based on the combination of hybrid quadric (parabolic and circular) cylinders, has been presented for electromagnetic applications. Closed-form expressions have been obtained for ray parameters required in the high-frequency mutual coupling computation of antenna pairs located arbitrarily on an aircraft wing.

  7. Design and Analysis of Hybrid CMOS SRAM Sense Amplifier

    Directory of Open Access Journals (Sweden)

    Karishma Bajaj

    2012-03-01

    Full Text Available Sense amplifiers are one of the very important peripheral components of CMOS memories. In a Hybrid Sense amplifier both current and voltage sensing techniques are used which makes it a better selection than a conventional current or voltage sense amplifiers. The hybrid sense amplifier works in three phases-Offset cancellation (200ps, Access phase (500ps and Evaluation phase. The offset cancellation is done simultaneously with word line decoding, so as to speed up the process. The sensing range of the hybrid sense amplifier is improved from 1.18mV to 92mV. Also hybrid sense amplifier consumes very low energy of about 6.84fj. This sense amplifier is analyzed with a column of 512 SRAM cells at 180nm technology node and compared to CMOS conventional voltage sense amplifier. The circuit consumes an average power of 1.57 µW with a negligible offset of 149.3µV.

  8. Sensorless Suitability Analysis of Hybrid PM Machines for Electric Vehicles

    DEFF Research Database (Denmark)

    Matzen, Torben Nørregaard; Rasmussen, Peter Omand

    2009-01-01

    Electrical machines for traction in electric vehicles are an essential component which attract attention with respect to machine design and control as a part of the emerging renewable industry. For the hybrid electric machine to replace the familiar behaviour of the combustion engine torque...

  9. Combined analysis of cervical smears. Cytopathology, image cytometry and in situ hybridization

    DEFF Research Database (Denmark)

    Multhaupt, H; Bruder, E; Elit, L

    1993-01-01

    This study was an attempt to correlate the Bethesda System of Papanicolaou smear classification with DNA content by image analysis and the presence of human papillomavirus (HPV) as determined by in situ hybridization. DNA histograms were classified as normal diploid, diploid proliferative......, polyploid and aneuploid. HPV in situ hybridization was performed with a cocktail of probes specific to HPV types 6, 11, 16 and 18. There was a good correlation between normal cytology and normal DNA histograms. Cytologically normal smears with bacterial or fungal infections showed a high proliferation index....... Four of five cases cytologically suspicious for HPV infection had HPV by in situ hybridization....

  10. APPLICATION OF PENALTY FUNCTION METHOD IN ISOPARAMETRIC HYBRID FINITE ELEMENT ANALYSIS

    Institute of Scientific and Technical Information of China (English)

    CHEN Dao-zheng; JIAO Zhao-ping

    2005-01-01

    By the aid of the penalty function method, the equilibrium restriction conditions were introduced to the isoparametric hybrid finite element analysis, and the concrete application course of the penalty function method in three-dimensional isoparametric hybrid finite element was discussed. The separated penalty parameters method and the optimal hybrid element model with penalty balance were also presented.The penalty balance method can effectively refrain the parasitical stress on the premise of no additional degrees of freedom. The numeric experiment shows that the presented element not only is effective in improving greatly the numeric calculation precision of distorted grids but also has the universality.

  11. Evaluation of genotype x environment interactions in maize hybrids using GGE biplot analysis

    Directory of Open Access Journals (Sweden)

    Fatma Aykut Tonk

    2011-01-01

    Full Text Available Seventeen hybrid maize genotypes were evaluated at four different locations in 2005 and 2006 cropping seasonsunder irrigated conditions in Turkey. The analysis of variance showed that mean squares of environments (E, genotypes (G andGE interactions (GEI were highly significant and accounted for 74, 7 and 19 % of treatment combination sum squares, respectively.To determine the effects of GEI on grain yield, the data were subjected to the GGE biplot analysis. Maize hybrid G16 can be proposedas reliably growing in test locations for high grain yield. Also, only the Yenisehir location could be best representative of overalllocations for deciding about which experimental hybrids can be recommended for grain yield in this study. Consequently, using ofgrain yield per plant instead of grain yield per plot in hybrid maize breeding programs could be preferred by private companies dueto some advantages.

  12. Biometric analysis of interspecific hybrids between Rosa canina L. and Rosa rubiginosa L. (section Caninae DC. em. Christ.

    Directory of Open Access Journals (Sweden)

    Anna Sołtys-Lelek

    2016-06-01

    Full Text Available The article presents the biometric analysis of selected morphological features of interspecies hybrid Rosa canina L. × R. rubiginosa L. This hybrid was the result of spontaneous hybridization between the two species falling into section Caninae DC. em. Christ. So far, it has not been studied in terms of morphological characteristics, in particular with respect to the parental forms.

  13. Unexpected structural complexity of supernumerary marker chromosomes characterized by microarray comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Hing Anne V

    2008-04-01

    Full Text Available Abstract Background Supernumerary marker chromosomes (SMCs are structurally abnormal extra chromosomes that cannot be unambiguously identified by conventional banding techniques. In the past, SMCs have been characterized using a variety of different molecular cytogenetic techniques. Although these techniques can sometimes identify the chromosome of origin of SMCs, they are cumbersome to perform and are not available in many clinical cytogenetic laboratories. Furthermore, they cannot precisely determine the region or breakpoints of the chromosome(s involved. In this study, we describe four patients who possess one or more SMCs (a total of eight SMCs in all four patients that were characterized by microarray comparative genomic hybridization (array CGH. Results In at least one SMC from all four patients, array CGH uncovered unexpected complexity, in the form of complex rearrangements, that could have gone undetected using other molecular cytogenetic techniques. Although array CGH accurately defined the chromosome content of all but two minute SMCs, fluorescence in situ hybridization was necessary to determine the structure of the markers. Conclusion The increasing use of array CGH in clinical cytogenetic laboratories will provide an efficient method for more comprehensive characterization of SMCs. Improved SMC characterization, facilitated by array CGH, will allow for more accurate SMC/phenotype correlation.

  14. Design and analysis of a wheel-legged hybrid locomotion mechanism

    Directory of Open Access Journals (Sweden)

    Change Zheng

    2015-11-01

    Full Text Available A wheel-legged hybrid robot was put forward. First, the mechanical design of this chassis was introduced. Second, based on the kinematic analysis, comparison between the robot with the active transition system and that with the passive transition system was made. Third, the process of overcoming three kinds of obstacles was simulated. Finally, the conclusion can be made that this hybrid locomotion mechanism with the active transition system has good performance on rough terrains.

  15. Periodically-Scheduled Controller Analysis using Hybrid Systems Reachability and Continuization

    Science.gov (United States)

    2015-12-01

    algorithm is run, and actuator outputs are set. The physical world , on the other hand, evolves continuously. Models of the physical world may be given...An extra clock variable, c, is added to the hybrid automaton that ticks at rate one (ċ = 1). When the clock reaches the period, a transition is...Preliminary Reachability Analysis Although hybrid automata can model real-time scheduled controllers and plants as shown above, an important factor is

  16. Analysis of genetic diversity of maize hybrids in the regional tests in Sichuan and Southwest China

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In this study,analyses of phenotypic characters,SSR molecular markers and pedigrees were done to study the genetic diversity in 186 maize hybrids that were tested in regional trials in Sichuan and Southwest China.The results showed that there were differences in the variation coefficients of different characteristics,but all of the variation coefficients changed within a narrow range.Sixty pairs of simple sequence repeat (SSR) primer distributed on the ten chromosomes of maize produced stable amplified bands and 608 alleles were detected among the hybrids.The average number of alleles per locus was 10.1 ranging from 3 to 23.The values of polymorphism information content (PIC) for each SSR locus varied from 0.5179 to 0.9256 with an average of 0.7826.The genetic similarities of SSR marker pattern among the 186 hybrids ranged from 0.6067 to 0.9162,with an average of 0.7722.There were 16499 pairs of genetic similarity,in which 96.9% were 0.70000 to 0.9256.The cluster analysis showed that the hybrids could be classified into ten clusters,with 88.2% of the hybrids included in Cluster 4,Cluster 8 and Cluster 10.The analysis of pedigree sources of 51 hybrids showed that 36 hybrids had close genetic relationships with the hybrids developed by the Pioneer Company in the late 1980s and early 1990s in the United States,such as Y78599,Y7865 and Y78698,accounting for 70.58%.Meanwhile,13 hybrids had close genetic relationships with Y78599,accounting for 8.66%.The genetic similarities of SSR marker pattern among the 51 hybrids ranged from 0.66192 to 0.8799,with an average of 0.7686.There were 1196 pairs of genetic similarity ranged between 0.7000 to 0.8796,accounting for 93.80% of all the genetic similarity pairs.The cluster analysis showed that 88.2% of the 51 hybrids were in Cluster 4,Cluster 8 and Cluster 10,which indicated that similarity was high and genetic diversity narrow among the 186 hybrids.This showed that it is necessary to broaden the genetic basis of breeding

  17. Thermal analysis of solar biomass hybrid co-generation plants

    Science.gov (United States)

    Kaushika, N. D.; Mishra, Anuradha; Chakravarty, M. N.

    2005-12-01

    This article describes a co-generation plant based on the biogas being produced from the waste of distillery plant and highlights the possible configuration in which the plant can be hybridized with auxiliary solar energy source having the advantage of using financial incentives in several countries. In hybridization, the solar heat is used for heating the boiler feed water. The solar heat-generating unit consists of line focus parabolic trough collector, heat transportation system and heat delivery unit such as heat exchanger. The simulation model of heat and mass transfer processes in the solar field as well as the balance of the system is developed to investigate the technological feasibility of the concept in terms of plant yield and matching of subsystems.

  18. Capacity analysis of inhomogeneous hybrid wireless networks using directional antennas

    Institute of Scientific and Technical Information of China (English)

    WU Feng; ZHU Jiang; TIAN Yi-long; ZOU Jian-bin

    2016-01-01

    Most of studies on network capacity are based on the assumption that all the nodes are uniformly distributed, which means that the networks are characterized by homogeneity. However, many realistic networks exhibit inhomogeneity due to natural and man-made reasons. In this work, the capacity of inhomogeneous hybrid networks with directional antennas for the first time is studied. By setting different node distribution probabilities, the whole network can be devided into dense cells and sparse cells. On this basis, an inhomogeneous hybrid network model is proposed. The network can exhibit significant inhomogeneity due to the coexistence of two types of cells. Then, we derive the network capacity and maximize the capacity under different channel allocation schemes. Finally, how the network parameters influence the network capacity is analyzed. It is found that if there are plenty of base stations, the per-node throughput can achieve constant order, and if the beamwidth of directional antenna is small enough, the network capacity can scale.

  19. Hybrid Scenario Based Performance Analysis of DSDV and DSSR

    CERN Document Server

    Majumder, Koushik; 10.5121/ijcsit.2010.2305

    2010-01-01

    The area of mobile ad hoc networking has received considerable attention of the research community in recent years. These networks have gained immense popularity primarily due to their infrastructure-less mode of operation which makes them a suitable candidate for deployment in emergency scenarios like relief operation, battlefield etc., where either the pre-existing infrastructure is totally damaged or it is not possible to establish a new infrastructure quickly. However, MANETs are constrained due to the limited transmission range of the mobile nodes which reduces the total coverage area. Sometimes the infrastructure-less ad hoc network may be combined with a fixed network to form a hybrid network which can cover a wider area with the advantage of having less fixed infrastructure. In such a combined network, for transferring data, we need base stations which act as gateways between the wired and wireless domains. Due to the hybrid nature of these networks, routing is considered a challenging task. Several r...

  20. Coexistence analysis of diploid and triploid hybrid water frogs

    Science.gov (United States)

    Apri, M.; Suandi, D.; Soewono, E.

    2014-02-01

    A dynamical model for genotype distributions of all hybrid populations of Pelophylax esculentus in the absence of differential survival is studied here. Assuming that under natural condition the parental genotypes LL and RR do not survive into adult stage, the dynamic is then reduced into three-dimensional dynamical system of classes LR, LLR, LRR genotypes. Coexistence of diploid (LR) and triploid (LLR and LRR) genotypes is analyzed here.

  1. Delta-Complete Analysis for Bounded Reachability of Hybrid Systems

    Science.gov (United States)

    2014-07-16

    can occur in realistic hybrid sys- tems, such as polynomials, trigonometric functions , and solutions of Lipschitz-continuous ODEs. The goal of this...systems are Type 2 computable, such as polynomials, exponentiation, logarithm, trigonometric functions , and solution functions of Lipschitz-continuous...comes from the need of solving logic formulas over the real numbers with nonlinear functions , which is notoriously hard. Recently, we have defined the δ

  2. Hybrid Threat Center of Gravity Analysis: Cutting the Gordian Knot

    Science.gov (United States)

    2016-04-04

    observed “the response from Jerusalem was both quick and violent, surprising Hezbollah’s leadership and triggering a month-long conflict that, in...urban areas that caught the IDF completely by surprise . Peters notes three distinct advantages employed by Hezbollah in the development of its hybrid...Ukraine. These “green men” had no identifying marks or uniforms yet operated with amazing efficiency and tactical proficiency.2 No shots were fired

  3. The Gwaii Haanas PV hybrid system : analysis of system operation

    Energy Technology Data Exchange (ETDEWEB)

    Ross, M. [GPCo Inc., Varennes, PQ (Canada); Turcotte, D.; Sheriff, F. [Natural Resources Canada, Varennes, PQ (Canada). CANMET Energy Technology Centre

    2003-05-01

    The operation of the photovoltaic/battery/genset hybrid power system at the Gwaii Haanas National Park Reserve warden station in British Columbia has been monitored since July 2001 as part of the Canada Centre for Mineral and Energy Technology (CANMET) Energy Technology Centre-Varennes Photovoltaic Hybrid Power Systems Program. The data collected has been used to validate hybrid system simulation tools being developed under the sponsorship of the Program. The analyzed data, along with the simulation tools, provided insight into the operation of the Gwaii Haanas power system. It also assisted in identifying the strengths and weaknesses of the system. Data indicates that the system functions well and is appropriately dimensioned and configured. The modules are arranged in two sub-arrays, with modules connected in parallel, showing remarkable tolerance to shading of part of the array. Almost complete discharge of the batteries occurs during the winter, when the Park residence is unoccupied. During the summer, users should keep track of the battery state-of-charge. Some recommendations were made to prolong the battery life. 1 ref., 1 tab., 16 figs.

  4. Hybrid Psychology: The marriage of discourse analysis with neuroscience

    Directory of Open Access Journals (Sweden)

    Rom Harré

    2010-07-01

    Full Text Available As the 21st Century opened the controversial and unstable discipline of `academic psychology’ seemed to separating into two radically distinct and perhaps irreconcilable domains. Discursive psychology focused on the management of meaning in a world of norms while Neuropsychology focused on the investigation of brain and cognitive processes. These two domains can be reconciled in a hybrid science that brings them together into a synthesis more powerful than anything psychologists have achieved before. In this paper means Hybrid psychology depends on the intuition that while brains can be assimilated into the world of persons, people cannot be assimilated into the world of cell structures and molecular processes. The project of setting up a hybrid science, in which the symbol using capacities of human beings are brought into a unified scheme with the organic aspects of members of the species homo sapiens, demands the dissolution of the mind-body problem, somehow setting it aside as an illusion, based on a mistaken presupposition.

  5. Deletion of 14q24.1 approximately q24.3 in a patient with acute lymphoblastic leukemia: a hidden chromosomal anomaly detected by array-based comparative genomic hybridization.

    Science.gov (United States)

    Xu, Weihong; Lu, Xianglan; Kim, YoungMi; Luo, Ying; Martin, Mallory; Mulvihill, John J; Li, Shibo

    2008-08-01

    A 4-year-old patient, who was newly diagnosed with acute lymphoblastic leukemia (ALL), was referred to us for cytogenetic evaluation. He had a normal karyotype by G-banded chromosome analysis, and a deletion of the ETV6 (alias TEL) gene was determined by fluorescence in situ hybridization analysis using DNA probes specific for t(12;21), which leads to ETV6/RUNX1 (alias TEL/AML1) gene fusion, but no translocation was found between the two genes. To find out if there were possibly additional subtle chromosomal changes undetectable by routine cytogenetics, high-density 385K oligo array comparative genomic hybridization (CGH) assay was performed. Besides the confirmation of the 12p deletion, a deletion of a 12-megabase (Mb) chromosomal segment on 14q24.1 approximately q24.3 was also detected. Within the deleted 12-Mb region, there were a total of 155 genes and at least 28 of these were cancer-related genes. A similar approach by array CGH in patients with ALL, especially in those patients with 12p deletion, could help to determine the significance of this rare event.

  6. HYBRID SULFUR PROCESS REFERENCE DESIGN AND COST ANALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    Gorensek, M.; Summers, W.; Boltrunis, C.; Lahoda, E.; Allen, D.; Greyvenstein, R.

    2009-05-12

    This report documents a detailed study to determine the expected efficiency and product costs for producing hydrogen via water-splitting using energy from an advanced nuclear reactor. It was determined that the overall efficiency from nuclear heat to hydrogen is high, and the cost of hydrogen is competitive under a high energy cost scenario. It would require over 40% more nuclear energy to generate an equivalent amount of hydrogen using conventional water-cooled nuclear reactors combined with water electrolysis compared to the proposed plant design described herein. There is a great deal of interest worldwide in reducing dependence on fossil fuels, while also minimizing the impact of the energy sector on global climate change. One potential opportunity to contribute to this effort is to replace the use of fossil fuels for hydrogen production by the use of water-splitting powered by nuclear energy. Hydrogen production is required for fertilizer (e.g. ammonia) production, oil refining, synfuels production, and other important industrial applications. It is typically produced by reacting natural gas, naphtha or coal with steam, which consumes significant amounts of energy and produces carbon dioxide as a byproduct. In the future, hydrogen could also be used as a transportation fuel, replacing petroleum. New processes are being developed that would permit hydrogen to be produced from water using only heat or a combination of heat and electricity produced by advanced, high temperature nuclear reactors. The U.S. Department of Energy (DOE) is developing these processes under a program known as the Nuclear Hydrogen Initiative (NHI). The Republic of South Africa (RSA) also is interested in developing advanced high temperature nuclear reactors and related chemical processes that could produce hydrogen fuel via water-splitting. This report focuses on the analysis of a nuclear hydrogen production system that combines the Pebble Bed Modular Reactor (PBMR), under development by

  7. Hybridization kinetics analysis of an oligonucleotide microarray for microRNA detection

    Institute of Scientific and Technical Information of China (English)

    Botao Zhao; Shuo Ding; Wei Li; Youxin Jin

    2011-01-01

    MicroRNA (miRNA) microarrays have been successfully used for profiling miRNA expression in many physiological processes such as development, differentiation, oncogenesis,and other disease processes. Detecting miRNA by miRNA microarray is actually based on nucleic acid hybridization between target molecules and their corresponding complementary probes. Due to the small size and high degree of similarity among miRNA sequences, the hybridization condition must be carefully optimized to get specific and reliable signals. Previously, we reported a microarray platform to detect miRNA expression. In this study, we evaluated the sensitivity and specificity of our microarray platform. After systematic analysis, we determined an optimized hybridization condition with high sensitivity and specificity for miRNA detection. Our results would be helpful for other hybridization-based miRNA detection methods, such as northern blot and nuclease protection assay.

  8. EVALUATION OF HYBRIDIZATION BETWEEN PANGASIUS DJAMBAL BLEEKER 1846 AND PANGASIANODON HYPOPHTHALMUS (SAUVAGE 1878: BIOMETRIC CHARACTERIZATION AND GROWTH ANALYSIS

    Directory of Open Access Journals (Sweden)

    Rudhy Gustiano

    2007-06-01

    Full Text Available Possible use of pangasiid hybrids in aquaculture might generate potential impacts on wild populations. Therefore, rapid identification tools in the field such as growth rate are urgently needed. This study examines morphological characters and growth performance of P. djambal and P. hypophthalmus and their reciprocal hybrids. A detailed morphological study analysed 32 morphometric measurements and 5 meristic counts on hybrids of Pangasius djambal and P. hypophthalmus. Morphometric analysis and meristic counts showed that the reciprocal hybrids have intermediate characters except for gill rakers number which were lower than that of parental species. In general, the hybrids have tendency to be like P. hypophthalmus rather than P. djambal. The only typical character P. djambal appearing in hybrids is teeth shape, both vomerine and palatine. It was shown that the true hybrids have seven pelvic fin rays. Eight months of growth comparison in earthen ponds showed that the hybrids have a better performance for specific growth rate than the parental stock.

  9. Establishment of a new human pleomorphic malignant fibrous histiocytoma cell line, FU-MFH-2: molecular cytogenetic characterization by multicolor fluorescence in situ hybridization and comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Isayama Teruto

    2010-11-01

    Full Text Available Abstract Background Pleomorphic malignant fibrous histiocytoma (MFH is one of the most frequent malignant soft tissue tumors in adults. Despite the considerable amount of research on MFH cell lines, their characterization at a molecular cytogenetic level has not been extensively analyzed. Methods and results We established a new permanent human cell line, FU-MFH-2, from a metastatic pleomorphic MFH of a 72-year-old Japanese man, and applied multicolor fluorescence in situ hybridization (M-FISH, Urovysion™ FISH, and comparative genomic hybridization (CGH for the characterization of chromosomal aberrations. FU-MFH-2 cells were spindle or polygonal in shape with oval nuclei, and were successfully maintained in vitro for over 80 passages. The histological features of heterotransplanted tumors in severe combined immunodeficiency mice were essentially the same as those of the original tumor. Cytogenetic and M-FISH analyses displayed a hypotriploid karyotype with numerous structural aberrations. Urovysion™ FISH revealed a homozygous deletion of the p16INK4A locus on chromosome band 9p21. CGH analysis showed a high-level amplification of 9q31-q34, gains of 1p12-p34.3, 2p21, 2q11.2-q21, 3p, 4p, 6q22-qter, 8p11.2, 8q11.2-q21.1, 9q21-qter, 11q13, 12q24, 15q21-qter, 16p13, 17, 20, and X, and losses of 1q43-qter, 4q32-qter, 5q14-q23, 7q32-qter, 8p21-pter, 8q23, 9p21-pter, 10p11.2-p13, and 10q11.2-q22. Conclusion The FU-MFH-2 cell line will be a particularly useful model for studying molecular pathogenesis of human pleomorphic MFH.

  10. Hybrid Vortex Method for the Aerodynamic Analysis of Wind Turbine

    Directory of Open Access Journals (Sweden)

    Hao Hu

    2015-01-01

    Full Text Available The hybrid vortex method, in which vortex panel method is combined with the viscous-vortex particle method (HPVP, was established to model the wind turbine aerodynamic and relevant numerical procedure program was developed to solve flow equations. The panel method was used to calculate the blade surface vortex sheets and the vortex particle method was employed to simulate the blade wake vortices. As a result of numerical calculations on the flow over a wind turbine, the HPVP method shows significant advantages in accuracy and less computation resource consuming. The validation of the aerodynamic parameters against Phase VI wind turbine experimental data is performed, which shows reasonable agreement.

  11. Using a Hybrid Cost-FMEA Analysis for Wind Turbine Reliability Analysis

    Directory of Open Access Journals (Sweden)

    Nacef Tazi

    2017-02-01

    Full Text Available Failure mode and effects analysis (FMEA has been proven to be an effective methodology to improve system design reliability. However, the standard approach reveals some weaknesses when applied to wind turbine systems. The conventional criticality assessment method has been criticized as having many limitations such as the weighting of severity and detection factors. In this paper, we aim to overcome these drawbacks and develop a hybrid cost-FMEA by integrating cost factors to assess the criticality, these costs vary from replacement costs to expected failure costs. Then, a quantitative comparative study is carried out to point out average failure rate, main cause of failure, expected failure costs and failure detection techniques. A special reliability analysis of gearbox and rotor-blades are presented.

  12. Power quality analysis of hybrid renewable energy system

    Directory of Open Access Journals (Sweden)

    Rinchin W. Mosobi

    2015-12-01

    Full Text Available An hybrid renewable energy sources consisting of solar photovoltaic, wind energy system, and a microhydro system is proposed in this paper. This system is suitable for supplying electricity to isolated locations or remote villages far from the grid supply. The solar photovoltaic system is modeled with two power converters, the first one being a DC-DC converter along with an maximum power point tracking to achieve a regulated DC output voltage and the second one being a DC-AC converter to obtain AC output. The wind energy system is modeled with a wind-turbine prime mover with varying wind speed and fixed pitch angle to drive an self excited induction generator (SEIG. Owing to inherent drooping characteristics of the SEIG, a closed loop turbine input system is incorporated. The microhydro system is modeled with a constant input power to drive an SEIG. The three different sources are integrated through an AC bus and the proposed hybrid system is supplied to R, R-L, and induction motor loads. A static compensator is proposed to improve the load voltage and current profiles; it also mitigates the harmonic contents of the voltage and current. The static synchronous compensator is realized by means of a three-phase IGBT-based current-controlled voltage source inverter with a self-supporting DC bus. The complete system is modeled and simulated using Matlab/Simulink. The simulation results obtained illustrate the feasibility of the proposed system and are found to be satisfactory.

  13. Analysis of a Hybrid Solar-Assisted Trigeneration System

    Directory of Open Access Journals (Sweden)

    Elisa Marrasso

    2016-09-01

    Full Text Available A hybrid solar-assisted trigeneration system is analyzed in this paper. The system is composed of a 20 m2 solar field of evacuated tube collectors, a natural gas fired micro combined heat and power system delivering 12.5 kW of thermal power, an absorption heat pump (AHP with a nominal cooling power of 17.6 kW, two storage tanks (hot and cold and an electric auxiliary heater (AH. The plant satisfies the energy demand of an office building located in Naples (Southern Italy. The electric energy of the cogenerator is used to meet the load and auxiliaries electric demand; the interactions with the grid are considered in cases of excess or over requests. This hybrid solution is interesting for buildings located in cities or historical centers with limited usable roof surface to install a conventional solar heating and cooling (SHC system able to achieve high solar fraction (SF. The results of dynamic simulation show that a tilt angle of 30° maximizes the SF of the system on annual basis achieving about 53.5%. The influence on the performance of proposed system of the hot water storage tank (HST characteristics (volume, insulation is also studied. It is highlighted that the SF improves when better insulated and bigger HSTs are considered. A maximum SF of about 58.2% is obtained with a 2000 L storage, whereas the lower thermal losses take place with a better insulated 1000 L tank.

  14. Power flow analysis for droop controlled LV hybrid AC-DC microgrids with virtual impedance

    DEFF Research Database (Denmark)

    Li, Chendan; Chaudhary, Sanjay; Vasquez, Juan Carlos

    2014-01-01

    The AC-DC hybrid microgrid is an effective form of utilizing different energy resources and the analysis of this system requires a proper power flow algorithm. This paper proposes a suitable power flow algorithm for LV hybrid AC-DC microgrid based on droop control and virtual impedance. Droop...... and virtual impedance concepts for AC network, DC network and interlinking converter are reviewed so as to model it in the power flow analysis. The validation of the algorithm is verified by comparing it with steady state results from detailed time domain simulation. The effectiveness of the proposed...

  15. Transcriptomic analysis of Crassostrea sikamea × Crassostrea angulata hybrids in response to low salinity stress

    Science.gov (United States)

    Yan, Lulu; Su, Jiaqi; Wang, Zhaoping; Yan, Xiwu; Yu, Ruihai; Ma, Peizhen; Li, Yangchun; Du, Junpeng

    2017-01-01

    Hybrid oysters often show heterosis in growth rate, weight, survival and adaptability to extremes of salinity. Oysters have also been used as model organisms to study the evolution of host-defense system. To gain comprehensive knowledge about various physiological processes in hybrid oysters under low salinity stress, we performed transcriptomic analysis of gill tissue of Crassostrea sikamea ♀ × Crassostrea angulata♂ hybrid using the deep-sequencing platform Illumina HiSeq. We exploited the high-throughput technique to delineate differentially expressed genes (DEGs) in oysters maintained in hypotonic conditions. A total of 199,391 high quality unigenes, with average length of 644 bp, were generated. Of these 35 and 31 genes showed up- and down-regulation, respectively. Functional categorization and pathway analysis of these DEGs revealed enrichment for immune mechanism, apoptosis, energy metabolism and osmoregulation under low salinity stress. The expression patterns of 41 DEGs in hybrids and their parental species were further analyzed by quantitative real-time PCR (qRT-PCR). This study will serve as a platform for subsequent gene expression analysis regarding environmental stress. Our findings will also provide valuable information about gene expression to better understand the immune mechanism, apoptosis, energy metabolism and osmoregulation in hybrid oysters under low salinity stress. PMID:28182701

  16. Yield stability and adaptability of maize hybrids based on GGE biplot analysis characteristics

    Directory of Open Access Journals (Sweden)

    Marcio Balestre

    2009-01-01

    Full Text Available The objective of this study was to evaluate stability and adaptability of the grain yield of commercial intervarietalmaize hybrids by the GGE (Genotype and Genotype by Environment Interaction biplot and AMMI (Additive Main Effects andMultiplicative Interaction analyses. Two intervarietal hybrids (BIO 2 and BIO4 were evaluated together with single, doubleand three-way cross hybrids. The performance of the intervarietal hybrid BIO 4 was superior to all double and three-waycross hybrids and outmatched the single-cross hybrids by 43%. In terms of stability, BIO 2 was more stable than BIO4, whichis desirable, but biological stability, which is not necessarily desirable, was also observed, since the yield was below theenvironmental mean. The graphical GGE biplot analysis was superior to the AMMI1 since a greater portion of the sum ofsquares of GE and G+GE was captured and the predictive accuracy was higher. On the other hand, the AMMI2 graphoutperformed the GGE biplot in predictive accuracy and explanation of G + GE and GE, although the difference in accuracywas smaller than between GGE2 and AMMI1.

  17. Sample preparation and in situ hybridization techniques for automated molecular cytogenetic analysis of white blood cells

    Energy Technology Data Exchange (ETDEWEB)

    Rijke, F.M. van de; Vrolijk, H.; Sloos, W. [Leiden Univ. (Netherlands)] [and others

    1996-06-01

    With the advent in situ hybridization techniques for the analysis of chromosome copy number or structure in interphase cells, the diagnostic and prognostic potential of cytogenetics has been augmented considerably. In theory, the strategies for detection of cytogenetically aberrant cells by in situ hybridization are simple and straightforward. In practice, however, they are fallible, because false classification of hybridization spot number or patterns occurs. When a decision has to be made on molecular cytogenetic normalcy or abnormalcy of a cell sample, the problem of false classification becomes particularly prominent if the fraction of aberrant cells is relatively small. In such mosaic situations, often > 200 cells have to be evaluated to reach a statistical sound figure. The manual enumeration of in situ hybridization spots in many cells in many patient samples is tedious. Assistance in the evaluation process by automation of microscope functions and image analysis techniques is, therefore, strongly indicated. Next to research and development of microscope hardware, camera technology, and image analysis, the optimization of the specimen for the (semi)automated microscopic analysis is essential, since factors such as cell density, thickness, and overlap have dramatic influences on the speed and complexity of the analysis process. Here we describe experiments that have led to a protocol for blood cell specimen that results in microscope preparations that are well suited for automated molecular cytogenetic analysis. 13 refs., 4 figs., 1 tab.

  18. Modeling, analysis and control of fuel cell hybrid power systems

    Science.gov (United States)

    Suh, Kyung Won

    Transient performance is a key characteristic of fuel cells, that is sometimes more critical than efficiency, due to the importance of accepting unpredictable electric loads. To fulfill the transient requirement in vehicle propulsion and portable fuel cell applications, a fuel cell stack is typically coupled with a battery through a DC/DC converter to form a hybrid power system. Although many power management strategies already exist, they all rely on low level controllers that realize the power split. In this dissertation we design controllers that realize various power split strategies by directly manipulating physical actuators (low level commands). We maintain the causality of the electric dynamics (voltage and current) and investigate how the electric architecture affects the hybridization level and the power management. We first establish the performance limitations associated with a stand-alone and power-autonomous fuel cell system that is not supplemented by an additional energy storage and powers all its auxiliary components by itself. Specifically, we examine the transient performance in fuel cell power delivery as it is limited by the air supplied by a compressor driven by the fuel cell itself. The performance limitations arise from the intrinsic coupling in the fluid and electrical domain between the compressor and the fuel cell stack. Feedforward and feedback control strategies are used to demonstrate these limitations analytically and with simulations. Experimental tests on a small commercial fuel cell auxiliary power unit (APU) confirm the dynamics and the identified limitations. The dynamics associated with the integration of a fuel cell system and a DC/DC converter is then investigated. Decentralized and fully centralized (using linear quadratic techniques) controllers are designed to regulate the power system voltage and to prevent fuel cell oxygen starvation. Regulating these two performance variables is a difficult task and requires a compromise

  19. The optimizations of CGH generation algorithms based on multiple GPUs for 3D dynamic holographic display

    Science.gov (United States)

    Yang, Dan; Liu, Juan; Zhang, Yingxi; Li, Xin; Wang, Yongtian

    2016-10-01

    Holographic display has been considered as a promising display technology. Currently, low-speed generation of holograms with big holographic data is one of crucial bottlenecks for three dimensional (3D) dynamic holographic display. To solve this problem, the acceleration method computation platform is presented based on look-up table point source method. The computer generated holograms (CGHs) acquisition is sped up by offline file loading and inline calculation optimization, where a pure phase CGH with gigabyte data is encoded to record an object with 10 MB sampling data. Both numerical simulation and optical experiment demonstrate that the CGHs with 1920×1080 resolution by the proposed method can be applied to the 3D objects reconstruction with high quality successfully. It is believed that the CGHs with huge data can be generated by the proposed method with high speed for 3D dynamic holographic display in near future.

  20. Analysis of extensive air showers with the hybrid code SENECA

    CERN Document Server

    Ortiz, J A; Medina-Tanco, G; Ortiz, Jeferson A.; Souza, Vitor de; Medina-Tanco, Gustavo

    2005-01-01

    The ultrahigh energy tail of the cosmic ray spectrum has been explored with unprecedented detail. For this reason, new experiments are exerting a severe pressure on extensive air shower modeling. Detailed fast codes are in need in order to extract and understand the richness of information now available. In this sense we explore the potential of SENECA, an efficient hybrid tridimensional simulation code, as a valid practical alternative to full Monte Carlo simulations of extensive air showers generated by ultrahigh energy cosmic rays. We discuss the influence of this approach on the main longitudinal characteristics of proton, iron nucleus and gamma induced air showers for different hadronic interaction models. We also show the comparisons of our predictions with those of CORSIKA code.

  1. Analysis of extensive air showers with the hybrid code SENECA

    Science.gov (United States)

    Ortiz, Jeferson A.; de Souza, Vitor; Medina-Tanco, Gustavo

    The ultrahigh energy tail of the cosmic ray spectrum has been explored with unprecedented detail. For this reason, new experiments are exerting a severe pressure on extensive air shower modeling. Detailed fast codes are in need in order to extract and understand the richness of information now available. In this sense we explore the potential of SENECA, an efficient hybrid tridimensional simulation code, as a valid practical alternative to full Monte Carlo simulations of extensive air showers generated by ultrahigh energy cosmic rays. We discuss the influence of this approach on the main longitudinal characteristics of proton, iron nucleus and gamma induced air showers for different hadronic interaction models. We also show the comparisons of our predictions with those of CORSIKA code.

  2. A dynamical system analysis of hybrid metric-Palatini cosmologies

    CERN Document Server

    Carloni, Sante; Lobo, Francisco S N

    2015-01-01

    The so called $f(X)$ hybrid metric-Palatini gravity presents a unique viable generalisation of the $f(R)$ theories within the metric-affine formalism. Here the cosmology of the $f(X)$ theories is studied using the dynamical system approach. The method consists of formulating the propagation equation in terms of suitable (expansion-normalised) variables as an autonomous system. The fixed points of the system then represent exact cosmological solutions described by power-law or de Sitter expansion. The formalism is applied to two classes of $f(X)$ models, revealing both standard cosmological fixed points and new accelerating solutions that can be attractors in the phase space. In addition, the fixed point with vanishing expansion rate are considered with special care in order to characterise the stability of Einstein static spaces and bouncing solutions.

  3. Flexural analysis of palm fiber reinforced hybrid polymer matrix composite

    Science.gov (United States)

    Venkatachalam, G.; Gautham Shankar, A.; Raghav, Dasarath; Santhosh Kiran, R.; Mahesh, Bhargav; Kumar, Krishna

    2015-07-01

    Uncertainty in availability of fossil fuels in the future and global warming increased the need for more environment friendly materials. In this work, an attempt is made to fabricate a hybrid polymer matrix composite. The blend is a mixture of General Purpose Resin and Cashew Nut Shell Liquid, a natural resin extracted from cashew plant. Palm fiber, which has high strength, is used as reinforcement material. The fiber is treated with alkali (NaOH) solution to increase its strength and adhesiveness. Parametric study of flexure strength is carried out by varying alkali concentration, duration of alkali treatment and fiber volume. Taguchi L9 Orthogonal array is followed in the design of experiments procedure for simplification. With the help of ANOVA technique, regression equations are obtained which gives the level of influence of each parameter on the flexure strength of the composite.

  4. Hybrid Additive Manufacturing Technologies - An Analysis Regarding Potentials and Applications

    Science.gov (United States)

    Merklein, Marion; Junker, Daniel; Schaub, Adam; Neubauer, Franziska

    Imposing the trend of mass customization of lightweight construction in industry, conventional manufacturing processes like forming technology and chipping production are pushed to their limits for economical manufacturing. More flexible processes are needed which were developed by the additive manufacturing technology. This toolless production principle offers a high geometrical freedom and an optimized utilization of the used material. Thus load adjusted lightweight components can be produced in small lot sizes in an economical way. To compensate disadvantages like inadequate accuracy and surface roughness hybrid machines combining additive and subtractive manufacturing are developed. Within this paper the principles of mainly used additive manufacturing processes of metals and their possibility to be integrated into a hybrid production machine are summarized. It is pointed out that in particular the integration of deposition processes into a CNC milling center supposes high potential for manufacturing larger parts with high accuracy. Furthermore the combination of additive and subtractive manufacturing allows the production of ready to use products within one single machine. Additionally actual research for the integration of additive manufacturing processes into the production chain will be analyzed. For the long manufacturing time of additive production processes the combination with conventional manufacturing processes like sheet or bulk metal forming seems an effective solution. Especially large volumes can be produced by conventional processes. In an additional production step active elements can be applied by additive manufacturing. This principle is also investigated for tool production to reduce chipping of the high strength material used for forming tools. The aim is the addition of active elements onto a geometrical simple basis by using Laser Metal Deposition. That process allows the utilization of several powder materials during one process what

  5. VizieR Online Data Catalog: Spectroscopy of main-belt Ch/Cgh-type asteroids (Vernazza+, 2016)

    Science.gov (United States)

    Vernazza, P.; Marsset, M.; Beck, P.; Binzel, R. P.; Birlan, M.; Cloutis, E. A.; DeMeo, F. E.; Dumas, C.; Hiroi, T.

    2016-09-01

    We conducted an extensive spectroscopic survey in the near-infrared range of 70 main-belt Ch/Cgh-type asteroids and 4 Ch/Cgh-type families and combined these measurements with available visible wavelength spectra. New data presented here are near-infrared asteroid spectral measurements for Ch- and Cgh-type asteroids from 0.7-2.5μm obtained using SpeX, the low- to medium-resolution near-IR spectrograph and imager on the 3m NASA InfraRed Telescope Facility (IRTF) located on Mauna Kea, HI. Observing runs were conducted remotely primarily from the Observatory of Paris-Meudon, France between 2010 April and 2012 January. The spectrograph SpeX, combined with a 0.8*15arcsec slit, was used in the low-resolution prism mode for acquisition of the spectra in the 0.7-2.5μm wavelength range. In order to monitor the high luminosity and variability of the sky in the near-IR, the telescope was moved along the slit during the acquisition of the data so as to obtain a sequence of spectra located at two different positions (A and B) on the array. In addition, we complemented our data set with additional near-infrared spectra retrieved from the Small Main-Belt Asteroid Spectroscopic Survey (SMASS) database (http://smass.mit.edu/). Combining these near-infrared measurements with available visible wavelength spectra (Bus, 1999PhDT........50B; Lazzaro et al., 2004Icar..172..179L) allows for the first time an extensive visible and near-infrared (VNIR) spectral database of main-belt Ch and Cgh types with D>45km (78% or 49/63 of all Ch and Cgh types listed in SMASS; see Table1). (1 data file).

  6. Transcriptome Analysis Identifies Key Candidate Genes Mediating Purple Ovary Coloration in Asiatic Hybrid Lilies

    Science.gov (United States)

    Xu, Leifeng; Yang, Panpan; Yuan, Suxia; Feng, Yayan; Xu, Hua; Cao, Yuwei; Ming, Jun

    2016-01-01

    Lily tepals have a short lifespan. Once the tepals senesce, the ornamental value of the flower is lost. Some cultivars have attractive purple ovaries and fruits which greatly enhance the ornamental value of Asiatic hybrid lilies. However, little is known about the molecular mechanisms of anthocyanin biosynthesis in Asiatic hybrid lily ovaries. To investigate the transcriptional network that governs purple ovary coloration in Asiatic hybrid lilies, we obtained transcriptome data from green ovaries (S1) and purple ovaries (S2) of Asiatic “Tiny Padhye”. Comparative transcriptome analysis revealed 4228 differentially expressed genes. Differential expression analysis revealed that ten unigenes including four CHS genes, one CHI gene, one F3H gene, one F3′H gene, one DFR gene, one UFGT gene, and one 3RT gene were significantly up-regulated in purple ovaries. One MYB gene, LhMYB12-Lat, was identified as a key transcription factor determining the distribution of anthocyanins in Asiatic hybrid lily ovaries. Further qPCR results showed unigenes related to anthocyanin biosynthesis were highly expressed in purple ovaries of three purple-ovaried Asiatic hybrid lilies at stages 2 and 3, while they showed an extremely low level of expression in ovaries of three green-ovaried Asiatic hybrid lilies during all developmental stages. In addition, shading treatment significantly decreased pigment accumulation by suppressing the expression of several unigenes related to anthocyanin biosynthesis in ovaries of Asiatic “Tiny Padhye”. Lastly, a total of 15,048 Simple Sequence Repeats (SSRs) were identified in 13,710 sequences, and primer pairs for SSRs were designed. The results could further our understanding of the molecular mechanisms of anthocyanin biosynthesis in Asiatic hybrid lily ovaries. PMID:27879624

  7. Array-based comparative genomic hybridization analysis reveals chromosomal copy number aberrations associated with clinical outcome in canine diffuse large B-cell lymphoma.

    Directory of Open Access Journals (Sweden)

    Arianna Aricò

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

  8. Genetic analysis of X-linked hybrid sterility in the house mouse.

    Science.gov (United States)

    Storchová, Radka; Gregorová, Sona; Buckiová, Daniela; Kyselová, Vendula; Divina, Petr; Forejt, Jirí

    2004-07-01

    Hybrid sterility is a common postzygotic reproductive isolation mechanism that appears in the early stages of speciation of various organisms. Mus musculus musculus and Mus musculus domesticus represent two recently separated mouse subspecies particularly suitable for genetic studies of hybrid sterility. Here we show that the introgression of Chr X of M. m. musculus origin (PWD/Ph inbred strain, henceforth PWD) into the genetic background of the C57BL/6J (henceforth B6) inbred strain (predominantly of M. m. domesticus origin) causes male sterility. The X-linked hybrid sterility is associated with reduced testes weight, lower sperm count, and morphological abnormalities of sperm heads. The analysis of recombinant Chr Xs in sterile and fertile males as well as quantitative trait locus (QTL) analysis of several fertility parameters revealed an oligogenic nature of the X-linked hybrid sterility. The Hstx1 locus responsible for male sterility was mapped near DXMit119 in the central part of Chr X. To ensure full sterility, the PWD allele of Hstx1 has to be supported with the PWD allelic form of loci in at least one proximal and/or one distal region of Chr X. Mapping and cloning of Hstx1 and other genes responsible for sterility of B6-X PWD Y B6 males could help to elucidate the special role of Chr X in hybrid sterility and consequently in speciation.

  9. Energy performance analysis for a photovoltaic, diesel, battery hybrid power supply system

    CSIR Research Space (South Africa)

    Tazvinga, Henerica

    2010-03-01

    Full Text Available This paper looks at an energy performance analysis for a photovoltaic, diesel, and battery hybrid power supply system. The procedure starts by the identification of the hourly load requirements for a typical target consumer and the concept of load...

  10. SINGLE CELL DEGENERATE OLIGONUCLEOTIDE PRIMER-PCR AND COMPARATIVE GENOMIC HYBRIDIZATION WITH MODIFIED CONTROL REFERENCE

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    For investigating the possibility of applying degenerate oligonucleotide primer PCR (DOP-PCR) and comparative genomic hybridization (CGH) technique to analyses of genomic genetics in a single cell, the whole genomic DNA of a single cell with XX, XY, XO, XXY, +13 or +21 was amplified by DOP-PCR. Single cell DOP-PCR CGHs with conventional and modified control references, the genomic DNA and a single cell DOP-PCR product from normal male, were carried out respectively. The results showed that the average profile of the fluorescence intensity ratio in CGH with the genomic DNA as reference fluctuates much and that the standard deviation in about 30% haploid is beyond the normal limits. False positive hyper-representation was found to exist in X chromosome while trisomy 13 and 21 were not detected. However, the distributions of the mean and the standard deviation of the ratio in the CGH with DOP-PCR product as reference were quite acceptable. The copy number changes of chromosome X,Y,13 and 21 were revealed. Those results suggested that there is unrandom unequal amplification in a single cell DOP-PCR. Using a single DOP-PCR product as reference can decrease its influence on CGH. Single cell DOP-PCR-CGH and its application in the genetic analyses of preimplantation embryo or fetal cell in maternal blood may be possible.

  11. Chromosomal imbalances detected in primary bone tumors by comparative genomic hybridization and interphase fluorescence in situ hybridization

    Directory of Open Access Journals (Sweden)

    Baruffi Marcelo Razera

    2003-01-01

    Full Text Available We applied a combination of comparative genomic hybridization (CGH and fluorescence in situ hybridization (FISH, to characterize the genetic aberrations in three osteosarcomas (OS and one Ewing's sarcoma. CGH identified recurrent chromosomal losses at 10p14-pter and gains at 8q22.3-24.1 in OS. Interphase FISH allowed to confirm 8q gain in two cases. A high amplification level of 11q12-qter was detected in one OS. The Ewing's sarcoma showed gain at 1p32-36.1 as the sole chromosome alteration. These studies demonstrate the value of molecular cytogenetic methods in the characterization of recurrent genomic alterations in bone tumor tissue.

  12. Study and Analysis of Congestion Management in Hybrid Electric Market

    Directory of Open Access Journals (Sweden)

    Moayed Mohseni

    2013-01-01

    Full Text Available The congestion management system is a systematic approach, collaboratively developed and implemented throughout a metropolitan region that provides for the safe and effective management and operation of new and existing transportation facilities through the use of demand reduction and operational management strat­e­gies. In this paper we try to present some points which should be investigated in congestion management problems. We calculate different kinds of congestion problems which may be occurred in our network. Here, the hybrid model is used to solve problems in the electricity market to solve the congestion problem in the network and Benders techniques is used together with an optimal power flow (OPF. In fact, by using of Benders algorithm the problem is divided into two major and minor problems. Therefore, the major problem related to the economy sector and no network is included and the minor problem is to solve the network and examine the accuracy of the network. Benders algorithm has been tested on a standard network IEEE 24 bus and Matlab software is used to implement the algorithm.

  13. Thermoeconomic Analysis of Hybrid Power Plant Concepts for Geothermal Combined Heat and Power Generation

    Directory of Open Access Journals (Sweden)

    Florian Heberle

    2014-07-01

    Full Text Available We present a thermo-economic analysis for a low-temperature Organic Rankine Cycle (ORC in a combined heat and power generation (CHP case. For the hybrid power plant, thermal energy input is provided by a geothermal resource coupled with the exhaust gases of a biogas engine. A comparison to alternative geothermal CHP concepts is performed by considering variable parameters like ORC working fluid, supply temperature of the heating network or geothermal water temperature. Second law efficiency as well as economic parameters show that hybrid power plants are more efficient compared to conventional CHP concepts or separate use of the energy sources.

  14. Performance Analysis of Hybrid PV/Diesel Energy System in Western Region of Saudi Arabia

    OpenAIRE

    Makbul A. M. Ramli; Ayong Hiendro; H. R. E. H. Bouchekara

    2014-01-01

    The potential implementation of hybrid photovoltaic (PV)/diesel energy system in western region of Saudi Arabia is analyzed in this paper. The solar radiation intensity considered in this study is in the range of 4.15–7.17 kWh/m2/day. The HOMER software is used to perform the technical and economical analysis of the system. Three different system configurations, namely, stand-alone diesel system, and hybrid PV/diesel system with and without battery storage element, will be evaluated and discu...

  15. Design tradeoff studies and sensitivity analysis, appendices B1 - B4. [hybrid electric vehicles

    Science.gov (United States)

    1979-01-01

    Documentation is presented for a program which separately computes fuel and energy consumption for the two modes of operation of a hybrid electric vehicle. The distribution of daily travel is specified as input data as well as the weights which the component driving cycles are given in each of the composite cycles. The possibility of weight reduction through the substitution of various materials is considered as well as the market potential for hybrid vehicles. Data relating to battery compartment weight distribution and vehicle handling analysis is tabulated.

  16. Analysis of the Fuel Efficiency of a Hybrid Electric Drive with an Electric Power Splitter

    Directory of Open Access Journals (Sweden)

    D. Čundev

    2008-01-01

    Full Text Available This paper presents the results of an analysis of the fuel efficiency of a hybrid electric car drive, with an electric power splitter based on a double rotor synchronous permanent magnet generator. The results have been obtained through a precisely determined mathematical model and by simulating the characteristics of all essential values for the entire drive. This work is related to the experimental working stand for electric and hybrid car drive research, which has been developed at the Faculty of Electrical Engineering (FEE at CTU in Prague. 

  17. A stable hybrid containing haploid genomes of two obligate diploid Candida species.

    Science.gov (United States)

    Chakraborty, Uttara; Mohamed, Aiyaz; Kakade, Pallavi; Mugasimangalam, Raja C; Sadhale, Parag P; Sanyal, Kaustuv

    2013-08-01

    Candida albicans and Candida dubliniensis are diploid, predominantly asexual human-pathogenic yeasts. In this study, we constructed tetraploid (4n) strains of C. albicans of the same or different lineages by spheroplast fusion. Induction of chromosome loss in the tetraploid C. albicans generated diploid or near-diploid progeny strains but did not produce any haploid progeny. We also constructed stable heterotetraploid somatic hybrid strains (2n + 2n) of C. albicans and C. dubliniensis by spheroplast fusion. Heterodiploid (n + n) progeny hybrids were obtained after inducing chromosome loss in a stable heterotetraploid hybrid. To identify a subset of hybrid heterodiploid progeny strains carrying at least one copy of all chromosomes of both species, unique centromere sequences of various chromosomes of each species were used as markers in PCR analysis. The reduction of chromosome content was confirmed by a comparative genome hybridization (CGH) assay. The hybrid strains were found to be stably propagated. Chromatin immunoprecipitation (ChIP) assays with antibodies against centromere-specific histones (C. albicans Cse4/C. dubliniensis Cse4) revealed that the centromere identity of chromosomes of each species is maintained in the hybrid genomes of the heterotetraploid and heterodiploid strains. Thus, our results suggest that the diploid genome content is not obligatory for the survival of either C. albicans or C. dubliniensis. In keeping with the recent discovery of the existence of haploid C. albicans strains, the heterodiploid strains of our study can be excellent tools for further species-specific genome elimination, yielding true haploid progeny of C. albicans or C. dubliniensis in future.

  18. Analysis of a model of fuel cell - gas turbine hybrid power system for enhanced energy efficiency

    Science.gov (United States)

    Calay, Rajnish K.; Mustafa, Mohamad Y.; Virk, Mohammad S.; Mustafa, Mahmoud F.

    2012-11-01

    A simple mathematical model to evaluate the performance of FC-GT hybrid system is presented in this paper. The model is used to analyse the influence of various parameters on the performance of a typical hybrid system, where excess heat rejected from the solid-oxide fuel cell stack is utilised to generate additional power through a gas turbine system and to provide heat energy for space heating. The model is based on thermodynamic analysis of various components of the plant and can be adapted for various configurations of the plant components. Because there are many parameters defining the efficiency and work output of the hybrid system, the technique is based on mathematical and graphical optimisation of various parameters; to obtain the maximum efficiency for a given plant configuration.

  19. Multiscale tomographic analysis of polymer-nanoparticle hybrid materials for solar cells

    Science.gov (United States)

    Lopez-Haro, Miguel; Jiu, Tonggang; Bayle-Guillemaud, Pascale; Jouneau, Pierre-Henri; Chandezon, Frédéric

    2013-10-01

    The present work focuses on the study of the three-dimensional (3D) morphology of polymer and nanoparticle hybrid nanocomposites used as active layers in solution-processed solar cells. The hybrid consists of blends of regioregular poly(3-alkylthiophene) and CdSe nanorods. Electron tomography (ET) analysis performed in high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) allows resolving single nanorods in the hybrid blend. These results are compared with those obtained using focused ion beam coupled with scanning electron microscopy (FIB-SEM), operated in a so-called 3D ``slice-and-view'' mode. This technique allows 3D information to be obtained on a whole device stack (hybrid active layers plus electrodes and the substrate) for significantly larger surface areas than with ET (~10 vs. ~0.1 μm2). The combination of ET and 3D FIB ``slice-and-view'' reconstructions provides complementary and coherent information on the 3D morphology of the hybrid systems at different length scales. Phase separation between the nanoparticles and the polymer is investigated by a quantitative analysis of the reconstructed volumes and is related to the performances of the hybrid devices.The present work focuses on the study of the three-dimensional (3D) morphology of polymer and nanoparticle hybrid nanocomposites used as active layers in solution-processed solar cells. The hybrid consists of blends of regioregular poly(3-alkylthiophene) and CdSe nanorods. Electron tomography (ET) analysis performed in high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) allows resolving single nanorods in the hybrid blend. These results are compared with those obtained using focused ion beam coupled with scanning electron microscopy (FIB-SEM), operated in a so-called 3D ``slice-and-view'' mode. This technique allows 3D information to be obtained on a whole device stack (hybrid active layers plus electrodes and the substrate) for

  20. Analysis of composition and microstructural uniformity of hybrid glass/carbon fibre composites

    DEFF Research Database (Denmark)

    Beauson, Justine; Markussen, Christen Malte; Madsen, Bo

    2013-01-01

    In hybrid fibre composites, the intermixing of the two types of fibres imposes challenges to obtain materials with a well-defined and uniform microstructure. In the present paper, the composition and the microstructural uniformity of hybrid glass/carbon fibre composites mixed at the fibre bundle...... fibre volume fractions are determined using volumetric calculations. A model is presented to predict the interrelation of volume fractions in hybrid fibre composites. The microstructural uniformity of the composites is analysed by the determined variation in composite volume fractions. Two analytical...... level are investigated. The different levels of compositions in the composites are defined and experimentally determined. The composite volume fractions are determined using an image analysis based procedure. The global fibre volume fractions are determined using a gravimetrical based method. The local...

  1. Flexural, Impact Properties and Sem Analysis of Bamboo and Glass Fiber Reinforced Polyester Hybrid Composites

    Directory of Open Access Journals (Sweden)

    Raghavendra Rao. H

    2014-08-01

    Full Text Available The Flexural, Impact properties and Scanning electron microscope analysis of Bamboo/glass fibers Reinforced polyester Hybrid composites were studied. The effect of alkali treatment of the bamboo fibers on these properties was also studied. It was observed that the Flexural, impact properties of the hybrid composite increase with glass fiber content. These properties found to be higher when alkali treated bamboo fibers were used in the hybrid composites. The elimination of amorphous hemi-cellulose with alkali treated leading to higher crystallinity of the bamboo fibers with alkali treatment may be responsible for these observations. The author investigated the interfacial bonding between Glass/Bamboo reinforced polyester composites. The effect of alkali treatment on the bonding between Glass/Bamboo composites was also studied.

  2. Combined analysis of cervical smears. Cytopathology, image cytometry and in situ hybridization.

    Science.gov (United States)

    Multhaupt, H; Bruder, E; Elit, L; Rothblat, I; Warhol, M

    1993-01-01

    This study was an attempt to correlate the Bethesda System of Papanicolaou smear classification with DNA content by image analysis and the presence of human papillomavirus (HPV) as determined by in situ hybridization. DNA histograms were classified as normal diploid, diploid proliferative, polyploid and aneuploid. HPV in situ hybridization was performed with a cocktail of probes specific to HPV types 6, 11, 16 and 18. There was a good correlation between normal cytology and normal DNA histograms. Cytologically normal smears with bacterial or fungal infections showed a high proliferation index. HPV infection correlated with DNA polyploidy but was seen in 15 of 29 smears classified as cytologically normal. Morphologically abnormal Papanicolaou smears correlated with aneuploid DNA content. Smears classified as intraepithelial neoplasia correlated with aneuploid DNA content in all 12 cases. Four of five cases cytologically suspicious for HPV infection had HPV by in situ hybridization.

  3. Analysis of the Hybrid Power System for High-Altitude Unmanned Aircraft

    Directory of Open Access Journals (Sweden)

    Kangwen Sun

    2015-01-01

    Full Text Available The application of single solar array on high-altitude unmanned aircraft will waste energy because of its low conversion efficiency. Furthermore, since its energy utilization is limited, the surface temperature of solar array will rise to 70°C due to the waste solar energy, thus reducing the electrical performance of the solar array. In order to reuse the energy converted into heat by solar array, a hybrid power system is presented in this paper. In the hybrid power system, a new electricity-generating method is adopted to spread the photovoltaic cell on the wing surface and arrange photothermal power in the wing box section. Because the temperature on the back of photovoltaic cell is high, it can be used as the high-temperature heat source. The lower wing surface can be a low-temperature cold source. A high-altitude unmanned aircraft was used to analyze the performances of pure solar-powered aircraft and hybrid powered aircraft. The analysis result showed that the hybrid system could reduce the area of wing by 19% and that high-altitude unmanned aircraft with a 35 m or less wingspan could raise the utilization rate of solar energy per unit area after adopting the hybrid power system.

  4. A hybrid approach to device integration on a genetic analysis platform

    Science.gov (United States)

    Brennan, Des; Jary, Dorothee; Kurg, Ants; Berik, Evgeny; Justice, John; Aherne, Margaret; Macek, Milan; Galvin, Paul

    2012-10-01

    Point-of-care (POC) systems require significant component integration to implement biochemical protocols associated with molecular diagnostic assays. Hybrid platforms where discrete components are combined in a single platform are a suitable approach to integration, where combining multiple device fabrication steps on a single substrate is not possible due to incompatible or costly fabrication steps. We integrate three devices each with a specific system functionality: (i) a silicon electro-wetting-on-dielectric (EWOD) device to move and mix sample and reagent droplets in an oil phase, (ii) a polymer microfluidic chip containing channels and reservoirs and (iii) an aqueous phase glass microarray for fluorescence microarray hybridization detection. The EWOD device offers the possibility of fully integrating on-chip sample preparation using nanolitre sample and reagent volumes. A key challenge is sample transfer from the oil phase EWOD device to the aqueous phase microarray for hybridization detection. The EWOD device, waveguide performance and functionality are maintained during the integration process. An on-chip biochemical protocol for arrayed primer extension (APEX) was implemented for single nucleotide polymorphism (SNiP) analysis. The prepared sample is aspirated from the EWOD oil phase to the aqueous phase microarray for hybridization. A bench-top instrumentation system was also developed around the integrated platform to drive the EWOD electrodes, implement APEX sample heating and image the microarray after hybridization.

  5. EVALUATION OF HYBRIDIZATION BETWEEN PANGASIUS DJAMBAL BLEEKER 1846 AND PANGASIANODON HYPOPHTHALMUS (SAUVAGE 1878): BIOMETRIC CHARACTERIZATION AND GROWTH ANALYSIS

    OpenAIRE

    Rudhy Gustiano; Anang Hari Kristanto

    2007-01-01

    Possible use of pangasiid hybrids in aquaculture might generate potential impacts on wild populations. Therefore, rapid identification tools in the field such as growth rate are urgently needed. This study examines morphological characters and growth performance of P. djambal and P. hypophthalmus and their reciprocal hybrids. A detailed morphological study analysed 32 morphometric measurements and 5 meristic counts on hybrids of Pangasius djambal and P. hypophthalmus. Morphometric analysis an...

  6. Comparative genomic hybridization of microdissected samples from different stages in the development of a seminoma and a non-seminoma

    NARCIS (Netherlands)

    Looijenga, LHJ; Rosenberg, C; van Gurp, RJHLM; Geelen, E; van Echten-Arends, J; de Jong, B; Mostert, M

    2000-01-01

    Human testicular germ cell tumours (TGCTs) of adolescents and adults, both seminomas and non-seminomas, originate from intratubular germ cell neoplasia (IGCN). Comparative genomic hybridization (CGH) was applied to microdissected samples from different stages of the development of a seminoma and a m

  7. Comparative genomic hybridization of microdissected samples from different stages in the development of a seminoma and a non-seminoma

    NARCIS (Netherlands)

    Looijenga, LHJ; Rosenberg, C; van Gurp, RJHLM; Geelen, E; van Echten-Arends, J; de Jong, B; Mostert, M

    Human testicular germ cell tumours (TGCTs) of adolescents and adults, both seminomas and non-seminomas, originate from intratubular germ cell neoplasia (IGCN). Comparative genomic hybridization (CGH) was applied to microdissected samples from different stages of the development of a seminoma and a

  8. Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors.

    NARCIS (Netherlands)

    Veltman, J.A.; Fridlyand, J.; Pejavar, S.; Olshen, A.B.; Korkola, J.E.; Vries, S. de; Carroll, P.; Kuo, W.L.; Pinkel, D.; Albertson, D.; Cordon-Cardo, C.; Jain, A.N.; Waldman, F.M.

    2003-01-01

    Genome-wide copy number profiles were characterized in 41 primary bladder tumors using array-based comparative genomic hybridization (array CGH). In addition to previously identified alterations in large chromosomal regions, alterations were identified in many small genomic regions, some with high-l

  9. Prenatal diagnosis of Wolf-Hirschhorn syndrome confirmed by comparative genomic hybridization array: report of two cases and review of the literature

    Directory of Open Access Journals (Sweden)

    Sifakis Stavros

    2012-02-01

    Full Text Available Abstract Wolf-Hirschhorn syndrome (WHS is a well known genetic condition caused by a partial deletion of the short arm of chromosome 4. The great variability in the extent of the 4p deletion and the possible contribution of additional genetic rearrangements lead to a wide spectrum of clinical manifestations. The majority of the reports of prenatally diagnosed WHS cases are associated with large 4p deletions identified by conventional chromosome analysis; however, the widespread clinical use of novel molecular techniques such as array comparative genomic hybridization (a-CGH has increased the detection rate of submicroscopic chromosomal aberrations associated with WHS phenotype. We provide a report of two fetuses with WHS presenting with intrauterine growth restriction as an isolated finding or combined with oligohydramnios and abnormal Doppler waveform in umbilical artery and uterine arteries. Standard karyotyping demonstrated a deletion on chromosome 4 in both cases [del(4(p15.33 and del(4(p15.31, respectively] and further application of a-CGH confirmed the diagnosis and offered a precise characterization of the genetic defect. A detailed review of the currently available literature on the prenatal diagnostic approach of WHS in terms of fetal sonographic assessment and molecular cytogenetic investigation is also provided.

  10. Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples.

    Science.gov (United States)

    Zhou, Qinghua; Wu, Shen-Yin; Amato, Katherine; DiAdamo, Autumn; Li, Peining

    2016-03-20

    Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants (CNVs) in products of conception (POC) and the underlying gene-dosage-sensitive mechanisms causing spontaneous abortions remain largely unknown. In this study, array comparative genomic hybridization (aCGH) analysis was performed as a salvage procedure for 128 POC culture failure (POC-CF) samples and as a supplemental procedure for 106 POC normal karyotype (POC-NK) samples. Chromosomal abnormalities were detected in 10% of POC-CF and pathogenic CNVs were detected in 3.9% of POC-CF and 5.7% of POC-NK samples. Compiled results from this study and relevant case series through a literature review demonstrated an abnormality detection rate (ADR) of 35% for chromosomal abnormalities in POC-CF samples, 3.7% for pathogenic CNVs in POC-CF samples, and 4.6% for pathogenic CNVs in POC-NK samples. Ingenuity Pathway Analysis (IPA) was performed on the genes from pathogenic CNVs found in POC samples. The denoted primary gene networks suggested that apoptosis and cell proliferation pathways are involved in miscarriage. In summary, a similar spectrum of cytogenomic abnormalities was observed in POC culture success and POC-CF samples. A threshold effect correlating the number of dosage-sensitive genes in a chromosome with the observed frequency of autosomal trisomy is proposed. A rationalized approach using firstly fluorescence in situ hybridization (FISH) testing with probes of chromosomes X/Y/18, 13/21, and 15/16/22 for common aneuploidies and polyploidies and secondly aCGH for other cytogenomic abnormalities is recommended for POC-CF samples.

  11. Hybrid molecular dynamics simulation for plasma induced damage analysis

    Science.gov (United States)

    Matsukuma, Masaaki

    2016-09-01

    In order to enable further device size reduction (also known as Moore's law) and improved power performance, the semiconductor industry is introducing new materials and device structures into the semiconductor fabrication process. Materials now include III-V compounds, germanium, cobalt, ruthenium, hafnium, and others. The device structure in both memory and logic has been evolving from planar to three dimensional (3D). One such device is the FinFET, where the transistor gate is a vertical fin made either of silicon, silicon-germanium or germanium. These changes have brought renewed interests in the structural damages caused by energetic ion bombardment of the fin sidewalls which are exposed to the ion flux from the plasma during the fin-strip off step. Better control of the physical damage of the 3D devices requires a better understanding of the damage formation mechanisms on such new materials and structures. In this study, the damage formation processes by ion bombardment have been simulated for Si and Ge substrate by Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid simulations and compared to the results from the classical molecular dynamics (MD) simulations. In our QM/MM simulations, the highly reactive region in which the structural damage is created is simulated with the Density Functional based Tight Binding (DFTB) method and the region remote from the primary region is simulated using classical MD with the Stillinger-Weber and Moliere potentials. The learn on the fly method is also used to reduce the computational load. Hence our QM/MM simulation is much faster than the full QC-MD simulations and the original QM/MM simulations. The amorphous layers profile simulated with QM/MM have obvious differences in their thickness for silicon and germanium substrate. The profile of damaged structure in the germanium substrate is characterized by a deeper tail then in silicon. These traits are also observed in the results from the mass selected ion beam

  12. The strength of the hybrid braking calipers analysis

    Institute of Scientific and Technical Information of China (English)

    Li Weitao; Yu Haiqing; Jiang Xiaoyan

    2015-01-01

    The braking system is an important part to ensure the safety of the vehicle, so the strength analysis is essential to the brake caliper. In this article, the forces will be mixed in the caliper brake systems theoretical analysis, and based on the actual working conditions established calipers ABAQUS finite element model to simulate calipers provide a theoretical basis for the structural design of the brake caliper.

  13. Nonlinear Analysis and Preliminary Testing Results of a Hybrid Wing Body Center Section Test Article

    Science.gov (United States)

    Przekop, Adam; Jegley, Dawn C.; Rouse, Marshall; Lovejoy, Andrew E.; Wu, Hsi-Yung T.

    2015-01-01

    A large test article was recently designed, analyzed, fabricated, and successfully tested up to the representative design ultimate loads to demonstrate that stiffened composite panels with through-the-thickness reinforcement are a viable option for the next generation large transport category aircraft, including non-conventional configurations such as the hybrid wing body. This paper focuses on finite element analysis and test data correlation of the hybrid wing body center section test article under mechanical, pressure and combined load conditions. Good agreement between predictive nonlinear finite element analysis and test data is found. Results indicate that a geometrically nonlinear analysis is needed to accurately capture the behavior of the non-circular pressurized and highly-stressed structure when the design approach permits local buckling.

  14. ANALYSIS OF ASSEMBLY SUITABILITY OF THE HYBRID NODE BASED ON WELD DISTORTION PREDICTION MODELS

    Directory of Open Access Journals (Sweden)

    Tomasz Urbański

    2015-08-01

    Full Text Available The article presents an analysis of assembly suitability of the innovative hybrid node. Weld distortions are a factor that affects significantly the quality of a structure during its pre-fabrication stage, thus increasing manufacturing costs . For the purposes of this analysis, such distortion forms were chosen that are the highest-ranking ones in the technological hierarchy. The analysis was performed taking advantage of significant parameters in order to demonstrate the possibilities of using mathematical models determined on the basis of a designed experiment to modify the construction technology as early as during the stage of the hybrid node’s manufacture. It was shown that using the above-mentioned theoretical models a technological assessment of the structural component can be performed by selecting such system of parameters that will produce distortions at a level acceptable from the point of view of further assembly suitability.

  15. New class of hybrid EoS and Bayesian M - R data analysis

    Energy Technology Data Exchange (ETDEWEB)

    Alvarez-Castillo, D. [JINR Dubna, Bogoliubov Laboratory of Theoretical Physics, Dubna (Russian Federation); Ayriyan, A.; Grigorian, H. [JINR Dubna, Laboratory of Information Technologies, Dubna (Russian Federation); Benic, S. [University of Zagreb, Department of Physics, Zagreb (Croatia); Blaschke, D. [JINR Dubna, Bogoliubov Laboratory of Theoretical Physics, Dubna (Russian Federation); National Research Nuclear University (MEPhI), Moscow (Russian Federation); Typel, S. [GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt (Germany)

    2016-03-15

    We explore systematically a new class of two-phase equations of state (EoS) for hybrid stars that is characterized by three main features: (1) stiffening of the nuclear EoS at supersaturation densities due to quark exchange effects (Pauli blocking) between hadrons, modelled by an excluded volume correction; (2) stiffening of the quark matter EoS at high densities due to multiquark interactions; and (3) possibility for a strong first-order phase transition with an early onset and large density jump. The third feature results from a Maxwell construction for the possible transition from the nuclear to a quark matter phase and its properties depend on the two parameters used for (1) and (2), respectively. Varying these two parameters, one obtains a class of hybrid EoS that yields solutions of the Tolman-Oppenheimer-Volkoff (TOV) equations for sequences of hadronic and hybrid stars in the mass-radius diagram which cover the full range of patterns according to the Alford-Han-Prakash classification following which a hybrid star branch can be either absent, connected or disconnected with the hadronic one. The latter case often includes a tiny connected branch. The disconnected hybrid star branch, also called ''third family'', corresponds to high-mass twin stars characterized by the same gravitational mass but different radii. We perform a Bayesian analysis and demonstrate that the observation of such a pair of high-mass twin stars would have a sufficient discriminating power to favor hybrid EoS with a strong first-order phase transition over alternative EoS. (orig.)

  16. Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features

    National Research Council Canada - National Science Library

    Shaw-Smith, C; Redon, R; Rickman, L; Rio, M; Willatt, L; Fiegler, H; Firth, H; Sanlaville, D; Winter, R; Colleaux, L; Bobrow, M; Carter, N P

    2004-01-01

    ...). The presence of subtle DNA copy number changes was investigated by array-CGH in 50 patients with learning disability and dysmorphism, employing a DNA microarray constructed from large insert clones...

  17. Reconstruction and analysis of hybrid composite shells using meshless methods

    Science.gov (United States)

    Bernardo, G. M. S.; Loja, M. A. R.

    2017-02-01

    The importance of focusing on the research of viable models to predict the behaviour of structures which may possess in some cases complex geometries is an issue that is growing in different scientific areas, ranging from the civil and mechanical engineering to the architecture or biomedical devices fields. In these cases, the research effort to find an efficient approach to fit laser scanning point clouds, to the desired surface, has been increasing, leading to the possibility of modelling as-built/as-is structures and components' features. However, combining the task of surface reconstruction and the implementation of a structural analysis model is not a trivial task. Although there are works focusing those different phases in separate, there is still an effective need to find approaches able to interconnect them in an efficient way. Therefore, achieving a representative geometric model able to be subsequently submitted to a structural analysis in a similar based platform is a fundamental step to establish an effective expeditious processing workflow. With the present work, one presents an integrated methodology based on the use of meshless approaches, to reconstruct shells described by points' clouds, and to subsequently predict their static behaviour. These methods are highly appropriate on dealing with unstructured points clouds, as they do not need to have any specific spatial or geometric requirement when implemented, depending only on the distance between the points. Details on the formulation, and a set of illustrative examples focusing the reconstruction of cylindrical and double-curvature shells, and its further analysis, are presented.

  18. Reconstruction and analysis of hybrid composite shells using meshless methods

    Science.gov (United States)

    Bernardo, G. M. S.; Loja, M. A. R.

    2017-06-01

    The importance of focusing on the research of viable models to predict the behaviour of structures which may possess in some cases complex geometries is an issue that is growing in different scientific areas, ranging from the civil and mechanical engineering to the architecture or biomedical devices fields. In these cases, the research effort to find an efficient approach to fit laser scanning point clouds, to the desired surface, has been increasing, leading to the possibility of modelling as-built/as-is structures and components' features. However, combining the task of surface reconstruction and the implementation of a structural analysis model is not a trivial task. Although there are works focusing those different phases in separate, there is still an effective need to find approaches able to interconnect them in an efficient way. Therefore, achieving a representative geometric model able to be subsequently submitted to a structural analysis in a similar based platform is a fundamental step to establish an effective expeditious processing workflow. With the present work, one presents an integrated methodology based on the use of meshless approaches, to reconstruct shells described by points' clouds, and to subsequently predict their static behaviour. These methods are highly appropriate on dealing with unstructured points clouds, as they do not need to have any specific spatial or geometric requirement when implemented, depending only on the distance between the points. Details on the formulation, and a set of illustrative examples focusing the reconstruction of cylindrical and double-curvature shells, and its further analysis, are presented.

  19. Rapid discrimination between four seagrass species using hybrid analysis.

    Science.gov (United States)

    Osathanunkul, M; Madesis, P; Ounjai, S; Suwannapoom, C; Jampeetong, A

    2015-04-27

    Biological species are traditionally identified based on their morphological features and the correct identification of species is critical in biological studies. However, some plant types, such as seagrass, are taxonomically problematic and difficult to identify. Furthermore, closely related seagrass species, such as Halophila spp, form a taxonomically unresolved complex. Although some seagrass taxa are easy to recognize, most species are difficult to identify without skilled taxonomic or molecular techniques. Barcoding coupled with High Resolution Melting analysis (BAR-HRM) offers a potentially reliable, rapid, and cost-effective method to confirm species. Here, DNA information of two chloroplast loci was used in combination with HRM analysis to discriminate four species of seagrass collected off the southern coast of Thailand. A distinct melting curve presenting one inflection point was generated for each species using rbcL primers. While the melting profiles of Cymodocea rotundata and Cymodocea serrulata were not statistically different, analysis of the normalized HRM curves produced with the rpoC primers allowed for their discrimination. The Bar-HRM technique showed promise in discriminating seagrass species and with further adaptations and improvements, could make for an effective and power tool for confirming seagrass species.

  20. Clinical trial involving sufferers and non-sufferers of cervicogenic headache (CGH): potential mechanisms of action of photobiomodulation (Conference Presentation)

    Science.gov (United States)

    Liebert, Ann D.; Bicknell, Brian

    2017-02-01

    Photobiomodulation (PBM) is an effective tool for the management of spinal pain including inflammation of facet joints. Apart from cervical and lumbar joint pain the upper cervical spine facet joint inflammation can result in the CGH (traumatic or atraumatic in origin). This condition affects children, adults and elders and is responsible for 19% of chronic headache and up to 33% of patients in pain clinics. The condition responds well to physiotherapy, facet joint injection, radiofrequency neurotomy and surgery at a rate of 75%. The other 25% being unresponsive to treatment with no identified features of unresponsiveness. In other conditions of chronic unresponsive cervical pain have responded to photobiomodulation at a level of 80% in the short and medium term. A clinical trial was therefore conducted on a cohort of atraumatic patients from the ages of 5-93 (predominantly Neurologist referred / familial sufferers 2/3 generations vertically and laterally) who had responded to a course of PBM and physiotherapy. The CGH sufferers and their non CGH suffering relatives over these generations were then compared for features that distinguish the two groups. Fifty parameters were tested (anthropmetric, movement and neural tension tests included) and there was a noted difference in tandem stance between the groups (.04 significance with repeated measures). As this impairment is common to benign ataxia and migrainous vertigo and in these conditions there is an ion channelopathy (especially potassium channelopathy). A postulated mechanism of action of PBM would involve modulation of ion channels and this is discussed in this presentation.

  1. A Hybrid Latent Class Analysis Modeling Approach to Analyze Urban Expressway Crash Risk.

    Science.gov (United States)

    Yu, Rongjie; Wang, Xuesong; Abdel-Aty, Mohamed

    2017-02-07

    Crash risk analysis is rising as a hot research topic as it could reveal the relationships between traffic flow characteristics and crash occurrence risk, which is beneficial to understand crash mechanisms which would further refine the design of Active Traffic Management System (ATMS). However, the majority of the current crash risk analysis studies have ignored the impact of geometric characteristics on crash risk estimation while recent studies proved that crash occurrence risk was affected by the various alignment features. In this study, a hybrid Latent Class Analysis (LCA) modeling approach was proposed to account for the heterogeneous effects of geometric characteristics. Crashes were first segmented into homogenous subgroups, where the optimal number of latent classes was identified based on bootstrap likelihood ratio tests. Then, separate crash risk analysis models were developed using Bayesian random parameter logistic regression technique; data from Shanghai urban expressway system were employed to conduct the empirical study. Different crash risk contributing factors were unveiled by the hybrid LCA approach and better model goodness-of-fit was obtained while comparing to an overall total crash model. Finally, benefits of the proposed hybrid LCA approach were discussed.

  2. Performance analysis on a hybrid air-conditioning system of a green building

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Q.; Wang, R.Z.; Dai, Y.J.; Zhai, X.Q. [Shanghai Jiao Tong University (China). School of Mechanical Engineering

    2006-05-15

    This paper presents the performance analysis on a hybrid air-conditioning system according to the hybrid building energy system of the green building demonstration project in Shanghai, in which a 150 m{sup 2} solar collector is used to power two 10 kW adsorption chillers, a vapor compression heat pump is used to cool air in the evaporating end while the condensing heating at about 80{sup o}C is fully used to regenerate a liquid desiccant dehumidification system. In the hybrid system, the sensible cooling to the air is treated mainly by solar adsorption cooling and vapor compression cooling, whereas the latent heat is treated by the liquid desiccant dehumidification system with regeneration from the condensing heat of the heat pump. The results show that the performance of this system is 44.5% higher than conventional vapor compression system at a latent load of 30% and this improving can be achieved by 73.8% at a 42% latent load. The optimal ratio of adsorption refrigerating power to total cooling load for this kind of hybrid systems is also studied in this paper. (author)

  3. A hybrid analysis method for linear dynamic soil-structure interaction in time and frequency domain

    Institute of Scientific and Technical Information of China (English)

    丁海平; 廖振鹏

    2001-01-01

    A hybrid analysis method in time and frequency domains for linear soil-structure interaction is presented. First, the time domain solution of the system with Rayleigh damping excited by a short time impulse is obtained by the decoupling numerical simulation technique of near-field wave motion. Then, the corresponding frequency domain solution can be got by Fourier transform. According to the relationship between damping value and dynamic re-sponse of a system, the solution of the system with complex damping can be got by Taylor expansion. The hybrid method makes the best of decoupling and explicit algorithm in time domain, and increases the calculation efficien-cy for linear soil-structure interaction analysis.

  4. Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization (FISH)

    DEFF Research Database (Denmark)

    Ronander, Elena; Bengtsson, Dominique C; Joergensen, Louise;

    2012-01-01

    and the consequence of differential binding on the clinical outcome of P. falciparum infections. Recently, the mutually exclusive transcription paradigm has been called into doubt by transcription assays based on individual P. falciparum transcript identification in single infected erythrocytic cells using RNA...... fluorescent in situ hybridization (FISH) analysis of var gene transcription by the parasite in individual nuclei of P. falciparum IE(1). Here, we present a detailed protocol for carrying out the RNA-FISH methodology for analysis of var gene transcription in single-nuclei of P. falciparum infected human...... erythrocytes. The method is based on the use of digoxigenin- and biotin- labeled antisense RNA probes using the TSA Plus Fluorescence Palette System(2) (Perkin Elmer), microscopic analyses and freshly selected P. falciparum IE. The in situ hybridization method can be used to monitor transcription...

  5. Finite Element Analysis of Adaptive-Stiffening and Shape-Control SMA Hybrid Composites

    Science.gov (United States)

    Gao, Xiujie; Burton, Deborah; Turner, Travis L.; Brinson, Catherine

    2005-01-01

    Shape memory alloy hybrid composites with adaptive-stiffening or morphing functions are simulated using finite element analysis. The composite structure is a laminated fiber-polymer composite beam with embedded SMA ribbons at various positions with respect to the neutral axis of the beam. Adaptive stiffening or morphing is activated via selective resistance heating of the SMA ribbons or uniform thermal loads on the beam. The thermomechanical behavior of these composites was simulated in ABAQUS using user-defined SMA elements. The examples demonstrate the usefulness of the methods for the design and simulation of SMA hybrid composites. Keywords: shape memory alloys, Nitinol, ABAQUS, finite element analysis, post-buckling control, shape control, deflection control, adaptive stiffening, morphing, constitutive modeling, user element

  6. Mobile 3D quality of experience evaluation: a hybrid data collection and analysis approach

    Science.gov (United States)

    Utriainen, Timo; Häyrynen, Jyrki; Jumisko-Pyykkö, Satu; Boev, Atanas; Gotchev, Atanas; Hannuksela, Miska M.

    2011-02-01

    The paper presents a hybrid approach to study the user's experienced quality of 3D visual content on mobile autostereoscopic displays. It combines extensive subjective tests with collection and objective analysis of eye-tracked data. 3D cues which are significant for mobiles are simulated in the generated 3D test content. The methodology for conducting subjective quality evaluation includes hybrid data-collection of quantitative quality preferences, qualitative impressions, and binocular eye-tracking. We present early results of the subjective tests along with eye movement reaction times, areas of interest and heatmaps obtained from raw eye-tracked data after statistical analysis. The study contributes to the question what is important to be visualized on portable auto-stereoscopic displays and how to maintain and visually enhance the quality of 3D content for such displays.

  7. A novel image compression-encryption hybrid algorithm based on the analysis sparse representation

    Science.gov (United States)

    Zhang, Ye; Xu, Biao; Zhou, Nanrun

    2017-06-01

    Recent advances on the compressive sensing theory were invoked for image compression-encryption based on the synthesis sparse model. In this paper we concentrate on an alternative sparse representation model, i.e., the analysis sparse model, to propose a novel image compression-encryption hybrid algorithm. The analysis sparse representation of the original image is obtained with an overcomplete fixed dictionary that the order of the dictionary atoms is scrambled, and the sparse representation can be considered as an encrypted version of the image. Moreover, the sparse representation is compressed to reduce its dimension and re-encrypted by the compressive sensing simultaneously. To enhance the security of the algorithm, a pixel-scrambling method is employed to re-encrypt the measurements of the compressive sensing. Various simulation results verify that the proposed image compression-encryption hybrid algorithm could provide a considerable compression performance with a good security.

  8. Hybrid modeling and empirical analysis of automobile supply chain network

    Science.gov (United States)

    Sun, Jun-yan; Tang, Jian-ming; Fu, Wei-ping; Wu, Bing-ying

    2017-05-01

    Based on the connection mechanism of nodes which automatically select upstream and downstream agents, a simulation model for dynamic evolutionary process of consumer-driven automobile supply chain is established by integrating ABM and discrete modeling in the GIS-based map. Firstly, the rationality is proved by analyzing the consistency of sales and changes in various agent parameters between the simulation model and a real automobile supply chain. Second, through complex network theory, hierarchical structures of the model and relationships of networks at different levels are analyzed to calculate various characteristic parameters such as mean distance, mean clustering coefficients, and degree distributions. By doing so, it verifies that the model is a typical scale-free network and small-world network. Finally, the motion law of this model is analyzed from the perspective of complex self-adaptive systems. The chaotic state of the simulation system is verified, which suggests that this system has typical nonlinear characteristics. This model not only macroscopically illustrates the dynamic evolution of complex networks of automobile supply chain but also microcosmically reflects the business process of each agent. Moreover, the model construction and simulation of the system by means of combining CAS theory and complex networks supplies a novel method for supply chain analysis, as well as theory bases and experience for supply chain analysis of auto companies.

  9. Cost Effectiveness Analysis of Quasi-Static Wireless Power Transfer for Plug-In Hybrid Electric Transit Buses: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lijuan; Gonder, Jeff; Burton, Evan; Brooker, Aaron; Meintz, Andrew; Konan, Arnaud

    2015-11-11

    This study evaluates the costs and benefits associated with the use of a plug-in hybrid electric bus and determines the cost effectiveness relative to a conventional bus and a hybrid electric bus. A sensitivity sweep analysis was performed over a number of a different battery sizes, charging powers, and charging stations. The net present value was calculated for each vehicle design and provided the basis for the design evaluation. In all cases, given present day economic assumptions, the conventional bus achieved the lowest net present value while the optimal plug-in hybrid electric bus scenario reached lower lifetime costs than the hybrid electric bus. The study also performed parameter sensitivity analysis under low market potential assumptions and high market potential assumptions. The net present value of plug-in hybrid electric bus is close to that of conventional bus.

  10. Hybrid Finite Element Analysis of Free Edge Effect in Symmetric Composite Laminates

    Science.gov (United States)

    1983-06-01

    ANALYSIS OF FREE EDGE EFFECT IN L AUTHOR(S 61102F S.W. Lee237B J.J. Rhiu S.C. Won,, I ~ 7. PENOAMnG ORGANIZATION NAME(S) AND ADORES4 S) L. PERFORMING...ANALYSIS OF FREE EDGE EFFECT IN SYMMETRIC COMPOSITE LAMINATES S. W. Lee I 3. Phi S. C. Wong Department of Aerospace Engineering University of Maryland...collocation method. In this report, we present an efficient hybrid finite element method for analysis of interlaminar stress or free edge effect in

  11. Efficient Mooring Line Fatigue Analysis Using a Hybrid Method Time Domain Simulation Scheme

    DEFF Research Database (Denmark)

    Christiansen, Niels Hørbye; Voie, Per Erlend Torbergsen; Høgsberg, Jan Becker;

    2013-01-01

    Dynamic analyses of mooring line systems are computationally expensive. Over the last decades an extensive variety of methods to reduce this computational cost have been suggested. One method that has shown promising preliminary results is a hybrid method which combines finite element analysis...... and slow drift motion. The method is tested on a mooring line system of a floating offshore platform. After training a full fatigue analysis is carried out. The results show that the ANN with high precision provides top tension force histories two orders of magnitude faster than a full dynamic analysis...

  12. A microfluidic-based electrochemical biochip for label-free DNA hybridization analysis.

    Science.gov (United States)

    Ben-Yoav, Hadar; Dykstra, Peter H; Gordonov, Tanya; Bentley, William E; Ghodssi, Reza

    2014-09-10

    Miniaturization of analytical benchtop procedures into the micro-scale provides significant advantages in regards to reaction time, cost, and integration of pre-processing steps. Utilizing these devices towards the analysis of DNA hybridization events is important because it offers a technology for real time assessment of biomarkers at the point-of-care for various diseases. However, when the device footprint decreases the dominance of various physical phenomena increases. These phenomena influence the fabrication precision and operation reliability of the device. Therefore, there is a great need to accurately fabricate and operate these devices in a reproducible manner in order to improve the overall performance. Here, we describe the protocols and the methods used for the fabrication and the operation of a microfluidic-based electrochemical biochip for accurate analysis of DNA hybridization events. The biochip is composed of two parts: a microfluidic chip with three parallel micro-channels made of polydimethylsiloxane (PDMS), and a 3 x 3 arrayed electrochemical micro-chip. The DNA hybridization events are detected using electrochemical impedance spectroscopy (EIS) analysis. The EIS analysis enables monitoring variations of the properties of the electrochemical system that are dominant at these length scales. With the ability to monitor changes of both charge transfer and diffusional resistance with the biosensor, we demonstrate the selectivity to complementary ssDNA targets, a calculated detection limit of 3.8 nM, and a 13% cross-reactivity with other non-complementary ssDNA following 20 min of incubation. This methodology can improve the performance of miniaturized devices by elucidating on the behavior of diffusion at the micro-scale regime and by enabling the study of DNA hybridization events.

  13. Thermoeconomic Analysis of Hybrid Power Plant Concepts for Geothermal Combined Heat and Power Generation

    OpenAIRE

    Florian Heberle; Dieter Brüggemann

    2014-01-01

    We present a thermo-economic analysis for a low-temperature Organic Rankine Cycle (ORC) in a combined heat and power generation (CHP) case. For the hybrid power plant, thermal energy input is provided by a geothermal resource coupled with the exhaust gases of a biogas engine. A comparison to alternative geothermal CHP concepts is performed by considering variable parameters like ORC working fluid, supply temperature of the heating network or geothermal water temperature. Second law efficiency...

  14. Appendage modal coordinate truncation criteria in hybrid coordinate dynamic analysis. [for spacecraft attitude control

    Science.gov (United States)

    Likins, P.; Ohkami, Y.; Wong, C.

    1976-01-01

    The paper examines the validity of the assumption that certain appendage-distributed (modal) coordinates can be truncated from a system model without unacceptable degradation of fidelity in hybrid coordinate dynamic analysis for attitude control of spacecraft with flexible appendages. Alternative truncation criteria are proposed and their interrelationships defined. Particular attention is given to truncation criteria based on eigenvalues, eigenvectors, and controllability and observability. No definitive resolution of the problem is advanced, and exhaustive study is required to obtain ultimate truncation criteria.

  15. Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

    Science.gov (United States)

    Kitajima, Akira; Nonaka, Keisuke; Yoshioka, Terutaka; Ohta, Satoshi; Goto, Shingo; Toyoda, Atsushi; Fujiyama, Asao; Mochizuki, Takako; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

    2016-01-01

    Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy–Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies. PMID:27902727

  16. Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes.

    Science.gov (United States)

    Shimizu, Tokurou; Kitajima, Akira; Nonaka, Keisuke; Yoshioka, Terutaka; Ohta, Satoshi; Goto, Shingo; Toyoda, Atsushi; Fujiyama, Asao; Mochizuki, Takako; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

    2016-01-01

    Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy-Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.

  17. Genetic analysis of a family with super-male syndrome%一个超雄综合征伴Yqh+家系的遗传学分析

    Institute of Scientific and Technical Information of China (English)

    张建林; 李海波; 姜胜华; 陈瑛; 张玉泉

    2014-01-01

    Objective To identify the genetic cause for a family featuring language retardation using combined cytogenetic and molecular genetic methods.Methods Following conventional G-banded karyotype analysis,the additional Y chromosome was identified by fluorescence in situ hybridization (FISH) and multiplex ligation dependent probe amplification (MLPA).Whole genome array-comparative genomic hybridization (aCGH) was also carried out to detect minor structural chromosomal abnormalities.Results The proband's karyotype was determined as 47,XY,+?,and the unknown aberrant chromosome was identified as Yqh+ with FISH,MLPA and aCGH.No other chromosomal abnormality was found in the pedigree.Conclusion Cytogenetic methods combined with FISH,MLPA,and aCGH can efficiently identify the origin of unknown chromosomes and provide accurate clues for clinical diagnosis and treatment.%目的 对1例语言发育迟缓患儿及其家系成员进行细胞和分子遗传学分析,寻找其致病原因.方法 常规外周血G显带分析后,应用荧光原位杂交(fluorescence in situ hybridization,FISH)技术、多重连接依赖探针扩增(multiplex ligation dependent probe amplification,MLPA)技术和微阵列比较基因组杂交(array-comparative genomic hybridization,aCGH)技术明确鉴定异常染色体.结果 患儿G显带染色体核型为47,XY,+?,不明来源的染色体经FISH结果证实为Y染色体,MLPA结果显示Y染色体探针增加,aCGH也显示Y染色体的拷贝数增加.未发现家系成员有其它染色体异常.结论 患儿的额外染色体为Y染色体.FISH、MLPA和aCGH等技术与细胞遗传学联合应用有助于准确鉴别不明来源的染色体,为临床诊疗提供准确的遗传学依据.

  18. Hybrid Powder - Single Crystal X-Ray Diffraction Instrument for Planetary Mineralogical Analysis of Unprepared Samples Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose to develop a planetary exploration XRD/XRF instrument based on a hybrid diffraction approach that complements powder XRD analysis, similar to that of the...

  19. Improving molecular diagnosis of aniridia and WAGR syndrome using customized targeted array-based CGH

    Science.gov (United States)

    Vallespín, Elena; Villaverde, Cristina; Martín-Arenas, Rubén; Vélez-Monsalve, Camilo; Lorda-Sánchez, Isabel; Nevado, Julián; Trujillo-Tiebas, María José; Lapunzina, Pablo; Ayuso, Carmen; Corton, Marta

    2017-01-01

    Chromosomal deletions at 11p13 are a frequent cause of congenital Aniridia, a rare pan-ocular genetic disease, and of WAGR syndrome, accounting up to 30% of cases. First-tier genetic testing for newborn with aniridia, to detect 11p13 rearrangements, includes Multiplex Ligation-dependent Probe Amplification (MLPA) and karyotyping. However, neither of these approaches allow obtaining a complete picture of the high complexity of chromosomal deletions and breakpoints in aniridia. Here, we report the development and validation of a customized targeted array-based comparative genomic hybridization, so called WAGR-array, for comprehensive high-resolution analysis of CNV in the WAGR locus. Our approach increased the detection rate in a Spanish cohort of 38 patients with aniridia, WAGR syndrome and other related ocular malformations, allowing to characterize four undiagnosed aniridia cases, and to confirm MLPA findings in four additional patients. For all patients, breakpoints were accurately established and a contiguous deletion syndrome, involving a large number of genes, was identified in three patients. Moreover, we identified novel microdeletions affecting 3' PAX6 regulatory regions in three families with isolated aniridia. This tool represents a good strategy for the genetic diagnosis of aniridia and associated syndromes, allowing for a more accurate CNVs detection, as well as a better delineation of breakpoints. Our results underline the clinical importance of performing exhaustive and accurate analysis of chromosomal rearrangements for patients with aniridia, especially newborns and those without defects in PAX6 after diagnostic screening. PMID:28231309

  20. An isothermal primer extension method for whole genome amplification of fresh and degraded DNA: applications in comparative genomic hybridization, genotyping and mutation screening.

    Science.gov (United States)

    Lee, Cheryl I P; Leong, Siew Hong; Png, Adrian E H; Choo, Keng Wah; Syn, Christopher; Lim, Dennis T H; Law, Hai Yang; Kon, Oi Lian

    2006-01-01

    We describe a protocol that uses a bioinformatically optimized primer in an isothermal whole genome amplification (WGA) reaction. Overnight incubation at 37 degrees C efficiently generates several hundred- to several thousand-fold increases in input DNA. The amplified product retains reasonably faithful quantitative representation of unamplified whole genomic DNA (gDNA). We provide protocols for applying this isothermal primer extension WGA protocol in three different techniques of genomic analysis: comparative genomic hybridization (CGH), genotyping at simple tandem repeat (STR) loci and screening for single base mutations in a common monogenic disorder, beta-thalassemia. gDNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues can also be amplified with this protocol.

  1. Performance Analysis of Hybrid PV/Diesel Energy System in Western Region of Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Makbul A. M. Ramli

    2014-01-01

    Full Text Available The potential implementation of hybrid photovoltaic (PV/diesel energy system in western region of Saudi Arabia is analyzed in this paper. The solar radiation intensity considered in this study is in the range of 4.15–7.17 kWh/m2/day. The HOMER software is used to perform the technical and economical analysis of the system. Three different system configurations, namely, stand-alone diesel system, and hybrid PV/diesel system with and without battery storage element, will be evaluated and discussed. The analysis will be addressed to the impact of PV penetration and battery storage on energy production, cost of energy, number of operational hours of diesel generators, fuel savings, and reduction of carbon emission for the given configurations. The simulation results indicate that the energy cost of the hybrid PV/diesel/battery system with 15% PV penetration, battery storage of 186.96 MWh, and energy demand of 32,962 MWh/day is $0.117/kWh.

  2. Phenotypic Variability and Diversity Analysis of Bean Traits of Some Cocoa Hybrids in Nigeria

    Directory of Open Access Journals (Sweden)

    A.V. Oyedokun

    2011-03-01

    Full Text Available It is essential to understand the economic potential and superiority among cocoa hybrids. Therefore, the present study aims at detecting variability among cocoa hybrids for bean index in Nigeria. Dried bean of fourteen genotypes of cocoa were evaluated for their bean values. Analysis of variance (ANOVA was used to understand the variability among the fourteen genotypes and Principal Component Analysis (PCA was employed to identify distinguishing traits and the grouping of the genotypes based on similarities. The fourteen cocoa genotypes were significantly (p≤0.05 different from each other with respect to weight of one bean, bean length, width, thickness, 100 bean weight, bean length to width, length to thickness and width to thickness ratio. All the studied morphometric characters exhibited high (>70% broad sense heritability. G8, the hybrid between T53/5 and N38 was the most superior genotype for bean weight and some other bean characteristics. The mass of seventy-four dried cocoa bean of G8 approximated 100 g. The first three Principal Component axes explained 91% of the total variation and the PCA grouped the fourteen genotypes into four distinct clusters. Genotypes could be selected for specific traits and improvement of traits seemed to be genetically reliable.

  3. Developmental Analysis of Genetic Behavior of Brown Rice Width in indica-japonica Hybrids

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiao-ming; SHI Chun-hai; YE Shen-hai; QI Yong-bin

    2006-01-01

    The developmental genetic behaviors of brown rice width (BRW) have been studied in indica-japonica hybrid rice (Oryza sativa L.), in which seven indica male sterile lines and five japonica restorer lines were applied, by using the developmental genetic models and corresponding statistical approaches for quantitative traits of triploid in cereal crops. The BRW of indica-japonica hybrid rice was co-determined by gene expression of triploid endosperm, cytoplasm, diploid maternal plant and their genotype ×environmental interaction effects. Unconditional analysis showed that the endosperm additive and maternal additive effects were predominant for the development of BRW from early- to late-stage of the grain development, but the endosperm dominant effect together with maternal effect and cytoplasmic effect became the major factor determing the BRW at the ripening stage. Moreover,conditional analysis found that there were new onset and offset of gene expression at different developmental stages of BRW in indica-japonica hybrid rice. Maternal and cytoplasm general heritabilities and their interaction heritabilities were more important compared to other components of heritability for BRW at all the five developmental stages.

  4. Sensitivity Analysis of Hybrid Propulsion Transportation System for Human Mars Expeditions

    Science.gov (United States)

    Chai, Patrick R.; Joyce, Ryan T.; Kessler, Paul D.; Merrill, Raymond G.; Qu, Min

    2017-01-01

    The National Aeronautics and Space Administration continues to develop and refine various transportation options to successfully field a human Mars campaign. One of these transportation options is the Hybrid Transportation System which utilizes both solar electric propulsion and chemical propulsion. The Hybrid propulsion system utilizes chemical propulsion to perform high thrust maneuvers, where the delta-V is most optimal when ap- plied to save time and to leverage the Oberth effect. It then utilizes solar electric propulsion to augment the chemical burns throughout the interplanetary trajectory. This eliminates the need for the development of two separate vehicles for crew and cargo missions. Previous studies considered single point designs of the architecture, with fixed payload mass and propulsion system performance parameters. As the architecture matures, it is inevitable that the payload mass and the performance of the propulsion system will change. It is desirable to understand how these changes will impact the in-space transportation system's mass and power requirements. This study presents an in-depth sensitivity analysis of the Hybrid crew transportation system to payload mass growth and solar electric propulsion performance. This analysis is used to identify the breakpoints of the current architecture and to inform future architecture and campaign design decisions.

  5. A novel hybrid Neumann expansion method for stochastic analysis of mistuned bladed discs

    Science.gov (United States)

    Yuan, Jie; Allegri, Giuliano; Scarpa, Fabrizio; Patsias, Sophoclis; Rajasekaran, Ramesh

    2016-05-01

    The paper presents a novel hybrid method to enhance the computational efficiency of matrix inversions during the stochastic analysis of mistuned bladed disc systems. The method is based on the use of stochastic Neumann expansion in the frequency domain, coupled with a matrix factorization in the neighbourhood of the resonant frequencies. The number of the expansion terms is used as an indicator to select the matrix inversion technique to be used, without introducing any additional computational cost. The proposed method is validated using two case studies, where the dynamics an aero-engine bladed disc is modelled first using a lumped parameter approach and then with high-fidelity finite element analysis. The frequency responses of the blades are evaluated according to different mistuning patterns via stiffness or mass perturbations under the excitation provided by the engine orders. Results from standard matrix factorization methods are used to benchmark the responses obtained from the proposed hybrid method. Unlike classic Neumann expansion methods, the new technique can effectively update the inversion of an uncertain matrix with no convergence problems during Monte Carlo simulations. The novel hybrid method is more computationally efficient than standard techniques, with no accuracy loss.

  6. Thermoeconomic analysis of SOFC-GT hybrid systems fed by liquid fuels

    Energy Technology Data Exchange (ETDEWEB)

    Santin, Marco; Traverso, Alberto; Magistri, Loredana; Massardo, Aristide [TPG-DIMSET, University of Genoa, Via Montallegro 1, 16145 Genoa (Italy)

    2010-02-15

    In the distributed power generation market, Solid Oxide Fuel Cell-Gas Turbine (SOFC-GT) hybrids are an attractive option. Prototypes are being tested around the world with different types of fuel, but mainly natural gas. In this publication, a study of SOFC-GT hybrids for operation with liquid fuels is presented. Two liquid fuels were investigated, methanol and kerosene, in four layouts, taking into account different fuel processing strategies. A 500 kW class hybrid system (HS) was analysed. Web-based ThermoEconomic Modular Program (WTEMP) software, developed by the Thermochemical Power Group of the University of Genoa, was used for the thermodynamic and investment analysis. Performance was calculated based on zero-dimensional component models. The economic assessment was performed with a through-life cost analysis approach. The cost of the conventional components was calculated with WTEMP cost equations. As a final result, methanol-fuelled HSs are shown to stand out for both their thermodynamic and economic performance. (author)

  7. Meiotic analysis of interspecific hybrids between Capsicum frutescens and Capsicum chinense

    Directory of Open Access Journals (Sweden)

    Nádia Fernandes Moreira

    2017-04-01

    Full Text Available The aim of this study was to observe the genetic relationship between C. frutescens (UENF 1636 and C. chinense (UENF 1785 based on the meiotic behavior, on the meiotic index, and on pollen viability of their F1 hybrids. For meiotic analysis and meiotic index, flower buds were collected and fixed for 24 hours in ethanol: acetic acid (3:1, and then transferred to 70% ethanol, and stored in a freezer. Slides preparation for meiosis, meiotic index and pollen viability was carried out according to the laboratory’s protocol. Hybrid meiosis was regular, and 12 pairs of chromosomes were observed in diakinesis, as well as a few anomalies. The MI of 88.16%, as well as the pollen viability of 72.5%, were satisfactory. Given the results, it was confirmed the genetic proximity of these species, which are classified in the Capsicum annuum gene complex.

  8. Energy-saving analysis of hydraulic hybrid excavator based on common pressure rail.

    Science.gov (United States)

    Shen, Wei; Jiang, Jihai; Su, Xiaoyu; Karimi, Hamid Reza

    2013-01-01

    Energy-saving research of excavators is becoming one hot topic due to the increasing energy crisis and environmental deterioration recently. Hydraulic hybrid excavator based on common pressure rail (HHEC) provides an alternative with electric hybrid excavator because it has high power density and environment friendly and easy to modify based on the existing manufacture process. This paper is focused on the fuel consumption of HHEC and the actuator dynamic response to assure that the new system can save energy without sacrificing performance. Firstly, we introduce the basic principle of HHEC; then, the sizing process is presented; furthermore, the modeling period which combined mathematical analysis and experiment identification is listed. Finally, simulation results show that HHEC has a fast dynamic response which can be accepted in engineering and the fuel consumption can be reduced 21% to compare the original LS excavator and even 32% after adopting another smaller engine.

  9. Fluorescence Image Analyzer - FLIMA: software for quantitative analysis of fluorescence in situ hybridization.

    Science.gov (United States)

    Silva, H C M; Martins-Júnior, M M C; Ribeiro, L B; Matoso, D A

    2017-03-30

    The Fluorescence Image Analyzer (FLIMA) software was developed for the quantitative analysis of images generated by fluorescence in situ hybridization (FISH). Currently, the images of FISH are examined without a coefficient that enables a comparison between them. Through GD Graphics Library, the FLIMA software calculates the amount of pixels on image and recognizes each present color. The coefficient generated by the algorithm shows the percentage of marks (probes) hybridized on the chromosomes. This software can be used for any type of image generated by a fluorescence microscope and is able to quantify digoxigenin probes exhibiting a red color, biotin probes exhibiting a green color, and double-FISH probes (digoxigenin and biotin used together), where the white color is displayed.

  10. Hybrid FDTD Analysis for Periodic On-Chip Terahertz (THZ) Structures

    Energy Technology Data Exchange (ETDEWEB)

    Hussein, Yasser A.; Spencer, James E.; /SLAC

    2005-06-07

    We present electromagnetic analysis and radiation efficiency calculations for on-chip terahertz (THz) structures based on a hybrid, finite-difference, time-domain (HFDTD) technique. The method employs the FDTD technique to calculate S-parameters for one cell of a periodic structure. The transmission ABCD matrix is then estimated and multiplied by itself n times to obtain the n-cell periodic structure ABCD parameters that are then converted back to S-parameters. Validation of the method is carried out by comparing the results of the hybrid technique with FDTD calculations of the entire periodic structure as well as with HFSS which all agree quite well. This procedure reduces the CPU-time and allows efficient design and optimization of periodic THz radiation sources. Future research will involve coupling of Maxwell's equations with a more detailed, physics-based transport model for higher-order effects.

  11. Graphene coated fiber optic surface plasmon resonance biosensor for the DNA hybridization detection: Simulation analysis

    Science.gov (United States)

    Shushama, Kamrun Nahar; Rana, Md. Masud; Inum, Reefat; Hossain, Md. Biplob

    2017-01-01

    In this paper, a graphene coated optical fiber surface plasmon resonance (SPR) biosensor is presented for the detection of DNA Hybridization. For the proposed sensor, a four layer model (fiber core /metal /sensing layer /sample) where a sheet of graphene (biomolecular recognition elements (BRE)) acting as a sensing layer is coated around the gold film because graphene enhances the sensitivity of fiber optic SPR biosensor. Numerical analysis shows the variation of resonance wavelength and spectrum of transmitted power for mismatched DNA strands and for complementary DNA strands. For mismatched DNA strands variation is negligible whereas for complementary DNA strands is considerably countable. Proposed sensor successfully distinguishes hybridization and single nucleotide polymorphisms (SNP) by observing the variation level of resonance wavelength and spectrum of transmitted power.

  12. One hybrid model combining singular spectrum analysis and LS + ARMA for polar motion prediction

    Science.gov (United States)

    Shen, Yi; Guo, Jinyun; Liu, Xin; Wei, Xiaobei; Li, Wudong

    2017-01-01

    Accurate real-time polar motion parameters play an important role in satellite navigation and positioning and spacecraft tracking. To meet the needs for real-time and high-accuracy polar motion prediction, a hybrid model that integrated singular spectrum analysis (SSA), least-squares (LS) extrapolation and an autoregressive moving average (ARMA) model was proposed. SSA was applied to separate the trend, the annual and the Chandler components from a given polar motion time series. LS extrapolation models were constructed for the separated trend, annual and Chandler components. An ARMA model was established for a synthetic sequence that contained the remaining SSA component and the residual series of LS fitting. In applying this hybrid model, multiple sets of polar motion predictions with lead times of 360 days were made based on an IERS 08 C04 series. The results showed that the proposed method could effectively predict the polar motion parameters.

  13. Techno-economic analysis of a hybrid mini-grid system for Fiji islands

    Energy Technology Data Exchange (ETDEWEB)

    Lal, Sandeep; Raturi, Atul [Univ. of South Pacific, Suva (Fiji). School of Engineering and Physics

    2012-07-01

    The Pacific Island Countries constantly struggle with the challenges of high petroleum dependence for their electricity production and lack of adequate energy services. It is possible to alleviate the energy poverty by utilizing abundant renewable energy resources available in the region. The objective of this work is to investigate the feasibility of a wind/solar photovoltaic/diesel generator-based hybrid power system in a remote location in Fiji islands. We used the Hybrid Optimisation Model for Electric Renewables (HOMER) software to simulate the system and perform system optimisation analysis. The system characteristics were studied in terms of optimal configuration, net present cost and the cost of energy. An entirely renewable energy-based configuration is feasible if 10% annual capacity shortage is allowed, while for a scenario with no capacity shortage, addition of a diesel generator is necessary. The addition of renewable energy components results in greenhouse gas reduction which could be used for carbon trading. (orig.)

  14. Price competition and equilibrium analysis in multiple hybrid channel supply chain

    Science.gov (United States)

    Kuang, Guihua; Wang, Aihu; Sha, Jin

    2017-06-01

    The amazing boom of Internet and logistics industry prompts more and more enterprises to sell commodity through multiple channels. Such market conditions make the participants of multiple hybrid channel supply chain compete each other in traditional and direct channel at the same time. This paper builds a two-echelon supply chain model with a single manufacturer and a single retailer who both can choose different channel or channel combination for their own sales, then, discusses the price competition and calculates the equilibrium price under different sales channel selection combinations. Our analysis shows that no matter the manufacturer and retailer choose same or different channel price to compete, the equilibrium price does not necessarily exist the equilibrium price in the multiple hybrid channel supply chain and wholesale price change is not always able to coordinate supply chain completely. We also present the sufficient and necessary conditions for the existence of equilibrium price and coordination wholesale price.

  15. Genomic compositions and phylogenetic analysis of Shigella boydii subgroup

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Comparative Genomic Hybridization (CGH) microarray analysis was used to compare the genomic compositions of all eighteen Shigella boydii serotype representative strains. The results indicated the genomic "backbone" of this subgroup contained 2552 ORFs homologous to nonpathogenic E. coli K12. Compared with the genome of K12199 ORFs were found to be absent in all S. boydii serotype representatives, including mainly outer membrane protein genes and O-antigen biosynthesis genes. Yet the specific ORFs of S. boydii subgroup contained basically bacteriophage genes and the function unknown (FUN) genes. Some iron metabolism, transport and type II secretion system related genes were found in most representative strains. According to the CGH phylogenetic analysis, the eighteen S. boydii serotype representatives were divided into four groups, in which serotype C13 strain was remarkably distinguished from the other serotype strains. This grouping result corresponded to the distribution of some metabolism related genes. Furthermore, the analysis of genome backbone genes, specific genes, and the phylogenetic trees allowed us to discover the evolution laws of S. boydii and to find out important clues to pathogenesis research, vaccination and the therapeutic medicine development.

  16. Feature-based Analysis of Large-scale Spatio-Temporal Sensor Data on Hybrid Architectures.

    Science.gov (United States)

    Saltz, Joel; Teodoro, George; Pan, Tony; Cooper, Lee; Kong, Jun; Klasky, Scott; Kurc, Tahsin

    2013-08-01

    Analysis of large sensor datasets for structural and functional features has applications in many domains, including weather and climate modeling, characterization of subsurface reservoirs, and biomedicine. The vast amount of data obtained from state-of-the-art sensors and the computational cost of analysis operations create a barrier to such analyses. In this paper, we describe middleware system support to take advantage of large clusters of hybrid CPU-GPU nodes to address the data and compute-intensive requirements of feature-based analyses in large spatio-temporal datasets.

  17. Finite Element Analysis and Test Results Comparison for the Hybrid Wing Body Center Section Test Article

    Science.gov (United States)

    Przekop, Adam; Jegley, Dawn C.; Rouse, Marshall; Lovejoy, Andrew E.

    2016-01-01

    This report documents the comparison of test measurements and predictive finite element analysis results for a hybrid wing body center section test article. The testing and analysis efforts were part of the Airframe Technology subproject within the NASA Environmentally Responsible Aviation project. Test results include full field displacement measurements obtained from digital image correlation systems and discrete strain measurements obtained using both unidirectional and rosette resistive gauges. Most significant results are presented for the critical five load cases exercised during the test. Final test to failure after inflicting severe damage to the test article is also documented. Overall, good comparison between predicted and actual behavior of the test article is found.

  18. Comparative genomic hybridization of germ cell tumors of the adult testis : Confirmation of karyotypic findings and identification of a 12p-amplicon

    NARCIS (Netherlands)

    Mostert, MMC; vandePol, M; Weghuis, DO; Suijkerbuijk, RF; vanKessel, AG; vanEchten, J; Looijenga, LHJ

    1996-01-01

    Comparative genomic hybridization (CGH) was carried out on 15 primary testicular germ cell tumors (TGCT) of adolescents and adults and two metastatic residual tumors after chemotherapeutic treatment. The results were compared with karyotypic data obtained form the same tumor specimens after direct h

  19. Prenatal diagnosis and molecular cytogenetic analysis of a de novo isodicentric chromosome 18

    Science.gov (United States)

    Zhang, Yanliang; Dai, Yong; Ren, Jinghui; Wang, Linqian

    2010-01-01

    Isodicentric chromosome 18 [idic(18)] is rare structural aberration. We report on a prenatal case described by conventional and molecular cytogenetic analyses. The sonography at 24 weeks of gestation revealed multiple fetal anomalies; radial aplasia and ventricular septal defect were significant features. Routine karyotyping showed a derivative chromosome replacing one normal chromosome 18. The parental karyotypes were normal, indicating that the derivative chromosome was de novo. Array comparative genomic hybridization (array-CGH) revealed 18p11.21→qter duplication and 18p11.21→pter deletion for genomic DNA of the fetus. The breakpoint was located at 18p11.21 (between 12104527 bp and 12145199 bp from the telomere of 18p). Thus, the derivative chromosome was ascertained as idic(18)(qter→p11.21::p11.21→qter). Fluorescent in situ hybridization (FISH) confirmed that the derivative chromosome was idic(18). Our report describes a rare isodicentric chromosome 18 and demonstrates that array-CGH is a useful complementary tool to cytogenetic analysis for reliable identifying derivative chromosome. PMID:20864786

  20. PolyA-Mediated DNA Assembly on Gold Nanoparticles for Thermodynamically Favorable and Rapid Hybridization Analysis.

    Science.gov (United States)

    Zhu, Dan; Song, Ping; Shen, Juwen; Su, Shao; Chao, Jie; Aldalbahi, Ali; Zhou, Ziang; Song, Shiping; Fan, Chunhai; Zuo, Xiaolei; Tian, Yang; Wang, Lianhui; Pei, Hao

    2016-05-03

    Understanding the behavior of biomolecules on nanointerface is critical in bioanalysis, which is great challenge due to the instability and the difficulty to control the orientation and loading density of biomolecules. Here, we investigated the thermodynamics and kinetics of DNA hybridization on gold nanoparticle, with the aim to improve the efficiency and speed of DNA analysis. We achieved precise and quantitative surface control by applying a recently developed poly adenines (polyA)-based assembly strategy on gold nanoparticles (DNA-AuNPs). PolyA served as an effective anchoring block based on the preferential binding with the AuNP surface and the appended recognition block adopted an upright conformation that favors DNA hybridization. The lateral spacing and surface density of DNA on AuNPs can be systematically modulated by adjusting the length of polyA block. We found the stability of duplex on AuNP was enhanced with the increasing length of polyA block. When the length of polyA block reached to 40 bases, the thermodynamic properties were more similar to that of duplex in solution. Fast hybridization rate was observed on the diblock DNA-AuNPs and was increased along with the length of polyA block. We consider the high stability and excellent hybridization performance come from the minimization of the DNA-DNA and DNA-AuNP interactions with the use of polyA block. This study provides better understanding of the behavior of biomolecules on the nanointerface and opens new opportunities to construct high-efficiency and high-speed biosensors for DNA analysis.

  1. Chromosomal aberrations in benign and malignant Bilharzia-associated bladder lesions analyzed by comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Ibrahim Muntaser

    2002-03-01

    Full Text Available Abstract Background Bilharzia-associated bladder cancer (BAC is a major health problem in countries where urinary schistosomiasis is endemic. Characterization of the genetic alterations in this cancer might enhance our understanding of the pathogenic mechanisms of the disease but, in contrast to nonbilharzia bladder cancer, BAC has rarely been the object of such scrutiny. In the present study, we aimed to characterize chromosomal imbalances in benign and malignant post-bilharzial lesions, and to determine whether their unique etiology yields a distinct cytogenetic profile as compared to chemically induced bladder tumors. Methods DNAs from 20 archival paraffin-embedded post-bilharzial bladder lesions (6 benign and 14 malignant obtained from Sudanese patients (12 males and 8 females with a history of urinary bilharziasis were investigated for chromosomal imbalances using comparative genomic hybridization (CGH. Subsequent FISH analysis with pericentromeric probes was performed on paraffin sections of the same cases to confirm the CGH results. Results Seven of the 20 lesions (6 carcinomas and one granuloma showed chromosomal imbalances varying from 1 to 6 changes. The most common chromosomal imbalances detected were losses of 1p21-31, 8p21-pter, and 9p and gain of 19p material, seen in three cases each, including the benign lesion. Conclusion Most of the detected imbalances have been repeatedly reported in non-bilharzial bladder carcinomas, suggesting that the cytogenetic profiles of chemical- and bilharzia-induced carcinomas are largely similar. However, loss of 9p seems to be more ubiquitous in BAC than in bladder cancer in industrialized countries.

  2. Identification of novel deletions of 15q11q13 in Angelman syndrome by array-CGH: molecular characterization and genotype-phenotype correlations.

    Science.gov (United States)

    Sahoo, Trilochan; Bacino, Carlos A; German, Jennifer R; Shaw, Chad A; Bird, Lynne M; Kimonis, Virginia; Anselm, Irinia; Waisbren, Susan; Beaudet, Arthur L; Peters, Sarika U

    2007-09-01

    Angelman syndrome (AS) is a neurodevelopmental disorder characterized by mental retardation, absent speech, ataxia, and a happy disposition. Deletions of the 15q11q13 region are found in approximately 70% of AS patients. The deletions are sub-classified into class I and class II based on their sizes of approximately 6.8 and approximately 6.0, respectively, with two different proximal breakpoints and a common distal breakpoint. Utilizing a chromosome 15-specific comparative genomic hybridization genomic microarray (array-CGH), we have identified, determined the deletion sizes, and mapped the breakpoints in a cohort of 44 cases, to relate those breakpoints to the genomic architecture and derive more precise genotype-phenotype correlations. Interestingly four patients of the 44 studied (9.1%) had novel and unusually large deletions, and are reported here. This is the first report of very large deletions of 15q11q13 resulting in AS; the largest deletion being >10.6 Mb. These novel deletions involve three different distal breakpoints, two of which have been earlier shown to be involved in the generation of isodicentric 15q chromosomes (idic15). Additionally, precise determination of the deletion breakpoints reveals the presence of directly oriented low-copy repeats (LCRs) flanking the recurrent and novel breakpoints. The LCRs are adequate in size, orientation, and homology to enable abnormal recombination events leading to deletions and duplications. This genomic organization provides evidence for a common mechanism for the generation of both common and rare deletion types. Larger deletions result in a loss of several genes outside the common Angelman syndrome-Prader-Willi syndrome (AS-PWS) critical interval, and a more severe phenotype.

  3. GSVD comparison of patient-matched normal and tumor aCGH profiles reveals global copy-number alterations predicting glioblastoma multiforme survival.

    Directory of Open Access Journals (Sweden)

    Cheng H Lee

    Full Text Available Despite recent large-scale profiling efforts, the best prognostic predictor of glioblastoma multiforme (GBM remains the patient's age at diagnosis. We describe a global pattern of tumor-exclusive co-occurring copy-number alterations (CNAs that is correlated, possibly coordinated with GBM patients' survival and response to chemotherapy. The pattern is revealed by GSVD comparison of patient-matched but probe-independent GBM and normal aCGH datasets from The Cancer Genome Atlas (TCGA. We find that, first, the GSVD, formulated as a framework for comparatively modeling two composite datasets, removes from the pattern copy-number variations (CNVs that occur in the normal human genome (e.g., female-specific X chromosome amplification and experimental variations (e.g., in tissue batch, genomic center, hybridization date and scanner, without a-priori knowledge of these variations. Second, the pattern includes most known GBM-associated changes in chromosome numbers and focal CNAs, as well as several previously unreported CNAs in >3% of the patients. These include the biochemically putative drug target, cell cycle-regulated serine/threonine kinase-encoding TLK2, the cyclin E1-encoding CCNE1, and the Rb-binding histone demethylase-encoding KDM5A. Third, the pattern provides a better prognostic predictor than the chromosome numbers or any one focal CNA that it identifies, suggesting that the GBM survival phenotype is an outcome of its global genotype. The pattern is independent of age, and combined with age, makes a better predictor than age alone. GSVD comparison of matched profiles of a larger set of TCGA patients, inclusive of the initial set, confirms the global pattern. GSVD classification of the GBM profiles of an independent set of patients validates the prognostic contribution of the pattern.

  4. Molecular Dissection Using Array Comparative Genomic Hybridization and Clinical Evaluation of An Infertile Male Carrier of An Unbalanced Y;21 Translocation: A Case Report and Review of The Literature.

    Science.gov (United States)

    Orrico, Alfredo; Marseglia, Giuseppina; Pescucci, Chiara; Cortesi, Ambra; Piomboni, Paola; Giansanti, Andrea; Gerundino, Francesca; Ponchietti, Roberto

    2016-01-01

    Chromosomal defects are relatively frequent in infertile men however, translocations between the Y chromosome and autosomes are rare and less than 40 cases of Y-autosome translocation have been reported. In particular, only three individuals has been described with a Y;21 translocation, up to now. We report on an additional case of an infertile man in whom a Y;21 translocation was associated with the deletion of a large part of the Y chromosome long arm. Applying various techniques, including conventional cytogenetic procedures, fluorescence in situ hybridisation (FISH) analysis and array comparative genomic hybridization (array-CGH) studies, we identified a derivative chromosome originating from a fragment of the short arm of the chromosome Y translocated on the short arm of the 21 chromosome. The Y chromosome structural rearrangement resulted in the intactness of the entire short arm, including the sex-determining region Y (SRY) and the short stature homeobox (SHOX) loci, although translocated on the 21 chromosome, and the loss of a large part of the long arm of the Y chromosome, including azoospermia factor-a (AZFa), AZFb, AZFc and Yq heterochromatin regions. This is the first case in which a (Yp;21p) translocation has been ascertained using an array-CGH approach, thus reporting details of such a rearrangement at higher resolution.

  5. High-resolution genome-wide array-based comparative genome hybridization reveals cryptic chromosome changes in AML and MDS cases with trisomy 8 as the sole cytogenetic aberration.

    Science.gov (United States)

    Paulsson, K; Heidenblad, M; Strömbeck, B; Staaf, J; Jönsson, G; Borg, A; Fioretos, T; Johansson, B

    2006-05-01

    Although trisomy 8 as the sole chromosome aberration is the most common numerical abnormality in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), little is known about its pathogenetic effects. Considering that +8 is a frequent secondary change in AML/MDS, cryptic--possibly primary--genetic aberrations may occur in cases with trisomy 8 as the apparently single anomaly. However, no such hidden anomalies have been reported. We performed a high-resolution genome-wide array-based comparative genome hybridization (array CGH) analysis of 10 AML/MDS cases with isolated +8, utilizing a 32K bacterial artificial chromosome array set, providing >98% coverage of the genome with a resolution of 100 kb. Array CGH revealed intrachromosomal imbalances, not corresponding to known genomic copy number polymorphisms, in 4/10 cases, comprising nine duplications and hemizygous deletions ranging in size from 0.5 to 2.2 Mb. A 1.8 Mb deletion at 7p14.1, which had occurred prior to the +8, was identified in MDS transforming to AML. Furthermore, a deletion including ETV6 was present in one case. The remaining seven imbalances involved more than 40 genes. The present results show that cryptic genetic abnormalities are frequent in trisomy 8-positive AML/MDS cases and that +8 as the sole cytogenetic aberration is not always the primary genetic event.

  6. GISH, AFLP and PCR-RFLP analysis of an intergeneric somatic hybrid combining Goutou sour orange and Poncirus trifoliata.

    Science.gov (United States)

    Fu, C H; Chen, C L; Guo, W W; Deng, X X

    2004-11-01

    Intergeneric somatic hybrids combining Goutou sour orange (Citrus aurantium L.) with trifoliate orange Poncirus trifoliata (L.) Raf] were produced by electrofusion and their genetic inheritance analyzed by amplified fragment length polymorphism (AFLP), genomic in situ hybridization (GISH), and PCR-restriction fragment length polymorphism (PCR-RFLP). Sixteen mini-calluses were obtained after 20 days of culture; they all developed into embryoids on EME500 medium. Following several subcultures on shoot induction medium for a total culture period of 6 months, shoots regenerated. The plants grew vigorously with a well-developed root system and exhibited the trifoliate leaf character of P. trifoliata. Ploidy analysis verified that all of the regenerates were tetraploids (2 n=4 x=36) as expected. GISH analysis confirmed that 18 chromosomes came from trifoliate orange and the remaining 18 from Goutou sour orange, as with most symmetric somatic hybrid plants; moreover, chromosome translocations were also observed in one plant. AFLP analysis of 16 regenerates and their fusion parents indicated that all of the somatic hybrids except one were genetically uniform. Analysis of the somatic hybrid cytoplasmic genomes with universal primers revealed that their chloroplast DNA (cpDNA) banding patterns were identical to those of the mesophyll parent trifoliate orange, while their mitochondria (mt) genomes were of the callus parent sour orange. The potential of GISH in Citrus somatic hybrid analysis is discussed.

  7. Chromosome-specific segmentation revealed by structural analysis of individually isolated chromosomes.

    Science.gov (United States)

    Kitada, Kunio; Taima, Akira; Ogasawara, Kiyomoto; Metsugi, Shouichi; Aikawa, Satoko

    2011-04-01

    Analysis of structural rearrangements at the individual chromosomal level is still technologically challenging. Here we optimized a chromosome isolation method using fluorescent marker-assisted laser-capture and laser-beam microdissection and applied it to structural analysis of two aberrant chromosomes found in a lung cancer cell line. A high-density array-comparative genomic hybridization (array-CGH) analysis of DNA samples prepared from each of the chromosomes revealed that these two chromosomes contained 296 and 263 segments, respectively, ranging from 1.5 kb to 784.3 kb in size, derived from different portions of chromosome 8. Among these segments, 242 were common in both aberrant chromosomes, but 75 were found to be chromosome-specific. Sequences of 263 junction sites connecting the ends of segments were determined using a PCR/Sanger-sequencing procedure. Overlapping microhomologies were found at 169 junction sites. Junction partners came from various portions of chromosome 8 and no biased pattern in the positional distribution of junction partners was detected. These structural characteristics suggested the occurrence of random fragmentation of the entire chromosome 8 followed by random rejoining of these fragments. Based on that, we proposed a model to explain how these aberrant chromosomes are formed. Through these structural analyses, it was demonstrated that the optimized chromosome isolation method described here can provide high-quality chromosomal DNA for high resolution array-CGH analysis and probably for massively parallel sequencing analysis.

  8. Expressed sequence tag analysis of functional genes associated with adventitious rooting in Liriodendron hybrids.

    Science.gov (United States)

    Zhong, Y D; Sun, X Y; Liu, E Y; Li, Y Q; Gao, Z; Yu, F X

    2016-06-24

    Liriodendron hybrids (Liriodendron chinense x L. tulipifera) are important landscaping and afforestation hardwood trees. To date, little genomic research on adventitious rooting has been reported in these hybrids, as well as in the genus Liriodendron. In the present study, we used adventitious roots to construct the first cDNA library for Liriodendron hybrids. A total of 5176 expressed sequence tags (ESTs) were generated and clustered into 2921 unigenes. Among these unigenes, 2547 had significant homology to the non-redundant protein database representing a wide variety of putative functions. Homologs of these genes regulated many aspects of adventitious rooting, including those for auxin signal transduction and root hair development. Results of quantitative real-time polymerase chain reaction showed that AUX1, IRE, and FB1 were highly expressed in adventitious roots and the expression of AUX1, ARF1, NAC1, RHD1, and IRE increased during the development of adventitious roots. Additionally, 181 simple sequence repeats were identified from 166 ESTs and more than 91.16% of these were dinucleotide and trinucleotide repeats. To the best of our knowledge, the present study reports the identification of the genes associated with adventitious rooting in the genus Liriodendron for the first time and provides a valuable resource for future genomic studies. Expression analysis of selected genes could allow us to identify regulatory genes that may be essential for adventitious rooting.

  9. Performance Analysis of a Hybrid Overset Multi-Block Application on Multiple Architectures

    Science.gov (United States)

    Djomehri, M. Jahed; Biswas, Rupak

    2003-01-01

    This paper presents a detailed performance analysis of a multi-block overset grid compu- tational fluid dynamics app!ication on multiple state-of-the-art computer architectures. The application is implemented using a hybrid MPI+OpenMP programming paradigm that exploits both coarse and fine-grain parallelism; the former via MPI message passing and the latter via OpenMP directives. The hybrid model also extends the applicability of multi-block programs to large clusters of SNIP nodes by overcoming the restriction that the number of processors be less than the number of grid blocks. A key kernel of the application, namely the LU-SGS linear solver, had to be modified to enhance the performance of the hybrid approach on the target machines. Investigations were conducted on cacheless Cray SX6 vector processors, cache-based IBM Power3 and Power4 architectures, and single system image SGI Origin3000 platforms. Overall results for complex vortex dynamics simulations demonstrate that the SX6 achieves the highest performance and outperforms the RISC-based architectures; however, the best scaling performance was achieved on the Power3.

  10. MULTICRITERIA HYBRID FLOW SHOP SCHEDULING PROBLEM: LITERATURE REVIEW, ANALYSIS, AND FUTURE RESEARCH

    Directory of Open Access Journals (Sweden)

    Marcia de Fatima Morais

    2014-12-01

    Full Text Available This research focuses on the Hybrid Flow Shop production scheduling problem, which is one of the most difficult problems to solve. The literature points to several studies that focus the Hybrid Flow Shop scheduling problem with monocriteria functions. Despite of the fact that, many real world problems involve several objective functions, they can often compete and conflict, leading researchers to concentrate direct their efforts on the development of methods that take consider this variant into consideration. The goal of the study is to review and analyze the methods in order to solve the Hybrid Flow Shop production scheduling problem with multicriteria functions in the literature. The analyses were performed using several papers that have been published over the years, also the parallel machines types, the approach used to develop solution methods, the type of method develop, the objective function, the performance criterion adopted, and the additional constraints considered. The results of the reviewing and analysis of 46 papers showed opportunities for future research on this topic, including the following: (i use uniform and dedicated parallel machines, (ii use exact and metaheuristics approaches, (iv develop lower and uppers bounds, relations of dominance and different search strategies to improve the computational time of the exact methods,  (v develop  other types of metaheuristic, (vi work with anticipatory setups, and (vii add constraints faced by the production systems itself.

  11. Three-dimensional hybrid-stress finite element analysis of composite laminates with cracks and cutouts

    Science.gov (United States)

    Wang, S. S.

    1985-01-01

    A three-dimensional hybrid-stress finite element analysis of composite laminates containing cutouts and cracks is presented. Fully three-dimensional, hexahedral isoparametric elements of the hybrid-stress model are formulated on the basis of the Hellinger-Reissner variational principle. Traction-free edges, cutouts, and crack surfaces are modeled by imposition of exact traction boundary conditions along element surfaces. Special boundary and surface elements are constructed by introducing proper constraints on assumed stress functions. The Lagrangian multiplier technique is used to enforce ply-interface continuity conditions in hybrid bimaterial composite elements for modeling the interface region in a composite laminate. Two examples are given to illustrate the capability of the present method of approach: (1) the well-known delamination problem in an angle-ply laminate, and (2) the important problem of a composite laminate containing a circular hole. Results are presented in detail for each case. Implications of interlaminar and intralaminar crack initiation, growth and fracture in composites containing cracks and cutouts are discussed.

  12. Characteristic Analysis and Control of a Hybrid Excitation Linear Eddy Current Brake

    Directory of Open Access Journals (Sweden)

    Baoquan Kou

    2015-07-01

    Full Text Available In this paper, a novel hybrid excitation linear eddy current brake is presented as a braking system for high-speed road and rail vehicles. The presence of the permanent magnets (PMs, whose flux lines in the primary core are oppositely directed with respect to the flux lines by the excitation windings, has the effect of mitigating the saturation of the iron in the teeth of the primary core. This allows the brake to be fed with more intense currents, improving the braking force. First, using the magnetic equivalent circuit method and the layer theory approach, the analytical model of the hybrid excitation linear eddy current brake was developed, which can account for the saturation effects occurring in the iron parts. The saturation effects make the design and control of eddy current brakes more difficult. Second, the relationship between the braking force characteristics and the design parameters were analyzed to provide useful information to the designers of eddy current brakes. Then, the controller of the hybrid excitation linear eddy current brake was designed to control the amplitude of the braking force. Finally, experimental measurements were conducted to verify the validity of the theoretical analysis.

  13. Thermoeconomic analysis of pressurized hybrid SOFC systems with CO{sub 2} separation

    Energy Technology Data Exchange (ETDEWEB)

    Franzoni, A.; Magistri, L.; Traverso, A.; Massardo, A.F. [TPG-DiMSET, Universita di Genova, via Montallegro 1, 16145 Genoa (Italy)

    2008-02-15

    In this paper, the results of the thermodynamic and economic analyses of distributed power generation plants (1.5 MWe) are described and compared. The results of an exergetic analysis are also reported, as well as the thermodynamic details of the most significant streams of the plants. The integration of different hybrid solid oxide fuel cell (SOFC) system CO{sub 2} separation technologies characterizes the power plants proposed. A hybrid system with a tubular SOFC fed with natural gas with internal reforming has been taken as reference plant. Two different technologies have been considered for the same base system to obtain a low CO{sub 2} emission plant. The first technology involved a fuel decarbonization and CO{sub 2} separation process placed before the system feed, while the second integrated the CO{sub 2} separation and the energy cycle. The first option employed fuel processing, a technology (amine chemical absorption) viable for short-term implementation in real installations while the second option provided the CO{sub 2} separation by condensing the steam from the system exhaust. The results obtained, using a Web-based Thermo Economic Modular Program software, developed by the Thermochemical Power Group of the University of Genoa, showed that the thermodynamic and economic impact of the adoption of zero emission cycle layouts based on hybrid systems was relevant. (author)

  14. Computational analysis of electrical conduction in hybrid nanomaterials with embedded non-penetrating conductive particles

    Science.gov (United States)

    Cai, Jizhe; Naraghi, Mohammad

    2016-08-01

    In this work, a comprehensive multi-resolution two-dimensional (2D) resistor network model is proposed to analyze the electrical conductivity of hybrid nanomaterials made of insulating matrix with conductive particles such as CNT reinforced nanocomposites and thick film resistors. Unlike existing approaches, our model takes into account the impenetrability of the particles and their random placement within the matrix. Moreover, our model presents a detailed description of intra-particle conductivity via finite element analysis, which to the authors’ best knowledge has not been addressed before. The inter-particle conductivity is assumed to be primarily due to electron tunneling. The model is then used to predict the electrical conductivity of electrospun carbon nanofibers as a function of microstructural parameters such as turbostratic domain alignment and aspect ratio. To simulate the microstructure of single CNF, randomly positioned nucleation sites were seeded and grown as turbostratic particles with anisotropic growth rates. Particle growth was in steps and growth of each particle in each direction was stopped upon contact with other particles. The study points to the significant contribution of both intra-particle and inter-particle conductivity to the overall conductivity of hybrid composites. Influence of particle alignment and anisotropic growth rate ratio on electrical conductivity is also discussed. The results show that partial alignment in contrast to complete alignment can result in maximum electrical conductivity of whole CNF. High degrees of alignment can adversely affect conductivity by lowering the probability of the formation of a conductive path. The results demonstrate approaches to enhance electrical conductivity of hybrid materials through controlling their microstructure which is applicable not only to carbon nanofibers, but also many other types of hybrid composites such as thick film resistors.

  15. Selection of single blastocysts for fresh transfer via standard morphology assessment alone and with array CGH for good prognosis IVF patients: results from a randomized pilot study

    Directory of Open Access Journals (Sweden)

    Yang Zhihong

    2012-05-01

    Full Text Available Abstract Background Single embryo transfer (SET remains underutilized as a strategy to reduce multiple gestation risk in IVF, and its overall lower pregnancy rate underscores the need for improved techniques to select one embryo for fresh transfer. This study explored use of comprehensive chromosomal screening by array CGH (aCGH to provide this advantage and improve pregnancy rate from SET. Methods First-time IVF patients with a good prognosis (age Results For patients in Group A (n = 55, 425 blastocysts were biopsied and analyzed via aCGH (7.7 blastocysts/patient. Aneuploidy was detected in 191/425 (44.9% of blastocysts in this group. For patients in Group B (n = 48, 389 blastocysts were microscopically examined (8.1 blastocysts/patient. Clinical pregnancy rate was significantly higher in the morphology + aCGH group compared to the morphology-only group (70.9 and 45.8%, respectively; p = 0.017; ongoing pregnancy rate for Groups A and B were 69.1 vs. 41.7%, respectively (p = 0.009. There were no twin pregnancies. Conclusion Although aCGH followed by frozen embryo transfer has been used to screen at risk embryos (e.g., known parental chromosomal translocation or history of recurrent pregnancy loss, this is the first description of aCGH fully integrated with a clinical IVF program to select single blastocysts for fresh SET in good prognosis patients. The observed aneuploidy rate (44.9% among biopsied blastocysts highlights the inherent imprecision of SET when conventional morphology is used alone. Embryos randomized to the aCGH group implanted with greater efficiency, resulted in clinical pregnancy more often, and yielded a lower miscarriage rate than those selected without aCGH. Additional studies are needed to verify our pilot data and confirm a role for on-site, rapid aCGH for IVF patients contemplating fresh SET.

  16. Fuel cycle analysis based evaluation of the fuel and emissions reduction potential of adapting the hybrid technology to tricycles

    Energy Technology Data Exchange (ETDEWEB)

    Biona, J.B.M. [Don Bosco Technical College, Mandaluyong City (Philippines); De La Salle University, Center for Engineering and Sustainable Development Research, Manila (Philippines); Culaba, A.B. [De La Salle University, Center for Engineering and Sustainable Development Research, Manila (Philippines); Purvis, M.R.I. [University of Portsmouth, Department of Mechanical Design and Engineering, Portsmouth (United Kingdom)

    2008-02-15

    A preliminary analysis has been conducted to investigate the fuel use and emissions reduction potential of incorporating hybrid systems to two stroke powered tricycles in Metro Manila. Carbureted and direct injection two stroke engine hybrid systems were investigated and compared with the impact of shifting to four stroke engines. Results showed that hybridized direct injection retrofitted two stroke powered systems would be able to provide far better environmental and fuel reduction benefits than the shift to new four strokes tricycles. It is thus recommended that the development of such technology specifically for tricycles be seriously pursued. (orig.)

  17. 22q13.3 Deletion Syndrome : Clinical and Molecular Analysis Using Array CGH

    NARCIS (Netherlands)

    Dhar, S. U.; del Gaudio, D.; German, J. R.; Peters, S. U.; Ou, Z.; Bader, P. I.; Berg, J. S.; Blazo, M.; Brown, C. W.; Graham, B. H.; Grebe, T. A.; Lalani, S.; Irons, M.; Sparagana, S.; Williams, M.; Phillips, J. A.; Beaudet, A. L.; Stankiewicz, P.; Patel, A.; Cheung, S. W.; Sahoo, T.

    2010-01-01

    The 22q13.3 deletion syndrome results from loss of terminal segments of varying sizes at 22qter. Few genotype phenotype correlations have been found but all patients have mental retardation and severe delay, or absence of, expressive speech. We carried out clinical and molecular characterization of

  18. General and hybrid correlation nuclear magnetic resonance analysis of phosphorus in Phytophthora palmivora.

    Science.gov (United States)

    Kirwan, Gemma M; Fernandez, David I; Niere, Julie O; Adams, Michael J

    2012-10-01

    Generalized two-dimensional (Gen2D) correlation analysis and hybrid correlation analysis have been applied to a series of dynamic (31)P nuclear magnetic resonance (NMR) spectra to monitor the in vivo metabolic changes of the plant pathogen Phytophthora palmivora in the presence and absence of phosphonate over an 18-h period. Results indicate that phosphonate exposure causes cleavage in organism polyphosphate chains as well as an increase in total sugar phosphates. In the presence of phosphonate, the NMR resonances attributed to terminal polyphosphate phosphorus reduced at a lower rate than those of middle polyphosphate phosphorus, indicating a change in average chain length and suggesting cleavage in the middle of the chain as well as at the ends. The correlation analysis techniques serve to identify and confirm spectral regions undergoing major change in the time-series data and facilitate the analysis of these dynamic changes.

  19. A HYBRID SYSTEM FOR DYNAMIC ANALYSIS AND DESIGN OF COUPLED SHEAR WALLS

    Directory of Open Access Journals (Sweden)

    A BERRAIS

    2000-06-01

    Full Text Available Non-linear dynamic analysis techniques are rapidly being developed and have been recognized as indispensable tools. However, their use in the design office requires special experience. Consequently they are not generally accepted as analysis/design tools. Additionally, uncertainties are associated with the determination of the earthquake forces, the stiffness and strength of the structure; the selection of the mathematical models; and the form of the earthquake. In this paper a hybrid system for the non-linear dynamic analysis/design of coupled shear walls is briefly described. The system combines expert system technology with finite element method to carry out the dynamic analysis of coupled walls under earthquake forces. The system has been implemented using Quintec-Prolog, Quintec-Flex and FORTRAN 77, and runs on a SUN SPARC station under Unix system.

  20. An efficient hybrid reliability analysis method with random and interval variables

    Science.gov (United States)

    Xie, Shaojun; Pan, Baisong; Du, Xiaoping

    2016-09-01

    Random and interval variables often coexist. Interval variables make reliability analysis much more computationally intensive. This work develops a new hybrid reliability analysis method so that the probability analysis (PA) loop and interval analysis (IA) loop are decomposed into two separate loops. An efficient PA algorithm is employed, and a new efficient IA method is developed. The new IA method consists of two stages. The first stage is for monotonic limit-state functions. If the limit-state function is not monotonic, the second stage is triggered. In the second stage, the limit-state function is sequentially approximated with a second order form, and the gradient projection method is applied to solve the extreme responses of the limit-state function with respect to the interval variables. The efficiency and accuracy of the proposed method are demonstrated by three examples.

  1. [Accidental finding of a cri du chat syndrome in an adult patient by means of array-CGH].

    Science.gov (United States)

    Ferreirós-Martínez, Raquel; López-Manzanares, Lydia; Alonso-Cerezo, Concepción

    2014-07-16

    Introduccion. El sindrome cri du chat (SCDC) tiene su origen en una delecion parcial o total del brazo corto del cromosoma 5, y es uno de los sindromes de delecion cromosomica mas frecuentes en humanos. La mayoria de los pacientes se diagnostica entre el primer mes y el primer año de vida, si bien aqui se describe el hallazgo de un SCDC en una mujer con sospecha de ataxia espinocerebelar y antecedentes familiares de trastorno bipolar y ataxia, con especial atencion a las caracteristicas clinicas y las tecnicas diagnosticas que permitieron su identificacion. Caso clinico. Mujer de 46 años que presentaba una inteligencia limite, intervenida a los 43 años de faquectomia bilateral. El inicio de la sintomatologia fue durante la infancia, e incluia hipoacusia, ataxia, disartria, disfagia, depresion, deterioro cognitivo y trastorno bipolar. La exploracion fisica revelo microcefalia, micrognatia, pies equinos y ataxia. Se realizo cariotipo y array-CGH en sangre periferica. La paciente presentaba una traslocacion que involucraba los cromosomas 5 y 15, y una inversion del cromosoma 9: 45,XX,inv9(p11q13);t(5,15)(p15.33;q11.2). El array-CGH mostro una delecion de 2,91 Mb en 5p15.33, formula genomica arr 5p15.33 (151537-3057771)x1, que involucraba 20 genes, incluyendo el gen TERT. Conclusiones. La delecion de multiples genes confirmo el diagnostico de SCDC y es la responsable del fenotipo de la paciente. Se pone de manifiesto la importancia de utilizar tecnicas adecuadas de diagnostico (array-CGH, cariotipo en sangre periferica) y la correcta eleccion de estas.

  2. Numerical analysis of the forced convective heat transfer on Al2O3-Cu/water hybrid nanofluid

    Science.gov (United States)

    Rahman, Mohd Rosdzimin Abdul; Leong, Kin Yuen; Idris, Azam Che; Saad, Mohd Rashdan; Anwar, Mahmood

    2017-05-01

    A numerical investigation to elucidate thermal behavior of hybrid nanofluids consisting of Al2O3 and Cu nanoparticles at ratio of 90:10 was conducted. Numerical domain of a two-dimensional axisymmetric copper tube with a length of 1000 and 10 mm in diameter is used. A uniform axial velocity is assigned at the velocity inlet based on the Reynolds number. The outer wall of the tube consists of non-slip wall condition with a constant heat flux. The assumptions of this numerical analysis are; (1) there is a steady state analysis, (2) effective thermo-physical properties of the nanofluid are depend on the volume concentration, and (3) fluid is continuum. It is found that the dominant nanoparticle in the hybrid nanofluids strongly influences the thermal behavior of the hybrid nanofluids. It was also found that the heat transfer coefficient increases as the volume concentration of the hybrid nanoparticle increases in base fluids and the Reynolds number.

  3. Small-Signal Analysis of Autonomous Hybrid Distributed Generation Systems in Presence of Ultracapacitor and Tie-Line Operation

    Science.gov (United States)

    Ray, Prakash K.; Mohanty, Soumya R.; Kishor, Nand

    2010-07-01

    This paper presents small-signal analysis of isolated as well as interconnected autonomous hybrid distributed generation system for sudden variation in load demand, wind speed and solar radiation. The hybrid systems comprise of different renewable energy resources such as wind, photovoltaic (PV) fuel cell (FC) and diesel engine generator (DEG) along with the energy storage devices such as flywheel energy storage system (FESS) and battery energy storage system (BESS). Further ultracapacitors (UC) as an alternative energy storage element and interconnection of hybrid systems through tie-line is incorporated into the system for improved performance. A comparative assessment of deviation of frequency profile for different hybrid systems in the presence of different storage system combinations is carried out graphically as well as in terms of the performance index (PI), ie integral square error (ISE). Both qualitative and quantitative analysis reflects the improvements of the deviation in frequency profiles in the presence of the ultracapacitors (UC) as compared to other energy storage elements.

  4. Molecular Cytogenetic Analysis of Spontaneous Interspecific Hybrid Between Oryza sativa and Oryza minuta

    Directory of Open Access Journals (Sweden)

    Chuan-deng YI

    2008-12-01

    Full Text Available Genomic in situ hybridization (GISH is a powerful tool to characterize parental chromosomes in interspecific hybrids, including the behaviour of autosynapsis and chromosome pairing. It was used to distinguish the chromosomes of Oryza sativa from wild species in a spontaneous interspecific hybrid and to investigate the chromosome pairing at metaphase I in meiosis of the hybrid in this study. The hybrid was a triploid with 36 chromosomes according to the chromosome number investigated in mitosis of root tips. During metaphase I of meiosis in the hybrid, less chromosome pairing was observed and most of the chromosomes existed as univalent. Based on GISH and FISH (Fluorescent in situ hybridization analyses, the chromosomes of the hybrid were composed of genomes A, B and C. Thus, it was believed that the hybrid was the result of natural hybridization between cultivated rice and wild species O. minuta which was planted in experimental fields.

  5. Hybrid optimization for 13C metabolic flux analysis using systems parametrized by compactification

    Directory of Open Access Journals (Sweden)

    Frick Oliver

    2008-03-01

    Full Text Available Abstract Background The importance and power of isotope-based metabolic flux analysis and its contribution to understanding the metabolic network is increasingly recognized. Its application is, however, still limited partly due to computational inefficiency. 13C metabolic flux analysis aims to compute in vivo metabolic fluxes in terms of metabolite balancing extended by carbon isotopomer balances and involves a nonlinear least-squares problem. To solve the problem more efficiently, improved numerical optimization techniques are necessary. Results For flux computation, we developed a gradient-based hybrid optimization algorithm. Here, independent flux variables were compactified into [0, 1-ranged variables using a single transformation rule. The compactified parameters could be discriminated between non-identifiable and identifiable variables after model linearization. The developed hybrid algorithm was applied to the central metabolism of Bacillus subtilis with only succinate and glutamate as carbon sources. This creates difficulties caused by symmetry of succinate leading to limited introduction of 13C labeling information into the system. The algorithm was found to be superior to its parent algorithms and to global optimization methods both in accuracy and speed. The hybrid optimization with tolerance adjustment quickly converged to the minimum with close to zero deviation and exactly re-estimated flux variables. In the metabolic network studied, some fluxes were found to be either non-identifiable or nonlinearly correlated. The non-identifiable fluxes could correctly be predicted a priori using the model identification method applied, whereas the nonlinear flux correlation was revealed only by identification runs using different starting values a posteriori. Conclusion This fast, robust and accurate optimization method is useful for high-throughput metabolic flux analysis, a posteriori identification of possible parameter correlations, and

  6. Well-posedness and stability analysis of hybrid feedback systems using Shkalikov's theory

    Directory of Open Access Journals (Sweden)

    Piotr Grabowski

    2006-01-01

    Full Text Available The modern method of analysis of the distributed parameter systems relies on the transformation of the dynamical model to an abstract differential equation on an appropriately chosen Banach or, if possible, Hilbert space. A linear dynamical model in the form of a first order abstract differential equation is considered to be well-posed if its right-hand side generates a strongly continuous semigroup. Similarly, a dynamical model in the form of a second order abstract differential equation is well-posed if its right-hand side generates a strongly continuous cosine family of operators. Unfortunately, the presence of a feedback leads to serious complications or even excludes a direct verification of assumptions of the Hille-Phillips-Yosida and/or the Sova-Fattorini Theorems. The class of operators which are similar to a normal discrete operator on a Hilbert space describes a wide variety of linear operators. In the papers [Grabowski P., Well–posedness and stability analysis of hybrid feedback systems, Journal of Mathematical Systems, Estimation and Control 6 (1996, 121–124 (summary, full electronic manuscript – retrieval code 15844, Grabowski P., Spectral approach to well–posedness and stability analysis of hybrid feedback systems, In: Wajs W., Grabowski P. (Eds., Studies in Automatics, 1996, Kraków, Wydawnictwa AGH, 104–139] two groups of similarity criteria for a given hybrid closed-lop system operator are given. The criteria of the first group are based on some perturbation results, and of the second, on the application of Shkalikov's theory of the Sturm-Liouville eigenproblems with a spectral parameter in the boundary conditions. In the present paper we continue those investigations showing certain advanced applications of the Shkalikov's theory. The results are illustrated by feedback control systems examples governed by wave and beam equations with increasing degree of complexity of the boundary conditions.

  7. Hybrid Bernstein Block-Pulse Functions Method for Second Kind Integral Equations with Convergence Analysis

    Directory of Open Access Journals (Sweden)

    Mohsen Alipour

    2014-01-01

    Full Text Available We introduce a new combination of Bernstein polynomials (BPs and Block-Pulse functions (BPFs on the interval [0, 1]. These functions are suitable for finding an approximate solution of the second kind integral equation. We call this method Hybrid Bernstein Block-Pulse Functions Method (HBBPFM. This method is very simple such that an integral equation is reduced to a system of linear equations. On the other hand, convergence analysis for this method is discussed. The method is computationally very simple and attractive so that numerical examples illustrate the efficiency and accuracy of this method.

  8. Hybrid-finite-element analysis of some nonlinear and 3-dimensional problems of engineering fracture mechanics

    Science.gov (United States)

    Atluri, S. N.; Nakagaki, M.; Kathiresan, K.

    1980-01-01

    In this paper, efficient numerical methods for the analysis of crack-closure effects on fatigue-crack-growth-rates, in plane stress situations, and for the solution of stress-intensity factors for arbitrary shaped surface flaws in pressure vessels, are presented. For the former problem, an elastic-plastic finite element procedure valid for the case of finite deformation gradients is developed and crack growth is simulated by the translation of near-crack-tip elements with embedded plastic singularities. For the latter problem, an embedded-elastic-singularity hybrid finite element method, which leads to a direct evaluation of K-factors, is employed.

  9. Parametric study and performance analysis of hybrid rocket motors with double-tube configuration

    Science.gov (United States)

    Yu, Nanjia; Zhao, Bo; Lorente, Arnau Pons; Wang, Jue

    2017-03-01

    The practical implementation of hybrid rocket motors has historically been hampered by the slow regression rate of the solid fuel. In recent years, the research on advanced injector designs has achieved notable results in the enhancement of the regression rate and combustion efficiency of hybrid rockets. Following this path, this work studies a new configuration called double-tube characterized by injecting the gaseous oxidizer through a head end injector and an inner tube with injector holes distributed along the motor longitudinal axis. This design has demonstrated a significant potential for improving the performance of hybrid rockets by means of a better mixing of the species achieved through a customized injection of the oxidizer. Indeed, the CFD analysis of the double-tube configuration has revealed that this design may increase the regression rate over 50% with respect to the same motor with a conventional axial showerhead injector. However, in order to fully exploit the advantages of the double-tube concept, it is necessary to acquire a deeper understanding of the influence of the different design parameters in the overall performance. In this way, a parametric study is carried out taking into account the variation of the oxidizer mass flux rate, the ratio of oxidizer mass flow rate injected through the inner tube to the total oxidizer mass flow rate, and injection angle. The data for the analysis have been gathered from a large series of three-dimensional numerical simulations that considered the changes in the design parameters. The propellant combination adopted consists of gaseous oxygen as oxidizer and high-density polyethylene as solid fuel. Furthermore, the numerical model comprises Navier-Stokes equations, k-ε turbulence model, eddy-dissipation combustion model and solid-fuel pyrolysis, which is computed through user-defined functions. This numerical model was previously validated by analyzing the computational and experimental results obtained for

  10. FEM-based Analysis of a Hybrid Synchronous Generator with Skewed Stator Slots

    Directory of Open Access Journals (Sweden)

    MUNTEANU, A.

    2011-11-01

    Full Text Available The paper presents a simulation study of a hybrid synchronous generator (dual excitation system - permanent magnets and electromagnets with skewed stator slots. The main goal is to establish if the skewing of the slots brings a significant improvement of the air-gap flux density and of the induced stator voltage. The skewness angle is the parameter in discussion. The study is based on finite element method analysis. Due to the particular geometry of the stator slots, a multilayer approach is employed.

  11. Identification of differentially expressed genes in rat silicosis model by suppression subtractive hybridization analysis

    Institute of Scientific and Technical Information of China (English)

    Zhongyuan Jin; Chunyan Fu; Jifang Wen; Baoan Liu; Deyun Feng; Chen Chen; Xiang Li; Yongbin Hu; Jinwu Peng; Yu Liu; Jing Du

    2008-01-01

    The critical molecular mechanism in the development of the pulmonary fibrosis remains unknown, leaving diagnosed patients with a poor prognosis. To isolate the genes specifi-cally up-regulated in pulmonary fibrosis, we established a rat silicosis model 360 d after treatment with crystalline silica suspension. Radiographs of chests showed that some scattered high-density shadows appeared in the lung field.Typical microscopic fibrosing silicotic nodules formed in the lung,alveolar epithelial cells and bronchial epithelial cells,particularly around the partial fibrosing silicotic nodules;some of them showed atypical hyperplasia that suggested a correlation between silicosis and lung cancer.Suppression subtractive hybridization analysis was performed to compare gene expression in lung tissue with silicosis and normal lung tissue.Reverse transcription-polymerase chain rection showed that the expressions of seven novel cDNA sequences identified by suppression subtractive hybridization in lung tissue with silicosis differed from normal lung tissue. Bioinformatics analysis showed that 47 positive clones rep-resented 35 genes containing two putative proteins and four predicted similar proteins.The analysis also showed that some screened genes in silicosis,such as prolyl 4-hydroxylases,actin-related protein-2/3 complex and acidic mammalian chitinase,have not been previously reported.These genes may provide new clues for investigating the molecular mechanisms in the development of pulmonary fibrosis.

  12. Earthscape, a Multi-Purpose Interactive 3d Globe Viewer for Hybrid Data Visualization and Analysis

    Science.gov (United States)

    Sarthou, A.; Mas, S.; Jacquin, M.; Moreno, N.; Salamon, A.

    2015-08-01

    The hybrid visualization and interaction tool EarthScape is presented here. The software is able to display simultaneously LiDAR point clouds, draped videos with moving footprint, volume scientific data (using volume rendering, isosurface and slice plane), raster data such as still satellite images, vector data and 3D models such as buildings or vehicles. The application runs on touch screen devices such as tablets. The software is based on open source libraries, such as OpenSceneGraph, osgEarth and OpenCV, and shader programming is used to implement volume rendering of scientific data. The next goal of EarthScape is to perform data analysis using ENVI Services Engine, a cloud data analysis solution. EarthScape is also designed to be a client of Jagwire which provides multisource geo-referenced video fluxes. When all these components will be included, EarthScape will be a multi-purpose platform that will provide at the same time data analysis, hybrid visualization and complex interactions. The software is available on demand for free at france@exelisvis.com.

  13. EARTHSCAPE, A MULTI-PURPOSE INTERACTIVE 3D GLOBE VIEWER FOR HYBRID DATA VISUALIZATION AND ANALYSIS

    Directory of Open Access Journals (Sweden)

    A. Sarthou

    2015-08-01

    Full Text Available The hybrid visualization and interaction tool EarthScape is presented here. The software is able to display simultaneously LiDAR point clouds, draped videos with moving footprint, volume scientific data (using volume rendering, isosurface and slice plane, raster data such as still satellite images, vector data and 3D models such as buildings or vehicles. The application runs on touch screen devices such as tablets. The software is based on open source libraries, such as OpenSceneGraph, osgEarth and OpenCV, and shader programming is used to implement volume rendering of scientific data. The next goal of EarthScape is to perform data analysis using ENVI Services Engine, a cloud data analysis solution. EarthScape is also designed to be a client of Jagwire which provides multisource geo-referenced video fluxes. When all these components will be included, EarthScape will be a multi-purpose platform that will provide at the same time data analysis, hybrid visualization and complex interactions. The software is available on demand for free at france@exelisvis.com.

  14. Multicolor in situ hybridization and linkage analysis order Charcot-Marie-Tooth type I (CMTIA) gene-region markers

    Energy Technology Data Exchange (ETDEWEB)

    Lebo, R.V.; Lynch, E.D.; Golbus, M.S. (Univ. of California, San Francisco (United States)); Bird, T.D. (Univ. of Washington, Seattle (United States)); Barker, D.F.; O' Connell, P.; Chance, P.F. (Univ. of Utah, Salt Lake City (United States))

    1992-01-01

    This study demonstrates a clear and current role for multicolor in situ hybridization in expediting positional cloning studies of unknown disease genes. Nine polymorphic DNA cosmids have been mapped to eight ordered locations spanning the Charcot-Marie-Tooth type 1 (CMT1A) disease gene region in distal band 17p11.2, by multicolor in situ hybridization. When used with linkage analysis, these methods have generated a fine physical map and have firmly assigned the CMT1A gene to distal band 17p11.2. Linkage analysis with four CMT1A pedigrees mapped the CMT1A gene with respect to two flanking markers. Additional loci were physically mapped and ordered by in situ hybridization and analysis of phase-known recombinants in CMT1A pedigrees. These data demonstrate the ability of in situ hybridization to resolve loci within 0.5 Mb on early-metaphase chromosomes. Multicolor in situ hybridization also excluded the possibility of pericentric inversions in two unrelated patients with CMT1 and neurofibromatosis type 1. When used with pulsed-field gel electrophoresis, multicolor in situ hybridization can establish physical location, order, and distance in closely spaced chromosome loci.

  15. Hybrid transfinite element modeling/analysis of nonlinear heat conduction problems involving phase change

    Science.gov (United States)

    Tamma, Kumar K.; Railkar, Sudhir B.

    1988-01-01

    The present paper describes the applicability of hybrid transfinite element modeling/analysis formulations for nonlinear heat conduction problems involving phase change. The methodology is based on application of transform approaches and classical Galerkin schemes with finite element formulations to maintain the modeling versatility and numerical features for computational analysis. In addition, in conjunction with the above, the effects due to latent heat are modeled using enthalpy formulations to enable a physically realistic approximation to be dealt computationally for materials exhibiting phase change within a narrow band of temperatures. Pertinent details of the approach and computational scheme adapted are described in technical detail. Numerical test cases of comparative nature are presented to demonstrate the applicability of the proposed formulations for numerical modeling/analysis of nonlinear heat conduction problems involving phase change.

  16. Study on the application of ArraY-CGH in the detection of unexplained malformation fetus%ArraY-CGH技术在不明原因畸形胎儿检测中的应用研究

    Institute of Scientific and Technical Information of China (English)

    侯建伟; 董晓燕; 许日华

    2016-01-01

    目的:探讨ArraY⁃CGH技术(微阵列比较基因组杂交技术)在不明原因畸形胎儿检测中的应用.方法:选取2013-01/2015-10新疆维吾尔自治区克拉玛依中心医院收治的不明原因畸形胎儿102例作为研究对象,对所选胎儿采取CNVs(全基因组拷贝数变异)进行筛查,获取畸形胎儿不明原因中CNVs检出率,并分析CNVs与畸形胎儿的相关性,采用此方法来评估ArraY⁃CGH对不明原因畸形胎儿可能的遗传病因诊断作用.结果:25/102例患儿中发现33个CNVs(重复16个、缺失17个),总发生率为32.35%(33/102),CNVs平均长度1321 kb.对3/25例患者父母血样进行鉴定,判定CNVs 是否是家族遗传,其中1例具有新生CNVs,余下2例为父亲遗传.携带MR/ DD 致病相关CNVs 的患儿检出率为15.69%(16/102).结论:基因组CNVs 相关的微缺失重复,是造成不明原因畸形胎儿的原因之一,高分辨ArraY⁃CGH 技术可在不明原因畸形胎儿中发现更多的遗传病因,帮助和提高不明原因畸形胎儿的分子诊断水平.%AIM: To investigate the application of ArraY⁃CGH ( microarray comparative genomic hybridization ) in the detection of unexplained malformation fetus. METHODS: A total of 102 unexplained malformation fetus admitted into Central Hospital of Karamay from January 2013 to October 2015 were selected as the objects of research, and they were given CNVs ( genome⁃wide copy number variations) screening to acquire CNVs detection rate of unexplained malformation fetus and analyze the correlations between CNVs and malformation fetus, which could evaluate the diagnosis effect of possible genetic etiology of ArraY⁃CGH for un⁃explained malformation fetus. RESULTS: A total of 33 cases of CNVs was found from 25/102 ( 16 repeat, 17 missing) , and the total incidence rate was 32.35%( 33/102 ) , and the average length of CNVs was 1321 kb. The blood

  17. pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis

    Directory of Open Access Journals (Sweden)

    de Chassey Benoît

    2009-10-01

    Full Text Available Abstract Background High-throughput screening of protein-protein interactions opens new systems biology perspectives for the comprehensive understanding of cell physiology in normal and pathological conditions. In this context, yeast two-hybrid system appears as a promising approach to efficiently reconstruct protein interaction networks at the proteome-wide scale. This protein interaction screening method generates a large amount of raw sequence data, i.e. the ISTs (Interaction Sequence Tags, which urgently need appropriate tools for their systematic and standardised analysis. Findings We develop pISTil, a bioinformatics pipeline combined with a user-friendly web-interface: (i to establish a standardised system to analyse and to annotate ISTs generated by two-hybrid technologies with high performance and flexibility and (ii to provide high-quality protein-protein interaction datasets for systems-level approach. This pipeline has been validated on a large dataset comprising more than 11.000 ISTs. As a case study, a detailed analysis of ISTs obtained from yeast two-hybrid screens of Hepatitis C Virus proteins against human cDNA libraries is also provided. Conclusion We have developed pISTil, an open source pipeline made of a collection of several applications governed by a Perl script. The pISTil pipeline is intended to laboratories, with IT-expertise in system administration, scripting and database management, willing to automatically process large amount of ISTs data for accurate reconstruction of protein interaction networks in a systems biology perspective. pISTil is publicly available for download at http://sourceforge.net/projects/pistil.

  18. Multilayer interparticle linking hybrid MOF-199 for noninvasive enrichment and analysis of plant hormone ethylene.

    Science.gov (United States)

    Zhang, Zhuomin; Huang, Yichun; Ding, Weiwei; Li, Gongke

    2014-04-01

    Ethylene, an important plant hormone, is of utmost importance during many developmental processes of plants. However, the efficient enrichment and analysis of trace ethylene still remains a challenge. A simple and mild multilayer interparticle linking strategy was proposed to fabricate a novel hybrid MOF-199 enrichment coating. Strong chemical interparticle linkages throughout the coating improved the durability and reproducibility of hybrid MOF-199 coating dramatically. This coating performed a significant extraction superiority of ethylene over commonly used commercial coatings, attributed to the multiple interactions including "molecular sieving effect", hydrogen bonding, open metal site interaction, and π-π affinity. The hybridization of multiwalled carbon nanotubes (MWCNTs) with MOF-199 further improved the enrichment capability and also acted as a hydrophobic "shield" to prevent the open metal sites of MOF-199 from being occupied by water molecules, which effectively improved the moisture-resistant property of MOF-199/CNTs coating. Finally, this novel enrichment method was successfully applied for the noninvasive analysis of trace ethylene, methanol, and ethanol from fruit samples with relatively high humidity. The low detection limit was 0.016 μg/L for ethylene. It was satisfactory that trace ethylene could be actually detected from fruit samples by this noninvasive method. Good recoveries of spiked grape, wampee, blueberry, and durian husk samples were obtained in the range of 90.0-114%, 79.4-88.6%, 78.5-86.8%, and 85.2-105% with the corresponding relative standard deviations of 4.8-9.8%, 6.9-8.9%, 3.8-8.1%, and 9.3-10.5% (n = 3), respectively.

  19. High efficiency production and genomic in situ hybridization analysis of Brassica aneuploids and homozygous plants

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Interspecific and intergeneric hybridizations have been widely used in plant genetics and breeding to construct stocks for genetic analysis and to introduce into crops the desirable traits and genes from their relatives. The intergeneric crosses between Brassica juncea (L.) Czern. & Coss., B. carinata A. Braun and Orychophragmus violaceus (L.) O. E. Schulz were made and the plants produced were subjected to genomic in situ hybridization analysis. The mixoploids from the cross with B. juncea were divided into three groups. The partially fertile mixoploids in the first group (2n = 36-42) mainly contained the somatic cells and pollen mother cells (PMCs) with the 36 chromosomes of B. juncea and additional chromosomes of O. violaceus. The mixoploids (2n = 30-36) in the second and third groups were morphologically quite similar to the mother plants B. juncea and showed nearly normal fertility. The plants in the second group produced the majority of PMCs (2n = 36) with their chromosomes paired and segregated normally, but 1-4 pairs of the O. violaceus chromosomes were included in some PMCs. The plants in the third group produced only PMCs with the 36 B. juncea chromosomes, which were paired and segregated normally. The mixoploids (2n = 29-34) from the cross with B. carinata produced the majority of PMCs (2n = 34) with normal chromosome pairing and segregation, but some plants had some PMCs with 1-3 pairs of chromosomes from O. violaceus and other plants had only PMCs with the B. carinata chromosomes. The Brassica homozygous plants and aneuploids with complete or partial chromosome complements of Brassica parents and various numbers of O. violaceus chromosomes were derived from these progeny plants. The results in this study provided the molecular cytogenetic evidence for the separation of parental genomes which was previously proposed to occur in the hybridizations of these two genera.

  20. Genetic molecular analysis of Coffea arabica (Rubiaceae hybrids using SRAP markers

    Directory of Open Access Journals (Sweden)

    Manoj Kumar Mishra

    2011-06-01

    Full Text Available In Coffea arabica (arabica coffee, the phenotypic as well as genetic variability has been found low because of the narrow genetic basis and self fertile nature of the species. Because of high similarity in phenotypic appearance among the majority of arabica collections, selection of parental lines for inter-varietals hybridization and identification of resultant hybrids at an early stage of plant growth is difficult. DNA markers are known to be reliable in identifying closely related cultivars and hybrids. Sequence Related Amplified Polymorphism (SRAP is a new molecular marker technology developed based on PCR. In this paper, sixty arabica-hybrid progenies belonging to six crosses were analyzed using 31 highly polymorphic SRAP markers. The analysis revealed seven types of SRAP marker profiles which are useful in discriminating the parents and hybrids. The number of bands amplified per primer pair ranges from 6.13 to 8.58 with average number of seven bands. Among six hybrid combinations, percentage of bands shared between hybrids and their parents ranged from 66.29% to 85.71% with polymorphic bands varied from 27.64% to 60.0%. Percentage of hybrid specific fragments obtained in various hybrid combinations ranged from 0.71% to 10.86% and ascribed to the consequence of meiotic recombination. Based on the similarity index calculation, it was observed that F1 hybrids share maximum number of bands with the female parent compared to male parent. The results obtained in the present study revealed the effectiveness of SRAP technique in cultivar identification and hybrid analysis in this coffee species. Rev. Biol. Trop. 59 (2: 607-617. Epub 2011 June 01.En Coffea arabica (café arabica, el fenotipo y la variabilidad genética son bajos debido a la estrecha base genética y la autofecundación de la especie. Por su alta similitud fenotípica entre la mayoría de las colecciones de arábica, la selección de líneas parentales para hibridación entre

  1. Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons

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    Karsens Harma A

    2008-02-01

    Full Text Available Abstract Background Array-based comparative genome hybridization (aCGH is commonly used to determine the genomic content of bacterial strains. Since prokaryotes in general have less conserved genome sequences than eukaryotes, sequence divergences between the genes in the genomes used for an aCGH experiment obstruct determination of genome variations (e.g. deletions. Current normalization methods do not take into consideration sequence divergence between target and microarray features and therefore cannot distinguish a difference in signal due to systematic errors in the data or due to sequence divergence. Results We present supervised Lowess, or S-Lowess, an application of the subset Lowess normalization method. By using a predicted subset of array features with minimal sequence divergence between the analyzed strains for the normalization procedure we remove systematic errors from dual-dye aCGH data in two steps: (1 determination of a subset of conserved genes (i.e. likely conserved genes, LCG; and (2 using the LCG for subset Lowess normalization. Subset Lowess determines the correction factors for systematic errors in the subset of array features and normalizes all array features using these correction factors. The performance of S-Lowess was assessed on aCGH experiments in which differentially labeled genomic DNA fragments of Lactococcus lactis IL1403 and L. lactis MG1363 strains were hybridized to IL1403 DNA microarrays. Since both genomes are sequenced and gene deletions identified, the success rate of different aCGH normalization methods in detecting these deletions in the MG1363 genome were determined. S-Lowess detects 97% of the deletions, whereas other aCGH normalization methods detect up to only 60% of the deletions. Conclusion S-Lowess is implemented in a user-friendly web-tool accessible from http://bioinformatics.biol.rug.nl/websoftware/s-lowess. We demonstrate that it outperforms existing normalization methods and maximizes

  2. Analysis of [Gossypium capitis-viridis × (G.hirsutum × G.australe)2] Trispecific Hybrid and Selected Characteristics.

    Science.gov (United States)

    Chen, Di; Wu, Yuxiang; Zhang, Xiling; Li, Fuguang

    2015-01-01

    Speciation is always a contentious and challenging issue following with the presence of gene flow. In Gossypium, there are many valuable resources and wild diploid cotton especially C and B genome species possess some excellent traits which cultivated cotton always lacks. In order to explore character transferring rule from wild cotton to upland tetraploid cotton, the [G. capitis-viridis × (G. hirsutum × G. australe)2] triple hybrid was synthesized by interspecies hybridization and chromosome doubling. Morphology comparisons were measured among this hybrid and its parents. It showed that trispecific hybrid F1 had some intermediate morphological characters like leaf style between its parents and some different characters from its parents, like crawl growth characteristics and two kind flower color. It is highly resistant to insects comparing with other cotton species by four year field investigation. By cytogenetic analysis, triple hybrid was further confirmed by meiosis behavior of pollen mother cells. Comparing with regular meiosis of its three parents, it was distinguished by the occurrence of polyads with various numbers of unbalanced microspores and finally generating various abnormal pollen grains. All this phenomenon results in the sterility of this hybrid. This hybrid was further identified by SSR marker from DNA molecular level. It showed that 98 selected polymorphism primers amplified effective bands in this hybrids and its parents. The genetic proportion of three parents in this hybrid is 47.8% from G. hirsutum, 14.3% from G. australe, 7.0% from G. capitis-viridis, and 30.9% recombination bands respectively. It was testified that wild genetic material has been transferred into cultivated cotton and this new germplasm can be incorporated into cotton breeding program.

  3. Analysis of [Gossypium capitis-viridis × (G.hirsutum × G.australe2] Trispecific Hybrid and Selected Characteristics.

    Directory of Open Access Journals (Sweden)

    Di Chen

    Full Text Available Speciation is always a contentious and challenging issue following with the presence of gene flow. In Gossypium, there are many valuable resources and wild diploid cotton especially C and B genome species possess some excellent traits which cultivated cotton always lacks. In order to explore character transferring rule from wild cotton to upland tetraploid cotton, the [G. capitis-viridis × (G. hirsutum × G. australe2] triple hybrid was synthesized by interspecies hybridization and chromosome doubling. Morphology comparisons were measured among this hybrid and its parents. It showed that trispecific hybrid F1 had some intermediate morphological characters like leaf style between its parents and some different characters from its parents, like crawl growth characteristics and two kind flower color. It is highly resistant to insects comparing with other cotton species by four year field investigation. By cytogenetic analysis, triple hybrid was further confirmed by meiosis behavior of pollen mother cells. Comparing with regular meiosis of its three parents, it was distinguished by the occurrence of polyads with various numbers of unbalanced microspores and finally generating various abnormal pollen grains. All this phenomenon results in the sterility of this hybrid. This hybrid was further identified by SSR marker from DNA molecular level. It showed that 98 selected polymorphism primers amplified effective bands in this hybrids and its parents. The genetic proportion of three parents in this hybrid is 47.8% from G. hirsutum, 14.3% from G. australe, 7.0% from G. capitis-viridis, and 30.9% recombination bands respectively. It was testified that wild genetic material has been transferred into cultivated cotton and this new germplasm can be incorporated into cotton breeding program.

  4. Large Improvements in MS/MS Based Peptide Identification Rates using a Hybrid Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cannon, William R.; Rawlins, Mitchell M.; Baxter, Douglas J.; Callister, Stephen J.; Lipton, Mary S.; Bryant, Donald A.

    2011-05-06

    We have developed a hybrid method for identifying peptides from global proteomics studies that significantly increases sensitivity and specificity in matching peptides to tandem mass spectra using database searches. The method increased the number of spectra that can be assigned to a peptide in a global proteomics study by 57-147% at an estimated false discovery rate of 5%, with clear room for even greater improvements. The approach combines the general utility of using consensus model spectra typical of database search methods1-3 with the accuracy of the intensity information contained in spectral libraries4-6. This hybrid approach is made possible by recent developments that elucidated the statistical framework common to both data analysis and statistical thermodynamics, resulting in a chemically inspired approach to incorporating fragment intensity information into both database searches and spectral library searches. We applied this approach to proteomics analysis of Synechococcus sp. PCC 7002, a cyanobacterium that is a model organism for studies of photosynthetic carbon fixation and biofuels development. The increased specificity and sensitivity of this approach allowed us to identify many more peptides involved in the processes important for photoautotrophic growth.

  5. Hybrid sentiment analysis utilizing multiple indicators to determine temporal shifts of opinion in OSNs

    Science.gov (United States)

    White, Joshua S.; Hall, Robert T.; Fields, Jeremy; White, Holly M.

    2016-05-01

    Utilization of traditional sentiment analysis for predicting the outcome of an event on a social network depends on: precise understanding of what topics relate to the event, selective elimination of trends that don't fit, and in most cases, expert knowledge of major players of the event. Sentiment analysis has traditionally taken one of two approaches to derive a quantitative value from qualitative text. These approaches include the bag of words model", and the usage of "NLP" to attempt a real understanding of the text. Each of these methods yield very similar accuracy results with the exception of some special use cases. To do so, however, they both impose a large computational burden on the analytic system. Newer approaches have this same problem. No matter what approach is used, SA typically caps out around 80% in accuracy. However, accuracy is the result of both polarity and degree of polarity, nothing else. In this paper we present a method for hybridizing traditional SA methods to better determine shifts in opinion over time within social networks. This hybridization process involves augmenting traditional SA measurements with contextual understanding, and knowledge about writers' demographics. Our goal is to not only to improve accuracy, but to do so with minimal impact to computation requirements.

  6. A Mathematical and Numerical Model for the Analysis of Hybrid Rocket Motors

    Directory of Open Access Journals (Sweden)

    Florin MINGIREANU

    2011-12-01

    Full Text Available The hybrid rocket motors (HRM use a two-phase propellant system. This offers some remarkable advantages but also arises some difficulties like the neutralization of their instabilities. The non-acoustic combustion instabilities are high-amplitude pressure oscillations that have too low frequencies to be associated with acoustics. Acoustic type combustion instabilities are self-excited oscillations generated by the interaction between acoustic waves and combustion. The goal of the present work is to develop a simplified model of the coupling of the hybrid combustion process with the complete unsteady flow, starting from the combustion port and ending with the nozzle. This model must be useful for transient and stability analysis and also for scaling of HRMs. The numerical results obtained with our model show a good agreement with published experimental and numerical results. The computational and stability analysis models developed in this work are simple, computationally efficient and offer the advantage of taking into account a large number of functional and constructive parameters that are used by the engineers.

  7. Quantitative data analysis methods for bead-based DNA hybridization assays using generic flow cytometry platforms.

    Science.gov (United States)

    Corrie, S R; Lawrie, G A; Battersby, B J; Ford, K; Rühmann, A; Koehler, K; Sabath, D E; Trau, M

    2008-05-01

    Bead-based assays are in demand for rapid genomic and proteomic assays for both research and clinical purposes. Standard quantitative procedures addressing raw data quality and analysis are required to ensure the data are consistent and reproducible across laboratories independent of flow platform. Quantitative procedures have been introduced spanning raw histogram analysis through to absolute target quantitation. These included models developed to estimate the absolute number of sample molecules bound per bead (Langmuir isotherm), relative quantitative comparisons (two-sided t-tests), and statistical analyses investigating the quality of raw fluorescence data. The absolute target quantitation method revealed a concentration range (below probe saturation) of Cy5-labeled synthetic cytokeratin 19 (K19) RNA of c.a. 1 x 10(4) to 500 x 10(4) molecules/bead, with a binding constant of c.a. 1.6 nM. Raw hybridization frequency histograms were observed to be highly reproducible across 10 triplex assay replicates and only three assay replicates were required to distinguish overlapping peaks representing small sequence mismatches. This study provides a quantitative scheme for determining the absolute target concentration in nucleic acid hybridization reactions and the equilibrium binding constants for individual probe/target pairs. It is envisaged that such studies will form the basis of standard analytical procedures for bead-based cytometry assays to ensure reproducibility in inter- and intra-platform comparisons of data between laboratories. (c) 2008 International Society for Advancement of Cytometry.

  8. Technology-Driven and Evidence-Based Genomic Analysis for Integrated Pediatric and Prenatal Genetics Evaluation

    Institute of Scientific and Technical Information of China (English)

    Yuan Wei; Fang Xu; Peining Li

    2013-01-01

    The first decade since the completion of the Human Genome Project has been marked with rapid development of genomic technologies and their immediate clinical applications.Genomic analysis using oligonucleotide array comparative genomic hybridization (aCGH) or single nucleotide polymorphism (SNP) chips has been applied to pediatric patients with developmental and intellectual disabilities (DD/ID),multiple congenital anomalies (MCA) and autistic spectrum disorders (ASD).Evaluation of analytical and clinical validities of aCGH showed > 99% sensitivity and specificity and increased analytical resolution by higher density probe coverage.Reviews of case series,multi-center comparison and large patient-control studies demonstrated a diagnostic yield of 12%-20%; approximately 60% of these abnormalities were recurrent genomic disorders.This pediatric experience has been extended toward prenatal diagnosis.A series of reports indicated approximately 10% of pregnancies with ultrasound-detected structural anomalies and normal cytogenetic findings had genomic abnormalities,and 30% of these abnormalities were syndromic genomic disorders.Evidence-based practice guidelines and standards for implementing genomic analysis and web-delivered knowledge resources for interpreting genomic findings have been established.The progress from this technology-driven and evidence-based genomic analysis provides not only opportunities to dissect disease-causing mechanisms and develop rational therapeutic interventions but also important lessons for integrating genomic sequencing into pediatric and prenatal genetic evaluation.

  9. Molecular analysis of a case of nevus of ota showing progressive evolution to melanoma with intermediate stages resembling cellular blue nevus.

    Science.gov (United States)

    Gerami, Pedram; Pouryazdanparast, Pedram; Vemula, Swapna; Bastian, Boris C

    2010-05-01

    Nevus of Ota is a variant of congenital nevus, which is morphologically paucicellular and resembles a common blue nevus. Although nevus of Ota is a risk factor for uveal melanoma in white people, the development of cutaneous melanoma within nevus of Ota is a very rare occurrence with only a few reported cases. We present a case of a long-standing nevus of Ota, with radiologic imaging demonstrating a large retro-orbital mass and a biopsy showing melanoma. The histopathology of the eye exenteration specimen illustrated various stages of melanocytic progression including areas resembling a nevus of Ota, blue nevus, cellular blue nevus, and melanoma. There was heterogeneity in the overtly malignant sections with some areas displaying expansile nodules of blander appearing spindled cells, whereas other areas were composed of epithelioid cells with higher mitotic counts and zones of necrosis. The extensive lesion also infiltrated the soft tissue and bone. We performed gene mutation analysis for GNAQ, BRAF, NRAS, and KIT and fluorescence in situ hybridization (FISH) targeting commonly altered chromosomal loci in melanoma and comparative genomic hybridization (CGH). Copy number changes typical of melanoma were identified by both FISH and CGH in the morphologically malignant areas illustrating the relationship of tumor progression and the progressive acquisition of genetic aberrations.

  10. Gene expression analysis of the ovary of hybrid females of Xenopus laevis and X. muelleri

    Directory of Open Access Journals (Sweden)

    Malone John H

    2008-03-01

    Full Text Available Abstract Background Interspecific hybrids of frogs of the genus Xenopus result in sterile hybrid males and fertile hybrid females. Previous work has demonstrated a dramatic asymmetrical pattern of misexpression in hybrid males compared to the two parental species with relatively few genes misexpressed in comparisons of hybrids and the maternal species (X. laevis and dramatically more genes misexpressed in hybrids compared to the paternal species (X. muelleri. In this work, we examine the gene expression pattern in hybrid females of X. laevis × X. muelleri to determine if this asymmetrical pattern of expression also occurs in hybrid females. Results We find a similar pattern of asymmetry in expression compared to males in that there were more genes differentially expressed between hybrids and X. muelleri compared to hybrids and X. laevis. We also found a dramatic increase in the number of misexpressed genes with hybrid females having about 20 times more genes misexpressed in ovaries compared to testes of hybrid males and therefore the match between phenotype and expression pattern is not supported. Conclusion We discuss these intriguing findings in the context of reproductive isolation and suggest that divergence in female expression may be involved in sterility of hybrid males due to the inherent sensitivity of spermatogenesis as defined by the faster male evolution hypothesis for Haldane's rule.

  11. Hybrid Microfluidic Platform for Multifactorial Analysis Based on Electrical Impedance, Refractometry, Optical Absorption and Fluorescence

    Directory of Open Access Journals (Sweden)

    Fábio M. Pereira

    2016-10-01

    Full Text Available This paper describes the development of a novel microfluidic platform for multifactorial analysis integrating four label-free detection methods: electrical impedance, refractometry, optical absorption and fluorescence. We present the rationale for the design and the details of the microfabrication of this multifactorial hybrid microfluidic chip. The structure of the platform consists of a three-dimensionally patterned polydimethylsiloxane top part attached to a bottom SU-8 epoxy-based negative photoresist part, where microelectrodes and optical fibers are incorporated to enable impedance and optical analysis. As a proof of concept, the chip functions have been tested and explored, enabling a diversity of applications: (i impedance-based identification of the size of micro beads, as well as counting and distinguishing of erythrocytes by their volume or membrane properties; (ii simultaneous determination of the refractive index and optical absorption properties of solutions; and (iii fluorescence-based bead counting.

  12. Optimization of process parameters in drilling of fibre hybrid composite using Taguchi and grey relational analysis

    Science.gov (United States)

    Vijaya Ramnath, B.; Sharavanan, S.; Jeykrishnan, J.

    2017-03-01

    Nowadays quality plays a vital role in all the products. Hence, the development in manufacturing process focuses on the fabrication of composite with high dimensional accuracy and also incurring low manufacturing cost. In this work, an investigation on machining parameters has been performed on jute-flax hybrid composite. Here, the two important responses characteristics like surface roughness and material removal rate are optimized by employing 3 machining input parameters. The input variables considered are drill bit diameter, spindle speed and feed rate. Machining is done on CNC vertical drilling machine at different levels of drilling parameters. Taguchi’s L16 orthogonal array is used for optimizing individual tool parameters. Analysis Of Variance is used to find the significance of individual parameters. The simultaneous optimization of the process parameters is done by grey relational analysis. The results of this investigation shows that, spindle speed and drill bit diameter have most effect on material removal rate and surface roughness followed by feed rate.

  13. A new damage diagnosis approach for NC machine tools based on hybrid Stationary subspace analysis

    Science.gov (United States)

    Gao, Chen; Zhou, Yuqing; Ren, Yan

    2017-05-01

    This paper focused on the damage diagnosis for NC machine tools and put forward a damage diagnosis method based on hybrid Stationary subspace analysis (SSA), for improving the accuracy and visibility of damage identification. First, the observed single sensor signal was reconstructed to multi-dimensional signals by the phase space reconstruction technique, as the inputs of SSA. SSA method was introduced to separate the reconstructed data into stationary components and non-stationary components without the need for independency and prior information of the origin signals. Subsequently, the selected non-stationary components were analysed for training LS-SVM (Least Squares Support Vector Machine) classifier model, in which several statistic parameters in the time and frequency domains were exacted as the sample of LS-SVM. An empirical analysis in NC milling machine tools is developed, and the result shows high accuracy of the proposed approach.

  14. Hybridization of DCT and SVD in the Implementation and Performance Analysis of Video Watermarking

    Directory of Open Access Journals (Sweden)

    Ved Vyas Dwivedi

    2012-06-01

    Full Text Available In this Paper, We worked and documented the implementation and performance analysis of digital video watermarking that uses the hybrid features of two of the most powerful transform domain processing of the video and fundamentals of the linear algebra. We have taken into the account fundamentals of Discrete Cosine Transform and Singular Value Decomposition for the development of the proposed algorithm. We first used the Singular Value Decomposition and then used the singular values for the insertion of the message behind the video. Finally we used two of the visual quality matrices for the analysis purpose. We also applied various attacks on the video and found the proposed scheme more robust.

  15. Unified performance analysis of hybrid-ARQ with incremental redundancy over free-space optical channels

    KAUST Repository

    Zedini, Emna

    2014-09-01

    In this paper, we carry out a unified performance analysis of hybrid automatic repeat request (HARQ) with incremental redundancy (IR) from an information theoretic perspective over a point-to-point free-space optical (FSO) system. First, we introduce a novel unified expression for the distribution of a single FSO link modeled by the Gamma fading that accounts for pointing errors subject to both types of detection techniques at the receiver side (i.e. heterodyne detection and intensity modulation with direct detection (IM/DD)). Then, we provide analytical expressions for the outage probability, the average number of transmissions, and the average transmission rate for HARQ with IR, assuming a maximum number of rounds for the HARQ protocol. In our study, the communication rate per HARQ round is constant. Our analysis demonstrates the importance of HARQ in improving the performance and reliability of FSO communication systems. All the given results are verified via computer-based Monte-Carlo simulations.

  16. A 91 kb microdeletion at Xq26.2 involving the GPC3 gene in a female fetus with Simpson-Golabi-Behmel syndrome detected by prenatal arrayCGH

    DEFF Research Database (Denmark)

    Ramsing, Mette; Becher, Naja Helene; Christensen, Rikke

    A 91 kb microdeletion at Xq26.2 involving the GPC3 gene in a female fetus with Simpson-Golabi-Behmel syndrome detected by prenatal arrayCGH......A 91 kb microdeletion at Xq26.2 involving the GPC3 gene in a female fetus with Simpson-Golabi-Behmel syndrome detected by prenatal arrayCGH...

  17. Comparative Analysis on Rice Plant Type of Two Super Hybrids and Shanyou63

    Institute of Scientific and Technical Information of China (English)

    LU Chuan-gen; ZOU Jiang-shi

    2003-01-01

    The characteristics of plant type and physiological indices for photosynthesis were analyzedusing two super hybrid rices, Liangyoupeijiu and LiangyouE32 as materials, and an indica hybrid, Shan-you63 as a control. Based on the present analysis and various theories and breeding practices on rice planttype, a model of plant ideotype for super hybrid rice (indica) in the lower reaches of Yangtze River Valleywas proposed. This was: a length of 35 - 40 cm for top leaf with a width of 2 cm, and that of 50 - 55 cmand 55 - 60 crm, respectively, for the second and third leaves from top, meanwhile, having a leaf angle of5°, 10° and 15° respectively, and a curvature of 1 - 1.5 cm-1 for the leaf face at heading stage; the upper-most three leaves keeping their activities for as long as 70 d, which could lead a LAI of 3 at full ripeness;loose plant type with thin (SLW=2.5- 3 gcm-2 , dry weight) and curve-slant leaves during early growingstage, and compact plant type by thick (SLW = 4 - 5 gcm-2 ) and erect leaves during the middle and lategrowing stages; with a coefficient of light extinction of 0.3 - 0.4, which allowed for an optimal LAI high of8 - 10 during the middle growth period; plant height of 110 -120 cm, with 2 -4 cm basal internode and along uppermost internode occupying 45 % of total stem length; 25 - 28 cm panicle with 8 - 10 spikelets percentimeter showing bend-type in ripening; a rich chlorophyll which led to a high net photosynthetic rate,and tolerance to light shading and photooxidation which is of benefit to increasing the adaptability to varyinglight conditions.

  18. Molecular Cytogenetic Analysis of Spontaneous Interspecific Hybrid Between Oryza sativa and Oryza minuta

    Institute of Scientific and Technical Information of China (English)

    YI Chuan-deng; CHENG Xu; WANG Bei-bei; LIANG Guo-hua; GONG Zhi-yun; TANG Shu-zhu; GU Ming-hong

    2008-01-01

    Genomic in situ hybridization (GISH) is a powerful tool to characterize parental chromosomes in interspecific hybrids, including the behaviour of autosynapsis and chromosome paidng. It was used to distinguish the chromosomes of Oryza sativa from wild species in a spontaneous interspecific hybdd and to investigate the chromosome pairing at metaphase I in meiosis of the hybdd in this study. The hybrid was a triploid with 36 chromosomes according to the chromosome nurnber investigated in mitosis of root tips. During metaphase I of meiosis in the hybrid, less chromosome pairing was observed and most of the chromosomes existed as univalent. Based on GISH and FISH (Fluorescent in situ hybridization) analyses, the chromosomes of the hybrid were composed of genomes A, B and C. Thus, it was believed that the hybrid was the result of natural hybridization between cultivated rice and wild species O. minuta which was planted in experimental fields.

  19. PanCGHweb: a web tool for genotype calling in pangenome CGH data.

    NARCIS (Netherlands)

    Bayjanov, J.; Siezen, R.J.; Hijum, S.A.F.T. van

    2010-01-01

    A pangenome is the total of genes present in strains of the same species. Pangenome microarrays allow determining the genomic content of bacterial strains more accurately than conventional comparative genome hybridization microarrays. PanCGHweb is the first tool that effectively calls genotype based

  20. Analphoid supernumerary marker chromosome characterized by aCGH and FISH as inv dup(3(q25.33qter de novo in a child with dysmorphic features and streaky pigmentation: case report

    Directory of Open Access Journals (Sweden)

    Pramathan R

    2008-08-01

    Full Text Available Abstract Background Small supernumerary marker chromosomes (sSMC occur in 0.075% of unselected prenatal and in 0.044% of consecutively studied postnatal cases. Individuals with sSMC present with varying phenotype, ranging from normal to extremely mild or severe depending on the chromosomal region involved, the euchromatic content present and degree of mosaicism. Except for chromosomes 15 and 22, the number of reported cases of sSMC is extremely small to provide us with a good genotype-phenotype correlation. Analphoid sSMC are even rarer. To our knowledge only eight cases of analphoid inversion-duplication 3q sSMC are reported so far. Results We describe here a one month old female child with several dysmorphic features and with a de novo analphoid supernumerary marker chromosome only in cultured skin fibroblast cells and not in lymphocytes. The marker was characterized as analphoid inversion-duplication 3q25.33-qter by oligo array comparative genomic hybridization (aCGH and fluorescence in situ hybridization (FISH studies. The final skin fibroblast karyotype was interpreted as 47,XX,+der(3.ish inv dup(3(qter-q25.33::q25.33-qter(subtel 3q+,subtel 3q+ de novo. Conclusion In addition to the eight reported cases of analphoid inversion-duplication 3q supernumerary marker in the literature, this is yet another case of 3q sSMC with a new breakpoint at 3q25.33 and with varying phenotype as described in the case report. Identification of more and more similar cases of analphoid inversion-duplication 3q marker will help in establishing a better genotype-phenotype correlation. The study further demonstrates that aCGH in conjunction with routine cytogenetics and FISH is very useful in precisely identifying and characterizing a marker chromosome, and more importantly help in providing with an accurate genetic diagnosis and better counseling to the family.

  1. Analysis and design of permanent magnet biased magnetic bearing based on hybrid factor

    Directory of Open Access Journals (Sweden)

    Jinji Sun

    2016-03-01

    Full Text Available In this article, hybrid factor is proposed for hybrid magnetic bearing. The hybrid factor is defined as the ratio of the force produced by the permanent magnet and the forces produced by the permanent magnet and current in hybrid magnetic bearing. It is deduced from a certain radial hybrid magnetic bearing using its important parameters such as the current stiffness and displacement stiffness at first and then the dynamic model of magnetically suspended rotor system is established. The relationship between structural parameters and control system parameters is analyzed based on the hybrid factor. Some influencing factors of hybrid factor in hybrid magnetic bearing, such as the size of the permanent magnet, length of air gap, and area of the stator poles, are analyzed in this article. It can be concluded that larger hybrid factor can be caused by the smaller power loss according to the definition of hybrid factor mentioned above. Meanwhile, the hybrid factor has a maximum value, which is related to control system parameters such as proportional factor expect for structural parameters. Finally, the design steps of parameters of hybrid magnetic bearing can be concluded.

  2. Analysis of Hybrid-Electric Propulsion System Designs for Small Unmanned Aircraft Systems

    Science.gov (United States)

    2010-03-01

    arrival of the Insight, nearly every major automotive manufacturer has released its own hybrid model. The Toyota Prius , released to the US in 2001, has...dominated the hybrid marketplace with US sales topping 1,000,000 in March 2009.17 The Prius features a power-split hybrid system enabling use of an

  3. Design tradeoff studies and sensitivity analysis. Appendices B1-B4. [HYBRID

    Energy Technology Data Exchange (ETDEWEB)

    1979-05-25

    These four appendices to the report on the Near-Term Hybrid Vehicle (NTHV) report contain information on: HYBRID computer program documentation; material substitution study for advanced hybrid vehicles; NTHV market potential; battery compartment weight distribution; and vehicle handling dynamics. (LCL)

  4. Performance Analysis of High-Speed Deep/Shallow Recessed Hybrid Bearing

    Directory of Open Access Journals (Sweden)

    Lei Wang

    2013-01-01

    Full Text Available The present paper proposes a theoretical analysis of the performance of deep/shallow recessed hybrid bearing. It is intended that, on the basis of the numerical results drawn from this study, appropriate shallow recess depth and width can be determined for use in the bearing design process. By adopting bulk flow theory, the turbulent Reynolds equation and energy equation are modified and solved numerically including concentrated inertia effects at the recess edge with different depth and width of shallow recess. The results indicate that the load capacity, drag torque increases as the depth of shallow recess is shallower and the width ratio (half angle of deep recess versus half angle of shallow recess is smaller. In contrast, the flow rate decreases as the depth of shallow recess is shallower and the width ratio is smaller. Nevertheless, the appropriate design of the depth and width of shallow recess might well induce the performance of high-speed deep/shallow recessed hybrid bearing.

  5. Techno-economic Analysis of a Wind-Diesel Hybrid Power System in the South Algeria

    Directory of Open Access Journals (Sweden)

    Khaireddine Allali

    2015-07-01

    Full Text Available The electrical energy is often produced with the help of diesel generators in isolated areas in the Saharan region. While the latter requiring relatively little investment because is generally expensive to exploit due to the transportation to remote areas adds extra cost, significant fuel consumption and relatively high maintenance cost, etc. Moreover, the electricity production by the diesel is ineffective, presents significant environmental risks. But these isolated areas have significant wind energy potential; which is good position for the exploitation of clean and sustainable wind energy. The use of wind-diesel power system is widely recommended especially to reduce fuel consumption and in this way to reduce system operating costs and environmental impact. The subject of this paper is to present the techno-economic analysis of a wind-diesel hybrid power system. In this context, the contribution envisaged with this research is to collaborate on the optimal design of a hybrid power system including a wind turbine generator, a diesel generator and an energy storage system for powering a continuous way an isolated site in the South Algerian installed power of 120 kW.This system has a high control strategy for the management of different power sources (wind, diesel, battery that depending to weather conditions, especially wind speed values and the power demanded by the consumer load.

  6. Analysis of PV-FC Hybrid System Operation Considering Sale Electricity

    Directory of Open Access Journals (Sweden)

    Amirali Shahkoomahalli

    2013-06-01

    Full Text Available This paper presents a hybrid power generation system modeling and simulation with the objective of electricity sale to distribution network (DN which consists of photovoltaic (PV module, proton exchange membrane (PEM fuel cell (FC, hydrogen storage tank (HST and electrolyzer (EL.Since last researches in optimal FC and PV application aimed in power electronic approach, In this paper the application between FC and PV is considered with the aim of maximizing profit gained due to electricity sale revenue to DN. The revenue from electricity sale to DN considering electricity price in low load, shoulder load and peak load hours is considered as the system profit. Also in a sensitivity analysis the impact of technical parameters of hybrid system components is investigated on system profit. The results showed that the system saves the electricity by hydrogen storage in HST in low load hours and sale it with more prices in shoulder load hours to DN. Also the obtained results show that several technical parameters of PV and PEM FC have considerable impact on system operation and profit.

  7. Cycle Analysis of Micro Gas Turbine-Molten Carbonate Fuel Cell Hybrid System

    Science.gov (United States)

    Kimijima, Shinji; Kasagi, Nobuhide

    A hybrid system based on a micro gas turbine (µGT) and a high-temperature fuel cell, i.e., molten carbonate fuel cell (MCFC) or solid oxide fuel cell (SOFC), is expected to achieve a much higher efficiency than conventional distributed power generation systems. In this study, a cycle analysis method and the performance evaluation of a µGT-MCFC hybrid system, of which the power output is 30kW, are investigated to clarify its feasibility. We developed a general design strategy in which a low fuel input to a combustor and higher MCFC operating temperature result in a high power generation efficiency. A high recuperator temperature effectiveness and a moderate steam-carbon ratio are the requirements for obtaining a high material strength in a turbine. In addition, by employing a combustor for complete oxidation of MCFC effluents without additional fuel input, i.e., a catalytic combustor, the power generation efficiency of a µGT-MCFC is achieved at over 60%(LHV).

  8. Multivariable analysis of effects of various methods of magnesium application of LG 2244 maize hybrid

    Directory of Open Access Journals (Sweden)

    Jan Bocianowski

    2013-03-01

    Full Text Available The paper presents a multivariable approach to the estimation of variability for quantitative traits after using the seven methods of magnesium application of the “stay-green” type of maize (Zea mays L. hybrid. The 13 characteristics of LG 2244 hybrid were under consideration in three years (2006-2008: grain yield, moisture of grain, 1000 grain yield, dry matter of a single plant, dry matter yield, uptake of N, uptake of P, uptake of K, uptake of Mg, uptake of Ca, chlorophyll a, chlorophyll b and chlorophyll a+b content. The obtained results were computed with statistical multivariable methods of application. Canonical variable analysis (in each year independent has proved to be an effective tool for clear assessing of differences among the studied methods of magnesium application. The most diverse methods were: C and E (in 2006, A and F (in 2007, and B as G (in 2008. The most similar methods (in respect of 13 traits simultaneously were: B and C (in 2006, D and E (in 2007, and C and E (in 2008. Mahalanobis’ distances between methods of magnesium application in individual years of the study were not significantly correlated.

  9. Time-series analysis with a hybrid Box-Jenkins ARIMA and neural network model

    Institute of Scientific and Technical Information of China (English)

    Dilli R Aryal; WANG Yao-wu(王要武)

    2004-01-01

    Time-series analysis is important to a wide range of disciplines transcending both the physical and social sciences for proactive policy decisions. Statistical models have sound theoretical basis and have been successfully used in a number of problem domains in time series forecasting. Due to power and flexibility, Box-Jenkins ARIMA model has gained enormous popularity in many areas and research practice for the last three decades.More recently, the neural networks have been shown to be a promising alternative tool for modeling and forecasting owing to their ability to capture the nonlinearity in the data. However, despite the popularity and the superiority of ARIMA and ANN models, the empirical forecasting performance has been rather mixed so that no single method is best in every situation. In this study, a hybrid ARIMA and neural networks model to time series forecasting is proposed. The basic idea behind the model combination is to use each model's unique features to capture different patterns in the data. With three real data sets, empirical results evidently show that the hybrid model outperforms ARIMA and ANN model noticeably in terms of forecasting accuracy used in isolation.

  10. Finite element analysis of hybrid energy harvesting of piezoelectric and electromagnetic

    Directory of Open Access Journals (Sweden)

    Muhammad Yazid Muhammad Ammar Faris

    2017-01-01

    Full Text Available Harvesting energy from ambient vibrations is a highly required method because of the wide range of available sources that produce vibration energy application from industrial machinery to human motion application. In this paper, the implementation of harvesting energy from two technologies to form a hybrid energy harvester system was analyzed. These two technologies involve the piezoelectric harvesting energy and the electromagnetic harvesting energy. A finite element model was developed using the Ansys software with the harmonic analysis solver to analyze and examine hybrid harvesting energy system. Both power output generated from the magnet and the piezoelectric is then combined to form one unit of energy. Further, it was found that the result shows the system generate the maximum power output of 14.85 μW from 100 Hz, 4.905 m/s2, and 0.6 cm3 for resonance frequency, acceleration, and the volume respectively from the optimal energy harvester design. Normalized Power Density (NPD result of 10.29 kgs/m3 comparable with other literature also can be used in energy harvesting system for vibration application.

  11. Optimization and Static Stress Analysis of Hybrid Fiber Reinforced Composite Leaf Spring

    Directory of Open Access Journals (Sweden)

    Luay Muhammed Ali Ismaeel

    2015-01-01

    Full Text Available A monofiber reinforced composite leaf spring is proposed as an alternative to the typical steel one as it is characterized by high strength-to-weight ratio. Different reinforcing schemes are suggested to fabricate the leaf spring. The composite and the typical steel leaf springs are subjected to the same working conditions. A weight saving of about more than 60% can be achieved while maintaining the strength for the structures under consideration. The objective of the present study was to replace material for leaf spring. This study suggests various materials of hybrid fiber reinforced plastics (HFRP. Also the effects of shear moduli of the fibers, matrices, and the composites on the composites performance and responses are discussed. The results and behaviors of each are compared with each other and verified by comparison with analytical solution; a good convergence is found between them. The elastic properties of the hybrid composites are calculated using rules of mixtures and Halpin-Tsi equation through the software of MATLAB v-7. The problem is also analyzed by the technique of finite element analysis (FEA through the software of ANSYS v-14. An element modeling was done for every leaf with eight-node 3D brick element (SOLID185 3D 8-Node Structural Solid.

  12. Hybrid motion sensing and experimental modal analysis using collocated smartphone camera and accelerometers

    Science.gov (United States)

    Ozer, Ekin; Feng, Dongming; Feng, Maria Q.

    2017-10-01

    State-of-the-art multisensory technologies and heterogeneous sensor networks propose a wide range of response measurement opportunities for structural health monitoring (SHM). Measuring and fusing different physical quantities in terms of structural vibrations can provide alternative acquisition methods and improve the quality of the modal testing results. In this study, a recently introduced SHM concept, SHM with smartphones, is focused to utilize multisensory smartphone features for a hybridized structural vibration response measurement framework. Based on vibration testing of a small-scale multistory laboratory model, displacement and acceleration responses are monitored using two different smartphone sensors, an embedded camera and accelerometer, respectively. Double-integration or differentiation among different measurement types is performed to combine multisensory measurements on a comparative basis. In addition, distributed sensor signals from collocated devices are processed for modal identification, and performance of smartphone-based sensing platforms are tested under different configuration scenarios and heterogeneity levels. The results of these tests show a novel and successful implementation of a hybrid motion sensing platform through multiple sensor type and device integration. Despite the heterogeneity of motion data obtained from different smartphone devices and technologies, it is shown that multisensory response measurements can be blended for experimental modal analysis. Getting benefit from the accessibility of smartphone technology, similar smartphone-based dynamic testing methodologies can provide innovative SHM solutions with mobile, programmable, and cost-free interfaces.

  13. An exergetic/energetic/economic analysis of three hydrogen production processes - Electrolysis, hybrid, and thermochemical

    Science.gov (United States)

    Funk, J. E.; Eisermann, W.

    This paper presents the results of a combined first and second law analysis, along with capital and operating costs, for hydrogen production from water by means of electrolytic, hybrid, and thermochemical processes. The processes are SPE and Lurgi electrolysis with light water reactor power generation and sulfur cycle hybrid, thermochemical and SPE electrolysis with a very high temperature reactor primary energy source. Energy and Exergy (2nd law) flow diagrams for the process are shown along with the location and magnitude of the process irreversibilities. The overall process thermal (1st law) efficiencies vary from 25 to 51% and the exergetic (2nd law) efficiencies, referred to the fuel for the primary energy source, vary from 22 to 45%. Capital and operating costs, escalated to 1979 dollars, are shown for each process for both the primary energy source and the hydrogen production plant. All costs were taken from information available in the open literature and are for a plant capacity of 100 x 10 to the 6th SCF/day. Production costs vary from 10 to 18 $/GJ, based on the higher heating value of hydrogen, and are based on a 90% plant operating factor with a 21% annual charge on total capital costs.

  14. Hybrid Integration of Taguchi Parametric Design, Grey Relational Analysis, and Principal Component Analysis Optimization for Plastic Gear Production

    Directory of Open Access Journals (Sweden)

    Nik Mizamzul Mehat

    2014-01-01

    Full Text Available The identification of optimal processing parameters is an important practice in the plastic injection moulding industry because of the significant effect of such parameters on plastic part quality and cost. However, the optimization design of injection moulding process parameters can be difficult because more than one quality characteristic is used in the evaluation. This study systematically develops a hybrid optimization method for multiple quality characteristics by integrating the Taguchi parameter design, grey relational analysis, and principal component analysis. A plastic gear is used to demonstrate the efficiency and validity of the proposed hybrid optimization method in controlling all influential injection moulding processing parameters during plastic gear manufacturing. To minimize the shrinkage behaviour in tooth thickness, addendum circle, and dedendum circle of moulded gear, the optimal combination of different process parameters is determined. The case study demonstrates that the proposed optimization method can produce plastic-moulded gear with minimum shrinkage behaviour of 1.8%, 1.53%, and 2.42% in tooth thickness, addendum circle, and dedendum circle, respectively; these values are less than the values in the main experiment. Therefore, shrinkage-related defects that lead to severe failure in plastic gears can be effectively minimized while satisfying the demand of the global plastic gear industry.

  15. Evolutionary insights into scleractinian corals using comparative genomic hybridizations

    Directory of Open Access Journals (Sweden)

    Aranda Manuel

    2012-09-01

    Full Text Available Abstract Background Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization. Results Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate. Conclusions The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than

  16. A modified hybrid uncertain analysis method for dynamic response field of the LSOAAC with random and interval parameters

    Science.gov (United States)

    Zi, Bin; Zhou, Bin

    2016-07-01

    For the prediction of dynamic response field of the luffing system of an automobile crane (LSOAAC) with random and interval parameters, a hybrid uncertain model is introduced. In the hybrid uncertain model, the parameters with certain probability distribution are modeled as random variables, whereas, the parameters with lower and upper bounds are modeled as interval variables instead of given precise values. Based on the hybrid uncertain model, the hybrid uncertain dynamic response equilibrium equation, in which different random and interval parameters are simultaneously included in input and output terms, is constructed. Then a modified hybrid uncertain analysis method (MHUAM) is proposed. In the MHUAM, based on random interval perturbation method, the first-order Taylor series expansion and the first-order Neumann series, the dynamic response expression of the LSOAAC is developed. Moreover, the mathematical characteristics of extrema of bounds of dynamic response are determined by random interval moment method and monotonic analysis technique. Compared with the hybrid Monte Carlo method (HMCM) and interval perturbation method (IPM), numerical results show the feasibility and efficiency of the MHUAM for solving the hybrid LSOAAC problems. The effects of different uncertain models and parameters on the LSOAAC response field are also investigated deeply, and numerical results indicate that the impact made by the randomness in the thrust of the luffing cylinder F is larger than that made by the gravity of the weight in suspension Q . In addition, the impact made by the uncertainty in the displacement between the lower end of the lifting arm and the luffing cylinder a is larger than that made by the length of the lifting arm L .

  17. PanCGHweb: a web tool for genotype calling in pangenome CGH data

    OpenAIRE

    Bayjanov, Jumamurat R.; Siezen, Roland J.; van Hijum, Sacha A. F. T.

    2010-01-01

    Summary: A pangenome is the total of genes present in strains of the same species. Pangenome microarrays allow determining the genomic content of bacterial strains more accurately than conventional comparative genome hybridization microarrays. PanCGHweb is the first tool that effectively calls genotype based on pangenome microarray data. Availability: PanCGHweb, the web tool is accessible from: http://bamics2.cmbi.ru.nl/websoftware/pancgh/ Contact:

  18. Rate-prediction structure complexity analysis for multi-view video coding using hybrid genetic algorithms

    Science.gov (United States)

    Liu, Yebin; Dai, Qionghai; You, Zhixiang; Xu, Wenli

    2007-01-01

    Efficient exploitation of the temporal and inter-view correlation is critical to multi-view video coding (MVC), and the key to it relies on the design of prediction chain structure according to the various pattern of correlations. In this paper, we propose a novel prediction structure model to design optimal MVC coding schemes along with tradeoff analysis in depth between compression efficiency and prediction structure complexity for certain standard functionalities. Focusing on the representation of the entire set of possible chain structures rather than certain typical ones, the proposed model can given efficient MVC schemes that adaptively vary with the requirements of structure complexity and video source characteristics (the number of views, the degrees of temporal and interview correlations). To handle large scale problem in model optimization, we deploy a hybrid genetic algorithm which yields satisfactory results shown in the simulations.

  19. Hybrid pigments resulting from several guest dyes onto γ-alumina host: A spectroscopic analysis

    Science.gov (United States)

    Pérez, Erik; Ibarra, Ilich A.; Guzmán, Ariel; Lima, Enrique

    2017-02-01

    The synthesis of hybrid pigments was made from combination of γ-Al2O3 and some organic chromophores such as carminic acid, alizarin, purpurin, curcumin, fluorescein and betacyanins. The γ-Al2O3 was obtained through sol-gel synthesis with 2-propanol and aluminium tri-sec-butoxide (ATB). This article presents some spectroscopic evidences related to the formation of aluminium complexes between coordinative unsaturated sites (CUS) of aluminium and some organic groups (carboxylic acid, quaternary ammonium and β-keto enol) present in the chromophores structure. The physicochemical properties upcoming from a spectroscopic analysis point out that these materials can be applied in the design of new materials with potential uses in artworks and in the field of cultural heritage.

  20. Aeromechanical stability analysis of a multirotor vehicle model representing a hybrid heavy lift airship (HHLA)

    Science.gov (United States)

    Venkatesan, C.; Friedmann, P. P.

    1984-01-01

    Hybrid Heavy Lift Airship (HHLA) is a proposed candidate vehicle aimed at providing heavy lift capability at low cost. This vehicle consists of a buoyant envelope attached to a supporting structure to which four rotor systems, taken from existing helicopters are attached. Nonlinear equations of motion capable of modelling the dynamics of this coupled multi-rotor/support frame/vehicle system have been developed. Using these equations of motion the aeroelastic and aeromechanical stability analysis is performed aimed at identifying potential instabilities which could occur for this type of vehicle. The coupling between various blade, supporting structure and rigid body modes is identified. Furthermore, the effects of changes in buoyancy ratio (Buoyant lift/total weight) on the dynamic characteristics of the vehicle are studied. The dynamic effects found are of considerable importance for the design of such vehicles. The analytical model developed is also useful for studying the aeromechanical stability of single rotor and tandem rotor coupled rotor/fuselage systems.

  1. Hybrid independent component analysis and twin support vector machine learning scheme for subtle gesture recognition.

    Science.gov (United States)

    Naik, Ganesh R; Kumar, Dinesh K; Jayadeva

    2010-10-01

    Myoelectric signal classification is one of the most difficult pattern recognition problems because large variations in surface electromyogram features usually exist. In the literature, attempts have been made to apply various pattern recognition methods to classify surface electromyography into components corresponding to the activities of different muscles, but this has not been very successful, as some muscles are bigger and more active than others. This results in dataset discrepancy during classification. Multicategory classification problems are usually solved by solving many, one-versus-rest binary classification tasks. These subtasks unsurprisingly involve unbalanced datasets. Consequently, we need a learning methodology that can take into account unbalanced datasets in addition to large variations in the distributions of patterns corresponding to different classes. Here, we attempt to address the above issues using hybrid features extracted from independent component analysis and twin support vector machine techniques.

  2. Performance Analysis of a Hybrid One-Sided Magnetic Exciter Mounted on a Piezoelectric Stack

    Directory of Open Access Journals (Sweden)

    A. Nandi

    2010-01-01

    Full Text Available The present work proposes a non-contact hybrid exciter especially useful for harmonic excitation of lightly damped structures/rotors. In the proposed exciter an electromagnet is placed on a piezoelectric stack and the extension of the piezoelectric stack is made almost equal to the displacement of the structure using a simple tracking control. This largely eliminates stiffness coupling between the structure/rotor and the exciter and non-linearity in the excitation force due to the vibration of the structure/rotor. The stiffness and inertia of the piezoelectric stack is considered in the analysis. A SIMULINK model of the combined structure and the exciter is developed for a full time-domain simulation of the excitation system.

  3. A NEW HYBRID FORECASTING ALGORITHM AND ITS APPLICATION IN ECONOMIC ANALYSIS

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    There exists a great deal of periodic non-stationary processes in natural, social and economical phenomenon. It is very important to realize the dynamic analysis and real-time forecast within a period. In this letter, a wavelet-Kalman hybrid estimation and forecasting algorithm based on step-by-step filtering with the real-time and recursion property is put forward. It combines the advantages of Kalman filter and wavelet transform. Utilizing the information provided by multisensor effectively, this algorithm can realize not only real-time tracking and dynamic multi-step forecasting within a period, but also the dynamic forecasting between periods, and it has a great value to the system decision-making. Simulation results show that this algorithm is valuable.

  4. Finite-Element Analysis of Jute- and Coir-Fiber-Reinforced Hybrid Composite Multipanel Plates

    Science.gov (United States)

    Nirbhay, M.; Misra, R. K.; Dixit, A.

    2015-09-01

    Natural-fiber-reinforced polymer composite materials are rapidly gaining interest worldwide both in terms of research and industrial applications. The present work includes the characterization and modeling of jute- and coir-fiber-reinforced hybrid composite materials. The mechanical behavior of a two-panel plate and a sixpanel box structure is analyzed under various loading regimes by using the finite-element software ABAQUS®. Exhaustive parametric studies are also performed to obtain a clear insight into the relationships between various parameters and deflections of the panels and stress distributions in them. Deflections of both the structures are compared and found to be in good agreement with published results. To determine the mechanical behavior of natural-fiber-reinforced composite panels, a finite-element analysis is performed.

  5. Taxonomy of pasteurella anatipestifer. 1. DNA base composition and DNA-DNA hybridization analysis.

    Science.gov (United States)

    Bangun, A; Johnson, J L; Tripathy, D N

    1987-01-01

    DNA was isolated from 15 strains of Pasteurella anatipestifer and from one strain each of Moraxella nonliquefaciens, M. bovis, Pasteurella multocida, P. haemolytica, P. gallinarum, P. pneumotropica, and P. ureae. The guanine-plus-cytosine contents of P. anatipestifer ranged from 32 to 35 mole %, whereas those of Moraxella and Pasteurella spp. were much higher, ranging from 40 to 45 mole %. DNA-DNA hybridization analysis revealed that homology of nine P. anatipestifer strains to strains ATCC 11845 and PA 15 was 52 to 100%, whereas homology of Moraxella and Pasteurella strains to these strains was only 3 to 17%. Similarly, homology of P. anatipestifer strains, Moraxella, and Pasteurella species other than P. multocida to P. multocida reference strain P-2192 was low. These results strongly suggest that P. anatipestifer is genetically unrelated to either Pasteurella or Moraxella.

  6. An aggregation method of Markov graphs for the reliability analysis of hybrid systems

    Energy Technology Data Exchange (ETDEWEB)

    Schoenig, Raphael [Centre de Recherche en Automatique de Nancy (CRAN), 2, avenue de la Foret de Haye, 54516 Vandoeuvre-les-Nancy (France) and GFI Consulting, 12, rue Rouget de Lisle, 92442 Issy les Moulineaux (France)]. E-mail: raphael.schoenig@mpsa.com; Aubry, Jean-Francois [Centre de Recherche en Automatique de Nancy (CRAN), 2, avenue de la Foret de Haye, 54516 Vandoeuvre-les-Nancy (France)]. E-mail: jean-francois.aubry@isi.u-nancy.fr; Cambois, Thierry [PSA Peugeot Citroen, 18, rue des Fauvelles, 92256 La Garenne Colombes (France)]. E-mail: thierry.cambois@mpsa.com; Hutinet, Tony [GFI Consulting, 12, rue Rouget de Lisle, 92442 Issy les Moulineaux (France)]. E-mail: thutinet@gfi.fr

    2006-02-01

    To meet always increasing safety requirements in car industry, design and safety assessment methods are developed in order to fit the complexity of new embedded mecatronic systems. Hybrid (discrete/continuous) and dynamic features, specific to these systems, require choosing a suitable formalism. These features should also be considered in safety studies made all through the system design. The aim of this paper is to propose a quantitative analysis method based on the construction of an aggregated Markov graph, which allows a limitation of the combinatorial expansion. This graph is directly deducted from the Petri net modelling of the system. It is composed by a set of functional modes and a set of transitions to which statistical information regarding the system dynamics has been added.

  7. Diagnostic support for glaucoma using retinal images: a hybrid image analysis and data mining approach.

    Science.gov (United States)

    Yu, Jin; Abidi, Syed Sibte Raza; Artes, Paul; McIntyre, Andy; Heywood, Malcolm

    2005-01-01

    The availability of modern imaging techniques such as Confocal Scanning Laser Tomography (CSLT) for capturing high-quality optic nerve images offer the potential for developing automatic and objective methods for diagnosing glaucoma. We present a hybrid approach that features the analysis of CSLT images using moment methods to derive abstract image defining features. The features are then used to train classifers for automatically distinguishing CSLT images of normal and glaucoma patient. As a first, in this paper, we present investigations in feature subset selction methods for reducing the relatively large input space produced by the moment methods. We use neural networks and support vector machines to determine a sub-set of moments that offer high classification accuracy. We demonstratee the efficacy of our methods to discriminate between healthy and glaucomatous optic disks based on shape information automatically derived from optic disk topography and reflectance images.

  8. A study on flow distribution for integrated hybrid actuator by analysis of reed valve

    Energy Technology Data Exchange (ETDEWEB)

    Woo, Jang Mi; Kang, Seung Hwan; Ko, Han Seo [Sungkyunkwan University, Suwon (Korea, Republic of); Goo, Nam Seo; Li, Yong Zhe [Konkuk University, Seoul (Korea, Republic of)

    2016-05-15

    Many studies have been conducted recently on an integrated hybrid actuator due to the increasing need for unmanned aircraft and guided weapons. In this study, flow distribution was analyzed for a reed valve which was used for flow regulation to improve the performance of the actuator. By using a Fluid structural interaction (FSI) technique with Computational fluid dynamics (CFD) having a moving mesh, numerical analysis was performed according to the thickness, shape and driving frequency of the reed valve. From the calculated results, the maximum performance of the reed valve was found at the valve thickness of 0.15 mm and the driving frequency of 250 Hz for a no-load state. The optimum thickness and shape for the valve for each driving frequency were also realized.

  9. Analysis of a hybrid renewable energy system on the Mures valley using Homer

    Directory of Open Access Journals (Sweden)

    Dumitru Cristian Dragoş

    2011-12-01

    Full Text Available Renewable energy technologies offer the promise of clean, abundant energy gathered from self-renewing resources such as the sun, wind, earth, and plants. Virtually all regions of the world have renewable resources of one type or another. This paper deals with the modeling and analysis of a hybrid system based on renewable energy resources, located on the Mureş valley, using a dedicated software named HOMER. Different types and topologies of renewable resources for the energy supply are analyzed; a small consumer situated on the Mureş Valley is modeled based on a load curve. Finally, the energy flows between the renewable energy system and the local supplying network are analyzed.

  10. Highlighting hybridity: A critical discourse analysis of teacher talk in science classrooms

    Science.gov (United States)

    Hanrahan, Mary U.

    2006-01-01

    There is evidence that alienation from science is linked to the dominant discourse practices of science classrooms (cf. Lemke, J. L. (1990). Talking Science: Language, Learning, and Values. Norwood, NJ: Ablex). Yet, in secondary science education it is particularly hard to find evidence of curriculum reform that includes explicit changes in pedagogic discourses to accommodate the needs of students from a wide range of backgrounds. However, such evidence does exist and needs to be highlighted wherever it is found to help address social justice concerns in science education. In this article, I show how critical discourse analysis can be used to explore a way of challenging the dominant discourse in teacher - student interactions in science classrooms. My findings suggest a new way of moving toward more socially just science curricula in middle years and secondary classrooms by using hybrid discourses that can serve emancipatory purposes.

  11. A hybrid of bees algorithm and flux balance analysis (BAFBA) for the optimisation of microbial strains.

    Science.gov (United States)

    Choon, Yee Wen; Mohamad, Mohd Saberi; Deris, Safaai; Illias, Rosli Md

    2014-01-01

    The development of microbial production system has become popular in recent years as microbial hosts offer a number of unique advantages for both native and heterologous small-molecules. However, the main drawback is low yield or productivity of the desired products. Optimisation algorithms are implemented in previous works to identify the effects of gene knockout. Nevertheless, the previous works faced performance issue. Thus, a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) is proposed in this paper to improve the performance in predicting optimal sets of gene deletion for maximising the growth rate and production yield of certain metabolite. This paper involves two datasets which are E. coli and S. cerevisiae. The list of knockout genes, growth rate and production yield after the deletion are the results from the experiments. BAFBA presents better results compared to the other methods and the identified list may be useful in solving genetic engineering problems.

  12. MorphologiCal and Cytogenetic Analysis on the Advanced Generations of Generic Hybrids between Brassica napus and Orychophragmus violaceu

    Institute of Scientific and Technical Information of China (English)

    Zhigang ZHAO; Dezhi DU; Zaiyun LI

    2012-01-01

    Objective This study aimed to reveal the genetic changes of advanced generation hybrids between Brassica napus and Orychophragmus violaceus. [Method] The morphological characteristics such as the plant shape, branching sites, leaf shape, leaf color, primary branches and secondary branches, as well as the cytolog- ical characteristics of the advanced generation hybrids (Fs-F10) between B. napus and O. violaceus were observed. [Result] The morphology analysis revealed that the hybrid progeny was more like B. rapa in leaf shape, leaf color, plant shape and ear- ly flowering phenotype, whereas more like B. napus in number of secondary branch- es, silique length and 1 000-seed weight. Analysis on the cytogenetics characteristics showed that these advanced inbred progenies were hypoploids with less than 38 chromosomes; moreover, all the chromosomes from O. violaceus had been lost. Chromosome pairings at meiotic diakinesis of hybrids between the advanced inbred progenies and B. rapa revealed that chromosomes lost in hypoploids possibly be- longed to the C genome of B. oleracea. With generations developing, chromosomes number of plants from two populations gradually increased and developed into the number of B. napus (2n=38). [Conclusion] This study will provide reference to reveal the source of chromosome lost in hypoploids and the morphological change of hybrids.

  13. HeteroGenius: A Framework for Hybrid Analysis of Heterogeneous Software Specifications

    Directory of Open Access Journals (Sweden)

    Manuel Giménez

    2014-01-01

    Full Text Available Nowadays, software artifacts are ubiquitous in our lives being an essential part of home appliances, cars, cell phones, and even in more critical activities like aeronautics and health sciences. In this context software failures may produce enormous losses, either economical or, in the worst case, in human lives. Software analysis is an area in software engineering concerned with the application of diverse techniques in order to prove the absence of errors in software pieces. In many cases different analysis techniques are applied by following specific methodological combinations that ensure better results. These interactions between tools are usually carried out at the user level and it is not supported by the tools. In this work we present HeteroGenius, a framework conceived to develop tools that allow users to perform hybrid analysis of heterogeneous software specifications. HeteroGenius was designed prioritising the possibility of adding new specification languages and analysis tools and enabling a synergic relation of the techniques under a graphical interface satisfying several well-known usability enhancement criteria. As a case-study we implemented the functionality of Dynamite on top of HeteroGenius.

  14. Uncertainty analysis and design optimization of hybrid rocket motor powered vehicle for suborbital flight

    Directory of Open Access Journals (Sweden)

    Zhu Hao

    2015-06-01

    Full Text Available In this paper, we propose an uncertainty analysis and design optimization method and its applications on a hybrid rocket motor (HRM powered vehicle. The multidisciplinary design model of the rocket system is established and the design uncertainties are quantified. The sensitivity analysis of the uncertainties shows that the uncertainty generated from the error of fuel regression rate model has the most significant effect on the system performances. Then the differences between deterministic design optimization (DDO and uncertainty-based design optimization (UDO are discussed. Two newly formed uncertainty analysis methods, including the Kriging-based Monte Carlo simulation (KMCS and Kriging-based Taylor series approximation (KTSA, are carried out using a global approximation Kriging modeling method. Based on the system design model and the results of design uncertainty analysis, the design optimization of an HRM powered vehicle for suborbital flight is implemented using three design optimization methods: DDO, KMCS and KTSA. The comparisons indicate that the two UDO methods can enhance the design reliability and robustness. The researches and methods proposed in this paper can provide a better way for the general design of HRM powered vehicles.

  15. Hybrid Evidence Theory-based Finite Element/Statistical Energy Analysis method for mid-frequency analysis of built-up systems with epistemic uncertainties

    Science.gov (United States)

    Yin, Shengwen; Yu, Dejie; Yin, Hui; Lü, Hui; Xia, Baizhan

    2017-09-01

    Considering the epistemic uncertainties within the hybrid Finite Element/Statistical Energy Analysis (FE/SEA) model when it is used for the response analysis of built-up systems in the mid-frequency range, the hybrid Evidence Theory-based Finite Element/Statistical Energy Analysis (ETFE/SEA) model is established by introducing the evidence theory. Based on the hybrid ETFE/SEA model and the sub-interval perturbation technique, the hybrid Sub-interval Perturbation and Evidence Theory-based Finite Element/Statistical Energy Analysis (SIP-ETFE/SEA) approach is proposed. In the hybrid ETFE/SEA model, the uncertainty in the SEA subsystem is modeled by a non-parametric ensemble, while the uncertainty in the FE subsystem is described by the focal element and basic probability assignment (BPA), and dealt with evidence theory. Within the hybrid SIP-ETFE/SEA approach, the mid-frequency response of interest, such as the ensemble average of the energy response and the cross-spectrum response, is calculated analytically by using the conventional hybrid FE/SEA method. Inspired by the probability theory, the intervals of the mean value, variance and cumulative distribution are used to describe the distribution characteristics of mid-frequency responses of built-up systems with epistemic uncertainties. In order to alleviate the computational burdens for the extreme value analysis, the sub-interval perturbation technique based on the first-order Taylor series expansion is used in ETFE/SEA model to acquire the lower and upper bounds of the mid-frequency responses over each focal element. Three numerical examples are given to illustrate the feasibility and effectiveness of the proposed method.